RX DOI; 10.1021/pr9007688. RX PUBMED; 19954172. RA Pham T.K., Sierocinski P., van der Oost J., Wright P.C.; RT "Quantitative proteomic analysis of Sulfolobus solfataricus membrane RT proteins."; RL J Proteome Res 9(2):1165-1172(2010). XX RX DOI; 10.1371/journal.pcbi.1000210. RX PUBMED; 18974823. RA Puchalka J., Oberhardt M.A., Godinho M., Bielecka A., Regenhardt D., RA Timmis K.N., Papin J.A., Martins dos Santos V.A.; RT "Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 RT metabolic network facilitates applications in biotechnology."; RL PLoS Comput Biol 4(10):e1000210(2008). XX RX DOI; 10.1111/j.1758-2229.2009.00093.x. RA García Vanina, Godoy Patricia, Daniels Craig, Hurtado Ana, Ramos Juan, RA Segura Ana; RT "Functional analysis of new transporters involved in stress tolerance RT inPseudomonas putidaDOT-T1E"; XX RX DOI; 10.1111/j.1462-2920.2009.02124.x. RA Herrera M.Carmen, Duque Estrella, Rodríguez-Herva José J., RA Fernández-Escamilla Ana M., Ramos Juan; RT "Identification and characterization of the PhhR regulon inPseudomonas RT putida"; XX RX DOI; 10.1186/1471-2164-11-202. RA Alam M.Tauqeer, Merlo Maria Elena, (stream) The STREAM Consortium, RA Hodgson David, Wellington Elizabeth, Takano Eriko, Breitling Rainer; RT "Metabolic modeling and analysis of the metabolic switch in Streptomyces RT coelicolor"; RL BMC Genomics(2010). XX RX DOI; 10.1186/1471-2164-11-10. RX PUBMED; 20053288. RA Nieselt K., Battke F., Herbig A., Bruheim P., Wentzel A., Jakobsen O.M., RA Sletta H., Alam M.T., Merlo M.E., Moore J., Omara W.A., Morrissey E.R., RA Juarez-Hermosillo M.A., Rodriguez-Garcia A., Nentwich M., Thomas L., RA Iqbal M., Legaie R., Gaze W.H., Challis G.L., Jansen R.C., Dijkhuizen L., RA Rand D.A., Wild D.L., Bonin M., Reuther J., Wohlleben W., Smith M.C., RA Burroughs N.J., Martin J.F., Hodgson D.A., Takano E., Breitling R., RA Ellingsen T.E., Wellington E.M.; RT "The dynamic architecture of the metabolic switch in Streptomyces RT coelicolor."; RL BMC Genomics 11:10(2010). XX RX DOI; 10.1371/journal.pone.0002724. RX PUBMED; 18628968. RA Mehra S., Charaniya S., Takano E., Hu W.S.; RT "A bistable gene switch for antibiotic biosynthesis: the butyrolactone RT regulon in Streptomyces coelicolor."; RL PLoS One 3(7):e2724(2008). XX RX DOI; 10.1016/S0076-6879(09)04806-X. RX PUBMED; 19374982. RA Hsiao N.H., Gottelt M., Takano E.; RT "Chapter 6. Regulation of antibiotic production by bacterial hormones."; RL Methods Enzymol 458:143-157(2009). XX RX DOI; 10.1038/nrmicro1797. RX PUBMED; 18026122. RA Breitling R., Vitkup D., Barrett M.P.; RT "New surveyor tools for charting microbial metabolic maps."; RL Nat Rev Microbiol 6(2):156-161(2008). XX RX DOI; 10.1093/bioinformatics/btm536. RX PUBMED; 18003642. RA Jourdan F., Breitling R., Barrett M.P., Gilbert D.; RT "MetaNetter: inference and visualization of high-resolution metabolomic RT networks."; RL Bioinformatics 24(1):143-145(2008). XX RX DOI; 10.1093/bioinformatics/btn642. RX PUBMED; 19095699. RA Rogers S., Scheltema R.A., Girolami M., Breitling R.; RT "Probabilistic assignment of formulas to mass peaks in metabolomics RT experiments."; RL Bioinformatics 25(4):512-518(2009). XX RX DOI; 10.1002/pmic.200800314. RX PUBMED; 18937253. RA Scheltema R.A., Kamleh A., Wildridge D., Ebikeme C., Watson D.G., RA Barrett M.P., Jansen R.C., Breitling R.; RT "Increasing the mass accuracy of high-resolution LC-MS data using RT background ions: a case study on the LTQ-Orbitrap."; RL Proteomics 8(22):4647-4656(2008). XX RX DOI; 10.1099/mic.0.2008/019539-0. RX PUBMED; 18667568. RA Santos-Beneit F., Rodriguez-Garcia A., Franco-Dominguez E., Martin J.F.; RT "Phosphate-dependent regulation of the low- and high-affinity transport RT systems in the model actinomycete Streptomyces coelicolor."; RL Microbiology (Reading) 154(Pt 8):2356-2370(2008). XX RX DOI; 10.1093/nar/gkp162. RX PUBMED; 19321498. RA Rodriguez-Garcia A., Sola-Landa A., Apel K., Santos-Beneit F., Martin J.F.; RT "Phosphate control over nitrogen metabolism in Streptomyces coelicolor: RT direct and indirect negative control of glnR, glnA, glnII and amtB RT expression by the response regulator PhoP."; RL Nucleic Acids Res 37(10):3230-3242(2009). XX RX DOI; 10.1099/mic.0.023275-0. RX PUBMED; 19332834. RA Malm S., Tiffert Y., Micklinghoff J., Schultze S., Joost I., Weber I., RA Horst S., Ackermann B., Schmidt M., Wohlleben W., Ehlers S., Geffers R., RA Reuther J., Bange F.C.; RT "The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD RT and the response regulator GlnR in nitrate assimilation of Mycobacterium RT tuberculosis."; RL Microbiology (Reading) 155(Pt 4):1332-1339(2009). XX RX DOI; 10.1111/j.1365-2958.2007.06092.x. RX PUBMED; 18179599. RA Tiffert Y., Supra P., Wurm R., Wohlleben W., Wagner R., Reuther J.; RT "The Streptomyces coelicolor GlnR regulon: identification of new GlnR RT targets and evidence for a central role of GlnR in nitrogen metabolism in RT actinomycetes."; RL Mol Microbiol 67(4):861-880(2008). XX RX DOI; 10.1016/S0065-2164(07)00007-X. RX PUBMED; 18395130. RA Gaze W., O'Neill C., Wellington E., Hawkey P.; RT "Antibiotic resistance in the environment, with particular reference to RT MRSA."; RL Adv Appl Microbiol 63:249-280(2008). XX RX DOI; 10.1128/AAC.00652-07. RX PUBMED; 19064898. RA Byrne-Bailey K.G., Gaze W.H., Kay P., Boxall A.B., Hawkey P.M., RA Wellington E.M.; RT "Prevalence of sulfonamide resistance genes in bacterial isolates from RT manured agricultural soils and pig slurry in the United Kingdom."; RL Antimicrob Agents Chemother 53(2):696-702(2009). XX RX DOI; 10.2390/biecoll-jib-2009-107. RX PUBMED; 20134075. RA Saqi M., Dobson R.J., Kraben P., Hodgson D.A., Wild D.L.; RT "An approach to pathway reconstruction using whole genome metabolic models RT and sensitive sequence searching."; RL J Integr Bioinform 6(1):107(2009). XX RX DOI; 10.1093/bioinformatics/btp642. RX PUBMED; 19933161. RA Krause F., Uhlendorf J., Lubitz T., Schulz M., Klipp E., Liebermeister W.; RT "Annotation and merging of SBML models with semanticSBML."; RL Bioinformatics 26(3):421-422(2010). XX RX DOI; 10.1111/j.1567-1364.2010.00630.x. RX PUBMED; 20491939. RA Navarrete C., Petrezselyova S., Barreto L., Martinez J.L., Zahradka J., RA Arino J., Sychrova H., Ramos J.; RT "Lack of main K+ uptake systems in Saccharomyces cerevisiae cells affects RT yeast performance in both potassium-sufficient and potassium-limiting RT conditions."; RL FEMS Yeast Res 10(5):508-517(2010). XX RX DOI; 10.1016/j.febslet.2010.04.042. RX PUBMED; 20412803. RA Casado C., Yenush L., Melero C., Ruiz Mdel C., Serrano R., Perez-Valle J., RA Arino J., Ramos J.; RT "Regulation of Trk-dependent potassium transport by the calcineurin pathway RT involves the Hal5 kinase."; RL FEBS Lett 584(11):2415-2420(2010). XX RX DOI; 10.1128/MMBR.00042-09. RX PUBMED; 20197501. RA Arino J., Ramos J., Sychrova H.; RT "Alkali metal cation transport and homeostasis in yeasts."; RL Microbiol Mol Biol Rev 74(1):95-120(2010). XX RX PUBMED; 20238415. RA Gerber S., Hasenbrink G., Hendriksen W., Van Heusden P., Ludwig J., RA Klipp E., Lichtenberg-Frate H.; RT "Graphical analysis and experimental evaluation of Saccharomyces cerevisiae RT PTRK1|2 and PBMH1|2 promoter region."; RL Genome Inform 22:11-20(2010). XX RX DOI; 10.1042/BJ20091909. RX PUBMED; 20028335. RA Ferrer-Dalmau J., Gonzalez A., Platara M., Navarrete C., Martinez J.L., RA Barreto L., Ramos J., Arino J., Casamayor A.; RT "Ref2, a regulatory subunit of the yeast protein phosphatase 1, is a novel RT component of cation homoeostasis."; RL Biochem J 426(3):355-364(2010). XX RX DOI; 10.1016/j.ygeno.2009.07.004. RX PUBMED; 19631734. RA van Heusden G.P.; RT "14-3-3 Proteins: insights from genome-wide studies in yeast."; RL Genomics 94(5):287-293(2009). XX RX DOI; 10.1074/jbc.M109.059956. RX PUBMED; 20197279. RA Zotova L., Aleschko M., Sponder G., Baumgartner R., Reipert S., Prinz M., RA Schweyen R.J., Nowikovsky K.; RT "Novel components of an active mitochondrial K(+)/H(+) exchange."; RL J Biol Chem 285(19):14399-14414(2010). XX RX DOI; 10.1038/npre.2009.3093.1. RA Liebermeister Wolfram, Krause Falko, Uhlendorf Jannis, Lubitz Timo, RA Klipp Edda; RT "SemanticSBML: a tool for annotating, checking, and merging of biochemical RT models in SBML format"; RL Nature Precedings(2009). XX RX DOI; 10.1016/j.funbio.2009.11.002. RT "Saccharomyces cerevisiae BY4741 and W303-1A laboratory strains differ in RT salt tolerance"; RL Fungal Biology(2010). XX RX PUBMED; 17822389. RA Rojas I., Golebiewski M., Kania R., Krebs O., Mir S., Weidemann A., RA Wittig U.; RT "Storing and annotating of kinetic data."; RL In Silico Biol 7(2 Suppl):S37-S44(2007). XX RX DOI; 10.1007/s11538-010-9530-7. RX PUBMED; 20238180. RA Jabbari S., Heap J.T., King J.R.; RT "Mathematical modelling of the sporulation-initiation network in Bacillus RT subtilis revealing the dual role of the putative quorum-sensing signal RT molecule PhrA."; RL Bull Math Biol 73(1):181-211(2011). XX RX DOI; 10.1007/s00285-009-0291-6. RX PUBMED; 19688348. RA Jabbari S., King J.R., Koerber A.J., Williams P.; RT "Mathematical modelling of the agr operon in Staphylococcus aureus."; RL J Math Biol 61(1):17-54(2010). XX RX DOI; 10.1016/j.mbs.2010.03.001. RX PUBMED; 20214910. RA Jabbari S., King J.R., Williams P.; RT "A mathematical investigation of the effects of inhibitor therapy on three RT putative phosphorylation cascades governing the two-component system of the RT agr operon."; RL Math Biosci 225(2):115-131(2010). XX RX DOI; 10.1093/bioinformatics/btq242. RX PUBMED; 20444837. RA Rodriguez-Fernandez M., Banga J.R.; RT "SensSB: a software toolbox for the development and sensitivity analysis of RT systems biology models."; RL Bioinformatics 26(13):1675-1676(2010). XX RX DOI; 10.1111/j.1365-2958.2009.06624.x. RX PUBMED; 19220751. RA Santos-Beneit F., Rodriguez-Garcia A., Sola-Landa A., Martin J.F.; RT "Cross-talk between two global regulators in Streptomyces: PhoP and AfsR RT interact in the control of afsS, pstS and phoRP transcription."; RL Mol Microbiol 72(1):53-68(2009). XX RX DOI; 10.1371/journal.pone.0010727. RX PUBMED; 20502716. RA Bonowski F., Kitanovic A., Ruoff P., Holzwarth J., Kitanovic I., Bui V.N., RA Lederer E., Wolfl S.; RT "Computer controlled automated assay for comprehensive studies of enzyme RT kinetic parameters."; RL PLoS One 5(5):e10727(2010). XX RX DOI; 10.1016/j.febslet.2009.11.018. RX PUBMED; 19913018. RA Westerhoff H.V., Winder C., Messiha H., Simeonidis E., Adamczyk M., RA Verma M., Bruggeman F.J., Dunn W.; RT "Systems biology: the elements and principles of life."; RL FEBS Lett 583(24):3882-3890(2009). XX RX DOI; 10.1128/AEM.00344-09. RX PUBMED; 19465534. RA Jonsson M., Saleihan Z., Nes I.F., Holo H.; RT "Construction and characterization of three lactate dehydrogenase-negative RT Enterococcus faecalis V583 mutants."; RL Appl Environ Microbiol 75(14):4901-4903(2009). XX RX DOI; 10.1111/j.1365-2958.2010.07283.x. RT "How mathematical modelling elucidates signalling in B. subtilis"; XX RX DOI; 10.1017/S0031182010000466. RX PUBMED; 20444304. RA Bakker B.M., Krauth-Siegel R.L., Clayton C., Matthews K., Girolami M., RA Westerhoff H.V., Michels P.A., Breitling R., Barrett M.P.; RT "The silicon trypanosome."; RL Parasitology 137(9):1333-1341(2010). XX RX DOI; 10.1017/S003118201000017X. RX PUBMED; 20158937. RA Barrett M.P., Bakker B.M., Breitling R.; RT "Metabolomic systems biology of trypanosomes."; RL Parasitology 137(9):1285-1290(2010). XX RX DOI; 10.1111/j.1365-2958.2010.07188.x. RX PUBMED; 20487272. RA Hyyrylainen H.L., Marciniak B.C., Dahncke K., Pietiainen M., Courtin P., RA Vitikainen M., Seppala R., Otto A., Becher D., Chapot-Chartier M.P., RA Kuipers O.P., Kontinen V.P.; RT "Penicillin-binding protein folding is dependent on the PrsA RT peptidyl-prolyl cis-trans isomerase in Bacillus subtilis."; RL Mol Microbiol 77(1):108-127(2010). XX RX DOI; 10.1128/JB.00756-07. RX PUBMED; 17586624. RA Reeves A., Gerth U., Volker U., Haldenwang W.G.; RT "ClpP modulates the activity of the Bacillus subtilis stress response RT transcription factor, sigmaB."; RL J Bacteriol 189(17):6168-6175(2007). XX RX DOI; 10.1111/j.1365-2958.2007.05891.x. RX PUBMED; 17725564. RA Towe S., Leelakriangsak M., Kobayashi K., Van Duy N., Hecker M., Zuber P., RA Antelmann H.; RT "The MarR-type repressor MhqR (YkvE) regulates multiple RT dioxygenases/glyoxalases and an azoreductase which confer resistance to RT 2-methylhydroquinone and catechol in Bacillus subtilis."; RL Mol Microbiol 66(1):40-54(2007). XX RX DOI; 10.1111/j.1365-2958.2008.06110.x. RX PUBMED; 18208493. RA Leelakriangsak M., Huyen N.T., Towe S., van Duy N., Becher D., Hecker M., RA Antelmann H., Zuber P.; RT "Regulation of quinone detoxification by the thiol stress sensing RT DUF24/MarR-like repressor, YodB in Bacillus subtilis."; RL Mol Microbiol 67(5):1108-1124(2008). XX RX DOI; 10.1586/14789450.5.1.77. RX PUBMED; 18282125. RA Antelmann H., Hecker M., Zuber P.; RT "Proteomic signatures uncover thiol-specific electrophile resistance RT mechanisms in Bacillus subtilis."; RL Expert Rev Proteomics 5(1):77-90(2008). XX RX DOI; 10.1111/j.1742-4658.2008.06776.x. RX PUBMED; 19049517. RA Barnett J.P., van der Ploeg R., Eijlander R.T., Nenninger A., Mendel S., RA Rozeboom R., Kuipers O.P., van Dijl J.M., Robinson C.; RT "The twin-arginine translocation (Tat) systems from Bacillus subtilis RT display a conserved mode of complex organization and similar substrate RT recognition requirements."; RL FEBS J 276(1):232-243(2009). XX RX DOI; 10.1128/JB.00099-08. RX PUBMED; 18326565. RA Commichau F.M., Gunka K., Landmann J.J., Stulke J.; RT "Glutamate metabolism in Bacillus subtilis: gene expression and enzyme RT activities evolved to avoid futile cycles and to allow rapid responses to RT perturbations of the system."; RL J Bacteriol 190(10):3557-3564(2008). XX RX DOI; 10.1002/pmic.200701081. RX PUBMED; 18491319. RA Dreisbach A., Otto A., Becher D., Hammer E., Teumer A., Gouw J.W., RA Hecker M., Volker U.; RT "Monitoring of changes in the membrane proteome during stationary phase RT adaptation of Bacillus subtilis using in vivo labeling techniques."; RL Proteomics 8(10):2062-2076(2008). XX RX DOI; 10.1016/j.jtbi.2008.04.037. RX PUBMED; 18573504. RA Frey S., Millat T., Hohmann S., Wolkenhauer O.; RT "How quantitative measures unravel design principles in multi-stage RT phosphorylation cascades."; RL J Theor Biol 254(1):27-36(2008). XX RX DOI; 10.1038/nrmicro1932. RX PUBMED; 18628769. RA Gorke B., Stulke J.; RT "Carbon catabolite repression in bacteria: many ways to make the most out RT of nutrients."; RL Nat Rev Microbiol 6(8):613-624(2008). XX RX DOI; 10.1002/pmic.200800278. RX PUBMED; 19003856. RA Hecker M., Antelmann H., Buttner K., Bernhardt J.; RT "Gel-based proteomics of Gram-positive bacteria: a powerful tool to address RT physiological questions."; RL Proteomics 8(23-24):4958-4975(2008). XX RX DOI; 10.1111/j.1365-2958.2008.06438.x. RX PUBMED; 18786145. RA Kirstein J., Strahl H., Moliere N., Hamoen L.W., Turgay K.; RT "Localization of general and regulatory proteolysis in Bacillus subtilis RT cells."; RL Mol Microbiol 70(3):682-694(2008). XX RX DOI; 10.1016/j.tim.2008.10.003. RX PUBMED; 19059781. RA Kouwen T.R., van Dijl J.M.; RT "Interchangeable modules in bacterial thiol-disulfide exchange pathways."; RL Trends Microbiol 17(1):6-12(2009). XX RX DOI; 10.1128/AEM.00894-08. RX PUBMED; 18952880. RA Kouwen T.R., Dubois J.Y., Freudl R., Quax W.J., van Dijl J.M.; RT "Modulation of thiol-disulfide oxidoreductases for increased production of RT disulfide-bond-containing proteins in Bacillus subtilis."; RL Appl Environ Microbiol 74(24):7536-7545(2008). XX RX DOI; 10.1016/j.biosystems.2008.03.007. RX PUBMED; 18474306. RA Millat T., Sreenath S.N., Soebiyanto R.P., Avva J., Cho K.H., RA Wolkenhauer O.; RT "The role of dynamic stimulation pattern in the analysis of bistable RT intracellular networks."; RL Biosystems 92(3):270-281(2008). XX RX DOI; 10.1128/JB.00848-08. RX PUBMED; 18757537. RA Singh K.D., Schmalisch M.H., Stulke J., Gorke B.; RT "Carbon catabolite repression in Bacillus subtilis: quantitative analysis RT of repression exerted by different carbon sources."; RL J Bacteriol 190(21):7275-7284(2008). XX RX DOI; 10.1111/j.1365-2958.2008.06332.x. RX PUBMED; 18643936. RA Reder A., Hoper D., Weinberg C., Gerth U., Fraunholz M., Hecker M.; RT "The Spx paralogue MgsR (YqgZ) controls a subregulon within the general RT stress response of Bacillus subtilis."; RL Mol Microbiol 69(5):1104-1120(2008). XX RX DOI; 10.1002/pmic.200800009. RX PUBMED; 18546160. RA Westers L., Westers H., Zanen G., Antelmann H., Hecker M., Noone D., RA Devine K.M., van Dijl J.M., Quax W.J.; RT "Genetic or chemical protease inhibition causes significant changes in the RT Bacillus subtilis exoproteome."; RL Proteomics 8(13):2704-2713(2008). XX RX DOI; 10.1186/1475-2859-7-10. RX PUBMED; 18394159. RA Zweers J.C., Barak I., Becher D., Driessen A.J., Hecker M., Kontinen V.P., RA Saller M.J., Vavrova L., van Dijl J.M.; RT "Towards the development of Bacillus subtilis as a cell factory for RT membrane proteins and protein complexes."; RL Microb Cell Fact 7:10(2008). XX RX DOI; 10.1128/AAC.01189-08. RX PUBMED; 19047653. RA Dubois J.Y., Kouwen T.R., Schurich A.K., Reis C.R., Ensing H.T., Trip E.N., RA Zweers J.C., van Dijl J.M.; RT "Immunity to the bacteriocin sublancin 168 Is determined by the SunI (YolF) RT protein of Bacillus subtilis."; RL Antimicrob Agents Chemother 53(2):651-661(2009). XX RX DOI; 10.1111/j.1365-2958.2008.06568.x. RX PUBMED; 19170879. RA Nguyen T.T., Eiamphungporn W., Mader U., Liebeke M., Lalk M., Hecker M., RA Helmann J.D., Antelmann H.; RT "Genome-wide responses to carbonyl electrophiles in Bacillus subtilis: RT control of the thiol-dependent formaldehyde dehydrogenase AdhA and cysteine RT proteinase YraA by the MerR-family regulator YraB (AdhR)."; RL Mol Microbiol 71(4):876-894(2009). XX RX DOI; 10.1002/pmic.200800580. RX PUBMED; 19180538. RA Kouwen T.R., van der Ploeg R., Antelmann H., Hecker M., Homuth G., RA Mader U., van Dijl J.M.; RT "Overflow of a hyper-produced secretory protein from the Bacillus Sec RT pathway into the Tat pathway for protein secretion as revealed by RT proteogenomics."; RL Proteomics 9(4):1018-1032(2009). XX RX DOI; 10.1002/pmic.200800483. RX PUBMED; 19160392. RA Kouwen T.R., Antelmann H., van der Ploeg R., Denham E.L., Hecker M., RA van Dijl J.M.; RT "MscL of Bacillus subtilis prevents selective release of cytoplasmic RT proteins in a hypotonic environment."; RL Proteomics 9(4):1033-1043(2009). XX RX DOI; 10.1159/000308512. RX PUBMED; 20389117. RA Pietack N., Becher D., Schmidl S.R., Saier M.H., Hecker M., Commichau F.M., RA Stulke J.; RT "In vitro phosphorylation of key metabolic enzymes from Bacillus subtilis: RT PrkC phosphorylates enzymes from different branches of basic metabolism."; RL J Mol Microbiol Biotechnol 18(3):129-140(2010). XX RX DOI; 10.1093/bioinformatics/btn588. RX PUBMED; 19008250. RA Brouwer R.W., van Hijum S.A., Kuipers O.P.; RT "MINOMICS: visualizing prokaryote transcriptomics and proteomics data in a RT genomic context."; RL Bioinformatics 25(1):139-140(2009). XX RX DOI; 10.1074/mcp.M800546-MCP200. RX PUBMED; 19193632. RA Commichau F.M., Rothe F.M., Herzberg C., Wagner E., Hellwig D., RA Lehnik-Habrink M., Hammer E., Volker U., Stulke J.; RT "Novel activities of glycolytic enzymes in Bacillus subtilis: interactions RT with essential proteins involved in mRNA processing."; RL Mol Cell Proteomics 8(6):1350-1360(2009). XX RX DOI; 10.1128/JB.01484-09. RX PUBMED; 20154131. RA de Jong I.G., Veening J.W., Kuipers O.P.; RT "Heterochronic phosphorelay gene expression as a source of heterogeneity in RT Bacillus subtilis spore formation."; RL J Bacteriol 192(8):2053-2067(2010). XX RX DOI; 10.1093/database/bap012. RX PUBMED; 20157485. RA Florez L.A., Roppel S.F., Schmeisky A.G., Lammers C.R., Stulke J.; RT "A community-curated consensual annotation that is continuously updated: RT the Bacillus subtilis centred wiki SubtiWiki."; RL Database (Oxford) 2009:bap012(2009). XX RX DOI; 10.1128/AAC.00439-09. RX PUBMED; 19738010. RA Kouwen T.R., Trip E.N., Denham E.L., Sibbald M.J., Dubois J.Y., RA van Dijl J.M.; RT "The large mechanosensitive channel MscL determines bacterial RT susceptibility to the bacteriocin sublancin 168."; RL Antimicrob Agents Chemother 53(11):4702-4711(2009). XX RX DOI; 10.1007/s00253-009-2212-4. RX PUBMED; 19727703. RA Kouwen T.R., van Dijl J.M.; RT "Applications of thiol-disulfide oxidoreductases for optimized in vivo RT production of functionally active proteins in Bacillus."; RL Appl Microbiol Biotechnol 85(1):45-52(2009). XX RX DOI; 10.1128/AEM.01671-09. RX PUBMED; 19948853. RA Kouwen T.R., Nielsen A.K., Denham E.L., Dubois J.Y., Dorenbos R., RA Rasmussen M.D., Quax W.J., Freudl R., van Dijl J.M.; RT "Contributions of the pre- and pro-regions of a Staphylococcus hyicus RT lipase to secretion of a heterologous protein by Bacillus subtilis."; RL Appl Environ Microbiol 76(3):659-669(2010). XX RX DOI; 10.1099/mic.0.035790-0. RX PUBMED; 19959575. RA Lammers C.R., Florez L.A., Schmeisky A.G., Roppel S.F., Mader U., RA Hamoen L., Stulke J.; RT "Connecting parts with processes: SubtiWiki and SubtiPathways integrate RT gene and pathway annotation for Bacillus subtilis."; RL Microbiology (Reading) 156(Pt 3):849-859(2010). XX RX DOI; 10.1016/j.ab.2009.04.030. RX PUBMED; 19397887. RA Liebeke M., Wunder A., Lalk M.; RT "A rapid microwave-assisted derivatization of bacterial metabolome samples RT for gas chromatography/mass spectrometry analysis."; RL Anal Biochem 401(2):312-314(2010). XX RX DOI; 10.1128/JB.00937-09. RX PUBMED; 19837798. RA Pother D.C., Liebeke M., Hochgrafe F., Antelmann H., Becher D., Lalk M., RA Lindequist U., Borovok I., Cohen G., Aharonowitz Y., Hecker M.; RT "Diamide triggers mainly S Thiolations in the cytoplasmic proteomes of RT Bacillus subtilis and Staphylococcus aureus."; RL J Bacteriol 191(24):7520-7530(2009). XX RX DOI; 10.1128/MMBR.00037-08. RX PUBMED; 19721087. RA van Hijum S.A., Medema M.H., Kuipers O.P.; RT "Mechanisms and evolution of control logic in prokaryotic transcriptional RT regulation."; RL Microbiol Mol Biol Rev 73(3):481-509, Table of Contents(2009). XX RX DOI; 10.1007/s00018-009-0160-x. RX PUBMED; 19823765. RA Yuan J., Zweers J.C., van Dijl J.M., Dalbey R.E.; RT "Protein transport across and into cell membranes in bacteria and RT archaea."; RL Cell Mol Life Sci 67(2):179-199(2010). XX RX DOI; 10.1128/AEM.01560-09. RX PUBMED; 19820159. RA Zweers J.C., Wiegert T., van Dijl J.M.; RT "Stress-responsive systems set specific limits to the overproduction of RT membrane proteins in Bacillus subtilis."; RL Appl Environ Microbiol 75(23):7356-7364(2009). XX RX DOI; 10.1016/j.jmb.2010.05.055. RX PUBMED; 20630473. RA Gunka K., Newman J.A., Commichau F.M., Herzberg C., Rodrigues C., RA Hewitt L., Lewis R.J., Stulke J.; RT "Functional dissection of a trigger enzyme: mutations of the bacillus RT subtilis glutamate dehydrogenase RocG that affect differentially its RT catalytic activity and regulatory properties."; RL J Mol Biol 400(4):815-827(2010). XX RX DOI; 10.1016/j.resmic.2009.03.008. RX PUBMED; 19403106. RA Hecker M., Reder A., Fuchs S., Pagels M., Engelmann S.; RT "Physiological proteomics and stress/starvation responses in Bacillus RT subtilis and Staphylococcus aureus."; RL Res Microbiol 160(4):245-258(2009). XX RX DOI; 10.1093/bioinformatics/btq469. RX PUBMED; 20739311. RA Asif H.M., Rolfe M.D., Green J., Lawrence N.D., Rattray M., Sanguinetti G.; RT "TFInfer: a tool for probabilistic inference of transcription factor RT activities."; RL Bioinformatics 26(20):2635-2636(2010). XX RX DOI; 10.1080/00207720903147746. RA Nikolov S., Lai X., Liebal Ulf, Wolkenhauer Olaf, Vera J.; RT "Integration of sensitivity and bifurcation analysis to detect critical RT processes in a model combining signalling and cell population dynamics"; RL Int. J. of Systems Sc.(2010). XX RX DOI; 10.1186/1752-0509-2-92. RA Vera Julio, Millat Thomas, Kolch Walter, Wolkenhauer Olaf; RT "Dynamics of receptor and protein transducer homodimerisation"; RL BMC Syst Biol(2008). XX RX DOI; 10.1524/auto.2008.0707. RA Wolkenhauer Olaf, Hofmeyr Jan-Hendrik S.; RT "Ein Beitrag zu einer Theorie lebender Zellen (A Contribution towards a RT Theory of Living Cells)"; RL at - Automatisierungstechnik(2008). XX RX DOI; 10.1007/s00253-010-2741-x. RA Janssen Holger, Döring Christina, Ehrenreich Armin, Voigt Birgit, RA Hecker Michael, Bahl Hubert, Fischer Ralf-Jörg; RT "A proteomic and transcriptional view of acidogenic and solventogenic RT steady-state cells of Clostridium acetobutylicum in a chemostat culture"; RL Appl Microbiol Biotechnol(2010). XX RX DOI; 10.1016/j.ymben.2010.10.001. RX PUBMED; 20933603. RA Meyer F.M., Gerwig J., Hammer E., Herzberg C., Commichau F.M., Volker U., RA Stulke J.; RT "Physical interactions between tricarboxylic acid cycle enzymes in Bacillus RT subtilis: evidence for a metabolon."; RL Metab Eng 13(1):18-27(2011). XX RX DOI; 10.1039/c005305h. RA Frey Simone, Sott Kristin, Smedh Maria, Millat Thomas, Dahl Peter, RA Wolkenhauer Olaf, Goksör Mattias; RT "A mathematical analysis of nuclear intensity dynamics for Mig1-GFP under RT consideration of bleaching effects and background noise in Saccharomyces RT cerevisiae"; RL Mol. BioSyst.