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Characterization of the Weimberg Pathway in Caulobacter crescentus

XyloCut

(Show All)

Abstract (Expand)

Caulobacter crescentus is a gram-negative bacterium that can utilize xylose as a substrate using the Weimberg pathway, which converts xylose to α-ketoglutarate in five steps without carbon loss. This ...

Authors: Henrik Almqvist, Celina Tufvegren, Lisa Wasserstrom, Gunnar Liden, Jonsdottir Glaser Sara

Date Published: 1st Jun 2018

Journal: Fermentation

DOI: 10.3390/fermentation4020044

Citation: Fermentation 4(2) : 44

Created: 13th Jun 2018 at 10:49, Last updated: 13th Jun 2018 at 10:51

pSSAlib: The partial-propensity stochastic chemical network simulator

Early Metabolic Injury (LiSyM-EMI - Pillar I)

Abstract (Expand)

Chemical reaction networks are ubiquitous in biology, and their dynamics is fundamentally stochastic. Here, we present the software library pSSAlib, which provides a complete and concise implementation ...

Authors: Lutz Brusch, Ostrenko Oleksandr,Incardona Pietro,Ramaswamy Rajesh,Sbalzarini Ivo F.

Date Published: 4th Dec 2017

Journal: PLoS Comput Biol

DOI: 10.1371/journal.pcbi.1005865

Citation: PLoS Comput Biol 13(12) : e1005865

Created: 8th Jun 2018 at 17:48, Last updated: 8th Jun 2018 at 17:49

A Predictive 3D Multi-Scale Model of Biliary Fluid Dynamics in the Liver Lobule.

Early Metabolic Injury (LiSyM-EMI - Pillar I)

Abstract (Expand)

Bile, the central metabolic product of the liver, is transported by the bile canaliculi network. The impairment of bile flow in cholestatic liver diseases has urged a demand for insights into its ...

Authors: Lutz Brusch, Meyer K.,Ostrenko O.,Bourantas G.,Morales-Navarrete H.,Porat-Shliom N.,Segovia-Miranda F.,Nonaka H.,Ghaemi A.,Verbavatz J. M.,Sbalzarini I.,Kalaidzidis Y.,Weigert R.,Zerial M.

Date Published: No date defined

Journal: Cell Syst

PubMed ID: 28330614

Citation: Cell Syst. 2017 Mar 22;4(3):277-290.e9. doi: 10.1016/j.cels.2017.02.008. Epub 2017 Mar 18.

Created: 8th Jun 2018 at 17:45

Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology.

Early Metabolic Injury (LiSyM-EMI - Pillar I)

Abstract (Expand)

Morpheus is a modeling environment for the simulation and integration of cell-based models with ordinary differential equations and reaction-diffusion systems. It allows rapid development of multiscale ...

Authors: Lutz Brusch, Starruss J.,de Back W.,Deutsch A.

Date Published: No date defined

Journal: Bioinformatics

PubMed ID: 24443380

Citation: Bioinformatics. 2014 May 1;30(9):1331-2. doi: 10.1093/bioinformatics/btt772. Epub 2014 Jan 17.

Created: 8th Jun 2018 at 17:26

Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis.

Example use cases

Abstract (Expand)

We used parameter scanning to emulate changes to the limiting rate for steps in a fitted model of glucose-derepressed yeast glycolysis. Three flux-control regimes were observed, two of which were under ...

Author: Pritchard L.,Kell D. B.

Date Published: No date defined

Journal: Eur J Biochem

PubMed ID: 12180966

Citation: Eur J Biochem. 2002 Aug;269(16):3894-904.

Created: 11th Apr 2018 at 13:50

Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data.

MESI-STRAT

Abstract (Expand)

Tryptophan is utilized in various metabolic routes including protein synthesis, serotonin, and melatonin synthesis and the kynurenine pathway. Perturbations in these pathways have been associated with ...

Authors: Ines Heiland, Mathias Ziegler, Stavrum A. K.,Schuster S.,Puntervoll P.

Date Published: No date defined

Journal: J Biol Chem

PubMed ID: 24129579

Citation: J Biol Chem. 2013 Nov 29;288(48):34555-66. doi: 10.1074/jbc.M113.474908. Epub 2013 Oct 15.

