Mario Stanke

发表

Faculty Opinions recommendation of OrthoFiller: utilising data from multiple species to improve the completeness of genome annotations.

Mario Stanke, 2017 .

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS

Katharina J. Hoff, Mario Stanke, Simone Lange, 2015, Bioinform..

Faculty Opinions recommendation of Significance evaluation in factor graphs.

Mario Stanke, 2018 .

Simultaneous gene finding in multiple genomes

Mario Stanke, Lizzy Gerischer, Stefanie König, 2016, Bioinform..

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1

Ming Zhang, Burkhard Morgenstern, Mario Stanke, 2006, Nucleic Acids Res..

Finding the missing honey bee genes: lessons learned from a genome upgrade

Dan Graur, Mario Stanke, Monica C Munoz-Torres, 2014, BMC Genomics.

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

David Haussler, Mario Stanke, Mark Diekhans, 2008, Bioinform..

jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus

Burkhard Morgenstern, Mario Stanke, Anne-Kathrin Schultz, 2012, Nucleic Acids Res..

jpHMM: Improving the reliability of recombination prediction in HIV-1

Ming Zhang, Burkhard Morgenstern, Mario Stanke, 2009, Nucleic Acids Res..

HIV classification using the coalescent theory

Ming Zhang, Fabian Schreiber, Burkhard Morgenstern, 2010, Bioinform..

A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes

Ming Zhang, Burkhard Morgenstern, Mario Stanke, 2006, BMC Bioinformatics.

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources

Burkhard Morgenstern, Mario Stanke, Stephan Waack, 2006, BMC Bioinformatics.

F1000Prime recommendation of Accurate multiple alignment of distantly related genome sequences using filtered spaced word matches as anchor points.

Mario Stanke, 2019 .

Whole-Genome Annotation with BRAKER.

Mario Stanke, Mark Borodovsky, Alexandre Lomsadze, 2019, Methods in molecular biology.

AUGUSTUS: ab initio prediction of alternative transcripts

Burkhard Morgenstern, Mario Stanke, Stephan Waack, 2006, Nucleic Acids Res..

Combining features in a graphical model to predict protein binding sites

Mario Stanke, Stephan Waack, Marlon Welter, 2015, Proteins.

Simultaneous gene finding in multiple genomes

Mario Stanke, Lizzy Gerischer, Stefanie König, 2015, PeerJ Prepr..

A novel hybrid gene prediction method employing protein multiple sequence alignments

Martin Kollmar, Mario Stanke, Stephan Waack, 2011, Bioinform..

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

Burkhard Morgenstern, Mario Stanke, B. Morgenstern, 2005, Nucleic Acids Res..

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

Mario Stanke, Stephan Waack, M. Stanke, 2003, ECCB.

Detection of viral sequence fragments of HIV-1 subfamilies yet unknown

Burkhard Morgenstern, Mario Stanke, Anne-Kathrin Schultz, 2011, BMC Bioinformatics.

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

Katharina J. Hoff, Mario Stanke, M. Stanke, 2013, Nucleic Acids Res..

The UCSC genome browser database: update 2007

David Haussler, Brian J. Raney, Jakob Skou Pedersen, 2006, Nucleic Acids Res..

Faculty Opinions recommendation of Whole-Genome Alignment and Comparative Annotation.

Mario Stanke, 2020 .

AUGUSTUS at MediGRID: Adaption of a bioinformatics application to grid computing for efficient genome analysis

Burkhard Morgenstern, Mario Stanke, Dietmar Sommerfeld, 2009, Future Gener. Comput. Syst..

VARUS: sampling complementary RNA reads from the sequence read archive

Mario Stanke, Felix Becker, Katharina J Hoff, 2019, BMC Bioinformatics.

AUGUSTUS: a web server for gene finding in eukaryotes

Burkhard Morgenstern, Mario Stanke, Stephan Waack, 2004, Nucleic Acids Res..

CRF-based models of protein surfaces improve protein-protein interaction site predictions

Mario Stanke, Stephan Waack, Zhijie Dong, 2014, BMC Bioinformatics.

BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database

Mario Stanke, Mark Borodovsky, Tomáš Brůna, 2020, bioRxiv.

Global, Highly Specific and Fast Filtering of Alignment Seeds

Mario Stanke, Matthis Ebel, Giovanna Migliorelli, 2020 .

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

Florian Odronitz, Martin Kollmar, Mario Stanke, 2008, BMC Bioinformatics.

Gene prediction with a hidden Markov model

Mario Stanke, M. Stanke, 2004 .

TSEBRA: transcript selector for BRAKER

Mario Stanke, Mark Borodovsky, Lars Gabriel, 2021, BMC Bioinformatics.

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

Erich Bornberg-Bauer, Peer Bork, Alexandre Souvorov, 2010, Science.

Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties

Mario Stanke, Manuel C Peitsch, Florian Martin, 2012, BMC Genomics.

Current methods for automated annotation of protein-coding genes.

Katharina J. Hoff, Mario Stanke, M. Stanke, 2015, Current opinion in insect science.

Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species

Mario Stanke, Jacques Corbeil, Sébastien Boisvert, 2011, Nucleic acids research.

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Mario Stanke, Donna M. Muzny, Sam Griffiths-Jones, 2017, BMC Biology.

The role of recombination in the emergence of a complex and dynamic HIV epidemic

Burkhard Morgenstern, Mario Stanke, Anne-Kathrin Schultz, 2010, Retrovirology.

Predicting Genes in Single Genomes with AUGUSTUS

Mario Stanke, M. Stanke, K. Hoff, 2018, Current protocols in bioinformatics.

Genome Sequence of Aedes aegypti, a Major Arbovirus Vector

Evgeny M. Zdobnov, Ian T. Paulsen, Jonathan Crabtree, 2007, Science.

Sequential selection of random vectors under a sum constraint

Mario Stanke, M. Stanke, 2004, Journal of Applied Probability.

The genome of the blood fluke Schistosoma mansoni

John P. Overington, Adhemar Zerlotini, Anna V. Protasio, 2009, Nature.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Mark Gerstein, Benedict Paten, Paul Flicek, 2017, bioRxiv.

Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics

Claire Fraser-Liggett, Albert J. Vilella, Mario Stanke, 2010, Science.

Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Mark Gerstein, Jane Loveland, Dent Earl, 2018, Nature Genetics.

The Genome of the Model Beetle and Pest Tribolium Castaneum Vertebrate-specific Orthologues Insect-specific Orthologues Homology Undetectable Similarity

Peer Bork, Alexandre Souvorov, Liangjiang Wang, 2022 .

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Mark Gerstein, Jane Loveland, Dent Earl, 2018, bioRxiv.