C. Benham

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WRITHING AND LINKING DENSITIES FOR CLOSED, CIRCULAR DNA

C. Benham, David Miller, 2000 .

Loss of FBP function arrests cellular proliferation and extinguishes c‐myc expression

D. Levens, C. Benham, L. He, 2000, The EMBO journal.

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes

Eva Rotenberg, Craig J. Benham, Peter F. Hallin, 2009, Standards in genomic sciences.

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

Tetsuo Ashizawa, Yuri L Lyubchenko, R. Sinden, 2003, Journal of molecular biology.

Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules

D. Levens, C. Benham, K. Metera, 2019, bioRxiv.

Single-molecule visualization of the effects of ionic strength and crowding on structure-mediated interactions in supercoiled DNA molecules

D. Levens, C. Benham, K. Metera, 2019, bioRxiv.

Denaturation: an example of a catastrophe. III. Phase diagrams for multistate transformations.

J. J. Kozak, C. Benham, 1977, Journal of theoretical biology.

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

F. Chédin, C. Benham, 2020, The Journal of Biological Chemistry.

In vivo decay kinetic parameters of hammerhead ribozymes.

R. Levitz, C. Benham, K. Drlica, 1994, Nucleic acids research.

Visualizing structure-mediated interactions in supercoiled DNA molecules

D. Levens, C. Benham, C. Leroux, 2018, bioRxiv.

Visualizing structure-mediated interactions in supercoiled DNA molecules

D. Levens, C. Benham, C. Leroux, 2018, bioRxiv.

Competitive superhelical transitions involving cruciform extrusion

C. Benham, Dina Zhabinskaya, 2013, Nucleic acids research.

Transcriptional augmentation: modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements).

C. Benham, C. Mielke, J. Bode, 2000, Critical reviews in eukaryotic gene expression.

Fatal connections: When DNA ends meet on the nuclear matrix

C. Benham, R. Marschalek, R. Strick, 2000, Journal of cellular biochemistry. Supplement.

Environmental influences on DNA superhelicity. The effect of ionic strength on superhelix conformation in solution.

C. Benham, G. Brady, M. Satkowski, 1987, Journal of molecular biology.

Expanding Flp-RMCE options: the potential of Recombinase Mediated Twin-Site Targeting (RMTT).

A. Schambach, C. Benham, J. Bode, 2014, Gene.

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

T. Przytycka, D. Levens, C. Benham, 2017, Cell systems.

Persistence lengths of DNA obtained from Brownian dynamics simulations.

S. P. Mielke, Niels Grønbech-Jensen, C. Benham, 2009, The journal of physical chemistry. A.

Mathematics of DNA structure, function and interactions

D. Swigon, S. Harvey, W. Olson, 2009 .

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

C. Benham, Rajiv R. P. Singh, 2006, Physical review letters.

Superhelical Duplex Destabilization and the Recombination Position Effect

Cheryl L. Sershen, J. Mell, C. Benham, 2011, PloS one.

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

A. Schäffer, E. Gertz, T. Przytycka, 2014, Nucleic acids research.

X-ray scattering from randomly oriented superhelices. Circular superhelical DNA.

C. Benham, G. Brady, D. B. Fein, 1980, Biophysical journal.

Theoretical analysis of transitions between B- and Z-conformations in torsionally stressed DNA

C. Benham, 1980, Nature.

Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation

A. Louis, C. Benham, C. Laughton, 2016, Nucleic acids research.

Germ-line transcripts of the immunoglobulin lambda J-C clusters in the mouse: characterization of the initiation sites and regulatory elements.

C. Benham, S. Weiss, J. Bode, 2001, Molecular immunology.

Statistical mechanical analysis of competing conformational transitions in superhelical DNA.

C. Benham, 1983, Cold Spring Harbor symposia on quantitative biology.

Correlations between Scaffold/matrix Attachment Region (s/mar) Binding Activity and Dna Duplex Destabilization Energy

Chengpeng Bi, Sandra Götze, C. Benham, 2022 .

From DNA structure to gene expression: mediators of nuclear compartmentalization and dynamics

H. Heng, S. Krawetz, C. Benham, 2004, Chromosome Research.

Mitotic stability of an episomal vector containing a human scaffold/matrix-attached region is provided by association with nuclear matrix

A. Baiker, H. Lipps, C. Benham, 2000, Nature Cell Biology.

An influenza virus containing nine different RNA segments.

C. Benham, P. Palese, M. Enami, 1991, Virology.

Analysis of biomathematically predicted Scaffold / Matrix Attached Regions (S/MARs) by three different approaches

Jürgen Bode, Matthias Frisch, S. Goetze, 2001, German Conference on Bioinformatics.