Created: 28th Mar 2018 at 23:22

Suppression of indoleamine-2,3-dioxygenase 1 expression by promoter hypermethylation in ER-positive breast cancer.

MESI-STRAT

(Show All)

Abstract (Expand)

Kynurenine formation by tryptophan-catabolic indoleamine-2,3-dioxygenase 1 (IDO1) plays a key role in tumor immune evasion and inhibition of IDO1 is efficacious in preclinical models of breast cancer. ...

Authors: Ines Heiland, Karl-Heinz Kellner, Sarah Schott, Christiane Opitz, Dewi D. L.,Mohapatra S. R.,Blanco Cabanes S.,Adam I.,Somarribas Patterson L. F.,Berdel B.,Kahloon M.,Thurmann L.,Loth S.,Heilmann K.,Weichenhan D.,Mucke O.,Wimberger P.,Kuhlmann J. D.,Plass C.,Platten M.,Gerhauser C.,Trump S.

Date Published: No date defined

Journal: Oncoimmunology

PubMed ID: 28344890

Citation: Oncoimmunology. 2017 Jan 3;6(2):e1274477. doi: 10.1080/2162402X.2016.1274477. eCollection 2017.

Created: 21st Mar 2018 at 14:18

Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker.

MESI-STRAT

Abstract (Expand)

INTRODUCTION: Male breast cancer (MBC) is a rare and inadequately characterized disease. The aim of the present study was to characterize MBC tumors transcriptionally, to classify them into comprehensive ...

Author: Johansson I.,Nilsson C.,Berglund P.,Lauss M.,Ringner M.,Olsson H.,Luts L.,Sim E.,Thorstensson S.,Fjallskog M. L.,Hedenfalk I.

Date Published: No date defined

Journal: Breast Cancer Res

PubMed ID: 22333393

Citation: Breast Cancer Res. 2012 Feb 14;14(1):R31. doi: 10.1186/bcr3116.

Created: 19th Mar 2018 at 11:35

Copy number profiling by array comparative genomic hybridization identifies frequently occurring BRCA2-like male breast cancer.

MESI-STRAT

Abstract (Expand)

Genomic aberrations can be used to subtype breast cancer. In this study, we investigated DNA copy number (CN) profiles of 69 cases of male breast cancer (MBC) by array comparative genomic hybridization ...

Author: Biesma H. D.,Schouten P. C.,Lacle M. M.,Sanders J.,Brugman W.,Kerkhoven R.,Mandjes I.,van der Groep P.,van Diest P. J.,Linn S. C.

Date Published: No date defined

Journal: Genes Chromosomes Cancer

PubMed ID: 26355282

Citation: Genes Chromosomes Cancer. 2015 Dec;54(12):734-44. doi: 10.1002/gcc.22284. Epub 2015 Sep 10.

Created: 14th Mar 2018 at 11:09

Life-stage associated remodeling of lipid metabolism regulation in Atlantic salmon.

GenoSysFat, DigiSal

(Show All)

Abstract (Expand)

Atlantic salmon migrates from rivers to sea to feed, grow and develop gonads before returning to spawn in freshwater. The transition to marine habitats is associated with dramatic changes in the ...

Authors: Gareth Gillard, Thomas Harvey, Arne Gjuvsland, Yang Jin, Magny Sidsel Thomassen, Jacob Seilø Torgersen, Torgeir R. Hvidsten, Jon Olav Vik, Sandve Simen, Lien S.,Leaver M.

Date Published: No date defined

Journal: Mol Ecol

PubMed ID: 29431879

Citation: Mol Ecol. 2018 Feb 12. doi: 10.1111/mec.14533.

Created: 19th Feb 2018 at 13:18

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics.

de.NBI-SysBio

(Show All)

Abstract (Expand)

SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature ...

Authors: Ulrike Wittig, Maja Rey, Renate Kania, Wolfgang Müller, Weidemann A.

Date Published: No date defined

Journal: Nucleic Acids Res

PubMed ID: 29092055

Citation: Nucleic Acids Res. 2018 Jan 4;46(D1):D656-D660. doi: 10.1093/nar/gkx1065.

Created: 29th Jan 2018 at 09:32

Proteome turnover in the green alga Ostreococcus tauri by time course 15N metabolic labeling mass spectrometry.

