Mario Stanke

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Katharina HoffUniversity of GreifswaldVerified email at uni-greifswald.de
Burkhard MorgensternProfessor of Bioinformatics, University of GöttingenVerified email at gwdg.de
Stephan WaackProfessor für Informatik, Universität GöttingenVerified email at informatik.uni-goettingen.de
Mark BorodovskyRegents' Professor, Georgia TechVerified email at gatech.edu
Mark DiekhansUniversity of California, Santa Cruz; UC Santa Cruz Genomics InstituteVerified email at soe.ucsc.edu
Alex LomsadzeSenior Research Scientist, The Wallace H. Coulter Department of Biomedical Engineering at GeorgiaVerified email at gatech.edu
David HausslerScientific Director, UC Santa Cruz Genomics Institute, University of California, Santa CruzVerified email at soe.ucsc.edu
Bette KorberLos Alamos National LaboratoryVerified email at lanl.gov
Ming ZhangLos Alamos National LaboratoryVerified email at lanl.gov
Thomas LeitnerLos Alamos National LaboratoryVerified email at lanl.gov
Martin KollmarVerified email at nmr.mpibpc.mpg.de
Jakob Skou PedersenProfessor at Department of Molecular Medicine, Aarhus UniversityVerified email at ki.au.dk
W James KentUC Santa Cruz Genomics Institute, University of California Santa Cruz, UCSC Genome BrowserVerified email at soe.ucsc.edu
Hiram ClawsonUC Santa Cruz Genomics Institute, UCSC Genome BrowserVerified email at ucsc.edu
Kate RosenbloomUC Santa Cruz Genomics Institute, UCSC Genome BrowserVerified email at soe.ucsc.edu
Robert KuhnUC Santa Cruz Genomics Institute, UCSC Genome BrowserVerified email at soe.ucsc.edu
Brooke RheadSenior Statistical Geneticist, TempusVerified email at berkeley.edu
Ann ZweigUCSC Genome Browser, UC Santa Cruz Genomics InstituteVerified email at ucsc.edu
Galt BarberUC Santa Cruz Genomics Institute, UCSC Genome BrowserVerified email at folkplanet.com
Brian RaneyUniversity of California, Santa Cruz, UC Santa Cruz Genomics Institute, UCSC Genome BrowserVerified email at ucsc.edu

Mario Stanke

Professor of Bioinformatics, University of Greifswald

Verified email at uni-greifswald.de - Homepage

gene prediction comparative genome analysis machine learning probabilistical graphical models molecular evolution


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AUGUSTUS: ab initio prediction of alternative transcripts M Stanke, O Keller, I Gunduz, A Hayes, S Waack, B Morgenstern Nucleic acids research 34 (suppl_2), W435-W439, 2006	2180	2006
Using native and syntenically mapped cDNA alignments to improve de novo gene finding M Stanke, M Diekhans, R Baertsch, D Haussler Bioinformatics 24 (5), 637-644, 2008	1950	2008
Gene prediction with a hidden Markov model and a new intron submodel M Stanke, S Waack Bioinformatics-Oxford 19 (2), 215-225, 2003	1736	2003
The genome of the model beetle and pest Tribolium castaneum. S Richards, RA Gibbs, GM Weinstock, SJ Brown, R Denell, RW Beeman, ... Nature 452 (7190), 949-955, 2008	1480	2008
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints M Stanke, B Morgenstern Nucleic acids research 33 (suppl_2), W465-W467, 2005	1461	2005
Genome Sequence of Aedes aegypti, a Major Arbovirus Vector V Nene, JR Wortman, D Lawson, B Haas, C Kodira, Z Tu, B Loftus, Z Xi, ... Science 316 (5832), 1718-1723, 2007	1358	2007
AUGUSTUS: a web server for gene finding in eukaryotes M Stanke, R Steinkamp, S Waack, B Morgenstern Nucleic acids research 32 (suppl_2), W309-W312, 2004	1314	2004
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources M Stanke, O Schöffmann, B Morgenstern, S Waack BMC bioinformatics 7, 1-11, 2006	1253	2006
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database T Brůna, KJ Hoff, A Lomsadze, M Stanke, M Borodovsky NAR genomics and bioinformatics 3 (1), lqaa108, 2021	1242	2021
The genome of the blood fluke Schistosoma mansoni M Berriman, BJ Haas, PT LoVerde, RA Wilson, GP Dillon, GC Cerqueira, ... Nature 460 (7253), 352-358, 2009	1221	2009
The Amphimedon queenslandica genome and the evolution of animal complexity M Srivastava, O Simakov, J Chapman, B Fahey, MEA Gauthier, T Mitros, ... Nature 466 (7307), 720-726, 2010	1177	2010
BRAKER1: unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS KJ Hoff, S Lange, A Lomsadze, M Borodovsky, M Stanke Bioinformatics 32 (5), 767-769, 2016	1048	2016
Genome Sequence of the Pea Aphid Acyrthosiphon pisum International Aphid Genomics Consortium PLoS biology 8 (2), e1000313, 2010	1006	2010
Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species JH Werren, S Richards, CA Desjardins, O Niehuis, J Gadau, ... Science 327 (5963), 343-348, 2010	941	2010
Assessment of transcript reconstruction methods for RNA-seq T Steijger, JF Abril, PG Engström, F Kokocinski, TJ Hubbard, R Guigó, ... Nature methods 10 (12), 1177-1184, 2013	792	2013
Draft genome of the filarial nematode parasite Brugia malayi E Ghedin, S Wang, D Spiro, E Caler, Q Zhao, J Crabtree, JE Allen, ... Science 317 (5845), 1756-1760, 2007	729	2007
Whole-genome annotation with BRAKER KJ Hoff, A Lomsadze, M Borodovsky, M Stanke Gene prediction: methods and protocols, 65-95, 2019	615	2019
Draft genome sequence of the oilseed species Ricinus communis AP Chan, J Crabtree, Q Zhao, H Lorenzi, J Orvis, D Puiu, ... Nature biotechnology 28 (9), 951-956, 2010	602	2010
The UCSC genome browser database: 2008 update D Karolchik, RM Kuhn, R Baertsch, GP Barber, H Clawson, M Diekhans, ... Nucleic acids research 36 (suppl_1), D773-D779, 2007	599	2007
A novel hybrid gene prediction method employing protein multiple sequence alignments O Keller, M Kollmar, M Stanke, S Waack Bioinformatics 27 (6), 757-763, 2011	563	2011

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