Gene Finding
BRAKER3
Lars Gabriel, Tomas Bruna, Katharina J. Hoff, Matthis EbAlexandre Lomsadze, Mark Borodovsky, Mario Stanke
RAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA"
Genome Res 2024
PubMed |
bioRxiv
GeneMark-ETP
Tomas Bruna, Alexandre Lomsadze and Mark Borodovsky
"GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes"
Genome Res, 2024
PubMed |
bioRxiv
TSEBRA
Lars Gabriel, Katharina Hoff, Tomas Bruna, Mark Borodovsky and Mario Stanke
"TSEBRA: transcript selector for BRAKER"
BMC Bioinformatics, 2021, 22(566)
PubMed |
Article
StartLink+
Karl Gemayel, Alexandre Lomsadze and Mark Borodovsky
"StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes"
Frontiers in Bioinformatics, 2021 Dec; Volume 1
Article
GeneMark-HM
Alexandre Lomsadze, Christophe Bonny, Francesco Strozzi and Mark Borodovsky
"GeneMark-HM: improving gene prediction in DNA sequences of human microbiome"
NAR Genomics and Bioinformatics, 2021 May; 3(2):lqab047
PubMed |
Article
BRAKER2
Tomáš Brůna, Katharina J. Hoff, Alexandre Lomsadze, Mario Stanke, Mark Borodovsky
"BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database"
NAR Genomics and Bioinformatics, 2021 Jan; 3(1):lqaa108
PubMed |
Article |
bioRxiv
GeneMark-EP+
Tomáš Brůna, Alexandre Lomsadze, Mark Borodovsky
"GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins"
NAR Genomics and Bioinformatics, 2020 Jun; 2(2):lqaa026
PubMed |
Article |
bioRxiv
GeneMarkS-2
Alexandre Lomsadze, Karl Gemayel, Shiyuyun Tang and Mark Borodovsky
"Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes"
Genome Research, 2018 Jul; 28(7):1079-1089
PubMed |
Article |
bioRxiv
PGAP
Tatiana Tatusova, Michael DiCuccio, Azat Badretdin, Vyacheslav Chetvernin, Eric P. Nawrocki, Leonid Zaslavsky, Alexandre Lomsadze, Kim D. Pruitt, Mark Borodovsky and James Ostell
"NCBI prokaryotic genome annotation pipeline"
Nucleic Acids Research, 2016 Aug; 44(14):6614-24
PubMed |
Article
BRAKER1
Katharina J. Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky and Mario Stanke
"BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS"
Bioinformatics, 2016 Mar; 32(5):767-9
PubMed |
Article
GeneMarkS-T
Tang S, Lomsadze A and Borodovsky M
"Identification of protein coding regions in RNA transcripts"
Nucleic Acids Research, 2015 Jul; 43(12):e78
PubMed |
Article
GeneMark-ET
Lomsadze A., Burns P.D. and Borodovsky M.
"Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm."
Nucleic Acids Research, 2014 Sep; 42(15):e119
PubMed |
Article
MetaGeneMark
Zhu W., Lomsadze A. and Borodovsky M.
"Ab initio gene identification in metagenomic sequences."
Nucleic Acids Research, 2010 Jul; 38(12):e132
PubMed |
Article
GeneMark-ES, version 2
Ter-Hovhannisyan V., Lomsadze A., Chernoff Y. and Borodovsky M.
"Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training."
Genome Research, 2008 Dec; 18(12):1979-90
PubMed |
Article |
Supplemental Materials
GeneMark-ES, version 1
Lomsadze A., Ter-Hovhannisyan V., Chernoff Y. and Borodovsky M.
"Gene identification in novel eukaryotic genomes by self-training algorithm."
Nucleic Acids Research, 2005 Nov; 33(20):6494-506
PubMed |
Article
GeneMark Web Server
Besemer J. and Borodovsky M.
"GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses."
Nucleic Acids Research, 2005, Vol. 33, Web Server Issue, pp. W451-454
PubMed |
Article
VIOLIN
Mills R., Rozanov M., Lomsadze A., Tatusova T. and Borodovsky M.
"Improving gene annotation in complete viral genomes."