Millar group

Abstract (Expand)

Protein synthesis and degradation determine the cellular levels of proteins, and their control hence enables organisms to respond to environmental change. Experimentally, these are little known proteome ...

Author: Martin S. F.,Munagapati V. S.,Salvo-Chirnside E.,Kerr L. E.,Le Bihan T.

Date Published: No date defined

Journal: J Proteome Res

PubMed ID: 22077659

Citation: J Proteome Res. 2012 Jan 1;11(1):476-86. doi: 10.1021/pr2009302. Epub 2011 Dec 1.

Created: 14th Jan 2018 at 23:40

Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles.

Millar group

Abstract (Expand)

BACKGROUND: Unicellular cyanobacteria of the genus Cyanothece are recognized for their ability to execute nitrogen (N2)-fixation in the dark and photosynthesis in the light. An understanding of these ...

Author: Aryal U. K.,Stockel J.,Krovvidi R. K.,Gritsenko M. A.,Monroe M. E.,Moore R. J.,Koppenaal D. W.,Smith R. D.,Pakrasi H. B.,Jacobs J. M.

Date Published: No date defined

Journal: BMC Syst Biol

PubMed ID: 22133144

Citation: BMC Syst Biol. 2011 Dec 1;5:194. doi: 10.1186/1752-0509-5-194.

Created: 14th Jan 2018 at 23:38

Stable Core Gut Microbiota across the Freshwater-to-Saltwater Transition for Farmed Atlantic Salmon

GenoSysFat

(Show All)

Abstract (Expand)

Gut microbiota associations through habitat transitions are fundamentally important yet poorly understood. One such habitat transition is the migration from freshwater to saltwater for anadromous fish, ...

Authors: Inga Leena Angell, Jon Olav Vik, Lars Snipen, Rudi Knut,Pope Phillip B.,Sandve Simen Rød

Date Published: 15th Jan 2018

Journal: Appl Environ Microbiol

DOI: 10.1128/AEM.01974-17

Citation: Appl Environ Microbiol 84(2) : e01974-17

Created: 9th Jan 2018 at 14:26, Last updated: 9th Jan 2018 at 14:30

Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis.

Millar group

Abstract (Expand)

The diurnal cycle strongly influences many plant metabolic and physiological processes. Arabidopsis thaliana rosettes were harvested six times during 12-h-light/12-h-dark treatments to investigate ...

Author: Blasing O. E.,Gibon Y.,Gunther M.,Hohne M.,Morcuende R.,Osuna D.,Thimm O.,Usadel B.,Scheible W. R.,Stitt M.

Date Published: No date defined

Journal: Plant Cell

PubMed ID: 16299223

Citation: Plant Cell. 2005 Dec;17(12):3257-81. doi: 10.1105/tpc.105.035261. Epub 2005 Nov 18.

Created: 4th Dec 2017 at 22:36

Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes.

Millar group

Abstract (Expand)

The balance between the supply and utilization of carbon (C) changes continually. It has been proposed that plants respond in an acclimatory manner, modifying C utilization to minimize harmful periods ...

Author: Usadel B.,Blasing O. E.,Gibon Y.,Retzlaff K.,Hohne M.,Gunther M.,Stitt M.

Date Published: No date defined

Journal: Plant Physiol

PubMed ID: 18305208

Citation: Plant Physiol. 2008 Apr;146(4):1834-61. doi: 10.1104/pp.107.115592. Epub 2008 Feb 27.

Created: 4th Dec 2017 at 22:35

Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis.

Millar group, TiMet

Abstract (Expand)

Plants use the circadian clock to sense photoperiod length. Seasonal responses like flowering are triggered at a critical photoperiod when a light-sensitive clock output coincides with light or darkness. ...

Author: Flis A.,Sulpice R.,Seaton D. D.,Ivakov A. A.,Liput M.,Abel C.,Millar A. J.,Stitt M.

Date Published: No date defined

Journal: Plant Cell Environ

PubMed ID: 27075884

Citation: Plant Cell Environ. 2016 Sep;39(9):1955-81. doi: 10.1111/pce.12754. Epub 2016 Jul 15.

