Mark Borodovsky
Mark Borodovsky
Regents' Professor, Georgia Tech
Verified email at - Homepage
Cited by
Cited by
NCBI prokaryotic genome annotation pipeline
T Tatusova, M DiCuccio, A Badretdin, V Chetvernin, EP Nawrocki, ...
Nucleic acids research 44 (14), 6614-6624, 2016
The complete genome sequence of the gastric pathogen Helicobacter pylori
JF Tomb, O White, AR Kerlavage, RA Clayton, GG Sutton, ...
Nature 388 (6642), 539-547, 1997
Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
CJ Bult, O White, GJ Olsen, L Zhou, RD Fleischmann, GG Sutton, ...
Science 273 (5278), 1058-1073, 1996
cag, a pathogenicity island of Helicobacter pylori, encodes type I-specific and disease-associated virulence factors
S Censini, C Lange, Z Xiang, JE Crabtree, P Ghiara, M Borodovsky, ...
Proceedings of the National Academy of Sciences 93 (25), 14648-14653, 1996
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
J Besemer, A Lomsadze, M Borodovsky
Nucleic acids research 29 (12), 2607-2618, 2001
GeneMark. hmm: new solutions for gene finding
AV Lukashin, M Borodovsky
Nucleic acids research 26 (4), 1107-1115, 1998
Ab initio gene identification in metagenomic sequences
W Zhu, A Lomsadze, M Borodovsky
Nucleic acids research 38 (12), e132-e132, 2010
The genome of woodland strawberry (Fragaria vesca)
V Shulaev, DJ Sargent, RN Crowhurst, TC Mockler, O Folkerts, ...
Nature genetics 43 (2), 109-116, 2011
GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses
J Besemer, M Borodovsky
Nucleic acids research 33 (suppl_2), W451-W454, 2005
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database
T Brůna, KJ Hoff, A Lomsadze, M Stanke, M Borodovsky
NAR genomics and bioinformatics 3 (1), lqaa108, 2021
BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS
KJ Hoff, S Lange, A Lomsadze, M Borodovsky, M Stanke
Bioinformatics 32 (5), 767-769, 2016
GENMARK: parallel gene recognition for both DNA strands
M Borodovsky, J McIninch
Computers & chemistry 17 (2), 123-133, 1993
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
V Ter-Hovhannisyan, A Lomsadze, YO Chernoff, M Borodovsky
Genome research 18 (12), 1979-1990, 2008
Gene identification in novel eukaryotic genomes by self-training algorithm
A Lomsadze, V Ter-Hovhannisyan, YO Chernoff, M Borodovsky
Nucleic acids research 33 (20), 6494-6506, 2005
Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
GA Wu, S Prochnik, J Jenkins, J Salse, U Hellsten, F Murat, X Perrier, ...
Nature biotechnology 32 (7), 656-662, 2014
The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex
G Blanc, G Duncan, I Agarkova, M Borodovsky, J Gurnon, A Kuo, ...
The Plant Cell 22 (9), 2943-2955, 2010
Whole-genome annotation with BRAKER
KJ Hoff, A Lomsadze, M Borodovsky, M Stanke
Gene prediction: methods and protocols, 65-95, 2019
Pan genome of the phytoplankton Emiliania underpins its global distribution
BA Read, J Kegel, MJ Klute, A Kuo, SC Lefebvre, F Maumus, C Mayer, ...
Nature 499 (7457), 209-213, 2013
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
JE Stajich, SK Wilke, D Ahrén, CH Au, BW Birren, M Borodovsky, C Burns, ...
Proceedings of the National Academy of Sciences 107 (26), 11889-11894, 2010
Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm
A Lomsadze, PD Burns, M Borodovsky
Nucleic acids research 42 (15), e119-e119, 2014
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