Publications

Abstract (Expand)

Tissues use feedback circuits in which cells send signals to each other to control their growth and survival. We show that such feed- back circuits are inherently unstable to mutants that misread the ...

Author: Karin Omer,Alon Uri

Date Published: 26th Jun 2017

Journal: Mol Syst Biol

Abstract (Expand)

Organisms use circadian clocks to generate 24-h rhythms in gene expression. However, the clock can interact with other pathways to generate shorter period oscillations. It remains unclear how these ...

Author: Martins Bruno MC,Das Arijit K,Antunes Liliana,Locke James CW

Date Published: 22nd Dec 2016

Journal: Mol Syst Biol

Abstract (Expand)

Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression ...

Author: Gustavsson Anna-Karin,Adiels Caroline B.,Mehlig Bernhard,Goksör Mattias

Date Published: 1st Aug 2015

Journal: Sci Rep

Abstract (Expand)

UNLABELLED: An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the ...

Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.,Kooi B.,Rohwer J. M.

Date Published: No date defined

Journal: FEBS J

Abstract (Expand)

UNLABELLED: In an accompanying paper [du Preez et al., (2012) FEBS J279, 2810-2822], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. Here we ...

Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.

Date Published: No date defined

Journal: FEBS J

Abstract:

Not specified

Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,du Preez Franco B.,Goksör Mattias

Date Published: 1st Aug 2012

Journal: Not specified

Abstract:

Not specified

Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,Goksör Mattias

Date Published: 3rd Jan 2014

Journal: Not specified

Abstract (Expand)

Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well ...

Authors: Stephan Christel, Malte Herold, Soeren Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson

Date Published: 1st Feb 2018

Journal: Appl Environ Microbiol

Abstract:

Not specified

Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,Kooi Bob,Goksör Mattias

Date Published: 1st Jun 2014

Journal: FEBS J

Abstract (Expand)

Cell volume is an important parameter for modelling cellular processes. Temperature-induced variability of cellular size, volume, intracellular granularity, a fraction of budding cells of yeast ...

Authors: Maksim Zakhartsev, Matthias Reuss

Date Published: 26th Apr 2018

Journal: Not specified

Abstract (Expand)

Photoperiod duration can be predicted from previous days, but irradiance fluctuates in an unpredictable manner. To investigate how allocation to starch responds to changes in these two environmental ...

Authors: Virginie Mengin, Pyl E. T.,Alexandre Moraes T.,Sulpice R.,Krohn N.,Encke B.,Stitt M.

Date Published: No date defined

Journal: Plant Cell Environ

Abstract:

Not specified

Authors: Johanna Krahmer, Ashwin Ganpudi, Ammad Abbas, Andrew Romanowski, Karen Halliday

Date Published: No date defined

Journal: Plant Physiol

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Crop biomass and yield are tightly linked to how the light signaling network translates information about the environment into allocation of resources, including photosynthates. Once activated, the ...

Authors: Andrej Arsovski, Jennifer Nemhauser, Zemke J. E.,Haagen B. D.,Kim S. H.

Date Published: No date defined

Journal: J Exp Bot

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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