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...
Taher, Leila, Ovcharenko, Ivan
Motivation: Several functional gene annotation databases have been developed in the recent years, and are widely used to infer the biological function of gene sets, by scrutinizing the attributes...
Identifying regulatory elements in eukaryotic genomes (2009)
Narlikar, Leelavati, Ovcharenko, Ivan
Proper development and functioning of an organism depends on precise spatial and temporal expression of all its genes. These coordinated expression-patterns are maintained primarily through the...
DiRE: identifying distant regulatory elements of co-expressed genes (2008)
Gotea, Valer, Ovcharenko, Ivan
Regulation of gene expression in eukaryotic genomes is established through a complex cooperative activity of proximal promoters and distant regulatory elements (REs) such as enhancers, repressors and...
Widespread Ultraconservation Divergence in Primates (2008)
The distribution and evolution of ultraconserved elements (UCEs, DNA stretches that are perfectly identical in primates and rodents) were examined in genomes of 3 primate species (human, chimpanzee,...
Gordon, Laurie, Yang, Shan, Tran-Gyamfi, Mary, Baggott, Dan, Christensen, Mari, Hamilton, Aaron, ...
The chicken genome draft sequence has provided a valuable resource for studies of an important agricultural and experimental model species and an important data set for comparative analysis. However,...
Loots, Gabriela, Ovcharenko, Ivan
Motivation: Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in...
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...
Gabriela Loots, Ivan Ovcharenko
Motivation: Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions in...
Identification of clustered YY1 binding sites in imprinting control regions (2006)
Do Kim, Jeong, Hinz, Angela K., Bergmann, Anne, Huang, Jennifer M., Ovcharenko, Ivan, Stubbs, Lisa, ...
Mammalian genomic imprinting is regulated by imprinting control regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In this study, the sequence...
Identification of clustered YY1 binding sites in imprinting control region (2006)
Kim, Jeong Do, Hinz, Angela K., Bergmann, Anne, Huang, Jennifer M., Ovcharenko, Ivan, Stubbs, Lisa, ...
Mammalian genomic imprinting is regulated by imprinting control regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In this study, the sequence...
Identifying synonymous regulatory elements in vertebrate genomes (2005)
Ivan Ovcharenko, Marcelo A. Nobrega
Synonymous gene regulation, defined by regulatory elements driving shared temporal and/or spatial aspects of gene expression, is most probably predicated on genomic elements that contain similar...
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...
Identifying synonymous regulatory elements in vertebrate genomes (2005)
Ovcharenko, Ivan, Nobrega, Marcelo A.
Synonymous gene regulation, defined by regulatory elements driving shared temporal and/or spatial aspects of gene expression, is most probably predicated on genomic elements that contain similar...
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...
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...
Human-zebrafish non-coding conserved elements act in vivo to regulate transcription (2005)
Shin, Jordan T., Priest, James R., Ovcharenko, Ivan, Ronco, Amy, Moore, Rachel K., Burns, C. Geoffrey, ...
Whole genome comparisons of distantly related species effectively predict biologically important sequences—core genes and cis-acting regulatory elements (REs)—but require experimentation to...
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms (2004)
Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, ...
We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken...
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...
CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments (2003)
Sharan, Roded, Ovcharenko, Ivan, Ben-Hur, Asa, Karp, Richard M.
Motivation: The binding of transcription factors to specific regulatory sequence elements is a primary mechanism for controlling gene transcription. Recent findings suggest a modular organization of...
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...
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...
Identifying synonymous regulatory elements in vertebrate genomes
Ovcharenko, Ivan, Nobrega, Marcelo A.
Synonymous gene regulation, defined by regulatory elements driving shared temporal and/or spatial aspects of gene expression, is most probably predicated on genomic elements that contain similar...
Human-zebrafish non-coding conserved elements act in vivo to regulate transcription
Shin, Jordan T., Priest, James R., Ovcharenko, Ivan, Ronco, Amy, Moore, Rachel K., Burns, C. Geoffrey, ...
Whole genome comparisons of distantly related species effectively predict biologically important sequences—core genes and cis-acting regulatory elements (REs)—but require experimentation to...
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...
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...
Identifying synonymous regulatory elements in vertebrate genomes
Ovcharenko, Ivan, Nobrega, Marcelo A.
Synonymous gene regulation, defined by regulatory elements driving shared temporal and/or spatial aspects of gene expression, is most probably predicated on genomic elements that contain similar...
Human-zebrafish non-coding conserved elements act in vivo to regulate transcription
Shin, Jordan T., Priest, James R., Ovcharenko, Ivan, Ronco, Amy, Moore, Rachel K., Burns, C. Geoffrey, ...
Whole genome comparisons of distantly related species effectively predict biologically important sequences—core genes and cis-acting regulatory elements (REs)—but require experimentation to...
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
Identification of clustered YY1 binding sites in imprinting control regions
Do Kim, Jeong, Hinz, Angela K., Bergmann, Anne, Huang, Jennifer M., Ovcharenko, Ivan, Stubbs, Lisa, ...
Mammalian genomic imprinting is regulated by imprinting control regions (ICRs) that are usually associated with tandem arrays of transcription factor binding sites. In this study, the sequence...
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...
Gordon, Laurie, Yang, Shan, Tran-Gyamfi, Mary, Baggott, Dan, Christensen, Mari, Hamilton, Aaron, ...
The chicken genome draft sequence has provided a valuable resource for studies of an important agricultural and experimental model species and an important data set for comparative analysis. However,...
DiRE: identifying distant regulatory elements of co-expressed genes
Gotea, Valer, Ovcharenko, Ivan
Regulation of gene expression in eukaryotic genomes is established through a complex cooperative activity of proximal promoters and distant regulatory elements (REs) such as enhancers, repressors and...
Widespread Ultraconservation Divergence in Primates
The distribution and evolution of ultraconserved elements (UCEs, DNA stretches that are perfectly identical in primates and rodents) were examined in genomes of 3 primate species (human, chimpanzee,...
Taher, Leila, Ovcharenko, Ivan
Motivation: Several functional gene annotation databases have been developed in the recent years, and are widely used to infer the biological function of gene sets, by scrutinizing the attributes...