(2011). XX RX DOI; 10.1128/AEM.01838-10. RX PUBMED; 21097579. RA Fiedler T., Bekker M., Jonsson M., Mehmeti I., Pritzschke A., Siemens N., RA Nes I., Hugenholtz J., Kreikemeyer B.; RT "Characterization of three lactic acid bacteria and their isogenic ldh RT deletion mutants shows optimization for YATP (cell mass produced per mole RT of ATP) at their physiological pHs."; RL Appl Environ Microbiol 77(2):612-617(2011). XX RX DOI; 10.1186/1752-0509-5-10. RT "A systems biology approach to investigate the effect of pH-induced gene RT regulation on solvent production by Clostridium acetobutylicum in RT continuous culture"; RL BMC Syst Biol(2011). XX RX DOI; 10.1007/978-1-60761-987-1_27. RX PUBMED; 21063964. RA Millat T., Wolkenhauer O., Fischer R.J., Bahl H.; RT "Modeling of cellular processes: methods, data, and requirements."; RL Methods Mol Biol 696:429-447(2011). XX RX DOI; 10.1074/jbc.M110.211144. RX PUBMED; 21252224. RA Rolfe M.D., Ter Beek A., Graham A.I., Trotter E.W., Asif H.M., RA Sanguinetti G., de Mattos J.T., Poole R.K., Green J.; RT "Transcript profiling and inference of Escherichia coli K-12 ArcA activity RT across the range of physiologically relevant oxygen concentrations."; RL J Biol Chem 286(12):10147-10154(2011). XX RX DOI; 10.2217/fmb.10.128. RX PUBMED; 21133689. RA Fiedler T., Sugareva V., Patenge N., Kreikemeyer B.; RT "Insights into Streptococcus pyogenes pathogenesis from transcriptome RT studies."; RL Future Microbiol 5(11):1675-1694(2010). XX RX DOI; 10.1186/1741-7007-8-54. RX PUBMED; 20459653. RA Yuzenkova Y., Bochkareva A., Tadigotla V.R., Roghanian M., Zorov S., RA Severinov K., Zenkin N.; RT "Stepwise mechanism for transcription fidelity."; RL BMC Biol 8:54(2010). XX RX DOI; 10.1111/j.1365-2958.2010.07113.x. RX PUBMED; 20233302. RA Veening J.W., Kuipers O.P.; RT "Gene position within a long transcript as a determinant for stochastic RT switching in bacteria."; RL Mol Microbiol 76(2):269-272(2010). XX RX DOI; 10.1016/j.tcb.2010.10.006. RX PUBMED; 21123069. RA Scholefield G., Veening J.W., Murray H.; RT "DnaA and ORC: more than DNA replication initiators."; RL Trends Cell Biol 21(3):188-194(2011). XX RX DOI; 10.1371/journal.pone.0009724. RX PUBMED; 20300532. RA Nijland R., Burgess J.G., Errington J., Veening J.W.; RT "Transformation of environmental Bacillus subtilis isolates by transiently RT inducing genetic competence."; RL PLoS One 5(3):e9724(2010). XX RX DOI; 10.1111/j.1365-2958.2009.06872.x. RX PUBMED; 19737355. RA Eberhardt A., Wu L.J., Errington J., Vollmer W., Veening J.W.; RT "Cellular localization of choline-utilization proteins in Streptococcus RT pneumoniae using novel fluorescent reporter systems."; RL Mol Microbiol 74(2):395-408(2009). XX RX DOI; 10.1101/gad.528209. RX PUBMED; 19684115. RA Veening J.W., Murray H., Errington J.; RT "A mechanism for cell cycle regulation of sporulation initiation in RT Bacillus subtilis."; RL Genes Dev 23(16):1959-1970(2009). XX RX DOI; 10.1093/nar/gkq1359. RX PUBMED; 21266474. RA Roghanian M., Yuzenkova Y., Zenkin N.; RT "Controlled interplay between trigger loop and Gre factor in the RNA RT polymerase active centre."; RL Nucleic Acids Res 39(10):4352-4359(2011). XX RX DOI; 10.1128/AEM.02485-10. RX PUBMED; 21296946. RA Mehmeti I., Jonsson M., Fergestad E.M., Mathiesen G., Nes I.F., Holo H.; RT "Transcriptome, proteome, and metabolite analyses of a lactate RT dehydrogenase-negative mutant of Enterococcus faecalis V583."; RL Appl Environ Microbiol 77(7):2406-2413(2011). XX RX DOI; 10.1073/pnas.0914424107. RX PUBMED; 20534498. RA Yuzenkova Y., Zenkin N.; RT "Central role of the RNA polymerase trigger loop in intrinsic RNA RT hydrolysis."; RL Proc Natl Acad Sci U S A 107(24):10878-10883(2010). XX RX DOI; 10.1103/PhysRevLett.105.220601. RX PUBMED; 21231375. RA Luksza M., Lassig M., Berg J.; RT "Significance analysis and statistical mechanics: an application to RT clustering."; RL Phys Rev Lett 105(22):220601(2010). XX RX DOI; 10.1093/nar/gkq1177. RX PUBMED; 21106498. RA Schumacher M.A., Sprehe M., Bartholomae M., Hillen W., Brennan R.G.; RT "Structures of carbon catabolite protein A-(HPr-Ser46-P) bound to diverse RT catabolite response element sites reveal the basis for high-affinity RT binding to degenerate DNA operators."; RL Nucleic Acids Res 39(7):2931-2942(2011). XX RX DOI; 10.1007/s00792-009-0280-0. RX PUBMED; 19802714. RA Zaparty M., Esser D., Gertig S., Haferkamp P., Kouril T., Manica A., RA Pham T.K., Reimann J., Schreiber K., Sierocinski P., Teichmann D., RA van Wolferen M., von Jan M., Wieloch P., Albers S.V., Driessen A.J., RA Klenk H.P., Schleper C., Schomburg D., van der Oost J., Wright P.C., RA Siebers B.; RT ""Hot standards" for the thermoacidophilic archaeon Sulfolobus RT solfataricus."; RL Extremophiles 14(1):119-142(2010). XX RX DOI; 10.1128/AAC.00696-09. RX PUBMED; 19995931. RA Chlebowicz M.A., Nganou K., Kozytska S., Arends J.P., Engelmann S., RA Grundmann H., Ohlsen K., van Dijl J.M., Buist G.; RT "Recombination between ccrC genes in a type V (5C2&5) staphylococcal RT cassette chromosome mec (SCCmec) of Staphylococcus aureus ST398 leads to RT conversion from methicillin resistance to methicillin susceptibility in RT vivo."; RL Antimicrob Agents Chemother 54(2):783-791(2010). XX RX DOI; 10.1128/JB.01276-10. RX PUBMED; 21169484. RA Tsompanidou E., Sibbald M.J., Chlebowicz M.A., Dreisbach A., Back J.W., RA van Dijl J.M., Buist G., Denham E.L.; RT "Requirement of the agr locus for colony spreading of Staphylococcus RT aureus."; RL J Bacteriol 193(5):1267-1272(2011). XX RX DOI; 10.1371/journal.pone.0009057. RX PUBMED; 20140229. RA Miller M., Donat S., Rakette S., Stehle T., Kouwen T.R., Diks S.H., RA Dreisbach A., Reilman E., Gronau K., Becher D., Peppelenbosch M.P., RA van Dijl J.M., Ohlsen K.; RT "Staphylococcal PknB as the first prokaryotic representative of the RT proline-directed kinases."; RL PLoS One 5(2):e9057(2010). XX RX DOI; 10.1089/omi.2010.0044. RX PUBMED; 20726779. RA Arino J.; RT "Integrative responses to high pH stress in S. cerevisiae."; RL OMICS 14(5):517-523(2010). XX RX DOI; 10.1111/j.1574-6968.2011.02214.x. RX PUBMED; 21241357. RA Ramos J., Arino J., Sychrova H.; RT "Alkali-metal-cation influx and efflux systems in nonconventional yeast RT species."; RL FEMS Microbiol Lett 317(1):1-8(2011). XX RX DOI; 10.1111/j.1365-2958.2010.07201.x. RA Mika Jacek, Van Den Bogaart Geert, Veenhoff Liesbeth, Krasnikov Victor, RA Poolman Bert; RT "Molecular sieving properties of the cytoplasm of Escherichia coli and RT consequences of osmotic stress"; XX RX DOI; 10.1016/j.copbio.2010.09.009. RX PUBMED; 20952181. RA Mika J.T., Poolman B.; RT "Macromolecule diffusion and confinement in prokaryotic cells."; RL Curr Opin Biotechnol 22(1):117-126(2011). XX RX DOI; 10.1111/j.1365-2958.2007.05705.x. RX PUBMED; 17462029. RA van den Bogaart G., Hermans N., Krasnikov V., Poolman B.; RT "Protein mobility and diffusive barriers in Escherichia coli: consequences RT of osmotic stress."; RL Mol Microbiol 64(3):858-871(2007). XX RX DOI; 10.1128/MMBR.00010-09. RX PUBMED; 19487732. RA Spitzer J., Poolman B.; RT "The role of biomacromolecular crowding, ionic strength, and RT physicochemical gradients in the complexities of life's emergence."; RL Microbiol Mol Biol Rev 73(2):371-388(2009). XX RX DOI; 10.1016/j.bbamem.2011.05.001. RX PUBMED; 21586269. RA Mika J.T., Moiset G., Cirac A.D., Feliu L., Bardaji E., Planas M., RA Sengupta D., Marrink S.J., Poolman B.; RT "Structural basis for the enhanced activity of cyclic antimicrobial RT peptides: the case of BPC194."; RL Biochim Biophys Acta 1808(9):2197-2205(2011). XX RX DOI; 10.1016/j.bpj.2011.03.057. RX PUBMED; 21575576. RA Cirac A.D., Moiset G., Mika J.T., Kocer A., Salvador P., Poolman B., RA Marrink S.J., Sengupta D.; RT "The molecular basis for antimicrobial activity of pore-forming cyclic RT peptides."; RL Biophys J 100(10):2422-2431(2011). XX RX DOI; 10.1111/j.1365-2958.2011.07722.x. RX PUBMED; 21651626. RA Minnen A., Attaiech L., Thon M., Gruber S., Veening J.W.; RT "SMC is recruited to oriC by ParB and promotes chromosome segregation in RT Streptococcus pneumoniae."; RL Mol Microbiol 81(3):676-688(2011). XX RX DOI; 10.3791/3145. RX PUBMED; 21841760. RA de Jong I.G., Beilharz K., Kuipers O.P., Veening J.W.; RT "Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using RT Automated Time-lapse Microscopy."; RL J Vis Exp (53)(2011). XX RX DOI; 10.1128/AEM.06604-11. RX PUBMED; 22038603. RA Mehmeti I., Faergestad E.M., Bekker M., Snipen L., Nes I.F., Holo H.; RT "Growth rate-dependent control in Enterococcus faecalis: effects on the RT transcriptome and proteome, and strong regulation of lactate RT dehydrogenase."; RL Appl Environ Microbiol 78(1):170-176(2012). XX RX DOI; 10.1038/emboj.2011.252. RX PUBMED; 21792175. RA Yuzenkova Y., Tadigotla V.R., Severinov K., Zenkin N.; RT "A new basal promoter element recognized by RNA polymerase core enzyme."; RL EMBO J 30(18):3766-3775(2011). XX RX DOI; 10.1038/emboj.2011.432. RX PUBMED; 22124324. RA Bochkareva A., Yuzenkova Y., Tadigotla V.R., Zenkin N.; RT "Factor-independent transcription pausing caused by recognition of the RT RNA-DNA hybrid sequence."; RL EMBO J 31(3):630-639(2012). XX RX DOI; 10.1093/nar/gkr1262. RX PUBMED; 22210860. RA Castro-Roa D., Zenkin N.; RT "In vitro experimental system for analysis of transcription-translation RT coupling."; RL Nucleic Acids Res 40(6):e45(2012). XX RX DOI; 10.1371/journal.pgen.1002160. RX PUBMED; 21814515. RA Perfeito L., Ghozzi S., Berg J., Schnetz K., Lassig M.; RT "Nonlinear fitness landscape of a molecular pathway."; RL PLoS Genet 7(7):e1002160(2011). XX RX DOI; 10.1371/journal.pcbi.1002352. RT "Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy RT Metabolism"; RL PLoS Comput Biol(2012). XX RX DOI; 10.1111/j.1742-4658.2012.08523.x. RX PUBMED; 22325620. RA Levering J., Musters M.W., Bekker M., Bellomo D., Fiedler T., de Vos W.M., RA Hugenholtz J., Kreikemeyer B., Kummer U., Teusink B.; RT "Role of phosphate in the central metabolism of two lactic acid bacteria--a RT comparative systems biology approach."; RL FEBS J 279(7):1274-1290(2012). XX RX DOI; 10.1016/j.jchromb.2011.10.036. RA Vielhauer Oliver, Zakhartsev Maksim, Horn Thomas, Takors Ralf, RA Reuss Matthias; RT "Simplified absolute metabolite quantification by gas RT chromatography–isotope dilution mass spectrometry on the basis of RT commercially available source material"; RL Journal of Chromatography B(2011). XX RT ; XX RX DOI; 10.1093/bioinformatics/btr312. RX PUBMED; 21622664. RA Wolstencroft K., Owen S., Horridge M., Krebs O., Mueller W., Snoep J.L., RA du Preez F., Goble C.; RT "RightField: embedding ontology annotation in spreadsheets."; RL Bioinformatics 27(14):2021-2022(2011). XX RX DOI; 10.1186/1471-2105-13-S1-S5. RX PUBMED; 22373396. RA Jupp S., Horridge M., Iannone L., Klein J., Owen S., Schanstra J., RA Wolstencroft K., Stevens R.; RT "Populous: a tool for building OWL ontologies from templates."; RL BMC Bioinformatics 13 Suppl 1(Suppl 1):S5(2012). XX RX DOI; 10.1038/ng.1054. RX PUBMED; 22281772. RA Sansone S.A., Rocca-Serra P., Field D., Maguire E., Taylor C., Hofmann O., RA Fang H., Neumann S., Tong W., Amaral-Zettler L., Begley K., Booth T., RA Bougueleret L., Burns G., Chapman B., Clark T., Coleman L.A., Copeland J., RA Das S., de Daruvar A., de Matos P., Dix I., Edmunds S., Evelo C.T., RA Forster M.J., Gaudet P., Gilbert J., Goble C., Griffin J.L., Jacob D., RA Kleinjans J., Harland L., Haug K., Hermjakob H., Ho Sui S.J., Laederach A., RA Liang S., Marshall S., McGrath A., Merrill E., Reilly D., Roux M., RA Shamu C.E., Shang C.A., Steinbeck C., Trefethen A., Williams-Jones B., RA Wolstencroft K., Xenarios I., Hide W.; RT "Toward interoperable bioscience data."; RL Nat Genet 44(2):121-126(2012). XX RX DOI; 10.1159/000320973. RX PUBMED; 21212688. RA Grimmler C., Janssen H., Krausse D., Fischer R.J., Bahl H., Durre P., RA Liebl W., Ehrenreich A.; RT "Genome-wide gene expression analysis of the switch between acidogenesis RT and solventogenesis in continuous cultures of Clostridium acetobutylicum."; RL J Mol Microbiol Biotechnol 20(1):1-15(2011). XX RT ; XX RX DOI; 10.1016/j.ab.2009.10.011. RA Zakhartsev Maksim, Bock Christian; RT "Miniaturized device for agitating a high-density yeast suspension that is RT suitable for in vivo nuclear magnetic resonance applications"; RL Analytical Biochemistry(2010). XX RX DOI; 10.1016/j.jbiotec.2011.03.015. RA Steinsiek Sonja, Frixel S., Stagge Stefan, Bettenbrock Katja; RT "Characterization of E. coli MG1655 and frdA and sdhC mutants at various RT aerobiosis levels"; RL Journal of Biotechnology(2011). XX RX DOI; 10.1016/j.jbiotec.2012.03.018. RA Schwarz Katrin, Kuit Wouter, Grimmler Christina, Ehrenreich Armin, RA Kengen Servé; RT "A transcriptional study of acidogenic chemostat cells of Clostridium RT acetobutylicum–cellular behavior in adaptation to n-butanol"; RL Journal of Biotechnology(2012). XX RX DOI; 10.1021/bp050381q. RA Schaub Jochen, Schiesling Carola, Reuss Matthias, Dauner Michael; RT "Integrated Sampling Procedure for Metabolome Analysis"; RL Biotechnol Progress(2006). XX RX DOI; 10.1126/science.1206848. RX PUBMED; 22383849. RA Nicolas P., Mader U., Dervyn E., Rochat T., Leduc A., Pigeonneau N., RA Bidnenko E., Marchadier E., Hoebeke M., Aymerich S., Becher D., RA Bisicchia P., Botella E., Delumeau O., Doherty G., Denham E.L., Fogg M.J., RA Fromion V., Goelzer A., Hansen A., Hartig E., Harwood C.R., Homuth G., RA Jarmer H., Jules M., Klipp E., Le Chat L., Lecointe F., Lewis P., RA Liebermeister W., March A., Mars R.A., Nannapaneni P., Noone D., Pohl S., RA Rinn B., Rugheimer F., Sappa P.K., Samson F., Schaffer M., Schwikowski B., RA Steil L., Stulke J., Wiegert T., Devine K.M., Wilkinson A.J., RA van Dijl J.M., Hecker M., Volker U., Bessieres P., Noirot P.; RT "Condition-dependent transcriptome reveals high-level regulatory RT architecture in Bacillus subtilis."; RL Science 335(6072):1103-1106(2012). XX RX DOI; 10.1039/C2MB25031D. RA Liebal Ulf, Sappa Praveen kumar, Millat Thomas, Steil Leif, Homuth Georg, RA Voelker Uwe, Wolkenhauer Olaf; RT "Proteolysis of beta-galactosidase following SigmaB activation in Bacillus RT subtilis"; RL Mol. BioSyst.(2012). XX RX DOI; 10.1099/mic.0.047357-0. RX PUBMED; 21233158. RA Brill J., Hoffmann T., Putzer H., Bremer E.; RT "T-box-mediated control of the anabolic proline biosynthetic genes of RT Bacillus subtilis."; RL Microbiology (Reading) 157(Pt 4):977-987(2011). XX RX DOI; 10.1111/j.1365-2958.2007.06071.x. RX PUBMED; 18086213. RA Commichau F.M., Stulke J.; RT "Trigger enzymes: bifunctional proteins active in metabolism and in RT controlling gene expression."; RL Mol Microbiol 67(4):692-702(2008). XX RX DOI; 10.1002/9783527629237.ch18. RA Commichau Fabian M., Stlke Jrg; RT "Signal Transduction by Trigger Enzymes: Bifunctional Enzymes and RT Transporters Controlling Gene Expression"; RL Bacterial Signaling(2009). XX RX DOI; 10.1002/bies.201000127. RX PUBMED; 21254151. RA de Jong I.G., Haccou P., Kuipers O.P.; RT "Bet hedging or not? A guide to proper classification of microbial survival RT strategies."; RL Bioessays 33(3):215-223(2011). XX RX DOI; 10.1002/pmic.201100174. RX PUBMED; 21800427. RA Fasehee H., Westers H., Bolhuis A., Antelmann H., Hecker M., Quax W.J., RA Mirlohi A.F., van Dijl J.M., Ahmadian G.; RT "Functional analysis of the sortase YhcS in Bacillus subtilis."; RL Proteomics 11(19):3905-3913(2011). XX RX DOI; 10.1186/1752-0509-5-5. RX PUBMED; 21219666. RA Florez L.A., Gunka K., Polania R., Tholen S., Stulke J.; RT "SPABBATS: A pathway-discovery method based on Boolean satisfiability that RT facilitates the characterization of suppressor mutants."; RL BMC Syst Biol 5:5(2011). XX RX DOI; 10.1093/bioinformatics/btq585. RX PUBMED; 20947526. RA Florez L.A., Lammers C.R., Michna R., Stulke J.; RT "CellPublisher: a web platform for the intuitive visualization and sharing RT of metabolic, signalling and regulatory pathways."; RL Bioinformatics 26(23):2997-2999(2010). XX RX DOI; 10.1007/s00253-010-2854-2. RX PUBMED; 20821203. RA Kohlstedt M., Becker J., Wittmann C.; RT "Metabolic fluxes and beyond-systems biology understanding and engineering RT of microbial metabolism."; RL Appl Microbiol Biotechnol 88(5):1065-1075(2010). XX RX DOI; 10.1111/j.1574-6968.2011.02456.x. RX PUBMED; 22092971. RA Landmann J.J., Werner S., Hillen W., Stulke J., Gorke B.; RT "Carbon source control of the phosphorylation state of the Bacillus RT subtilis carbon-flux regulator Crh in vivo."; RL FEMS Microbiol Lett 327(1):47-53(2012). XX RX DOI; 10.1111/j.1742-4658.2012.08604.x. RX PUBMED; 22512862. RA Wunsche A., Hammer E., Bartholomae M., Volker U., Burkovski A., Seidel G., RA Hillen W.; RT "CcpA forms complexes with CodY and RpoA in Bacillus subtilis."; RL FEBS J 279(12):2201-2214(2012). XX RX DOI; 10.1128/JB.05500-11. RX PUBMED; 21803996. RA Lehnik-Habrink M., Newman J., Rothe F.M., Solovyova A.S., Rodrigues C., RA Herzberg C., Commichau F.M., Lewis R.J., Stulke J.; RT "RNase Y in Bacillus subtilis: a Natively disordered protein that is the RT functional equivalent of RNase E from Escherichia coli."; RL J Bacteriol 193(19):5431-5441(2011). XX RX DOI; 10.1111/j.1365-2958.2011.07777.x. RX PUBMED; 21815947. RA Lehnik-Habrink M., Schaffer M., Mader U., Diethmaier C., Herzberg C., RA Stulke J.; RT "RNA processing in Bacillus subtilis: identification of targets of the RT essential RNase Y."; RL Mol Microbiol 81(6):1459-1473(2011). XX RX DOI; 10.1039/c0mb00315h. RX PUBMED; 21327190. RA Liebeke M., Dorries K., Zuhlke D., Bernhardt J., Fuchs S., Pane-Farre J., RA Engelmann S., Volker U., Bode R., Dandekar T., Lindequist U., Hecker M., RA Lalk M.; RT "A metabolomics and proteomics study of the adaptation of Staphylococcus RT aureus to glucose starvation."; RL Mol Biosyst 7(4):1241-1253(2011). XX RX DOI; 10.1111/j.1365-2958.2008.06382.x. RX PUBMED; 18673455. RA Liebeke M., Pother D.C., van Duy N., Albrecht D., Becher D., Hochgrafe F., RA Lalk M., Hecker M., Antelmann H.; RT "Depletion of thiol-containing proteins in response to quinones in Bacillus RT subtilis."; RL Mol Microbiol 69(6):1513-1529(2008). XX RX DOI; 10.1371/journal.pone.0018140. RX PUBMED; 21479178. RA van der Ploeg R., Mader U., Homuth G., Schaffer M., Denham E.L., RA Monteferrante C.G., Miethke M., Marahiel M.A., Harwood C.R., Winter T., RA Hecker M., Antelmann H., van Dijl J.M.; RT "Environmental salinity determines the specificity and need for RT Tat-dependent secretion of the YwbN protein in Bacillus subtilis."; RL PLoS One 6(3):e18140(2011). XX RT ; XX RX DOI; 10.1016/j.copbio.2010.10.003. RX PUBMED; 21074401. RA Mader U., Nicolas P., Richard H., Bessieres P., Aymerich S.; RT "Comprehensive identification and quantification of microbial RT transcriptomes by genome-wide unbiased methods."; RL Curr Opin Biotechnol 22(1):32-41(2011). XX RX DOI; 10.1093/nar/gkr923. RX PUBMED; 22096228. RA Mader U., Schmeisky A.G., Florez L.A., Stulke J.; RT "SubtiWiki--a comprehensive community resource for the model organism RT Bacillus subtilis."; RL Nucleic Acids Res 40(Database issue):D1278-D1287(2012). XX RX DOI; 10.1016/j.jmb.2011.12.024. RX PUBMED; 22198292. RA Newman J.A., Hewitt L., Rodrigues C., Solovyova A.S., Harwood C.R., RA Lewis R.J.; RT "Dissection of the network of interactions that links RNA processing with RT glycolysis in the Bacillus subtilis degradosome."; RL J Mol Biol 416(1):121-136(2012). XX RX DOI; 10.1007/978-3-642-20198-1_15. RA Pittelkow Marco, Bremer Erhard; RT "Cellular Adjustments of Bacillus subtilis and Other Bacilli to Fluctuating RT Salinities"; RL Halophiles and Hypersaline Environments(2011). XX RX DOI; 10.1261/rna.2837311. RX PUBMED; 21947264. RA Manful T., Fadda A., Clayton C.; RT "The role of the 5'-3' exoribonuclease XRNA in transcriptome-wide mRNA RT degradation."; RL RNA 17(11):2039-2047(2011). XX RX DOI; 10.1093/nar/gkr1046. RX PUBMED; 22102587. RA Wittig U., Kania R., Golebiewski M., Rey M., Shi L., Jong L., Algaa E., RA Weidemann A., Sauer-Danzwith H., Mir S., Krebs O., Bittkowski M., RA Wetsch E., Rojas I., Muller W.; RT "SABIO-RK--database for biochemical reaction kinetics."; RL Nucleic Acids Res 40(Database issue):D790-D796(2012). XX RX DOI; 10.1038/nbt.2243. RA Marx Vivien; RT "My data are your data"; RL Nat Biotechnol(2012). XX RT ; XX RX DOI; 10.1111/j.1742-4658.2012.08658.x. RX PUBMED; 22686585. RA du Preez F.B., van Niekerk D.D., Snoep J.L.; RT "From steady-state to synchronized yeast glycolytic oscillations II: model RT validation."; RL FEBS J 279(16):2823-2836(2012). XX RX DOI; 10.1111/j.1742-4658.2012.08665.x. RX PUBMED; 22712534. RA du Preez F.B., van Niekerk D.D., Kooi B., Rohwer J.M., Snoep J.L.; RT "From steady-state to synchronized yeast glycolytic oscillations I: model RT construction."; RL FEBS J 279(16):2810-2822(2012). XX RX DOI; 10.1098/rsob.120091. RX PUBMED; 22870390. RA Rolfe M.D., Ocone A., Stapleton M.R., Hall S., Trotter E.W., Poole R.K., RA Sanguinetti G., Green J.; RT "Systems analysis of transcription factor activities in environments with RT stable and dynamic oxygen concentrations."; RL Open Biol 2(7):120091(2012). XX RT ; XX RX DOI; 10.1016/j.bbabio.2012.09.014. RT "‘Domino’ systems biology and the ‘A’ of ATP"; RL Biochimica et Biophysica Acta (BBA) - Bioenergetics(2012). XX RX DOI; 10.1002/cpe.2941. RA Wolstencroft Katy, Owen Stuart, Horridge Matthew, Jupp Simon, Krebs Olga, RA Snoep Jacky, du Preez Franco, Müller Wolfgang, Stevens Robert, RA Goble Carole; RT "Stealthy annotation of experimental biology by spreadsheets"; RL Concurrency and Computation: Practice and Experience(2013). XX RX DOI; 10.1007/s00239-012-9503-6. RX PUBMED; 22544085. RA Zenkin N.; RT "Hypothesis: emergence of translation as a result of RNA helicase RT evolution."; RL J Mol Evol 74(5-6):249-256(2012). XX RT ; XX RX DOI; 10.1111/j.1462-2920.2012.02892.x. RX PUBMED; 23033921. RA de Jong I.G., Veening J.W., Kuipers O.P.; RT "Single cell analysis of gene expression patterns during carbon starvation RT in Bacillus subtilis reveals large phenotypic variation."; RL Environ Microbiol 14(12):3110-3121(2012). XX RX DOI; 10.1186/1752-0509-6-144. RX PUBMED; 23171476. RA Kolar M., Meier J., Mustonen V., Lassig M., Berg J.; RT "GraphAlignment: Bayesian pairwise alignment of biological networks."; RL BMC Syst Biol 6:144(2012). XX RX DOI; 10.1128/JB.01502-12. RT "Glucose Transport in Escherichia coli Mutant Strains with Defects in Sugar RT Transport Systems"; RL Journal of Bacteriology(2012). XX RX DOI; 10.1128/JB.06197-11. RX PUBMED; 22001508. RA Meyer F.M., Jules M., Mehne F.M., Le Coq D., Landmann J.J., Gorke B., RA Aymerich S., Stulke J.; RT "Malate-mediated carbon catabolite repression in Bacillus subtilis involves RT the HPrK/CcpA pathway."; RL J Bacteriol 193(24):6939-6949(2011). XX RX DOI; 10.1128/JB.06470-11. RX PUBMED; 22178973. RA Gunka K., Tholen S., Gerwig J., Herzberg C., Stulke J., Commichau F.M.; RT "A high-frequency mutation in Bacillus subtilis: requirements for the RT decryptification of the gudB glutamate dehydrogenase gene."; RL J Bacteriol 194(5):1036-1044(2012). XX RX DOI; 10.1111/1574-6968.12041. RX PUBMED; 23136871. RA Meyer F.M., Stulke J.; RT "Malate metabolism in Bacillus subtilis: distinct roles for three classes RT of malate-oxidizing enzymes."; RL FEMS Microbiol Lett 339(1):17-22(2013). XX RX DOI; 10.1111/j.1365-2958.2012.08072.x. RX PUBMED; 22568516. RA Lehnik-Habrink M., Lewis R.J., Mader U., Stulke J.; RT "RNA degradation in Bacillus subtilis: an interplay of essential endo- and RT exoribonucleases."; RL Mol Microbiol 84(6):1005-1017(2012). XX RX DOI; 10.1186/1471-2164-13-401. RX PUBMED; 22900538. RA Marciniak B.C., Pabijaniak M., de Jong A., Duhring R., Seidel G., RA Hillen W., Kuipers O.P.; RT "High- and low-affinity cre boxes for CcpA binding in Bacillus subtilis RT revealed by genome-wide analysis."; RL BMC Genomics 13:401(2012). XX RX DOI; 10.1021/pr300866f. RX PUBMED; 23256564. RA Goosens V.J., Otto A., Glasner C., Monteferrante C.C., van der Ploeg R., RA Hecker M., Becher D., van Dijl J.M.; RT "Novel twin-arginine translocation pathway-dependent phenotypes of Bacillus RT subtilis unveiled by quantitative proteomics."; RL J Proteome Res 12(2):796-807(2013). XX RX DOI; 10.1128/JB.01475-12. RX PUBMED; 23175651. RA Lehnik-Habrink M., Rempeters L., Kovacs A.T., Wrede C., Baierlein C., RA Krebber H., Kuipers O.P., Stulke J.; RT "DEAD-Box RNA helicases in Bacillus subtilis have multiple functions and RT act independently from each other."; RL J Bacteriol 195(3):534-544(2013). XX RX DOI; 10.1128/JB.01505-12. RX PUBMED; 23175650. RA Hoffmann T., Wensing A., Brosius M., Steil L., Volker U., Bremer E.; RT "Osmotic control of opuA expression in Bacillus subtilis and its modulation RT in response to intracellular glycine betaine and proline pools."; RL J Bacteriol 195(3):510-522(2013). XX RX DOI; 10.1016/j.ejps.2011.08.017. RX PUBMED; 21888969. RA Geenen S., du Preez F.B., Reed M., Nijhout H.F., Kenna J.G., Wilson I.D., RA Westerhoff H.V., Snoep J.L.; RT "A mathematical modelling approach to assessing the reliability