Research Topics
Genomes and Genes | G HatfieldSummaryAffiliation: University of California Country: USA Publications
Research Grants
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Detail Information
Publications
DNA topology-mediated control of global gene expression in Escherichia coliG 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...- Differential analysis of DNA microarray gene expression dataG 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... - Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanismMichael L Opel
Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
Mol Microbiol 53:665-74. 2004.... - Global gene expression profiling in Escherichia coli K12. The effects of leucine-responsive regulatory proteinShe 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... - Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energyKimberly 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.... - Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcAKirsty 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... - DNA deformation energy as an indirect recognition mechanism in protein-DNA interactionsKimberly 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... 
Pressure dissociation of integration host factor-DNA complexes reveals flexibility-dependent structural variation at the protein-DNA interfaceDonald 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...- Application of a generalized MWC model for the mathematical simulation of metabolic pathways regulated by allosteric enzymesTarek 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... - GRA1 protein vaccine confers better immune response compared to codon-optimized GRA1 DNA vaccineMert 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... - 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... - The role of DNA deformation energy at individual base steps for the identification of DNA-protein binding sitesNicholas 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... - Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNRKirsty 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... - Optimizing scaleup yield for protein production: Computationally Optimized DNA Assembly (CODA) and Translation EngineeringG 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.... - Identification of hair cycle-associated genes from time-course gene expression profile data by using replicate varianceKevin 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... - An enzyme mechanism language for the mathematical modeling of metabolic pathwaysChin-Rang Yang
Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA
Bioinformatics 21:774-80. 2005..In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations... - Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learningSamuel A Danziger
Institute for Genomics and Bioinformatics, University of California, Irvine, Irvine, California, United States of America
PLoS Comput Biol 5:e1000498. 2009.... - TY3 GAG3 protein forms ordered particles in Escherichia coliLiza 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... - HB tag modules for PCR-based gene tagging and tandem affinity purification in Saccharomyces cerevisiaeChristian Tagwerker
University of California Irvine, Department of Biological Chemistry, School of Medicine, Irvine, CA 92697-1700, USA
Yeast 23:623-32. 2006.... - Ty3 capsid mutations reveal early and late functions of the amino-terminal domainLiza 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... - A mathematical model for the branched chain amino acid biosynthetic pathways of Escherichia coli K12Chin 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... - Ty3 nucleocapsid controls localization of particle assemblyLiza 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... - Effects of exercise on gene expression in human peripheral blood mononuclear cellsPeter 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... 
Recombinant human collagen and biomimetic variants using a de novo gene optimized for modular assemblySam 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...- Computationally Optimised DNA Assembly of synthetic genesLiza 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 Grants
- A Functional Census of p53 Cancer and Suppressor MutantsG 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. ..
- Global Regulatory Networks in Escherichia ColiG Hatfield; Fiscal Year: 2006..abstract_text> ..
- BRANCHED CHAIN AMINO ACID BIOSYNTHESIS IN E COLIG 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. ..
- BRANCHED CHAIN AMINO ACID BIOSYNTHESIS IN E COLIG 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. ..