Bmc Bioinformatics, Nameeta Shah, Michael V Teplitsky, Simon Minovitsky, Len A Pennacchio, Philip Hugenholtz, ...
Software SNP-VISTA: An interactive SNP visualization tool
Multiple Whole Genome Alignments and Novel Biomedical Applications at the VISTA Portal (2008)
Brudno, Michael, Poliakov, Alexander, Minovitsky, Simon, Ratnere, Igor, Dubchak, Inna
The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the...
Shengyin Gu, Iain Anderson, Victor Kunin, Michael Cipriano, Simon Minovitsky, Nina Amenta, ...
Summary: We describe a general multiplatform exploratory tool called TreeQ-Vista, designed for presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic...
Shengyin Gu, Iain Anderson, Victor Kunin, Michael Cipriano, Simon Minovitsky, Nina Amenta, ...
Summary: We describe a general multiplatform exploratory tool called TreeQ-Vista, designed for presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic...
§ To whom correspondence should be addressed (2008)
Nameeta Shah, Michael V. Teplitsky, Simon Minovitsky, Len A. Pennacchio, Philip Hugenholtz, Bernd Hamann, ...
Background Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide...
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences (2007)
Minovitsky, Simon, Stegmaier, Philip, Kel, Alexander, Kondrashov, Alexey S, Dubchak, Inna
Abstract Background A substantial fraction of non-coding DNA sequences of multicellular eukaryotes is under selective constraint. In particular, ~5% of the human genome consists of conserved...
Das, Debopriya, Clark, Tyson A., Schweitzer, Anthony, Yamamoto, Miki, Marr, Henry, Arribere, Josh, ...
Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify...
Multiple whole genome alignments and novel biomedical applications at the VISTA portal (2007)
Brudno, Michael, Poliakov, Alexander, Minovitsky, Simon, Ratnere, Igor, Dubchak, Inna
The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the...
Gu, Shengyin, Anderson, Iain, Kunin, Victor, Cipriano, Michael, Minovitsky, Simon, Weber, Gunther, ...
Summary: We describe a general multiplatform exploratory tool called TreeQ-Vista, designed for presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic...
Gu, Shengyin, Anderson, Iain, Kunin, Victor, Cipriano, Michael, Minovitsky, Simon, Weber, Gunther, ...
Summary: We describe a general multiplatform exploratory tool called TreeQ-Vista, designed for presenting functional annotations in a phylogenetic context. Traits, such as phenotypic and genomic...
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences (2007)
Minovitsky, Simon, Stegmaier, Philip, Kel, Alexander, Kondrashov, Alexey S., Dubchak, Inna
Background: A substantial fraction of non-coding DNA sequences of multicellular eukaryotes is under selective constraint. In particular, ~;5 percent of the human genome consists of conserved...
Kazakov, Alexei E., Cipriano, Michael J., Novichkov, Pavel S., Minovitsky, Simon, Vinogradov, Dmitry V., Arkin, Adam, ...
RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several...
VISTA Enhancer Browser--a database of tissue-specific human enhancers (2007)
Visel, Axel, Minovitsky, Simon, Dubchak, Inna, Pennacchio, Len A.
Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This...
VISTA Enhancer Browser--A Database of Tissue-Specific Human Enhancers (2006)
Visel, Axel, Minovitsky, Simon, Dubchak, Inna, Pennacchio, Len A.
Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This...
Kazakov, Alexei E., Cipriano, Michael J., Novichkov, Pavel S., Minovitsky, Simon, Vinogradov, Dmitry V., Arkin, Adam, ...
RegTransBase, a manually curated database of regulatory interactions in prokaryotes, captures the knowledge in published scientific literature using a controlled vocabulary. Although a number of...
Das, Debopriya, Clark, Tyson A., Schweitzer, Anthony, Marr, Henry, Yamamoto, Miki L., Parra, Marilyn K., ...
In Vivo Enhancer Analysis Chromosome 16 Conserved Noncoding Sequences (2006)
Pennacchio, Len A., Ahituv, Nadav, Moses, Alan M., Nobrega, Marcelo, Prabhakar, Shyam, Shoukry, Malak, ...
