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GeneMark.hmm: new solutions for gene finding.
Lukashin AV, Borodovsky M. Lukashin AV, et al. Among authors: borodovsky m. Nucleic Acids Res. 1998 Feb 15;26(4):1107-15. doi: 10.1093/nar/26.4.1107. Nucleic Acids Res. 1998. PMID: 9461475 Free PMC article.
Probabilistic models for biological sequences: selection and Maximum Likelihood estimation.
Ekisheva S, Borodovsky M. Ekisheva S, et al. Among authors: borodovsky m. Int J Bioinform Res Appl. 2006;2(3):305-24. doi: 10.1504/IJBRA.2006.010607. Int J Bioinform Res Appl. 2006. PMID: 18048168
NCBI prokaryotic genome annotation pipeline.
Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. Tatusova T, et al. Among authors: borodovsky m. Nucleic Acids Res. 2016 Aug 19;44(14):6614-24. doi: 10.1093/nar/gkw569. Epub 2016 Jun 24. Nucleic Acids Res. 2016. PMID: 27342282 Free PMC article.
TrueSight: a new algorithm for splice junction detection using RNA-seq.
Li Y, Li-Byarlay H, Burns P, Borodovsky M, Robinson GE, Ma J. Li Y, et al. Among authors: borodovsky m. Nucleic Acids Res. 2013 Feb 1;41(4):e51. doi: 10.1093/nar/gks1311. Epub 2012 Dec 18. Nucleic Acids Res. 2013. PMID: 23254332 Free PMC article.
UnSplicer: mapping spliced RNA-Seq reads in compact genomes and filtering noisy splicing.
Burns PD, Li Y, Ma J, Borodovsky M. Burns PD, et al. Among authors: borodovsky m. Nucleic Acids Res. 2014 Feb;42(4):e25. doi: 10.1093/nar/gkt1141. Epub 2013 Nov 19. Nucleic Acids Res. 2014. PMID: 24259430 Free PMC article.
Protein secondary structure prediction for a single-sequence using hidden semi-Markov models.
Aydin Z, Altunbasak Y, Borodovsky M. Aydin Z, et al. Among authors: borodovsky m. BMC Bioinformatics. 2006 Mar 30;7:178. doi: 10.1186/1471-2105-7-178. BMC Bioinformatics. 2006. PMID: 16571137 Free PMC article.
Eukaryotic gene prediction using GeneMark.hmm-E and GeneMark-ES.
Borodovsky M, Lomsadze A. Borodovsky M, et al. Curr Protoc Bioinformatics. 2011 Sep;Chapter 4:Unit 4.6.1-10. doi: 10.1002/0471250953.bi0406s35. Curr Protoc Bioinformatics. 2011. PMID: 21901742 Free PMC article.
Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm.
Antonov I, Borodovsky M. Antonov I, et al. Among authors: borodovsky m. J Bioinform Comput Biol. 2010 Jun;8(3):535-51. doi: 10.1142/s0219720010004847. J Bioinform Comput Biol. 2010. PMID: 20556861
Ab initio gene identification in metagenomic sequences.
Zhu W, Lomsadze A, Borodovsky M. Zhu W, et al. Among authors: borodovsky m. Nucleic Acids Res. 2010 Jul;38(12):e132. doi: 10.1093/nar/gkq275. Epub 2010 Apr 19. Nucleic Acids Res. 2010. PMID: 20403810 Free PMC article.
Prokaryotic gene prediction using GeneMark and GeneMark.hmm.
Borodovsky M, Mills R, Besemer J, Lomsadze A. Borodovsky M, et al. Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.5. doi: 10.1002/0471250953.bi0405s01. Curr Protoc Bioinformatics. 2003. PMID: 18428700
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