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    Dubchak, Inna

    TitleComputer Senior Sci/Engr
    SchoolLawrence Berkeley National Lab
    DepartmentJoint Genome Institute
    Address1 Cyclotron Road
    Berkeley CA 94720
    Phone925/296-5713
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Mansueto L, Fuentes RR, Borja FN, Detras J, Abriol-Santos JM, Chebotarov D, Sanciangco M, Palis K, Copetti D, Poliakov A, Dubchak I, Solovyev V, Wing RA, Hamilton RS, Mauleon R, McNally KL, Alexandrov N. Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res. 2017 Jan 04; 45(D1):D1075-D1081. PMID: 27899667.
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      2. Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS. s(54)-dependent regulome in Desulfovibrio vulgaris Hildenborough. BMC Genomics. 2015; 16(1):919. PMID: 26555820.
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      3. Yang S, Oksenberg N, Takayama S, Heo SJ, Poliakov A, Ahituv N, Dubchak I, Boffelli D. Functionally conserved enhancers with divergent sequences in distant vertebrates. BMC Genomics. 2015; 16(1):882. PMID: 26519295.
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      4. Cantor M, Nordberg H, Smirnova T, Hess M, Tringe S, Dubchak I. Elviz - exploration of metagenome assemblies with an interactive visualization tool. BMC Bioinformatics. 2015; 16:130. PMID: 25928663.
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      5. Dubchak I, Balasubramanian S, Wang S, Meyden C, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC. An integrative computational approach for prioritization of genomic variants. PLoS One. 2014; 9(12):e114903. PMID: 25506935.
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      6. Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov PS, Dubchak I, Arkin AP, Wall JD. Rex (Encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough Is a Repressor of Sulfate Adenylyl Transferase and Is Regulated by NADH. J Bacteriol. 2015 Jan 1; 197(1):29-39. PMID: 25313388.
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      7. Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B. Alignathon: a competitive assessment of whole-genome alignment methods. Genome Res. 2014 Dec; 24(12):2077-89. PMID: 25273068.
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      8. Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, Hussey SG, Pinard D, van der Merwe K, Singh P, van Jaarsveld I, Silva-Junior OB, Togawa RC, Pappas MR, Faria DA, Sansaloni CP, Petroli CD, Yang X, Ranjan P, Tschaplinski TJ, Ye CY, Li T, Sterck L, Vanneste K, Murat F, Soler M, Clemente HS, Saidi N, Cassan-Wang H, Dunand C, Hefer CA, Bornberg-Bauer E, Kersting AR, Vining K, Amarasinghe V, Ranik M, Naithani S, Elser J, Boyd AE, Liston A, Spatafora JW, Dharmwardhana P, Raja R, Sullivan C, Romanel E, Alves-Ferreira M, Külheim C, Foley W, Carocha V, Paiva J, Kudrna D, Brommonschenkel SH, Pasquali G, Byrne M, Rigault P, Tibbits J, Spokevicius A, Jones RC, Steane DA, Vaillancourt RE, Potts BM, Joubert F, Barry K, Pappas GJ, Strauss SH, Jaiswal P, Grima-Pettenati J, Salse J, Van de Peer Y, Rokhsar DS, Schmutz J. The genome of Eucalyptus grandis. Nature. 2014 Jun 19; 510(7505):356-62. PMID: 24919147.
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      9. Poliakov A, Foong J, Brudno M, Dubchak I. GenomeVISTA-an integrated software package for whole-genome alignment and visualization. Bioinformatics. 2014 Sep 15; 30(18):2654-5. PMID: 24860159.
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      10. Sulakhe D, Balasubramanian S, Xie B, Berrocal E, Feng B, Taylor A, Chitturi B, Dave U, Agam G, Xu J, Börnigen D, Dubchak I, Gilliam TC, Maltsev N. High-throughput translational medicine: challenges and solutions. Adv Exp Med Biol. 2014; 799:39-67. PMID: 24292961.
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      11. Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao X, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res. 2014 Jan 1; 42(1):D699-704. PMID: 24297253.
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      12. Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I, Smirnova T, Grigoriev IV, Dubchak I. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates. Nucleic Acids Res. 2014 Jan 1; 42(1):D26-31. PMID: 24225321.
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      13. Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA. RegPrecise 3.0 - A resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics. 2013; 14:745. PMID: 24175918.
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      14. Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS. New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria. J Bacteriol. 2013 Oct; 195(19):4466-75. PMID: 23913324.
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      15. Dubchak I, Munoz M, Poliakov A, Salomonis N, Minovitsky S, Bodmer R, Zambon AC. Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data. Bioinformatics. 2013 Aug 15; 29(16):2059-61. PMID: 23736530.
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      16. Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, Dubchak I. RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics. 2013; 14:213. PMID: 23547897.
