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51

Denaturation: An Example of a Catastrophe

John J. Kozak and Craig J. Benham

Journal:

Proceedings of the National Academy of Sciences

Year:

1974

Language:

english

File:

PDF, 801 KB

english, 1974

52

Elastic Model of Supercoiling

Craig J. Benham

Journal:

Proceedings of the National Academy of Sciences

Year:

1977

Language:

english

File:

PDF, 1.06 MB

english, 1977

53

Torsional Stress and Local Denaturation in Supercoiled DNA

Craig J. Benham

Journal:

Proceedings of the National Academy of Sciences

Year:

1979

Language:

english

File:

PDF, 1.06 MB

english, 1979

54

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

Turan, Soeren, Qiao, Junhua, Madden, Sally, Benham, Craig, Kotz, Marina, Schambach, Axel, Bode, Juergen

Journal:

Year:

2014

Language:

english

File:

PDF, 1.82 MB

english, 2014

55

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

Levens, David, Benham, Craig J

Journal:

Physical Biology

Year:

2011

Language:

english

File:

PDF, 420 KB

english, 2011

56

Development of Ribozymes That Target Stathmin, a Major Regulator of the Mitotic Spindle

Mistry, Sucharita J., Benham, Craig J., Atweh, George F.

Journal:

Antisense and Nucleic Acid Drug Development

Year:

2001

Language:

english

File:

PDF, 270 KB

english, 2001

57

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

Benham, Craig J., Bi, Chengpeng

Journal:

Journal of Computational Biology

Year:

2004

Language:

english

File:

PDF, 223 KB

english, 2004

58

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

Fye, Richard M., Benham, Craig J.

Journal:

Physical Review E

Year:

1999

Language:

english

File:

PDF, 319 KB

english, 1999

59

Theoretical analysis of the helix-coil transition in positively superhelical DNA at high temperatures

Benham, Craig J.

Journal:

Physical Review E

Year:

1996

File:

PDF, 689 KB

1996

60

Comment on “Can One Predict DNA Transcription Start Sites by Studying Bubbles?”

Benham, Craig J., Singh, Rajiv R. P.

Journal:

Physical Review Letters

Year:

2006

Language:

english

File:

PDF, 84 KB

english, 2006

61

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

Mielke, Steven P., Fink, William H., Krishnan, V. V., Grønbech-Jensen, Niels, Benham, Craig J.

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 776 KB

english, 2004

62

Monte Carlo analysis of conformational transitions in superhelical DNA

Sun, Hongzhi, Mezei, Mihaly, Fye, Richard, Benham, Craig J.

Journal:

The Journal of Chemical Physics

Year:

1995

Language:

english

File:

PDF, 427 KB

english, 1995

63

Hen's Teeth and Whale's Feet: Generalized Characters and Their Compatibility

BENHAM, CRAIG, KANNAN, SAMPATH, PATERSON, MICHAEL, WARNOW, TANDY

Journal:

Journal of Computational Biology

Year:

1995

Language:

english

File:

PDF, 1.27 MB

english, 1995

64

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

Mielke, Steven P., Gro̸nbech-Jensen, Niels, Krishnan, V. V., Fink, William H., Benham, Craig J.

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 780 KB

english, 2005

65

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

Benham, Craig J.

Journal:

The Journal of Chemical Physics

Year:

1990

Language:

english

File:

PDF, 1.15 MB

english, 1990

66

Onset of writhing in circular elastic polymers

Benham, Craig J.

Journal:

Physical Review A

Year:

1989

Language:

english

File:

PDF, 179 KB

english, 1989

67

In vivo decay kinetic parameters of hammerhead ribozymes

Sioud, Mouldy, Opstad, Anne, Zhao, Jiang-Qin, Levitz, Ruth, Benham, Craig, Drlica, Karl

Journal:

Nucleic Acids Research

Year:

1994

Language:

english

File:

PDF, 410 KB

english, 1994

68

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

Benham, Craig J.

Journal:

Year:

1996

Language:

english

File:

PDF, 621 KB

english, 1996

69

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

Zhabinskaya, Dina, Benham, Craig J., Ioshikhes, Ilya

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.41 MB

english, 2012

70

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

Zhabinskaya, Dina, Benham, Craig J., Dokholyan, Nikolay V.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 713 KB

english, 2011

71

Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites

Bauer, Amy L., Hlavacek, William S., Unkefer, Pat J., Mu, Fangping, Benham, Craig

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 890 KB

english, 2010

72

Superhelical Destabilization in Regulatory Regions of Stress Response Genes

Wang, Huiquan, Benham, Craig J.

Journal:

PLoS Computational Biology

Year:

2008

Language:

english

File:

PDF, 611 KB

english, 2008

73

The influence of tertiary structural restraints on conformational transitions in superhelical DNA

Benham, Craig J.

