Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast

[1]  U. Sauer,et al.  Systems biology of microbial metabolism. , 2010, Current opinion in microbiology.

[2]  Stefan J. Jol,et al.  Differential glucose repression in common yeast strains in response to HXK2 deletion. , 2010, FEMS yeast research.

[3]  Uwe Sauer,et al.  Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates , 2010, BMC Systems Biology.

[4]  F. Robert,et al.  Transcriptional regulation of nonfermentable carbon utilization in budding yeast. , 2010, FEMS yeast research.

[5]  Gary D Bader,et al.  The Genetic Landscape of a Cell , 2010, Science.

[6]  Michael Snyder,et al.  Systems biology from a yeast omics perspective , 2009, FEBS letters.

[7]  Pamela A. Silver,et al.  Eukaryotic systems broaden the scope of synthetic biology , 2009, The Journal of cell biology.

[8]  Pamela K. Kreeger,et al.  Cancer systems biology: a network modeling perspective , 2009, Carcinogenesis.

[9]  Lukas N. Mueller,et al.  Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics , 2009, Cell.

[10]  I. Simon,et al.  Backup in gene regulatory networks explains differences between binding and knockout results , 2009, Molecular systems biology.

[11]  U. Sauer,et al.  13C-based metabolic flux analysis , 2009, Nature Protocols.

[12]  James R Broach,et al.  How Saccharomyces responds to nutrients. , 2008, Annual review of genetics.

[13]  Richard Bonneau.  Learning biological networks: from modules to dynamics. , 2008, Nature chemical biology.

[14]  Henry H. N. Lam,et al.  A database of mass spectrometric assays for the yeast proteome , 2008, Nature Methods.

[15]  Guy Karlebach,et al.  Modelling and analysis of gene regulatory networks , 2008, Nature Reviews Molecular Cell Biology.

[16]  Jens Nielsen,et al.  Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks , 2008, BMC Systems Biology.

[17]  U. Sauer,et al.  Cyclic AMP-Dependent Catabolite Repression Is the Dominant Control Mechanism of Metabolic Fluxes under Glucose Limitation in Escherichia coli , 2008, Journal of bacteriology.

[18]  W. Heideman,et al.  Protein Kinase A, TOR, and Glucose Transport Control the Response to Nutrient Repletion in Saccharomyces cerevisiae , 2007, Eukaryotic Cell.

[19]  Patrick J. Killion,et al.  Genetic reconstruction of a functional transcriptional regulatory network , 2007, Nature Genetics.

[20]  U. Sauer,et al.  Article number: 62 REVIEW Metabolic networks in motion: 13 C-based flux analysis , 2022 .

[21]  J. Heitman,et al.  Peroxisome Function Regulates Growth on Glucose in the Basidiomycete Fungus Cryptococcus neoformans , 2006, Eukaryotic Cell.

[22]  M. Gerstein,et al.  Genomic analysis of the hierarchical structure of regulatory networks , 2006, Proceedings of the National Academy of Sciences.

[23]  L. Aravind,et al.  Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. , 2006, Journal of molecular biology.

[24]  T. Ideker,et al.  Supporting Online Material for A Systems Approach to Mapping DNA Damage Response Pathways , 2006 .

[25]  Pooja Jain,et al.  The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae , 2005, Nucleic Acids Res..

[26]  Jens Nielsen,et al.  Improvement of Galactose Uptake in Saccharomyces cerevisiae through Overexpression of Phosphoglucomutase: Example of Transcript Analysis as a Tool in Inverse Metabolic Engineering , 2005, Applied and Environmental Microbiology.

[27]  R. Rolfes,et al.  DNA-Bound Bas1 Recruits Pho2 To Activate ADE Genes in Saccharomyces cerevisiae , 2005, Eukaryotic Cell.

[28]  U. Sauer,et al.  Metabolic functions of duplicate genes in Saccharomyces cerevisiae. , 2005, Genome research.

[29]  A. Hinnebusch.  Translational regulation of GCN4 and the general amino acid control of yeast. , 2005, Annual review of microbiology.

[30]  Nicola Zamboni,et al.  FiatFlux – a software for metabolic flux analysis from 13C-glucose experiments , 2005, BMC Bioinformatics.

