G Hatfield

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint DNA topology-mediated control of global gene expression in Escherichia coli
    G Wesley Hatfield
    Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, California 92697, USA
    Annu Rev Genet 36:175-203. 2002
  2. ncbi request reprint Differential analysis of DNA microarray gene expression data
    G Wesley Hatfield
    Department of Microbiology, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
    Mol Microbiol 47:871-7. 2003
  3. ncbi request reprint Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism
    Michael L Opel
    Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
    Mol Microbiol 53:665-74. 2004
  4. ncbi request reprint Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein
    She pin Hung
    Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
    J Biol Chem 277:40309-23. 2002
  5. ncbi request reprint Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy
    Kimberly A Aeling
    Institute for Genomics and Bioinformatics, Department of Microbiology and Molecular Genetics, School of Medicine, University of California 92697, USA
    J Biol Chem 281:39236-48. 2006
  6. ncbi request reprint Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA
    Kirsty A Salmon
    Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095 1489, USA
    J Biol Chem 280:15084-96. 2005
  7. ncbi request reprint DNA deformation energy as an indirect recognition mechanism in protein-DNA interactions
    Kimberly A Aeling
    Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, 92697 3425, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:117-25. 2007
  8. pmc Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interface
    Donald F Senear
    Department of Molecular Biology and Biochemistry, College of Medicine, University of California, Irvine, CA 92697, USA
    Nucleic Acids Res 35:1761-72. 2007
  9. ncbi request reprint Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes
    Tarek S Najdi
    Institute for Genomics and Bioinformatics, Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, Irvine, California 92697, USA
    J Bioinform Comput Biol 4:335-55. 2006
  10. ncbi request reprint GRA1 protein vaccine confers better immune response compared to codon-optimized GRA1 DNA vaccine
    Mert Döşkaya
    Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
    Vaccine 25:1824-37. 2007

