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Items: 26

1.

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
2.

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.

3.

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):.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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
11.

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.

12.

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.

13.

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
14.

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.

15.

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.

16.

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.

17.

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
18.

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
19.

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.

20.

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
21.

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
22.

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.

23.

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.

24.

Improving gene annotation of complete viral genomes.

Mills R, Rozanov M, Lomsadze A, Tatusova T, Borodovsky M.

Nucleic Acids Res. 2003 Dec 1;31(23):7041-55.

25.
26.

Interaction of above-Fermi-edge magnetoexciton states from different subbands in dense two-dimensional electron magnetoplasma.

Kulik LV, Petinova AV, Kulakovskii VD, Andersson TG, Wang S, Lomsadze AV.

Phys Rev B Condens Matter. 1995 Jun 15;51(24):17654-17659. No abstract available.

PMID:
9978795

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