NCBI DCODE.org Comparative Genomics Developments :: Publications

SynoR :: https://synor.dcode.org    I. Ovcharenko and M.A. Nobrega, Identifying synonymous regulatory elements in vertebrate genomes, Nucleic Acids Research, 33, W403-7, (2005) [PDF].

ECR Browser :: https://ecrbrowser.dcode.org     I. Ovcharenko, M.A. Nobrega, G.G. Loots, and L. Stubbs, ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes, Nucleic Acids Research, 32(Web Server Issue), W280-W286 (2004) [PDF]

Mulan :: https://mulan.dcode.org     I. Ovcharenko, G.G. Loots, B.M. Giardine, M. Hou, J. Ma, R.C. Hardison, L. Stubbs, and W. Miller, Mulan: Multiple-sequence local alignment and visualization for studying function and evolution, Genome Research, 15(1), 184-194, (2005) [PDF]

zPicture :: https://zpicture.dcode.org     I. Ovcharenko, G.G. Loots, R.C. Hardison, W. Miller, Lisa Stubbs, zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles, Genome Research, 14(3), 472-477 (2004) [PDF]

eShadow :: https://eshadow.dcode.org     I. Ovcharenko, D. Boffelli, and G.G. Loots, eShadow: A Tool for Comparing Closely Related Sequences, Genome Research, 14(6), 1191-1198 (2004) [PDF]

rVista 2.0 :: https://rvista.dcode.org     G.G. Loots and I. Ovcharenko, rVISTA 2.0: evolutionary analysis of transcription factor binding sites, Nucleic Acids Research, 32(Web Server Issue), W217-W221 (2004) [PDF]     G.G. Loots, I. Ovcharenko, L. Pachter, I. Dubchak, E.M. Rubin, Comparative sequence-based approach to high-throughput discovery of functional regulatory elements, Genome Research 12(5), 832-839 (2002) [PDF]

Creme 2.0 :: https://creme.dcode.org     R. Sharan, A. Ben-Hur, G.G. Loots, and I. Ovcharenko, CREME: Cis-Regulatory Module Explorer for the human genome, Nucleic Acids Research, 32(Web Server Issue), W253-W256 (2004) [PDF]     R. Sharan*, I. Ovcharenko*, A. Ben-Hur, R.Karp, CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments, Bioinformatics, Suppl. 1, i283-i291, (2003) [PDF]

Array2BIO :: https://array2bio.dcode.org     G.G. Loots, P.S. Chain, S. Mabery, A. Rasley, E. Garcia, and I. Ovcharenko, Array2BIO: from microarray expression data to functional annotation of co-regulated genes, BMC Bioinformatics, 7(1), 307 (2006) [PDF]

ECRbase :: https://ecrbase.dcode.org     G.G. Loots and I. Ovcharenko, ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes, Bioinformatics, 23(1), 122-124 (2007) [PDF].

Research based on dcode.org tools and methods     I. Ovcharenko, G.G. Loots, M.A. Nobrega, R.C. Hardison, W. Miller, and L. Stubbs, Evolution and functional classification of vertebrate gene deserts, Genome Research, 15(1), 137-145, (2005) [PDF]     I. Ovcharenko, L. Stubbs, and G.G. Loots, Interpreting mammalian evolution using Fugu genome comparisons, Genomics, 84(5), 890-895 (2004) [PDF]     M. Nobrega*, I. Ovcharenko*, V. Afzal, E. Rubin, Scanning Human Gene Deserts for Long-Range Enhancers, Science 302(5644), 413 (2003) [PDF, Supporting Online Material]     D. Boffelli, J. MacAuliffe, D. Ovcharenko, K. Lewis, I. Ovcharenko, L. Pachter, E. Rubin, Phylogenetic analysis of primate sequences reveals functional regions of the human genome, Science, 299(5611), 1391-4, (2003) [PDF]

Reviews     G.G. Loots and I. Ovcharenko, Dcode.org anthology of comparative genomic tools, Nucleic Acids Research, 33, W56-64, (2005) [PDF].     A. Heller, "Mining Genomes" in the June 2005 issue of the Science and Technology Review LLNL's magazine.     I. Ovcharenko and G.G. Loots, Finding the Needle in the Haystack: Computational Strategies for Discovering Regulatory Sequences in Genomes, Current Genomics, 4, 557-568, (2003) [PDF]     I. Ovcharenko and G.G. Loots, Comparative Genomics Tools for Exploring the Human Genome. CSHL Symposia on Quantitative Biology; The genome of Homo Sapiens, 68, 283-291, (2004) [PDF]

CSHL course on Computational Genomics     L. Stubbs and I. Ovcharenko, Algorithms for Genome Comparisons, Cold Spring Harbor Laboratory, November 5-11, 2003.