Craig Benham

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes
    Huiquan Wang
    UC Davis Genome Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
    Nucleic Acids Res 34:D373-8. 2006
  2. pmc The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome
    Eva M Strawbridge
    Department of Mathematics, University of Chicago, IL 60637, USA
    Curr Genet 56:321-40. 2010
  3. pmc Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress
    Huiquan Wang
    Genome Center, University of California, Davis, CA 95616, USA
    BMC Bioinformatics 7:248. 2006
  4. ncbi request reprint DNA mechanics
    Craig J Benham
    UC Davis Genome Center, University of California, Davis, CA 95616, USA
    Annu Rev Biomed Eng 7:21-53. 2005
  5. ncbi request reprint The analysis of stress-induced duplex destabilization in long genomic DNA sequences
    Craig J Benham
    UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
    J Comput Biol 11:519-43. 2004
  6. ncbi request reprint Brownian dynamics of double-stranded DNA in periodic systems with discrete salt
    Steven P Mielke
    UC Davis Genome Center, University of California, Davis, California 95616, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 77:031924. 2008
  7. ncbi request reprint WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA
    Chengpeng Bi
    UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
    Bioinformatics 20:1477-9. 2004
  8. ncbi request reprint Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA
    Steven P Mielke
    Biophysics Graduate Group, University of California, Davis, California 95616, USA
    J Chem Phys 123:124911. 2005
  9. pmc Theoretical analysis of the stress induced B-Z transition in superhelical DNA
    Dina Zhabinskaya
    UC Davis Genome Center, University of California, Davis, Davis California, United States of America
    PLoS Comput Biol 7:e1001051. 2011
  10. ncbi request reprint Transcription-driven twin supercoiling of a DNA loop: a Brownian dynamics study
    Steven P Mielke
    Biophysics Graduate Group, University of California, Davis, CA 95616, USA
    J Chem Phys 121:8104-12. 2004

