| NCBI prokaryotic genome annotation pipeline T Tatusova, M DiCuccio, A Badretdin, V Chetvernin, EP Nawrocki, ... Nucleic Acids Research, gkw569, 2016 | 5153 | 2016 |
| 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 | 2268 | 2001 |
| Ab initio gene identification in metagenomic sequences W Zhu, A Lomsadze, M Borodovsky Nucleic acids research 38 (12), e132-e132, 2010 | 1448 | 2010 |
| 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, 2015 | 926 | 2015 |
| 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 | 907 | 2008 |
| 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 | 871 | 2021 |
| 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 | 855 | 2005 |
| Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication NATURE BIOTECHNOLOGY, 2014 | 639 | 2014 |
| 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 | 514 | 2013 |
| Whole-genome annotation with BRAKER K Hoff, A Lomsadze, M Borodovsky, M Stanke Methods in molecular biology (Clifton, NJ) 1962, 65, 2019 | 488 | 2019 |
| 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 | 487 | 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 | 439 | 2014 |
| Prokaryotic gene prediction using GeneMark and GeneMark. hmm M Borodovsky, R Mills, J Besemer, A Lomsadze Current Protocols in Bioinformatics, 4.5. 1-4.5. 16, 2003 | 360 | 2003 |
| The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation G Blanc, I Agarkova, J Grimwood, A Kuo, A Brueggeman, DD Dunigan, ... Genome biology 13 (5), 1-12, 2012 | 359 | 2012 |
| The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle W Wang, G Haberer, H Gundlach, C Gläßer, T Nussbaumer, MC Luo, ... Nature communications 5, 2014 | 323 | 2014 |
| Identification of protein coding regions in RNA transcripts S Tang, A Lomsadze, M Borodovsky Nucleic acids research 43 (12), e78-e78, 2015 | 314 | 2015 |
| GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins T Brůna, A Lomsadze, M Borodovsky NAR Genomics and Bioinformatics 2 (2), lqaa026, 2020 | 248 | 2020 |
| Identification of proteins associated with murine cytomegalovirus virions LM Kattenhorn, R Mills, M Wagner, A Lomsadze, V Makeev, ... Journal of virology 78 (20), 11187-11197, 2004 | 205 | 2004 |
| Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes A Lomsadze, K Gemayel, S Tang, M Borodovsky Genome research 28 (7), 1079-1089, 2018 | 148 | 2018 |
| The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants R Wóycicki, J Witkowicz, P Gawroński, J Dąbrowska, A Lomsadze, ... PLoS One 6 (7), e22728, 2011 | 139 | 2011 |