of RT biomarkers of glutathione metabolism."; RL Eur J Pharm Sci 46(4):233-243(2012). XX RX DOI; 10.1016/j.ejps.2011.06.006. RX PUBMED; 21704158. RA Kolodkin A., Boogerd F.C., Plant N., Bruggeman F.J., Goncharuk V., RA Lunshof J., Moreno-Sanchez R., Yilmaz N., Bakker B.M., Snoep J.L., RA Balling R., Westerhoff H.V.; RT "Emergence of the silicon human and network targeting drugs."; RL Eur J Pharm Sci 46(4):190-197(2012). XX RX DOI; 10.1186/1752-0509-5-198. RX PUBMED; 22172142. RA Waltemath D., Adams R., Bergmann F.T., Hucka M., Kolpakov F., Miller A.K., RA Moraru I.I., Nickerson D., Sahle S., Snoep J.L., Le Novere N.; RT "Reproducible computational biology experiments with SED-ML--the Simulation RT Experiment Description Markup Language."; RL BMC Syst Biol 5:198(2011). XX RX DOI; 10.1128/JB.05490-11. RX PUBMED; 21784929. RA Brill J., Hoffmann T., Bleisteiner M., Bremer E.; RT "Osmotically controlled synthesis of the compatible solute proline is RT critical for cellular defense of Bacillus subtilis against high RT osmolarity."; RL J Bacteriol 193(19):5335-5346(2011). XX RX DOI; 10.1128/AEM.01040-12. RX PUBMED; 22685134. RA Hoffmann T., von Blohn C., Stanek A., Moses S., Barzantny H., Bremer E.; RT "Synthesis, release, and recapture of compatible solute proline by RT osmotically stressed Bacillus subtilis cells."; RL Appl Environ Microbiol 78(16):5753-5762(2012). XX RX DOI; 10.1128/AEM.01934-12. RA Zaprasis Adrienne, Brill J., Thuring M., Wunsche G., Heun M., Barzantny H., RA Hoffmann Tamara, Bremer Erhard; RT "Osmoprotection of Bacillus subtilis through Import and Proteolysis of RT Proline-Containing Peptides"; RL Applied and Environmental Microbiology(2012). XX RX DOI; 10.1039/c1ib00042j. RX PUBMED; 22052476. RA Holcombe M., Adra S., Bicak M., Chin S., Coakley S., Graham A.I., Green J., RA Greenough C., Jackson D., Kiran M., MacNeil S., Maleki-Dizaji A., RA McMinn P., Pogson M., Poole R., Qwarnstrom E., Ratnieks F., Rolfe M.D., RA Smallwood R., Sun T., Worth D.; RT "Modelling complex biological systems using an agent-based approach."; RL Integr Biol (Camb) 4(1):53-64(2012). XX RX DOI; 10.1073/pnas.0804943106. RX PUBMED; 19261852. RA Jervis A.J., Crack J.C., White G., Artymiuk P.J., Cheesman M.R., RA Thomson A.J., Le Brun N.E., Green J.; RT "The O2 sensitivity of the transcription factor FNR is controlled by Ser24 RT modulating the kinetics of [4Fe-4S] to [2Fe-2S] conversion."; RL Proc Natl Acad Sci U S A 106(12):4659-4664(2009). XX RX DOI; 10.1016/j.mib.2009.01.008. RX PUBMED; 19246238. RA Green J., Crack J.C., Thomson A.J., LeBrun N.E.; RT "Bacterial sensors of oxygen."; RL Curr Opin Microbiol 12(2):145-151(2009). XX RX DOI; 10.1128/AEM.01507-12. RX PUBMED; 22843529. RA Sharma P., Hellingwerf K.J., de Mattos M.J., Bekker M.; RT "Uncoupling of substrate-level phosphorylation in Escherichia coli during RT glucose-limited growth."; RL Appl Environ Microbiol 78(19):6908-6913(2012). XX RX DOI; 10.1111/j.1742-4658.2012.08608.x. RA Sharma Poonam, Teixeira de Mattos Joost, Hellingwerf Klaas J., RA Bekker Martijn; RT "On the function of the various quinone species in RT Escherichia coli"; XX RX DOI; 10.1186/1752-0509-7-3. RA Liebal Ulf, Millat Thomas, Marles-Wright Jon, Lewis Rick, Wolkenhauer Olaf; RT "Simulations of stressosome activation emphasize allosteric interactions RT between RsbR and RsbT"; RL BMC Syst Biol(2013). XX RX DOI; 10.1111/1751-7915.12033. RT "Integrative modelling of pH-dependent enzyme activity and transcriptomic RT regulation of the acetone-butanol-ethanol fermentation of RT Clostridium acetobutylicum RT in continuous culture"; RL Microbial Biotechnology(2013). XX RX DOI; 10.1007/s00253-013-4860-7. RX PUBMED; 23640360. RA Millat T., Janssen H., Thorn G.J., King J.R., Bahl H., Fischer R.J., RA Wolkenhauer O.; RT "A shift in the dominant phenotype governs the pH-induced metabolic switch RT of Clostridium acetobutylicumin phosphate-limited continuous cultures."; RL Appl Microbiol Biotechnol 97(14):6451-6466(2013). XX RX DOI; 10.1074/jbc.M113.458265. RA Feldman-Salit Anna, Hering Silvio, Messiha H., Veith Nadine, Cojocaru Vlad, RA Sieg Antje, Westerhoff Hans V., Kreikemeyer Bernd, Wade Rebecca, RA Fiedler Tomas; RT "Regulation of the Activity of Lactate Dehydrogenases from Four Lactic Acid RT Bacteria"; RL Journal of Biological Chemistry(2013). XX RX DOI; 10.1074/jbc.M113.483289. RX PUBMED; 23814051. RA Leroux A.E., Haanstra J.R., Bakker B.M., Krauth-Siegel R.L.; RT "Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione RT synthetase by kinetic analysis and computational modeling."; RL J Biol Chem 288(33):23751-23764(2013). XX RX DOI; 10.1016/j.pep.2013.07.002. RT "Kinetic characterization of arginine deiminase and carbamate kinase from RT Streptococcus pyogenes M49"; RL Protein Expression and Purification(2013). XX RX DOI; 10.1371/journal.pcbi.1003159. RT "Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate RT Kinase in Lactic Acid Bacteria"; RL PLoS Comput Biol(2013). XX RX DOI; 10.1111/febs.12438. RX PUBMED; 23865479. RA Kouril T., Esser D., Kort J., Westerhoff H.V., Siebers B., Snoep J.L.; RT "Intermediate instability at high temperature leads to low pathway RT efficiency for an in vitro reconstituted system of gluconeogenesis in RT Sulfolobus solfataricus."; RL FEBS J 280(18):4666-4680(2013). XX RX DOI; 10.1007/978-3-642-41338-4_14. RT "Semantic Data and Models Sharing in Systems Biology: The Just Enough RT Results Model and the SEEK Platform"; RL Advanced Information Systems Engineering(2013). XX RX DOI; 10.1016/B978-0-12-800143-1.00003-8. RX PUBMED; 24797926. RA Achcar F., Fadda A., Haanstra J.R., Kerkhoven E.J., Kim D.H., Leroux A.E., RA Papamarkou T., Rojas F., Bakker B.M., Barrett M.P., Clayton C., RA Girolami M., Krauth-Siegel R.L., Matthews K.R., Breitling R.; RT "The silicon trypanosome: a test case of iterative model extension in RT systems biology."; RL Adv Microb Physiol 64:115-143(2014). XX RT ; XX RX DOI; 10.1371/journal.pone.0075412. RX PUBMED; 24116043. RA Sharma P., Stagge S., Bekker M., Bettenbrock K., Hellingwerf K.J.; RT "Kinase activity of ArcB from Escherichia coli is subject to regulation by RT both ubiquinone and demethylmenaquinone."; RL PLoS One 8(10):e75412(2013). XX RX DOI; 10.1016/B978-0-12-800143-1.00002-6. RX PUBMED; 24797925. RA Bettenbrock K., Bai H., Ederer M., Green J., Hellingwerf K.J., Holcombe M., RA Kunz S., Rolfe M.D., Sanguinetti G., Sawodny O., Sharma P., Steinsiek S., RA Poole R.K.; RT "Towards a systems level understanding of the oxygen response of RT Escherichia coli."; RL Adv Microb Physiol 64:65-114(2014). XX RX DOI; 10.1128/AEM.02033-13. RX PUBMED; 23956387. RA Overkamp W., Beilharz K., Detert Oude Weme R., Solopova A., Karsens H., RA Kovacs A., Kok J., Kuipers O.P., Veening J.W.; RT "Benchmarking various green fluorescent protein variants in Bacillus RT subtilis, Streptococcus pneumoniae, and Lactococcus lactis for live cell RT imaging."; RL Appl Environ Microbiol 79(20):6481-6490(2013). XX RX DOI; 10.1186/1475-2859-11-34. RX PUBMED; 22433058. RA Poblete-Castro I., Escapa I.F., Jager C., Puchalka J., Lam C.M., RA Schomburg D., Prieto M.A., Martins dos Santos V.A.; RT "The metabolic response of P. putida KT2442 producing high levels of RT polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: RT highlights from a multi-level omics approach."; RL Microb Cell Fact 11:34(2012). XX RX DOI; 10.1111/j.1462-2920.2011.02430.x. RX PUBMED; 21355971. RA Frank S., Klockgether J., Hagendorf P., Geffers R., Schock U., Pohl T., RA Davenport C.F., Tummler B.; RT "Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray RT transcriptomics."; RL Environ Microbiol 13(5):1309-1326(2011). XX RT ; XX RX DOI; 10.1016/B978-0-12-800143-1.00001-4. RA Ariño Joaquin, Aydar Ebru, Drulhe Samuel, Ganser Daniel, Jorrin Jesus, RA Kahm Matthias, Krause Falko, Petrezselyova Silvia, Yenush Lynne, RA Zimmermannová Olga, van Heusden G.Paul H., Kschischo Maik, Ludwig Jost, RA Palmer Chris, Ramos Jose, Sychrova Hana; RT "Systems Biology of Monovalent Cation Homeostasis in Yeast"; RL Advances in Microbial Systems Biology(2014). XX RX DOI; 10.1371/journal.pcbi.1003371. RX PUBMED; 24339766. RA Kerkhoven E.J., Achcar F., Alibu V.P., Burchmore R.J., Gilbert I.H., RA Trybilo M., Driessen N.N., Gilbert D., Breitling R., Bakker B.M., RA Barrett M.P.; RT "Handling uncertainty in dynamic models: the pentose phosphate pathway in RT Trypanosoma brucei."; RL PLoS Comput Biol 9(12):e1003371(2013). XX RX DOI; 10.1371/journal.pntd.0002012. RX PUBMED; 23350008. RA Pieretti S., Haanstra J.R., Mazet M., Perozzo R., Bergamini C., Prati F., RA Fato R., Lenaz G., Capranico G., Brun R., Bakker B.M., Michels P.A., RA Scapozza L., Bolognesi M.L., Cavalli A.; RT "Naphthoquinone derivatives exert their antitrypanosomal activity via a RT multi-target mechanism."; RL PLoS Negl Trop Dis 7(1):e2012(2013). XX RX DOI; 10.1016/j.ijpara.2012.04.009. RX PUBMED; 22580731. RA Haanstra J.R., van Tuijl A., van Dam J., van Winden W., Tielens A.G., RA van Hellemond J.J., Bakker B.M.; RT "Proliferating bloodstream-form Trypanosoma brucei use a negligible part of RT consumed glucose for anabolic processes."; RL Int J Parasitol 42(7):667-673(2012). XX RX DOI; 10.1093/nar/gku790. RX PUBMED; 25190458. RA Yuzenkova Y., Gamba P., Herber M., Attaiech L., Shafeeq S., Kuipers O.P., RA Klumpp S., Zenkin N., Veening J.W.; RT "Control of transcription elongation by GreA determines rate of gene RT expression in Streptococcus pneumoniae."; RL Nucleic Acids Res 42(17):10987-10999(2014). XX RX DOI; 10.1111/mmi.12764. RX PUBMED; 25145465. RA Fadda A., Ryten M., Droll D., Rojas F., Farber V., Haanstra J.R., Merce C., RA Bakker B.M., Matthews K., Clayton C.; RT "Transcriptome-wide analysis of trypanosome mRNA decay reveals complex RT degradation kinetics and suggests a role for co-transcriptional degradation RT in determining mRNA levels."; RL Mol Microbiol 94(2):307-326(2014). XX RX DOI; 10.1093/nar/gku839. RX PUBMED; 25245949. RA Bhogale P.M., Sorg R.A., Veening J.W., Berg J.; RT "What makes the lac-pathway switch: identifying the fluctuations that RT trigger phenotype switching in gene regulatory systems."; RL Nucleic Acids Res 42(18):11321-11328(2014). XX RT ; XX RX DOI; 10.3389/fmicb.2014.00124. RX PUBMED; 24723921. RA Ederer M., Steinsiek S., Stagge S., Rolfe M.D., Ter Beek A., Knies D., RA Teixeira de Mattos M.J., Sauter T., Green J., Poole R.K., Bettenbrock K., RA Sawodny O.; RT "A mathematical model of metabolism and regulation provides a systems-level RT view of how Escherichia coli responds to oxygen."; RL Front Microbiol 5:124(2014). XX RX DOI; 10.1371/journal.pcbi.1003595. RX PUBMED; 24763195. RA Bai H., Rolfe M.D., Jia W., Coakley S., Poole R.K., Green J., Holcombe M.; RT "Agent-based modeling of oxygen-responsive transcription factors in RT Escherichia coli."; RL PLoS Comput Biol 10(4):e1003595(2014). XX RX DOI; 10.1016/j.mib.2014.09.006. RA Szöör Balázs, Haanstra Jurgen, Gualdrón-López Melisa, Michels Paul AM; RT "Evolution, dynamics and specialized functions of glycosomes in metabolism RT and development of trypanosomatids"; RL Current Opinion in Microbiology(2014). XX RX DOI; 10.4056/sigs.5279417. RA Waltemath Dagmar, Bergmann Frank T., Chaouiya Claudine, Czauderna Tobias, RA Gleeson Padraig, Goble Carole, Golebiewski Martin, Hucka Michael, RA Juty Nick, Krebs Olga, Le Novère Nicolas, Mi Huaiyu, Moraru Ion I., RA Myers Chris J., Nickerson David, Olivier Brett G., Rodriguez Nicolas, RA Schreiber Falk, Smith Lucian, Zhang Fengkai, Bonnet Eric; RT "Meeting report from the fourth meeting of the Computational Modeling in RT Biology Network (COMBINE)"; RL Standards in Genomic Sciences(2014). XX RX DOI; 10.1128/AEM.03279-14. RX PUBMED; 25527553. RA Veith N., Solheim M., van Grinsven K.W., Olivier B.G., Levering J., RA Grosseholz R., Hugenholtz J., Holo H., Nes I., Teusink B., Kummer U.; RT "Using a genome-scale metabolic model of Enterococcus faecalis V583 to RT assess amino acid uptake and its impact on central metabolism."; RL Appl Environ Microbiol 81(5):1622-1633(2015). XX RX DOI; 10.3389/fcell.2015.00017. RX PUBMED; 25853130. RA Stanford N.J., Millard P., Swainston N.; RT "RobOKoD: microbial strain design for (over)production of target RT compounds."; RL Front Cell Dev Biol 3:17(2015). XX RX DOI; 10.1038/msb.2012.53. RX PUBMED; 23149687. RA Schaber J., Baltanas R., Bush A., Klipp E., Colman-Lerner A.; RT "Modelling reveals novel roles of two parallel signalling pathways and RT homeostatic feedbacks in yeast."; RL Mol Syst Biol 8:622(2012). XX RT ; XX RX DOI; 10.1371/journal.ppat.1004573. RX PUBMED; 25569684. RA Poenisch M., Metz P., Blankenburg H., Ruggieri A., Lee J.Y., Rupp D., RA Rebhan I., Diederich K., Kaderali L., Domingues F.S., Albrecht M., RA Lohmann V., Erfle H., Bartenschlager R.; RT "Identification of HNRNPK as regulator of hepatitis C virus particle RT production."; RL PLoS Pathog 11(1):e1004573(2015). XX RX DOI; 10.1111/febs.13237. RA Penkler Gerald, du Toit Francois, Adams Waldo, Rautenbach Marina, RA Palm Daniel C., van Niekerk Dawie, Snoep Jacky; RT "Construction and validation of a detailed kinetic model of glycolysis in RT Plasmodium falciparum"; RL FEBS J(2015). XX RT ; XX RX DOI; 10.1016/j.chom.2010.12.002. RX PUBMED; 21238945. RA Reiss S., Rebhan I., Backes P., Romero-Brey I., Erfle H., Matula P., RA Kaderali L., Poenisch M., Blankenburg H., Hiet M.S., Longerich T., RA Diehl S., Ramirez F., Balla T., Rohr K., Kaul A., Buhler S., Pepperkok R., RA Lengauer T., Albrecht M., Eils R., Schirmacher P., Lohmann V., RA Bartenschlager R.; RT "Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is RT essential for integrity of the membranous replication compartment."; RL Cell Host Microbe 9(1):32-45(2011). XX RX DOI; 10.1016/j.jtherbio.2015.05.008. RA Zakhartsev Maksim, Yang Xuelian, Reuss Matthias, Pörtner Hans Otto; RT "Metabolic efficiency in yeast Saccharomyces cerevisiae in relation to RT temperature dependent growth and biomass yield"; RL Journal of Thermal Biology(2015). XX RX DOI; 10.1007/s11306-014-0700-8. RA Zakhartsev Maksim, Vielhauer Oliver, Horn Thomas, Yang Xuelian, RA Reuss Matthias; RT "Fast sampling for quantitative microbial metabolomics: new aspects on cold RT methanol quenching: metabolite co-precipitation"; RL Metabolomics(2015). XX RX DOI; 10.1038/msb.2009.68. RA Piques Maria, Schulze Waltraud X, Höhne Melanie, Usadel Björn, Gibon Yves, RA Rohwer Johann, Stitt Mark; RT "Ribosome and transcript copy numbers, polysome occupancy and enzyme RT dynamics in Arabidopsis"; RL Mol Syst Biol(2009). XX RX DOI; 10.1038/nmeth.f.303. RX PUBMED; 20383131. RA Caporaso J.G., Kuczynski J., Stombaugh J., Bittinger K., Bushman F.D., RA Costello E.K., Fierer N., Pena A.G., Goodrich J.K., Gordon J.I., RA Huttley G.A., Kelley S.T., Knights D., Koenig J.E., Ley R.E., RA Lozupone C.A., McDonald D., Muegge B.D., Pirrung M., Reeder J., RA Sevinsky J.R., Turnbaugh P.J., Walters W.A., Widmann J., Yatsunenko T., RA Zaneveld J., Knight R.; RT "QIIME allows analysis of high-throughput community sequencing data."; RL Nat Methods 7(5):335-336(2010). XX RX DOI; 10.1038/msb.2011.50. RA Bachmann J., Raue A., Schilling Marcel, Böhm Martin, Kreutz C., Kaschek D., RA Busch H., Gretz N., Lehmann W.D., Timmer Jens, Klingmüller Ursula; RT "Division of labor by dual feedback regulators controls JAK2/STAT5 RT signaling over broad ligand range"; RL Molecular Systems Biology(2011). XX RX DOI; 10.1038/ng1201-365. RX PUBMED; 11726920. RA Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., RA Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., Gaasterland T., RA Glenisson P., Holstege F.C., Kim I.F., Markowitz V., Matese J.C., RA Parkinson H., Robinson A., Sarkans U., Schulze-Kremer S., Stewart J., RA Taylor R., Vilo J., Vingron M.; RT "Minimum information about a microarray experiment (MIAME)-toward standards RT for microarray data."; RL Nat Genet 29(4):365-371(2001). XX RX DOI; 10.1038/msb.2010.102. RA Kolodkin Alexey N, Bruggeman Frank J, Plant Nick, Moné Martijn J, RA Bakker Barbara M, Campbell Moray J, van Leeuwen Johannes P T M, RA Carlberg Carsten, Snoep Jacky, Westerhoff Hans V; RT "Design principles of nuclear receptor signaling: how complex networking RT improves signal transduction"; RL Mol Syst Biol(2010). XX RX DOI; 10.1073/pnas.88.16.7328. RX PUBMED; 1831270. RA Tyson J.J.; RT "Modeling the cell division cycle: cdc2 and cyclin interactions."; RL Proc Natl Acad Sci U S A 88(16):7328-7332(1991). XX RX DOI; 10.1073/pnas.0804672105. RX PUBMED; 18669651. RA Stefan M.I., Edelstein S.J., Le Novere N.; RT "An allosteric model of calmodulin explains differential activation of PP2B RT and CaMKII."; RL Proc Natl Acad Sci U S A 105(31):10768-10773(2008). XX RX DOI; 10.1038/nature17164. RX PUBMED; 27088604. RA Lien S., Koop B.F., Sandve S.R., Miller J.R., Kent M.P., Nome T., RA Hvidsten T.R., Leong J.S., Minkley D.R., Zimin A., Grammes F., Grove H., RA Gjuvsland A., Walenz B., Hermansen R.A., von Schalburg K., Rondeau E.B., RA Di Genova A., Samy J.K., Olav Vik J., Vigeland M.D., Caler L., Grimholt U., RA Jentoft S., Vage D.I., de Jong P., Moen T., Baranski M., Palti Y., RA Smith D.R., Yorke J.A., Nederbragt A.J., Tooming-Klunderud A., RA Jakobsen K.S., Jiang X., Fan D., Hu Y., Liberles D.A., Vidal R., Iturra P., RA Jones S.J., Jonassen I., Maass A., Omholt S.W., Davidson W.S.; RT "The Atlantic salmon genome provides insights into rediploidization."; RL Nature 533(7602):200-205(2016). XX RX DOI; 10.1097/MNM.0000000000000550. RX PUBMED; 27218430. RA Hirose Y., Kaida H., Kawahara A., Matono S., Tanaka T., Kurata S., Kage M., RA Ishibashi M., Abe T.; RT "Molecular biological correlation of fluorine-18 fluorodeoxyglucose uptake RT in esophageal squamous cell carcinoma."; RL Nucl Med Commun 37(10):1053-1061(2016). XX RX DOI; 10.1099/mic.0.000314. RA Buetti-Dinh Antoine, Dethlefsen Olga, Friedman Ran, Dopson Mark; RT "Transcriptomic analysis reveals how a lack of potassium ions increases RT Sulfolobus acidocaldarius sensitivity to pH changes"; XX RX DOI; 10.1021/bi00557a009. RA Crouch Thomas H., Klee Claude B.; RT "Positive cooperative binding of calcium to bovine brain calmodulin"; RL Biochemistry(1980). XX RX DOI; 10.1093/bioinformatics/btq461. RX PUBMED; 20709691. RA Edgar R.C.; RT "Search and clustering orders of magnitude faster than BLAST."; RL Bioinformatics 26(19):2460-2461(2010). XX RX DOI; 10.1038/nmeth.2604. RX PUBMED; 23955772. RA Edgar R.C.; RT "UPARSE: highly accurate OTU sequences from microbial amplicon reads."; RL Nat Methods 10(10):996-998(2013). XX RX DOI; 10.12688/f1000research.9211.1. RA König Matthias; RT "cy3sabiork: A Cytoscape app for visualizing kinetic data from SABIO-RK"; RL F1000Res(2016). XX RT ; XX RX DOI; 10.1111/febs.13615. RA van Niekerk Dawie, Penkler Gerald P., du Toit Francois, Snoep Jacky; RT "Targeting glycolysis in the malaria parasite RT Plasmodium falciparum"; RL FEBS J(2016). XX RX DOI; 10.1042/BST20150145. RA Snoep Jacky, Green Kathleen, Eicher J., Palm D.C., Penkler G., du Toit F., RA Walters N., Burger R., Westerhoff H.V., van Niekerk Dawie; RT "Quantitative analysis of drug effects at the whole-body level: a case RT study for glucose metabolism in malaria patients"; RL Biochemical Society Transactions(2015). XX RX DOI; 10.1016/j.jchromb.2011.10.036. RA Vielhauer Oliver, Zakhartsev Maksim, Horn Thomas, Takors Ralf, RA Reuss Matthias; RT "Simplified absolute metabolite quantification by gas RT chromatography–isotope dilution mass spectrometry on the basis of RT commercially available source material"; RL Journal of Chromatography B(2011). XX RX DOI; 10.1109/TCBB.2016.2550451. RA Stalidzans Egils, Mozga Ivars, Sulins Jurijs, Zikmanis Peteris; RT "Search for a minimal set of parameters by assessing the total optimisation RT potential for a dynamic model of a biochemical network"; RL IEEE/ACM Trans. Comput. Biol. and Bioinf.(2016). XX RX DOI; 10.1371/journal.pcbi.1004192. RX PUBMED; 25905717. RA D'Alessandro L.A., Samaga R., Maiwald T., Rho S.H., Bonefas S., Raue A., RA Iwamoto N., Kienast A., Waldow K., Meyer R., Schilling M., Timmer J., RA Klamt S., Klingmuller U.; RT "Disentangling the Complexity of HGF Signaling by Combining Qualitative and RT Quantitative Modeling."; RL PLoS Comput Biol 11(4):e1004192(2015). XX RX DOI; 10.1016/j.exphem.2016.02.004. RX PUBMED; 26911671. RA Wuchter P., Vetter M., Saffrich R., Diehlmann A., Bieback K., Ho A.D., RA Horn P.; RT "Evaluation of GMP-compliant culture media for in vitro expansion of human RT bone marrow mesenchymal stromal cells."; RL Exp Hematol 44(6):508-518(2016). XX RX DOI; 10.1126/scisignal.aab1967. RX PUBMED; 26838549. RA Iwamoto N., D'Alessandro L.A., Depner S., Hahn B., Kramer B.A., RA Lucarelli P., Vlasov A., Stepath M., Bohm M.E., Deharde D., Damm G., RA Seehofer D., Lehmann W.D., Klingmuller U., Schilling M.; RT "Context-specific flow through the MEK/ERK module produces cell- and RT ligand-specific patterns of ERK single and double phosphorylation."; RL Sci Signal 9(413):ra13(2016). XX RX DOI; 10.1007/s00441-015-2348-8. RX PUBMED; 26829941. RA Wuchter P., Saffrich R., Giselbrecht S., Nies C., Lorig H., Kolb S., RA Ho A.D., Gottwald E.; RT "Microcavity arrays as an in vitro model system of the bone marrow niche RT for hematopoietic stem cells."; RL Cell Tissue Res 364(3):573-584(2016). XX RX DOI; 10.1093/bioinformatics/btv405. RX PUBMED; 26142188. RA Raue A., Steiert B., Schelker M., Kreutz C., Maiwald T., Hass H., RA Vanlier J., Tonsing C., Adlung L., Engesser R., Mader W., Heinemann T., RA Hasenauer J., Schilling M., Hofer T., Klipp E., Theis F., Klingmuller U., RA Schoberl B., Timmer J.; RT "Data2Dynamics: a modeling environment tailored to parameter estimation in RT dynamical systems."; RL Bioinformatics 31(21):3558-3560(2015). XX RX DOI; 10.1021/pr5006923. RX PUBMED; 25333863. RA Boehm M.E., Adlung L., Schilling M., Roth S., Klingmuller U., Lehmann W.D.; RT "Identification of isoform-specific dynamics in phosphorylation-dependent RT STAT5 dimerization by quantitative mass spectrometry and mathematical RT modeling."; RL J Proteome Res 13(12):5685-5694(2014). XX RX DOI; 10.1038/leu.2014.273. RX PUBMED; 25227910. RA Malcherek G., Jin N., Huckelhoven A.G., Mani J., Wang L., Gern U., RA Diehlmann A., Wuchter P., Schmitt A., Chen B., Ho A.D., Schmitt M.; RT "Mesenchymal stromal cells inhibit proliferation of virus-specific CD8(+) T RT cells."; RL Leukemia 28(12):2388-2394(2014). XX RX DOI; 10.1016/j.jcyt.2014.04.002. RX PUBMED; 24856898. RA Wuchter P., Bieback K., Schrezenmeier H., Bornhauser M., Muller L.P., RA Bonig H., Wagner W., Meisel R., Pavel P., Tonn T., Lang P., Muller I., RA Renner M., Malcherek G., Saffrich R., Buss E.C., Horn P., Rojewski M., RA Schmitt A., Ho A.D., Sanzenbacher R., Schmitt M.; RT "Standardization of Good Manufacturing Practice-compliant production of RT bone marrow-derived human mesenchymal stromal cells for immunotherapeutic RT applications."; RL Cytotherapy 17(2):128-139(2015). XX RT ; XX RX DOI; 10.1016/j.biomaterials.2013.11.011. RX PUBMED; 24269154. RA Hanke M., Hoffmann I., Christophis C., Schubert M., Hoang V.T., RA Zepeda-Moreno A., Baran N., Eckstein V., Wuchter P., Rosenhahn A., Ho A.D.; RT "Differences between healthy hematopoietic progenitors and leukemia cells RT with respect to CD44 mediated rolling versus adherence behavior on RT hyaluronic acid coated surfaces."; RL Biomaterials 35(5):1411-1419(2014). XX RX DOI; 10.1016/j.jcyt.2013.07.007. RX PUBMED; 24119647. RA Ludwig A., Saffrich R., Eckstein V., Bruckner T., Wagner W., Ho A.D., RA Wuchter P.; RT "Functional potentials of human hematopoietic progenitor cells are RT maintained by mesenchymal stromal cells and not impaired by plerixafor."; RL Cytotherapy 16(1):111-121(2014). XX RX DOI; 10.1055/s-0033-1343346. RX PUBMED; 24006170. RA Schmitt M., Muller L.P., Keysser G., Lorenz H.M., Ho A.D., Wuchter P.; RT "[Mesenchymal stroma cells (MSCs) for the treatment of rheumatic RT disease]."; RL Dtsch Med Wochenschr 138(37):1852-1855(2013). XX RX DOI; 10.1126/science.1184913. RX PUBMED; 20488988. RA Becker V., Schilling M., Bachmann J., Baumann U., Raue A., Maiwald T., RA Timmer J., Klingmuller U.; RT "Covering a broad dynamic range: information processing at the RT erythropoietin receptor."; RL Science 328(5984):1404-1408(2010). XX RX DOI; 10.1111/mmi.13498. RX PUBMED; 27611014. RA Wolf J., Stark H., Fafenrot K., Albersmeier A., Pham T.K., Muller K.B., RA Meyer B.H., Hoffmann L., Shen L., Albaum S.P., Kouril T., RA Schmidt-Hohagen K., Neumann-Schaal M., Brasen C., Kalinowski J., RA Wright P.C., Albers S.V., Schomburg D., Siebers B.; RT "A systems biology approach reveals major metabolic changes in the RT thermoacidophilic archaeon Sulfolobus solfataricus in response to the RT carbon source L-fucose versus D-glucose."; RL Mol Microbiol 102(5):882-908(2016). XX RX DOI; 10.1111/j.1742-4658.2005.05037.x. RX PUBMED; 16336276. RA Schilling M., Maiwald T., Bohl S., Kollmann M., Kreutz C., Timmer J., RA Klingmuller U.; RT "Computational processing and error reduction strategies for standardized RT quantitative data in biological networks."; RL FEBS J 272(24):6400-6411(2005). XX RX DOI; 10.2390/biecoll-jib-2013-220. RX PUBMED; 23549603. RA