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GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses.
Besemer J, Borodovsky M. Besemer J, et al. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W451-4. doi: 10.1093/nar/gki487. Nucleic Acids Res. 2005. PMID: 15980510 Free PMC article.
Prokaryotic gene prediction using GeneMark and GeneMark.hmm.
Borodovsky M, Mills R, Besemer J, Lomsadze A. Borodovsky M, et al. Among authors: besemer j. Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.5. doi: 10.1002/0471250953.bi0405s01. Curr Protoc Bioinformatics. 2003. PMID: 18428700
GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.
Besemer J, Lomsadze A, Borodovsky M. Besemer J, et al. Nucleic Acids Res. 2001 Jun 15;29(12):2607-18. doi: 10.1093/nar/29.12.2607. Nucleic Acids Res. 2001. PMID: 11410670 Free PMC article.
Heuristic approach to deriving models for gene finding.
Besemer J, Borodovsky M. Besemer J, et al. Nucleic Acids Res. 1999 Oct 1;27(19):3911-20. doi: 10.1093/nar/27.19.3911. Nucleic Acids Res. 1999. PMID: 10481031 Free PMC article.
The structure of unstable constitutive revertants of mutant galOP-308::IS2-I.
Delius H, Charlier D, Besemer J. Delius H, et al. Mol Gen Genet. 1980;179(2):391-7. doi: 10.1007/BF00425470. Mol Gen Genet. 1980. PMID: 6258016
Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum.
Slupska MM, King AG, Fitz-Gibbon S, Besemer J, Borodovsky M, Miller JH. Slupska MM, et al. Among authors: besemer j. J Mol Biol. 2001 Jun 1;309(2):347-60. doi: 10.1006/jmbi.2001.4669. J Mol Biol. 2001. PMID: 11371158
The isolation of IS1 and IS2 DNA.
Schmidt F, Besemer J, Starlinger P. Schmidt F, et al. Mol Gen Genet. 1976 May 7;145(2):145-54. doi: 10.1007/BF00269586. Mol Gen Genet. 1976. PMID: 934052
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