Created: 4th Dec 2017 at 14:22

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Millar group

Abstract (Expand)

bioRxiv preprint 2017 Plants respond to seasonal cues such as the photoperiod, to adapt to current conditions and to prepare for environmental changes in the season to come. To assess photoperiodic ...

Authors: Daniel Seaton, Andrew Millar, Graf Alexander,Baerenfaller Katja,Stitt Mark,Gruissem Wilhelm

Date Published: No date defined

Journal: Not specified

DOI: 10.1101/182071

Citation: Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

Created: 16th Nov 2017 at 13:06, Last updated: 16th Nov 2017 at 13:11

Nutzung von Persistent Identifiern zur Umsetzung der FAIR-Prinzipien in Datenablageplattformen für die medizinische Forschung

WG Infrastructure for Translational Research

Abstract:

Not specified

Authors: None

Date Published: 24th Oct 2017

Journal: Not specified

Citation: Knopp C. Nutzung von Persistent Identifiern zur Umsetzung der FAIR-Prinzipien in Datenablageplattformen für die medizinische Forschung [Bachelorarbeit]. Göttingen: Georg-August-Universität; 2017.

Created: 17th Oct 2017 at 20:58

Photoreceptor effects on plant biomass, resource allocation, and metabolic state

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Abstract (Expand)

Plants sense the light environment through an ensemble of photoreceptors. Members of the phytochrome class of light receptors are known to play a critical role in seedling establishment, and are among ...

Author: Yang Deyue,Seaton Daniel D.,Krahmer Johanna,Halliday Karen J.

Date Published: 5th Jul 2016

Journal: Proc Natl Acad Sci USA

DOI: 10.1073/pnas.1601309113

Citation: Proc Natl Acad Sci USA 113(27) : 7667

Created: 6th Oct 2017 at 15:57, Last updated: 6th Oct 2017 at 16:01

Large-Scale Transposition Mutagenesis of Streptomyces coelicolor Identifies Hundreds of Genes Influencing Antibiotic Biosynthesis.

SYSTERACT

Abstract (Expand)

Gram-positive Streptomyces bacteria produce thousands of bioactive secondary metabolites, including antibiotics. To systematically investigate genes affecting secondary metabolism, we developed a ...

Author: Xu Z.,Wang Y.,Chater K. F.,Ou H. Y.,Xu H. H.,Deng Z.,Tao M.

Date Published: 8th Jan 2017

Journal: Appl Environ Microbiol

PubMed ID: 28062460

Citation: Appl Environ Microbiol. 2017 Mar 2;83(6). pii: e02889-16. doi: 10.1128/AEM.02889-16. Print 2017 Mar 15.

Created: 8th Sep 2017 at 14:21

Linking circadian time to growth rate quantitatively via carbon metabolism

Millar group

(Show All)

Abstract (Expand)

Predicting a multicellular organism's phenotype quantitatively from its genotype is challenging, as genetic effects must propagate up time and length scales. Circadian clocks are intracellular ...

Authors: Yin Hoon Chew, Daniel Seaton, Andrew Millar, Mengin Virginie,Flis Anna,Mugford Sam T.,Smith Alison M.,Stitt Mark

Date Published: No date defined

Journal: Not specified

DOI: 10.1101/105437

Citation: Linking circadian time to growth rate quantitatively via carbon metabolism

Created: 4th Sep 2017 at 13:53, Last updated: 4th Sep 2017 at 13:58

Miniaturized and automated adaptive laboratory evolution: Evolving Corynebacterium glutamicum towards an improved d-xylose utilization.

XyloCut

(Show All)

Abstract (Expand)

Adaptive Laboratory Evolution (ALE) is increasingly being used as a technique for untargeted strain optimization. This work aimed at developing an automated and miniaturized ALE approach based on ...

Authors: Niklas Tenhaef, Christian Brüsseler, Jan Marienhagen, Stephan Noack, Radek A.,Muller M. F.,Wiechert W.,Polen T.

Date Published: 30th May 2017

Journal: Bioresour Technol

PubMed ID: 28552568

Citation: Bioresour Technol. 2017 May 12. pii: S0960-8524(17)30709-5. doi: 10.1016/j.biortech.2017.05.055.

Created: 29th Aug 2017 at 12:08

Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus.

