A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

Robustness of Nutrient Signaling Is Maintained by Interconnectivity Between Signal Transduction Pathways

(2019) Niek Welkenhuysen et al.   Frontiers in Physiology

Revisiting the Crabtree/Warburg effect in a dynamic perspective: a fitness advantage against sugar-induced cell death

(2018) Elisabetta de Alteriis et al.   CELL CYCLE

A Boolean network of the crosstalk between IGF and Wnt signaling in aging satellite cells

(2018) Lea Siegle et al.   PLoS One

Understanding the role of interactions between host and Mycobacterium tuberculosis under hypoxic condition: an in silico approach

(2018) Tungadri Bose et al.   BMC GENOMICS

Caloric Restriction Extends Yeast Chronological Life Span by Optimizing the Snf1 (AMPK) Signaling Pathway

(2017) Margaret B. Wierman et al.   MOLECULAR AND CELLULAR BIOLOGY

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Fructose-1,6-bisphosphate couples glycolytic flux to activation of Ras

(2017) Ken Peeters et al.   Nature Communications

Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources

(2016) Joao A. Paulo et al.   Journal of Proteomics

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

(2016) Junyoung O Park et al.   Nature Chemical Biology

Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

(2016) Avlant Nilsson et al.   Scientific Reports

Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations

(2015) Margaret B. Wierman et al.   Aging-US

FlexFlux: combining metabolic flux and regulatory network analyses

(2015) Lucas Marmiesse et al.   BMC Systems Biology

Snf1 Phosphorylates Adenylate Cyclase and Negatively Regulates Protein Kinase A-dependent Transcription inSaccharomyces cerevisiae

(2015) Raffaele Nicastro et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines

(2015) Mingcong Wang et al.   PROTEOMICS

Targeting AMPK for cancer prevention and treatment

(2015) Weidong Li et al.   Oncotarget

State Transitions in the TORC1 Signaling Pathway and Information Processing in Saccharomyces cerevisiae

(2014) J. E. Hughes Hallett et al.   GENETICS

Multiscale Computational Models of Complex Biological Systems

(2013) Joseph Walpole et al.   Annual Review of Biomedical Engineering

A Tumor Suppressor Complex with GAP Activity for the Rag GTPases That Signal Amino Acid Sufficiency to mTORC1

(2013) L. Bar-Peled et al.   SCIENCE

Genome-wide location analysis reveals an important overlap between the targets of the yeast transcriptional regulators Rds2 and Adr1

(2012) Nitnipa Soontorngun et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Glucose-induced posttranslational activation of protein phosphatases PP2A and PP1 in yeast

(2012) Dries Castermans et al.   CELL RESEARCH

Nutritional Control of Growth and Development in Yeast

(2012) J. R. Broach   GENETICS

In VivoPhosphorylation of Ser21and Ser83during Nutrient-induced Activation of the Yeast Protein Kinase A (PKA) Target Trehalase

(2012) Wim Schepers et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Leucyl-tRNA Synthetase Controls TORC1 via the EGO Complex

(2012) Grégory Bonfils et al.   MOLECULAR CELL

YeastMine—an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit

(2012) Rama Balakrishnan et al.   Database-The Journal of Biological Databases and Curation

Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters

(2012) Roi Adadi et al.   PLoS Computational Biology

Protein Kinase A Contributes to the Negative Control of Snf1 Protein Kinase in Saccharomyces cerevisiae

(2011) LaKisha Barrett et al.   EUKARYOTIC CELL

Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing

(2011) J. J. Smith et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae

(2009) Tobias S Christensen et al.   BMC Systems Biology

The localization and concentration of  thePDE2-encoded high-affinity cAMP phosphodiesterase is regulated by cAMP-dependent protein kinase A in the yeastSaccharomyces cerevisiae

(2009) Yun Hu et al.   FEMS YEAST RESEARCH

The Yeast GATA Factor Gat1 Occupies a Central Position in Nitrogen Catabolite Repression-Sensitive Gene Activation

(2009) I. Georis et al.   MOLECULAR AND CELLULAR BIOLOGY

The Vam6 GEF Controls TORC1 by Activating the EGO Complex

(2009) Matteo Binda et al.   MOLECULAR CELL

Sfp1 Interaction with TORC1 and Mrs6 Reveals Feedback Regulation on TOR Signaling

(2009) Harri Lempiäinen et al.   MOLECULAR CELL

AMPK in Health and Disease

(2009) Gregory R. Steinberg et al.   PHYSIOLOGICAL REVIEWS

Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3

(2008) Jakub Westholm et al.   BMC GENOMICS

Caffeine extends yeast lifespan by targeting TORC1

(2008) Valeria Wanke et al.   MOLECULAR MICROBIOLOGY

Promoter Binding by the Adr1 Transcriptional Activator May Be Regulated by Phosphorylation in the DNA-Binding Region

(2008) Nataly Kacherovsky et al.   PLoS One

SNF1/AMPK pathways in yeast

(2007) Kristina Hedbacker   Frontiers in Bioscience-Landmark