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      17. Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS. Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. J Bacteriol. 2013 Jan; 195(1):29-38. PMID: 23086211.
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      18. Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA. RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics. Nucleic Acids Res. 2012 Jul; 40(Web Server issue):W604-8. PMID: 22700702.
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      19. Grigoriev IV, Nordberg H, Shabalov I, Aerts A, Cantor M, Goodstein D, Kuo A, Minovitsky S, Nikitin R, Ohm RA, Otillar R, Poliakov A, Ratnere I, Riley R, Smirnova T, Rokhsar D, Dubchak I. The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res. 2012 Jan; 40(Database issue):D26-32. PMID: 22110030.
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      20. Lukashin I, Novichkov P, Boffelli D, Paciorkowski AR, Minovitsky S, Yang S, Dubchak I. VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies. Bioinformatics. 2011 Sep 15; 27(18):2595-7. PMID: 21791533.
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      21. Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011; 12 Suppl 1:S3. PMID: 21810205.
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      22. Gerasimova A, Kazakov AE, Arkin AP, Dubchak I, Gelfand MS. Comparative genomics of the dormancy regulons in mycobacteria. J Bacteriol. 2011 Jul; 193(14):3446-52. PMID: 21602344.
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      23. Kochetov AV, Volkova OA, Poliakov A, Dubchak I, Rogozin IB. Tandem termination signal in plant mRNAs. Gene. 2011 Jul 15; 481(1):1-6. PMID: 21539902.
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      24. Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W299-307. PMID: 20542910.
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      25. Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS. The genome of the Western clawed frog Xenopus tropicalis. Science. 2010 Apr 30; 328(5978):633-6. PMID: 20431018.
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      26. Khoueiry P, Rothbächer U, Ohtsuka Y, Daian F, Frangulian E, Roure A, Dubchak I, Lemaire P. A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites. Curr Biol. 2010 May 11; 20(9):792-802. PMID: 20434338.
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      27. Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T. Visualizing genomes: techniques and challenges. Nat Methods. 2010 Mar; 7(3 Suppl):S5-S15. PMID: 20195257.
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      28. Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak I, Alm EJ, Arkin AP. MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res. 2010 Jan; 38(Database issue):D396-400. PMID: 19906701.
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      29. Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010 Jan; 38(Database issue):D111-8. PMID: 19884135.
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      30. 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. PMID: 19496056.
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      31. Worden AZ, Lee JH, Mock T, Rouzé P, Simmons MP, Aerts AL, Allen AE, Cuvelier ML, Derelle E, Everett MV, Foulon E, Grimwood J, Gundlach H, Henrissat B, Napoli C, McDonald SM, Parker MS, Rombauts S, Salamov A, Von Dassow P, Badger JH, Coutinho PM, Demir E, Dubchak I, Gentemann C, Eikrem W, Gready JE, John U, Lanier W, Lindquist EA, Lucas S, Mayer KF, Moreau H, Not F, Otillar R, Panaud O, Pangilinan J, Paulsen I, Piegu B, Poliakov A, Robbens S, Schmutz J, Toulza E, Wyss T, Zelensky A, Zhou K, Armbrust EV, Bhattacharya D, Goodenough UW, Van de Peer Y, Grigoriev IV. Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science. 2009 Apr 10; 324(5924):268-72. PMID: 19359590.
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      32. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG. The Sorghum bicolor genome and the diversification of grasses. Nature. 2009 Jan 29; 457(7229):551-6. PMID: 19189423.
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      33. Dubchak I, Poliakov A, Kislyuk A, Brudno M. Multiple whole-genome alignments without a reference organism. Genome Res. 2009 Apr; 19(4):682-9. PMID: 19176791.
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      34. 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. PMID: 19070576.
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      35. 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. PMID: 18978059.
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      36. 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. PMID: 18845571.
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      37. 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. PMID: 18820024.
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      38. Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-I T, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS. The amphioxus genome and the evolution of the chordate karyotype. Nature. 2008 Jun 19; 453(7198):1064-71. PMID: 18563158.
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      39. Minovitsky S, Stegmaier P, Kel A, Kondrashov AS, Dubchak I. Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. BMC Genomics. 2007; 8:378. PMID: 17945028.
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      40. 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. PMID: 17933782.
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      41. 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. PMID: 17932063.
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      42. Bazykin GA, Kondrashov FA, Brudno M, Poliakov A, Dubchak I, Kondrashov AS. Extensive parallelism in protein evolution. Biol Direct. 2007; 2:20. PMID: 17705846.
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      43. 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. PMID: 17626050.
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      44. 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. PMID: 17488840.