Shi L., Jong L., Wittig U., Lucarelli P., Stepath M., Mueller S., RA D'Alessandro L.A., Klingmuller U., Muller W.; RT "Excemplify: a flexible template based solution, parsing and managing data RT in spreadsheets for experimentalists."; RL J Integr Bioinform 10(2):220(2013). XX RX DOI; 10.7554/eLife.13308. RA Matz-Soja Madlen, Rennert Christiane, Schönefeld Kristin, Aleithe Susanne, RA Boettger Jan, Schmidt-Heck Wolfgang, Weiss Thomas S, Hovhannisyan Amalya, RA Zellmer Sebastian, Klöting Nora, Schulz Angela, Kratzsch Jürgen, RA Guthke Reinhardt, Gebhardt Rolf; RT "Hedgehog signaling is a potent regulator of liver lipid metabolism and RT reveals a GLI-code associated with steatosis"; XX RX DOI; 10.1103/PhysRevE.90.023303. RA Tönsing Christian, Timmer Jens, Kreutz Clemens; RT "Cause and cure of sloppiness in ordinary differential equation models"; RL Phys. Rev. E(2014). XX RX DOI; 10.1111/j.1751-7915.2010.00219.x. RA Gomez-Escribano Juan Pablo, Bibb Mervyn J.; RT "Engineering Streptomyces coelicolor for heterologous expression of RT secondary metabolite gene clusters"; XX RX DOI; 10.1038/sdata.2016.18. RX PUBMED; 26978244. RA Wilkinson M.D., Dumontier M., Aalbersberg I.J., Appleton G., Axton M., RA Baak A., Blomberg N., Boiten J.W., da Silva Santos L.B., Bourne P.E., RA Bouwman J., Brookes A.J., Clark T., Crosas M., Dillo I., Dumon O., RA Edmunds S., Evelo C.T., Finkers R., Gonzalez-Beltran A., Gray A.J., RA Groth P., Goble C., Grethe J.S., Heringa J., 't Hoen P.A., Hooft R., RA Kuhn T., Kok R., Kok J., Lusher S.J., Martone M.E., Mons A., Packer A.L., RA Persson B., Rocca-Serra P., Roos M., van Schaik R., Sansone S.A., RA Schultes E., Sengstag T., Slater T., Strawn G., Swertz M.A., Thompson M., RA van der Lei J., van Mulligen E., Velterop J., Waagmeester A., RA Wittenburg P., Wolstencroft K., Zhao J., Mons B.; RT "The FAIR Guiding Principles for scientific data management and RT stewardship."; RL Sci Data 3:160018(2016). XX RX DOI; 10.1007/978-1-4419-7046-6_1. RX PUBMED; 21431541. RA Battke F., Herbig A., Wentzel A., Jakobsen O.M., Bonin M., Hodgson D.A., RA Wohlleben W., Ellingsen T.E., Nieselt K.; RT "A technical platform for generating reproducible expression data from RT Streptomyces coelicolor batch cultivations."; RL Adv Exp Med Biol 696:3-15(2011). XX RX DOI; 10.1093/nar/gks205. RX PUBMED; 22406834. RA Iqbal M., Mast Y., Amin R., Hodgson D.A., Wohlleben W., Burroughs N.J.; RT "Extracting regulator activity profiles by integration of de novo motifs RT and expression data: characterizing key regulators of nutrient depletion RT responses in Streptomyces coelicolor."; RL Nucleic Acids Res 40(12):5227-5239(2012). XX RX DOI; 10.1074/mcp.M111.013797. RX PUBMED; 22147733. RA Thomas L., Hodgson D.A., Wentzel A., Nieselt K., Ellingsen T.E., Moore J., RA Morrissey E.R., Legaie R., Wohlleben W., Rodriguez-Garcia A., Martin J.F., RA Burroughs N.J., Wellington E.M., Smith M.C.; RT "Metabolic switches and adaptations deduced from the proteomes of RT Streptomyces coelicolor wild type and phoP mutant grown in batch culture."; RL Mol Cell Proteomics 11(2):M111.013797(2012). XX RX DOI; 10.1007/s00253-011-3644-1. RX PUBMED; 22033567. RA Waldvogel E., Herbig A., Battke F., Amin R., Nentwich M., Nieselt K., RA Ellingsen T.E., Wentzel A., Hodgson D.A., Wohlleben W., Mast Y.; RT "The PII protein GlnK is a pleiotropic regulator for morphological RT differentiation and secondary metabolism in Streptomyces coelicolor."; RL Appl Microbiol Biotechnol 92(6):1219-1236(2011). XX RX DOI; 10.1186/1752-0509-6-59. RX PUBMED; 22676814. RA Wentzel A., Bruheim P., Overby A., Jakobsen O.M., Sletta H., Omara W.A., RA Hodgson D.A., Ellingsen T.E.; RT "Optimized submerged batch fermentation strategy for systems scale studies RT of metabolic switching in Streptomyces coelicolor A3(2)."; RL BMC Syst Biol 6:59(2012). XX RX DOI; 10.3390/metabo2010178. RX PUBMED; 24957373. RA Wentzel A., Sletta H., Ellingsen T.E., Bruheim P.; RT "Intracellular Metabolite Pool Changes in Response to Nutrient Depletion RT Induced Metabolic Switching in Streptomyces coelicolor."; RL Metabolites 2(1):178-194(2012). XX RX DOI; 10.1093/nar/gkw1032. RX PUBMED; 27899646. RA Wolstencroft K., Krebs O., Snoep J.L., Stanford N.J., Bacall F., RA Golebiewski M., Kuzyakiv R., Nguyen Q., Owen S., Soiland-Reyes S., RA Straszewski J., van Niekerk D.D., Williams A.R., Malmstrom L., Rinn B., RA Muller W., Goble C.; RT "FAIRDOMHub: a repository and collaboration environment for sharing systems RT biology research."; RL Nucleic Acids Res 45(D1):D404-D407(2017). XX RX DOI; 10.1371/journal.pcbi.1005049. RX PUBMED; 27494133. RA Merkle R., Steiert B., Salopiata F., Depner S., Raue A., Iwamoto N., RA Schelker M., Hass H., Wasch M., Bohm M.E., Mucke O., Lipka D.B., Plass C., RA Lehmann W.D., Kreutz C., Timmer J., Schilling M., Klingmuller U.; RT "Identification of Cell Type-Specific Differences in Erythropoietin RT Receptor Signaling in Primary Erythroid and Lung Cancer Cells."; RL PLoS Comput Biol 12(8):e1005049(2016). XX RX DOI; 10.1098/rsfs.2015.0103. RX PUBMED; 27051515. RA Nickerson D., Atalag K., de Bono B., Geiger J., Goble C., Hollmann S., RA Lonien J., Muller W., Regierer B., Stanford N.J., Golebiewski M., RA Hunter P.; RT "The Human Physiome: how standards, software and innovative service RT infrastructures are providing the building blocks to make it achievable."; RL Interface Focus 6(2):20150103(2016). XX RX DOI; 10.1093/bioinformatics/btw461. RX PUBMED; 27587694. RA Steiert B., Timmer J., Kreutz C.; RT "L1 regularization facilitates detection of cell type-specific parameters RT in dynamical systems."; RL Bioinformatics 32(17):i718-i726(2016). XX RX DOI; 10.1371/journal.pone.0162366. RX PUBMED; 27588423. RA Maiwald T., Hass H., Steiert B., Vanlier J., Engesser R., Raue A., RA Kipkeew F., Bock H.H., Kaschek D., Kreutz C., Timmer J.; RT "Driving the Model to Its Limit: Profile Likelihood Based Model RT Reduction."; RL PLoS One 11(9):e0162366(2016). XX RX DOI; 10.15252/msb.20167258. RX PUBMED; 28123004. RA Adlung L., Kar S., Wagner M.C., She B., Chakraborty S., Bao J., RA Lattermann S., Boerries M., Busch H., Wuchter P., Ho A.D., Timmer J., RA Schilling M., Hofer T., Klingmuller U.; RT "Protein abundance of AKT and ERK pathway components governs cell RT type-specific regulation of proliferation."; RL Mol Syst Biol 13(1):904(2017). XX RX DOI; 10.1098/rsob.150042. RX PUBMED; 26468131. RA Flis A., Fernandez A.P., Zielinski T., Mengin V., Sulpice R., Stratford K., RA Hume A., Pokhilko A., Southern M.M., Seaton D.D., McWatters H.G., Stitt M., RA Halliday K.J., Millar A.J.; RT "Defining the robust behaviour of the plant clock gene circuit with RT absolute RNA timeseries and open infrastructure."; RL Open Biol 5(10)(2015). XX RX DOI; 10.1093/pcp/pcp028. RX PUBMED; 19233867. RA Niwa Y., Yamashino T., Mizuno T.; RT "The circadian clock regulates the photoperiodic response of hypocotyl RT elongation through a coincidence mechanism in Arabidopsis thaliana."; RL Plant Cell Physiol 50(4):838-854(2009). XX RX DOI; 10.1093/pcp/pcm056. RX PUBMED; 17504813. RA Nakamichi N., Kita M., Niinuma K., Ito S., Yamashino T., Mizoguchi T., RA Mizuno T.; RT "Arabidopsis clock-associated pseudo-response regulators PRR9, PRR7 and RT PRR5 coordinately and positively regulate flowering time through the RT canonical CONSTANS-dependent photoperiodic pathway."; RL Plant Cell Physiol 48(6):822-832(2007). XX RX DOI; 10.1186/1471-2164-15-481. RX PUBMED; 24939016. RA Yadetie F., Karlsen O.A., Eide M., Hogstrand C., Goksoyr A.; RT "Liver transcriptome analysis of Atlantic cod (Gadus morhua) exposed to PCB RT 153 indicates effects on cell cycle regulation and lipid metabolism."; RL BMC Genomics 15(1):481(2014). XX RX DOI; 10.1016/j.aquatox.2012.09.013. RX PUBMED; 23103053. RA Yadetie F., Karlsen O.A., Lanzen A., Berg K., Olsvik P., Hogstrand C., RA Goksoyr A.; RT "Global transcriptome analysis of Atlantic cod (Gadus morhua) liver after RT in vivo methylmercury exposure suggests effects on energy metabolism RT pathways."; RL Aquat Toxicol 126:314-325(2013). XX RX DOI; 10.1186/s12864-016-2864-2. RX PUBMED; 27496535. RA Yadetie F., Bjorneklett S., Garberg H.K., Oveland E., Berven F., RA Goksoyr A., Karlsen O.A.; RT "Quantitative analyses of the hepatic proteome of methylmercury-exposed RT Atlantic cod (Gadus morhua) suggest oxidative stress-mediated effects on RT cellular energy metabolism."; RL BMC Genomics 17:554(2016). XX RX DOI; 10.1016/j.aquatox.2017.01.014. RA Karlsen Fekadu Yadetie; RT "Quantitative proteomics analysis reveals perturbation of lipid metabolic RT pathways in the liver of Atlantic cod (Gadus morhua) treated with PCB 153"; RL Aquatic Toxicology(2017). XX RX DOI; 10.1098/rsif.2013.0979. RX PUBMED; 24335560. RA Seaton D.D., Ebenhoh O., Millar A.J., Pokhilko A.; RT "Regulatory principles and experimental approaches to the circadian control RT of starch turnover."; RL J R Soc Interface 11(91):20130979(2014). XX RX DOI; 10.15252/msb.20145766. RX PUBMED; 25600997. RA Seaton D.D., Smith R.W., Song Y.H., MacGregor D.R., Stewart K., Steel G., RA Foreman J., Penfield S., Imaizumi T., Millar A.J., Halliday K.J.; RT "Linked circadian outputs control elongation growth and flowering in RT response to photoperiod and temperature."; RL Mol Syst Biol 11(1):776(2015). XX RX DOI; 10.1073/pnas.1410238111. RX PUBMED; 25197087. RA Chew Y.H., Wenden B., Flis A., Mengin V., Taylor J., Davey C.L., Tindal C., RA Thomas H., Ougham H.J., de Reffye P., Stitt M., Williams M., RA Muetzelfeldt R., Halliday K.J., Millar A.J.; RT "Multiscale digital Arabidopsis predicts individual organ and RT whole-organism growth."; RL Proc Natl Acad Sci U S A 111(39):E4127-E4136(2014). XX RX DOI; 10.1186/s12870-016-0868-3. RA Zakhartsev Maksim, Medvedeva Irina, Orlov Yuriy, Akberdin Ilya, Krebs Olga, RA Schulze Waltraud; RT "Metabolic model of central carbon and energy metabolisms of growing RT Arabidopsis thaliana in relation to sucrose translocation"; RL BMC Plant Biology(2016). XX RX DOI; 10.1016/j.jbiotec.2016.06.009. RX PUBMED; 27297548. RA Radek A., Muller M.F., Gatgens J., Eggeling L., Krumbach K., RA Marienhagen J., Noack S.; RT "Formation of xylitol and xylitol-5-phosphate and its impact on growth of RT d-xylose-utilizing Corynebacterium glutamicum strains."; RL J Biotechnol 231:160-166(2016). XX RX DOI; 10.1016/j.jbiotec.2014.09.026. RX PUBMED; 25304460. RA Radek A., Krumbach K., Gatgens J., Wendisch V.F., Wiechert W., Bott M., RA Noack S., Marienhagen J.; RT "Engineering of Corynebacterium glutamicum for minimized carbon loss during RT utilization of D-xylose containing substrates."; RL J Biotechnol 192 Pt A:156-160(2014). XX RX DOI; 10.1073/pnas.1118814109. RX PUBMED; 22496591. RA Wenden B., Toner D.L., Hodge S.K., Grima R., Millar A.J.; RT "Spontaneous spatiotemporal waves of gene expression from biological clocks RT in the leaf."; RL Proc Natl Acad Sci U S A 109(17):6757-6762(2012). XX RX DOI; 10.2390/biecoll-jib-2016-289. RX PUBMED; 28187405. RA Schreiber F., Bader G.D., Gleeson P., Golebiewski M., Hucka M., RA Le Novere N., Myers C., Nickerson D., Sommer B., Walthemath D.; RT "Specifications of Standards in Systems and Synthetic Biology: Status and RT Developments in 2016."; RL J Integr Bioinform 13(3):289(2016). XX RX DOI; 10.1007/s13222-016-0243-4. RA Müller Wolfgang, Bittkowski Meik, Golebiewski Martin, Kania Renate, RA Rey Maja, Weidemann Andreas, Wittig Ulrike; RT "SABIO-RK, von Daten in der Publikation zur Suchlösung für Spezialisten"; RL Datenbank-Spektrum(2017). XX RX DOI; 10.1016/j.febslet.2013.06.043. RX PUBMED; 23831062. RA Smallbone K., Messiha H.L., Carroll K.M., Winder C.L., Malys N., Dunn W.B., RA Murabito E., Swainston N., Dada J.O., Khan F., Pir P., Simeonidis E., RA Spasic I., Wishart J., Weichart D., Hayes N.W., Jameson D., Broomhead D.S., RA Oliver S.G., Gaskell S.J., McCarthy J.E., Paton N.W., Westerhoff H.V., RA Kell D.B., Mendes P.; RT "A model of yeast glycolysis based on a consistent kinetic characterisation RT of all its enzymes."; RL FEBS Lett 587(17):2832-2841(2013). XX RX DOI; 10.1007/978-3-642-33876-2_42. RA Wolstencroft Katy, Owen Stuart, Horridge Matthew, Müller Wolfgang, RA Bacall Finn, Snoep Jacky, du Preez Franco, Nguyen Quyen, Krebs Olga, RA Goble Carole; RT "RightField: Scientific Knowledge Acquisition by Stealth through RT Ontology-Enabled Spreadsheets"; RL Knowledge Engineering and Knowledge Management(2012). XX RX DOI; 10.1038/srep38699. RX PUBMED; 27922098. RA Koehorst J.J., van Dam J.C., van Heck R.G., Saccenti E., Dos Santos V.A., RA Suarez-Diez M., Schaap P.J.; RT "Comparison of 432 Pseudomonas strains through integration of genomic, RT functional, metabolic and expression data."; RL Sci Rep 6:38699(2016). XX RX DOI; 10.1371/journal.pcbi.1001116. RA Oberhardt Matthew A., Puchałka Jacek, Martins dos Santos Vitor, RA Papin Jason A.; RT "Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative RT Systems Analysis"; RL PLoS Comput Biol(2011). XX RX DOI; 10.1016/j.ymben.2012.09.006. RA Nikel Pablo I., de Lorenzo Victor; RT "Engineering an anaerobic metabolic regime in Pseudomonas putida KT2440 for RT the anoxic biodegradation of 1,3-dichloroprop-1-ene"; RL Metabolic Engineering(2013). XX RX DOI; 10.1002/biot.201000124. RA Sohn Seung Bum, Kim Tae Yong, Park Jong Myoung, Lee Sang Yup; RT "In silico RT genome-scale metabolic analysis of RT Pseudomonas putida RT KT2440 for polyhydroxyalkanoate synthesis, degradation of RT aromatics and anaerobic survival"; RL Biotechnology Journal(2010). XX RX DOI; 10.1038/msb.2013.6. RX PUBMED; 23549481. RA Wodke J.A., Puchalka J., Lluch-Senar M., Marcos J., Yus E., Godinho M., RA Gutierrez-Gallego R., dos Santos V.A., Serrano L., Klipp E., Maier T.; RT "Dissecting the energy metabolism in Mycoplasma pneumoniae through RT genome-scale metabolic modeling."; RL Mol Syst Biol 9:653(2013). XX RX DOI; 10.1039/c3mb70113a. RX PUBMED; 23598864. RA Maier T., Marcos J., Wodke J.A., Paetzold B., Liebeke M., RA Gutierrez-Gallego R., Serrano L.; RT "Large-scale metabolome analysis and quantitative integration with genomics RT and proteomics data in Mycoplasma pneumoniae."; RL Mol Biosyst 9(7):1743-1755(2013). XX RX PUBMED; 10. RA Schmoldt A., Benthe H.F., Haberland G.; RT "Digitoxin metabolism by rat liver microsomes."; RL Biochem Pharmacol 24(17):1639-1641(1975). XX RX DOI; 10.1111/febs.14105. RA Stark Helge, Wolf Jacqueline, Albersmeier Andreas, Pham Trong Khoa, RA Hofmann Julia D., Siebers Bettina, Kalinowski Jörn, Wright Phil, RA Neumann-Schaal Meina, Schomburg Dietmar; RT "Oxidative Stickland reactions in an obligate aerobic organism - amino acid RT catabolism in the Crenarchaeon RT Sulfolobus solfataricus"; RL FEBS J(2017). XX RA Lindhorst Henning, Lucia Sergio, Findeisen Rolf, Waldherr Steffen; RT "Modeling metabolic networks including gene expression and uncertainties"; XX RX DOI; 10.1371/journal.pone.0180331. RX PUBMED; 28692669. RA Figueiredo A.S., Kouril T., Esser D., Haferkamp P., Wieloch P., RA Schomburg D., Ruoff P., Siebers B., Schaber J.; RT "Systems biology of the modified branched Entner-Doudoroff pathway in RT Sulfolobus solfataricus."; RL PLoS One 12(7):e0180331(2017). XX RX DOI; 10.1016/j.biortech.2017.05.055. RX PUBMED; 28552568. RA Radek A., Tenhaef N., Muller M.F., Brusseler C., Wiechert W., RA Marienhagen J., Polen T., Noack S.; RT "Miniaturized and automated adaptive laboratory evolution: Evolving RT Corynebacterium glutamicum towards an improved d-xylose utilization."; RL Bioresour Technol 245(Pt B):1377-1385(2017). XX RX DOI; 10.1101/105437. RA Chew Yin Hoon, Seaton Daniel, Mengin Virginie, Flis Anna, Mugford Sam T., RA Smith Alison M., Stitt Mark, Millar Andrew; RT "Linking circadian time to growth rate quantitatively RT via RT carbon metabolism"; XX RX DOI; 10.1128/AEM.02889-16. RX PUBMED; 28062460. RA Xu Z., Wang Y., Chater K.F., Ou H.Y., Xu H.H., Deng Z., Tao M.; RT "Large-Scale Transposition Mutagenesis of Streptomyces coelicolor RT Identifies Hundreds of Genes Influencing Antibiotic Biosynthesis."; RL Appl Environ Microbiol 83(6)(2017). XX RX DOI; 10.1073/pnas.1601309113. RA Yang Deyue, Seaton Daniel D., Krahmer Johanna, Halliday Karen J.; RT "Photoreceptor effects on plant biomass, resource allocation, and metabolic RT state"; RL Proc Natl Acad Sci USA(2016). XX RT "Nutzung von Persistent Identifiern zur Umsetzung der FAIR-Prinzipien in RT Datenablageplattformen für die medizinische Forschung"; XX RX DOI; 10.1101/182071. RA Seaton Daniel, Graf Alexander, Baerenfaller Katja, Stitt Mark, RA Millar Andrew, Gruissem Wilhelm; RT "Photoperiodic control of the Arabidopsis proteome reveals a translational RT coincidence mechanism"; XX RX DOI; 10.1111/pce.12754. RX PUBMED; 27075884. RA Flis A., Sulpice R., Seaton D.D., Ivakov A.A., Liput M., Abel C., RA Millar A.J., Stitt M.; RT "Photoperiod-dependent changes in the phase of core clock transcripts and RT global transcriptional outputs at dawn and dusk in Arabidopsis."; RL Plant Cell Environ 39(9):1955-1981(2016). XX RX DOI; 10.1104/pp.107.115592. RX PUBMED; 18305208. RA Usadel B., Blasing O.E., Gibon Y., Retzlaff K., Hohne M., Gunther M., RA Stitt M.; RT "Global transcript levels respond to small changes of the carbon status RT during progressive exhaustion of carbohydrates in Arabidopsis rosettes."; RL Plant Physiol 146(4):1834-1861(2008). XX RX DOI; 10.1105/tpc.105.035261. RX PUBMED; 16299223. RA Blasing O.E., Gibon Y., Gunther M., Hohne M., Morcuende R., Osuna D., RA Thimm O., Usadel B., Scheible W.R., Stitt M.; RT "Sugars and circadian regulation make major contributions to the global RT regulation of diurnal gene expression in Arabidopsis."; RL Plant Cell 17(12):3257-3281(2005). XX RX DOI; 10.1128/AEM.01974-17. RA Rudi Knut, Angell Inga Leena, Pope Phillip B., Vik Jon Olav, RA Sandve Simen Rød, Snipen Lars; RT "Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition RT for Farmed Atlantic Salmon"; RL Appl Environ Microbiol(2018). XX RX DOI; 10.1186/1752-0509-5-194. RX PUBMED; 22133144. RA Aryal U.K., Stockel J., Krovvidi R.K., Gritsenko M.A., Monroe M.E., RA Moore R.J., Koppenaal D.W., Smith R.D., Pakrasi H.B., Jacobs J.M.; RT "Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece RT ATCC51142 across light-dark diurnal cycles."; RL BMC Syst Biol 5:194(2011). XX RX DOI; 10.1021/pr2009302. RX PUBMED; 22077659. RA Martin S.F., Munagapati V.S., Salvo-Chirnside E., Kerr L.E., Le Bihan T.; RT "Proteome turnover in the green alga Ostreococcus tauri by time course 15N RT metabolic labeling mass spectrometry."; RL J Proteome Res 11(1):476-486(2012). XX RX DOI; 10.1093/nar/gkx1065. RX PUBMED; 29092055. RA Wittig U., Rey M., Weidemann A., Kania R., Muller W.; RT "SABIO-RK: an updated resource for manually curated biochemical reaction RT kinetics."; RL Nucleic Acids Res 46(D1):D656-D660(2018). XX RX DOI; 10.1111/mec.14533. RX PUBMED; 29431879. RA Gillard G., Harvey T.N., Gjuvsland A., Jin Y., Thomassen M., Lien S., RA Leaver M., Torgersen J.S., Hvidsten T.R., Vik J.O., Sandve S.R.; RT "Life-stage-associated remodelling of lipid metabolism regulation in RT Atlantic salmon."; RL Mol Ecol 27(5):1200-1213(2018). XX RX DOI; 10.1002/gcc.22284. RX PUBMED; 26355282. RA Biesma H.D., Schouten P.C., Lacle M.M., Sanders J., Brugman W., RA Kerkhoven R., Mandjes I., van der Groep P., van Diest P.J., Linn S.C.; RT "Copy number profiling by array comparative genomic hybridization RT identifies frequently occurring BRCA2-like male breast cancer."; RL Genes Chromosomes Cancer 54(12):734-744(2015). XX RX DOI; 10.1186/bcr3116. RX PUBMED; 22333393. RA Johansson I., Nilsson C., Berglund P., Lauss M., Ringner M., Olsson H., RA Luts L., Sim E., Thorstensson S., Fjallskog M.L., Hedenfalk I.; RT "Gene expression profiling of primary male breast cancers reveals two RT unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel RT prognostic biomarker."; RL Breast Cancer Res 14(1):R31(2012). XX RX DOI; 10.1080/2162402X.2016.1274477. RX PUBMED; 28344890. RA Dewi D.L., Mohapatra S.R., Blanco Cabanes S., Adam I., RA Somarribas Patterson L.F., Berdel B., Kahloon M., Thurmann L., Loth S., RA Heilmann K., Weichenhan D., Mucke O., Heiland I., Wimberger P., RA Kuhlmann J.D., Kellner K.H., Schott S., Plass C., Platten M., Gerhauser C., RA Trump S., Opitz C.A.; RT "Suppression of indoleamine-2,3-dioxygenase 1 expression by promoter RT hypermethylation in ER-positive breast cancer."; RL Oncoimmunology 6(2):e1274477(2017). XX RX DOI; 10.1074/jbc.M113.474908. RX PUBMED; 24129579. RA Stavrum A.K., Heiland I., Schuster S., Puntervoll P., Ziegler M.; RT "Model of tryptophan metabolism, readily scalable using tissue-specific RT gene expression data."; RL J Biol Chem 288(48):34555-34566(2013). XX RX DOI; 10.1046/j.1432-1033.2002.03055.x. RX PUBMED; 12180966. RA Pritchard L., Kell D.B.; RT "Schemes of flux control in a model of Saccharomyces cerevisiae RT glycolysis."; RL Eur J Biochem 269(16):3894-3904(2002). XX RX DOI; 10.1093/bioinformatics/btt772. RX PUBMED; 24443380. RA Starruss J., de Back W., Brusch L., Deutsch A.; RT "Morpheus: a user-friendly modeling environment for multiscale and RT multicellular systems biology."; RL Bioinformatics 30(9):1331-1332(2014). XX RX DOI; 10.1016/j.cels.2017.02.008. RX PUBMED; 28330614. RA Meyer K., Ostrenko O., Bourantas G., Morales-Navarrete H., Porat-Shliom N., RA Segovia-Miranda F., Nonaka H., Ghaemi A., Verbavatz J.M., Brusch L., RA Sbalzarini I., Kalaidzidis Y., Weigert R., Zerial M.; RT "A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver RT Lobule."; RL Cell Syst 4(3):277-290.e9(2017). XX RX DOI; 10.1371/journal.pcbi.1005865. RA Ostrenko Oleksandr, Incardona Pietro, Ramaswamy Rajesh, Brusch Lutz, RA Sbalzarini Ivo F.; RT "pSSAlib: The partial-propensity stochastic chemical network simulator"; RL PLoS Comput Biol(2017). XX RX DOI; 10.3390/fermentation4020044. RA Almqvist Henrik, Jonsdottir Glaser Sara, Tufvegren Celina, RA Wasserstrom Lisa, Liden Gunnar; RT "Characterization of the Weimberg Pathway in Caulobacter crescentus"; RL Fermentation(2018). XX RX DOI; 10.1093/jxb/ery080. RX PUBMED; 29514292. RA Arsovski A.A., Zemke J.E., Haagen B.D., Kim S.H., Nemhauser J.L.; RT "Phytochrome B regulates resource allocation in Brassica rapa."; RL J Exp Bot 69(11):2837-2846(2018). XX RX DOI; 10.1104/pp.17.01437. RX PUBMED; 29254984. RA Krahmer J., Ganpudi A., Abbas A., Romanowski A., Halliday K.J.; RT "Phytochrome, Carbon Sensing, Metabolism, and Plant Growth Plasticity."; RL Plant Physiol 176(2):1039-1048(2018). XX RX DOI; 10.1111/pce.13000. RX PUBMED; 28628949. RA Mengin V., Pyl E.T., Alexandre Moraes T., Sulpice R., Krohn N., Encke B., RA Stitt M.; RT "Photosynthate partitioning to starch in Arabidopsis thaliana is RT insensitive to light intensity but sensitive to photoperiod due to a RT restriction on growth in the light in short photoperiods."; RL Plant Cell Environ 40(11):2608-2627(2017). XX RX DOI; 10.1093/femsyr/foy052. RA Zakhartsev Maksim, Reuss Matthias; RT "Cell size and morphological properties of yeast Saccharomyces cerevisiae RT in relation to growth temperature"; XX RX DOI; 10.1038/srep09404. RA Gustavsson Anna-Karin, Adiels Caroline B., Mehlig Bernhard, Goksör Mattias; RT "Entrainment of heterogeneous glycolytic oscillations in single cells"; RL Sci Rep(2015). XX RX DOI; 10.1111/febs.12820. RA Gustavsson Anna-Karin, van Niekerk Dawie, Adiels Caroline B., Kooi Bob, RA Goksör Mattias, Snoep Jacky; RT "Allosteric regulation of phosphofructokinase controls the emergence of RT glycolytic oscillations in isolated yeast cells"; RL FEBS J(2014). XX RX DOI; 10.1128/AEM.02091-17. RA Christel Stephan, Herold Malte, Bellenberg Soeren, El Hajjami Mohamed, RA Buetti-Dinh Antoine, Pivkin Igor, Sand Wolfgang, Wilmes Paul, RA Poetsch Ansgar, Dopson Mark; RT "Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing RT Model Species RT Leptospirillum ferriphilum RT T"; RL Appl Environ Microbiol(2018). XX RX DOI; 10.1016/j.febslet.2013.11.028. RA Gustavsson Anna-Karin, van Niekerk Dawie, Adiels Caroline B., RA Goksör Mattias, Snoep Jacky; RT "Heterogeneity of glycolytic oscillatory behaviour in individual yeast RT cells"; XX RX DOI; 10.1111/j.1742-4658.2012.08639.x. RA Gustavsson Anna-Karin, van Niekerk Dawie, Adiels Caroline B., RA du Preez Franco B., Goksör Mattias, Snoep Jacky; RT "Sustained glycolytic oscillations in individual isolated yeast cells"; XX RX DOI; 10.1111/j.1742-4658.2012.08658.x. RX PUBMED; 22686585. RA du Preez F.B., van Niekerk D.D., Snoep J.L.; RT "From steady-state to synchronized yeast glycolytic oscillations II: model RT validation."; RL FEBS J 279(16):2823-2836(2012). XX RX DOI; 10.1111/j.1742-4658.2012.08665.x. RX PUBMED; 22712534. RA du Preez F.B., van Niekerk D.D., Kooi B., Rohwer J.M., Snoep J.L.; RT "From steady-state to synchronized yeast glycolytic oscillations I: model RT construction."; RL FEBS J 279(16):2810-2822(2012). XX RX DOI; 10.15252/msb.20167087. RA Martins Bruno MC, Das Arijit K, Antunes Liliana, Locke James CW; RT "Frequency doubling in the cyanobacterial circadian clock"; RL Mol Syst Biol(2016). XX RX DOI; 10.15252/msb.20177599. RA Karin Omer, Alon Uri; RT "Biphasic response as a mechanism against mutant takeover in tissue RT homeostasis circuits"; RL Mol Syst Biol(2017). XX RX DOI; 10.1002/hep.29389. RX PUBMED; 28727166. RA Hijmans B.S., Boss A., van Dijk T.H., Soty M., Wolters H., Mutel E., RA Groen A.K., Derks T.G.J., Mithieux G., Heerschap A., Reijngoud D.J., RA Rajas F., Oosterveer M.H.; RT "Hepatocytes contribute to residual glucose production in a mouse model for RT glycogen storage disease type Ia."; RL Hepatology 66(6):2042-2054(2017). XX RX DOI; 10.1038/ncomms13254. RX PUBMED; 27869123. RA Dalle Pezze P., Ruf S., Sonntag A.G., Langelaar-Makkinje M., Hall P., RA Heberle A.M., Razquin Navas P., van Eunen K., Tolle R.C., Schwarz J.J., RA Wiese H., Warscheid B., Deitersen J., Stork B., Fassler E., Schauble S., RA Hahn U., Horvatovich P., Shanley D.P., Thedieck K.; RT "A systems study reveals concurrent activation of AMPK and mTOR by amino RT acids."; RL Nat Commun 7:13254(2016). XX RX DOI; 10.1021/acs.jproteome.6b00419. RX PUBMED; 27447838. RA Wolters J.C., Ciapaite J., van Eunen K., Niezen-Koning K.E., Matton A., RA Porte R.J., Horvatovich P., Bakker B.M., Bischoff R., Permentier H.P.; RT "Translational Targeted Proteomics Profiling of Mitochondrial Energy RT Metabolic Pathways in Mouse and Human Samples."; RL J Proteome Res 15(9):3204-3213(2016). XX RX DOI; 10.1002/biot.201800180. RA Kumelj Tjasa, Sulheim Snorre, Wentzel Alexander, Almaas Eivind; RT "Predicting strain engineering strategies using iKS1317: a genome‐scale RT metabolic model of Streptomyces coelicolor"; RL Biotechnol. J.