Mario Stanke

31 papers B 1C 1Journal 28
YearRankTypeTitle / Venue / Authors
2024 J jnl
Tiberius: end-to-end deep learning with an HMM for gene prediction.
Bioinform.
Lars Gabriel, Felix Becker, Katharina Jasmin Hoff, Mario Stanke
2024 J jnl
learnMSA2: deep protein multiple alignments with large language and hidden Markov models.
Bioinform.
Felix Becker, Mario Stanke
2023 J jnl
Galba: genome annotation with miniprot and AUGUSTUS.
BMC Bioinform.
Tomás Bruna, Heng Li, Joseph Guhlin, Daniel Honsel, Steffen Herbold, Mario Stanke, Natalia Nenasheva, Matthis Ebel, Lars Gabriel, Katharina Jasmin Hoff
2022 B conf
Co-evolution of Spies and Resistance Fighters.
EvoApplications
Johanna Lange, Mario Stanke, Marc Ebner
2022 J jnl
End-to-end learning of evolutionary models to find coding regions in genome alignments.
Bioinform.
Darvin Mertsch, Mario Stanke
2022 J jnl
Global, highly specific and fast filtering of alignment seeds.
BMC Bioinform.
Matthis Ebel, Giovanna Migliorelli, Mario Stanke
2021 J jnl
TSEBRA: transcript selector for BRAKER.
BMC Bioinform.
Lars Gabriel, Katharina Jasmin Hoff, Tomás Bruna, Mark Borodovsky, Mario Stanke
2019 J jnl
VARUS: sampling complementary RNA reads from the sequence read archive.
BMC Bioinform.
Mario Stanke, Willy Bruhn, Felix Becker, Katharina Jasmin Hoff
2016 J jnl
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.
Bioinform.
Katharina Jasmin Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke
2016 J jnl
Simultaneous gene finding in multiple genomes.
Bioinform.
Stefanie König, Lars Romoth, Lizzy Gerischer, Mario Stanke
2015 J jnl
Simultaneous gene finding in multiple genomes.
PeerJ Prepr.
Stefanie König, Lars Romoth, Lizzy Gerischer, Mario Stanke
2014 J jnl
CRF-based models of protein surfaces improve protein-protein interaction site predictions.
BMC Bioinform.
Zhijie Dong, Keyu Wang, Truong Khanh Linh Dang, Mehmet Gültas, Marlon Welter, Torsten Wierschin, Mario Stanke, Stephan Waack
2013 J jnl
WebAUGUSTUS - a web service for training AUGUSTUS and predicting genes in eukaryotes.
Nucleic Acids Res.
Katharina Jasmin Hoff, Mario Stanke
2012 J jnl
jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus.
Nucleic Acids Res.
Anne-Kathrin Schultz, Ingo Bulla, Mariama Abdou-Chekaraou, Emmanuel Gordien, Burkhard Morgenstern, Fabien Zoulim, Paul Dény, Mario Stanke
2011 J jnl
A novel hybrid gene prediction method employing protein multiple sequence alignments.
Bioinform.
Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack
2011 J jnl
Detection of viral sequence fragments of HIV-1 subfamilies yet unknown.
BMC Bioinform.
Thomas Unterthiner, Anne-Kathrin Schultz, Jan Bulla, Burkhard Morgenstern, Mario Stanke, Ingo Bulla
2010 J jnl
HIV classification using the coalescent theory.
Bioinform.
Ingo Bulla, Anne-Kathrin Schultz, Fabian Schreiber, Ming Zhang, Thomas Leitner, Bette T. Korber, Burkhard Morgenstern, Mario Stanke
2009 J jnl
AUGUSTUS at MediGRID: Adaption of a bioinformatics application to grid computing for efficient genome analysis.
Future Gener. Comput. Syst.
Dietmar Sommerfeld, Thomas Lingner, Mario Stanke, Burkhard Morgenstern, Harald Richter
2009 J jnl
jpHMM: Improving the reliability of recombination prediction in HIV-1.
Nucleic Acids Res.
Anne-Kathrin Schultz, Ming Zhang, Ingo Bulla, Thomas Leitner, Bette T. Korber, Burkhard Morgenstern, Mario Stanke
2008 J jnl
Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species.
BMC Bioinform.
Oliver Keller, Florian Odronitz, Mario Stanke, Martin Kollmar, Stephan Waack
2008 J jnl
The UCSC Genome Browser Database: 2008 update.
Nucleic Acids Res.
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, Jakob Skou Pedersen, Andy Pohl, Brian J. Raney, Brooke L. Rhead, Kate R. Rosenbloom, Kayla E. Smith, Mario Stanke, Archana Thakkapallayil, Heather Trumbower, Ting Wang, Ann S. Zweig, David Haussler, W. James Kent
2008 J jnl
Using native and syntenically mapped cDNA alignments to improve
Bioinform.
Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler
2007 J jnl
The UCSC genome browser database: update 2007.
Nucleic Acids Res.
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, Brian J. Raney, Andy Pohl, Jakob Skou Pedersen, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Mark Diekhans, Hiram Clawson, Gill Bejerano, Galt P. Barber, Robert Baertsch, David Haussler, W. James Kent
2006 J jnl
A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes.
BMC Bioinform.
Anne-Kathrin Schultz, Ming Zhang, Thomas Leitner, Carla Kuiken, Bette T. Korber, Burkhard Morgenstern, Mario Stanke
2006 J jnl
AUGUSTUS:
Nucleic Acids Res.
Mario Stanke, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, Burkhard Morgenstern
2006 J jnl
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.
BMC Bioinform.
Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern, Stephan Waack
2006 J jnl
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.
Nucleic Acids Res.
Ming Zhang, Anne-Kathrin Schultz, Charles Calef, Carla Kuiken, Thomas Leitner, Bette T. Korber, Burkhard Morgenstern, Mario Stanke
2005 J jnl
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.
Nucleic Acids Res.
Mario Stanke, Burkhard Morgenstern
2004 J jnl
AUGUSTUS: a web server for gene finding in eukaryotes.
Nucleic Acids Res.
Mario Stanke, Rasmus Steinkamp, Stephan Waack, Burkhard Morgenstern
2004 — —
Gene prediction with a hidden Markov model.
Mario Stanke
2003 C conf
Gene prediction with a hidden Markov model and a new intron submodel.
ECCB
Mario Stanke, Stephan Waack