GeneMark: Relevant References

News | Books | Gene Finding Journal Publications | Issues in Gene Finding | DNA, proteins and cell systems modeling and analysis



Borodovsky M. and Ekisheva S.
Problems and Solutions in Biological Sequence Analysis
Cambridge University Press, 2006
Publisher | DOI | Amazon| Review | Review 2 | Russian Translation

Gene Finding

Lars Gabriel, Tomáš Brůna, Katharina J. Hoff, Matthis EbAlexandre Lomsadze, Mark Borodovsky, Mario Stanke
BRAKER3: Fully automated genome annotation using RNA-Seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA"
Under review
PubMed | bioRxiv

Tomas Bruna, Alexandre Lomsadze and Mark Borodovsky
"GeneMark-ETP: Automatic Gene Finding in Eukaryotic Genomes in Consistency with Extrinsic Data"
Under review
bioRxiv, 2023, January 5
PubMed | bioRxiv

Lars Gabriel, Katharina Hoff, Tomas Bruna, Mark Borodovsky and Mario Stanke
"TSEBRA: transcript selector for BRAKER"
BMC Bioinformatics, 2021, 22(566)
PubMed | Article

Karl Gemayel, Alexandre Lomsadze and Mark Borodovsky
"StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes"
Frontiers in Bioinformatics, 2021 Dec; Volume 1

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Issues in Gene Finding back to top

Aaron Pfennig, Alexandre Lomsadze, Borodovsky M.
"Annotation of Phage Genomes with Multiple Genetic Codes."
bioRxiv, 2022, July 2

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

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

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

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

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.

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.

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

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.

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.

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

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

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

Mitrophanov A.Yu. and Borodovsky M.
"Statistical significance in biological sequence analysis."
Briefings in Bioinformatics, 2006, Vol. 7, No.1, pp. 2-24

Mitrophanov A.Yu., Lomsadze A. and Borodovsky M.
"Sensitivity of hidden Markov models."
Journal of Applied Probability, 2005, Vol. 42, pp. 632-642

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

Jean-F. Tomb et al.
The complete genome sequence of the gastric pathogen Helicobacter pylori
Nature, 1997 August 7, 388(6642):539-47.

Carol Bult et al.
Complete Genome Sequence of the Methanogenic Archaeon, Methanococcus jannaschii
Science, 1996 Aug; Vol. 273. no. 5278, pp. 1058 - 1073

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

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