Craig J Benham

Craig J Benham

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Craig J Benham

Craig J Benham

Publications by authors named "Craig J Benham"

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Emerging roles for R-loop structures in the management of topological stress.

J Biol Chem 2020 Apr 27;295(14):4684-4695. Epub 2020 Feb 27.

Genome Center, University of California, Davis, California 95616

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http://dx.doi.org/10.1074/jbc.REV119.006364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7135976PMC
April 2020

Interplay between DNA sequence and negative superhelicity drives R-loop structures.

Proc Natl Acad Sci U S A 2019 03 8;116(13):6260-6269. Epub 2019 Mar 8.

Department of Molecular and Cellular Biology, University of California, Davis, CA 95616;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1819476116
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http://dx.doi.org/10.1073/pnas.1819476116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442632PMC
March 2019

Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome.

Cell Syst 2017 03 22;4(3):344-356.e7. Epub 2017 Feb 22.

Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2017.01.013DOI Listing
March 2017

SIST: stress-induced structural transitions in superhelical DNA.

Bioinformatics 2015 Feb 4;31(3):421-2. Epub 2014 Oct 4.

UC Davis Genome Center and Department of Mathematics, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu657DOI Listing
February 2015

Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation.

Nucleic Acids Res 2014 Nov 21;42(20):12367-79. Epub 2014 Oct 21.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

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http://dx.doi.org/10.1093/nar/gku921DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4227770PMC
November 2014

Competitive superhelical transitions involving cruciform extrusion.

Nucleic Acids Res 2013 Nov 22;41(21):9610-21. Epub 2013 Aug 22.

UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/nar/gkt733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834812PMC
November 2013

The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli.

Nucleic Acids Res 2013 Jul 25;41(12):5965-77. Epub 2013 Apr 25.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 8600 Rockville Pike, Bethesda, MD 20894, USA.

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http://dx.doi.org/10.1093/nar/gkt308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695496PMC
July 2013

Theoretical analysis of competing conformational transitions in superhelical DNA.

PLoS Comput Biol 2012 26;8(4):e1002484. Epub 2012 Apr 26.

UC Davis Genome Center, University of California, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3343103PMC
August 2012

Superhelical duplex destabilization and the recombination position effect.

PLoS One 2011 9;6(6):e20798. Epub 2011 Jun 9.

Baylor College of Medicine, Houston, Texas, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020798PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111454PMC
November 2011

DNA stress and strain, in silico, in vitro and in vivo.

Phys Biol 2011 Jun 13;8(3):035011. Epub 2011 May 13.

Laboratory of Pathology, National Cancer Institute, 10 Center Drive, Building 10, Room 2N106, Bethesda, MD 20892-1500, USA.

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http://dx.doi.org/10.1088/1478-3975/8/3/035011DOI Listing
June 2011

Theoretical analysis of the stress induced B-Z transition in superhelical DNA.

PLoS Comput Biol 2011 Jan 20;7(1):e1001051. Epub 2011 Jan 20.

UC Davis Genome Center, University of California, Davis, Davis California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1001051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024258PMC
January 2011

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome.

Curr Genet 2010 Aug 6;56(4):321-40. Epub 2010 May 6.

Department of Mathematics, University of Chicago, IL 60637, USA.

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http://dx.doi.org/10.1007/s00294-010-0302-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2908449PMC
August 2010

Persistence lengths of DNA obtained from Brownian dynamics simulations.

J Phys Chem A 2009 Apr;113(16):4213-6

NASA Goddard Institute for Space Studies, New York, New York 10025, USA.

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http://dx.doi.org/10.1021/jp8107599DOI Listing
April 2009

Visualization of the detailed structure of plasmid DNA.

J Phys Chem B 2008 Dec;112(51):16788-92

The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka 567-0047, Japan.

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http://pubs.acs.org/doi/abs/10.1021/jp804634s
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http://dx.doi.org/10.1021/jp804634sDOI Listing
December 2008

Brownian dynamics of double-stranded DNA in periodic systems with discrete salt.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 Mar 31;77(3 Pt 1):031924. Epub 2008 Mar 31.

UC Davis Genome Center, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1103/PhysRevE.77.031924DOI Listing
March 2008

Superhelical destabilization in regulatory regions of stress response genes.

PLoS Comput Biol 2008 Jan;4(1):e17

UC Davis Genome Center, University of California Davis, Davis, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0040017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211533PMC
January 2008

OriDB: a DNA replication origin database.

Nucleic Acids Res 2007 Jan 25;35(Database issue):D40-6. Epub 2006 Oct 25.

Institute of Medical Science, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK.

