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

af Benham Craig J, Wang Huiquan
Udgivet 2006-05-01

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

af Ak, Prashanth, Benham, Craig J
Udgivet 2005

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

af Wang, Huiquan, Benham, Craig J
Udgivet 2006

Superhelical Destabilization in Regulatory Regions of Stress Response Genes

af Wang, Huiquan, Benham, Craig J
Udgivet 2008

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

af Zhabinskaya, Dina, Benham, Craig J.
Udgivet 2011

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

af Zhabinskaya, Dina, Benham, Craig J.
Udgivet 2012

Competitive superhelical transitions involving cruciform extrusion

af Zhabinskaya, Dina, Benham, Craig J.
Udgivet 2013

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

af Chedin, Frederic, Benham, Craig J.
Udgivet i J Biol Chem (2020)

Denaturation: An Example of a Catastrophe

af Kozak, John J., Benham, Craig J.
Udgivet 1974

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

af Wang, Huiquan, Noordewier, Michiel, Benham, Craig J.
Udgivet 2004

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

af Wang, Huiquan, Kaloper, Miroslava, Benham, Craig J.
Udgivet 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

af Leblanc, Benoit P., Benham, Craig J., Clark, David J.
Udgivet 2000

The distribution of inverted repeat sequences in the Saccharomyces cerevisiae genome

af Strawbridge, Eva M., Benson, Gary, Gelfand, Yevgeniy, Benham, Craig J.
Udgivet 2010

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

af Zheng, Ying, Dubois, Wendy, Benham, Craig, Batchelor, Eric, Levens, David
Udgivet i Commun Biol (2020)

Superhelical Duplex Destabilization and the Recombination Position Effect

af Sershen, Cheryl L., Mell, Joshua C., Madden, Sally M., Benham, Craig J.
Udgivet 2011

Mathematics of DNA structure, function and interactions

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

OriDB: a DNA replication origin database

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

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

af Stolz, Robert, Sulthana, Shaheen, Hartono, Stella R., Malig, Maika, Benham, Craig J., Chedin, Frederic
Udgivet i 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

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

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

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