Nucleic Acids Research, 2003, Vol. 31, No. 23, 7041-7055
PubMed |
Article
GeneMarkS
Besemer J., Lomsadze A. and Borodovsky M.
"GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions."
Nucleic Acids Research, 2001, Vol. 29, No. 12, 2607-2618
PubMed |
Article
Heuristic Models
Besemer J. and Borodovsky M.
"Heuristic approach to deriving models for gene finding."
Nucleic Acids Research, 1999, Vol. 27, No. 19, pp. 3911-3920
PubMed |
Article
Frame-by-Frame
Shmatkov A.M., Melikyan A.A., Chernousko F.L. and Borodovsky M.
"Finding prokaryotic genes by the 'frame-by-frame' algorithm: targeting gene starts and overlapping genes."
Bioinformatics, 1999, Vol. 15, No. 11, pp. 874-886
PubMed |
Article
GeneMark-Genesis
Hayes W. and Borodovsky M.
"How to interpret an anonymous bacterial genome: machine learning approach to gene identification."
Genome Research, 1998, Vol. 8, No. 11, pp. 1154-1171
PubMed |
Article
GeneMark.hmm
Lukashin A. and Borodovsky M.
"GeneMark.hmm: new solutions for gene finding."
Nucleic Acids Research, 1998, Vol. 26, No. 4, pp. 1107-1115
PubMed |
Article
GeneMark
Borodovsky M. and McIninch J.
"GeneMark: parallel gene recognition for both DNA strands."
Computers & Chemistry, 1993, Vol. 17, No. 19, pp. 123-133
Abstract |
Article
Borodovsky M.Yu., McIninch J.
"Recognition of genes in DNA sequence with ambiguities"
Biosystems. , 1993;Vol 30(1-3), pp.161-71
PubMed |
Article
Three-periodic Markov chain models
Borodovsky M.Yu., Sprizhitskii Y.A., Golovanov E.I., and Aleksandrov A.A.
"Statistical Patterns in Primary Structures of the Functional Regions of the Genome in Escherichia Coli."
Molekular Biology, 1986, Vol. 20, pp. 826-833, 833-840, 1144-1150
Article
Issues in Gene Finding back to top
Aaron Pfennig, Alexandre Lomsadze, Borodovsky M.
MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes"
J Mol Biol, 2023
PubMed |
bioRxiv
Antonov I, Coakley A, Atkins JF, Baranov PV, Borodovsky M.
"Identification of the nature of reading frame transitions observed in prokaryotic genomes."
Nucleic Acids Research, 2013, 41(13):6514-30
PubMed |
Article
Burns PD, Li Y, Ma J, Borodovsky M.
"UnSplicer: mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing."
Nucleic Acids Research, 2013 Nov 19
PubMed |
Article |
Supplemental Materials
Antonov I., Baranov P. and Borodovsky M.
"GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences"
Nucleic Acids Research, Vol. 41, No. D1 (2013):D152-D156.
PubMed |
Article
Tang S., Antonov I. and Borodovsky M.
"MetaGeneTack: ab initio detection of frameshifts in metagenomic sequences."
Bioinformatics, Vol. 29, No. 1 (2013):114-116.
PubMed |
Article
Martin J., Zhu W., Passalacqua K., Bergman N. and Borodovsky M.
"Bacillus anthracis genome organization in light of whole transcriptome sequencing."
BMC Bioinformatics, 2010, 11(Suppl 3):S10 doi:10.1186/1471-2105-11-S3-S10
PubMed |
Article |
Supplemental Materials
Antonov I. and Borodovsky M.
"GeneTack: Frameshift Identification in Protein Coding Sequences by the Viterbi Algorithm."
J Bioinformatics and Computational Biology, Vol. 8, No. 3 (2010):1-17.
Medline |
Article
Azad R.K. and Borodovsky M.Y.
"Probabilistic methods of identifying genes in prokaryotic genomes: connections to the HMM theory."
Briefings in Bioinformatics, 2004, Vol. 5, No. 2, pp. 118-130
PubMed |
Article
Azad R.K. and Borodovsky M.
"Effects of choice of DNA sequence model structure on gene identification accuracy."
