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Items: 1 to 50 of 88

1.

Consent insufficient for data release-Response.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 May 3;364(6439):446. doi: 10.1126/science.aax7509. No abstract available.

PMID:
31048484
2.

Whole-Genome Annotation with BRAKER.

Hoff KJ, Lomsadze A, Borodovsky M, Stanke M.

Methods Mol Biol. 2019;1962:65-95. doi: 10.1007/978-1-4939-9173-0_5.

PMID:
31020555
3.

Toward unrestricted use of public genomic data.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I.

Science. 2019 Jan 25;363(6425):350-352. doi: 10.1126/science.aaw1280. No abstract available.

4.

Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.

Lomsadze A, Gemayel K, Tang S, Borodovsky M.

Genome Res. 2018 Jul;28(7):1079-1089. doi: 10.1101/gr.230615.117. Epub 2018 May 17.

5.

Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools.

Antonov IV, Mazurov E, Borodovsky M, Medvedeva YA.

Brief Bioinform. 2019 Mar 22;20(2):551-564. doi: 10.1093/bib/bby032.

PMID:
29697742
6.

The genome sequence and transcriptome of Potentilla micrantha and their comparison to Fragaria vesca (the woodland strawberry).

Buti M, Moretto M, Barghini E, Mascagni F, Natali L, Brilli M, Lomsadze A, Sonego P, Giongo L, Alonge M, Velasco R, Varotto C, Šurbanovski N, Borodovsky M, Ward JA, Engelen K, Cavallini A, Cestaro A, Sargent DJ.

Gigascience. 2018 Apr 1;7(4):1-14. doi: 10.1093/gigascience/giy010. Erratum in: Gigascience. 2018 Nov 1;7(11):.

7.

NCBI prokaryotic genome annotation pipeline.

Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J.

Nucleic Acids Res. 2016 Aug 19;44(14):6614-24. doi: 10.1093/nar/gkw569. Epub 2016 Jun 24.

8.

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.

Hoff KJ, Lange S, Lomsadze A, Borodovsky M, Stanke M.

Bioinformatics. 2016 Mar 1;32(5):767-9. doi: 10.1093/bioinformatics/btv661. Epub 2015 Nov 11.

9.

Identification of protein coding regions in RNA transcripts.

Tang S, Lomsadze A, Borodovsky M.

Nucleic Acids Res. 2015 Jul 13;43(12):e78. doi: 10.1093/nar/gkv227. Epub 2015 Apr 13.

10.

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm.

Lomsadze A, Burns PD, Borodovsky M.

Nucleic Acids Res. 2014 Sep;42(15):e119. doi: 10.1093/nar/gku557. Epub 2014 Jul 2.

11.

Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication.

Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astúa J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D.

Nat Biotechnol. 2014 Jul;32(7):656-62. doi: 10.1038/nbt.2906. Epub 2014 Jun 8.

12.

The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.

Wang W, Haberer G, Gundlach H, Gläßer C, Nussbaumer T, Luo MC, Lomsadze A, Borodovsky M, Kerstetter RA, Shanklin J, Byrant DW, Mockler TC, Appenroth KJ, Grimwood J, Jenkins J, Chow J, Choi C, Adam C, Cao XH, Fuchs J, Schubert I, Rokhsar D, Schmutz J, Michael TP, Mayer KF, Messing J.

Nat Commun. 2014;5:3311. doi: 10.1038/ncomms4311.

13.

Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite.

Borodovsky M, Lomsadze A.

Curr Protoc Microbiol. 2014 Feb 6;32:Unit 1E.7.. doi: 10.1002/9780471729259.mc01e07s32.

PMID:
24510847
14.

UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing.

Burns PD, Li Y, Ma J, Borodovsky M.

Nucleic Acids Res. 2014 Feb;42(4):e25. doi: 10.1093/nar/gkt1141. Epub 2013 Nov 19.

15.

Identification of the nature of reading frame transitions observed in prokaryotic genomes.

Antonov I, Coakley A, Atkins JF, Baranov PV, Borodovsky M.

Nucleic Acids Res. 2013 Jul;41(13):6514-30. doi: 10.1093/nar/gkt274. Epub 2013 May 6.

16.

TrueSight: a new algorithm for splice junction detection using RNA-seq.

Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, Ma J.

Nucleic Acids Res. 2013 Feb 1;41(4):e51. doi: 10.1093/nar/gks1311. Epub 2012 Dec 18.

17.

GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences.

Antonov I, Baranov P, Borodovsky M.

Nucleic Acids Res. 2013 Jan;41(Database issue):D152-6. doi: 10.1093/nar/gks1062. Epub 2012 Nov 17.

18.

MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences.

Tang S, Antonov I, Borodovsky M.

