Quantitative Operating Principles of Yeast Metabolism during Adaptation to Heat Stress.

[1]  S. Omholt,et al.  Scan-o-matic: High-Resolution Microbial Phenomics at a Massive Scale , 2015, G3: Genes, Genomes, Genetics.

[2]  Eberhard O. Voit,et al.  Dynamics of the Heat Stress Response of Ceramides with Different Fatty-Acyl Chain Lengths in Baker’s Yeast , 2015, PLoS Comput. Biol..

[3]  D. Renault,et al.  Abiotic stressors and stress responses: What commonalities appear between species across biological organization levels? , 2015, Environmental pollution.

[4]  J. Ariño,et al.  Coordinate responses to alkaline pH stress in budding yeast , 2015, Microbial cell.

[5]  D. Botstein,et al.  Characterizing the in vivo role of trehalose in Saccharomyces cerevisiae using the AGT1 transporter , 2015, Proceedings of the National Academy of Sciences.

[6]  K. Bidle.  The molecular ecophysiology of programmed cell death in marine phytoplankton. , 2015, Annual review of marine science.

[7]  M. Grbic,et al.  Reversion of developmental mode in insects: evolution from long germband to short germband in the polyembrionic wasp Macrocentrus cingulum Brischke , 2014, Evolution & development.

[8]  M. Yen,et al.  Examining the condition-specific antisense transcription in S. cerevisiae and S. paradoxus , 2014, BMC Genomics.

[9]  David Botstein,et al.  Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes , 2013, Proceedings of the National Academy of Sciences.

[10]  Luonan Chen.  Guest editorial. Computational systems biology. , 2013, IET systems biology.

[11]  V. Mootha,et al.  MCU encodes the pore conducting mitochondrial calcium currents , 2013, eLife.

[12]  Eberhard O. Voit,et al.  Coordination of Rapid Sphingolipid Responses to Heat Stress in Yeast , 2013, PLoS Comput. Biol..

[13]  Andreas Wagner,et al.  Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation. , 2013, Molecular biology and evolution.

[14]  U. Alon,et al.  Mutation Rules and the Evolution of Sparseness and Modularity in Biological Systems , 2013, PloS one.

[15]  J. Vik,et al.  Bridging the genotype–phenotype gap: what does it take? , 2013, The Journal of physiology.

[16]  W. Lim,et al.  Design principles of regulatory networks: searching for the molecular algorithms of the cell. , 2013, Molecular cell.

[17]  M. Munder,et al.  Molecular chaperones and stress-inducible protein-sorting factors coordinate the spatiotemporal distribution of protein aggregates , 2012, Molecular biology of the cell.

[18]  Marcel J. T. Reinders,et al.  Understanding Regulation of Metabolism through Feasibility Analysis , 2012, PloS one.

[19]  Sean R. Collins,et al.  Hierarchical modularity and the evolution of genetic interactomes across species. , 2012, Molecular cell.

[20]  Jennifer Abrams,et al.  Biology of the Heat Shock Response and Protein Chaperones: Budding Yeast (Saccharomyces cerevisiae) as a Model System , 2012, Microbiology and Molecular Reviews.

[21]  C. Grant,et al.  The Response to Heat Shock and Oxidative Stress in Saccharomyces cerevisiae , 2012, Genetics.

[22]  Yunpeng Wang,et al.  Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability , 2012, PLoS Comput. Biol..

[23]  C. Varela,et al.  Adaptive evolution of Saccharomyces cerevisiae to generate strains with enhanced glycerol production , 2011, Applied Microbiology and Biotechnology.

[24]  K. Struhl,et al.  Extensive divergence of yeast stress responses through transitions between induced and constitutive activation , 2011, Proceedings of the National Academy of Sciences.

[25]  R. Jayaraman.  Hypermutation and stress adaptation in bacteria , 2011, Journal of Genetics.

[26]  Gonzalo Guillén-Gosálbez,et al.  Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models , 2011, BMC Systems Biology.

[27]  J. Vik,et al.  Order‐preserving principles underlying genotype–phenotype maps ensure high additive proportions of genetic variance , 2011, Journal of evolutionary biology.

[28]  F. Dietrich,et al.  Oxidative Stress Survival in a Clinical Saccharomyces cerevisiae Isolate Is Influenced by a Major Quantitative Trait Nucleotide , 2011, Genetics.

[29]  G. Bellí,et al.  The oxidative stress response in yeast cells involves changes in the stability of Aft1 regulon mRNAs , 2011, Molecular microbiology.

[30]  A. Wagner,et al.  Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution , 2011, Journal of evolutionary biology.

[31]  S. Omholt,et al.  Methods for and results from the study of design principles in molecular systems. , 2011, Mathematical biosciences.

[32]  Insuk Lee,et al.  Towards Establishment of a Rice Stress Response Interactome , 2011, PLoS genetics.

[33]  In-Hee Lee,et al.  A filter-based feature selection approach for identifying potential biomarkers for lung cancer , 2011, Journal of Clinical Bioinformatics.

[34]  N. Alon,et al.  A Biological Solution to a Fundamental Distributed Computing Problem , 2011, Science.

[35]  Michael A. Savageau,et al.  Relating Mutant Genotype to Phenotype via Quantitative Behavior of the NADPH Redox Cycle in Human Erythrocytes , 2010, PloS one.

[36]  Gonzalo Guillén-Gosálbez,et al.  Optimization and evolution in metabolic pathways: global optimization techniques in Generalized Mass Action models. , 2010, Journal of biotechnology.

[37]  Rui Alves,et al.  Minimization of Biosynthetic Costs in Adaptive Gene Expression Responses of Yeast to Environmental Changes , 2010, PLoS Comput. Biol..