Bioinformatics, 2004, Vol. 20, No. 7, pp. 993-1005
PubMed |
Article
DNA, proteins and cell systems modeling and analysis back to top
Bruna T., R. Aryal, O. Dudchenko, D.J. Sargent, et al.
"A chromosome-length genome assembly and annotation of blackberry (Rubus argutus Link., cv. 'Hillquist')."
G3. Genes|Genomes|Genetics. 2022, 12
Article
Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, et al.
"Pan genome of the phytoplankton Emiliania underpins its global distribution."
Nature. 2013, 499(7457):209-13
PubMed|
Article
Junhuan Xu et al.
Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi.
BMC Genomics, 2011 Mar 24; 10.1186/1471-2164-12-161
Article
Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, et al.
"The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex"
Plant Cell. 2010, 22(9):2943-55.
PubMed|
Article
Guillaume Blanc et al.
The Chlorella variabilis NC64A Genome Reveals Adaptation to Photosymbiosis, Coevolution with Viruses, and Cryptic Sex
The Plant Cell, 2010 Sep 17; 10.1105/tpc.110.076406.
Article
Jason Stajich et al.
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus)
Proc Natl Acad Sci USA, 2010 Jun 29; 107(26):11889-94.
Article
Svetlana Ekisheva and Mark Borodovsky
"Uniform Accuracy of the Maximum Likelihood Estimates for Probabilistic Models of Biological Sequences."
Methodology and Computing in Applied Probability, 2009 Feb; 10.1007/s11009-009-9125-7
Article
Mitrophanov A.Yu. and Borodovsky M.
"Convergence rate estimation for the TKF91 model of biological sequence length evolution"
Math Biosci., 2007 Oct;209(2):470-85. Epub 2007 Mar 13.
PubMed |
Article
Piriyapongsa J., Polavarapu N., Borodovsky M. and McDonald J.
"Exonization of the LTR transposable elements in human genome"
BMC Genomics, 2007 Aug 28;8:291.
PubMed |
Article
Mitrophanov A.Yu., Churchward G. and Borodovsky M.
"Control of Streptococcus pyogenes virulence: Modeling of the CovR/S signal transduction system"
J Theor Biol., 2007 May 7;246(1):113-28. Epub 2006 Nov 21.
PubMed |
Article
Aydin Z., Altunbasak Y. and Borodovsky M.
"Protein secondary structure prediction for a single-sequence using hidden semi-Markov models."
BMC Bioinformatics, 2006 Mar 30;7:178
PubMed |
Article
Kim S.B., Tsui K. and Borodovsky M.
"Multiple testing in large-scale contingency tables: inferring patterns of pair-wise amino acid association in beta-sheets"
Int. J. Bioinformatics Research and Applications, 2006, Vol. 2, No. 2, pp 193-217
Article
Ekisheva S. and Borodovsky M.
"Probabilistic models for biological sequences: selection and Maximum Likelihood estimation"
Int. J. Bioinformatics Research and Applications, 2006, Vol. 2, No. 3, pp 305-324
Article
Mitrophanov A.Yu. and Borodovsky M.
"Statistical significance in biological sequence analysis."
Briefings in Bioinformatics, 2006, Vol. 7, No.1, pp. 2-24
PubMed |
Article
Mitrophanov A.Yu., Lomsadze A. and Borodovsky M.
"Sensitivity of hidden Markov models."
Journal of Applied Probability, 2005, Vol. 42, pp. 632-642
Article
Kattenhorn L.M., Mills R., Wagner M., Lomsadze A., Makeev V., Borodovsky M., Ploegh H.L. and Kessler B.M
"Identification of Proteins Associated with Murine Cytomegalovirus Virions."
Journal of Virology, 2004, Vol. 78, No. 20, pp. 11187-11197
PubMed |
Article
Jean-F. Tomb et al.
The complete genome sequence of the gastric pathogen Helicobacter pylori
Nature, 1997 August 7, 388(6642):539-47.
Article
Carol Bult et al.
Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
Science, 1996 Aug; Vol. 273. no. 5278, pp. 1058 - 1073
Article
Kleffe J. and Borodovsky M.
"First and second moment of counts of words in random texts generated by Markov chains"
Comput. Appl. Biosci., 1992, Vol. 8, No. 5, pp. 433-441
PubMed |
Article
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