(2018). XX RX DOI; 10.1016/j.cmet.2016.09.004. RA Fang Evandro Fei, Kassahun Henok, Croteau Deborah L., RA Scheibye-Knudsen Morten, Marosi Krisztina, Lu Huiming, RA Shamanna Raghavendra A., Kalyanasundaram Sumana, Bollineni Ravi Chand, RA Wilson Mark A., Iser Wendy B., Wollman Bradley N., Morevati Marya, Li Jun, RA Kerr Jesse S., Lu Qiping, Waltz Tyler B., Tian Jane, Sinclair David A., RA Mattson Mark P., Nilsen Marianne B., Bohr Vilhelm A.; RT "NAD + Replenishment Improves Lifespan and Healthspan in Ataxia RT Telangiectasia Models via Mitophagy and DNA Repair"; RL Cell Metabolism(2016). XX RX DOI; 10.1038/s41598-017-12662-3. RA Fakouri Nima Borhan, Durhuus Jon Ambæk, Regnell Christine Elisabeth, RA Angleys Maria, Desler Claus, Hasan-Olive Md Mahdi, Martín-Pardillos Ana, RA Tsaalbi-Shtylik Anastasia, Thomsen Kirsten, Lauritzen Martin, RA Bohr Vilhelm A., de Wind Niels, Bergersen Linda Hildegard, Rasmussen Tim; RT "Rev1 contributes to proper mitochondrial function via the RT PARP-NAD+-SIRT1-PGC1α axis"; RL Sci Rep(2017). XX RX DOI; 10.1016/j.gdata.2016.04.013. RX PUBMED; 27222814. RA Liu B., Ertesvag H., Aasen I.M., Vadstein O., Brautaset T., Heggeset T.M.; RT "Draft genome sequence of the docosahexaenoic acid producing RT thraustochytrid Aurantiochytrium sp. T66."; RL Genom Data 8:115-116(2016). XX RX DOI; 10.3354/aei00297. RA Jin Yang, Angell Inga Leena, Simen Sandve, Snipen Lars, Olsen Y, Rudi knut; RT "Atlantic salmon raised with diets low in long-chain polyunsaturated n-3 RT fatty acids in freshwater have a Mycoplasma-dominated gut microbiota at RT sea"; RL Aquacult. Environ. Interact.(2019). XX RX DOI; 10.1002/bit.26289. RX PUBMED; 28295202. RA Zhang Z.T., Taylor S., Wang Y.; RT "In situ esterification and extractive fermentation for butyl butyrate RT production with Clostridium tyrobutyricum."; RL Biotechnol Bioeng 114(7):1428-1437(2017). XX RX DOI; 10.1002/bit.24618. RX PUBMED; 22833369. RA van den Berg C., Heeres A.S., van der Wielen L.A., Straathof A.J.; RT "Simultaneous Clostridial fermentation, lipase-catalyzed esterification, RT and ester extraction to enrich diesel with butyl butyrate."; RL Biotechnol Bioeng 110(1):137-142(2013). XX RX DOI; 10.1093/bib/bby087. RA Neal Maxwell Lewis, König Matthias, Nickerson David, Mısırlı Göksel, RA Kalbasi Reza, Dräger Andreas, Atalag Koray, Chelliah Vijayalakshmi, RA Cooling Michael T, Cook Daniel L, Crook Sharon, de Alba Miguel, RA Friedman Samuel, Garny Alan, Gennari John H, Gleeson Padraig, RA Golebiewski Martin, Hucka Mike, Juty Nick, Myers Chris, Olivier Brett G, RA Sauro Herbert M, Scharm Martin, Snoep Jacky, Toure Vasundra, Wipat Anil, RA Wolkenhauer Olaf, Waltemath Dagmar; RT "Harmonizing semantic annotations for computational models in biology"; RL Briefings in Bioinformatics(2019). XX RX DOI; 10.1515/jib-2018-0013. RA Schreiber Falk, Bader Gary D., Gleeson Padraig, Golebiewski Martin, RA Hucka Mike, Keating Sarah M., Novère Nicolas Le, Myers Chris, RA Nickerson David, Sommer Björn, Waltemath Dagmar; RT "Specifications of Standards in Systems and Synthetic Biology: Status and RT Developments in 2017"; RL Journal of Integrative Bioinformatics(2018). XX RX DOI; 10.1038/sdata.2016.18. RA Wilkinson Mark D., Dumontier Michel, Aalbersberg IJsbrand Jan, RA Appleton Gabrielle, Axton Myles, Baak Arie, Blomberg Niklas, RA Boiten Jan-Willem, da Silva Santos Luiz Bonino, Bourne Philip E., RA Bouwman Jildau, Brookes Anthony J., Clark Tim, Crosas Mercè, Dillo Ingrid, RA Dumon Olivier, Edmunds Scott, Evelo Chris T., Finkers Richard, RA Gonzalez-Beltran Alejandra, Gray Alasdair J.G., Groth Paul, Goble Carole, RA Grethe Jeffrey S., Heringa Jaap, ’t Hoen Peter A.C, Hooft Rob, Kuhn Tobias, RA Kok Ruben, Kok Joost, Lusher Scott J., Martone Maryann E., Mons Albert, RA Packer Abel L., Persson Bengt, Rocca-Serra Philippe, Roos Marco, RA van Schaik Rene, Sansone Susanna-Assunta, Schultes Erik, Sengstag Thierry, RA Slater Ted, Strawn George, Swertz Morris A., Thompson Mark, RA van der Lei Johan, van Mulligen Erik, Velterop Jan, Waagmeester Andra, RA Wittenburg Peter, Wolstencroft Katherine, Zhao Jun, Mons Barend; RT "The FAIR Guiding Principles for scientific data management and RT stewardship"; RL Sci. Data(2016). XX RX DOI; 10.1099/mic.0.000542. RX PUBMED; 28982396. RA Kouril T., Eicher J.J., Siebers B., Snoep J.L.; RT "Phosphoglycerate kinase acts as a futile cycle at high temperature."; RL Microbiology (Reading) 163(11):1604-1612(2017). XX RX DOI; 10.3389/fmicb.2019.00757. RX PUBMED; 31031731. RA Haferkamp P., Tjaden B., Shen L., Brasen C., Kouril T., Siebers B.; RT "The Carbon Switch at the Level of Pyruvate and Phosphoenolpyruvate in RT Sulfolobus solfataricus P2."; RL Front Microbiol 10:757(2019). XX RX DOI; 10.1101/267104. RA Kinmonth-Schultz Hannah A, MacEwen Melissa J, Seaton Daniel, Millar Andrew, RA Imaizumi Takato, Kim Soo-Hyung; RT "Mechanistic model of temperature influence on flowering through RT whole-plant accumulation of FT"; XX RX DOI; 10.1074/jbc.M115.654129. RX PUBMED; 26432643. RA VanLinden M.R., Dolle C., Pettersen I.K., Kulikova V.A., Niere M., RA Agrimi G., Dyrstad S.E., Palmieri F., Nikiforov A.A., Tronstad K.J., RA Ziegler M.; RT "Subcellular Distribution of NAD+ between Cytosol and Mitochondria RT Determines the Metabolic Profile of Human Cells."; RL J Biol Chem 290(46):27644-27659(2015). XX RX DOI; 10.1038/s41477-018-0253-3. RX PUBMED; 30250277. RA Song Y.H., Kubota A., Kwon M.S., Covington M.F., Lee N., Taagen E.R., RA Laboy Cintron D., Hwang D.Y., Akiyama R., Hodge S.K., Huang H., RA Nguyen N.H., Nusinow D.A., Millar A.J., Shimizu K.K., Imaizumi T.; RT "Molecular basis of flowering under natural long-day conditions in RT Arabidopsis."; RL Nat Plants 4(10):824-835(2018). XX RX DOI; 10.1101/287862. RA Noordally Zeenat B., Hindle Matthew M., Martin Sarah F., Seaton Daniel, RA Simpson Ian, Le Bihan Thierry, Millar Andrew; RT "Circadian protein regulation in the green lineage I. A phospho-dawn RT anticipates light onset before proteins peak in daytime."; XX RX DOI; 10.1101/232397. RA Buskin Adriana, Zhu Lili, Chichagova Valeria, Basu Basudha, RA Mozaffari-Jovin Sina, Dolan David, Droop Alastair, Collin Joseph, RA Bronstein Revital, Mehrotra Sudeep, Farkas Michael, Hilgen Gerrit, RA White Kathryn, Hallam Dean, Bialas Katarzyna, Chung Git, Mellough Carla, RA Ding Yuchun, Krasnogor Natalio, Przyborski Stefan, Al-Aama Jumana, RA Alharthi Sameer, Xu Yaobo, Wheway Gabrielle, Szymanska Katarzyna, RA McKibbin Martin, Inglehearn Chris F, Elliott David J, Lindsay Susan, RA Ali Robin R, Steel David H, Armstrong Lyle, Sernagor Evelyne, Pierce Eric, RA Luehrmann Reinhard, Grellscheid Sushma Nagaraja, Johnson Colin A, RA Lako Majlinda; RT "Human iPSC-derived RPE and retinal organoids reveal impaired alternative RT splicing of genes involved in pre-mRNA splicing in PRPF31 autosomal RT dominant retinitis pigmentosa"; XX RX DOI; 10.7557/5.4510. RA Oefelein Timon; RT "Delivering on open data: Current practices in data sharing, and challenges RT ahead!"; RL Septentrio Conference Series(2018). XX RX DOI; 10.1038/s41598-019-43862-8. RA Datsomor Alex K., Zic Nikola, Li Keshuai, Olsen Rolf E., Jin Yang, RA Vik Jon Olav, Edvardsen Rolf B., Grammes Fabian, Wargelius Anna, Winge Per; RT "CRISPR/Cas9-mediated ablation of elovl2 in Atlantic salmon (Salmo salar RT L.) inhibits elongation of polyunsaturated fatty acids and induces Srebp-1 RT and target genes"; RL Sci Rep(2019). XX RX DOI; 10.1186/s12915-016-0327-5. RX PUBMED; 27927213. RA van Eunen K., Volker-Touw C.M., Gerding A., Bleeker A., Wolters J.C., RA van Rijt W.J., Martines A.M., Niezen-Koning K.E., Heiner R.M., RA Permentier H., Groen A.K., Reijngoud D.J., Derks T.G., Bakker B.M.; RT "Living on the edge: substrate competition explains loss of robustness in RT mitochondrial fatty-acid oxidation disorders."; RL BMC Biol 14(1):107(2016). XX RX DOI; 10.1002/adsc.201801530. RA Roldán Raquel, Hernández Karel, Joglar Jesús, Bujons Jordi, Parella Teodor, RA Fessner Wolf Dieter, Clapés Pere; RT "Aldolase-Catalyzed Asymmetric Synthesis of N-Heterocycles by Addition of RT Simple Aliphatic Nucleophiles to Aminoaldehydes"; RL Adv. Synth. Catal.(2019). XX RX DOI; 10.1002/cbic.201600609. RA Zhou Chaoqiang, Saravanan Thangavelu, Lorillière Marion, Wei Dongzhi, RA Charmantray Franck, Hecquet Laurence, Fessner Wolf Dieter, Yi Dong; RT "Second-Generation Engineering of a Thermostable Transketolase (TK RT Gst RT ) for Aliphatic Aldehyde Acceptors with Either Improved or RT Reversed Stereoselectivity"; RL ChemBioChem(2017). XX RX DOI; 10.1002/adsc.201900109. RT "One‐Pot Cascade Synthesis of (3S)‐Hydroxyketones Catalyzed by RT Transketolase via Hydroxypyruvate Generated in Situ from d‐Serine by RT d‐Amino Acid Oxidase"; RL Volume361, Issue11 Special Issue: Biocatalysis, Pages 2550-2558(2019). XX RX DOI; 10.1021/acscatal.9b01646. RA Marín-Valls Roser, Hernández Karel, Bolte Michael, Joglar Jesús, RA Bujons Jordi, Clapés Pere; RT "Chemoenzymatic Hydroxymethylation of Carboxylic Acids by Tandem RT Stereodivergent Biocatalytic Aldol Reaction and Chemical Decarboxylation"; RL ACS Catal.(2019). XX RX DOI; 10.1039/c2ob25357g. RA Karjalainen Oskari K., Koskinen Ari M.P.; RT "Diastereoselective synthesis of vicinal amino alcohols"; RL Org. Biomol. Chem.(2012). XX RX DOI; 10.1016/j.marenvres.2019.02.003. RX PUBMED; 30803754. RA Dale K., Muller M.B., Tairova Z., Khan E.A., Hatlen K., Grung M., RA Yadetie F., Lille-Langoy R., Blaser N., Skaug H.J., Lyche J.L., Arukwe A., RA Hylland K., Karlsen O.A., Goksoyr A.; RT "Contaminant accumulation and biological responses in Atlantic cod (Gadus RT morhua) caged at a capped waste disposal site in Kollevag, Western RT Norway."; RL Mar Environ Res 145:39-51(2019). XX RX DOI; 10.1021/acs.est.9b00637. RX PUBMED; 31090407. RA Khan E.A., Bertotto L.B., Dale K., Lille-Langoy R., Yadetie F., RA Karlsen O.A., Goksoyr A., Schlenk D., Arukwe A.; RT "Modulation of Neuro-Dopamine Homeostasis in Juvenile Female Atlantic Cod ( RT Gadus morhua) Exposed to Polycyclic Aromatic Hydrocarbons and RT Perfluoroalkyl Substances."; RL Environ Sci Technol 53(12):7036-7044(2019). XX RX DOI; 10.1089/zeb.2018.1712. RX PUBMED; 31216234. RA van Steijn L., Verbeek F.J., Spaink H.P., Merks R.M.H.; RT "Predicting Metabolism from Gene Expression in an Improved Whole-Genome RT Metabolic Network Model of Danio rerio."; RL Zebrafish 16(4):348-362(2019). XX RX DOI; 10.1038/s41573-019-0016-5. RA Platten Michael, Nollen Ellen A.A., Röhrig Ute F., Fallarino Francesca, RA Opitz Christiane; RT "Tryptophan metabolism as a common therapeutic target in cancer, RT neurodegeneration and beyond"; RL Nature Reviews Drug Discovery(2019). XX RX DOI; 10.3389/fonc.2019.00962. RA Zimmer Philipp, Schmidt Frank, Prentzell Mirja Tamara, Berdel Bianca, RA Wiskemann Joachim, Kellner Karl-Heinz, Debus Jürgen, Ulrich Cornelia, RA Opitz Christiane, Steindorf Karen; RT "Resistance Exercise Reduces Kynurenine Pathway Metabolites in Breast RT Cancer Patients Undergoing Radiotherapy"; RL Front. Oncol.(2019). XX RX DOI; 10.1016/j.mex.2019.10.011. RA Hill Meredith, Mason Dayna, Monteiro Marques Tânia, RA Gama Carvalho Margarida, Tran Nham; RT "Developing A Virus-MicroRNA Interactome Using Cystoscope"; RL MethodsX(2019). XX RX DOI; 10.1016/j.virol.2018.05.022. RX PUBMED; 29935424. RA Sais D., Zhang X., Marques T.M., Rose B., Khoury S., Hill M., Deutsch F., RA Lyons J.G., Gama-Carvalho M., Tran N.; RT "Human papillomavirus 16 E6 modulates the expression of miR-496 in RT oropharyngeal cancer."; RL Virology 521:149-157(2018). XX RX DOI; 10.1038/s41598-018-29990-7. RA Garcia-Vaquero Marina L., Gama-Carvalho Margarida, Rivas Javier De Las, RA Pinto Francisco R.; RT "Searching the overlap between network modules with specific betweeness RT (S2B) and its application to cross-disease analysis"; RL Sci Rep(2018). XX RX DOI; 10.15252/embj.201694335. RX PUBMED; 27993935. RA Amaral A.J., Andrade J., Foxall R.B., Matoso P., Matos A.M., Soares R.S., RA Rocha C., Ramos C.G., Tendeiro R., Serra-Caetano A., Guerra-Assuncao J.A., RA Santa-Marta M., Goncalves J., Gama-Carvalho M., Sousa A.E.; RT "miRNA profiling of human naive CD4 T cells links miR-34c-5p to cell RT activation and HIV replication."; RL EMBO J 36(3):346-360(2017). XX RX DOI; 10.1111/jnc.13945. RX PUBMED; 28054357. RA Gama-Carvalho M., L Garcia-Vaquero M., R Pinto F., Besse F., Weis J., RA Voigt A., Schulz J.B., De Las Rivas J.; RT "Linking amyotrophic lateral sclerosis and spinal muscular atrophy through RT RNA-transcriptome homeostasis: a genomics perspective."; RL J Neurochem 141(1):12-30(2017). XX RX DOI; 10.1093/nar/gky049. RA Iyer Lavanya M, Nagarajan Sankari, Woelfer Monique, Schoger Eric, RA Khadjeh Sara, Zafiriou Maria Patapia, Kari Vijayalakshmi, Herting Jonas, RA Pang Sze Ting, Weber Marc, Rathjens Franziska S, Fischer Ralf-Jörg, RA Toischer Karl, Hasenfuss Gerd, Noack Steffi, Johnsen Steven A, RA Zelarayán Laura C; RT "A context-specific cardiac β-catenin and GATA4 interaction influences RT TCF7L2 occupancy and remodels chromatin driving disease progression in the RT adult heart"; XX RX DOI; 10.1093/nar/gkw1032. RX PUBMED; 27899646. RA Wolstencroft K., Krebs O., Snoep J.L., Stanford N.J., Bacall F., RA Golebiewski M., Kuzyakiv R., Nguyen Q., Owen S., Soiland-Reyes S., RA Straszewski J., van Niekerk D.D., Williams A.R., Malmstrom L., Rinn B., RA Muller W., Goble C.; RT "FAIRDOMHub: a repository and collaboration environment for sharing systems RT biology research."; RL Nucleic Acids Res 45(D1):D404-D407(2017). XX RX DOI; 10.1101/845818. RA Petek Marko, Zagorscak Maja, Ramsak Ziva, Sanders Sheri, Tseng Elizabeth, RA Zouine Mohamed, Coll Rius Anna, Gruden Kristina; RT "Cultivar-specific transcriptome and pan-transcriptome reconstruction of RT tetraploid potato"; XX RX DOI; 10.26508/lsa.201800257. RA Heberle Alexander, Razquin Navas Patricia, Langelaar-Makkinje Miriam, RA Kasack Katharina, Sadik Ahmed, Faessler Erik, Hahn Udo, RA Marx-Stoelting Philip, Opitz Christiane, Sers Christine, Heiland Ines, RA Schäuble Sascha, Thedieck Kathrin; RT "The PI3K and MAPK/p38 pathways control stress granule assembly in a RT hierarchical manner"; RL Life Sci. Alliance(2019). XX RX DOI; 10.1038/492180a. RA Vaux David L.; RT "Know when your numbers are significant"; RL Nature(2012). XX RX DOI; 10.1038/protex.2016.032. RA bhardwaj vikash, bhardwaj Vikash, Krebs Olga; RT "Parallel DNA Polymerase Chain Reaction (PD-PCR)"; RL Protocol Exchange(2016). XX RX DOI; 10.1128/JB.00399-15. RX PUBMED; 26148714. RA Mock J., Zheng Y., Mueller A.P., Ly S., Tran L., Segovia S., Nagaraju S., RA Kopke M., Durre P., Thauer R.K.; RT "Energy Conservation Associated with Ethanol Formation from H2 and CO2 in RT Clostridium autoethanogenum Involving Electron Bifurcation."; RL J Bacteriol 197(18):2965-2980(2015). XX RX DOI; 10.1016/j.aquatox.2018.06.003. RX PUBMED; 29929084. RA Yadetie F., Zhang X., Hanna E.M., Aranguren-Abadia L., Eide M., Blaser N., RA Brun M., Jonassen I., Goksoyr A., Karlsen O.A.; RT "RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) RT precision-cut liver slices exposed to benzo[a]pyrene and RT 17alpha-ethynylestradiol."; RL Aquat Toxicol 201:174-186(2018). XX RX DOI; 10.1038/msb.2012.6. RX PUBMED; 22395476. RA Pokhilko A., Fernandez A.P., Edwards K.D., Southern M.M., Halliday K.J., RA Millar A.J.; RT "The clock gene circuit in Arabidopsis includes a repressilator with RT additional feedback loops."; RL Mol Syst Biol 8:574(2012). XX RX DOI; 10.1371/journal.pcbi.1003705. RA Fogelmark Karl, Troein Carl; RT "Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock"; RL PLoS Comput Biol(2014). XX RX DOI; 10.1002/hep.22284. RX PUBMED; 18459129. RA Herrema H., Derks T.G., van Dijk T.H., Bloks V.W., Gerding A., Havinga R., RA Tietge U.J., Muller M., Smit G.P., Kuipers F., Reijngoud D.J.; RT "Disturbed hepatic carbohydrate management during high metabolic demand in RT medium-chain acyl-CoA dehydrogenase (MCAD)-deficient mice."; RL Hepatology 47(6):1894-1904(2008). XX RX DOI; 10.1038/s41467-020-14830-y. RA Shen Lu, Kohlhaas Martha, Enoki Junichi, Meier Roland, RA Schönenberger Bernhard, Wohlgemuth Roland, Kourist Robert, Niemeyer Felix, RA van Niekerk Dawie, Bräsen Christopher, Niemeyer Jochen, Snoep Jacky, RA Siebers Bettina; RT "A combined experimental and modelling approach for the Weimberg pathway RT optimisation"; RL Nat Commun(2020). XX RX DOI; 10.1016/j.jsbmb.2018.06.013. RA Barnard Monique, Quanson Jonathan L., Mostaghel Elahe, Pretorius Elzette, RA Snoep Jacky, Storbeck Karl-Heinz; RT "11-Oxygenated androgen precursors are the preferred substrates for RT aldo-keto reductase 1C3 (AKR1C3): Implications for castration resistant RT prostate cancer"; RL The Journal of Steroid Biochemistry and Molecular Biology(2018). XX RX DOI; 10.1101/647776. RA Kolodkin Alexey, Sharma Raju Prasad, Colangelo Anna Maria, RA Ignatenko Andrew, Martorana Francesca, Jennen Danyel, Briede Jacco J., RA Brady Nathan, Barberis Matteo, Mondeel Thierry D.G.A., Papa Michele, RA Kumar Vikas, Peters Bernhard, Skupin Alexander, Alberghina Lilia, RA Balling Rudi, Westerhoff Hans V.; RT "Design principles of ROS dynamic networks relevant to precision therapies RT for age-related diseases"; XX RX DOI; 10.1093/bioinformatics/btaa068. RA Scharm Martin, Wolkenhauer Olaf, Jalili Mahdi, Salehzadeh-Yazdi Ali; RT "GEMtractor: extracting views into genome-scale metabolic models"; RL Bioinformatics(2020). XX RX DOI; 10.1101/796722. RA Sulheim Snorre, Kumelj Tjasa, van Dissel Dino, Salehzadeh-Yazdi Ali, RA Du Chao, van Wezel Gilles P., Nieselt Kay, Almaas Eivind, RA Wentzel Alexander, Kerkhoven Eduard; RT "Genome-scale Model Constrained by Proteomics Reveals Metabolic Changes in RT Streptomyces coelicolor RT M1152 Compared to M145"; XX RX DOI; 10.1038/s41598-019-50758-0. RA Martines Anne-Claire M.F., Gerding Albert, Stolle Sarah, RA Vieira-Lara Marcel A., Wolters Justina C., Jurdzinski Angelika, RA Bongiovanni Laura, de Bruin Alain, van der Vlies Pieter, RA van der Vries Gerben, Bloks Vincent W., Derks Terry G.J., RA Reijngoud Dirk-Jan, Bakker Barbara; RT "Transcriptome analysis suggests a compensatory role of the cofactors RT coenzyme A and NAD+ in medium-chain acyl-CoA dehydrogenase knockout mice"; RL Scientific Reports(2019). XX RX DOI; 10.1101/2020.03.22.002386. RA Gordon David E., Jang Gwendolyn M., Bouhaddou Mehdi, Xu Jiewei, RA Obernier Kirsten, O’Meara Matthew J., Guo Jeffrey Z., Swaney Danielle L., RA Tummino Tia A., Hüttenhain Ruth, Kaake Robyn M., Richards Alicia L., RA Tutuncuoglu Beril, Foussard Helene, Batra Jyoti, Haas Kelsey, Modak Maya, RA Kim Minkyu, Haas Paige, Polacco Benjamin J., Braberg Hannes, RA Fabius Jacqueline M., Eckhardt Manon, Soucheray Margaret, RA Bennett Melanie J., Cakir Merve, McGregor Michael J, Li Qiongyu, RA Naing Zun Zar Chi, Zhou Yuan, Peng Shiming, Kirby Ilsa T., Melnyk James E., RA Chorba John S., Lou Kevin, Dai Shizhong A., Shen Wenqi, Shi Ying, RA Zhang Ziyang, Barrio-Hernandez Inigo, Memon Danish, RA Hernandez-Armenta Claudia, Mathy Christopher J.P., Perica Tina, RA Pilla Kala B., Ganesan Sai J., Saltzberg Daniel J., Ramachandran Rakesh, RA Liu Xi, Rosenthal Sara B., Calviello Lorenzo, Venkataramanan Srivats, RA Lin Yizhu, Wankowicz Stephanie A., Bohn Markus, Trenker Raphael, RA Young Janet M., Cavero Devin, Hiatt Joe, Roth Theo, Rathore Ujjwal, RA Subramanian Advait, Noack Julia, Hubert Mathieu, Roesch Ferdinand, RA Vallet Thomas, Meyer Björn, White Kris M., Miorin Lisa, Agard David, RA Emerman Michael, Ruggero Davide, García-Sastre Adolfo, Jura Natalia, RA Zastrow Mark von, Taunton Jack, Schwartz Olivier, Vignuzzi Marco, RA d’Enfert Christophe, Mukherjee Shaeri, Jacobson Matt, Malik Harmit S., RA Fujimori Danica G., Ideker Trey, Craik Charles S., Floor Stephen, RA Fraser James S., Gross John, Sali Andrej, Kortemme Tanja, Beltrao Pedro, RA Shokat Kevan, Shoichet Brian K., Krogan Nevan J.; RT "A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets RT and Potential Drug-Repurposing"; XX RX DOI; 10.1101/2020.03.13.991455. RA Lukassen Soeren, Chua Robert Lorenz, Trefzer Timo, Kahn Nicolas C., RA Schneider Marc A., Muley Thomas, Winter Hauke, Meister Michael, RA Veith Carmen, Boots Agnes W., Hennig Bianca P., Kreuter Michael, RA Conrad Christian, Eils Roland; RT "SARS-CoV-2 receptor ACE2 and TMPRSS2 are predominantly expressed in a RT transient secretory cell type in subsegmental bronchial branches"; XX RX DOI; 10.1101/2020.03.05.979260. RA Pfaender Stephanie, Mar Katrina B., Michailidis Eleftherios, RA Kratzel Annika, Hirt Dagny, V’kovski Philip, Fan Wenchun, Ebert Nadine, RA Stalder Hanspeter, Kleine-Weber Hannah, Hoffmann Markus, RA Hoffmann H.Heinrich, Saeed Mohsan, Dijkman Ronald, Steinmann Eike, RA Wight-Carter Mary, Hanners Natasha W., Pöhlmann Stefan, Gallagher Tom, RA Todt Daniel, Zimmer Gert, Rice Charles M., Schoggins John W., Thiel Volker; RT "LY6E impairs coronavirus fusion and confers immune control of viral RT disease"; XX RX DOI; 10.1101/2020.02.19.956581. RA Walls Alexandra C., Park Young-Jun, Tortorici M.Alexandra, Wall Abigail, RA McGuire Andrew T., Veesler David; RT "Structure, function and antigenicity of the SARS-CoV-2 spike RT glycoprotein"; XX RX DOI; 10.1101/2020.02.08.926006. RA Meng Tong, Cao Hao, Zhang Hao, Kang Zijian, Xu Da, Gong Haiyi, Wang Jing, RA Li Zifu, Cui Xingang, Xu Huji, Wei Haifeng, Pan Xiuwu, Zhu Rongrong, RA Xiao Jianru, Zhou Wang, Cheng Liming, Liu Jianmin; RT "The insert sequence in SARS-CoV-2 enhances spike protein cleavage by RT TMPRSS"; XX RX DOI; 10.1101/2020.03.10.986398. RA Brielle Esther S., Schneidman-Duhovny Dina, Linial Michal; RT "The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 RT human receptor"; XX RX DOI; 10.1016/j.antiviral.2020.104742. RA Coutard B., Valle C., de Lamballerie X., Canard B., Seidah N.G., RA Decroly E.; RT "The spike glycoprotein of the new coronavirus 2019-nCoV contains a RT furin-like cleavage site absent in CoV of the same clade"; RL Antiviral Research(2020). XX RX DOI; 10.1016/j.cell.2020.02.052. RA Hoffmann Markus, Kleine-Weber Hannah, Schroeder Simon, Krüger Nadine, RA Herrler Tanja, Erichsen Sandra, Schiergens Tobias S., Herrler Georg, RA Wu Nai-Huei, Nitsche Andreas, Müller Marcel A., Drosten Christian, RA Pöhlmann Stefan; RT "SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a RT Clinically Proven Protease Inhibitor"; RL Cell(2020). XX RX DOI; 10.1038/s41564-020-0688-y. RA Letko Michael, Marzi Andrea, Munster Vincent; RT "Functional assessment of cell entry and receptor usage for SARS-CoV-2 and RT other lineage B betacoronaviruses"; RL Nature Microbiology(2020). XX RX DOI; 10.1101/2020.03.14.988345. RA Wang Ke, Chen Wei, Zhou Yu-Sen, Lian Jian-Qi, Zhang Zheng, Du Peng, RA Gong Li, Zhang Yang, Cui Hong-Yong, Geng Jie-Jie, Wang Bin, Sun Xiu-Xuan, RA Wang Chun-Fu, Yang Xu, Lin Peng, Deng Yong-Qiang, Wei Ding, Yang Xiang-Min, RA Zhu Yu-Meng, Zhang Kui, Zheng Zhao-Hui, Miao Jin-Lin, Guo Ting, Shi Ying, RA Zhang Jun, Fu Ling, Wang Qing-Yi, Bian Huijie, Zhu Ping, Chen Zhi-Nan; RT "SARS-CoV-2 invades host cells via a novel route: CD147-spike protein"; XX RX DOI; 10.1126/science.abb2507. RA Wrapp Daniel, Wang Nianshuang, Corbett Kizzmekia S., Goldsmith Jory A., RA Hsieh Ching-Lin, Abiona Olubukola, Graham Barney S., McLellan Jason S.; RT "Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation"; RL Science(2020). XX RX DOI; 10.1101/2020.02.29.971101. RA Wu Aiping, Niu Peihua, Wang Lulan, Zhou Hangyu, Zhao Xiang, Wang Wenling, RA Wang Jingfeng, Ji Chengyang, Ding Xiao, Wang Xianyue, Lu Roujian, RA Gold Sarah, Aliyari Saba, Zhang Shilei, Vikram Ellee, Zou Angela, RA Lenh Emily, Chen Janet, Ye Fei, Han Na, Peng Yousong, Guo Haitao, RA Wu Guizhen, Jiang Taijiao, Tan Wenjie, Cheng Genhong; RT "Mutations, Recombination and Insertion in the Evolution of 2019-nCoV"; XX RX DOI; 10.1073/pnas.0605402103. RA Lu W., Zheng B.