Author details

Full Name

Mario Stanke

Affiliation

Institut fur Mathematik und Informatik, Universitat Greifswald

ORCID

Career Start Year

2003

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37398387	BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA.	bioRxiv	2024
37090650	GALBA: Genome Annotation with Miniprot and AUGUSTUS.	bioRxiv	2023
35060608	End-to-end learning of evolutionary models to find coding regions in genome alignments.	Bioinformatics	2022
35689182	Global, highly specific and fast filtering of alignment seeds.	BMC Bioinformatics	2022
36399060	learnMSA: learning and aligning large protein families.	Gigascience	2022
34108946	<i>Pseudomonas</i> Strains Induce Transcriptional and Morphological Changes and Reduce Root Colonization of <i>Verticillium</i> spp.	Front Microbiol	2021
33575650	BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.	NAR Genom Bioinform	2021
34823473	TSEBRA: transcript selector for BRAKER.	BMC Bioinformatics	2021
33955130	A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum.	Mol Plant Pathol	2021
33947700	The genomic basis of evolutionary differentiation among honey bees.	Genome Res	2021
31937263	Enhanced genome assembly and a new official gene set for Tribolium castaneum.	BMC Genomics	2020
30466165	Predicting Genes in Single Genomes with AUGUSTUS.	Curr Protoc Bioinformatics	2019
31703556	VARUS: sampling complementary RNA reads from the sequence read archive.	BMC Bioinformatics	2019
31020558	Multi-Genome Annotation with AUGUSTUS.	Methods Mol Biol	2019
31020555	Whole-Genome Annotation with BRAKER.	Methods Mol Biol	2019
30674272	Effects of adult temperature on gene expression in a butterfly: identifying pathways associated with thermal acclimation.	BMC Evol Biol	2019
29277866	Comparative Genome Annotation.	Methods Mol Biol	2018
29884752	Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.	Genome Res	2018
30275530	Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.	Nat Genet	2018
29563166	Repeat associated mechanisms of genome evolution and function revealed by the <i>Mus caroli</i> and <i>Mus pahari</i> genomes.	Genome Res	2018
29787441	Exome Sequencing Discloses Ionizing-radiation-induced DNA Variants in the Genome of Human Gingiva Fibroblasts.	Health Phys	2018
28544481	Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.	Hum Mutat	2017
28209133	House spider genome uncovers evolutionary shifts in the diversity and expression of black widow venom proteins associated with extreme toxicity.	BMC Genomics	2017
28756775	The house spider genome reveals an ancient whole-genome duplication during arachnid evolution.	BMC Biol	2017
28536194	Wild tobacco genomes reveal the evolution of nicotine biosynthesis.	Proc Natl Acad Sci U S A	2017
27466621	Simultaneous gene finding in multiple genomes.	Bioinformatics	2016
26559507	BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS.	Bioinformatics	2016
25663045	Combining features in a graphical model to predict protein binding sites.	Proteins	2015
32846689	Current methods for automated annotation of protein-coding genes.	Curr Opin Insect Sci	2015
26334912	Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target.	BMC Genomics	2015
26215380	The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology.	Nat Commun	2015
24404173	ClassyFlu: classification of influenza A viruses with Discriminatively trained profile-HMMs.	PLoS One	2014
25523483	Tissue-specific transcriptomics, chromosomal localization, and phylogeny of chemosensory and odorant binding proteins from the red flour beetle Tribolium castaneum reveal subgroup specificities for olfaction or more general functions.	BMC Genomics	2014
25124108	CRF-based models of protein surfaces improve protein-protein interaction site predictions.	BMC Bioinformatics	2014
24950814	The Chlamydomonas genome project: a decade on.	Trends Plant Sci	2014
24433459	Verticillium transcription activator of adhesion Vta2 suppresses microsclerotia formation and is required for systemic infection of plant roots.	New Phytol	2014
24479613	Finding the missing honey bee genes: lessons learned from a genome upgrade.	BMC Genomics	2014
23471408	Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote.	Science	2013
23700307	WebAUGUSTUS--a web service for training AUGUSTUS and predicting genes in eukaryotes.	Nucleic Acids Res	2013
21998295	Genome sequencing of the lizard parasite Leishmania tarentolae reveals loss of genes associated to the intracellular stage of human pathogenic species.	Nucleic Acids Res	2012
23190529	Design of a tobacco exon array with application to investigate the differential cadmium accumulation property in two tobacco varieties.	BMC Genomics	2012
22600739	jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus.	Nucleic Acids Res	2012
21216780	A novel hybrid gene prediction method employing protein multiple sequence alignments.	Bioinformatics	2011
21432999	Concerted action of the new Genomic Peptide Finder and AUGUSTUS allows for automated proteogenomic annotation of the Chlamydomonas reinhardtii genome.	Proteomics	2011
21481263	Detection of viral sequence fragments of HIV-1 subfamilies yet unknown.	BMC Bioinformatics	2011
20075255	Functional and evolutionary insights from the genomes of three parasitoid Nasonia species.	Science	2010
20729833	Draft genome sequence of the oilseed species Ricinus communis.	Nat Biotechnol	2010
20686567	The Amphimedon queenslandica genome and the evolution of animal complexity.	Nature	2010
20929810	Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics.	Science	2010
20547848	Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).	Proc Natl Acad Sci U S A	2010

1 - 50 of 73

Boris R Jankovic

4700 King Abdullah University of Science and Technology

Career Start Year 2011

Number of shared co-authors 2

Sayed Mohammad Ebrahim Sahraeian

Roche Sequencing Solutions Inc.

