Biochemistry Option Divisions of Biology and Chemistry and Chemical (2009)
Christopher A. Voigt, D. Benjamin Gordon, Stephen L. Mayo, Engineering California, Howard Hughes Medical
A goal of computational protein design is to compute an amino acid sequence de novo that will fold into a de®ned backbone structure (Street & Mayo, 1999). This is adif®cult task, as protein...
Biochemistry Option Divisions of Biology and Chemistry and Chemical (2008)
Christopher A. Voigt, D. Benjamin Gordon, Stephen L. Mayo, Engineering California, Howard Hughes Medical
A goal of computational protein design is to compute an amino acid sequence de novo that will fold into a de®ned backbone structure (Street & Mayo, 1999). This is a dif®cult task, as protein...
BIOINFORMATICS ORIGINAL PAPER Sequence analysis (2008)
Kenzie D. Macisaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, ...
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data Vol. 22 no. 4 2006, pages 423–429 doi:10.1093/bioinformatics/bti815
Introduction Exact Rotamer Optimization for Protein Design (2008)
D. Benjamin Gordon, Geoffrey K. Hom, Stephen L. Mayo, Niles A. Pierce
Networks in Saccharomyces cerevisiae (2008)
S. Nicholson, S. Some, B. Kone, J. Clim, Tong Ihn Lee, Nicola J. Rinaldi, ...
transport (32). The model was also used for tracer forecasts during the MINOS campaign. 40. E. Roeckner et al. “The atmospheric general circulation model ECHAM-4: Model description and simulation...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. (2008)
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein-DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets (2008)
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...
An improved map of conserved regulatory sites for Saccharomyces cerevisiae (2006)
MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
Abstract Background The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was...
Kenzie D. Macisaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, ...
Motivation: Genome-wide chromatin-immunoprecipitation (ChIPchip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover...
Gordon, D. Benjamin, Nekludova, Lena, McCallum, Scott, Fraenkel, Ernest
Summary: TAMO (Tools for Analysis of MOtifs) is an object-oriented computational framework for interpreting transcriptional regulation using DNA-sequence motifs. To simplify the application of...
Gordon, D. Benjamin, Nekludova, Lena, McCallum, Scott, Fraenkel, Ernest
Summary: TAMO (Tools for Analysis of MOtifs) is an object-oriented computational framework for interpreting transcriptional regulation using DNA-sequence motifs. To simplify the application of...
MacIsaac, Kenzie D., Gordon, D. Benjamin, Nekludova, Lena, Odom, Duncan T., Schreiber, Joerg, Gifford, David K., ...
Motivation: Genome-wide chromatin-immunoprecipitation (ChIP-chip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover...
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets
Johnson, David S., Li, Wei, Gordon, D. Benjamin, Bhattacharjee, Arindam, Curry, Bo, Ghosh, Jayati, ...
The most widely used method for detecting genome-wide protein–DNA interactions is chromatin immunoprecipitation on tiling microarrays, commonly known as ChIP-chip. Here, we conducted the first...