Ivan Ovcharenko, Gabriela G. Loots, Ross C. Hardison, Webb Miller, Lisa Stubbs
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an...
Predicting tissue-specific enhancers in the human genome (2007)
Pennacchio, Len A., Loots, Gabriela G., Nobrega, Marcelo A., Ovcharenko, Ivan
Determining how transcriptional regulatory signals are encoded in vertebrate genomes is essential for understanding the origins of multicellular complexity; yet the genetic code of vertebrate gene...
Predicting Tissue-Specific Enhancers in the Human Genome (2006)
Pennacchio, Len A., Loots, Gabriela G., Nobrega, Marcelo A., Ovcharenko, Ivan
Determining how transcriptional regulatory signals are encoded in vertebrate genomes is essential for understanding the origins of multi-cellular complexity; yet the genetic code of vertebrate gene...
Array2BIO: from microarray expression data to functional annotation of co-regulated genes (2006)
Loots, Gabriela G, Chain, Patrick SG, Mabery, Shalini, Rasley, Amy, Garcia, Emilio, Ovcharenko, Ivan
Abstract Background There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease (2005)
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can negatively impact human development and health, yet due to the difficulty of detecting these critical sequences we predominantly focus on coding sequences...
doi:10.1093/nar/gki355 Dcode.org anthology of comparative genomic tools (2005)
Gabriela G. Loots, Ivan Ovcharenko
Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to...
Dcode.org anthology of comparative genomic tools (2005)
Loots, Gabriela G., Ovcharenko, Ivan
Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease (2005)
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can have a negative impact on human development and health, yet because of the difficulty of detecting these critical sequences, we predominantly focus on...
Evolution and functional classification of vertebrate gene deserts (2005)
Ovcharenko, Ivan, Loots, Gabriela G., Nobrega, Marcelo A., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct...
Ovcharenko, Ivan, Loots, Gabriela G., Giardine, Belinda M., Hou, Minmei, Ma, Jian, Hardison, Ross C., ...
Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease (2005)
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can have a negative impact on human development and health, yet because of the difficulty of detecting these critical sequences, we predominantly focus on...
Strategies for characterising cis-regulatory elements in Xenopus (2005)
Khokha, Mustafa K., Loots, Gabriela G.
Understanding the cis-regulatory architecture of metazoan organisms is the greatest challenge facing genome biology today. In vertebrate organisms, distinct sequence elements mediate transcriptional...
eShadow: A tool for comparing closely related sequences (2004)
Ovcharenko, Ivan, Boffelli, Dario, Loots, Gabriela G.
Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing,...
CREME: Cis-Regulatory Module Explorer for the human genome (2004)
Roded Sharan, Asa Ben-hur, Gabriela G. Loots, Ivan Ovcharenko
The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription...
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles (2004)
Ovcharenko, Ivan, Loots, Gabriela G., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an...
eShadow: A Tool for Comparing Closely Related Sequences (2004)
Ovcharenko, Ivan, Boffelli, Dario, Loots, Gabriela G.
Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing,...
rVISTA 2.0: evolutionary analysis of transcription factor binding sites (2004)
Loots, Gabriela G., Ovcharenko, Ivan
Identifying and characterizing the transcription factor binding site (TFBS) patterns of cis-regulatory elements represents a challenge, but holds promise to reveal the regulatory language the genome...
CREME: Cis-Regulatory Module Explorer for the human genome (2004)
Sharan, Roded, Ben-Hur, Asa, Loots, Gabriela G., Ovcharenko, Ivan
The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription...
Ovcharenko, Ivan, Nobrega, Marcelo A., Loots, Gabriela G., Stubbs, Lisa
With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have...
Ovcharenko, Ivan, Loots, Gabriela G., Giardine, Belinda M., Hou, Minmei, Ma, Jian, Hardison, Ross C., ...
Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of...
Evolution and functional classification of vertebrate gene deserts (2004)
Ovcharenko, Ivan, Loots, Gabriela G., Nobrega, Marcelo A., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct...
Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons (2000)
Dubchak, Inna, Brudno, Michael, Loots, Gabriela G., Pachter, Lior, Mayor, Chris, Rubin, Edward M., ...
rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites
Loots, Gabriela G., Ovcharenko, Ivan, Pachter, Lior, Dubchak, Inna, Rubin, Edward M.
Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVISTA, for high-throughput...
Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons
Dubchak, Inna, Brudno, Michael, Loots, Gabriela G., Pachter, Lior, Mayor, Chris, Rubin, Edward M., ...
Human and mouse genomic sequence comparisons are being increasingly used to search for evolutionarily conserved gene regulatory elements. Large-scale human–mouse DNA comparison studies have...
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
Ovcharenko, Ivan, Loots, Gabriela G., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an...
eShadow: A Tool for Comparing Closely Related Sequences
Ovcharenko, Ivan, Boffelli, Dario, Loots, Gabriela G.
Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing,...
Ovcharenko, Ivan, Nobrega, Marcelo A., Loots, Gabriela G., Stubbs, Lisa
With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have...
rVISTA 2.0: evolutionary analysis of transcription factor binding sites
Loots, Gabriela G., Ovcharenko, Ivan
Identifying and characterizing the transcription factor binding site (TFBS) patterns of cis-regulatory elements represents a challenge, but holds promise to reveal the regulatory language the genome...
CREME: Cis-Regulatory Module Explorer for the human genome
Sharan, Roded, Ben-Hur, Asa, Loots, Gabriela G., Ovcharenko, Ivan
The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription...
Evolution and functional classification of vertebrate gene deserts
Ovcharenko, Ivan, Loots, Gabriela G., Nobrega, Marcelo A., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct...
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Ovcharenko, Ivan, Loots, Gabriela G., Giardine, Belinda M., Hou, Minmei, Ma, Jian, Hardison, Ross C., ...
Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of...
Dcode.org anthology of comparative genomic tools
Loots, Gabriela G., Ovcharenko, Ivan
Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can have a negative impact on human development and health, yet because of the difficulty of detecting these critical sequences, we predominantly focus on...
Array2BIO: from microarray expression data to functional annotation of co-regulated genes
Loots, Gabriela G, Chain, Patrick SG, Mabery, Shalini, Rasley, Amy, Garcia, Emilio, Ovcharenko, Ivan
rVista for Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites
Loots, Gabriela G., Ovcharenko, Ivan, Pachter, Lior, Dubchak, Inna, Rubin, Edward M.
Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool, rVISTA, for high-throughput...
Active Conservation of Noncoding Sequences Revealed by Three-Way Species Comparisons
Dubchak, Inna, Brudno, Michael, Loots, Gabriela G., Pachter, Lior, Mayor, Chris, Rubin, Edward M., ...
Human and mouse genomic sequence comparisons are being increasingly used to search for evolutionarily conserved gene regulatory elements. Large-scale human–mouse DNA comparison studies have...
zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles
Ovcharenko, Ivan, Loots, Gabriela G., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Comparative sequence analysis has evolved as an essential technique for identifying functional coding and noncoding elements conserved throughout evolution. Here, we introduce zPicture, an...
eShadow: A Tool for Comparing Closely Related Sequences
Ovcharenko, Ivan, Boffelli, Dario, Loots, Gabriela G.
Primate sequence comparisons are difficult to interpret due to the high degree of sequence similarity shared between such closely related species. Recently, a novel method, phylogenetic shadowing,...
Ovcharenko, Ivan, Nobrega, Marcelo A., Loots, Gabriela G., Stubbs, Lisa
With an increasing number of vertebrate genomes being sequenced in draft or finished form, unique opportunities for decoding the language of DNA sequence through comparative genome alignments have...
rVISTA 2.0: evolutionary analysis of transcription factor binding sites
Loots, Gabriela G., Ovcharenko, Ivan
Identifying and characterizing the transcription factor binding site (TFBS) patterns of cis-regulatory elements represents a challenge, but holds promise to reveal the regulatory language the genome...
CREME: Cis-Regulatory Module Explorer for the human genome
Sharan, Roded, Ben-Hur, Asa, Loots, Gabriela G., Ovcharenko, Ivan
The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Eukaryotic genes are often regulated by several transcription...
Evolution and functional classification of vertebrate gene deserts
Ovcharenko, Ivan, Loots, Gabriela G., Nobrega, Marcelo A., Hardison, Ross C., Miller, Webb, Stubbs, Lisa
Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct...
Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
Ovcharenko, Ivan, Loots, Gabriela G., Giardine, Belinda M., Hou, Minmei, Ma, Jian, Hardison, Ross C., ...
Multiple-sequence alignment analysis is a powerful approach for understanding phylogenetic relationships, annotating genes, and detecting functional regulatory elements. With a growing number of...
Dcode.org anthology of comparative genomic tools
Loots, Gabriela G., Ovcharenko, Ivan
Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to...
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease
Loots, Gabriela G., Kneissel, Michaela, Keller, Hansjoerg, Baptist, Myma, Chang, Jessie, Collette, Nicole M., ...
Mutations in distant regulatory elements can have a negative impact on human development and health, yet because of the difficulty of detecting these critical sequences, we predominantly focus on...
Array2BIO: from microarray expression data to functional annotation of co-regulated genes
Loots, Gabriela G, Chain, Patrick SG, Mabery, Shalini, Rasley, Amy, Garcia, Emilio, Ovcharenko, Ivan
Predicting tissue-specific enhancers in the human genome
Pennacchio, Len A., Loots, Gabriela G., Nobrega, Marcelo A., Ovcharenko, Ivan
Determining how transcriptional regulatory signals are encoded in vertebrate genomes is essential for understanding the origins of multicellular complexity; yet the genetic code of vertebrate gene...