Career Start Year 2010

Number of shared co-authors 13

Salvador Capella-Gutierrez

Spanish National Bioinformatics Institute (INB/ELIXIR-ES)

Career Start Year 2009

Number of shared co-authors 34

Nuno A Fonseca

European Bioinformatics Institute

Career Start Year 2008

Number of shared co-authors 20

Christophe Dessimoz

University of Lausanne

Career Start Year 2005

Number of shared co-authors 13

Daniel R Zerbino

European Bioinformatics Institute

Career Start Year 2005

Number of shared co-authors 15

Dariusz Przybylski

Howard Hughes Medical Institute, Brandeis University

Career Start Year 2001

Number of shared co-authors 17

Suleyman Cenk Sahinalp

National Cancer Institute, National Institutes of Health

Career Start Year 2001

Number of shared co-authors 5

Tyler Alioto

Universitat de Barcelona (UB)

Career Start Year 2001

Number of shared co-authors 74

Martin C Frith

Artificial Intelligence Research Center, University of Tokyo

Career Start Year 2001

Number of shared co-authors 6

Gunnar R??tsch

ETH Zurich

Career Start Year 1999

Number of shared co-authors 10

Kevin Bryson

University of Glasgow

Career Start Year 1999

Number of shared co-authors 8

Knut Reinert

Institut fur Informatik, Freie Universitat Berlin

Career Start Year 1998

Number of shared co-authors 24

Anton Nekrutenko

The Pennsylvania State University, University Park

Career Start Year 1998

Number of shared co-authors 31

Ian Holmes

University of California berkeley

Career Start Year 1998

Number of shared co-authors 39

Michele Clamp

Harvard University

Career Start Year 1998

Number of shared co-authors 65

Iddo Friedberg

Iowa State University

Career Start Year 1997

Number of shared co-authors 15

Stefano Lonardi

University of California Riverside

Career Start Year 1996

Number of shared co-authors 4

Martin G Reese

Fabric Genomics Inc.

Career Start Year 1996

Number of shared co-authors 27

Richa Agarwala

National Center for Biotechnology Information, National Institutes of Health

Career Start Year 1995

Number of shared co-authors 37

Bonnie Berger

Massachusetts Institute of Technology

Career Start Year 1994

Number of shared co-authors 8

Terry Gaasterland

Scripps Institution of Oceanography, University of California San Diego

Career Start Year 1994

Number of shared co-authors 49

Inna Dubchak

Lawrence Berkeley National Laboratory

Career Start Year 1993

Number of shared co-authors 53

Simon Kasif

Boston University

Career Start Year 1993

Number of shared co-authors 24

Erik L L Sonnhammer

Stockholm University

Career Start Year 1992

Number of shared co-authors 5

Martijn A Huynen

Radboud University Medical Centre Nijmegen

Career Start Year 1992

Number of shared co-authors 4

Jaap Heringa

VU University Amsterdam

Career Start Year 1991

Number of shared co-authors 3

Miguel A Andrade-Navarro

Institute of Organismic and Molecular Evolution, Johannes Gutenberg University

Career Start Year 1991

Number of shared co-authors 3

Nomi L Harris

Lawrence Berkely National Laboratory, Massachusetts Institute of Technology, Princeton University

Career Start Year 1990

Number of shared co-authors 33

Pavel A Pevzner

University of California

Career Start Year 1987

Number of shared co-authors 36

row(s) 1 - 30 of 30

Burkhard Morgenstern

Institute of Microbiology and Genetics

Co-authored papers 15

Mark Borodovsky

Georgia Institute of Technology

Co-authored papers 6

Mark Diekhans

Genomics Institute, University of California Santa Cruz

Co-authored papers 6

Bette Korber

Co-authored papers 5

Gregor Bucher

Johann-Friedrich-Blumenbach Institute, University of Gottingen

Co-authored papers 5

Robert M Waterhouse

University of Lausanne

Co-authored papers 5

Claire M Fraser

Institute for Genome Sciences, University of Maryland School of Medicine

Co-authored papers 5

Kim C Worley

Baylor College of Medicine

Co-authored papers 5

Jennifer R Wortman

Broad Institute of MIT and Harvard

Co-authored papers 5

Brian J Haas

Broad Institute of MIT and Harvard

Co-authored papers 5

David Haussler

Genomics Institute, University of California Santa Cruz

Co-authored papers 4

Christine G Elsik

University of Missouri

Co-authored papers 4

Richard A Gibbs

Baylor College of Medicine

Co-authored papers 4

Owen White

Institute for Genome Sciences, University of Maryland School of Medicine

Co-authored papers 4

Ernst A Wimmer

Georg August University

Co-authored papers 4

Stephen Richards

Baylor College of Medicine

Co-authored papers 4

Donna M Muzny

Baylor College of Medicine

Co-authored papers 4

Zhijian Tu

Department of Biochemistry and the Fralin Life Sciences Institute, Virginia Tech

Co-authored papers 3

Lan Zhang

Baylor College of Medicine

Co-authored papers 3

Peter W Atkinson

University of California riverside

Co-authored papers 3

Thomas M Keane

European Bioinformatics Institute

Co-authored papers 3

Ian T Fiddes

Liver Center and Diabetes Center, University of California san francisco

Co-authored papers 3

Martin Klingler

Friedrich-Alexander-University Erlangen-Nurnberg

Co-authored papers 3

Nico Posnien

Johann-Friedrich-Blumenbach Institute, University Goettingen

Co-authored papers 3

Chinnappa D Kodira

GE Global Research Center

Co-authored papers 3

Dan Graur

University of Houston

Co-authored papers 3

Evgenia V Kriventseva

University of Geneva Medical School

Co-authored papers 3

Siegfried Roth

University of Cologne

Co-authored papers 3

Eran Elhaik

Lund University

Co-authored papers 3

Evgeny M Zdobnov

University of Geneva

Co-authored papers 3

1 - 30

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