-J., Xu K., Schwarz W., Du L., Wong C.K.L., Chen J., RA Duan S., Deubel V., Sun B.; RT "Severe acute respiratory syndrome-associated coronavirus 3a protein forms RT an ion channel and modulates virus release"; RL Proceedings of the National Academy of Sciences(2006). XX RX DOI; 10.1128/JVI.78.13.6723-6734.2004. RA Tan Y.-J., Teng E., Shen S., Tan T.H.P., Goh P.-Y., Fielding B.C., RA Ooi E.-E., Tan H.-C., Lim S.G., Hong W.; RT "A Novel Severe Acute Respiratory Syndrome Coronavirus Protein, U274, Is RT Transported to the Cell Surface and Undergoes Endocytosis"; RL Journal of Virology(2004). XX RX DOI; 10.1038/nature03712. RA Imai Yumiko, Kuba Keiji, Rao Shuan, Huan Yi, Guo Feng, Guan Bin, Yang Peng, RA Sarao Renu, Wada Teiji, Leong-Poi Howard, Crackower Michael A., RA Fukamizu Akiyoshi, Hui Chi-Chung, Hein Lutz, Uhlig Stefan, RA Slutsky Arthur S., Jiang Chengyu, Penninger Josef M.; RT "Angiotensin-converting enzyme 2 protects from severe acute lung failure"; RL Nature(2005). XX RX DOI; 10.1128/JVI.79.15.10083-10087.2005. RA Tan Y.-J., Tham P.-Y., Chan D.Z.L., Chou C.-F., Shen S., Fielding B.C., RA Tan T.H.P., Lim S.G., Hong W.; RT "The Severe Acute Respiratory Syndrome Coronavirus 3a Protein Up-Regulates RT Expression of Fibrinogen in Lung Epithelial Cells"; RL Journal of Virology(2005). XX RX DOI; 10.1113/expphysiol.2007.040048. RA Imai Yumiko, Kuba Keiji, Penninger Josef M.; RT "The discovery of angiotensin-converting enzyme 2 and its role in acute RT lung injury in mice: Discovery of ACE2 and its role in acute lung injury"; RL Experimental Physiology(2008). XX RX DOI; 10.1016/j.biocel.2009.04.019. RA Chan Chak-Ming, Tsoi Ho, Chan Wing-Man, Zhai Shenyu, Wong Ching-On, RA Yao Xiaoqiang, Chan Wood-Yee, Tsui Stephen Kwok-Wing, Chan Ho Yin Edwin; RT "The ion channel activity of the SARS-coronavirus 3a protein is linked to RT its pro-apoptotic function"; RL The International Journal of Biochemistry & Cell Biology(2009). XX RX DOI; 10.1371/journal.pone.0008342. RA Minakshi Rinki, Padhan Kartika, Rani Manjusha, Khan Nabab, Ahmad Faizan, RA Jameel Shahid; RT "The SARS Coronavirus 3a Protein Causes Endoplasmic Reticulum Stress and RT Induces Ligand-Independent Downregulation of the Type 1 Interferon RT Receptor"; RL PLoS ONE(2009). XX RX DOI; 10.3389/fmicb.2019.00050. RA Chen I-Yin, Moriyama Miyu, Chang Ming-Fu, Ichinohe Takeshi; RT "Severe Acute Respiratory Syndrome Coronavirus Viroporin 3a Activates the RT NLRP3 Inflammasome"; RL Frontiers in Microbiology(2019). XX RX DOI; 10.1186/1752-0509-6-117. RA Shoemaker Jason E, Fukuyama Satoshi, Eisfeld Amie J, Muramoto Yukiko, RA Watanabe Shinji, Watanabe Tokiko, Matsuoka Yukiko, Kitano Hiroaki, RA Kawaoka Yoshihiro; RT "Integrated network analysis reveals a novel role for the cell cycle in RT 2009 pandemic influenza virus-induced inflammation in macaque lungs"; RL BMC Systems Biology(2012). XX RX DOI; 10.1371/journal.ppat.1004856. RA Shoemaker Jason E., Fukuyama Satoshi, Eisfeld Amie J., Zhao Dongming, RA Kawakami Eiryo, Sakabe Saori, Maemura Tadashi, Gorai Takeo, RA Katsura Hiroaki, Muramoto Yukiko, Watanabe Shinji, Watanabe Tokiko, RA Fuji Ken, Matsuoka Yukiko, Kitano Hiroaki, Kawaoka Yoshihiro; RT "An Ultrasensitive Mechanism Regulates Influenza Virus-Induced RT Inflammation"; RL PLOS Pathogens(2015). XX RX DOI; 10.1101/2020.02.23.20026690. RA Liao Minfeng, Liu Yang, Yuan Jin, Wen Yanling, Xu Gang, Zhao Juanjuan, RA Chen Lin, Li Jinxiu, Wang Xin, Wang Fuxiang, Liu Lei, Zhang Shuye, RA Zhang Zheng; RT "The landscape of lung bronchoalveolar immune cells in COVID-19 revealed by RT single-cell RNA sequencing"; XX RX DOI; 10.20944/preprints202003.0206.v1. RT "Therapeutic Approaches for COVID-19 Based on the Dynamics of RT Interferon-mediated Immune Responses"; XX RX DOI; 10.1038/s41591-020-0819-2. RA Thevarajan Irani, Nguyen Thi H.O., Koutsakos Marios, Druce Julian, RA Caly Leon, van de Sandt Carolien E., Jia Xiaoxiao, Nicholson Suellen, RA Catton Mike, Cowie Benjamin, Tong Steven Y.C., Lewin Sharon R., RA Kedzierska Katherine; RT "Breadth of concomitant immune responses prior to patient recovery: a case RT report of non-severe COVID-19"; RL Nature Medicine(2020). XX RX DOI; 10.1053/j.gastro.2020.02.055. RA Xiao Fei, Tang Meiwen, Zheng Xiaobin, Liu Ye, Li Xiaofeng, Shan Hong; RT "Evidence for gastrointestinal infection of SARS-CoV-2"; RL Gastroenterology(2020). XX RX DOI; 10.1084/jem.20050828. RA Gu Jiang, Gong Encong, Zhang Bo, Zheng Jie, Gao Zifen, Zhong Yanfeng, RA Zou Wanzhong, Zhan Jun, Wang Shenglan, Xie Zhigang, Zhuang Hui, RA Wu Bingquan, Zhong Haohao, Shao Hongquan, Fang Weigang, Gao Dongshia, RA Pei Fei, Li Xingwang, He Zhongpin, Xu Danzhen, Shi Xeying, RA Anderson Virginia M., Leong Anthony S.-Y.; RT "Multiple organ infection and the pathogenesis of SARS"; RL Journal of Experimental Medicine(2005). XX RX DOI; 10.1101/2020.03.13.990226. RA Bao Linlin, Deng Wei, Gao Hong, Xiao Chong, Liu Jiayi, Xue Jing, Lv Qi, RA Liu Jiangning, Yu Pin, Xu Yanfeng, Qi Feifei, Qu Yajin, Li Fengdi, RA Xiang Zhiguang, Yu Haisheng, Gong Shuran, Liu Mingya, Wang Guanpeng, RA Wang Shunyi, Song Zhiqi, Zhao Wenjie, Han Yunlin, Zhao Linna, Liu Xing, RA Wei Qiang, Qin Chuan; RT "Reinfection could not occur in SARS-CoV-2 infected rhesus macaques"; XX RX DOI; 10.1101/2020.02.06.20020974. RA Guan Wei-jie, Ni Zheng-yi, Hu Yu, Liang Wen-hua, Ou Chun-quan, RA He Jian-xing, Liu Lei, Shan Hong, Lei Chun-liang, Hui David SC, Du Bin, RA Li Lan-juan, Zeng Guang, Yuen Kowk-Yung, Chen Ru-chong, Tang Chun-li, RA Wang Tao, Chen Ping-yan, Xiang Jie, Li Shi-yue, Wang Jin-lin, RA Liang Zi-jing, Peng Yi-xiang, Wei Li, Liu Yong, Hu Ya-hua, Peng Peng, RA Wang Jian-ming, Liu Ji-yang, Chen Zhong, Li Gang, Zheng Zhi-jian, RA Qiu Shao-qin, Luo Jie, Ye Chang-jiang, Zhu Shao-yong, Zhong Nan-shan; RT "Clinical characteristics of 2019 novel coronavirus infection in China"; XX RX DOI; 10.1016/S0140-6736(20)30183-5. RA Huang Chaolin, Wang Yeming, Li Xingwang, Ren Lili, Zhao Jianping, Hu Yi, RA Zhang Li, Fan Guohui, Xu Jiuyang, Gu Xiaoying, Cheng Zhenshun, Yu Ting, RA Xia Jiaan, Wei Yuan, Wu Wenjuan, Xie Xuelei, Yin Wen, Li Hui, Liu Min, RA Xiao Yan, Gao Hong, Guo Li, Xie Jungang, Wang Guangfa, Jiang Rongmeng, RA Gao Zhancheng, Jin Qi, Wang Jianwei, Cao Bin; RT "Clinical features of patients infected with 2019 novel coronavirus in RT Wuhan, China"; RL The Lancet(2020). XX RX DOI; 10.1111/all.14289. RA Dong Xiang, Cao Yi-yuan, Lu Xiao-xia, Zhang Jin-jin, Du Hui, Yan You-qin, RA Akdis Cezmi A., Gao Ya-dong; RT "Eleven Faces of Coronavirus Disease 2019"; RL Allergy(2020). XX RX DOI; 10.1101/2020.03.07.982264. RA Lokugamage Kumari G., Hage Adam, Schindewolf Craig, Rajsbaum Ricardo, RA Menachery Vineet D.; RT "SARS-CoV-2 is sensitive to type I interferon pretreatment"; XX RX DOI; 10.1016/S1473-3099(20)30132-8. RA Stebbing Justin, Phelan Anne, Griffin Ivan, Tucker Catherine, Oechsle Olly, RA Smith Dan, Richardson Peter; RT "COVID-19: combining antiviral and anti-inflammatory treatments"; RL The Lancet Infectious Diseases(2020). XX RX DOI; 10.1101/2020.03.04.20031237. RA Rao Shitao, Lau Alexandria, So Hon-Cheong; RT "Exploring diseases/traits and blood proteins causally related to RT expression of ACE2, the putative receptor of 2019-nCov: A Mendelian RT Randomization analysis"; XX RX DOI; 10.20944/preprints202003.0286.v1. RA Li Xu, Yu Jinchao, Zhang Zhiming, Ren Jing, Peluffo Alex E., Zhang Wen, RA Zhao Yujie, Yan Kaijing, Cohen Daniel, Wang Wenjia; RT "Network Bioinformatics Analysis Provides Insight into Drug Repurposing for RT COVID-2019"; XX RX DOI; 10.1016/j.antiviral.2011.02.008. RA Schwarz Silvia, Wang Kai, Yu Wenjing, Sun Bing, Schwarz Wolfgang; RT "Emodin inhibits current through SARS-associated coronavirus 3a protein"; RL Antiviral Research(2011). XX RX DOI; 10.1099/vir.0.19424-0. RA Thiel Volker, Ivanov Konstantin A., Putics Ákos, Hertzig Tobias, RA Schelle Barbara, Bayer Sonja, Weißbrich Benedikt, Snijder Eric J., RA Rabenau Holger, Doerr Hans Wilhelm, Gorbalenya Alexander E., Ziebuhr John; RT "Mechanisms and enzymes involved in SARS coronavirus genome expression"; RL Journal of General Virology(2003). XX RX DOI; 10.1016/j.jpha.2020.03.001. RA Li Xiaowei, Geng Manman, Peng Yizhao, Meng Liesu, Lu Shemin; RT "Molecular immune pathogenesis and diagnosis of COVID-19"; RL Journal of Pharmaceutical Analysis(2020). XX RX DOI; 10.1128/JCM.00187-20. RA Khan Suliman, Siddique Rabeea, Shereen Muhammad Adnan, Ali Ashaq, RA Liu Jianbo, Bai Qian, Bashir Nadia, Xue Mengzhou; RT "The emergence of a novel coronavirus (SARS-CoV-2), their biology and RT therapeutic options"; RL Journal of Clinical Microbiology(2020). XX RX DOI; 10.1080/22221751.2020.1736644. RA Fung Sin-Yee, Yuen Kit-San, Ye Zi-Wei, Chan Chi-Ping, Jin Dong-Yan; RT "A tug-of-war between severe acute respiratory syndrome coronavirus 2 and RT host antiviral defence: lessons from other pathogenic viruses"; RL Emerging Microbes & Infections(2020). XX RX DOI; 10.1007/s12250-020-00207-4. RA Fu Yajing, Cheng Yuanxiong, Wu Yuntao; RT "Understanding SARS-CoV-2-Mediated Inflammatory Responses: From Mechanisms RT to Potential Therapeutic Tools"; RL Virologica Sinica(2020). XX RX DOI; 10.1002/jmv.25681. RA Chen Yu, Liu Qianyun, Guo Deyin; RT "Emerging coronaviruses: Genome structure, replication, and pathogenesis"; RL Journal of Medical Virology(2020). XX RX DOI; 10.1146/annurev-micro-020518-115759. RA Fung To Sing, Liu Ding Xiang; RT "Human Coronavirus: Host-Pathogen Interaction"; RL Annual Review of Microbiology(2019). XX RX DOI; 10.3390/v7041700. RA Ujike Makoto, Taguchi Fumihiro; RT "Incorporation of Spike and Membrane Glycoproteins into Coronavirus RT Virions"; RL Viruses(2015). XX RX DOI; 10.1016/S0065-3527(06)66005-3. RA Masters Paul S.; RT "The Molecular Biology of Coronaviruses"; RL Advances in Virus Research(2006). XX RX DOI; 10.1007/978-1-4899-1531-3_1. RA Siddell Stuart G.; RT "The Coronaviridae: An Introduction"; RL The Coronaviridae(1995). XX RX DOI; 10.1016/j.mib.2014.05.005. RA Kindler Eveline, Thiel Volker; RT "To sense or not to sense viral RNA—essentials of coronavirus innate immune RT evasion"; RL Current Opinion in Microbiology(2014). XX RX DOI; 10.1016/j.coviro.2017.11.002. RA Zheng Jian, Perlman Stanley; RT "Immune responses in influenza A virus and human coronavirus infections: an RT ongoing battle between the virus and host"; RL Current Opinion in Virology(2018). XX RX DOI; 10.1007/s12250-015-3683-3. RA Wong Lok-Yin Roy, Lui Pak-Yin, Jin Dong-Yan; RT "A molecular arms race between host innate antiviral response and emerging RT human coronaviruses"; RL Virologica Sinica(2016). XX RX DOI; 10.1007/s00281-017-0629-x. RA Channappanavar Rudragouda, Perlman Stanley; RT "Pathogenic human coronavirus infections: causes and consequences of RT cytokine storm and immunopathology"; RL Seminars in Immunopathology(2017). XX RX DOI; 10.3389/fimmu.2020.00211. RA Zhao Chunyuan, Zhao Wei; RT "NLRP3 Inflammasome-A Key Player in Antiviral Responses"; RL Frontiers in Immunology(2020). XX RX DOI; 10.1002/jmv.25685. RA Li Geng, Fan Yaohua, Lai Yanni, Han Tiantian, Li Zonghui, Zhou Peiwen, RA Pan Pan, Wang Wenbiao, Hu Dingwen, Liu Xiaohong, Zhang Qiwei, Wu Jianguo; RT "Coronavirus infections and immune responses"; RL Journal of Medical Virology(2020). XX RX DOI; 10.1007/82_2017_25. RA de Wilde Adriaan H., Snijder Eric J., Kikkert Marjolein, RA van Hemert Martijn J.; RT "Host Factors in Coronavirus Replication"; RL Roles of Host Gene and Non-coding RNA Expression in Virus Infection(2018). XX RX DOI; 10.1038/nrmicro2147. RA Perlman Stanley, Netland Jason; RT "Coronaviruses post-SARS: update on replication and pathogenesis"; RL Nature Reviews Microbiology(2009). XX RX DOI; 10.1093/infdis/jiv476. RA Wu Zhiqiang, Yang Li, Ren Xianwen, Zhang Junpeng, Yang Fan, Zhang Shuyi, RA Jin Qi; RT "ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of RT Human Severe Acute Respiratory Syndrome Coronavirus"; RL The Journal of Infectious Diseases(2016). XX RX DOI; 10.1002/jmv.25700. RA Ceraolo Carmine, Giorgi Federico M.; RT "Genomic variance of the 2019-nCoV coronavirus"; RL Journal of Medical Virology(2020). XX RX DOI; 10.1128/JVI.01048-15. RA Lau Susanna K.P., Feng Yun, Chen Honglin, Luk Hayes K.H., Yang Wei-Hong, RA Li Kenneth S.M., Zhang Yu-Zhen, Huang Yi, Song Zhi-Zhong, Chow Wang-Ngai, RA Fan Rachel Y.Y., Ahmed Syed Shakeel, Yeung Hazel C., Lam Carol S.F., RA Cai Jian-Piao, Wong Samson S.Y., Chan Jasper F.W., Yuen Kwok-Yung, RA Zhang Hai-Lin, Woo Patrick C.Y.; RT "Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is RT Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through RT Recombination"; RL Journal of Virology(2015). XX RX DOI; 10.1080/22221751.2020.1719902. RA Chan Jasper Fuk-Woo, Kok Kin-Hang, Zhu Zheng, Chu Hin, To Kelvin Kai-Wang, RA Yuan Shuofeng, Yuen Kwok-Yung; RT "Genomic characterization of the 2019 novel human-pathogenic coronavirus RT isolated from a patient with atypical pneumonia after visiting Wuhan"; RL Emerging Microbes & Infections(2020). XX RX DOI; 10.1038/s41598-018-33487-8. RA Muth Doreen, Corman Victor Max, Roth Hanna, Binger Tabea, Dijkman Ronald, RA Gottula Lina Theresa, Gloza-Rausch Florian, Balboni Andrea, Battilani Mara, RA Rihtarič Danijela, Toplak Ivan, Ameneiros Ramón Seage, Pfeifer Alexander, RA Thiel Volker, Drexler Jan Felix, Müller Marcel Alexander, RA Drosten Christian; RT "Attenuation of replication by a 29 nucleotide deletion in SARS-coronavirus RT acquired during the early stages of human-to-human transmission"; RL Scientific Reports(2018). XX RX DOI; 10.26434/chemrxiv.11938173.v5. RA Wenzhong Liu, Hualan Li; RT "COVID-19: Attacks the 1-Beta Chain of Hemoglobin and Captures the RT Porphyrin to Inhibit Human Heme Metabolism"; XX RX DOI; 10.1056/NEJMsr2005760. RA Vaduganathan Muthiah, Vardeny Orly, Michel Thomas, McMurray John J.V., RA Pfeffer Marc A., Solomon Scott D.; RT "Renin–Angiotensin–Aldosterone System Inhibitors in Patients with RT Covid-19"; RL New England Journal of Medicine(2020). XX RX DOI; 10.1016/j.virol.2017.11.012. RA Shirato Kazuya, Kawase Miyuki, Matsuyama Shutoku; RT "Wild-type human coronaviruses prefer cell-surface TMPRSS2 to endosomal RT cathepsins for cell entry"; RL Virology(2018). XX RX DOI; 10.1038/s41422-020-0305-x. RA Xia Shuai, Liu Meiqin, Wang Chao, Xu Wei, Lan Qiaoshuai, Feng Siliang, RA Qi Feifei, Bao Linlin, Du Lanying, Liu Shuwen, Qin Chuan, Sun Fei, RA Shi Zhengli, Zhu Yun, Jiang Shibo, Lu Lu; RT "Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly RT potent pan-coronavirus fusion inhibitor targeting its spike protein that RT harbors a high capacity to mediate membrane fusion"; RL Cell Research(2020). XX RX DOI; 10.3390/v12040360. RA Srinivasan Suhas, Cui Hongzhu, Gao Ziyang, Liu Ming, Lu Senbao, RA Mkandawire Winnie, Narykov Oleksandr, Sun Mo, Korkin Dmitry; RT "Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved RT Functional Regions of Viral Proteins"; RL Viruses(2020). XX RX DOI; 10.1111/tra.12387. RA Yamauchi Yohei, Greber Urs F.; RT "Principles of Virus Uncoating: Cues and the Snooker Ball"; RL Traffic(2016). XX RX DOI; 10.7150/ijbs.45498. RA Yang Naidi, Shen Han-Ming; RT "Targeting the Endocytic Pathway and Autophagy Process as a Novel RT Therapeutic Strategy in COVID-19"; RL International Journal of Biological Sciences(2020). XX RX DOI; 10.1016/S0140-6736(20)30566-3. RA Zhou Fei, Yu Ting, Du Ronghui, Fan Guohui, Liu Ying, Liu Zhibo, Xiang Jie, RA Wang Yeming, Song Bin, Gu Xiaoying, Guan Lulu, Wei Yuan, Li Hui, Wu Xudong, RA Xu Jiuyang, Tu Shengjin, Zhang Yi, Chen Hua, Cao Bin; RT "Clinical course and risk factors for mortality of adult inpatients with RT COVID-19 in Wuhan, China: a retrospective cohort study"; RL The Lancet(2020). XX RX DOI; 10.1056/NEJMoa2002032. RA Guan Wei-jie, Ni Zheng-yi, Hu Yu, Liang Wen-hua, Ou Chun-quan, RA He Jian-xing, Liu Lei, Shan Hong, Lei Chun-liang, Hui David S.C., Du Bin, RA Li Lan-juan, Zeng Guang, Yuen Kwok-Yung, Chen Ru-chong, Tang Chun-li, RA Wang Tao, Chen Ping-yan, Xiang Jie, Li Shi-yue, Wang Jin-lin, RA Liang Zi-jing, Peng Yi-xiang, Wei Li, Liu Yong, Hu Ya-hua, Peng Peng, RA Wang Jian-ming, Liu Ji-yang, Chen Zhong, Li Gang, Zheng Zhi-jian, RA Qiu Shao-qin, Luo Jie, Ye Chang-jiang, Zhu Shao-yong, Zhong Nan-shan; RT "Clinical Characteristics of Coronavirus Disease 2019 in China"; RL New England Journal of Medicine(2020). XX RX DOI; 10.1128/JVI.01281-09. RA Chen J., Lau Y.F., Lamirande E.W., Paddock C.D., Bartlett J.H., Zaki S.R., RA Subbarao K.; RT "Cellular Immune Responses to Severe Acute Respiratory Syndrome Coronavirus RT (SARS-CoV) Infection in Senescent BALB/c Mice: CD4+ T Cells Are Important RT in Control of SARS-CoV Infection"; RL Journal of Virology(2010). XX RX DOI; 10.1016/j.chom.2016.01.007. RA Channappanavar Rudragouda, Fehr Anthony R., Vijay Rahul, Mack Matthias, RA Zhao Jincun, Meyerholz David K., Perlman Stanley; RT "Dysregulated Type I Interferon and Inflammatory Monocyte-Macrophage RT Responses Cause Lethal Pneumonia in SARS-CoV-Infected Mice"; RL Cell Host & Microbe(2016). XX RX DOI; 10.1101/2020.02.18.20024364. RA Diao Bo, Wang Chenhui, Tan Yingjun, Chen Xiewan, Liu Ying, Ning Lifeng, RA Chen Li, Li Min, Liu Yueping, Wang Gang, Yuan Zilin, Feng Zeqing, RA Wu Yuzhang, Chen Yongwen; RT "Reduction and Functional Exhaustion of T Cells in Patients with RT Coronavirus Disease 2019 (COVID-19)"; XX RX DOI; 10.1172/JCI137244. RA Chen Guang, Wu Di, Guo Wei, Cao Yong, Huang Da, Wang Hongwu, Wang Tao, RA Zhang Xiaoyun, Chen Huilong, Yu Haijing, Zhang Xiaoping, Zhang Minxia, RA Wu Shiji, Song Jianxin, Chen Tao, Han Meifang, Li Shusheng, Luo Xiaoping, RA Zhao Jianping, Ning Qin; RT "Clinical and immunologic features in severe and moderate Coronavirus RT Disease 2019"; RL Journal of Clinical Investigation(2020). XX RX DOI; 10.1038/s41421-020-0153-3. RA Zhou Yadi, Hou Yuan, Shen Jiayu, Huang Yin, Martin William, Cheng Feixiong; RT "Network-based drug repurposing for novel coronavirus RT 2019-nCoV/SARS-CoV-2"; RL Cell Discovery(2020). XX RX DOI; 10.1101/2020.03.21.990770. RA Ju Bin, Zhang Qi, Ge Xiangyang, Wang Ruoke, Yu Jiazhen, Shan Sisi, RA Zhou Bing, Song Shuo, Tang Xian, Yu Jinfang, Ge Jiwan, Lan Jun, Yuan Jing, RA Wang Haiyan, Zhao Juanjuan, Zhang Shuye, Wang Youchun, Shi Xuanling, RA Liu Lei, Wang Xinquan, Zhang Zheng, Zhang Linqi; RT "Potent human neutralizing antibodies elicited by SARS-CoV-2 infection"; XX RX DOI; 10.1016/j.micinf.2005.02.006. RA Qiu Maofeng, Shi Yuling, Guo Zhaobiao, Chen Zeliang, He Rongqiao, RA Chen Runsheng, Zhou Dongsheng, Dai Erhei, Wang Xiaoyi, Si Bingyin, RA Song Yajun, Li Jingxiang, Yang Ling, Wang Jin, Wang Hongxia, Pang Xin, RA Zhai Junhui, Du Zongmin, Liu Ying, Zhang Yong, Li Linhai, Wang Jian, RA Sun Bing, Yang Ruifu; RT "Antibody responses to individual proteins of SARS coronavirus and their RT neutralization activities"; RL Microbes and Infection(2005). XX RX DOI; 10.3390/ijms19020487. RA Xia Shuai, Xu Wei, Wang Qian, Wang Cong, Hua Chen, Li Weihua, Lu Lu, RA Jiang Shibo; RT "Peptide-Based Membrane Fusion Inhibitors Targeting HCoV-229E Spike Protein RT HR1 and HR2 Domains"; RL International Journal of Molecular Sciences(2018). XX RX DOI; 10.1038/nrmicro.2016.81. RA de Wit Emmie, van Doremalen Neeltje, Falzarano Darryl, Munster Vincent J.; RT "SARS and MERS: recent insights into emerging coronaviruses"; RL Nature Reviews Microbiology(2016). XX RA Wu Canrong, Yang Yueying, Liu Yang, Zhang Peng, Wang Yali, Li Hua, RA Wang Qiqi, Xu Yang, Li Mingxue, Zheng Mengzhu, Chen Lixia; RT "Furin, a potential therapeutic target for COVID-19"; XX RX DOI; 10.26434/chemrxiv.11871402.v4. RA Smith Micholas, Smith Jeremy C.; RT "Repurposing Therapeutics for COVID-19: Supercomputer-Based Docking to the RT SARS-CoV-2 Viral Spike Protein and Viral Spike Protein-Human ACE2 RT Interface"; XX RX DOI; 10.1073/pnas.1919250117. RA Nilsson Avlant, Haanstra Jurgen, Engqvist Martin, Gerding Albert, RA Bakker Barbara, Klingmüller Ursula, Teusink Bas, Nielsen Jens; RT "Quantitative analysis of amino acid metabolism in liver cancer links RT glutamate excretion to nucleotide synthesis"; RL Proceedings of the National Academy of Sciences(2020). XX RX DOI; 10.1002/ijc.29649. RX PUBMED; 26095926. RA Wichmann G., Rosolowski M., Krohn K., Kreuz M., Boehm A., Reiche A., RA Scharrer U., Halama D., Bertolini J., Bauer U., Holzinger D., Pawlita M., RA Hess J., Engel C., Hasenclever D., Scholz M., Ahnert P., Kirsten H., RA Hemprich A., Wittekind C., Herbarth O., Horn F., Dietz A., Loeffler M.; RT "The role of HPV RNA transcription, immune response-related gene expression RT and disruptive TP53 mutations in diagnostic and prognostic profiling of RT head and neck cancer."; RL Int J Cancer 137(12):2846-2857(2015). XX RX DOI; 10.1101/2020.04.28.20075788. RA Wang Zichen, Zheutlin Amanda B, Kao Yu-Han, Ayers Kristin L, Gross Susan J, RA Kovatch Patricia, Nirenberg Sharon, Charney Alexander W, Nadkarni Girish N, RA O'Reilly Paul F, Just Allan C, Horowitz Carol R, Martin Glenn, RA Branch Andrea D, Glicksberg Benjamin S, Charney Dennis S, Reich David L, RA Oh William K, Schadt Eric E, Chen Rong, Li Li; RT "Analysis of hospitalized COVID-19 patients in the Mount Sinai Health RT System using electronic medical records (EMR) reveals important prognostic RT factors for improved clinical outcomes"; XX RX DOI; 10.1002/cctc.201901756. RA Lorillière Marion, Guérard‐Hélaine Christine, Gefflaut Thierry, RA Fessner Wolf Dieter, Clapés Pere, Charmantray Franck, Hecquet Laurence; RT "Convergent RT in situ RT Generation of Both Transketolase Substrates RT via RT Transaminase and Aldolase Reactions for Sequential One‐Pot, RT Three‐Step Cascade Synthesis of Ketoses"; RL ChemCatChem(2019). XX RX DOI; 10.1002/humu.21489. RA Thiele Susanne, de Sanctis Luisa, Werner Ralf, Grötzinger Joachim, RA Aydin Cumhur, Jüppner Harald, Bastepe Murat, Hiort Olaf; RT "Functional characterization of GNAS mutations found in patients with RT pseudohypoparathyroidism type Ic defines a new subgroup of RT pseudohypoparathyroidism affecting selectively Gsα-receptor interaction"; RL Human Mutation(2011). XX RX DOI; 10.1021/acs.jced.9b00555. RA Xu Xinmeng, Range Jan, Gygli Gudrun, Pleiss Juergen; RT "Analysis of Thermophysical Properties of Deep Eutectic Solvents by Data RT Integration"; RL Journal of Chemical & Engineering Data(2020). XX RX DOI; 10.1021/acs.jmedchem.8b02021. RX PUBMED; 30908048. RA Linciano P., Pozzi C., Iacono L.D., di Pisa F., Landi G., Bonucci A., RA Gul S., Kuzikov M., Ellinger B., Witt G., Santarem N., Baptista C., RA Franco C., Moraes C.B., Muller W., Wittig U., Luciani R., Sesenna A., RA Quotadamo A., Ferrari S., Pohner I., Cordeiro-da-Silva A., Mangani S., RA Costantino L., Costi M.P.; RT "Enhancement of Benzothiazoles as Pteridine Reductase-1 Inhibitors for the RT Treatment of Trypanosomatidic Infections."; RL J Med Chem 62(8):3989-4012(2019). XX RX DOI; 10.1016/j.ejmech.2020.112047. RX PUBMED; 31982652. RA Linciano P., Cullia G., Borsari C., Santucci M., Ferrari S., Witt G., RA Gul S., Kuzikov M., Ellinger B., Santarem N., Cordeiro da Silva A., RA Conti P., Bolognesi M.L., Roberti M., Prati F., Bartoccini F., Retini M., RA Piersanti G., Cavalli A., Goldoni L., Bertozzi S.M., Bertozzi F., RA Brambilla E., Rizzo V., Piomelli D., Pinto A., Bandiera T., Costi M.P.; RT "Identification of a 2,4-diaminopyrimidine scaffold targeting Trypanosoma RT brucei pteridine reductase 1 from the LIBRA compound library screening RT campaign."; RL Eur J Med Chem 189:112047(2020). XX RX DOI; 10.1021/acsmedchemlett.8b00565. RX PUBMED; 30996791. RA Borsari C., Santarem N., Macedo S., Jimenez-Anton M.D., Torrado J.J., RA Olias-Molero A.I., Corral M.J., Tait A., Ferrari S., Costantino L., RA Luciani R., Ponterini G., Gul S., Kuzikov M., Ellinger B., Behrens B., RA Reinshagen J., Alunda J.M., Cordeiro-da-Silva A., Costi M.P.; RT "SAR Studies and Biological Characterization of a Chromen-4-one Derivative RT as an Anti-Trypanosoma brucei Agent."; RL ACS Med Chem Lett 10(4):528-533(2019). XX RX DOI; 10.1201/9781351011655. RA Jayaprakash Venkatesan, Castagnolo Daniele, Özkay Yusuf; RT "Medicinal Chemistry of Neglected and Tropical Diseases"; XX RX DOI; 10.1021/acsinfecdis.8b00358. RX PUBMED; 31012301. RA Landi G., Linciano P., Borsari C., Bertolacini C.P., Moraes C.B., RA Cordeiro-da-Silva A., Gul S., Witt G., Kuzikov M., Costi M.P., Pozzi C., RA Mangani S.; RT "Structural Insights into the Development of Cycloguanil Derivatives as RT Trypanosoma brucei Pteridine-Reductase-1 Inhibitors."; RL ACS Infect Dis 5(7):1105-1114(2019). XX RX DOI; 10.1177/2472555218823171. RX PUBMED; 30784368. RA Moraes C.B., Witt G., Kuzikov M., Ellinger B., Calogeropoulou T., RA Prousis K.C., Mangani S., Di Pisa F., Landi G., Iacono L.D., Pozzi C., RA Freitas-Junior L.H., Dos Santos Pascoalino B., Bertolacini C.P., RA Behrens B., Keminer O., Leu J., Wolf M., Reinshagen J., RA Cordeiro-da-Silva A., Santarem N., Venturelli A., Wrigley S., RA Karunakaran D., Kebede B., Pohner I., Muller W., Panecka-Hofman J., RA Wade R.C., Fenske M., Clos J., Alunda J.M., Corral M.J., Uliassi E., RA Bolognesi M.L., Linciano P., Quotadamo