Publications by authors named "Craig Benham"

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D
DNA superhelicity.
Craig J Benham

Nucleic Acids Res· January 2024

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Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation.
Cynthia Shaheen, Cameron Hastie, Kimberly Metera, Shane Scott, Zhi Zhang, Craig Benham

Nucleic Acids Res· March 2022

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FUBP1 and FUBP2 enforce distinct epigenetic setpoints for MYC expression in primary single murine cells.
Ying Zheng, Wendy Dubois, Craig Benham, Eric Batchelor, David Levens

Commun Biol· October 2020

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Emerging roles for R-loop structures in the management of topological stress.
Frederic Chedin, Craig J Benham

J Biol Chem· April 2020

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Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules.
Shane Scott, Cynthia Shaheen, Brendon McGuinness, Kimberly Metera, Fedor Kouzine, Craig J Benham

Nucleic Acids Res· July 2019

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Interplay between DNA sequence and negative superhelicity drives R-loop structures.
Robert Stolz, Shaheen Sulthana, Stella R Hartono, Maika Malig, Craig J Benham

Proc Natl Acad Sci U S A· March 2019

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Visualizing structure-mediated interactions in supercoiled DNA molecules.
Shane Scott, Zhi Ming Xu, Fedor Kouzine, Daniel J Berard, Cynthia Shaheen, Craig J Benham

Nucleic Acids Res· May 2018

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Permanganate/S1 Nuclease Footprinting Reveals Non-B DNA Structures with Regulatory Potential across a Mammalian Genome.
Fedor Kouzine, Damian Wojtowicz, Laura Baranello, Arito Yamane, Steevenson Nelson, Craig J Benham

Cell Syst· March 2017

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Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.
Thana Sutthibutpong, Christian Matek, Craig Benham, Gabriel G Slade, Agnes Noy

Nucleic Acids Res· November 2016

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SIST: stress-induced structural transitions in superhelical DNA.
Dina Zhabinskaya, Sally Madden, Craig J Benham

Bioinformatics· February 2015

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Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation.
Xiangjun Du, E Michael Gertz, Damian Wojtowicz, Dina Zhabinskaya, David Levens, Craig J Benham

Nucleic Acids Res· November 2014

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Expanding Flp-RMCE options: the potential of Recombinase Mediated Twin-Site Targeting (RMTT).
Soeren Turan, Junhua Qiao, Sally Madden, Craig Benham, Marina Kotz

Gene· August 2014

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Competitive superhelical transitions involving cruciform extrusion.
Dina Zhabinskaya, Craig J Benham

Nucleic Acids Res· November 2013

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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.
Xiangjun Du, Damian Wojtowicz, Albert A Bowers, David Levens, Craig J Benham

Nucleic Acids Res· July 2013

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Theoretical analysis of competing conformational transitions in superhelical DNA.
Dina Zhabinskaya, Craig J Benham

PLoS Comput Biol· August 2012

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S
Superhelical duplex destabilization and the recombination position effect.
Cheryl L Sershen, Joshua C Mell, Sally M Madden, Craig J Benham

PLoS One· November 2011

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DNA stress and strain, in silico, in vitro and in vivo.
David Levens, Craig J Benham

Phys Biol· June 2011

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Theoretical analysis of the stress induced B-Z transition in superhelical DNA.
Dina Zhabinskaya, Craig J Benham

PLoS Comput Biol· January 2011

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The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome.
Eva M Strawbridge, Gary Benson, Yevgeniy Gelfand, Craig J Benham

Curr Genet· August 2010

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GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes.
Peter F Hallin, Hans-Henrik Stærfeldt, Eva Rotenberg, Tim T Binnewies, Craig J Benham

Stand Genomic Sci· September 2009

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Persistence lengths of DNA obtained from Brownian dynamics simulations.
Steven P Mielke, Craig J Benham, Niels Grønbech-Jensen

J Phys Chem A· April 2009

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Visualization of the detailed structure of plasmid DNA.
Hiroyuki Tanaka, Steven P Mielke, Craig J Benham, Tomoji Kawai

J Phys Chem B· December 2008

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Brownian dynamics of double-stranded DNA in periodic systems with discrete salt.
Steven P Mielke, Niels Grønbech-Jensen, Craig J Benham

Phys Rev E Stat Nonlin Soft Matter Phys· March 2008

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Superhelical destabilization in regulatory regions of stress response genes.
Huiquan Wang, Craig J Benham

PLoS Comput Biol· January 2008

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O
OriDB: a DNA replication origin database.
Conrad A Nieduszynski, Shin-ichiro Hiraga, Prashanth Ak, Craig J Benham, Anne D Donaldson

Nucleic Acids Res· January 2007

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