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Items: 1 to 50 of 110

1.

Complete Genome Sequence of a Virulent African Swine Fever Virus from a Domestic Pig in Ukraine.

Kovalenko G, Ducluzeau AL, Ishchenko L, Sushko M, Sapachova M, Rudova N, Solodiankin O, Gerilovych A, Dagdag R, Redlinger M, Bezymennyi M, Frant M, Lange CE, Dubchak I, Mezhenskyi AA, Nychyk S, Bortz E, Drown DM.

Microbiol Resour Announc. 2019 Oct 17;8(42). pii: e00883-19. doi: 10.1128/MRA.00883-19.

2.

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport.

Rajeev L, Garber ME, Zane GM, Price MN, Dubchak I, Wall JD, Novichkov PS, Mukhopadhyay A, Kazakov AE.

Environ Microbiol. 2019 Feb;21(2):784-799. doi: 10.1111/1462-2920.14500. Epub 2019 Jan 16.

PMID:
30536693
3.

KBase: The United States Department of Energy Systems Biology Knowledgebase.

Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D.

Nat Biotechnol. 2018 Jul 6;36(7):566-569. doi: 10.1038/nbt.4163. No abstract available.

4.

Genomic variation in 3,010 diverse accessions of Asian cultivated rice.

Wang W, Mauleon R, Hu Z, Chebotarov D, Tai S, Wu Z, Li M, Zheng T, Fuentes RR, Zhang F, Mansueto L, Copetti D, Sanciangco M, Palis KC, Xu J, Sun C, Fu B, Zhang H, Gao Y, Zhao X, Shen F, Cui X, Yu H, Li Z, Chen M, Detras J, Zhou Y, Zhang X, Zhao Y, Kudrna D, Wang C, Li R, Jia B, Lu J, He X, Dong Z, Xu J, Li Y, Wang M, Shi J, Li J, Zhang D, Lee S, Hu W, Poliakov A, Dubchak I, Ulat VJ, Borja FN, Mendoza JR, Ali J, Li J, Gao Q, Niu Y, Yue Z, Naredo MEB, Talag J, Wang X, Li J, Fang X, Yin Y, Glaszmann JC, Zhang J, Li J, Hamilton RS, Wing RA, Ruan J, Zhang G, Wei C, Alexandrov N, McNally KL, Li Z, Leung H.

Nature. 2018 May;557(7703):43-49. doi: 10.1038/s41586-018-0063-9. Epub 2018 Apr 25.

5.

Conserved genomic collinearity as a source of broadly applicable, fast evolving, markers to resolve species complexes: A case study using the lichen-forming genus Peltigera section Polydactylon.

Magain N, Miadlikowska J, Mueller O, Gajdeczka M, Truong C, Salamov AA, Dubchak I, Grigoriev IV, Goffinet B, Sérusiaux E, Lutzoni F.

Mol Phylogenet Evol. 2017 Dec;117:10-29. doi: 10.1016/j.ympev.2017.08.013. Epub 2017 Aug 30.

PMID:
28860010
6.

Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

D'Souza M, Sulakhe D, Wang S, Xie B, Hashemifar S, Taylor A, Dubchak I, Conrad Gilliam T, Maltsev N.

Methods Mol Biol. 2017;1613:85-99. doi: 10.1007/978-1-4939-7027-8_5.

PMID:
28849559
7.

Rice SNP-seek database update: new SNPs, indels, and queries.

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.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1075-D1081. doi: 10.1093/nar/gkw1135. Epub 2016 Nov 29.

8.

σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.

Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS.

BMC Genomics. 2015 Nov 10;16:919. doi: 10.1186/s12864-015-2176-y.

9.

Functionally conserved enhancers with divergent sequences in distant vertebrates.

Yang S, Oksenberg N, Takayama S, Heo SJ, Poliakov A, Ahituv N, Dubchak I, Boffelli D.

BMC Genomics. 2015 Oct 30;16:882. doi: 10.1186/s12864-015-2070-7.

10.

Elviz - exploration of metagenome assemblies with an interactive visualization tool.

Cantor M, Nordberg H, Smirnova T, Hess M, Tringe S, Dubchak I.

BMC Bioinformatics. 2015 Apr 28;16:130. doi: 10.1186/s12859-015-0566-4.

11.

An integrative computational approach for prioritization of genomic variants.

Dubchak I, Balasubramanian S, Wang S, Cem M, 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.