Collaborators

Detail Information

Publications25

  1. ncbi request reprint DNA topology-mediated control of global gene expression in Escherichia coli
    G Wesley Hatfield
    Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, California 92697, USA
    Annu Rev Genet 36:175-203. 2002
    ..This model is illustrated by the DNA supercoiling-dependent mechanisms that coordinate basal expression levels of operons of the ilv regulon both with one another and with cellular growth conditions...
  2. ncbi request reprint Differential analysis of DNA microarray gene expression data
    G Wesley Hatfield
    Department of Microbiology, Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, CA 92697, USA
    Mol Microbiol 47:871-7. 2003
    ..This method provides a probability of differential expression for each gene based on experiment-wide false-positive and -negative levels driven by experimental error and biological variance...
  3. ncbi request reprint Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism
    Michael L Opel
    Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
    Mol Microbiol 53:665-74. 2004
    ....
  4. ncbi request reprint Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory protein
    She pin Hung
    Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
    J Biol Chem 277:40309-23. 2002
    ..This allows the experimenter to compute posterior probabilities of differential expression for each individual differential gene expression measurement...
  5. ncbi request reprint Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy
    Kimberly A Aeling
    Institute for Genomics and Bioinformatics, Department of Microbiology and Molecular Genetics, School of Medicine, University of California 92697, USA
    J Biol Chem 281:39236-48. 2006
    ....
  6. ncbi request reprint Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA
    Kirsty A Salmon
    Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095 1489, USA
    J Biol Chem 280:15084-96. 2005
    ..The strict statistical analyses that we have performed on our data allow us to predict that 1139 genes in the E. coli genome are regulated either directly or indirectly by the ArcA protein with a 99% confidence level...
  7. ncbi request reprint DNA deformation energy as an indirect recognition mechanism in protein-DNA interactions
    Kimberly A Aeling
    Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, 92697 3425, USA
    IEEE/ACM Trans Comput Biol Bioinform 4:117-25. 2007
    ..Deformation energy may also have a predictive capacity for the underlying catalytic mechanism of DNA-binding enzymes...
  8. pmc Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interface
    Donald F Senear
    Department of Molecular Biology and Biochemistry, College of Medicine, University of California, Irvine, CA 92697, USA
    Nucleic Acids Res 35:1761-72. 2007
    ..Biol. 310, 379-401, 2001). We propose that the volume changes reflect differences in hydration that arise from structural variation at IHF-DNA interfaces while the resulting energetic compensation maintains the same net binding energy...
  9. ncbi request reprint Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymes
    Tarek S Najdi
    Institute for Genomics and Bioinformatics, Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, Irvine, California 92697, USA
    J Bioinform Comput Biol 4:335-55. 2006
    ..This model predicts the partition of enzyme activities in the steady state which paves the way for a more generalized prediction of the behavior of bifunctional enzymes...
  10. ncbi request reprint GRA1 protein vaccine confers better immune response compared to codon-optimized GRA1 DNA vaccine
    Mert Döşkaya
    Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
    Vaccine 25:1824-37. 2007
    ..Immune response and protection conferred by codon-optimized GRA1 DNA vaccine was slightly better than wild type GRA1 DNA vaccine...
  11. ncbi request reprint How noisy and replicable are DNA microarry data?
    Suman Sundaresh
    Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
    Int J Bioinform Res Appl 1:31-50. 2005
    ..Replicability is assessed quantitatively using correlation analysis as a global measure and differential expression analysis and ANOVA at the level of individual genes...
  12. ncbi request reprint The role of DNA deformation energy at individual base steps for the identification of DNA-protein binding sites
    Nicholas R Steffen
    Department of Information and Computer Science, University of California, Irvine, CA 92697, USA
    Genome Inform 13:153-62. 2002
    ..We show that a perceptron can be trained to use the deformation propensity at each step in a sequence to generate such weights...
  13. ncbi request reprint Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR
    Kirsty Salmon
    Department of Microbiology, Immunology, and Molecular Genetics and The Molecular Biology Institute, UCLA, Los Angeles, Cal ifornia, 90095 1489, USA
    J Biol Chem 278:29837-55. 2003
    ..In particular, we describe an approach for identifying gene expression patterns (clusters) obtained from multiple perturbation experiments based on a subset of genes that exhibit high probability for differential expression values...
  14. ncbi request reprint Optimizing scaleup yield for protein production: Computationally Optimized DNA Assembly (CODA) and Translation Engineering
    G Wesley Hatfield
    The Institute for Genomics and Bioinformatics, Donald Bren School of Information and Computer Sciences, University of California, Irvine, CA 92497, USA
    Biotechnol Annu Rev 13:27-42. 2007
    ....
  15. pmc Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate variance
    Kevin K Lin
    Department of Biological Chemistry, Institute for Genomics and Bioinformatics, University of California, Irvine, CA 92697, USA
    Proc Natl Acad Sci U S A 101:15955-60. 2004
    ..The same computational approach should be generally useful for identifying genes associated with cyclic processes from complex tissues...
  16. ncbi request reprint An enzyme mechanism language for the mathematical modeling of metabolic pathways
    Chin Rang Yang
    Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
    Bioinformatics 21:774-80. 2005
    ....
  17. pmc Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning
    Samuel A Danziger
    Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
    PLoS Comput Biol 5:e1000498. 2009
    ....
  18. pmc TY3 GAG3 protein forms ordered particles in Escherichia coli
    Liza S Z Larsen
    Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
    Virology 370:223-7. 2008
    ..These results indicate that assembly can be driven through interactions among capsid subunits in the particle, but that the nucleocapsid domain, likely in association with RNA, confers order upon this process...
  19. ncbi request reprint HB tag modules for PCR-based gene tagging and tandem affinity purification in Saccharomyces cerevisiae
    Christian Tagwerker
    University of California Irvine, Department of Biological Chemistry, School of Medicine, Irvine, CA 92697 1700, USA
    Yeast 23:623-32. 2006
    ....
  20. pmc Ty3 capsid mutations reveal early and late functions of the amino-terminal domain
    Liza S Z Larsen
    Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, USA
    J Virol 81:6957-72. 2007
    ..Particle formation was generally resistant to localized substitutions, possibly indicating that multiple domains are involved...
  21. ncbi request reprint A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12
    Chin Rang Yang
    Department of Microbiology and Molecular Genetics, College of Medicine, University of California at Irvine, Irvine, California 92697, USA
    J Biol Chem 280:11224-32. 2005
    ..This model simulates the results of experimental measurements...
  22. pmc Ty3 nucleocapsid controls localization of particle assembly
    Liza S Z Larsen
    Department of Biological Chemistry, D240 Med Sci I, University of California, Irvine, CA 92697 1700, USA
    J Virol 82:2501-14. 2008
    ..We hypothesize that the NC domain acts as a molecular switch to control Gag3 conformational states that affect both assembly and localization...
  23. ncbi request reprint Effects of exercise on gene expression in human peripheral blood mononuclear cells
    Peter H Connolly
    Department of Pediatrics, University of California, Irvine, California 92697, USA
    J Appl Physiol 97:1461-9. 2004
    ..40-fold). A single bout of heavy exercise substantially alters PBMC gene expression characterized in many cases by a brisk activation and deactivation of genes associated with stress, inflammation, and tissue repair...
  24. doi request reprint Recombinant human collagen and biomimetic variants using a de novo gene optimized for modular assembly
    Sam Wei Polly Chan
    Department of Chemical Engineering and Materials Science, University of California, Irvine, California 92697, USA
    Biomacromolecules 11:1460-9. 2010
    ..This work shows the flexibility of our strategy for designing and assembling specifically tailored biomimetic collagen polymers with re-engineered properties...
  25. pmc Computationally Optimised DNA Assembly of synthetic genes
    Liza S Z Larsen
    CODA Genomics Inc, Laguna Hills, CA 92653, USA
    Int J Bioinform Res Appl 4:324-36. 2008
    ..The CODA algorithm and these biological methods enable fast, simple and reliable assemblies of sequence-correct full-length genes...

Research Grants13

  1. A Functional Census of p53 Cancer and Suppressor Mutants
    G Hatfield; Fiscal Year: 2007
    ..Variations of this basic strategy apply to each of our Specific Aims, which all rely on closely coordinated experiment and computation. ..
  2. Global Regulatory Networks in Escherichia Coli
    G Hatfield; Fiscal Year: 2006
    ..abstract_text> ..
  3. BRANCHED CHAIN AMINO ACID BIOSYNTHESIS IN E COLI
    G Hatfield; Fiscal Year: 2004
    ..These experiments will further provide a wealth of information for future studies concerning the operon specific and global regulation of carbon and energy metabolism genes during aerobic to anaerobic growth transitions. ..
  4. BRANCHED CHAIN AMINO ACID BIOSYNTHESIS IN E COLI
    G Hatfield; Fiscal Year: 2000
    ..These and other experiments has led him to propose a "DNA structural-transmission model" for regulation of the ilvG promoter by IHF. His proposed new experiments are aimed towards testing a number of predictions of this model. ..