SulfoSys, SulfoSys - Biotec

(Show All)

Abstract (Expand)

Sulfolobus solfataricus is a thermoacidophilic Archaeon that thrives in terrestrial hot springs (solfatares) with optimal growth at 80 degrees C and pH 2-4. It catabolizes specific carbon sources, such ...

Authors: Sofia Figueiredo, Theresa Kouril, Patrick Haferkamp, Patricia Wieloch, Dietmar Schomburg, Peter Ruoff, Bettina Siebers, Jörg Schaber, Esser D.

Date Published: 12th Jul 2017

Journal: PLoS One

PubMed ID: 28692669

Citation: PLoS One. 2017 Jul 10;12(7):e0180331. doi: 10.1371/journal.pone.0180331. eCollection 2017.

Created: 15th Aug 2017 at 12:17

Modeling metabolic networks including gene expression and uncertainties

ROBUSTYEAST

Abstract (Expand)

Constraint based methods, such as the Flux Balance Analysis, are widely used to model cellular growth processes without relying on extensive information on the regulatory features. The regulation is ...

Authors: Henning Lindhorst, Steffen Waldherr, Lucia Sergio,Findeisen Rolf

Date Published: 13th Jun 2017

Journal: Not specified

Citation: arXiv:1609.08961

Created: 6th Jul 2017 at 13:49

Oxidative Stickland reactions in an obligate aerobic organism - amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus

SulfoSys - Biotec

(Show All)

Abstract (Expand)

The thermoacidophilic Crenarchaeon Sulfolobus solfataricus is a model organism for archaeal adaptation to extreme environments and renowned for its ability to degrade a broad variety of substrates. It ...

Authors: Helge Stark, Jacqueline Wolf, Andreas Albersmeier, Trong Khoa Pham, Bettina Siebers, Phil Wright, Dietmar Schomburg, Hofmann Julia D.,Kalinowski Jörn,Neumann-Schaal Meina

Date Published: 29th May 2017

Journal: FEBS J

DOI: 10.1111/febs.14105

Citation: FEBS J 86 : 156

Created: 5th Jun 2017 at 23:00, Last updated: 5th Jun 2017 at 23:01

Digitoxin metabolism by rat liver microsomes.

Example use cases

Abstract:

Not specified

Author: Schmoldt A.,Benthe H. F.,Haberland G.

Date Published: 1st Sep 1975

Journal: Biochem Pharmacol

PubMed ID: 10

Citation: Biochem Pharmacol. 1975 Sep 1;24(17):1639-41.

Created: 8th May 2017 at 15:49

Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae.

MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine

Abstract (Expand)

Systems metabolomics, the identification and quantification of cellular metabolites and their integration with genomics and proteomics data, promises valuable functional insights into cellular biology. ...

Authors: Luis Serrano, Maier T.,Marcos J.,Wodke J. A.,Paetzold B.,Liebeke M.,Gutierrez-Gallego R.

Date Published: 20th Apr 2013

Journal: Mol Biosyst

PubMed ID: 23598864

Citation: Mol Biosyst. 2013 Jul;9(7):1743-55. doi: 10.1039/c3mb70113a. Epub 2013 Apr 19.

Created: 8th May 2017 at 10:30

Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling.

MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine

(Show All)

Abstract (Expand)

Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of ...

Authors: Judith Wodke, Eva Yus, Luis Serrano, Edda Klipp, Puchalka J.,Lluch-Senar M.,Marcos J.,Godinho M.,Gutierrez-Gallego R.,dos Santos V. A.,Maier T.

Date Published: 4th Apr 2013

Journal: Mol Syst Biol

PubMed ID: 23549481

Citation: Mol Syst Biol. 2013;9:653. doi: 10.1038/msb.2013.6.

Created: 8th May 2017 at 09:31

In silico genome-scale metabolic analysis of Pseudomonas putida KT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival

EmPowerPutida

Abstract:

Not specified

Author: Sohn Seung Bum,Kim Tae Yong,Park Jong Myoung,Lee Sang Yup

Date Published: 1st Jul 2010

Journal: Biotechnology Journal

DOI: 10.1002/biot.201000124

Citation: Biotechnology Journal 5(7) : 739

Created: 19th Apr 2017 at 11:47, Last updated: 19th Apr 2017 at 11:47

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