Bioinformatics. 2013 Jan 1;29(1):114-6. doi: 10.1093/bioinformatics/bts636. Epub 2012 Nov 4.

19.

The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation.

Blanc G, Agarkova I, Grimwood J, Kuo A, Brueggeman A, Dunigan DD, Gurnon J, Ladunga I, Lindquist E, Lucas S, Pangilinan J, Pröschold T, Salamov A, Schmutz J, Weeks D, Yamada T, Lomsadze A, Borodovsky M, Claverie JM, Grigoriev IV, Van Etten JL.

Genome Biol. 2012 May 25;13(5):R39. doi: 10.1186/gb-2012-13-5-r39.

20.

Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES.

Borodovsky M, Lomsadze A.

Curr Protoc Bioinformatics. 2011 Sep;Chapter 4:Unit 4.6.1-10. doi: 10.1002/0471250953.bi0406s35.

21.

Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite.

Borodovsky M, Lomsadze A.

Curr Protoc Bioinformatics. 2011 Sep;Chapter 4:Unit 4.5.1-17. doi: 10.1002/0471250953.bi0405s35.

PMID:
21901741
22.

The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants.

Wóycicki R, Witkowicz J, Gawroński P, Dąbrowska J, Lomsadze A, Pawełkowicz M, Siedlecka E, Yagi K, Pląder W, Seroczyńska A, Śmiech M, Gutman W, Niemirowicz-Szczytt K, Bartoszewski G, Tagashira N, Hoshi Y, Borodovsky M, Karpiński S, Malepszy S, Przybecki Z.

PLoS One. 2011;6(7):e22728. doi: 10.1371/journal.pone.0022728. Epub 2011 Jul 28.

23.

Guest editors' introduction to the special section on bioinformatics research and applications.

Borodovsky M, Przytycka TM, Rajasekaran S, Zelikovsky A.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):865-6. No abstract available.

PMID:
21812137
24.

A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.

Sharma V, Firth AE, Antonov I, Fayet O, Atkins JF, Borodovsky M, Baranov PV.

Mol Biol Evol. 2011 Nov;28(11):3195-211. doi: 10.1093/molbev/msr155. Epub 2011 Jun 14.

25.

Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi.

Xu J, Linning R, Fellers J, Dickinson M, Zhu W, Antonov I, Joly DL, Donaldson ME, Eilam T, Anikster Y, Banks T, Munro S, Mayo M, Wynhoven B, Ali J, Moore R, McCallum B, Borodovsky M, Saville B, Bakkeren G.

BMC Genomics. 2011 Mar 24;12:161. doi: 10.1186/1471-2164-12-161.

26.

Uniform Accuracy of the Maximum Likelihood Estimates for Probabilistic Models of Biological Sequences.

Ekisheva S, Borodovsky M.

Methodol Comput Appl Probab. 2011 Mar 1;13(1):105-120.

27.

The genome of woodland strawberry (Fragaria vesca).

Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJ, Williams KP, Holt SH, Ruiz Rojas JJ, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW Jr, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Lopez Girona E, Zdepski A, Wang W, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM.

Nat Genet. 2011 Feb;43(2):109-16. doi: 10.1038/ng.740. Epub 2010 Dec 26.

28.

2K09 and thereafter : the coming era of integrative bioinformatics, systems biology and intelligent computing for functional genomics and personalized medicine research.

Yang JY, Niemierko A, Bajcsy R, Xu D, Athey BD, Zhang A, Ersoy OK, Li GZ, Borodovsky M, Zhang JC, Arabnia HR, Deng Y, Dunker AK, Liu Y, Ghafoor A.

BMC Genomics. 2010 Dec 1;11 Suppl 3:I1. doi: 10.1186/1471-2164-11-S3-I1.

29.

The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex.

Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, Lindquist E, Lucas S, Pangilinan J, Polle J, Salamov A, Terry A, Yamada T, Dunigan DD, Grigoriev IV, Claverie JM, Van Etten JL.

Plant Cell. 2010 Sep;22(9):2943-55. doi: 10.1105/tpc.110.076406. Epub 2010 Sep 17.

30.

Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm.

Antonov I, Borodovsky M.

J Bioinform Comput Biol. 2010 Jun;8(3):535-51.

PMID:
20556861
31.

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).

