Stefanie Nachtweide and Mario Stanke (2019), Multi-Genome Annotation with AUGUSTUS. Methods Mol Biol., 1962:139-160. doi: 10.1007/978-1-4939-9173-0_8. PubMed PMID: 31020558
Hoff KJ, Lomsadze A, Borodovsky M, Stanke M. (2019), Whole-Genome Annotation with BRAKER. Methods Mol Biol., 1962:65-95. doi: 10.1007/978-1-4939-9173-0_5. PubMed PMID: 31020555.
Hoff KJ. ,Stanke M. (2018). Predicting genes in single genomes with AUGUSTUS. Current Protocols in Bioinformatics, e57. doi: 10.1002/cpbi.57. manuscript (PDF)
Stefanie König, Lars Romoth, Lizzy Gerischer, and Mario Stanke (2016) Simultaneous gene finding in multiple genomes. Bioinformatics, 32 (22): 3388-3395, doi: 10.1093/bioinformatics/btw494
Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008) Using native and syntenically mapped cDNA alignments to improve de novo gene finding. Bioinformatics, doi: 10.1093/bioinformatics/btn013
Mario Stanke, Ana Tzvetkova, Burkhard Morgenstern (2006) "AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome" BMC Genome Biology, 7(Suppl 1):S11
Mario Stanke , Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, Burkhard Morgenstern (2006) "AUGUSTUS: ab initio prediction of alternative transcripts" Nucleic Acids Research, 34: W435-W439.
Mario Stanke, Oliver Schoeffmann, Burkhard Morgenstern and Stephan Waack "Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources", BMC Bioinformatics, 7:62 (2006)
Mario Stanke and Burkhard Morgenstern (2005) "AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints", Nucleic Acids Research, 33, W465-W467
Mario Stanke, Rasmus Steinkamp, Stephan Waack and Burkhard Morgenstern, "AUGUSTUS: a web server for gene finding in eukaryotes" (2004), Nucleic Acids Research, Vol. 32, W309-W312
Mario Stanke (2003), Gene Prediction with a Hidden-Markov Model. Ph.D. thesis, Universitaet Goettingen, http://webdoc.sub.gwdg.de/diss/2004/stanke/
Mario Stanke and Stephan Waack (2003), Gene Prediction with a Hidden-Markov Model and a new Intron Submodel. Bioinformatics, Vol. 19, Suppl. 2, pages ii215-ii225