A., Ferrari S., Santucci M., RA Borsari C., Costi M.P., Gul S.; RT "Accelerating Drug Discovery Efforts for Trypanosomatidic Infections Using RT an Integrated Transnational Academic Drug Discovery Platform."; RL SLAS Discov 24(3):346-361(2019). XX RX DOI; 10.1039/c9pp00026g. RX PUBMED; 30900698. RA Vanossi D., Caselli M., Pavesi G., Borsari C., Linciano P., Costi M.P., RA Ponterini G.; RT "Excited-state intramolecular proton transfer in a bioactive flavonoid RT provides fluorescence observables for recognizing its engagement with RT target proteins."; RL Photochem Photobiol Sci 18(9):2270-2280(2019). XX RX DOI; 10.1016/bs.armc.2018.08.002. RA Borsari Chiara, Quotadamo Antonio, Ferrari Stefania, Venturelli Alberto, RA Cordeiro-da-Silva Anabela, Santarem Nuno, Costi Maria Paola; RT "Scaffolds and Biological Targets Avenue to Fight Against Drug Resistance RT in Leishmaniasis"; RL Neglected Diseases: Extensive Space for Modern Drug Discovery(2018). XX RX DOI; 10.1016/j.ejps.2018.06.002. RX PUBMED; 29883726. RA Jimenez-Anton M.D., Garcia-Calvo E., Gutierrez C., Escribano M.D., RA Kayali N., Luque-Garcia J.L., Olias-Molero A.I., Corral M.J., Costi M.P., RA Torrado J.J., Alunda J.M.; RT "Pharmacokinetics and disposition of miltefosine in healthy mice and RT hamsters experimentally infected with Leishmania infantum."; RL Eur J Pharm Sci 121:281-286(2018). XX RX DOI; 10.1016/j.ejmech.2018.01.043. RX PUBMED; 29407968. RA Linciano P., Moraes C.B., Alcantara L.M., Franco C.H., Pascoalino B., RA Freitas-Junior L.H., Macedo S., Santarem N., Cordeiro-da-Silva A., Gul S., RA Witt G., Kuzikov M., Ellinger B., Ferrari S., Luciani R., Quotadamo A., RA Costantino L., Costi M.P.; RT "Aryl thiosemicarbazones for the treatment of trypanosomatidic RT infections."; RL Eur J Med Chem 146:423-434(2018). XX RX DOI; 10.1002/cmdc.201700786. RX PUBMED; 29451361. RA Uliassi E., Piazzi L., Belluti F., Mazzanti A., Kaiser M., Brun R., RA Moraes C.B., Freitas-Junior L.H., Gul S., Kuzikov M., Ellinger B., RA Borsari C., Costi M.P., Bolognesi M.L.; RT "Development of a Focused Library of Triazole-Linked RT Privileged-Structure-Based Conjugates Leading to the Discovery of Novel RT Phenotypic Hits against Protozoan Parasitic Infections."; RL ChemMedChem 13(7):678-683(2018). XX RX DOI; 10.1016/j.ejmech.2016.12.017. RX PUBMED; 28064141. RA Borsari C., Santarem N., Torrado J., Olias A.I., Corral M.J., Baptista C., RA Gul S., Wolf M., Kuzikov M., Ellinger B., Witt G., Gribbon P., RA Reinshagen J., Linciano P., Tait A., Costantino L., Freitas-Junior L.H., RA Moraes C.B., Bruno Dos Santos P., Alcantara L.M., Franco C.H., RA Bertolacini C.D., Fontana V., Tejera Nevado P., Clos J., Alunda J.M., RA Cordeiro-da-Silva A., Ferrari S., Costi M.P.; RT "Methoxylated 2'-hydroxychalcones as antiparasitic hit compounds."; RL Eur J Med Chem 126:1129-1135(2017). XX RX DOI; 10.1111/cbdd.12941. RX PUBMED; 28079302. RA Bruno S., Uliassi E., Zaffagnini M., Prati F., Bergamini C., Amorati R., RA Paredi G., Margiotta M., Conti P., Costi M.P., Kaiser M., Cavalli A., RA Fato R., Bolognesi M.L.; RT "Molecular basis for covalent inhibition of glyceraldehyde-3-phosphate RT dehydrogenase by a 2-phenoxy-1,4-naphthoquinone small molecule."; RL Chem Biol Drug Des 90(2):225-235(2017). XX RX DOI; 10.3390/molecules22030426. RX PUBMED; 28282886. RA Di Pisa F., Landi G., Dello Iacono L., Pozzi C., Borsari C., Ferrari S., RA Santucci M., Santarem N., Cordeiro-da-Silva A., Moraes C.B., RA Alcantara L.M., Fontana V., Freitas-Junior L.H., Gul S., Kuzikov M., RA Behrens B., Pohner I., Wade R.C., Costi M.P., Mangani S.; RT "Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing RT Anti-Parasitic Activity."; RL Molecules 22(3)(2017). XX RX DOI; 10.3390/molecules22122166. RX PUBMED; 29211037. RA Herrmann F.C., Sivakumar N., Jose J., Costi M.P., Pozzi C., Schmidt T.J.; RT "In Silico Identification and In Vitro Evaluation of Natural Inhibitors of RT Leishmania major Pteridine Reductase I."; RL Molecules 22(12)(2017). XX RX DOI; 10.1021/acsomega.7b00473. RX PUBMED; 28983525. RA Linciano P., Dawson A., Pohner I., Costa D.M., Sa M.S., RA Cordeiro-da-Silva A., Luciani R., Gul S., Witt G., Ellinger B., Kuzikov M., RA Gribbon P., Reinshagen J., Wolf M., Behrens B., Hannaert V., RA Michels P.A.M., Nerini E., Pozzi C., di Pisa F., Landi G., Santarem N., RA Ferrari S., Saxena P., Lazzari S., Cannazza G., Freitas-Junior L.H., RA Moraes C.B., Pascoalino B.S., Alcantara L.M., Bertolacini C.P., Fontana V., RA Wittig U., Muller W., Wade R.C., Hunter W.N., Mangani S., Costantino L., RA Costi M.P.; RT "Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma RT brucei Pteridine Reductase in Support of Early-Stage Drug Discovery."; RL ACS Omega 2(9):5666-5683(2017). XX RX DOI; 10.1016/j.bbagen.2017.09.012. RX PUBMED; 28939533. RA Panecka-Hofman J., Pohner I., Spyrakis F., Zeppelin T., Di Pisa F., RA Dello Iacono L., Bonucci A., Quotadamo A., Venturelli A., Mangani S., RA Costi M.P., Wade R.C.; RT "Comparative mapping of on-targets and off-targets for the discovery of RT anti-trypanosomatid folate pathway inhibitors."; RL Biochim Biophys Acta Gen Subj 1861(12):3215-3230(2017). XX RX DOI; 10.1016/j.pt.2017.04.007. RX PUBMED; 28529130. RA Pierce R.J., MacDougall J., Leurs R., Costi M.P.; RT "The Future of Drug Development for Neglected Tropical Diseases: How the RT European Commission Can Continue to Make a Difference."; RL Trends Parasitol 33(8):581-583(2017). XX RX DOI; 10.1016/j.ejmech.2017.10.005. RX PUBMED; 29031061. RA Uliassi E., Fiorani G., Krauth-Siegel R.L., Bergamini C., Fato R., RA Bianchini G., Carlos Menendez J., Molina M.T., Lopez-Montero E., Falchi F., RA Cavalli A., Gul S., Kuzikov M., Ellinger B., Witt G., Moraes C.B., RA Freitas-Junior L.H., Borsari C., Costi M.P., Bolognesi M.L.; RT "Crassiflorone derivatives that inhibit Trypanosoma brucei RT glyceraldehyde-3-phosphate dehydrogenase (TbGAPDH) and Trypanosoma cruzi RT trypanothione reductase (TcTR) and display trypanocidal activity."; RL Eur J Med Chem 141:138-148(2017). XX RX DOI; 10.1021/acs.jmedchem.6b00698. RX PUBMED; 27411733. RA Borsari C., Luciani R., Pozzi C., Poehner I., Henrich S., Trande M., RA Cordeiro-da-Silva A., Santarem N., Baptista C., Tait A., Di Pisa F., RA Dello Iacono L., Landi G., Gul S., Wolf M., Kuzikov M., Ellinger B., RA Reinshagen J., Witt G., Gribbon P., Kohler M., Keminer O., Behrens B., RA Costantino L., Tejera Nevado P., Bifeld E., Eick J., Clos J., Torrado J., RA Jimenez-Anton M.D., Corral M.J., Alunda J.M., Pellati F., Wade R.C., RA Ferrari S., Mangani S., Costi M.P.; RT "Profiling of Flavonol Derivatives for the Development of RT Antitrypanosomatidic Drugs."; RL J Med Chem 59(16):7598-7616(2016). XX RX DOI; 10.2174/0929867322666151015120804. RX PUBMED; 26477622. RA Gaspar L., Moraes C.B., Freitas-Junior L.H., Ferrari S., Costantino L., RA Costi M.P., Coron R.P., Smith T.K., Siqueira-Neto J.L., McKerrow J.H., RA Cordeiro-da-Silva A.; RT "Current and Future Chemotherapy for Chagas Disease."; RL Curr Med Chem 22(37):4293-4312(2015). XX RX DOI; 10.1101/2020.07.27.20162636. RA Sass Julian, Bartschke Alexander, Lehne Moritz, Essenwanger Andrea, RA Rinaldi Eugenia, Rudolph Stefanie, Heitmann Kai Uwe, RA Vehreschild Joerg Janne, von Kalle Christof, Thun Sylvia; RT "The German Corona Consensus Dataset (GECCO): A standardized dataset for RT COVID-19 research"; XX RX DOI; 10.1515/jib-2020-0005. RA Waltemath Dagmar, Golebiewski Martin, Blinov Michael, Gleeson Padraig, RA Hermjakob Henning, Hucka Mike, Inau Esther Thea, Keating Sarah M, RA König Matthias, Krebs Olga, Malik-Sheriff Rahuman S, Nickerson David, RA Oberortner Ernst, Sauro Herbert M, Schreiber Falk, Smith Maggie, RA Stefan Melanie, Wittig Ulrike, Myers Chris J; RT "The first 10 years of the international coordination network for standards RT in systems and synthetic biology (COMBINE)"; RL Journal of Integrative Bioinformatics(2020). XX RX DOI; 10.1515/jib-2020-0022. RA Schreiber Falk, Sommer Björn, Czauderna Tobias, Golebiewski Martin, RA Gorochowski Thomas E., Hucka Mike, Keating Sarah M., König Matthias, RA Myers Chris, Nickerson David, Waltemath Dagmar; RT "Specifications of standards in systems and synthetic biology: status and RT developments in 2020"; RL Journal of Integrative Bioinformatics(2020). XX RX DOI; 10.1007/978-1-4939-9736-7_17. RX PUBMED; 31602618. RA Stanford N.J., Scharm M., Dobson P.D., Golebiewski M., Hucka M., RA Kothamachu V.B., Nickerson D., Owen S., Pahle J., Wittig U., Waltemath D., RA Goble C., Mendes P., Snoep J.; RT "Data Management in Computational Systems Biology: Exploring Standards, RT Tools, Databases, and Packaging Best Practices."; RL Methods Mol Biol 2049:285-314(2019). XX RX DOI; 10.1515/jib-2019-0035. RA Schreiber Falk, Sommer Björn, Bader Gary D., Gleeson Padraig, RA Golebiewski Martin, Hucka Mike, Keating Sarah M., König Matthias, RA Myers Chris, Nickerson David, Waltemath Dagmar; RT "Specifications of Standards in Systems and Synthetic Biology: Status and RT Developments in 2019"; RL Journal of Integrative Bioinformatics(2019). XX RX DOI; 10.1016/B978-0-12-809633-8.20471-8. RA Golebiewski Martin; RT "Data Formats for Systems Biology and Quantitative Modeling"; RL Encyclopedia of Bioinformatics and Computational Biology(2019). XX RX DOI; 10.1109/WSC.2017.8247840. RA Myers Chris J., Bader Gary, Gleeson Padraig, Golebiewski Martin, RA Hucka Mike, Le Novere Nicolas, Nickerson David, Schreiber Falk, RA Waltemath Dagmar; RT "A brief history of COMBINE"; RL 2017 Winter Simulation Conference (WSC)(2017). XX RX DOI; 10.1093/insilicoplants/diz006. RA Kinmonth-Schultz Hannah, MacEwen Melissa J S, Seaton Daniel, Millar Andrew, RA Imaizumi Takato, Kim Soo-Hyung; RT "An explanatory model of temperature influence on flowering through RT whole-plant accumulation of FLOWERING LOCUS T in Arabidopsis thaliana"; RL in silico Plants(2019). XX RX DOI; 10.1038/s41540-020-0138-8. RA Westerhoff Hans V., Kolodkin Alexey; RT "Advice from a systems-biology model of the corona epidemics"; RL npj Systems Biology and Applications(2020). XX RX DOI; 10.1007/s10822-017-0035-4. RX PUBMED; 28688090. RA Jedwabny W., Panecka-Hofman J., Dyguda-Kazimierowicz E., Wade R.C., RA Sokalski W.A.; RT "Application of a simple quantum chemical approach to ligand fragment RT scoring for Trypanosoma brucei pteridine reductase 1 inhibition."; RL J Comput Aided Mol Des 31(8):715-728(2017). XX RX DOI; 10.1093/nar/gkx277. RX PUBMED; 28431137. RA Stank A., Kokh D.B., Horn M., Sizikova E., Neil R., Panecka J., Richter S., RA Wade R.C.; RT "TRAPP webserver: predicting protein binding site flexibility and detecting RT transient binding pockets."; RL Nucleic Acids Res 45(W1):W325-W330(2017). XX RX DOI; 10.1007/s00253-014-5634-6. RA González-Peñas H., Lu-Chau Thelmo, Moreira Maria Teresa, Lema J.M.; RT "Solvent screening methodology for in situ ABE extractive fermentation"; RL Applied Microbiology and Biotechnology(2014). XX RX DOI; 10.1016/j.tips.2012.05.004. RX PUBMED; 22709554. RA Vilardaga J.P., Gardella T.J., Wehbi V.L., Feinstein T.N.; RT "Non-canonical signaling of the PTH receptor."; RL Trends Pharmacol Sci 33(8):423-431(2012). XX RX DOI; 10.1016/j.sbi.2020.05.003. RX PUBMED; 32615371. RA Sheludko Y.V., Fessner W.D.; RT "Winning the numbers game in enzyme evolution - fast screening methods for RT improved biotechnology proteins."; RL Curr Opin Struct Biol 63:123-133(2020). XX RX DOI; 10.1021/jacs.0c09994. RA Marín-Valls Roser, Hernandez Karel, Bolte Michael, Parella Teodor, RA Joglar Jesús, Bujons Jordi, Clapés Pere; RT "Biocatalytic Construction of Quaternary Centers by Aldol Addition of 3, RT 3-Disubstituted 2-Oxoacid Derivatives to Aldehydes"; RL Journal of the American Chemical Society(2020). XX RX DOI; 10.1016/j.celrep.2019.11.104. RX PUBMED; 31875560. RA Kolbe E., Aleithe S., Rennert C., Spormann L., Ott F., Meierhofer D., RA Gajowski R., Stopel C., Hoehme S., Kucken M., Brusch L., Seifert M., RA von Schoenfels W., Schafmayer C., Brosch M., Hofmann U., Damm G., RA Seehofer D., Hampe J., Gebhardt R., Matz-Soja M.; RT "Mutual Zonated Interactions of Wnt and Hh Signaling Are Orchestrating the RT Metabolism of the Adult Liver in Mice and Human."; RL Cell Rep 29(13):4553-4567.e7(2019). XX RX DOI; 10.15252/msb.20198985. RX PUBMED; 32090478. RA Meyer K., Morales-Navarrete H., Seifert S., Wilsch-Braeuninger M., RA Dahmen U., Tanaka E.M., Brusch L., Kalaidzidis Y., Zerial M.; RT "Bile canaliculi remodeling activates YAP via the actin cytoskeleton during RT liver regeneration."; RL Mol Syst Biol 16(2):e8985(2020). XX RX DOI; 10.1038/s41540-020-00150-w. RX PUBMED; 33106503. RA N Kolodkin A., Sharma R.P., Colangelo A.M., Ignatenko A., Martorana F., RA Jennen D., Briede J.J., Brady N., Barberis M., Mondeel T.D.G.A., Papa M., RA Kumar V., Peters B., Skupin A., Alberghina L., Balling R., Westerhoff H.V.; RT "ROS networks: designs, aging, Parkinson's disease and precision RT therapies."; RL NPJ Syst Biol Appl 6(1):34(2020). XX RX DOI; 10.1016/bs.mie.2020.12.025. RA Welsing Gina, Wolter Birger, Hintzen Henric M.T., Tiso Till, Blank Lars; RT "Upcycling of hydrolyzed PET by microbial conversion to a fatty acid RT derivative"; RL Methods in Enzymology(2021). XX RX DOI; 10.1073/pnas.1902346116. RX PUBMED; 31341085. RA Bockwoldt M., Houry D., Niere M., Gossmann T.I., Reinartz I., Schug A., RA Ziegler M., Heiland I.; RT "Identification of evolutionary and kinetic drivers of NAD-dependent RT signaling."; RL Proc Natl Acad Sci U S A 116(32):15957-15966(2019). XX RX DOI; 10.1016/j.cell.2020.07.038. RA Sadik Ahmed, Somarribas Patterson Luis F., Öztürk Selcen, RA Mohapatra Soumya R., Panitz Verena, Secker Philipp F., Pfänder Pauline, RA Loth Stefanie, Salem Heba, Prentzell Mirja Tamara, Berdel Bianca, RA Iskar Murat, Faessler Erik, Reuter Friederike, Kirst Isabelle, RA Kalter Verena, Foerster Kathrin I., Jäger Evelyn, Guevara Carina Ramallo, RA Sobeh Mansour, Hielscher Thomas, Poschet Gernot, Reinhardt Annekathrin, RA Hassel Jessica C., Zapatka Marc, Hahn Udo, von Deimling Andreas, RA Hopf Carsten, Schlichting Rita, Escher Beate I., Burhenne Jürgen, RA Haefeli Walter E., Ishaque Naveed, Böhme Alexander, Schäuble Sascha, RA Thedieck Kathrin, Trump Saskia, Seiffert Martina, Opitz Christiane; RT "IL4I1 Is a Metabolic Immune Checkpoint that Activates the AHR and Promotes RT Tumor Progression"; RL Cell(2020). XX RX DOI; 10.1021/acs.analchem.0c00187. RA Metzler Lukas, Rehbein Ulrike, Schönberg Jan-Niklas, Brandstetter Thomas, RA Thedieck Kathrin, Rühe Jürgen; RT "Breaking the Interface: Efficient Extraction of Magnetic Beads from RT Nanoliter Droplets for Automated Sequential Immunoassays"; RL Analytical Chemistry(2020). XX RX DOI; 10.1038/s41416-019-0664-6. RX PUBMED; 31819194. RA Opitz C.A., Somarribas Patterson L.F., Mohapatra S.R., Dewi D.L., Sadik A., RA Platten M., Trump S.; RT "The therapeutic potential of targeting tryptophan catabolism in cancer."; RL Br J Cancer 122(1):30-44(2020). XX RX DOI; 10.1093/hmg/ddp079. RX PUBMED; 19224950. RA Maier E.M., Gersting S.W., Kemter K.F., Jank J.M., Reindl M., Messing D.D., RA Truger M.S., Sommerhoff C.P., Muntau A.C.; RT "Protein misfolding is the molecular mechanism underlying MCADD identified RT in newborn screening."; RL Hum Mol Genet 18(9):1612-1623(2009). XX RX DOI; 10.3390/microorganisms8050658. RA Zhu Xiaolin, Navarro Yurena, Mas Albert, Torija-Martínez María-Jesús, RA Beltran Casellas Gemma; RT "A Rapid Method for Selecting Non-Saccharomyces Strains with a Low Ethanol RT Yield"; RL Microorganisms(2020). XX RX DOI; 10.3390/foods9101373. RA Navarro Yurena, Torija-Martínez María-Jesús, Mas Albert, RA Beltran Casellas Gemma; RT "Viability-PCR Allows Monitoring Yeast Population Dynamics in Mixed RT Fermentations Including Viable but Non-Culturable Yeasts"; RL Foods(2020). XX RX DOI; 10.3390/microorganisms8020157. RA Roca-Mesa Helena, Sendra Sonia, Mas Albert, Beltran Casellas Gemma, RA Torija-Martínez María-Jesús; RT "Nitrogen Preferences during Alcoholic Fermentation of Different RT Non-Saccharomyces Yeasts of Oenological Interest"; RL Microorganisms(2020). XX RX DOI; 10.1093/bioinformatics/btz020. RA Hass Helge, Loos Carolin, Raimúndez-Álvarez Elba, Timmer Jens, RA Hasenauer Jan, Kreutz Clemens; RT "Benchmark problems for dynamic modeling of intracellular processes"; RL Bioinformatics(2019). XX RX DOI; 10.1101/2021.03.18.436071. RA Urquiza Garcia Uriel, Millar Andrew; RT "Testing the inferred transcription rates of a dynamic, gene network model RT in absolute units"; XX RX DOI; 10.1016/j.celrep.2021.108864. RA Kay Jennifer E., Corrigan Joshua J., Armijo Amanda L., Nazari Ilana S., RA Kohale Ishwar N., Torous Dorothea K., Avlasevich Svetlana L., RA Croy Robert G., Wadduwage Dushan N., Carrasco Sebastian E., RA Dertinger Stephen D., White Forest M., Essigmann John M., Samson Leona D., RA Engelward Bevin P.; RT "Excision of mutagenic replication-blocking lesions suppresses cancer but RT promotes cytotoxicity and lethality in nitrosamine-exposed mice"; RL Cell Reports(2021). XX RX DOI; 10.3390/microorganisms8060866. RA Walter Tatjana, Al Medani Nour, Burgardt Arthur, cankar Katarina, RA Ferrer Lenny, Kerbs Anastasia, Lee Jin-Ho, Mindt Melanie, Risse Joe Max, RA Wendisch Volker; RT "Fermentative N-Methylanthranilate Production by Engineered Corynebacterium RT glutamicum"; RL Microorganisms(2020). XX RX DOI; 10.3390/microorganisms8121945. RA Walter Tatjana, Veldmann Kareen H., Götker Susanne, Busche Tobias, RA Rückert Christian, Kashkooli Arman Beyraghdar, Paulus Jannik, RA cankar Katarina, Wendisch Volker; RT "Physiological Response of Corynebacterium glutamicum to Indole"; RL Microorganisms(2020). XX RX DOI; 10.1038/s41598-021-89948-0. RA Eide Marta, Zhang Xiaokang, Karlsen Odd André, Goldstone Jared V., RA Stegeman John, Jonassen Inge, Goksøyr Anders; RT "The chemical defensome of five model teleost fish"; RL Scientific Reports(2021). XX RX DOI; 10.3389/fmolb.2020.591406. RA Hanna Eileen Marie, Zhang Xiaokang, Eide Marta, Fallahi Shirin, RA Furmanek Tomasz, Yadetie Fekadu, Zielinski Tomasz, Goksøyr Anders, RA Jonassen Inge; RT "ReCodLiver0.9: Overcoming Challenges in Genome-Scale Metabolic RT Reconstruction of a Non-model Species"; RL Frontiers in Molecular Biosciences(2020). XX RX PUBMED; 10. RA Schmoldt A., Benthe H.F., Haberland G.; RT "Digitoxin metabolism by rat liver microsomes."; RL Biochem Pharmacol 24(17):1639-1641(1975). XX RX DOI; 10.3389/fgene.2019.00794. RA Olsvik Pål A., Larsen Anett Kristin, Berntssen Marc H.G., Goksøyr Anders, RA Karlsen Odd André, Yadetie Fekadu, Sanden Monica, Kristensen Torstein; RT "Effects of Agricultural Pesticides in Aquafeeds on Wild Fish Feeding on RT Leftover Pellets Near Fish Farms"; RL Frontiers in Genetics(2019). XX RX DOI; 10.1101/2021.04.15.439997. RA Doello Sofia, Neumann Niels, Spät Philipp, Maček Boris, Forchhammer Karl; RT "Regulatory phosphorylation site tunes Phosphoglucomutase 1 as a metabolic RT valve to control mobilization of glycogen stores"; XX RX DOI; 10.1371/journal.pcbi.1003705. RA Fogelmark Karl, Troein Carl; RT "Rethinking Transcriptional Activation in the Arabidopsis Circadian Clock"; RL PLoS Computational Biology(2014). XX RX DOI; 10.1093/insilicoplants/diab022. RA Urquiza Garcia Uriel, Millar Andrew; RT "Testing the inferred transcription rates of a dynamic, gene network model RT in absolute units (in silico Plants 2021)"; RL in silico Plants(2021). XX RX DOI; 10.1093/bib/bbx163. RX PUBMED; 29237040. RA Montagud A., Traynard P., Martignetti L., Bonnet E., Barillot E., RA Zinovyev A., Calzone L.; RT "Conceptual and computational framework for logical modelling of biological RT networks deregulated in diseases."; RL Brief Bioinform 20(4):1238-1249(2019). XX RX DOI; 10.1093/bioinformatics/bty766. RA Letort Gaelle, Montagud Arnau, Stoll Gautier, Heiland Randy, RA Barillot Emmanuel, Macklin Paul, Zinovyev Andrei, Calzone Laurence; RT "PhysiBoSS: a multi-scale agent-based modelling framework integrating RT physical dimension and cell signalling"; RL Bioinformatics(2019). XX RX DOI; 10.1186/1752-0509-6-116. RX PUBMED; 22932419. RA Stoll G., Viara E., Barillot E., Calzone L.; RT "Continuous time Boolean modeling for biological signaling: application of RT Gillespie algorithm."; RL BMC Syst Biol 6:116(2012). XX RX DOI; 10.1093/bioinformatics/btx123. RX PUBMED; 28881959. RA Stoll G., Caron B., Viara E., Dugourd A., Zinovyev A., Naldi A., RA Kroemer G., Barillot E., Calzone L.; RT "MaBoSS 2.0: an environment for stochastic Boolean modeling."; RL Bioinformatics 33(14):2226-2228(2017). XX RX DOI; 10.1101/2020.04.02.019075. RA Getz Michael, Wang Yafei, An Gary, Asthana Maansi, Becker Andrew, RA Cockrell Chase, Collier Nicholson, Craig Morgan, Davis Courtney L., RA Faeder James R., Ford Versypt Ashlee N., Mapder Tarunendu, RA Gianlupi Juliano F., Glazier James A., Hamis Sara, Heiland Randy, RA Hillen Thomas, Hou Dennis, Islam Mohammad Aminul, Jenner Adrianne L., RA Kurtoglu Furkan, Larkin Caroline I., Liu Bing, Macfarlane Fiona, RA Maygrundter Pablo, Morel Penelope A, Narayanan Aarthi, Ozik Jonathan, RA Pienaar Elsje, Rangamani Padmini, Saglam Ali Sinan, Shoemaker Jason Edward, RA Smith Amber M., Weaver Jordan J.A., Macklin Paul; RT "Iterative community-driven development of a SARS-CoV-2 tissue simulator"; XX RX DOI; 10.1093/bioinformatics/btaa484. RA Aghamiri Sara Sadat, Singh Vidisha, Naldi Aurélien, Helikar Tomáš, RA Soliman Sylvain, Niarakis Anna; RT "Automated inference of Boolean models from molecular interaction maps RT using CaSQ"; RL Bioinformatics(2020). XX RX DOI; 10.1007/s00018-021-03916-5. RX PUBMED; 34427691. RA Galow A.M., Kussauer S., Wolfien M., Brunner R.M., Goldammer T., David R., RA Hoeflich A.; RT "Quality control in scRNA-Seq can discriminate pacemaker cells: the mtRNA RT bias."; RL Cell Mol Life Sci 78(19-20):6585-6592(2021). XX RX DOI; 10.1016/j.coviro.2021.09.005. RA Plavec Zlatka, Poehner Ina, Poso Antti, Butcher Sarah J; RT "Virus structure and structure-based antivirals"; RL Current Opinion in Virology(2021). XX RX DOI; 10.1021/acscatal.1c02076. RA Ott Felix, Rabe Kersten S., Niemeyer Christof M., Gygli Gudrun; RT "Toward Reproducible Enzyme Modeling with Isothermal Titration RT Calorimetry"; RL ACS Catalysis(2021). XX RX DOI; 10.1021/acs.jcim.0c00018. RA Gygli Gudrun, Pleiss Juergen; RT "Simulation Foundry: Automated and F.A.I.R. Molecular Modeling"; RL Journal of Chemical Information and Modeling(2020). XX RX DOI; 10.15252/msb.202110387. RX PUBMED; 34664389. RA Ostaszewski M., Niarakis A., Mazein A., Kuperstein I., Phair R., RA Orta-Resendiz A., Singh V., Aghamiri S.S., Acencio M.L., Glaab E., RA Ruepp A., Fobo G., Montrone C., Brauner B., Frishman G., Monraz Gomez L.C., RA Somers J., Hoch M., Kumar Gupta S., Scheel J., Borlinghaus H., RA Czauderna T., Schreiber F., Montagud A., Ponce de Leon M., Funahashi A., RA Hiki Y., Hiroi N., Yamada T.G., Drager A., Renz A., Naveez M., Bocskei Z., RA Messina F., Bornigen D., Fergusson L., Conti M., Rameil M., Nakonecnij V., RA Vanhoefer J., Schmiester L., Wang M., Ackerman E.E., Shoemaker J.E., RA Zucker J., Oxford K., Teuton J., Kocakaya E., Summak G.Y., Hanspers K., RA Kutmon M., Coort S., Eijssen L., Ehrhart F., Rex D.A.B., Slenter D., RA Martens M., Pham N., Haw R., Jassal B., Matthews L., Orlic-Milacic M., RA Senff Ribeiro A., Rothfels K., Shamovsky V., Stephan R., Sevilla C., RA Varusai T., Ravel J.M., Fraser R., Ortseifen V., Marchesi S., Gawron P., RA Smula E., Heirendt L., Satagopam V., Wu G., Riutta A., Golebiewski M., RA Owen S., Goble C., Hu X., Overall R.W., Maier D., Bauch A., Gyori B.M., RA Bachman J.A., Vega C., Groues V., Vazquez M., Porras P., Licata L., RA Iannuccelli M., Sacco F., Nesterova A., Yuryev A., de Waard A., Turei D., RA Luna A., Babur O., Soliman S., Valdeolivas A., Esteban-Medina M., RA Pena-Chilet M., Rian K., Helikar T., Puniya B.L., Modos D., Treveil A., RA Olbei M., De Meulder B., Ballereau S., Dugourd A., Naldi A., Noel V., RA Calzone L., Sander C., Demir E., Korcsmaros T., Freeman T.C., Auge F., RA Beckmann J.S., Hasenauer J., Wolkenhauer O., Wilighagen E.L., Pico A.R., RA Evelo C.T., Gillespie M.E., Stein L.D., Hermjakob H., D'Eustachio P., RA Saez-Rodriguez J., Dopazo J., Valencia A., Kitano H., Barillot E., RA Auffray C., Balling R., Schneider R.; RT "COVID19 Disease Map, a computational knowledge repository of virus-host RT interaction mechanisms."; RL Mol Syst Biol 17(10):e10387(2021). XX RX DOI; 10.15252/msb.202110387. RA Ostaszewski Marek, Niarakis Anna, Mazein Alexander, Kuperstein Inna, RA Phair Robert, Orta‐Resendiz Aurelio, Singh Vidisha, AGHAMIRI Sara Sadat, RA Acencio Marcio, Glaab Enrico, Ruepp Andreas, Fobo Gisela, Montrone Corinna, RA Brauner Barbara, Frishman Goar, Monraz Gómez Luis Cristóbal, RA Somers Julia, Hoch Matti, Kumar Gupta Shailendra, Scheel Julia, RA Borlinghaus Hanna, Czauderna Tobias, Schreiber Falk, Montagud Arnau, RA Ponce de Leon Miguel, Funahashi Akira, Hiki Yusuke, Hiroi Noriko, RA Yamada Takahiro G, Dräger Andreas, Renz Alina, Naveez Muhammad, RA Bocskei Zsolt, Messina Francesco, Börnigen Daniela, Fergusson Liam, RA Conti Marta, Rameil Marius, Nakonecnij Vanessa, Vanhoefer Jakob, RA Schmiester Leonard, Wang Muying, Ackerman Emily, Shoemaker