Stajich JE, Wilke SK, Ahrén D, Au CH, Birren BW, Borodovsky M, Burns C, Canbäck B, Casselton LA, Cheng CK, Deng J, Dietrich FS, Fargo DC, Farman ML, Gathman AC, Goldberg J, Guigó R, Hoegger PJ, Hooker JB, Huggins A, James TY, Kamada T, Kilaru S, Kodira C, Kües U, Kupfer D, Kwan HS, Lomsadze A, Li W, Lilly WW, Ma LJ, Mackey AJ, Manning G, Martin F, Muraguchi H, Natvig DO, Palmerini H, Ramesh MA, Rehmeyer CJ, Roe BA, Shenoy N, Stanke M, Ter-Hovhannisyan V, Tunlid A, Velagapudi R, Vision TJ, Zeng Q, Zolan ME, Pukkila PJ.

Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11889-94. doi: 10.1073/pnas.1003391107. Epub 2010 Jun 14.

32.

Bacillus anthracis genome organization in light of whole transcriptome sequencing.

Martin J, Zhu W, Passalacqua KD, Bergman N, Borodovsky M.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S10. doi: 10.1186/1471-2105-11-S3-S10.

33.

Ab initio gene identification in metagenomic sequences.

Zhu W, Lomsadze A, Borodovsky M.

Nucleic Acids Res. 2010 Jul;38(12):e132. doi: 10.1093/nar/gkq275. Epub 2010 Apr 19.

34.

Frameshift detection in prokaryotic genomic sequences.

Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M.

Int J Bioinform Res Appl. 2009;5(4):458-77.

PMID:
19640832
35.

In silico identification of genes in bacteriophage DNA.

Kropinski AM, Borodovsky M, Carver TJ, Cerdeño-Tárraga AM, Darling A, Lomsadze A, Mahadevan P, Stothard P, Seto D, Van Domselaar G, Wishart DS.

Methods Mol Biol. 2009;502:57-89. doi: 10.1007/978-1-60327-565-1_6.

PMID:
19082552
36.

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.

Ter-Hovhannisyan V, Lomsadze A, Chernoff YO, Borodovsky M.

Genome Res. 2008 Dec;18(12):1979-90. doi: 10.1101/gr.081612.108. Epub 2008 Aug 29.

37.

Eukaryotic gene prediction using GeneMark.hmm.

Borodovsky M, Lomsadze A, Ivanov N, Mills R.

Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.6. doi: 10.1002/0471250953.bi0406s01.

PMID:
18428701
38.

Prokaryotic gene prediction using GeneMark and GeneMark.hmm.

Borodovsky M, Mills R, Besemer J, Lomsadze A.

Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.5. doi: 10.1002/0471250953.bi0405s01.

PMID:
18428700
39.

Probabilistic models for biological sequences: selection and Maximum Likelihood estimation.

Ekisheva S, Borodovsky M.

Int J Bioinform Res Appl. 2006;2(3):305-24.

PMID:
18048168
40.
41.

Evaluating the protein coding potential of exonized transposable element sequences.

Piriyapongsa J, Rutledge MT, Patel S, Borodovsky M, Jordan IK.

Biol Direct. 2007 Nov 26;2:31.

42.

Exonization of the LTR transposable elements in human genome.

Piriyapongsa J, Polavarapu N, Borodovsky M, McDonald J.

BMC Genomics. 2007 Aug 28;8:291.

43.

Convergence rate estimation for the TKF91 model of biological sequence length evolution.

Mitrophanov AY, Borodovsky M.

Math Biosci. 2007 Oct;209(2):470-85. Epub 2007 Mar 13.

PMID:
17448505
44.

Protein secondary structure prediction with semi Markov HMMs.

Aydin Z, Altunbasak Y, Borodovsky M.

Conf Proc IEEE Eng Med Biol Soc. 2004;4:2964-7.

PMID:
17270900
45.

Control of Streptococcus pyogenes virulence: modeling of the CovR/S signal transduction system.

Mitrophanov AY, Churchward G, Borodovsky M.

J Theor Biol. 2007 May 7;246(1):113-28. Epub 2006 Nov 21.

46.

Statistical significance in biological sequence analysis.

Mitrophanov AY, Borodovsky M.

Brief Bioinform. 2006 Mar;7(1):2-24. Review.

PMID:
16761361
47.

Protein secondary structure prediction for a single-sequence using hidden semi-Markov models.

Aydin Z, Altunbasak Y, Borodovsky M.

BMC Bioinformatics. 2006 Mar 30;7:178.

48.

Gene identification in novel eukaryotic genomes by self-training algorithm.

Lomsadze A, Ter-Hovhannisyan V, Chernoff YO, Borodovsky M.

Nucleic Acids Res. 2005 Nov 28;33(20):6494-506. Print 2005.

49.

GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.

Besemer J, Borodovsky M.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4.

50.

Identification of proteins associated with murine cytomegalovirus virions.

Kattenhorn LM, Mills R, Wagner M, Lomsadze A, Makeev V, Borodovsky M, Ploegh HL, Kessler BM.

J Virol. 2004 Oct;78(20):11187-97.

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