James Broach

Publications

• A Dynamic Interplay of Nucleosome and Msn2 Binding Regulates Kinetics of Gene Activation and Repression Following Stress
  Nucleic Acids Research. May, 2014  |   Pubmed ID: 24598258
• Genetic Heterogeneity of Amyotrophic Lateral Sclerosis: Implications for Clinical Practice and Research
  Muscle & Nerve. Jun, 2014  |   Pubmed ID: 24488689
• The Yeast Environmental Stress Response Regulates Mutagenesis Induced by Proteotoxic Stress
  PLoS Genetics. 2013  |   Pubmed ID: 23935537
• Nucleotide Degradation and Ribose Salvage in Yeast
  Molecular Systems Biology. 2013  |   Pubmed ID: 23670538
• Noise and Interlocking Signaling Pathways Promote Distinct Transcription Factor Dynamics in Response to Different Stresses
  Molecular Biology of the Cell. Jun, 2013  |   Pubmed ID: 23615444
• High Hydrostatic Pressure Activates Gene Expression That Leads to Ethanol Production Enhancement in a Saccharomyces Cerevisiae Distillery Strain
  Applied Microbiology and Biotechnology. Mar, 2013  |   Pubmed ID: 22915193
• High Hydrostatic Pressure Activates Transcription Factors Involved in Saccharomyces Cerevisiae Stress Tolerance
  Current Pharmaceutical Biotechnology. Dec, 2012  |   Pubmed ID: 23072392
• Nutritional Control of Growth and Development in Yeast
  Genetics. Sep, 2012  |   Pubmed ID: 22964838
• Regulation of Yeast Pyruvate Kinase by Ultrasensitive Allostery Independent of Phosphorylation
  Molecular Cell. Oct, 2012  |   Pubmed ID: 22902555
• Decoding Complex Chemical Mixtures with a Physical Model of a Sensor Array
  PLoS Computational Biology. Oct, 2011  |   Pubmed ID: 22046111
• Chromatin Remodelers Clear Nucleosomes from Intrinsically Unfavorable Sites to Establish Nucleosome-depleted Regions at Promoters
  Molecular Biology of the Cell. Jun, 2011  |   Pubmed ID: 21508315
• Yeast Cells Can Access Distinct Quiescent States
  Genes & Development. Feb, 2011  |   Pubmed ID: 21289062
• Initiation of the TORC1-regulated G0 Program Requires Igo1/2, Which License Specific MRNAs to Evade Degradation Via the 5'-3' MRNA Decay Pathway
  Molecular Cell. May, 2010  |   Pubmed ID: 20471941
• The Origin Recognition Complex Interacts with a Subset of Metabolic Genes Tightly Linked to Origins of Replication
  PLoS Genetics. Dec, 2009  |   Pubmed ID: 19997491
• Protein Kinase A and TORC1 Activate Genes for Ribosomal Biogenesis by Inactivating Repressors Encoded by Dot6 and Its Homolog Tod6
  Proceedings of the National Academy of Sciences of the United States of America. Nov, 2009  |   Pubmed ID: 19901341
• Chromatin-dependent Transcription Factor Accessibility Rather Than Nucleosome Remodeling Predominates During Global Transcriptional Restructuring in Saccharomyces Cerevisiae
  Molecular Biology of the Cell. Aug, 2009  |   Pubmed ID: 19494041
• Expression of CXCR4, a G-protein-coupled Receptor for CXCL12 in Yeast Identification of New-generation Inverse Agonists
  Methods in Enzymology. 2009  |   Pubmed ID: 19446737
• Microarray Profiling of Phage-display Selections for Rapid Mapping of Transcription Factor-DNA Interactions
  PLoS Genetics. Apr, 2009  |   Pubmed ID: 19360118
• Glucose Regulates Transcription in Yeast Through a Network of Signaling Pathways
  Molecular Systems Biology. 2009  |   Pubmed ID: 19225458
• Predicting Cellular Growth from Gene Expression Signatures
  PLoS Computational Biology. Jan, 2009  |   Pubmed ID: 19119411
• Ph.D. Training in Cancer Biology
  Cancer Research. Nov, 2008  |   Pubmed ID: 19010881
• Microarray Data Mining: a Novel Optimization-based Approach to Uncover Biologically Coherent Structures
  BMC Bioinformatics. 2008  |   Pubmed ID: 18538024
• How Saccharomyces Responds to Nutrients
  Annual Review of Genetics. 2008  |   Pubmed ID: 18303986
• Evaluation of Normalization and Pre-clustering Issues in a Novel Clustering Approach: Global Optimum Search with Enhanced Positioning
  Journal of Bioinformatics and Computational Biology. Aug, 2007  |   Pubmed ID: 17787062
• Protein Kinase A and Sch9 Cooperatively Regulate Induction of Autophagy in Saccharomyces Cerevisiae