Jason E, RA Zucker Jeremy, Oxford Kristie, Teuton Jeremy, Kocakaya Ebru, RA Summak Gökçe Yağmur, Hanspers Kristina, Kutmon Martina, Coort Susan, RA Eijssen Lars, Ehrhart Friederike, Rex Devasahayam Arokia Balaya, RA Slenter Denise, Martens Marvin, Pham Nhung, Haw Robin, Jassal Bijay, RA Matthews Lisa, Orlic‐Milacic Marija, Senff Ribeiro Andrea, Rothfels Karen, RA Shamovsky Veronica, Stephan Ralf, Sevilla Cristoffer, Varusai Thawfeek, RA Ravel Jean‐Marie, Fraser Rupsha, Ortseifen Vera, Marchesi Silvia, RA Gawron Piotr, Smula Ewa, Heirendt Laurent, Satagopam Venkata, Wu Guanming, RA Riutta Anders, Golebiewski Martin, Owen Stuart, Goble Carole, Hu Xiaoming, RA Overall Rupert, Maier Dieter, Bauch Angela, Gyori Benjamin, Bachman John, RA Vega Carlos, Grouès Valentin, Vazquez Miguel, Porras Pablo, Licata Luana, RA Iannuccelli Marta, Sacco Francesca, Nesterova Anastasia, Yuryev Anton, RA de Waard Anita, Turei Denes, Luna Augustin, Babur Ozgun, Soliman Sylvain, RA Valdeolivas Alberto, Esteban‐Medina Marina, Peña‐Chilet Maria, rian kinza, RA Helikar Tomas, Puniya Bhanwar Lal, Modos Dezso, Treveil Agatha, RA Olbei Marton, De Meulder Bertrand, Ballereau Stephane, Dugourd Aurélien, RA Naldi Aurelien, Noel Vincent, Calzone Laurence, Sander Chris, Demir Emek, RA Korcsmaros Tamas, Freeman Tom, Augé Franck, Beckmann Jacques S, RA Hasenauer Jan, Wolkenhauer Olaf, Wilighagen Egon L, Pico Alexander, RA Evelo Chris, Gillespie Marc, Stein Lincoln D, Hermjakob Henning, RA D'Eustachio Peter, Saez‐Rodriguez Julio, Dopazo Joaquin, Valencia Alfonso, RA Kitano Hiroaki, Barillot Emmanuel, Auffray Charles, Balling Rudi, RA Schneider Reinhard; RT "COVID19 Disease Map, a computational knowledge repository of virus–host RT interaction mechanisms"; RL Molecular Systems Biology(2021). XX RX DOI; 10.15252/msb.202110396. RA Liu Xiaonan, Huuskonen Sini, Laitinen Tuomo, Redchuk Taras, RA Bogacheva Mariia, Salokas Kari, Poehner Ina, Öhman Tiina, RA Tonduru Arun Kumar, Hassinen Antti, Gawriyski Lisa, Keskitalo Salla, RA Vartiainen Maria K, Pietiäinen Vilja, Poso Antti, Varjosalo Markku; RT "SARS‐CoV‐2–host proteome interactions for antiviral drug discovery"; RL Molecular Systems Biology(2021). XX RX DOI; 10.1515/cti-2021-0011. RA Metaxas Ioannis, Michailidi Emily, Stavrou Dimitris, Pavlidis Ioannis; RT "Educational reconstruction of size-depended-properties in nanotechnology RT for teaching in tertiary education"; RL Chemistry Teacher International(2021). XX RX DOI; 10.1039/D1CC04664K. RA Konia Eleni, Chatzicharalampous Konstantinos, Drakonaki Athina, RA Muenke Cornelia, Ermler Ulrich, Tsiotis Georgios, Pavlidis Ioannis; RT "Rational engineering of RT Luminiphilus syltensis RT ( RT R RT )-selective amine transaminase for the acceptance of bulky RT substrates"; RL Chemical Communications(2021). XX RX DOI; 10.3389/fimmu.2021.590532. RX PUBMED; 33679737. RA Mohapatra S.R., Sadik A., Sharma S., Poschet G., Gegner H.M., Lanz T.V., RA Lucarelli P., Klingmuller U., Platten M., Heiland I., Opitz C.A.; RT "Hypoxia Routes Tryptophan Homeostasis Towards Increased Tryptamine RT Production."; RL Front Immunol 12:590532(2021). XX RX DOI; 10.1073/pnas.1902346116. RA Bockwoldt Mathias, Houry Dorothee, Niere Marc, Gossmann Toni I., RA Reinartz Ines, Schug Alexander, Ziegler Mathias, Heiland Ines; RT "Identification of evolutionary and kinetic drivers of NAD-dependent RT signaling"; RL Proceedings of the National Academy of Sciences(2019). XX RX DOI; 10.3390/biom11060880. RX PUBMED; 34198503. RA Ziegler M., Monne M., Nikiforov A., Agrimi G., Heiland I., Palmieri F.; RT "Welcome to the Family: Identification of the NAD(+) Transporter of Animal RT Mitochondria as Member of the Solute Carrier Family SLC25."; RL Biomolecules 11(6)(2021). XX RX DOI; 10.1101/2021.11.09.467905. RA Mobasher Ghadeer, Mertová Lukrécia, Ghosh Sucheta, Krebs Olga, RA Heinlein Bettina, Müller Wolfgang; RT "Combining dictionary- and rule-based approximate entity linking with tuned RT BioBERT"; XX RX DOI; 10.1016/j.isci.2021.103222. RX PUBMED; 34712920. RA Yang H., Arif M., Yuan M., Li X., Shong K., Turkez H., Nielsen J., RA Uhlen M., Boren J., Zhang C., Mardinoglu A.; RT "A network-based approach reveals the dysregulated transcriptional RT regulation in non-alcoholic fatty liver disease."; RL iScience 24(11):103222(2021). XX RX DOI; 10.1038/ncomms4083. RX PUBMED; 24419221. RA Mardinoglu A., Agren R., Kampf C., Asplund A., Uhlen M., Nielsen J.; RT "Genome-scale metabolic modelling of hepatocytes reveals serine deficiency RT in patients with non-alcoholic fatty liver disease."; RL Nat Commun 5:3083(2014). XX RX DOI; 10.1371/journal.pcbi.1009259. RX PUBMED; 34383741. RA Abegaz F., Martines A.M.F., Vieira-Lara M.A., Rios-Morales M., RA Reijngoud D.J., Wit E.C., Bakker B.M.; RT "Bistability in fatty-acid oxidation resulting from substrate inhibition."; RL PLoS Comput Biol 17(8):e1009259(2021). XX RX DOI; 10.3389/fctls.2021.803850. RA Kaloudis Nikolaos, Zygouri Panagiota, Chalmpes Nikolaos, RA Spyrou Konstantinos, Gournis Dimitrios, Pavlidis Ioannis; RT "Effect of graphite oxide on the catalytic behavior of (S)-selective amine RT transaminases"; RL Frontiers in Catalysis(2021). XX RX DOI; 10.1007/s00216-021-03732-7. RA Dietze Jörn, van Pijkeren Alienke, Egger Anna-Sophia, Ziegler Mathias, RA Kwiatkowski Marcel, Heiland Ines; RT "Natural isotope correction improves analysis of protein modification RT dynamics"; RL Analytical and Bioanalytical Chemistry(2021). XX RX DOI; 10.1093/bioinformatics/bty917. RA Shafiee Kamalabad Mahdi, Heberle Alexander, Thedieck Kathrin, RA Grzegorczyk Marco; RT "Partially non-homogeneous dynamic Bayesian networks based on Bayesian RT regression models with partitioned design matrices"; RL Bioinformatics(2019). XX RX DOI; 10.1016/j.wasman.2021.12.044. RX PUBMED; 35030456. RA Siddiqui S.A., Ristow B., Rahayu T., Putra N.S., Widya Yuwono N., Nisa' K., RA Mategeko B., Smetana S., Saki M., Nawaz A., Nagdalian A.; RT "Black soldier fly larvae (BSFL) and their affinity for organic waste RT processing."; RL Waste Manag 140:1-13(2022). XX RX DOI; 10.21203/rs.3.rs-1300133/v1. RA Odaka Mitsuhiro, Magnin Morgan, Inoue Katsumi; RT "Gene Network Inference from Single-Cell Omics Data and Domain Knowledge RT for Constructing COVID-19-Specific ICAM1-Associated Pathways"; XX RX DOI; 10.1101/105437. RA Chew Yin Hoon, Seaton Daniel, Mengin Virginie, Flis Anna, Mugford Sam T., RA George Gavin M., Moulin Michael, Hume Alastair, Zeeman Samuel C., RA Fitzpatrick Teresa B., Smith Alison M., Stitt Mark, Millar Andrew; RT "The Arabidopsis Framework Model version 2 predicts the organism-level RT effects of circadian clock gene mis-regulation"; XX RX DOI; 10.3389/fimmu.2019.00152. RA Wang Hao, Lei Peng, Gamil Amr Ahmed Abdelrahim, Lagos Leidy, Yue Yang, RA Schirmer Kristin, Mydland Liv Torunn, Overland Margareth, Krogdahl Åshild, RA Kortner Trond M.; RT "Rainbow Trout (Oncorhynchus Mykiss) Intestinal Epithelial Cells as a Model RT for Studying Gut Immune Function and Effects of Functional Feed RT Ingredients"; RL Frontiers in Immunology(2019). XX RX DOI; 10.1371/journal.pcbi.1010194. RA Zakhartsev Maksim, Rotnes Filip, Gulla Marie, Oyas Ove, van Dam Jesse, RA Suarez Diez Maria, Grammes Fabian, Hafthorsson Robert, van Helvoirt Wout, RA Koehorst Jasper, Schaap Peter, Jin Yang, Mydland Liv Torunn, RA Gjuvsland Arne, Simen Sandve, Martins dos Santos Vitor, Vik Jon Olav; RT "SALARECON connects the Atlantic salmon genome to growth and feed RT efficiency"; RL PLOS Computational Biology(2022). XX RX DOI; 10.3389/fnhum.2017.00123. RA Kleemeyer Maike, Polk Thad A., Schaefer Sabine, Bodammer Nils C., RA Brechtel Lars, Lindenberger Ulman; RT "Exercise-Induced Fitness Changes Correlate with Changes in Neural RT Specificity in Older Adults"; RL Frontiers in Human Neuroscience(2017). XX RX DOI; 10.1111/1751-7915.14082. RA Krohn Ines, Menanteau‐Ledouble Simon, Hageskal Gunhild, RA Astafyeva Yekaterina, Jouannais Pierre, Nielsen Jeppe Lund, Pizzol Massimo, RA Wentzel Alexander, Streit Wolfgang R.; RT "Health benefits of microalgae and their microbiomes"; RL Microbial Biotechnology(2022). XX RX DOI; 10.1021/acs.est.2c00372. RA Jouannais Pierre, Hindersin Stefan, Löhn Sarah, Pizzol Massimo; RT "Stochastic LCA Model of Upscaling the Production of Microalgal Compounds"; RL Environmental Science & Technology(2022). XX RX DOI; 10.1128/spectrum.00633-22. RA Astafyeva Yekaterina, Gurschke Marno, Qi Minyue, Bergmann Lutgardis, RA Indenbirken Daniela, de Grahl Imke, Katzowitsch Elena, Reumann Sigrun, RA Hanelt Dieter, Alawi Malik, Streit Wolfgang R., Krohn Ines; RT "Microalgae and Bacteria Interaction—Evidence for Division of Diligence in RT the Alga Microbiota"; RL Microbiology Spectrum(2022). XX RX DOI; 10.3390/pr9071196. RA Sedlar Karel, Nykrynova Marketa, Bezdicek Matej, Branska Barbora, RA Lengerova Martina, Patakova Petra, Skutkova Helena; RT "Diversity and Evolution of Clostridium beijerinckii and Complete Genome of RT the Type Strain DSM 791T"; RL Processes(2021). XX RX PUBMED; 10. RA Schmoldt A., Benthe H.F., Haberland G.; RT "Digitoxin metabolism by rat liver microsomes."; RL Biochem Pharmacol 24(17):1639-1641(1975). XX RX DOI; 10.1101/2021.11.18.468977. RA Petek Marko, Zagorscak Maja, Blejec Andrej, Ramsak Ziva, Coll Anna, RA Baebler Špela, Gruden Kristina; RT "pISA-tree - a data management framework for life science research projects RT using a standardised directory tree"; XX RX DOI; 10.1021/acs.jafc.2c01042. RA Ferrer Lenny, Mindt Melanie, Suarez Diez Maria, Hentrich Thomas, RA Zagorscak Maja, Lee Jin-Ho, Gruden Kristina, Wendisch Volker, RA cankar Katarina; RT "Fermentative Indole Production via Bacterial Tryptophan Synthase Alpha RT Subunit and Plant Indole-3-Glycerol Phosphate Lyase Enzymes"; RL Journal of Agricultural and Food Chemistry(2022). XX RX DOI; 10.1093/insilicoplants/diac010. RA Chew Yin Hoon, Seaton Daniel, Mengin Virginie, Flis Anna, Mugford Sam T, RA George Gavin M, Moulin Michael, Hume Alastair, Zeeman Samuel C, RA Fitzpatrick Teresa B, Smith Alison M, Stitt Mark, Millar Andrew; RT "The RT Arabidopsis RT Framework Model version 2 predicts the organism-level effects RT of circadian clock gene mis-regulation"; RL in silico Plants(2022). XX RX DOI; 10.1038/s41598-022-26483-6. RA Albadry Mohamed, Höpfl Sebastian, Ehteshamzad Nadia, König Matthias, RA Böttcher Michael, Neumann Jasna, Lupp Amelie, Dirsch Olaf, Radde Nicole, RA Christ Bruno, Christ Madlen, Schwen Lars Ole, Laue Hendrik, RA Klopfleisch Robert, Dahmen Uta; RT "Periportal steatosis in mice affects distinct parameters of pericentral RT drug metabolism"; RL Scientific Reports(2022). XX RX DOI; 10.1128/AAC.00990-21. RA Watson Daniel J., Laing Lizahn, Gibhard Liezl, Wong Ho Ning, RA Haynes Richard K., Wiesner Lubbe; RT "Toward New Transmission-Blocking Combination Therapies: Pharmacokinetics RT of 10-Amino-Artemisinins and 11-Aza-Artemisinin and Comparison with RT Dihydroartemisinin and Artemether"; RL Antimicrobial Agents and Chemotherapy(2021). XX RX DOI; 10.1016/j.jpba.2018.09.024. RA Dai Tianming, Jiang Weifan, Guo Yike, Xie Yanxiang, Dai Renke; RT "Comparison of in vitro/in vivo blood distribution and pharmacokinetics of RT artemisinin, artemether and dihydroartemisinin in rats"; RL Journal of Pharmaceutical and Biomedical Analysis(2019). XX RX DOI; 10.1093/cid/ciaa368. RA McCarthy James S, Donini Cristina, Chalon Stephan, Woodford John, RA Marquart Louise, Collins Katharine A, Rozenberg Felix D, Fidock David A, RA Cherkaoui-Rbati Mohammed H, Gobeau Nathalie, Möhrle Jörg J; RT "A Phase 1, Placebo-controlled, Randomized, Single Ascending Dose Study and RT a Volunteer Infection Study to Characterize the Safety, Pharmacokinetics, RT and Antimalarial Activity of the RT Plasmodium RT Phosphatidylinositol 4-Kinase Inhibitor MMV390048"; RL Clinical Infectious Diseases(2020). XX RX DOI; 10.1186/1475-2875-10-263. RA Morris Lorna, Duparc Stephan, Borghini-Fuhrer Isabelle, Jung Kirsten, RA Shin Chang-Sik, Fleckenstein Lawrence; RT "Review of the clinical pharmacokinetics of artesunate and its active RT metabolite dihydroartemisinin following intravenous, intramuscular, oral or RT rectal administration"; RL Malaria Journal(2011). XX RX DOI; 10.1126/scitranslmed.aad9735. RA Paquet Tanya, Le Manach Claire, Cabrera Diego González, Younis Yassir, RA Henrich Philipp P., Abraham Tara S., Lee Marcus C.S., Basak Rajshekhar, RA Ghidelli-Disse Sonja, Lafuente-Monasterio María José, Bantscheff Marcus, RA Ruecker Andrea, Blagborough Andrew M., Zakutansky Sara E., RA Zeeman Anne-Marie, White Karen L., Shackleford David M., Mannila Janne, RA Morizzi Julia, Scheurer Christian, Angulo-Barturen Iñigo, RA Martínez María Santos, Ferrer Santiago, Sanz Laura María, RA Gamo Francisco Javier, Reader Janette, Botha Mariette, Dechering Koen J., RA Sauerwein Robert W., Tungtaeng Anchalee, Vanachayangkul Pattaraporn, RA Lim Chek Shik, Burrows Jeremy, Witty Michael J., Marsh Kennan C., RA Bodenreider Christophe, Rochford Rosemary, Solapure Suresh M., RA Jiménez-Díaz María Belén, Wittlin Sergio, Charman Susan A., RA Donini Cristina, Campo Brice, Birkholtz Lyn-Marie, Hanson Kirsten K., RA Drewes Gerard, Kocken Clemens H.M., Delves Michael J., Leroy Didier, RA Fidock David A., Waterson David, Street Leslie J., Chibale Kelly; RT "Antimalarial efficacy of MMV390048, an inhibitor of RT Plasmodium RT phosphatidylinositol 4-kinase"; RL Science Translational Medicine(2017). XX RX DOI; 10.2165/00003088-200039040-00002. RA Navaratnam Visweswaran, Mansor Sharif Mahsufi, Sit Nam-Weng, Grace James, RA Li Xiangcheng, Olliaro Piero; RT "Pharmacokinetics of Artemisinin-Type Compounds"; RL Clinical Pharmacokinetics(2000). XX RX DOI; 10.1128/AAC.01896-19. RA Sinxadi Phumla, Donini Cristina, Johnstone Hilary, Langdon Grant, RA Wiesner Lubbe, Allen Elizabeth, Duparc Stephan, Chalon Stephan, RA McCarthy James S., Lorch Ulrike, Chibale Kelly, Möhrle Jörg, RA Barnes Karen I.; RT "Safety, Tolerability, Pharmacokinetics, and Antimalarial Activity of the RT Novel RT Plasmodium RT Phosphatidylinositol 4-Kinase Inhibitor MMV390048 in Healthy RT Volunteers"; RL Antimicrobial Agents and Chemotherapy(2020). XX RX DOI; 10.1016/j.ejmech.2022.114952. RX PUBMED; 36462439. RA Papa A., Pasquini S., Galvani F., Cammarota M., Contri C., Carullo G., RA Gemma S., Ramunno A., Lamponi S., Gorelli B., Saponara S., Varani K., RA Mor M., Campiani G., Boscia F., Vincenzi F., Lodola A., Butini S.; RT "Development of potent and selective FAAH inhibitors with improved RT drug-like properties as potential tools to treat neuroinflammatory RT conditions."; RL Eur J Med Chem 246:114952(2023). XX RX DOI; 10.1039/d1md00246e. RA Johnson Alex D., Buhagiar Joseph A., Magri David; RT "4-Amino-1,8-naphthalimide–ferrocene conjugates as potential multi-targeted RT anticancer and fluorescent cellular imaging agents"; RL RSC Medicinal Chemistry(2021). XX RX DOI; 10.3390/cells10102711. RA Cattelani Cecilia, Lesiak Dominik, Liebscher Gudrun, Singer Isabel I., RA Stasyk Taras, Wallnöfer Moritz H., Heberle Alexander, Corti Corrado, RA Hess Michael W., Pfaller Kristian, Kwiatkowski Marcel, RA Pramstaller Peter P., Hicks Andrew A., Thedieck Kathrin, Müller Thomas, RA Huber Lukas A., Eca Guimaraes de Araujo Mariana; RT "The SZT2 Interactome Unravels New Functions of the KICSTOR Complex"; RL Cells(2021). XX RX DOI; 10.1093/database/baad005. RA Leaman Robert, Islamaj Rezarta, Adams Virginia, Alliheedi Mohammed A, RA Almeida Camila, Antunes Rui, Bevan Robert, Chang Antje, RA Erdengasileng Arslan, Hodgskiss Matthew, Ida Ryuki, Kim Dong-Hyun, RA Li Xiangcheng, Mercer Robert E, Mertová Lukrécia, Mobasher Ghadeer, RA Shin Hoo-Chang, Sung Mujeen, Tsujimura Tomoki, Yeh Wen-Chao, Lu Zhiyong; RT "Chemical identification and indexing in full-text articles: an overview of RT the NLM-Chem track at BioCreative VII"; RL Database(2023). XX RX DOI; 10.1002/adsc.202201190. RA Hecquet Laurence; RT "Synthesis of Deoxysugars from Aliphatic α-Ketoacids and Aldoses Catalyzed RT by Thermostable Transketolase Variants from Geobacillus RT stearothermophilus"; XX RX DOI; 10.1016/j.bioorg.2023.106615. RA Roussaki Marina, Magoulas George E., Fotopoulou Theano, Santarem Nuno, RA Barrias Emile, Poehner Ina, Luelmo Sara, Afroudakis Pantelis, RA Georgikopoulou Kalliopi, Nevado Paloma Tejera, Eick Julia, Bifeld Eugenia, RA Corral María J., Jiménez-Antón María Dolores, Ellinger Bernhard, RA Kuzikov Maria, Fragiadaki Irini, Scoulica Effie, Gul Sheraz, Clos Joachim, RA Prousis Kyriakos C., Torrado Juan J., Alunda José María, Wade Rebecca, RA de Souza Wanderley, Cordeiro-da-Silva Anabela, Calogeropoulou Theodora; RT "Design, synthesis and biological evaluation of antiparasitic RT dinitroaniline-ether phospholipid hybrids"; RL Bioorganic Chemistry(2023). XX RX DOI; 10.1042/BCJ20180757. RA van Niekerk Dawie, Gustavsson Anna-Karin, Mojica-Benavides Martin, RA Adiels Caroline B., Goksör Mattias, Snoep Jacky; RT "Phosphofructokinase controls the acetaldehyde-induced phase shift in RT isolated yeast glycolytic oscillators"; RL Biochemical Journal(2019). XX RX DOI; 10.1016/j.biosystems.2023.104969. RA Kouril Theresa, October Craig, Hollocks Stephanie, Odendaal Christoff, RA van Niekerk Dawie, Snoep Jacky; RT "Inhibitor titrations reveal low control of glyceraldehyde 3-phosphate RT dehydrogenase and high control of hexokinase on glycolytic flux in an RT aggressive triple-negative breast cancer cell line"; RL Biosystems(2023). XX RX DOI; 10.1002/cyto.a.20623. RA Lee Jamie A., Spidlen Josef, Boyce Keith, Cai Jennifer, Crosbie Nicholas, RA Dalphin Mark, Furlong Jeff, Gasparetto Maura, Goldberg Michael, RA Goralczyk Elizabeth M., Hyun Bill, Jansen Kirstin, Kollmann Tobias, RA Kong Megan, Leif Robert, McWeeney Shannon, Moloshok Thomas D., Moore Wayne, RA Nolan Garry, Nolan John, Nikolich-Zugich Janko, Parrish David, RA Purcell Barclay, Qian Yu, Selvaraj Biruntha, Smith Clayton, RA Tchuvatkina Olga, Wertheimer Anne, Wilkinson Peter, Wilson Christopher, RA Wood James, Zigon Robert, Scheuermann Richard H., Brinkman Ryan R.; RT "MIFlowCyt: The minimum information about a flow cytometry experiment"; RL Cytometry Part A(2008). XX RX DOI; 10.18653/v1/2023.bionlp-1.40. RA Mobasher Ghadeer, Müller Wolfgang, Krebs Olga, Gertz Michael; RT "WeLT: Improving Biomedical Fine-tuned Pre-trained Language Models with RT Cost-sensitive Learning"; RL The 22nd Workshop on Biomedical Natural Language Processing and BioNLP RL Shared Tasks(2023). XX RX DOI; 10.1007/s10456-022-09842-9. RX PUBMED; 35704148. RA Bonanini F., Kurek D., Previdi S., Nicolas A., Hendriks D., de Ruiter S., RA Meyer M., Clapes Cabrer M., Dinkelberg R., Garcia S.B., Kramer B., RA Olivier T., Hu H., Lopez-Iglesias C., Schavemaker F., Walinga E., Dutta D., RA Queiroz K., Domansky K., Ronden B., Joore J., Lanz H.L., Peters P.J., RA Trietsch S.J., Clevers H., Vulto P.; RT "In vitro grafting of hepatic spheroids and organoids on a microfluidic RT vascular bed."; RL Angiogenesis 25(4):455-470(2022). XX RX DOI; 10.1016/j.chroma.2023.464342. RX PUBMED; 37696124. RA Zhang Z., Singh M., Kindt A., Wegrzyn A.B., Pearson M.J., Ali A., RA Harms A.C., Baker P., Hankemeier T.; RT "Development of a targeted hydrophilic interaction liquid RT chromatography-tandem mass spectrometry based lipidomics platform applied RT to a coronavirus disease severity study."; RL J Chromatogr A 1708:464342(2023). XX RX DOI; 10.26434/chemrxiv-2023-h0w52. RA Singh Madhulika, Kiyuna Ligia Akemi, Odendaal Christoff, Bakker Barbara, RA HARMS Amy, Hankemeier Thomas; RT "Development of HILIC-MS/MS method for acyl-CoAs covering short- to RT long-chain species in a single analytical run"; XX RX DOI; 10.18420/BTW2023-57. RA Müller Wolfgang, Mertová Lukrécia; RT "ReStoRunT: Simple Recording, Storing, Running and Tracing changes in RT Spreadsheets"; RL Datenbanksysteme für Business, Technologie und Web(2023). XX RX DOI; 10.1021/acs.jproteome.2c00758. RA van Pijkeren Alienke, Egger Anna-Sophia, Hotze Madlen, Zimmermann Boris, RA Kipura Tobias, Grander Julia, Gollowitzer André, Koeberle Andreas, RA Bischoff Rainer, Thedieck Kathrin, Kwiatkowski Marcel; RT "Proteome Coverage after Simultaneous Proteo-Metabolome Liquid–Liquid RT Extraction"; RL Journal of Proteome Research(2023). XX RX DOI; 10.1101/2023.01.16.523931. RA Pfänder Pauline, Hensen Lucas, Navas Patricia Razquin, Solvay Marie, RA Prentzell Mirja Tamara, Sadik Ahmed, Heberle Alexander, Seifert Sophie, RA Regin Leon, Bausbacher Tobias, Egger Anna-Sophia, Hotze Madlen, RA Kipura Tobias, Berdel Bianca, Karabogdan Ivana, RA Somarribas Patterson Luis F., Reil Michele, Sayeeram Deepak, RA Peters Manuela, Pittol Jose Ramos, van ’t Land-Kuper Ineke, Börding Teresa, RA Trump Saskia, van Pijkeren Alienke, Zhang Ying, Loayza-Puch Fabricio, RA Kowar Alexander, Harder Sönke, Waltl Lorenz, Gollowitzer André, RA Kataura Tetsushi, Korolchuk Viktor I., Mohammed Shad A., Sievers Phillipp, RA Sahm Felix, Schlüter Hartmut, Koeberle Andreas, Hopf Carsten, RA Kwiatkowski Marcel, Sers Christine, van den Eynde Benoit, Opitz Christiane, RA Thedieck Kathrin; RT "Tryptophan stress activates EGFR-RAS-signaling to MTORC1 and p38/MAPK to RT sustain translation and AHR-dependent autophagy"; XX RX DOI; 10.1136/jitc-2023-006728. RA Solvay Marie, Holfelder Pauline, Klaessens Simon, Pilotte Luc, RA Stroobant Vincent, Lamy Juliette, Naulaerts Stefan, Spillier Quentin, RA Frédérick Raphaël, De Plaen Etienne, Sers Christine, Opitz Christiane, RA van den Eynde Benoit, Zhu Jingzhi; RT "Tryptophan depletion sensitizes the AHR pathway by increasing AHR RT expression and GCN2/LAT1-mediated kynurenine uptake, and potentiates RT induction of regulatory T lymphocytes"; RL Journal for ImmunoTherapy of Cancer(2023). XX RX DOI; 10.1016/j.bcp.2023.115798. RA Opitz Christiane, Holfelder Pauline, Prentzell Mirja Tamara, Trump Saskia; RT "The complex biology of aryl hydrocarbon receptor activation in cancer and RT beyond"; RL Biochemical Pharmacology(2023). XX RX DOI; 10.1042/BST20190730. RX PUBMED; 33544134. RA Heberle A.M., Rehbein U., Rodriguez Peiris M., Thedieck K.; RT "Finding new edges: systems approaches to MTOR signaling."; RL Biochem Soc Trans 49(1):41-54(2021). XX RX DOI; 10.15698/cst2022.08.270. RX PUBMED; 36447531. RA Abdellatif M., Eisenberg T., Heberle A.M., Thedieck K., Kroemer G., RA Sedej S.; RT "Cardiac PI3K p110alpha attenuation delays aging and extends lifespan."; RL Cell Stress 6(8):72-75(2022). XX RX DOI; 10.1038/s41467-023-41132-w. RA Jin Han, Zhang Cheng, Zwahlen Martin, von Feilitzen Kalle, Karlsson Max, RA Shi Mengnan, Yuan Meng, Song Xiya, Li Xiangyu, Yang Hong, Turkez Hasan, RA Fagerberg Linn, Uhlén Mathias, Mardinoglu Adil; RT "Systematic transcriptional analysis of human cell lines for gene RT expression landscape and tumor representation"; RL Nature Communications(2023). XX RX DOI; 10.1161/CIRCULATIONAHA.122.059863. RX PUBMED; 35616058. RA Abdellatif M., Trummer-Herbst V., Heberle A.M., Humnig A., Pendl T., RA Durand S., Cerrato G., Hofer S.J., Islam M., Voglhuber J., RA Ramos Pittol J.M., Kepp O., Hoefler G., Schmidt A., Rainer P.P., Scherr D., RA von Lewinski D., Bisping E., McMullen J.R., Diwan A., Eisenberg T., RA Madeo F., Thedieck K., Kroemer G., Sedej S.; RT "Fine-Tuning Cardiac Insulin-Like Growth Factor 1 Receptor Signaling to RT Promote Health and Longevity."; RL Circulation 145(25):1853-1866(2022). XX RX DOI; 10.1073/pnas.1902346116. RA Bockwoldt Mathias, Houry Dorothee, Niere Marc, Gossmann Toni I., RA Reinartz Ines, Schug Alexander, Ziegler Mathias, Heiland Ines; RT "Identification of evolutionary and kinetic drivers of NAD-dependent RT signaling"; RL Proceedings of the National Academy of Sciences(2019). XX RX DOI; 10.1093/database/baac037. RX PUBMED; 35653350. RA Feng B., Gao J.; RT "AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from RT biomedical literature."; RL Database (Oxford) 2022(2022). XX RX DOI; 10.1016/j.molmet.2023.101838. RA Alagere Krishnamurthy Kishore, Rutten M.G.S., Hoogerland J.A., RA van Dijk T.H., Bos T., Koehorst M., de Vries M.P., Kloosterhuis N.J., RA Havinga H., Schomakers B.V., van Weeghel M., Wolters J.C., Bakker Barbara, RA Oosterveer Maaike H.; RT "Hepatic ChREBP orchestrates intrahepatic carbohydrate metabolism to limit RT hepatic glucose 6-phosphate and glycogen accumulation in a mouse model for RT acute Glycogen Storage Disease type Ib"; RL Molecular Metabolism(2024). XX RX DOI; 10.1186/s12915-023-01652-9. RX PUBMED; 37667308. RA Odendaal C., Jager E.A., Martines A.M.F., Vieira-Lara M.A., RA Huijkman N.C.A., Kiyuna L.A., Gerding A., Wolters J.C., Heiner-Fokkema R., RA van Eunen K., Derks T.G.J., Bakker B.M.; RT "Personalised modelling of clinical heterogeneity between medium-chain RT acyl-CoA dehydrogenase patients."; RL BMC Biol 21(1):184(2023). XX RX DOI; 10.1097/HC9.0000000000000208. RX PUBMED; 37486964. RA Wolf S.D., Ehlting C., Muller-Dott S., Poschmann G., Petzsch P., RA Lautwein T., Wang S., Helm B., Schilling M., Saez-Rodriguez J., Vucur M., RA Stuhler K., Kohrer K., Tacke F., Dooley S., Klingmuller U., Luedde T., RA Bode J.G.; RT "Hepatocytes reprogram liver macrophages involving control of TGF-beta RT activation, influencing liver regeneration and injury."; RL Hepatol Commun 7(8)(2023). XX