| NCBI prokaryotic genome annotation pipeline T Tatusova, M DiCuccio, A Badretdin, V Chetvernin, EP Nawrocki, ... Nucleic acids research 44 (14), 6614-6624, 2016 | 5681 | 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 | 4411 | 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 | 3325 | 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 | 2604 | 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 | 2368 | 2001 |
| GeneMark. hmm: new solutions for gene finding AV Lukashin, M Borodovsky Nucleic acids research 26 (4), 1107-1115, 1998 | 2008 | 1998 |
| Ab initio gene identification in metagenomic sequences W Zhu, A Lomsadze, M Borodovsky Nucleic acids research 38 (12), e132-e132, 2010 | 1552 | 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 | 1347 | 2011 |
| 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 | 1183 | 2021 |
| GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses J Besemer, M Borodovsky Nucleic acids research 33 (suppl_2), W451-W454, 2005 | 1134 | 2005 |
| 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 | 1022 | 2016 |
| GENMARK: parallel gene recognition for both DNA strands M Borodovsky, J McIninch Computers & chemistry 17 (2), 123-133, 1993 | 965 | 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 | 962 | 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 | 926 | 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 | 665 | 2014 |
| Whole-genome annotation with BRAKER KJ Hoff, A Lomsadze, M Borodovsky, M Stanke Gene prediction: methods and protocols, 65-95, 2019 | 592 | 2019 |
| 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 | 582 | 2010 |
| 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 | 535 | 2013 |
| 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 | 503 | 2014 |
| 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 | 500 | 2010 |