The cylindrical Poisson–Boltzmann equation. I. Transformations and general solutions

C. Benham, 1983 .

FUBP1 and FUBP2 enforce distinct epigenetic setpoints for MYC expression in primary single murine cells

D. Levens, Eric Batchelor, C. Benham, 2020, Communications biology.

AT-rich Islands in Genomic DNA as a Novel Target for AT-specific DNA-reactive Antitumor Drugs* 210

C. Benham, S. Hardies, K. Rodriguez, 2001, The Journal of Biological Chemistry.

Integration Site Choice of a Feline Immunodeficiency Virus Vector

T. Casavant, T. Scheetz, B. Davidson, 2006, Journal of Virology.

NOTES Integration Site Choice of a Feline Immunodeﬁciency Virus Vector

T. Casavant, T. Scheetz, B. Davidson, 2006 .

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

Craig J. Benham, Dina Zhabinskaya, C. Benham, 2012, PLoS Comput. Biol..

Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions.

C. Benham, T. Kohwi-Shigematsu, J. Bode, 1997, Journal of molecular biology.

Sequential determination of ligands binding to discrete components in heterogeneous mixtures by iterative panning and blocking (IPAB).

D. Thaler, C. Benham, B. Messmer, 2000, Journal of molecular biology.

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

D. Levens, C. Benham, 2011, Physical biology.

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

Teresa M. Przytycka, Craig J. Benham, Damian Wojtowicz, 2013, Nucleic acids research.

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

M. Malig, F. Chédin, C. Benham, 2019, Proceedings of the National Academy of Sciences.

OriDB: a DNA replication origin database

Craig J. Benham, Prashanth Ak, Conrad A. Nieduszynski, 2006, Nucleic Acids Res..

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

Morten O. Christensen, C. Benham, C. Mielke, 2002, Journal of cellular biochemistry.

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

G. W. Hatfield, G Wesley Hatfield, C. Benham, 2002, Annual review of genetics.

Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation

B. Munsky, D. Levens, C. Benham, 2022, Nucleic acids research.

Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA

Craig J. Benham, Richard M. Fye, C. Benham, 1999 .

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

G. W. Hatfield, G Wesley Hatfield, Kimberly A. Aeling, 2004, Molecular microbiology.

The positive aspects of stress: strain initiates domain decondensation (SIDD).

C. Benham, S. Goetze, A. Gluch, 2006, Briefings in functional genomics & proteomics.

Theoretical analysis of competitive conformational transitions in torsionally stressed DNA.

C. Benham, C J Benham, 1981, Journal of molecular biology.

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

C. Benham, W. Bauer, Craig J Benham, 2002, Journal of molecular biology.

Disulfide bonding patterns and protein topologies

C. Benham, M. Saleet Jafri, 1993, Protein science : a publication of the Protein Society.

Activation of Gene Expression by a Novel DNA Structural Transmission Mechanism That Requires Supercoiling-induced DNA Duplex Destabilization in an Upstream Activating Sequence*

Craig J. Benham, G. W. Hatfield, G. Wesley Hatfield, 1998, The Journal of Biological Chemistry.

Peripheral doublet microtubules and wave generation in eukaryotic flagella.

P. Crowley, C. Benham, J. Morgan, 1981, Journal of theoretical biology.

Geometry and mechanics of DNA superhelicity

C. Benham, 1983, Biopolymers.

X-ray scattering from the superhelix in circular DNA.

C. Benham, G. Brady, D. Foos, 1983, Proceedings of the National Academy of Sciences of the United States of America.

Computational and in vitro analysis of destabilized DNA regions in the interferon gene cluster: potential of predicting functional gene domains.

C. Benham, S. Goetze, A. Gluch, 2003, Biochemistry.

Computational and in Vitro Analysis of Destabilized DNA Regions in the Interferon Gene Cluster: Potential of Predicting Functional Gene Domains †

C. Benham, S. Goetze, A. Gluch, 2003 .

Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA

Craig J. Benham, Dina Zhabinskaya, C. Benham, 2011, PLoS Comput. Biol..

Theoretical analysis of heteropolymeric transitions in superhelical DNA molecules of specified sequence

Craig J. Benham, C. Benham, 1990 .

Analysis of the Structure of a Natural Alternating d(TA)n Sequence in Yeast Chromatin

J. Pérez-Ortín, C. Benham, A. Aranda, 1997, Yeast.

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

S. P. Mielke, Niels Grønbech-Jensen, C. Benham, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

Kinetics of reactions involving DNA containing stress‐induced single‐stranded regions

C. Benham, 1980, Biopolymers.

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

G. Benson, C. Benham, Y. Gelfand, 2010, Current Genetics.

Superhelical Destabilization in Regulatory Regions of Stress Response Genes

Huiquan Wang, Craig J. Benham, C. Benham, 2008, PLoS Comput. Biol..