  Molecular Biology of the Cell. Oct, 2007  |   Pubmed ID: 17699586
• Sch9 is a Major Target of TORC1 in Saccharomyces Cerevisiae
  Molecular Cell. Jun, 2007  |   Pubmed ID: 17560372
• Cross-talk and Decision Making in MAP Kinase Pathways
  Nature Genetics. Mar, 2007  |   Pubmed ID: 17259986
• Functional Expression of CXCR4 in Saccharomyces Cerevisiae in the Development of Powerful Tools for the Pharmacological Characterization of CXCR4
  Methods in Molecular Biology (Clifton, N.J.). 2006  |   Pubmed ID: 16878688
• Single-cell Observations Reveal Intermediate Transcriptional Silencing States
  Molecular Cell. Jul, 2006  |   Pubmed ID: 16857588
• The Dynamics of Homologous Pairing During Mating Type Interconversion in Budding Yeast
  PLoS Genetics. Jun, 2006  |   Pubmed ID: 16789829
• Creation of GPCR-based Chemical Sensors by Directed Evolution in Yeast
  Protein Engineering, Design & Selection : PEDS. Jan, 2006  |   Pubmed ID: 16263727
• Design and Synthesis of Downsized Metastin (45-54) Analogs with Maintenance of High GPR54 Agonistic Activity
  Bioorganic & Medicinal Chemistry Letters. Jan, 2006  |   Pubmed ID: 16242330
• Mutations in the Nucleosome Core Enhance Transcriptional Silencing
  Molecular and Cellular Biology. Mar, 2005  |   Pubmed ID: 15713639
• Sense and Sensibility: Nutritional Response and Signal Integration in Yeast
  Current Opinion in Microbiology. Dec, 2004  |   Pubmed ID: 15556035
• Making the Right Choice--long-range Chromosomal Interactions in Development
  Cell. Nov, 2004  |   Pubmed ID: 15550239
• PP2A Phosphatase Activity is Required for Stress and Tor Kinase Regulation of Yeast Stress Response Factor Msn2p
  Eukaryotic Cell. Oct, 2004  |   Pubmed ID: 15470255
• A Dynamic Transcriptional Network Communicates Growth Potential to Ribosome Synthesis and Critical Cell Size
  Genes & Development. Oct, 2004  |   Pubmed ID: 15466158
• Ras and Gpa2 Mediate One Branch of a Redundant Glucose Signaling Pathway in Yeast
  PLoS Biology. May, 2004  |   Pubmed ID: 15138498
• The Saccharomyces Cerevisiae Recombination Enhancer Biases Recombination During Interchromosomal Mating-type Switching but Not in Interchromosomal Homologous Recombination
  Genetics. Mar, 2004  |   Pubmed ID: 15082540
• Metastin and Its Variant Forms Suppress Migration of Pancreatic Cancer Cells
  Biochemical and Biophysical Research Communications. Feb, 2004  |   Pubmed ID: 15013429
• The Ras/protein Kinase A Pathway Acts in Parallel with the Mob2/Cbk1 Pathway to Effect Cell Cycle Progression and Proper Bud Site Selection
  Eukaryotic Cell. Feb, 2004  |   Pubmed ID: 14871942
• Theoretical and Computational Studies of the Glucose Signaling Pathways in Yeast Using Global Gene Expression Data
  Biotechnology and Bioengineering. Dec, 2003  |   Pubmed ID: 14708127
• Molecular-size Reduction of a Potent CXCR4-chemokine Antagonist Using Orthogonal Combination of Conformation- and Sequence-based Libraries
  Angewandte Chemie (International Ed. in English). Jul, 2003  |   Pubmed ID: 12876735
• Constitutive Activation of CCR5 and CCR2 Induced by Conformational Changes in the Conserved TXP Motif in Transmembrane Helix 2
  The Journal of Biological Chemistry. Sep, 2003  |   Pubmed ID: 12837756
• Multiple Roles of Tap42 in Mediating Rapamycin-induced Transcriptional Changes in Yeast
  Molecular Cell. Jun, 2003  |   Pubmed ID: 12820961
• Making Good Neighbors: the Right Fence for the Right Job
  Nature Structural Biology. Apr, 2003  |   Pubmed ID: 12660719
• Rap1p and Other Transcriptional Regulators Can Function in Defining Distinct Domains of Gene Expression
  Nucleic Acids Research. Feb, 2003  |   Pubmed ID: 12582242
• Directional Bias During Mating Type Switching in Saccharomyces is Independent of Chromosomal Architecture
  The EMBO Journal. May, 2002  |   Pubmed ID: 11980725
• A Point Mutation That Confers Constitutive Activity to CXCR4 Reveals That T140 is an Inverse Agonist and That AMD3100 and ALX40-4C Are Weak Partial Agonists
  The Journal of Biological Chemistry. Jul, 2002  |   Pubmed ID: 11923301