[31]  Cheng-Yan Kao,et al.  A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae , 2005, Bioinform..

[32]  U. Sauer,et al.  Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism , 2005, Nature Genetics.

[33]  U. Sauer,et al.  Escherichia coli† , 2004 .

[34]  Jason A. Papin,et al.  Reconstruction of cellular signalling networks and analysis of their properties , 2005, Nature Reviews Molecular Cell Biology.

[35]  D. Fell.  Enzymes, metabolites and fluxes. , 2004, Journal of experimental botany.

[36]  J. Stelling,et al.  Robustness of Cellular Functions , 2004, Cell.

[37]  M. Gerstein,et al.  Genomic analysis of regulatory network dynamics reveals large topological changes , 2004, Nature.

[38]  Nicola J. Rinaldi,et al.  Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.

[39]  Uwe Sauer,et al.  TCA cycle activity in Saccharomyces cerevisiae is a function of the environmentally determined specific growth and glucose uptake rates. , 2004, Microbiology.

[40]  M. Carlson,et al.  Cyclic AMP-Dependent Protein Kinase Regulates the Subcellular Localization of Snf1-Sip1 Protein Kinase , 2004, Molecular and Cellular Biology.

[41]  Benjamin M. Bolstad,et al.  affy - analysis of Affymetrix GeneChip data at the probe level , 2004, Bioinform..

[42]  H. Boucherie,et al.  Dissecting regulatory networks by means of two‐dimensional gel electrophoresis: Application to the study of the diauxic shift in the yeast Saccharomyces cerevisiae , 2004, Proteomics.

[43]  D. Pe’er,et al.  Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.

[44]  Hans-Joachim Schüller,et al.  Transcriptional control of nonfermentative metabolism in the yeast Saccharomyces cerevisiae , 2003, Current Genetics.

[45]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[46]  S. Rafii,et al.  Splitting vessels: Keeping lymph apart from blood , 2003, Nature Medicine.

[47]  Nicola J. Rinaldi,et al.  Transcriptional Regulatory Networks in Saccharomyces cerevisiae , 2002, Science.

[48]  A. Kimura,et al.  Chromosomal gradient of histone acetylation established by Sas2p and Sir2p functions as a shield against gene silencing , 2002, Nature Genetics.

[49]  S. Knudsen,et al.  A new non-linear normalization method for reducing variability in DNA microarray experiments , 2002, Genome Biology.

[50]  Yaniv Ziv,et al.  Revealing modular organization in the yeast transcriptional network , 2002, Nature Genetics.

[51]  Ronald W. Davis,et al.  Functional profiling of the Saccharomyces cerevisiae genome , 2002, Nature.

[52]  H. Westerhoff,et al.  Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway , 2001, FEBS letters.

[53]  Fred Winston,et al.  NRG1 is required for glucose repression of the SUC2 and GAL genes of Saccharomyces cerevisiae , 2001, BMC Genetics.

[54]  C. Li,et al.  Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Robert Hermann,et al.  Methods for Intense Aeration, Growth, Storage, and Replication of Bacterial Strains in Microtiter Plates , 2000, Applied and Environmental Microbiology.

[56]  E. A. Packham,et al.  Control of glycolytic gene expression in the budding yeast (Saccharomyces cerevisiae) , 1995, Current Genetics.

[57]  Fred Winston,et al.  Construction of a set of convenient saccharomyces cerevisiae strains that are isogenic to S288C , 1995, Yeast.

[58]  L. Hood,et al.  Reverse Engineering of Biological Complexity , 2007 .

[59]  M. Knop,et al.  System of centromeric, episomal, and integrative vectors based on drug resistance markers for Saccharomyces cerevisiae. , 2006, BioTechniques.

[60]  F. Winston,et al.  NRG 1 is required for glucose repression of the SUC 2 and GAL genes of Saccharomyces cerevisiae , 2001 .

[61]  David Botstein,et al.  SGD: Saccharomyces Genome Database , 1998, Nucleic Acids Res..

[62]  S. Weinhouse.  On respiratory impairment in cancer cells. , 1956, Science.