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

od Benham Craig J, Wang Huiquan
Wydane 2006-05-01

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

od Ak, Prashanth, Benham, Craig J
Wydane 2005

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

od Wang, Huiquan, Benham, Craig J
Wydane 2006

Superhelical Destabilization in Regulatory Regions of Stress Response Genes

od Wang, Huiquan, Benham, Craig J
Wydane 2008

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

od Zhabinskaya, Dina, Benham, Craig J.
Wydane 2011

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

od Zhabinskaya, Dina, Benham, Craig J.
Wydane 2012

Competitive superhelical transitions involving cruciform extrusion

od Zhabinskaya, Dina, Benham, Craig J.
Wydane 2013

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

od Chedin, Frederic, Benham, Craig J.
Wydane w J Biol Chem (2020)

Denaturation: An Example of a Catastrophe

od Kozak, John J., Benham, Craig J.
Wydane 1974

Stress-Induced DNA Duplex Destabilization (SIDD) in the E. coli Genome: SIDD Sites Are Closely Associated With Promoters

od Wang, Huiquan, Noordewier, Michiel, Benham, Craig J.
Wydane 2004

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

od Wang, Huiquan, Kaloper, Miroslava, Benham, Craig J.
Wydane 2006

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

od Leblanc, Benoit P., Benham, Craig J., Clark, David J.
Wydane 2000

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

od Strawbridge, Eva M., Benson, Gary, Gelfand, Yevgeniy, Benham, Craig J.
Wydane 2010

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

od Zheng, Ying, Dubois, Wendy, Benham, Craig, Batchelor, Eric, Levens, David
Wydane w Commun Biol (2020)

Superhelical Duplex Destabilization and the Recombination Position Effect

od Sershen, Cheryl L., Mell, Joshua C., Madden, Sally M., Benham, Craig J.
Wydane 2011

Mathematics of DNA structure, function and interactions

od Benham, Craig John., Harvey, Stephen., Olson, Wilma K., Sumners, De Witt., Swigon, David.
Wydane 2009

OriDB: a DNA replication origin database

od Nieduszynski, Conrad A., Hiraga, Shin-ichiro, Ak, Prashanth, Benham, Craig J., Donaldson, Anne D.
Wydane 2007

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

od Stolz, Robert, Sulthana, Shaheen, Hartono, Stella R., Malig, Maika, Benham, Craig J., Chedin, Frederic
Wydane w Proc Natl Acad Sci U S A (2019)

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

od Du, Xiangjun, Wojtowicz, Damian, Bowers, Albert A., Levens, David, Benham, Craig J., Przytycka, Teresa M.
Wydane 2013

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

od He, Liusheng, Liu, Juhong, Collins, Irene, Sanford, Suzanne, O'Connell, Brian, Benham, Craig J., Levens, David
Wydane 2000