Alex Lomsadze
Alex Lomsadze
Senior Research Scientist, The Wallace H. Coulter Department of Biomedical Engineering at Georgia
Verified email at
Cited by
Cited by
NCBI prokaryotic genome annotation pipeline
T Tatusova, M DiCuccio, A Badretdin, V Chetvernin, EP Nawrocki, ...
Nucleic Acids Research, gkw569, 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
Ab initio gene identification in metagenomic sequences
W Zhu, A Lomsadze, M Borodovsky
Nucleic acids research 38 (12), e132-e132, 2010
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
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
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
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 AhrÚn, CH Au, BW Birren, M Borodovsky, C Burns, ...
Proceedings of the National Academy of Sciences 107 (26), 11889-11894, 2010
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
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
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
The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle
W Wang, G Haberer, H Gundlach, C Glń▀er, T Nussbaumer, MC Luo, ...
Nature communications 5, 2014
Whole-genome annotation with BRAKER
K Hoff, A Lomsadze, M Borodovsky, M Stanke
Methods in molecular biology (Clifton, NJ) 1962, 65, 2019
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
BRAKER2: Automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database
T Br¨na, KJ Hoff, A Lomsadze, M Stanke, M Borodovsky
NAR genomics and bioinformatics 3 (1), lqaa108, 2021
Identification of protein coding regions in RNA transcripts
S Tang, A Lomsadze, M Borodovsky
Nucleic acids research 43 (12), e78-e78, 2015
The genome sequence of the North-European cucumber (Cucumis sativus L.) unravels evolutionary adaptation mechanisms in plants
R Wˇycicki, J Witkowicz, P Gawro˝ski, J D▒browska, A Lomsadze, ...
PLoS One 6 (7), e22728, 2011
Gene identification in prokaryotic genomes, phages, metagenomes, and EST sequences with GeneMarkS suite
M Borodovsky, A Lomsadze
Current protocols in microbiology, 1E. 7.1-1E. 7.17, 2014
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
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