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Alex Lomsadze
Alex Lomsadze
Senior Research Scientist, The Wallace H. Coulter Department of Biomedical Engineering at Georgia
Verified email at gatech.edu
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Cited by
Cited by
Year
NCBI prokaryotic genome annotation pipeline
T Tatusova, M DiCuccio, A Badretdin, V Chetvernin, EP Nawrocki, ...
Nucleic Acids Research, gkw569, 2016
34222016
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
18532001
Ab initio gene identification in metagenomic sequences
W Zhu, A Lomsadze, M Borodovsky
Nucleic acids research 38 (12), e132-e132, 2010
10612010
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
7272008
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
6912015
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
6742005
Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication
NATURE BIOTECHNOLOGY, 2014
5262014
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
4382013
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
4302010
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
3122012
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
3032003
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
2852014
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
2592014
Whole-genome annotation with BRAKER
K Hoff, A Lomsadze, M Borodovsky, M Stanke
Methods in molecular biology (Clifton, NJ) 1962, 65, 2019
2542019
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
1882004
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
1732021
Identification of protein coding regions in RNA transcripts
S Tang, A Lomsadze, M Borodovsky
Nucleic acids research 43 (12), e78-e78, 2015
1692015
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
1202011
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
992014
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
882018
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