Selected publications of the group

2008

Putnam NH, et. al. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008 Jun 19;453(7198):1064-71.

Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res. 2008 Jan;36(Database issue):D528-33. Epub 2007 Oct 12.

Markowitz VM, Ivanova NN, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Hugenholtz P, Kyrpides NC. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res. 2008 Jan;36(Database issue):D534-8. Epub 2007 Oct 11.

2007

Dubchak I. Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools. Methods Mol Biol. 2007;395:3-16.

Minovitsky S, Stegmaier P, Kel A, Kondrashov AS, Dubchak I. Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. BMC Genomics. 2007 Oct 18;8:378.

Merchant SS, et. al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science. 2007 Oct 12;318(5848):245-50.

Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS. Extensive parallelism in protein evolution. Biol Direct. 2007 Aug 16;2:20.

Das D, Clark TA, Schweitzer A, Yamamoto M, Marr H, Arribere J, Minovitsky S, Poliakov A, Dubchak I, Blume JE, Conboy JG. A correlation with exon expression approach to identify cis-regulatory elements for tissue-specific alternative splicing. Nucleic Acids Res. 2007;35(14):4845-57. Epub 2007 Jul 10.

Brudno M, Poliakov A, Minovitsky S, Ratnere I, Dubchak I. Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W669-74. Epub 2007 May 8.

Palenik B, et. al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A. 2007 May 1;104(18):7705-10. Epub 2007 Apr 25.

Gu S, Anderson I, Kunin V, Cipriano M, Minovitsky S, Weber G, Amenta N, Hamann B, Dubchak I. TreeQ-VISTA: an interactive tree visualization tool with functional annotation query capabilities. Bioinformatics. 2007 Mar 15;23(6):764-6. Epub 2007 Jan 17.

Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I. RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 2007 Jan;35(Database issue):D407-12. Epub 2006 Nov 16.

Visel A, Minovitsky S, Dubchak I, Pennacchio LA. VISTA Enhancer Browser -- a database of tissue-specific human enhancers. Nucleic Acids Res. 2007 Jan;35(Database issue):D88-92. Epub 2006 Nov 27.

2006

Markowitz VM, et al. The integrated microbial genomes (IMG) system. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D344-8

Dubchak I. and Ryaboy D.V. VISTA Family of Computational Tools for Comparative Analysis of DNA Sequences and Whole Genomes. In: Gene Mapping, Discovery, And Expression: Methods And Protocols (Methods in Molecular Biology). Edited by Minou Bina, Humana Press, 2006.

Papatsenko D, Kislyuk A, Levine M, Dubchak I. Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics. 2006, 88(4):431-42. Epub 2006 May 11.

Tuskan, G.A., S.P. DiFazio, U. Hellsten, and et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 313:1596-604.

Tyler, B.M., S. Tripathy, X. Zhang, et al. (2006) Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science. 313:1261-6.

Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, Anderson I, Mavrommatis K, Kunin V, Garcia Martin H, Dubchak I, Hugenholtz P, Kyrpides NC. (2006) An experimental metagenome data management and analysis system. Bioinformatics. 22(14):e359-67.

Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I. RegTransBase -- a database of regulatory sequences and interactions in a wide range of prokaryotic genomes. Nucleic Acids Res. 2006 Nov 16; [Epub ahead of print].

Visel A, Minovitsky S, Dubchak I, Pennacchio LA. VISTA Enhancer Browser -- a database of tissue-specific human enhancers. Nucleic Acids Res. 2006 Nov 27; [Epub ahead of print] PMID: 17130149 [PubMed - as supplied by publisher].

Pennacchio LA, Ahituv N, Moses AM, Prabhakar S, Nobrega MA, Shoukry M, Minovitsky S, Dubchak I, Holt A, Lewis KD, Plajzer-Frick I, Akiyama J, De Val S, Afzal V, Black BL, Couronne O, Eisen MB, Visel A, Rubin EM. In vivo enhancer analysis of human conserved non-coding sequences. Nature. 2006 Nov 23;444(7118):499-502. Epub 2006 Nov 5.

2005

Michael Brudno and Inna Dubchak. Comparisons of Long Genomic Sequences: Algorithms and Applications. In: Handbook of Computational Molecular Biology, Chapman & Hall/CRC Computer & Information Science Series Volume: 9. Ed. S.Aluru, 2005

Eric J. Alm, Katherine H. Huang, Morgan N. Price, Richard P. Koche, Keith Keller, Inna L. Dubchak and Adam P. Arkin. The MicrobesOnline Web site for comparative genomics. Genome Res., 2005. 15:1015-1022

Zambon AC, Zhang L, Minovitsky S, Kanter JR, Prabhakar S, Salomonis N, Vranizan K, Dubchak I, Conklin BR, Insel PA. Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. Proc Natl Acad Sci U S A. 2005, 102(24):8561-6.

