Mario Stanke

According to our database, Mario Stanke authored at least 28 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

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., December, 2023

2022

Global, highly specific and fast filtering of alignment seeds.

Matthis Ebel, Giovanna Migliorelli, Mario Stanke

BMC Bioinform., 2022

End-to-end learning of evolutionary models to find coding regions in genome alignments.

Darvin Mertsch, Mario Stanke

Bioinform., 2022

Co-evolution of Spies and Resistance Fighters.

Johanna Lange, Mario Stanke, Marc Ebner

Proceedings of the Applications of Evolutionary Computation - 25th European Conference, 2022

2021

TSEBRA: transcript selector for BRAKER.

Lars Gabriel, Katharina Jasmin Hoff, Tomás Bruna, Mark Borodovsky, Mario Stanke

BMC Bioinform., 2021

2019

VARUS: sampling complementary RNA reads from the sequence read archive.

Mario Stanke, Willy Bruhn, Felix Becker, Katharina Jasmin Hoff

BMC Bioinform., 2019

2016

Simultaneous gene finding in multiple genomes.

Stefanie König, Lars Romoth, Lizzy Gerischer, Mario Stanke

Bioinform., 2016

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

2014

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

2013

WebAUGUSTUS - a web service for training AUGUSTUS and predicting genes in eukaryotes.

Katharina Jasmin Hoff, Mario Stanke

Nucleic Acids Res., 2013

2012

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

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

A novel hybrid gene prediction method employing protein multiple sequence alignments.

Oliver Keller, Martin Kollmar, Mario Stanke, Stephan Waack

Bioinform., 2011

2010

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

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

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

Future Gener. Comput. Syst., 2009

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, 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

Nucleic Acids Res., 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

Using native and syntenically mapped cDNA alignments to improve <i>de novo</i> gene finding.

Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler

Bioinform., 2008

2007

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, 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

Nucleic Acids Res., 2007

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

AUGUSTUS: <i>ab initio</i> prediction of alternative transcripts.

Mario Stanke, Oliver Keller, Irfan Gunduz, Alec Hayes, Stephan Waack, Burkhard Morgenstern

Nucleic Acids Res., 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

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

2005

AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints.

Mario Stanke, Burkhard Morgenstern

Nucleic Acids Res., 2005

2004

Gene prediction with a hidden Markov model.

Mario Stanke

PhD thesis, 2004

AUGUSTUS: a web server for gene finding in eukaryotes.

Mario Stanke, Rasmus Steinkamp, Stephan Waack, Burkhard Morgenstern

Nucleic Acids Res., 2004

2003

Gene prediction with a hidden Markov model and a new intron submodel.

Mario Stanke, Stephan Waack

Proceedings of the European Conference on Computational Biology (ECCB 2003), 2003