PLoS One. 2014 Dec 15;9(12):e114903. doi: 10.1371/journal.pone.0114903. eCollection 2014. Erratum in: PLoS One. 2015;10(4):e0124700. Meyden, Cem [corrected to Meydan, Cem].

12.

Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH.

Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov PS, Dubchak I, Arkin AP, Wall JD.

J Bacteriol. 2015 Jan 1;197(1):29-39. doi: 10.1128/JB.02083-14. Epub 2014 Oct 13.

13.

Alignathon: a competitive assessment of whole-genome alignment methods.

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.

Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1.

14.

[Case of young woman with Graves' disease and incomplete distal renal tubular acidosis with severe progress and cardiac arrest].

Klimm W, Kade G, Spaleniak S, Dubchak I, Niemczyk S.

Pol Merkur Lekarski. 2014 Jul;37(217):53-5. Polish.

PMID:
25154201
15.

The genome of Eucalyptus grandis.

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.

Nature. 2014 Jun 19;510(7505):356-62. doi: 10.1038/nature13308. Epub 2014 Jun 11.

PMID:
24919147
16.

[In the search for effective and safe dose of amikacin in patients with chronic kidney disease].

Gomółka M, Szamotulska K, Rymarz A, Brodowska-Kania D, Dubchak I, Piechota W, Jurkiewicz D, Niemczyk S.

Pol Merkur Lekarski. 2014 Apr;36(214):240-4. Polish.

PMID:
24868895
17.

GenomeVISTA--an integrated software package for whole-genome alignment and visualization.

Poliakov A, Foong J, Brudno M, Dubchak I.

Bioinformatics. 2014 Sep 15;30(18):2654-5. doi: 10.1093/bioinformatics/btu355. Epub 2014 May 23.

18.

MycoCosm portal: gearing up for 1000 fungal genomes.

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.

Nucleic Acids Res. 2014 Jan;42(Database issue):D699-704. doi: 10.1093/nar/gkt1183. Epub 2013 Dec 1.

19.

High-throughput translational medicine: challenges and solutions.

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.

Adv Exp Med Biol. 2014;799:39-67. doi: 10.1007/978-1-4614-8778-4_3. Review.

PMID:
24292961
20.

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates.

Nordberg H, Cantor M, Dusheyko S, Hua S, Poliakov A, Shabalov I, Smirnova T, Grigoriev IV, Dubchak I.

Nucleic Acids Res. 2014 Jan;42(Database issue):D26-31. doi: 10.1093/nar/gkt1069. Epub 2013 Nov 12.

21.

RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA.

BMC Genomics. 2013 Nov 1;14:745. doi: 10.1186/1471-2164-14-745.

22.

New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria.

Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS.

J Bacteriol. 2013 Oct;195(19):4466-75. doi: 10.1128/JB.00679-13. Epub 2013 Aug 2.

23.

Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data.

Dubchak I, Munoz M, Poliakov A, Salomonis N, Minovitsky S, Bodmer R, Zambon AC.

Bioinformatics. 2013 Aug 15;29(16):2059-61. doi: 10.1093/bioinformatics/btt318. Epub 2013 Jun 4.

24.

RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.

Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, Dubchak I.

BMC Genomics. 2013 Apr 2;14:213. doi: 10.1186/1471-2164-14-213.

25.

Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.

Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS.

J Bacteriol. 2013 Jan;195(1):29-38. doi: 10.1128/JB.01977-12. Epub 2012 Oct 19.

26.

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W604-8. doi: 10.1093/nar/gks562. Epub 2012 Jun 14.

27.

[Rapid course of Churge-Strauss syndrome--since appearance of asthma till development of renal failure and neurological complication].

Dubchak I, Gomółka M, Niemczyk S.

Pol Merkur Lekarski. 2012 Mar;32(189):170-2. Polish.

PMID:
22568182
28.

The genome portal of the Department of Energy Joint Genome Institute.

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.

Nucleic Acids Res. 2012 Jan;40(Database issue):D26-32. doi: 10.1093/nar/gkr947. Epub 2011 Nov 22.

29.

Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.

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.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S3. doi: 10.1186/1471-2164-12-S1-S3.

30.

VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies.

Lukashin I, Novichkov P, Boffelli D, Paciorkowski AR, Minovitsky S, Yang S, Dubchak I.

