Craig J. Benham

Publication Activity (10 Years)

Years Active: 1995-2015
Publications (10 Years): 1

Top Topics

Theoretical Analysis

Top Venues

PLoS Comput. Biol.

Publications

Dina Zhabinskaya, Sally Madden, Craig J. Benham
SIST: stress-induced structural transitions in superhelical DNA. Bioinform. 31 (3) (2015)
Dina Zhabinskaya, Craig J. Benham
Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA. PLoS Comput. Biol. 8 (4) (2012)
Dina Zhabinskaya, Craig J. Benham
Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA. PLoS Comput. Biol. 7 (1) (2011)
Huiquan Wang, Craig J. Benham
Superhelical Destabilization in Regulatory Regions of Stress Response Genes. PLoS Comput. Biol. 4 (1) (2008)
Conrad A. Nieduszynski, Shin-ichiro Hiraga, Prashanth Ak, Craig J. Benham, Anne D. Donaldson
OriDB: a DNA replication origin database. Nucleic Acids Res. 35 (Database-Issue) (2007)
Huiquan Wang, Miroslava Kaloper, Craig J. Benham
SIDDBASE: a database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes. Nucleic Acids Res. 34 (Database-Issue) (2006)
Huiquan Wang, Craig J. Benham
Promoter prediction and annotation of microbial genomes based on DNA sequence and structural responses to superhelical stress. BMC Bioinform. 7 (2006)
Huiquan Wang, Craig J. Benham
Annotation of Promoter Regions in Microbial Genomes Based on DNA Structural and Sequence Properties. Systems Biology and Regulatory Genomics (2005)
Prashanth Ak, Craig J. Benham
Susceptibility to Superhelically Driven DNA Duplex Destabilization: A Highly Conserved Property of Yeast Replication Origins. PLoS Comput. Biol. 1 (1) (2005)
Huiquan Wang, Craig J. Benham
Superhelically Destabilized Sites in the E. coli Genome: Implications for Promoter Prediction in Prokaryotes. German Conference on Bioinformatics (2004)
Craig J. Benham, Chengpeng Bi
The Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences. J. Comput. Biol. 11 (4) (2004)
Chengpeng Bi, Craig J. Benham
The Approximate Algorithm for Analysis of the Strand Separation Transition in Super helical DNA Using Nearest Neighbor Energetics. CSB (2003)
S. Goetze, A. Knopp, Craig J. Benham, Stephen A. Krawetz, Jürgen Bode
Biomathematical and in vitro analysis of destabilized regions in the interferon gene cluster. German Conference on Bioinformatics (2001)
A. Knopp, S. Goetze, Craig J. Benham, Matthias Frisch, Stephen A. Krawetz, Jürgen Bode
Analysis of biomathematically predicted Scaffold / Matrix Attached Regions (S/MARs) by three different approaches. German Conference on Bioinformatics (2001)
Craig J. Benham
In Silico Biology: The emergence of a new biological methodology. HERCMA (2001)
Craig J. Benham
Stress-Induced DNA Duplex Destabilization in Transcriptional Initiation. Pacific Symposium on Biocomputing (2001)
Craig J. Benham
The topologically driven strand separation transition in DNA - methods of analysis and biological significance. Mathematical Support for Molecular Biology (1998)
Richard M. Fye, Craig J. Benham
A formally exact method to numerically analyze local denaturation in superhelical DNA. RECOMB (1998)
Gabriela Hristescu, Craig J. Benham, Martin Farach
DNA Strand Separation Prediction: A Parallel Implementation. PDPTA (1997)
Craig J. Benham
Computation of DNA structural variability - a new predictor of DNA regulatory regions. Comput. Appl. Biosci. 12 (5) (1996)
Craig J. Benham
Sites of Superhelical DNA Duplex Destabilization occour at Specific Regulatory Regions. German Conference on Bioinformatics (1996)
Craig J. Benham, Sampath Kannan, Michael Paterson, Tandy J. Warnow
Hen's Teeth and Whale's Feet: Generalized Characters and Their Compatibility. J. Comput. Biol. 2 (4) (1995)
Craig J. Benham, Sampath Kannan, Tandy J. Warnow
Of Chicken Teeth and Mouse Eyes, or Generalized Character Compatibility. CPM (1995)