[38]  A. Sorribas,et al.  Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses , 2009, BMC Bioinformatics.

[39]  Michael A Savageau,et al.  Phenotypes and tolerances in the design space of biochemical systems , 2009, Proceedings of the National Academy of Sciences.

[40]  Uri Alon,et al.  An Analytically Solvable Model for Rapid Evolution of Modular Structure , 2009, PLoS Comput. Biol..

[41]  A. Long,et al.  Experimental evolution reveals natural selection on standing genetic variation , 2009, Nature Genetics.

[42]  É. Sucena,et al.  Rapid Experimental Evolution of Pesticide Resistance in C. elegans Entails No Costs and Affects the Mating System , 2008, PloS one.

[43]  Audrey P Gasch,et al.  Stress-activated genomic expression changes serve a preparative role for impending stress in yeast. , 2008, Molecular biology of the cell.

[44]  Enrique Herrero,et al.  Comprehensive Transcriptional Analysis of the Oxidative Response in Yeast* ♦ , 2008, Journal of Biological Chemistry.

[45]  A. Gasch.  Comparative genomics of the environmental stress response in ascomycete fungi , 2007, Yeast.

[46]  T. Reusch,et al.  Molecular ecology of global change , 2007, Molecular ecology.

[47]  M. Berovič,et al.  Heat shock on Saccharomyces cerevisiae inoculum increases glycerol production in wine fermentation , 2007, Biotechnology Letters.

[48]  M. Berovič,et al.  Influence of heat shock on glycerol production in alcohol fermentation. , 2007, Journal of bioscience and bioengineering.

[49]  Andrzej K. Konopka,et al.  Systems biology : principles, methods, and concepts , 2006 .

[50]  A. Sorribas,et al.  Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock , 2006, BMC Bioinformatics.

[51]  U. Alon,et al.  Spontaneous evolution of modularity and network motifs. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Geoff Holmes,et al.  Benchmarking Attribute Selection Techniques for Discrete Class Data Mining , 2003, IEEE Trans. Knowl. Data Eng..

[53]  Eberhard O Voit,et al.  Biochemical and genomic regulation of the trehalose cycle in yeast: review of observations and canonical model analysis. , 2003, Journal of theoretical biology.

[54]  E. Voit.  Design principles and operating principles: the yin and yang of optimal functioning. , 2003, Mathematical biosciences.

[55]  I. Jolliffe.  Principal Component Analysis , 2002 .

[56]  E. Nevo.  Inaugural Article: Evolution of genome-phenome diversity under environmental stress , 2001 .

[57]  E. Lander,et al.  Remodeling of yeast genome expression in response to environmental changes. , 2001, Molecular biology of the cell.

[58]  D. Botstein,et al.  Genomic expression programs in the response of yeast cells to environmental changes. , 2000, Molecular biology of the cell.

[59]  Michael R. Rose,et al.  Variation in the reversibility of evolution , 2000, Nature.

[60]  E. O. Voit,et al.  Biochemical systems analysis of genome-wide expression data , 2000, Bioinform..

[61]  H. Bohnert,et al.  Genomic approaches to plant stress tolerance. , 2000, Current opinion in plant biology.

[62]  M. Jacquet,et al.  The heat shock response in yeast: differential regulations and contributions of the Msn2p/Msn4p and Hsf1p regulons , 1999, Molecular microbiology.

[63]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[64]  Y. Hannun,et al.  Involvement of Yeast Sphingolipids in the Heat Stress Response of Saccharomyces cerevisiae * , 1997, The Journal of Biological Chemistry.

[65]  M. Cascante,et al.  Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model definition and nomenclature. , 1995, Mathematical biosciences.

[66]  A Sorribas,et al.  Comparative characterization of the fermentation pathway of Saccharomyces cerevisiae using biochemical systems theory and metabolic control analysis: model validation and dynamic behavior. , 1995, Mathematical biosciences.

[67]  H. Kacser,et al.  The control of flux. , 1995, Biochemical Society transactions.

[68]  R. Nickells,et al.  A role for glyceraldehyde-3-phosphate dehydrogenase in the development of thermotolerance in Xenopus laevis embryos , 1988, The Journal of cell biology.

[69]  Michael A. Savageau,et al.  Optimal design of feedback control by inhibition , 1975, Journal of Molecular Evolution.

[70]  Reinhart Heinrich,et al.  A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. , 1974, European journal of biochemistry.

[71]  M A Savageau,et al.  Concepts relating the behavior of biochemical systems to their underlying molecular properties. , 1971, Archives of biochemistry and biophysics.

[72]  M. Savageau,et al.  Parameter Sensitivity as a Criterion for Evaluating and Comparing the Performance of Biochemical Systems , 1971, Nature.

[73]  M. Savageau.  Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. , 1969, Journal of theoretical biology.

[74]  C. Darwin.  The Origin of Species by Means of Natural Selection, Or, The Preservation of Favoured Races in the Struggle for Life , 1859 .

[75]  Travis S. Bayer,et al.  Building synthetic systems to learn nature's design principles. , 2012, Advances in experimental medicine and biology.

[76]  J. F. Poyatos,et al.  On the search for design principles in biological systems. , 2012, Advances in experimental medicine and biology.

[77]  Orkun S. Soyer,et al.  Evolutionary principles underlying structure and response dynamics of cellular networks. , 2012, Advances in experimental medicine and biology.

[78]  John Huntington,et al.  System Design Principles , 2007 .

[79]  Jan Ihmels,et al.  Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae , 2004, Nature Biotechnology.

[80]  Stephen Wolfram,et al.  The Mathematica Book , 1996 .