Bioinformatics. 2011 Sep 15;27(18):2595-7. doi: 10.1093/bioinformatics/btr440. Epub 2011 Jul 26.

31.

Comparative genomics of the dormancy regulons in mycobacteria.

Gerasimova A, Kazakov AE, Arkin AP, Dubchak I, Gelfand MS.

J Bacteriol. 2011 Jul;193(14):3446-52. doi: 10.1128/JB.00179-11. Epub 2011 May 20.

32.

Tandem termination signal in plant mRNAs.

Kochetov AV, Volkova OA, Poliakov A, Dubchak I, Rogozin IB.

Gene. 2011 Jul 15;481(1):1-6. doi: 10.1016/j.gene.2011.04.002. Epub 2011 Apr 22.

33.

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.

Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W299-307. doi: 10.1093/nar/gkq531. Epub 2010 Jun 11.

34.

A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites.

Khoueiry P, Rothbächer U, Ohtsuka Y, Daian F, Frangulian E, Roure A, Dubchak I, Lemaire P.

Curr Biol. 2010 May 11;20(9):792-802. doi: 10.1016/j.cub.2010.03.063. Epub 2010 Apr 29.

35.

The genome of the Western clawed frog Xenopus tropicalis.

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.

Science. 2010 Apr 30;328(5978):633-6. doi: 10.1126/science.1183670.

36.

Visualizing genomes: techniques and challenges.

Nielsen CB, Cantor M, Dubchak I, Gordon D, Wang T.

Nat Methods. 2010 Mar;7(3 Suppl):S5-S15. doi: 10.1038/nmeth.1422. Epub 2010 Feb 25. Review.

PMID:
20195257
37.

MicrobesOnline: an integrated portal for comparative and functional genomics.

Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP.

Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400. doi: 10.1093/nar/gkp919. Epub 2009 Nov 11.

38.

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.

Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA.

Nucleic Acids Res. 2010 Jan;38(Database issue):D111-8. doi: 10.1093/nar/gkp894. Epub 2009 Nov 1.

39.

Obtaining comparative genomic data with the VISTA family of computational tools.

Ratnere I, Dubchak I.

Curr Protoc Bioinformatics. 2009 Jun;Chapter 10:Unit 10.6. doi: 10.1002/0471250953.bi1006s26.

PMID:
19496056
40.

Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas.

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.

Science. 2009 Apr 10;324(5924):268-72. doi: 10.1126/science.1167222.

41.

The Sorghum bicolor genome and the diversification of grasses.

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, Mehboob-ur-Rahman, Ware D, Westhoff P, Mayer KF, Messing J, Rokhsar DS.

Nature. 2009 Jan 29;457(7229):551-6. doi: 10.1038/nature07723.

PMID:
19189423
42.

Multiple whole-genome alignments without a reference organism.

Dubchak I, Poliakov A, Kislyuk A, Brudno M.

Genome Res. 2009 Apr;19(4):682-9. doi: 10.1101/gr.081778.108. Epub 2009 Jan 28.

43.

Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors.

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.

Cell. 2008 Dec 12;135(6):1053-64. doi: 10.1016/j.cell.2008.10.049.

44.

Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes.

Novichkov PS, Wolf YI, Dubchak I, Koonin EV.

J Bacteriol. 2009 Jan;191(1):65-73. doi: 10.1128/JB.01237-08. Epub 2008 Oct 31.

45.

ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.

Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I.

Nucleic Acids Res. 2009 Jan;37(Database issue):D448-54. doi: 10.1093/nar/gkn684. Epub 2008 Oct 9.

46.

Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria.

Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, Gelfand MS.

J Bacteriol. 2009 Jan;191(1):52-64. doi: 10.1128/JB.01175-08. Epub 2008 Sep 26.

47.

The amphioxus genome and the evolution of the chordate karyotype.

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.

Nature. 2008 Jun 19;453(7198):1064-71. doi: 10.1038/nature06967.

PMID:
18563158
49.

Short sequence motifs, overrepresented in mammalian conserved non-coding sequences.

Minovitsky S, Stegmaier P, Kel A, Kondrashov AS, Dubchak I.

BMC Genomics. 2007 Oct 18;8:378.

50.

The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions.

Markowitz VM, Szeto E, Palaniappan K, Grechkin Y, Chu K, Chen IM, Dubchak I, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC.

Nucleic Acids Res. 2008 Jan;36(Database issue):D528-33. Epub 2007 Oct 12.

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