* Corresponding authors Summary (2008)
Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, Wes Bethel, ...
The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by the growing...
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,...
Close sequence comparisons are sufficient to identify human cis-regulatory elements (2006)
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Close sequence comparisons are sufficient to identify human cis-regulatory elements (2006)
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Close Sequence Comparisons are Sufficient to Identify Human cis-Regulatory Elements (2005)
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...
Ahituv, Nadav, Prabhakar, Shyam, Poulin, Francis, Rubin, Edward M., Couronne, Olivier
Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout...
Ahituv, Nadav, Prabhakar, Shyam, Poulin, Francis, Rubin, Edward M., Couronne, Olivier
Our inability to associate distant regulatory elements with the genes they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle...
Ahituv, Nadav, Prabhakar, Shyam, Poulin, Francis, Rubin, Edward M., Couronne, Olivier
Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major...
The sequence and analysis of duplication rich human chromosome 16 (2004)
Martin, Joel, Han, Cliff, Gordon, Laurie A., Terry, Astrid, Prabhakar, Shyam, She, Xinwei, ...
We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by...
The complete sequence of human chromosome 5 (2004)
Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, State, ...
Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding...
Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments (2004)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Bethel, E. Wes, ...
We have developed Phylo-VISTA (Shah et al., 2003), an interactive software tool for analyzing multiple alignments by visualizing a similarity measure for DNA sequences of multiple species. The...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
The genome sequence of a second fruit fly, D. pseudoobscura, presents an opportunity for comparative analysis of a primary model organism D. melanogaster. The vast majority of Drosophila genes have...
Phylo-VISTA: Interactive Visualization of Multiple DNA Sequence Alignments (2004)
Nameeta Shah Olivier, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, Wes Bethel, ...
an Internet browser with Java Plug-in 1.4.2 and it is integrated into the global alignment program LAGAN at http://lagan.stanford.edu. Contact phylovista@lbl.gov 1 Introduction Large-scale genome...
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments (2004)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Wes Bethel, E., ...
Motivation The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by...
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments (2004)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Bethel, E. Wes, ...
Motivation: The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by...
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments (2004)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Wes Bethel, E., ...
Motivation The power of multi-sequence comparison for biological discovery is well established. The need for new capabilities to visualize and compare cross-species alignment data is intensified by...
Phylo-VISTA: An interactive visualization tool for multiple DNA sequence alignments (2003)
Shah, Nameeta, Couronne, Olivier, Pennacchio, Len A., Brudno, Michael, Batzoglou, Serafim, Bethel, E. Wes, ...
Motivation. The power of multi-sequence comparison for biological discovery is well established and sequence data from a growing list of organisms is becoming available. Thus, a need exists for...
Michael Brudno, Sanket Malde, Er Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, ...
Vol. 19 Suppl. 1 2003, pages i54–i62
Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments (2003)
Nameeta Shah, Olivier Couronne, Len A. Pennacchio, Michael Brudno, Serafim Batzoglou, E. Wes Bethel, ...
We have developed Phylo-VISTA (Shah et al., 2003) , an interactive software tool for analyzing multiple alignments by visualizing a similarity measure for DNA sequences of multiple species. The...
Michael Brudno, Sanket Malde, Er Poliakov, Chuong B. Do, Olivier Couronne, Inna Dubchak, ...
Vol. 19 Suppl. 1 2003, pages i54–i62
Strategies and Tools for Whole-Genome Alignments (2003)
Couronne, Olivier, Poliakov, Alexander, Bray, Nicolas, Ishkhanov, Tigran, Ryaboy, Dmitriy, Rubin, Edward, ...
The availability of the assembled mouse genome makes possible, for the first time, an alignment and comparison of two large vertebrate genomes. We investigated different strategies of alignment for...
Glocal alignment: finding rearrangements during alignment (2003)
Brudno, Michael, Malde, Sanket, Poliakov, Alexander, Do, Chuong B., Couronne, Olivier, Dubchak, Inna, ...
Motivation: To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align...
Strategies and tools for whole genome alignments (2002)
Couronne, Olivier, Poliakov, Alexander, Bray, Nicolas, Ishkhanov, Tigran, Ryaboy, Dmitriy, Rubin, Edward, ...
The availability of the assembled mouse genome makes possible, for the first time, an alignment and comparison of two large vertebrate genomes. We have investigated different strategies of alignment...
Strategies and Tools for Whole-Genome Alignments
Couronne, Olivier, Poliakov, Alexander, Bray, Nicolas, Ishkhanov, Tigran, Ryaboy, Dmitriy, Rubin, Edward, ...
The availability of the assembled mouse genome makes possible, for the first time, an alignment and comparison of two large vertebrate genomes. We investigated different strategies of alignment for...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout...
Strategies and Tools for Whole-Genome Alignments
Couronne, Olivier, Poliakov, Alexander, Bray, Nicolas, Ishkhanov, Tigran, Ryaboy, Dmitriy, Rubin, Edward, ...
The availability of the assembled mouse genome makes possible, for the first time, an alignment and comparison of two large vertebrate genomes. We investigated different strategies of alignment for...
Richards, Stephen, Liu, Yue, Bettencourt, Brian R., Hradecky, Pavel, Letovsky, Stan, Nielsen, Rasmus, ...
We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout...
Close sequence comparisons are sufficient to identify human cis-regulatory elements
Prabhakar, Shyam, Poulin, Francis, Shoukry, Malak, Afzal, Veena, Rubin, Edward M., Couronne, Olivier, ...
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of...