Mario Stanke

Affiliations

Institute for Mathematics and Computer Science, University of Greifswald, Greifswald, Germany.
Center for Functional Genomics of Microbes, University of Greifswald, Greifswald, Germany.

Publications (24)

A 20-kb lineage-specific genomic region tames virulence in pathogenic amphidiploid Verticillium longisporum.

Molecular plant pathology

Avec: Rebekka Harting , Jessica Starke , Harald Kusch , Stefanie Pöggeler , Isabel Maurus , Rabea Schlüter , Manuel Landesfeind , Ingo Bulla , Minou Nowrousian , Ronnie de Jonge , Gertrud Stahlhut , Katharina J Hoff , Kathrin P Aßhauer , Andrea Thürmer , Mario Stanke , Rolf Daniel , Burkhard Morgenstern , Bart P H J Thomma , James W Kronstad , Susanna A Braus-Stromeyer , Gerhard H Braus

Whole-Genome Annotation with BRAKER.

Methods in molecular biology (Clifton, N.J.)

Avec: Katharina J Hoff , Alexandre Lomsadze , Mark Borodovsky , Mario Stanke

Enhanced genome assembly and a new official gene set for Tribolium castaneum.

BMC genomics

Avec: Nicolae Herndon , Jennifer Shelton , Lizzy Gerischer , Panos Ioannidis , Maria Ninova , Jürgen Dönitz , Robert M Waterhouse , Chun Liang , Carsten Damm , Janna Siemanowski , Peter Kitzmann , Julia Ulrich , Stefan Dippel , Georg Oberhofer , Yonggang Hu , Jonas Schwirz , Magdalena Schacht , Sabrina Lehmann , Alice Montino , Nico Posnien , Daniela Gurska , Thorsten Horn , Jan Seibert , Iris M Vargas Jentzsch , Kristen A Panfilio , Jianwei Li , Ernst A Wimmer , Dominik Stappert , Siegfried Roth , Reinhard Schröder , Yoonseong Park , Michael Schoppmeier , Ho-Ryun Chung , Martin Klingler , Sebastian Kittelmann , Markus Friedrich , Rui Chen , Boran Altincicek , Andreas Vilcinskas , Evgeny Zdobnov , Sam Griffiths-Jones , Matthew Ronshaugen , Mario Stanke , Sue J Brown , Gregor Bucher

Frontiers in microbiology

Avec: Rebekka Harting , Alexandra Nagel , Kai Nesemann , Annalena M Höfer , Emmanouil Bastakis , Harald Kusch , Claire E Stanley , Martina Stöckli , Alexander Kaever , Katharina J Hoff , Mario Stanke , Andrew J deMello , Markus Künzler , Cara H Haney , Susanna A Braus-Stromeyer , Gerhard H Braus

BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA.

Genome research

Avec: Lars Gabriel , Tomáš Brůna , Katharina J Hoff , Matthis Ebel , Alexandre Lomsadze , Mark Borodovsky , Mario Stanke

GALBA: Genome Annotation with Miniprot and AUGUSTUS.

bioRxiv : the preprint server for biology

Avec: Tomáš Brůna , Heng Li , Joseph Guhlin , Daniel Honsel , Steffen Herbold , Mario Stanke , Natalia Nenasheva , Matthis Ebel , Lars Gabriel , Katharina J Hoff

Effects of adult temperature on gene expression in a butterfly: identifying pathways associated with thermal acclimation.

BMC evolutionary biology

Avec: Kristin Franke , Isabell Karl , Tonatiuh Pena Centeno , Barbara Feldmeyer , Christian Lassek , Vicencio Oostra , Katharina Riedel , Mario Stanke , Christopher W Wheat , Klaus Fischer

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

BMC bioinformatics

Avec: Mario Stanke , Willy Bruhn , Felix Becker , Katharina J Hoff

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

NAR genomics and bioinformatics

Avec: Tomáš Brůna , Katharina J Hoff , Alexandre Lomsadze , Mario Stanke , Mark Borodovsky

learnMSA: learning and aligning large protein families.

GigaScience

Avec: Felix Becker , Mario Stanke

learnMSA2: deep protein multiple alignments with large language and hidden Markov models.

Bioinformatics (Oxford, England)

Avec: Felix Becker , Mario Stanke

Comparative Genome Annotation.

Methods in molecular biology (Clifton, N.J.)

Avec: Stefanie Nachtweide , Lars Romoth , Mario Stanke

Survival According to Therapy Regimen for Small Intestinal Neuroendocrine Tumors.

Journal of clinical medicine

Avec: Christine Koch , Cornelia Bambey , Natalie Filmann , Marc Stanke , Oliver Waidmann , Gabriele Husmann , Joerg Bojunga

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

Bioinformatics (Oxford, England)

Avec: Darvin Mertsch , Mario Stanke

Multi-Genome Annotation with AUGUSTUS.

