Selected publications of the group members
2009
Ratnere I, Dubchak I.
Obtaining comparative genomic data with the VISTA family of computational tools.
Curr Protoc Bioinformatics. 2009 Jun;Chapter 10:Unit 10.6.
Worden AZ, Lee JH, Mock T, Rouzé P, et al.
Green evolution and dynamic adaptations revealed by genomes
of the marine picoeukaryotes Micromonas.
Science. 2009 Apr 10;324(5924):268-72.
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, et al.
The Sorghum bicolor genome and the diversification
of grasses.
Nature. 2009 Jan 29;457(7229):551-6.
Dubchak I, Poliakov A, Kislyuk A, Brudno M.
Multiple whole-genome alignments without a reference organism.
Genome Res. 2009 Apr;19(4):682-9. Epub 2009 Jan 28.
2008
De Val S, Chi NC, Meadows SM, Minovitsky S, Anderson JP, Harris IS, Ehlers ML, Agarwal P, Visel A, Xu SM, Pennacchio LA, Dubchak I, Krieg PA, Stainier DY, Black BL.
Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors.
Cell. 2008 Dec 12;135(6):1053-64.
Novichkov PS, Wolf YI, Dubchak I, Koonin EV.
Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes.
J Bacteriol. 2009 Jan;191(1):65-73. Epub 2008 Oct 31.
Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I.
ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.
Nucleic Acids Res. 2009 Jan;37(Database issue):D448-54. Epub 2008 Oct 9. .
Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, Gelfand MS.
Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria.
J Bacteriol. 2009 Jan;191(1):52-64. Epub 2008 Sep 26.
Putnam NH, Butts T, Ferrier DE, Furlong RF, et al.
The amphioxus genome and the evolution of the chordate karyotype.
Nature. 2008 Jun 19;453(7198):1064-71.
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.
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.
Merchant SS, Prochnik SE, Vallon O, Harris EH, et al.
The Chlamydomonas genome reveals the evolution of key animal and plant
functions.
Science. 2007 Oct 12;318(5848):245-50.
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.
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
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.
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.
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).
Methods Mol Biol. 2006;338:69-89.
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. 2006 Jul 15;22(14):e359-67.
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.
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].
Markowitz VM, et al.
The integrated microbial genomes (IMG) system.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D344-8
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
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
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 Feb 3;33(2):714-24. Print 2005.
Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, et al
Comparative genome sequencing of Drosophila
pseudoobscura: chromosomal, gene, and cis-element evolution.
Genome Res. 2005 Jan;15(1):1-18.
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
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.
Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, et al.l
The DNA sequence and biology of human
chromosome 19.
Nature. 2004 Apr 1;428(6982):529-35.
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 Mar 22;20(5):636-43. Epub 2004 Jan 22.
2003
Dubchak I, Frazer K.
Multi-species sequence comparison: the next frontier in genome annotation.
Genome Biol. 2003;4(12):122. Epub 2003 Nov 27.
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.
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.
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.
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 Dec 5;420(6915):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
Brudno M, Gelfand MS, Spengler S, Zorn M, Dubchak I, Conboy JG.
Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing.
Nucleic Acids Res. 2001 Jun 1;29(11):2338-48.
PMID: 11376152 [PubMed - indexed for MEDLINE]
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
Mayor, C., Brudno, M., Schwartz,J.R., Poliakov,A., Rubin,E.M., Frazer, K.A., Pachter, L.S., Dubchak, I.
VISTA : visualizing global DNA sequence alignments of arbitrary length.
Bioinformatics, 16: 1046-1047.
Dubchak,I., Brudno, M., Pachter, L.S., Loots, G.G., Mayor, C., Rubin, E.M., Frazer, K.A.
Active conservation of noncoding sequences revealed by three-way species comparisons.
Genome Res. 2000 Sep;10(9):1304-6.