Research Grants

Collaborators

Detail Information

Publications20

  1. pmc SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes
    Huiquan Wang
    UC Davis Genome Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
    Nucleic Acids Res 34:D373-8. 2006
    ..SIDDBASE is available at www.gc.ucdavis.edu/benham/siddbase...
  2. pmc The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome
    Eva M Strawbridge
    Department of Mathematics, University of Chicago, IL 60637, USA
    Curr Genet 56:321-40. 2010
    ..However, the S. cerevisiae genome is not enriched in those IRs that would extrude cruciforms, suggesting that this is not a common event. Various explanations for these results are considered...
  3. pmc Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress
    Huiquan Wang
    Genome Center, University of California, Davis, CA 95616, USA
    BMC Bioinformatics 7:248. 2006
    ..In this report we investigate how this structural property, either alone or together with other structural and sequence attributes, may be used to search prokaryotic genomes for promoters...
  4. ncbi request reprint DNA mechanics
    Craig J Benham
    UC Davis Genome Center, University of California, Davis, CA 95616, USA
    Annu Rev Biomed Eng 7:21-53. 2005
    ..Therefore, agreement between predicted structures and structures obtained experimentally, for example, by electron microscopy, does not in itself provide evidence for the correctness or completeness of any given model of DNA mechanics...
  5. ncbi request reprint The analysis of stress-induced duplex destabilization in long genomic DNA sequences
    Craig J Benham
    UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
    J Comput Biol 11:519-43. 2004
    ....
  6. ncbi request reprint Brownian dynamics of double-stranded DNA in periodic systems with discrete salt
    Steven P Mielke
    UC Davis Genome Center, University of California, Davis, California 95616, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 77:031924. 2008
    ..Such phenomena are likely to play an important role in the formation of alternative DNA secondary structures, suggesting the present methods will prove valuable to dynamic models of superhelical stress-induced DNA structural transitions...
  7. ncbi request reprint WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA
    Chengpeng Bi
    UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA
    Bioinformatics 20:1477-9. 2004
    ..AVAILABILITY: http://orange.genomecenter.ucdavis.edu/benham/sidd/index.html..
  8. ncbi request reprint Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA
    Steven P Mielke
    Biophysics Graduate Group, University of California, Davis, California 95616, USA
    J Chem Phys 123:124911. 2005
    ....
  9. pmc Theoretical analysis of the stress induced B-Z transition in superhelical DNA
    Dina Zhabinskaya
    UC Davis Genome Center, University of California, Davis, Davis California, United States of America
    PLoS Comput Biol 7:e1001051. 2011
    ..The approach developed here has the potential to illuminate the occurrence of Z-form regions in vivo, and the possible roles this transition may play in biological processes...
  10. ncbi request reprint Transcription-driven twin supercoiling of a DNA loop: a Brownian dynamics study
    Steven P Mielke
    Biophysics Graduate Group, University of California, Davis, CA 95616, USA
    J Chem Phys 121:8104-12. 2004
    ..Natl. Acad. Sci. U.S.A. 84, 7024 (1987)]. The properties of the chain at the onset of writhing agree well with predictions from theory, and the generated stress is ample for driving secondary structural transitions in physiological DNA...
  11. pmc Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters
    Huiquan Wang
    UC Davis Genome Center, University of California, Davis, California 95616, USA
    Genome Res 14:1575-84. 2004
    ..We describe how these observations may illuminate specific mechanisms of regulation, and assist in the computational identification of promoter locations in prokaryotes...
  12. 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
    ....
  13. pmc Superhelical destabilization in regulatory regions of stress response genes
    Huiquan Wang
    UC Davis Genome Center, University of California Davis, Davis, California, United States of America
    PLoS Comput Biol 4:e17. 2008
    ....
  14. 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...
  15. ncbi request reprint Comment on "Can one predict DNA transcription start sites by studying bubbles?"
    Craig J Benham
    Genome Center and Department of Mathematics, University of California Davis, CA 95616, USA
    Phys Rev Lett 97:059801; discussion 059802. 2006
  16. ncbi request reprint Extrusion of an imperfect palindrome to a cruciform in superhelical DNA: complete determination of energetics using a statistical mechanical model
    Craig J Benham
    Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
    J Mol Biol 316:563-81. 2002
    ..Our analysis also suggests that, at higher temperatures, significant denaturation at the base of an imperfect cruciform can successfully compete with extension of the cruciform arms...
  17. ncbi request reprint Multiple collagen I gene regulatory elements have sites of stress-induced DNA duplex destabilization and nuclear scaffold/matrix association potential
    Christian Mielke
    Department of Structural and Molecular Biology, University of Aarhus, Denmark
    J Cell Biochem 84:484-96. 2002
    ..They demonstrate the usefulness of computational analyses that predict SIDD properties in reliably identifying DNA elements involved in the structural organization of the eukaryotic genome and the regulation of its expression...
  18. ncbi request reprint Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats
    Vladimir N Potaman
    Laboratory of DNA Structure and Function, Center for Genome Research, Institute of Biosciences and Technology, Texas A and M University System Health Sciences Center, Houston, TX 77030 3303, USA
    J Mol Biol 326:1095-111. 2003
    ..A model is proposed in which unscheduled or aberrant DNA replication is a critical step in the expansion mutation...
  19. ncbi request reprint Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function
    Zhanna Polonskaya
    Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
    Virology 328:282-91. 2004
    ....
  20. pmc Integration site choice of a feline immunodeficiency virus vector
    Yubin Kang
    Program in Gene Therapy, Department of Pediatrics, University of Iowa, Iowa City, 52242, 52242, USA
    J Virol 80:8820-3. 2006
    ..FIV integration preferences are more similar to those of primate lentiviruses and distinct from those of Moloney murine leukemia virus, avian sarcoma leukosis virus, and foamy virus...

Research Grants2

  1. INFERRING CHROMOSOME ARCHITECTURE FROM GENOMIC SEQUENCE
    Craig Benham; Fiscal Year: 2002
    ..It will be used to develop a new generation of precisely targeted and regulated transfection vectors for gene therapy. ..