Superhelically Destabilized Sites in the E. coli Genome: Implications for Promoter Prediction in Prokaryotes

Huiquan Wang, Craig J. Benham, C. Benham, 2004, German Conference on Bioinformatics.

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

S. P. Mielke, Niels Grønbech-Jensen, V. Krishnan, 2004, The Journal of chemical physics.

S. P. Mielke, C. Benham, 2005, Annual review of biomedical engineering.

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

Chengpeng Bi, C. Benham, Chengpeng Bi, 2004, Bioinformatics.

An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled.

C. Benham, D. Clark, C J Benham, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions.

C. Benham, C J Benham, Craig J Benham, 1996, Journal of molecular biology.

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

Niels Grønbech-Jensen, S. P. Mielke, Niels Grønbech-Jensen, 2005, The Journal of chemical physics.

Torsional stress and local denaturation in supercoiled DNA.

C. Benham, C J Benham, 1979, Proceedings of the National Academy of Sciences of the United States of America.

Stable cruciform formation at inverted repeat sequences in supercoiled DNA

C. Benham, 1982, Biopolymers.

Energetics of the strand separation transition in superhelical DNA.

C. Benham, C J Benham, 1992, Journal of molecular biology.

Susceptibility to Superhelically Driven DNA Duplex Destabilization: A Highly Conserved Property of Yeast Replication Origins

Craig J. Benham, Prashanth Ak, C. Benham, 2005, PLoS Comput. Biol..

SIST: stress-induced structural transitions in superhelical DNA

Craig J. Benham, Dina Zhabinskaya, Sally Madden, 2015, Bioinform..

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

Huiquan Wang, Craig J. Benham, Miroslava Kaloper, 2005, Nucleic Acids Res..

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

C. Benham, J. Hearing, Craig J Benham, 2004, Virology.

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

M. Noordewier, C. Benham, Craig J Benham, 2004, Genome research.

The role of the stress resultant in determining mechanical equilibria of superhelical DNA.

C. Benham, 1987, Biopolymers.

Negative supercoiling increases the sensitivity of plasmid DNA to single-strand break induction by X-rays.

J. Miller, C. Benham, C. Swenberg, 1991, International Journal of Radiation Biology.

Effects of Torsional Stress on the Interaction of DNA with Radiation and Chemicals

Craig J. Benham, J. M. Nelson, John H. Miller, 1996 .

Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci.

C. Benham, C J Benham, Craig J. Benham, 1993, Proceedings of the National Academy of Sciences of the United States of America.

The equilibrium statistical mechanics of the helix–coil transition in torsionally stressed DNA

Craig J. Benham, C. Benham, 1980 .

Development of ribozymes that target stathmin, a major regulator of the mitotic spindle.

C. Benham, G. Atweh, S. Mistry, 2001, Antisense & nucleic acid drug development.

An elastic model of the large‐scale structure of duplex DNA

C. Benham, 1979, Biopolymers.

Elastic model of supercoiling.

C. Benham, 1977, Proceedings of the National Academy of Sciences of the United States of America.

The Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences

Chengpeng Bi, Craig J. Benham, C. Benham, 2004, J. Comput. Biol..

Denaturation: an example of a catastrophe.

J. J. Kozak, C. Benham, C J Benham, 1974, Proceedings of the National Academy of Sciences of the United States of America.

The approximate algorithm for analysis of the strand separation transition in superhelical DNA using nearest neighbor energetics

Chengpeng Bi, Craig J. Benham, C. Benham, 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

Computation of DNA structural variability - a new predictor of DNA regulatory regions

Craig J. Benham, C. Benham, 1996, Comput. Appl. Biosci..

OriDB : a DNA replication origin database

Conrad A. Nieduszynski, C. Benham, A. Donaldson, 2006 .

Stress-Induced DNA Duplex Destabilization in Transcriptional Initiation

Craig J. Benham, C. Benham, 2000, Pacific Symposium on Biocomputing.

Denaturation: an example of a catastrophe. II. Two-state transitions.

C. Benham, 1976, Journal of theoretical biology.

Catastrophes in statistical biophysics

J. J. Kozak, C. Benham, 1978 .

SIST: stress-induced structural transitions in superhelical DNA

C. Benham, Dina Zhabinskaya, Sally Madden, 2015, Bioinform..

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

G. W. Hatfield, Kimberly A. Aeling, Reid C. Johnson, 2004, Molecular microbiology.