The identification of enhancers with predicted specificities in vertebrate genomes remains a significant challenge that is hampered by a lack of experimentally validated training sets. In this study,...
SNP-VISTA: An interactive SNP visualization tool (2005)
Shah, Nameeta, Teplitsky, Michael V, Minovitsky, Simon, Pennacchio, Len A, Hugenholtz, Philip, Hamann, Bernd, ...
Abstract Background Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single...
SNP-VISTA: An interactive SNP visualization tool (2005)
Shah, Nameeta, Teplitsky, Michael V, Minovitsky, Simon, Pennacchio, Len A, Hugenholtz, Philip, Hamann, Bernd, ...
Background: Recent advances in sequencing technologies promise to provide a better understanding of the genetics of human disease as well as the evolution of microbial populations. Single Nucleotide...
Minovitsky, Simon, Gee, Sherry L., Schokrpur, Shiruyeh, Dubchak, Inna, Conboy, John G.
Previous studies have identified UGCAUG as an intron splicing enhancer that is frequently located adjacent to tissue-specific alternative exons in the human genome. Here, we show that UGCAUG is...
Minovitsky, Simon, Gee, Sherry L., Schokrpur, Shiruyeh, Dubchak, Inna, Conboy, John G.
Previous studies have identified UGCAUG as an intron splicing enhancer that is frequently located adjacent to tissue-specific alternative exons in the human genome. Here, we show that UGCAUG is...
Zambon, Alexander C., Zhang, Lingzhi, Minovitsky, Simon, Kanter, Joan R., Prabhakar, Shyam, Salomonis, Nathan, ...
Although a substantial number of hormones and drugs increase cellular cAMP levels, the global impact of cAMP and its major effector mechanism, protein kinase A (PKA), on gene expression is not known....
SNP-VISTA: An interactive SNP visualization tool
Shah, Nameeta, Teplitsky, Michael V, Minovitsky, Simon, Pennacchio, Len A, Hugenholtz, Philip, Hamann, Bernd, ...
Minovitsky, Simon, Gee, Sherry L., Schokrpur, Shiruyeh, Dubchak, Inna, Conboy, John G.
Previous studies have identified UGCAUG as an intron splicing enhancer that is frequently located adjacent to tissue-specific alternative exons in the human genome. Here, we show that UGCAUG is...
Zambon, Alexander C., Zhang, Lingzhi, Minovitsky, Simon, Kanter, Joan R., Prabhakar, Shyam, Salomonis, Nathan, ...
Although a substantial number of hormones and drugs increase cellular cAMP levels, the global impact of cAMP and its major effector mechanism, protein kinase A (PKA), on gene expression is not known....
SNP-VISTA: An interactive SNP visualization tool
Shah, Nameeta, Teplitsky, Michael V, Minovitsky, Simon, Pennacchio, Len A, Hugenholtz, Philip, Hamann, Bernd, ...
Kazakov, Alexei E., Cipriano, Michael J., Novichkov, Pavel S., Minovitsky, Simon, Vinogradov, Dmitry V., Arkin, Adam, ...
RegTransBase is a manually curated database of regulatory interactions in prokaryotes that captures the knowledge in public scientific literature using a controlled vocabulary. Although several...
VISTA Enhancer Browser—a database of tissue-specific human enhancers
Visel, Axel, Minovitsky, Simon, Dubchak, Inna, Pennacchio, Len A.
Despite the known existence of distant-acting cis-regulatory elements in the human genome, only a small fraction of these elements has been identified and experimentally characterized in vivo. This...
Multiple whole genome alignments and novel biomedical applications at the VISTA portal
Brudno, Michael, Poliakov, Alexander, Minovitsky, Simon, Ratnere, Igor, Dubchak, Inna
The VISTA portal for comparative genomics is designed to give biomedical scientists a unified set of tools to lead them from the raw DNA sequences through the alignment and annotation to the...
Das, Debopriya, Clark, Tyson A., Schweitzer, Anthony, Yamamoto, Miki, Marr, Henry, Arribere, Josh, ...
Correlation of motif occurrences with gene expression intensity is an effective strategy for elucidating transcriptional cis-regulatory logic. Here we demonstrate that this approach can also identify...