BIPAD: A web server for modeling bipartite sequence elements (2006)
Abstract Background Many dimeric protein complexes bind cooperatively to families of bipartite nucleic acid sequence elements, which consist of pairs of conserved half-site sequences separated by...
Tandem machine learning for the identification of genes regulated by transcription factors (2005)
Dinakarpandian, Deendayal, Raheja, Venetia, Mehta, Saumil, Schuetz, Erin G, Rogan, Peter K
Abstract Background The identification of promoter regions that are regulated by a given transcription factor has traditionally relied upon the identification and distributions of binding sites...
Bmc Bioinformatics, Deendayal Dinakarp, Venetia Raheja, Saumil Mehta, Erin G Schuetz, Peter K Rogan, ...
Research article Tandem machine learning for the identification of genes regulated by transcription factors
Newkirk, Heather L., Knoll, Joan H.M., Rogan, Peter K.
Cross-hybridization of repetitive sequences in genomic and expression arrays is reported to be suppressed with repeat-blocking nucleic acids (Cot-1 DNA). Contrary to expectation, we demonstrated that...
PK: Bipartite pattern discovery by entropy minimization-based multiple local alignment (2004)
Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel...
Bipartite pattern discovery by entropy minimization-based multiple local alignment (2004)
Bi, Chengpeng, Rogan, Peter K.
Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel...
Gadiraju, Sashidhar, Vyhlidal, Carrie A, Leeder, J Steven, Rogan, Peter K
Abstract Background We present Delila-genome , a software system for identification, visualization and analysis of protein binding sites in complete genome sequences. Binding sites are predicted by...
BioMed Central Open Access (2003)
Bmc Bioinformatics, Sashidhar Gadiraju, Carrie A Vyhlidal, J Steven Leeder, Peter K Rogan
Software Genome-wide prediction, display and refinement of binding sites with information theory-based models
Mottez, Estelle, Rogan, Peter K., Manuelidis, Laura
A clone of 7.1kb corresponding to the mouse L1 interspersed repeat family was selected for homology to a human interspersed repeat. This clone fairly represents mouse genomic members. Mapping of the...
Genome-wide prediction, display and refinement of binding sites with information theory-based models
Gadiraju, Sashidhar, Vyhlidal, Carrie A, Leeder, J Steven, Rogan, Peter K
Sequence-Based Design of Single-Copy Genomic DNA Probes for Fluorescence In Situ Hybridization
Rogan, Peter K., Cazcarro, Patricia M., Knoll, Joan H.M.
Chromosomal rearrangements are frequently monitored by fluorescence in situ hybridization (FISH) using large, recombinant DNA probes consisting of contiguous genomic intervals that are often distant...
Bipartite pattern discovery by entropy minimization-based multiple local alignment
Bi, Chengpeng, Rogan, Peter K.
Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel...
Tandem machine learning for the identification of genes regulated by transcription factors
Dinakarpandian, Deendayal, Raheja, Venetia, Mehta, Saumil, Schuetz, Erin G, Rogan, Peter K
Vockley, Jerry, Rogan, Peter K., Anderson, Bambi D., Willard, Jan, Seelan, Ratnam S., Smith, David I., ...
Isovaleric acidemia (IVA) is a recessive disorder caused by a deficiency of isovaleryl-CoA dehydrogenase (IVD). We have reported elsewhere nine point mutations in the IVD gene in fibroblasts of...
Newkirk, Heather L., Knoll, Joan H.M., Rogan, Peter K.
Cross-hybridization of repetitive sequences in genomic and expression arrays is reported to be suppressed with repeat-blocking nucleic acids (Cot-1 DNA). Contrary to expectation, we demonstrated that...
Genome-wide prediction, display and refinement of binding sites with information theory-based models
Gadiraju, Sashidhar, Vyhlidal, Carrie A, Leeder, J Steven, Rogan, Peter K
Sequence-Based Design of Single-Copy Genomic DNA Probes for Fluorescence In Situ Hybridization
Rogan, Peter K., Cazcarro, Patricia M., Knoll, Joan H.M.
Chromosomal rearrangements are frequently monitored by fluorescence in situ hybridization (FISH) using large, recombinant DNA probes consisting of contiguous genomic intervals that are often distant...
Bipartite pattern discovery by entropy minimization-based multiple local alignment
Bi, Chengpeng, Rogan, Peter K.
Many multimeric transcription factors recognize DNA sequence patterns by cooperatively binding to bipartite elements composed of half sites separated by a flexible spacer. We developed a novel...
Tandem machine learning for the identification of genes regulated by transcription factors
Dinakarpandian, Deendayal, Raheja, Venetia, Mehta, Saumil, Schuetz, Erin G, Rogan, Peter K
Vockley, Jerry, Rogan, Peter K., Anderson, Bambi D., Willard, Jan, Seelan, Ratnam S., Smith, David I., ...
Isovaleric acidemia (IVA) is a recessive disorder caused by a deficiency of isovaleryl-CoA dehydrogenase (IVD). We have reported elsewhere nine point mutations in the IVD gene in fibroblasts of...
Newkirk, Heather L., Knoll, Joan H.M., Rogan, Peter K.
Cross-hybridization of repetitive sequences in genomic and expression arrays is reported to be suppressed with repeat-blocking nucleic acids (Cot-1 DNA). Contrary to expectation, we demonstrated that...
Bloom Syndrome and Maternal Uniparental Disomy for Chromosome 15
Woodage, Trevor, Prasad, Madhuri, Dixon, Joanne W., Selby, Roslyn E., Romain, Dennis R., Columbano-Green, Letizia M., ...
Bloom syndrome (BS) is an autosomal recessive disorder characterized by increases in the frequency of sister-chromatid exchange and in the incidence of malignancy. Chromosome-transfer studies have...