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      45. Palenik B, Grimwood J, Aerts A, Rouzé P, Salamov A, Putnam N, Dupont C, Jorgensen R, Derelle E, Rombauts S, Zhou K, Otillar R, Merchant SS, Podell S, Gaasterland T, Napoli C, Gendler K, Manuell A, Tai V, Vallon O, Piganeau G, Jancek S, Heijde M, Jabbari K, Bowler C, Lohr M, Robbens S, Werner G, Dubchak I, Pazour GJ, Ren Q, Paulsen I, Delwiche C, Schmutz J, Rokhsar D, Van de Peer Y, Moreau H, Grigoriev IV. 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. PMID: 17460045.
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      46. 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. PMID: 17234642.
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      47. Dubchak I. Comparative analysis and visualization of genomic sequences using VISTA browser and associated computational tools. Methods Mol Biol. 2007; 395:3-16. PMID: 17993664.
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      48. 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. PMID: 17130149.
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      49. 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. PMID: 17142223.
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      50. 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. PMID: 17086198.
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      51. Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Déjardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjärvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leplé JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouzé P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 2006 Sep 15; 313(5793):1596-604. PMID: 16973872.
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      52. Tyler BM, Tripathy S, Zhang X, Dehal P, Jiang RH, Aerts A, Arredondo FD, Baxter L, Bensasson D, Beynon JL, Chapman J, Damasceno CM, Dorrance AE, Dou D, Dickerman AW, Dubchak I, Garbelotto M, Gijzen M, Gordon SG, Govers F, Grunwald NJ, Huang W, Ivors KL, Jones RW, Kamoun S, Krampis K, Lamour KH, Lee MK, McDonald WH, Medina M, Meijer HJ, Nordberg EK, Maclean DJ, Ospina-Giraldo MD, Morris PF, Phuntumart V, Putnam NH, Rash S, Rose JK, Sakihama Y, Salamov AA, Savidor A, Scheuring CF, Smith BM, Sobral BW, Terry A, Torto-Alalibo TA, Win J, Xu Z, Zhang H, Grigoriev IV, Rokhsar DS, Boore JL. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science. 2006 Sep 1; 313(5791):1261-6. PMID: 16946064.
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      53. Markowitz VM, Ivanova N, Palaniappan K, Szeto E, Korzeniewski F, Lykidis A, Anderson I, Mavromatis K, Mavrommatis K, Kunin V, Garcia Martin H, Dubchak I, Hugenholtz P, Kyrpides NC. An experimental metagenome data management and analysis system. Bioinformatics. 2006 Jul 15; 22(14):e359-67. PMID: 16873494.
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      54. Papatsenko D, Kislyuk A, Levine M, Dubchak I. Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics. 2006 Oct; 88(4):431-42. PMID: 16697139.
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      55. Dubchak I, Ryaboy DV. VISTA family of computational tools for comparative analysis of DNA sequences and whole genomes. Methods Mol Biol. 2006; 338:69-89. PMID: 16888351.
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      56. Markowitz VM, Korzeniewski F, Palaniappan K, Szeto E, Werner G, Padki A, Zhao X, Dubchak I, Hugenholtz P, Anderson I, Lykidis A, Mavromatis K, Ivanova N, Kyrpides NC. The integrated microbial genomes (IMG) system. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D344-8. PMID: 16381883.
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      57. 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; 6:145. PMID: 16336695.
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      58. Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, Dubchak I. SNP-VISTA: an interactive SNP visualization tool. BMC Bioinformatics. 2005; 6:292. PMID: 16336665.
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      59. Rodionov DA, Dubchak I, 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. PMID: 16261196.
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      60. Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak I, Arkin AP. The MicrobesOnline Web site for comparative genomics. Genome Res. 2005 Jul; 15(7):1015-22. PMID: 15998914.
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      61. 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 Jun 14; 102(24):8561-6. PMID: 15939874.
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      62. 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. PMID: 15691898.
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      63. Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res. 2005 Jan; 15(1):1-18. PMID: 15632085.
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      64. Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol. 2004; 5(11):R90. PMID: 15535866.
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      69. 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. PMID: 15060011.
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      70. Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004 Apr 1; 428(6982):493-521. PMID: 15057822.
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      73. Dubchak I, Frazer K. Multi-species sequence comparison: the next frontier in genome annotation. Genome Biol. 2003; 4(12):122. PMID: 14659006.
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      86. Ding CH, Dubchak I. Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics. 2001 Apr; 17(4):349-58. PMID: 11301304.
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      89. Mian IS, Dubchak I. Representing and reasoning about protein families using generative and discriminative methods. J Comput Biol. 2000; 7(6):849-62. PMID: 11382366.
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      98. Holbrook SR, Dubchak I, Kim SH. PROBE: a computer program employing an integrated neural network approach to protein structure prediction. Biotechniques. 1993 Jun; 14(6):984-9. PMID: 8333967.
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