Gene prediction with a hidden Markov model and a new intron submodel. - Mario Stanke; Stephan Waack (ECCB, 2003)

AUGUSTUS: a web server for gene finding in eukaryotes. - Mario Stanke; Rasmus Steinkamp; Stephan Waack; Burkhard Morgenstern (Nucleic Acids Res., 2004)

Gene prediction with a hidden Markov model. - Mario Stanke (2004)

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. - Mario Stanke; Burkhard Morgenstern (Nucleic Acids Res., 2005)

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes. - Anne-Kathrin Schultz; Ming Zhang; Thomas Leitner; Carla Kuiken; Bette T. Korber; Burkhard Morgenstern; Mario Stanke (BMC Bioinform., 2006)

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources. - Mario Stanke; Oliver Schöffmann; Burkhard Morgenstern; Stephan Waack (BMC Bioinform., 2006)

AUGUSTUS: ab initio prediction of alternative transcripts. - Mario Stanke; Oliver Keller; Irfan Gunduz; Alec Hayes; Stephan Waack; Burkhard Morgenstern (Nucleic Acids Res., 2006)

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. - Ming Zhang; Anne-Kathrin Schultz; Charles Calef; Carla Kuiken; Thomas Leitner; Bette T. Korber; Burkhard Morgenstern; Mario Stanke (Nucleic Acids Res., 2006)

The UCSC genome browser database: update 2007. - Robert M. Kuhn; Donna Karolchik; Ann S. Zweig; Heather Trumbower; Daryl J. Thomas; Archana Thakkapallayil; Charles W. Sugnet; Mario Stanke; Kayla E. Smith; Adam C. Siepel; Kate R. Rosenbloom; Brooke L. Rhead; et al. (Nucleic Acids Res., 2007)

Using native and syntenically mapped cDNA alignments to improve de novo gene finding. - Mario Stanke; Mark Diekhans; Robert Baertsch; David Haussler (Bioinform., 2008)

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species. - Oliver Keller; Florian Odronitz; Mario Stanke; Martin Kollmar; Stephan Waack (BMC Bioinform., 2008)

The UCSC Genome Browser Database: 2008 update. - Donna Karolchik; Robert M. Kuhn; Robert Baertsch; Galt P. Barber; Hiram Clawson; Mark Diekhans; Belinda Giardine; Rachel A. Harte; Angela S. Hinrichs; Fan Hsu; Kord M. Kober; Webb Miller; et al. (Nucleic Acids Res., 2008)

AUGUSTUS at MediGRID: Adaption of a bioinformatics application to grid computing for efficient genome analysis. - Dietmar Sommerfeld; Thomas Lingner; Mario Stanke; Burkhard Morgenstern; Harald Richter 001 (Future Gener. Comput. Syst., 2009)

jpHMM: Improving the reliability of recombination prediction in HIV-1. - Anne-Kathrin Schultz; Ming Zhang; Ingo Bulla; Thomas Leitner; Bette T. Korber; Burkhard Morgenstern; Mario Stanke (Nucleic Acids Res., 2009)

HIV classification using the coalescent theory. - Ingo Bulla; Anne-Kathrin Schultz; Fabian Schreiber; Ming Zhang; Thomas Leitner; Bette T. Korber; Burkhard Morgenstern; Mario Stanke (Bioinform., 2010)

A novel hybrid gene prediction method employing protein multiple sequence alignments. - Oliver Keller; Martin Kollmar; Mario Stanke; Stephan Waack (Bioinform., 2011)

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown. - Thomas Unterthiner; Anne-Kathrin Schultz; Jan Bulla; Burkhard Morgenstern; Mario Stanke; Ingo Bulla (BMC Bioinform., 2011)

jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. - Anne-Kathrin Schultz; Ingo Bulla; Mariama Abdou-Chekaraou; Emmanuel Gordien; Burkhard Morgenstern; Fabien Zoulim; Paul Dény; Mario Stanke (Nucleic Acids Res., 2012)

WebAUGUSTUS - a web service for training AUGUSTUS and predicting genes in eukaryotes. - Katharina Jasmin Hoff; Mario Stanke (Nucleic Acids Res., 2013)

CRF-based models of protein surfaces improve protein-protein interaction site predictions. - Zhijie Dong; Keyu Wang; Truong Khanh Linh Dang; Mehmet Gültas; Marlon Welter; Torsten Wierschin; Mario Stanke; Stephan Waack (BMC Bioinform., 2014)

Simultaneous gene finding in multiple genomes. - Stefanie König; Lars Romoth; Lizzy Gerischer; Mario Stanke (PeerJ Prepr., 2015)

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. - Katharina Jasmin Hoff; Simone Lange; Alexandre Lomsadze; Mark Borodovsky; Mario Stanke (Bioinform., 2016)

VARUS: sampling complementary RNA reads from the sequence read archive. - Mario Stanke; Willy Bruhn; Felix Becker; Katharina Jasmin Hoff (BMC Bioinform., 2019)

TSEBRA: transcript selector for BRAKER. - Lars Gabriel; Katharina Jasmin Hoff; Tomás Bruna; Mark Borodovsky; Mario Stanke (BMC Bioinform., 2021)

Co-evolution of Spies and Resistance Fighters. - Johanna Lange; Mario Stanke; Marc Ebner (EvoApplications, 2022)

End-to-end learning of evolutionary models to find coding regions in genome alignments. - Darvin Mertsch; Mario Stanke (Bioinform., 2022)

Global, highly specific and fast filtering of alignment seeds. - Matthis Ebel; Giovanna Migliorelli; Mario Stanke (BMC Bioinform., 2022)

Galba: genome annotation with miniprot and AUGUSTUS. - Tomás Bruna; Heng Li; Joseph Guhlin; Daniel Honsel; Steffen Herbold; Mario Stanke; Natalia Nenasheva; Matthis Ebel; Lars Gabriel; Katharina Jasmin Hoff (BMC Bioinform., 2023)

learnMSA2: deep protein multiple alignments with large language and hidden Markov models. - Felix Becker; Mario Stanke (Bioinform., 2024)