Journal:

Nucleic Acids Research

Year:

1987

Language:

english

File:

PDF, 565 KB

english, 1987

74

Persistence Lengths of DNA Obtained from Brownian Dynamics Simulations †

Mielke, Steven P., Benham, Craig J., Grønbech-Jensen, Niels

Journal:

Journal of Physical Chemistry A

Year:

2009

Language:

english

File:

PDF, 62 KB

english, 2009

75

Sites of Predicted Stress-Induced DNA Duplex Destabilization Occur Preferentially at Regulatory Loci

Craig J. Benham

Journal:

Proceedings of the National Academy of Sciences

Year:

1993

Language:

english

File:

PDF, 1.11 MB

english, 1993

76

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes

Hallin, Peter F., Stærfeldt, Hans-Henrik, Rotenberg, Eva, Binnewies, Tim T., Benham, Craig J., Ussery, David W.

Journal:

Standards in Genomic Sciences

Year:

2009

Language:

english

File:

PDF, 2.31 MB

english, 2009

77

10.1090/s0002-9939-01-05913-5

Benham, Craig, Lin, Xiao-Song, Miller, David

Journal:

Proceedings of the American Mathematical Society

Year:

2001

Language:

english

File:

PDF, 142 KB

english, 2001

78

Subspaces of Knot Spaces

Craig Benham, Xiao-Song Lin and David Miller

Journal:

Proceedings of the American Mathematical Society

Year:

2001

Language:

english

File:

PDF, 268 KB

english, 2001

79

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

Sutthibutpong, Thana, Matek, Christian, Benham, Craig, Slade, Gabriel G., Noy, Agnes, Laughton, Charles, K. Doye, Jonathan P., Louis, Ard A., Harris, Sarah A.

Journal:

Nucleic Acids Research

Year:

2016

Language:

english

File:

PDF, 1.55 MB

english, 2016

80

Single Molecule Visualization of Topology-Mediated Interactions in Supercoiled DNA

Scott, Shane, Ming Xu, Zhi, Kouzine, Fedor, Berard, Daniel, Shaheen, Cynthia, Saunders, Laura, Gravel, Barbara, Leroux, Catherine, Cayen-Cyr, Christopher, Levens, David, Benham, Craig, Leslie, Sabrina

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 42 KB

english, 2017

81

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

Kouzine, Fedor, Wojtowicz, Damian, Baranello, Laura, Yamane, Arito, Nelson, Steevenson, Resch, Wolfgang, Kieffer-Kwon, Kyong-Rim, Benham, Craig J., Casellas, Rafael, Przytycka, Teresa M., Levens, Davi

Journal:

Year:

2017

Language:

english

File:

PDF, 3.37 MB

english, 2017

82

Erratum: Monte Carlo analysis of conformational transitions in superhelical DNA [J. Chem. Phys. 103 , 8653 (1995)]

Sun, Hongzhi, Mezei, Mihaly, Fye, Richard, Benham, Craig

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 232 KB

english, 1996

83

Visualizing structure-mediated interactions in supercoiled DNA molecules

Scott, Shane, Xu, Zhi Ming, Kouzine, Fedor, Berard, Daniel J, Shaheen, Cynthia, Gravel, Barbara, Saunders, Laura, Hofkirchner, Alexander, Leroux, Catherine, Laurin, Jill, Levens, David, Benham, Craig

Journal:

Nucleic Acids Research

Year:

2018

Language:

english

File:

PDF, 1.09 MB

english, 2018

84

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

Ak, Prashanth, Benham, Craig J

Journal:

PLoS Computational Biology

Year:

2005

Language:

english

File:

PDF, 238 KB

english, 2005

85

Superhelical Duplex Destabilization and the Recombination Position Effect

Sershen, Cheryl L., Mell, Joshua C., Madden, Sally M., Benham, Craig J., Lustig, Arthur J.

Journal:

Year:

2011

Language:

english

File:

PDF, 427 KB

english, 2011

86

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

Scott, Shane, Shaheen, Cynthia, McGuinness, Brendon, Metera, Kimberly, Kouzine, Fedor, Levens, David, Benham, Craig J, Leslie, Sabrina

Journal:

Nucleic Acids Research

Year:

2019

Language:

english

File:

PDF, 983 KB

english, 2019

87

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

Scott, Shane, Shaheen, Cynthia, McGuinness, Brendon, Metera, Kimberly, Kouzine, Fedor, Levens, David, Benham, Craig J, Leslie, Sabrina

Journal:

Nucleic Acids Research

Year:

2019

File:

PDF, 983 KB

2019

88

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

Miller, John H., Nelson, John M., Fleck, Earl W., Benham, Craig J.

Journal:

Applied Occupational and Enviromental Hygiene

Year:

1996

Language:

english

File:

PDF, 524 KB

english, 1996

89

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

Chedin, Frederic, Benham, Craig J

Journal:

Journal of Biological Chemistry

Year:

2020

File:

PDF, 939 KB

2020

90

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

Zheng, Ying, Dubois, Wendy, Benham, Craig, Batchelor, Eric, Levens, David

Journal:

Communications Biology

Year:

2020

File:

PDF, 1.92 MB

2020

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