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HIV classification using the coalescent theory.
Bulla I, Schultz AK, Schreiber F, Zhang M, Leitner T, Korber B, Morgenstern B, Stanke M. Bulla I, et al. Bioinformatics. 2010 Jun 1;26(11):1409-15. doi: 10.1093/bioinformatics/btq159. Epub 2010 Apr 16. Bioinformatics. 2010. PMID: 20400454 Free PMC article.
WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes.
Hoff KJ, Stanke M. Hoff KJ, et al. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W123-8. doi: 10.1093/nar/gkt418. Epub 2013 May 21. Nucleic Acids Res. 2013. PMID: 23700307 Free PMC article.
Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
Stanke M, Diekhans M, Baertsch R, Haussler D. Stanke M, et al. Bioinformatics. 2008 Mar 1;24(5):637-44. doi: 10.1093/bioinformatics/btn013. Epub 2008 Jan 24. Bioinformatics. 2008. PMID: 18218656
Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species.
Keller O, Odronitz F, Stanke M, Kollmar M, Waack S. Keller O, et al. BMC Bioinformatics. 2008 Jun 13;9:278. doi: 10.1186/1471-2105-9-278. BMC Bioinformatics. 2008. PMID: 18554390 Free PMC article.
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus.
Schultz AK, Bulla I, Abdou-Chekaraou M, Gordien E, Morgenstern B, Zoaulim F, Dény P, Stanke M. Schultz AK, et al. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W193-8. doi: 10.1093/nar/gks414. Epub 2012 May 16. Nucleic Acids Res. 2012. PMID: 22600739 Free PMC article.
A novel hybrid gene prediction method employing protein multiple sequence alignments.
Keller O, Kollmar M, Stanke M, Waack S. Keller O, et al. Bioinformatics. 2011 Mar 15;27(6):757-63. doi: 10.1093/bioinformatics/btr010. Epub 2011 Jan 6. Bioinformatics. 2011. PMID: 21216780
jpHMM: improving the reliability of recombination prediction in HIV-1.
Schultz AK, Zhang M, Bulla I, Leitner T, Korber B, Morgenstern B, Stanke M. Schultz AK, et al. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W647-51. doi: 10.1093/nar/gkp371. Epub 2009 May 14. Nucleic Acids Res. 2009. PMID: 19443440 Free PMC article.
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.
Zhang M, Schultz AK, Calef C, Kuiken C, Leitner T, Korber B, Morgenstern B, Stanke M. Zhang M, et al. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W463-5. doi: 10.1093/nar/gkl255. Nucleic Acids Res. 2006. PMID: 16845050 Free PMC article.
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