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http://dx.doi.org/10.1093/nar/gkl758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1781122PMC
January 2007

Integration site choice of a feline immunodeficiency virus vector.

J Virol 2006 Sep;80(17):8820-3

Program in Gene Therapy, Department of Pediatrics, University of Iowa, Iowa City, 52242, 52242, USA.

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http://dx.doi.org/10.1128/JVI.00719-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1563849PMC
September 2006

Comment on "Can one predict DNA transcription start sites by studying bubbles?".

Phys Rev Lett 2006 Aug 2;97(5):059801; discussion 059802. Epub 2006 Aug 2.

Genome Center and Department of Mathematics, University of California-Davis, CA 95616, USA.

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http://dx.doi.org/10.1103/PhysRevLett.97.059801DOI Listing
August 2006

Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress.

BMC Bioinformatics 2006 May 5;7:248. Epub 2006 May 5.

Genome Center, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1186/1471-2105-7-248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1468432PMC
May 2006

SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes.

Nucleic Acids Res 2006 Jan;34(Database issue):D373-8

UC Davis Genome Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/nar/gkj007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347370PMC
January 2006

DNA mechanics.

Annu Rev Biomed Eng 2005 ;7:21-53

UC Davis Genome Center, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1146/annurev.bioeng.6.062403.132016DOI Listing
September 2005

Brownian dynamics simulations of sequence-dependent duplex denaturation in dynamically superhelical DNA.

J Chem Phys 2005 Sep;123(12):124911

Biophysics Graduate Group, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1063/1.2038767DOI Listing
September 2005

Susceptibility to superhelically driven DNA duplex destabilization: a highly conserved property of yeast replication origins.

PLoS Comput Biol 2005 Jun 24;1(1):e7. Epub 2005 Jun 24.

UC Davis Genome Center, University of California, Davis, USA.

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http://dx.doi.org/10.1371/journal.pcbi.0010007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1183513PMC
June 2005

The analysis of stress-induced duplex destabilization in long genomic DNA sequences.

J Comput Biol 2004 ;11(4):519-43

UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA.

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http://dx.doi.org/10.1089/cmb.2004.11.519DOI Listing
January 2005

Role for a region of helically unstable DNA within the Epstein-Barr virus latent cycle origin of DNA replication oriP in origin function.

Virology 2004 Oct;328(2):282-91

Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA.

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http://dx.doi.org/10.1016/j.virol.2004.07.023DOI Listing
October 2004

Transcription-driven twin supercoiling of a DNA loop: a Brownian dynamics study.

J Chem Phys 2004 Oct;121(16):8104-12

Biophysics Graduate Group, University of California, Davis, CA 95616, USA.

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http://dx.doi.org/10.1063/1.1799613DOI Listing
October 2004

Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters.

Genome Res 2004 Aug;14(8):1575-84

UC Davis Genome Center, University of California, Davis, California 95616, USA.

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http://dx.doi.org/10.1101/gr.2080004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC509266PMC
August 2004

Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism.

Mol Microbiol 2004 Jul;53(2):665-74

Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, CA 92697, USA.

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http://dx.doi.org/10.1111/j.1365-2958.2004.04147.xDOI Listing
July 2004

WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA.

Bioinformatics 2004 Jun 6;20(9):1477-9. Epub 2004 May 6.

UC Davis Genome Center, University of California, One Shields Avenue, Davis, CA 95616, USA.

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http://dx.doi.org/10.1093/bioinformatics/bth304DOI Listing
June 2004

DNA topology-mediated control of global gene expression in Escherichia coli.

Annu Rev Genet 2002 11;36:175-203. Epub 2002 Jun 11.

Department of Microbiology and Molecular Genetics, College of Medicine, University of California, Irvine, California 92697, USA.

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http://dx.doi.org/10.1146/annurev.genet.36.032902.111815DOI Listing
July 2003

Unpaired structures in SCA10 (ATTCT)n.(AGAAT)n repeats.

J Mol Biol 2003 Feb;326(4):1095-111

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.

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http://dx.doi.org/10.1016/s0022-2836(03)00037-8DOI Listing
February 2003

Multiple collagen I gene regulatory elements have sites of stress-induced DNA duplex destabilization and nuclear scaffold/matrix association potential.

J Cell Biochem 2002 ;84(3):484-96

Department of Structural and Molecular Biology, University of Aarhus, Denmark.

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March 2002

Extrusion of an imperfect palindrome to a cruciform in superhelical DNA: complete determination of energetics using a statistical mechanical model.

J Mol Biol 2002 Feb;316(3):563-81

Department of Biomathematical Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA.

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http://dx.doi.org/10.1006/jmbi.2001.5361DOI Listing
February 2002