Research Topics
| Ivan OvcharenkoSummaryAffiliation: Lawrence Livermore National Laboratory Country: USA Publications
| Collaborators
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Detail Information
Publications
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomesIvan Ovcharenko
Genome Biology Division and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
Nucleic Acids Res 32:W280-6. 2004..The interconnection of the ECR Browser with other DNA sequence analysis tools creates a unique portal for studying and exploring vertebrate genomes...- Identifying synonymous regulatory elements in vertebrate genomesIvan Ovcharenko
Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
Nucleic Acids Res 33:W403-7. 2005..SynoR is publicly available at http://synor.dcode.org... - Evolution and functional classification of vertebrate gene desertsIvan Ovcharenko
Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
Genome Res 15:137-45. 2005..Stable gene deserts resist chromosomal rearrangements and appear to harbor multiple distant regulatory elements physically linked to their neighboring genes, with the linearity of conservation invariant throughout vertebrate evolution... - Mulan: multiple-sequence local alignment and visualization for studying function and evolutionIvan Ovcharenko
Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
Genome Res 15:184-94. 2005..Source code for the aligners and the aligner-evaluation software can be freely downloaded from http://www.bx.psu.edu/miller_lab/... - Interpreting mammalian evolution using Fugu genome comparisonsIvan Ovcharenko
Genome Biology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L 441, Livermore, CA 94550, USA
Genomics 84:890-5. 2004..This newly defined threshold identifies 90% of all human/Fugu noncoding ECRs without the assistance of human-Fugu genome alignments and provides a very efficient filter for identifying functional human/mouse ECRs... - eShadow: a tool for comparing closely related sequencesIvan Ovcharenko
Energy, Environment, Biology and Institutional Computing EEBI, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
Genome Res 14:1191-8. 2004..Here, we describe the eShadow comparative tool and its potential uses for analyzing both multiple nucleotide and protein alignments to predict putative functional elements... - Dcode.org anthology of comparative genomic toolsGabriela G Loots
Genome Biology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L-441 Livermore, CA 94550, USA
Nucleic Acids Res 33:W56-64. 2005..Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the http://www.dcode.org/ website... - rVISTA 2.0: evolutionary analysis of transcription factor binding sitesGabriela G Loots
Genome Biology Division and EEBI Computing Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L-441, Livermore, CA 94550, USA
Nucleic Acids Res 32:W217-21. 2004..The rVISTA tool is publicly available at http://rvista.dcode.org/... - zPicture: dynamic alignment and visualization tool for analyzing conservation profilesIvan Ovcharenko
Energy, Environment, Biology and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
Genome Res 14:472-7. 2004..Finally, we describe how this tool can be efficiently applied to the analysis of nonvertebrate genomes, including those of microbial organisms... - ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomesGabriela Loots
CMLS 7000 East Avenue, Livermore, CA, 94550, USA
Bioinformatics 23:122-4. 2007..ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish and fugu genomes. It is freely accessible at http://ecrbase.dcode.org... - Human variation in short regions predisposed to deep evolutionary conservationGabriela G Loots
Biology and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
Mol Biol Evol 27:1279-88. 2010.... - Array2BIO: from microarray expression data to functional annotation of co-regulated genesGabriela G Loots
Lawrence Livermore National Laboratory, Livermore, California 94550, USA
BMC Bioinformatics 7:307. 2006..To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility... - Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regionsLaurie Gordon
Genome Biology Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
Genome Res 17:1603-13. 2007.... - Mulan: multiple-sequence alignment to predict functional elements in genomic sequencesGabriela G Loots
Lawrence Berkeley National Laboratory, USA
Methods Mol Biol 395:237-54. 2007.... - Predicting tissue-specific enhancers in the human genomeLen A Pennacchio
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
Genome Res 17:201-11. 2007..These results indicate the power of combining complementary genomic data sets as an initial computational foray into a global view of tissue-specific gene regulation in vertebrates... - Identification of clustered YY1 binding sites in imprinting control regionsJeong Do Kim
Department of Biological Sciences, Center for BioModular Multi Scale Systems, Louisiana State University, Baton Rouge, Louisiana 70803, USA
Genome Res 16:901-11. 2006..Overall, our identification of three additional clustered YY1 binding sites in imprinted domains suggests a significant role for YY1 in mammalian genomic imprinting... - Widespread ultraconservation divergence in primatesIvan Ovcharenko
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Mol Biol Evol 25:1668-76. 2008..Many of these genes are expressed in the central nervous system. Finally, UCE sequence variability within human populations has been identified, including population-specific nonsynonymous changes in protein-coding regions... - DiRE: identifying distant regulatory elements of co-expressed genesValer Gotea
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
Nucleic Acids Res 36:W133-9. 2008..Its integration with the Array2BIO server allows users to start their analysis with raw microarray expression data. The DiRE web server is freely available at http://dire.dcode.org... - Human-zebrafish non-coding conserved elements act in vivo to regulate transcriptionJordan T Shin
Cardiovascular Research Center and Cardiology Division, Massachusetts General Hospital and Harvard Medical School Charlestown, MA 02129, USA
Nucleic Acids Res 33:5437-45. 2005..Together, these data support the utility of comparative genomics of distantly related vertebrate species to identify REs and provide a scaleable, in vivo quantitative assay to define functional activity of candidate REs... - Generation and annotation of the DNA sequences of human chromosomes 2 and 4Ladeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St. Louis, Missouri 63108, USA
Nature 434:724-31. 2005..Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions... - A genetic variation map for chicken with 2.8 million single-nucleotide polymorphismsGane Ka-Shu Wong
Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China
Nature 432:717-22. 2004..In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases... - Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolutionLadeana W Hillier
Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
Nature 432:695-716. 2004..The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture... - CREME: Cis-Regulatory Module Explorer for the human genomeRoded Sharan
International Computer Science Institute, 1947 Center Street, Berkeley, CA 94704, USA
Nucleic Acids Res 32:W253-6. 2004..The identified cis-regulatory modules are statistically scored and significant combinations are reported and graphically visualized. Our web server is available at http://creme.dcode.org... - The DNA sequence and biology of human chromosome 19Jane Grimwood
Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Avenue, Palo Alto, California 94304, USA
Nature 428:529-35. 2004.... - Scanning human gene deserts for long-range enhancersMarcelo A Nobrega
U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
Science 302:413. 2003 - CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segmentsRoded Sharan
International Computer Science Institute, 1947 Center St, Suite 600, Berkeley CA 94704, USA
Bioinformatics 19:i283-91. 2003..In the cell cycle set five of the seven identified sets of genes were coherently expressed. On the stress response data four of the six detected sets fell predominantly into well-defined functional sub-categories... - Phylogenetic shadowing of primate sequences to find functional regions of the human genomeDario Boffelli
U S Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
Science 299:1391-4. 2003.... - rVista for comparative sequence-based discovery of functional transcription factor binding sitesGabriela G Loots
Genome Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
Genome Res 12:832-9. 2002....