Minovitsky S, Gee SL, Schokrpur S, Dubchak I, Conboy JG. The splicing regulatory element, UGCAUG, is phylogenetically and spatially conserved in introns that flank tissue-specific alternative exons. Nucleic Acids Res. 2005, 33(2):714-24.

Richards S et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 2005 Jan;15(1):1-18.

Donfack J, Schneider DH, Tan Z, Kurz T, Dubchak I, Frazer KA, Ober C. Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy. Respir Res. 2005 Dec 10;6(1):145

Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, Dubchak IL. SNP-VISTA: an interactive SNP visualization tool. BMC Bioinformatics. 2005 Dec 8;6:292

Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput Biol. 2005 Oct;1(5):e55. Epub 2005 Oct 28

2004

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9.

Imanishi T, et al. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol. 2004 Jun;2(6):e162. Epub 2004 Apr 20

Grimwood J, et al. The DNA sequence and biology of human chromosome 19. Nature. 2004 Apr 1;428(6982):529-35.

Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I. Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res. 2004 Apr;14(4):685-92.

Cooper GM, Brudno M, Stone EA, Dubchak I, Batzoglou S, Sidow A. Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res. 2004 Apr;14(4):539-48.

Gibbs RA, et al. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1;428(6982):493-521.

Shah N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Bethel EW, Rubin EM, Hamann B, Dubchak I. Phylo-VISTA: interactive visualization of multiple DNA sequence alignments. Bioinformatics. 2004, 20(5):636-43.

2003

Frazer, K.A, Elnitski, L., Church, D.M., Dubchak, I. , and Hardison, R.C.. Cross-species Sequence Comparisons: A Review of Methods and Available Resources. (2003) Genome Res., 2003 Jan;13(1):1-12.

Bray, N., Dubchak, I., and Pachter, L. AVID: A Global Alignment Program. (2003) Genome Res. 2003 Jan;13(1):97-102.

Couronne O., Poliakov A., Bray, N., Ishkhanov, T., Ryaboy, D., Rubin, E., Pachter L, Dubchak, I. Strategies and Tools for Whole Genome Alignments, Genome Res., 2003 Jan;13(1):73-80.

Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S.Glocal alignment: finding rearrangements during alignment. Bioinformatics. 2003 Jul;19 Suppl 1:I54-I62.

Banerjee, P., Bahlo, M., Schwartz, J., Loots, G.G., Houston, K.A., Dubchak, I., Speed, T.P, and Rubin, E.M. SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcriptiption factor binding site data. Mamm Genome. 2002 Oct;13(10):554-7.

2002

Wei, L., Liu, I., Dubchak, I. Shon, J., and Park, J. Comparative genomics approaches to study organism similarities and differences. J Biomed Inform.(2002) 35:142-50.

Waterston, et.al., Initial sequencing and comparative analysis of the mouse genome. Nature. ( 2002) 420:520-62.

Banerjee, P., Bahlo, M., Schwartz, J., Loots, G.G., Houston, K.A., Dubchak, I., Speed, T.P, a nd Rubin, E.M. SNPs in putative regulatory regions identified by human mouse comparative sequencing and transcription factor binding site data. Mamm Genome. (2002) 10:554-7.

Dubchak,I., Pachter, L. (2002) The computational challenges of applying comparative-based computational methods to whole genomes. Briefings in Bioinformatics, 3, 18.

Loots, G., Ovcharenko,I., Pachter,L., Dubchak,I., Rubin, E. rVISTA for comparative sequence-based discovery of functional transcription factor binding sites. (2002) Genome. Res. 12:832-839

2001

Carter, R. J., Dubchak, I., Holbrook, S.R., (2001) A computational approach to identify genes for functional RNAs in genomic sequences. Nucl. Acids. Res. 29: 3928-3938

Xing EP, Wolf DM, Dubchak I, Spengler S, Zorn M, Muchnik I, Kulikowski C. Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation. J Theor Biol. 2001 Sep 21;212(2):129-39.

2000

Dubchak,I., Brudno, M., Pachter, L.S., Loots, G.G., Mayor, C., Rubin, E.M., Frazer, K.A. (2000)Active conservation of noncoding sequences revealed by 3-way species comparisons. Genome Research, 10: 1304-1306

Mayor, C., Brudno, M., Schwartz,J.R., Poliakov,A., Rubin,E.M., Frazer, K.A., Pachter, L.S., Dubchak, I. (2000) VISTA: Visualizing global DNA sequence alignments of arbitrary length. Bioinformatics, 16: 1046-1047.