Methods in molecular biology (Clifton, N.J.)

Avec: Stefanie Nachtweide , Mario Stanke

Predicting Genes in Single Genomes with AUGUSTUS.

Current protocols in bioinformatics

Avec: Katharina J Hoff , Mario Stanke

TSEBRA: transcript selector for BRAKER.

BMC bioinformatics

Avec: Lars Gabriel , Katharina J Hoff , Tomáš Brůna , Mark Borodovsky , Mario Stanke

Global, highly specific and fast filtering of alignment seeds.

BMC bioinformatics

Avec: Matthis Ebel , Giovanna Migliorelli , Mario Stanke

Galba: genome annotation with miniprot and AUGUSTUS.

BMC bioinformatics

Avec: Tomáš Brůna , Heng Li , Joseph Guhlin , Daniel Honsel , Steffen Herbold , Mario Stanke , Natalia Nenasheva , Matthis Ebel , Lars Gabriel , Katharina J Hoff

BRAKER3: Fully automated genome annotation using RNA-Seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA.

bioRxiv : the preprint server for biology

Avec: Lars Gabriel , Tomáš Brůna , Katharina J Hoff , Matthis Ebel , Alexandre Lomsadze , Mark Borodovsky , Mario Stanke

Non-adiabatic effects in the H

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences

Avec: Paulo H R Amaral , Monika Stanke , Ludwik Adamowicz , Leonardo G Diniz , José R Mohallem , Alexander Alijah

The genomic basis of evolutionary differentiation among honey bees.

Genome research

Avec: Bertrand Fouks , Philipp Brand , Hung N Nguyen , Jacob Herman , Francisco Camara , Daniel Ence , Darren E Hagen , Katharina J Hoff , Stefanie Nachweide , Lars Romoth , Kimberly K O Walden , Roderic Guigo , Mario Stanke , Giuseppe Narzisi , Mark Yandell , Hugh M Robertson , Nikolaus Koeniger , Panuwan Chantawannakul , Michael C Schatz , Kim C Worley , Gene E Robinson , Christine G Elsik , Olav Rueppell

Application of YOLOv4 for Detection and Motion Monitoring of Red Foxes.

Animals : an open access journal from MDPI

Avec: Anne K Schütz , Verena Schöler , E Tobias Krause , Mareike Fischer , Thomas Müller , Conrad M Freuling , Franz J Conraths , Mario Stanke , Timo Homeier-Bachmann , Hartmut H K Lentz

Molecular Structure Theory without the Born-Oppenheimer Approximation: Rotationless Vibrational States of LiH.

The journal of physical chemistry. A

Avec: Saeed Nasiri , Sergiy Bubin , Monika Stanke , Ludwik Adamowicz

Réseau de co-auteurs

Katharina J Hoff 12 collaborations

Tomáš Brůna 6 collaborations

Mark Borodovsky 5 collaborations

Lars Gabriel 5 collaborations

Matthis Ebel 5 collaborations

Alexandre Lomsadze 4 collaborations

Felix Becker 3 collaborations

Rebekka Harting 2 collaborations

Harald Kusch 2 collaborations

Susanna A Braus-Stromeyer 2 collaborations

Gerhard H Braus 2 collaborations

Heng Li 2 collaborations

Joseph Guhlin 2 collaborations

Daniel Honsel 2 collaborations

Steffen Herbold 2 collaborations

Natalia Nenasheva 2 collaborations

Stefanie Nachtweide 2 collaborations

Lars Romoth 2 collaborations

Monika Stanke 2 collaborations

Ludwik Adamowicz 2 collaborations

Jessica Starke 1 collaboration

Stefanie Pöggeler 1 collaboration

Isabel Maurus 1 collaboration

Rabea Schlüter 1 collaboration

Manuel Landesfeind 1 collaboration

Ingo Bulla 1 collaboration

Minou Nowrousian 1 collaboration

Ronnie de Jonge 1 collaboration

Gertrud Stahlhut 1 collaboration

Kathrin P Aßhauer 1 collaboration

Andrea Thürmer 1 collaboration

Rolf Daniel 1 collaboration

Burkhard Morgenstern 1 collaboration

Bart P H J Thomma 1 collaboration

James W Kronstad 1 collaboration

Nicolae Herndon 1 collaboration

Jennifer Shelton 1 collaboration

Lizzy Gerischer 1 collaboration

Panos Ioannidis 1 collaboration

Maria Ninova 1 collaboration

Jürgen Dönitz 1 collaboration

Robert M Waterhouse 1 collaboration

Chun Liang 1 collaboration

Carsten Damm 1 collaboration

Janna Siemanowski 1 collaboration

Peter Kitzmann 1 collaboration

Julia Ulrich 1 collaboration

Stefan Dippel 1 collaboration

Georg Oberhofer 1 collaboration

Yonggang Hu 1 collaboration

Jonas Schwirz 1 collaboration

Magdalena Schacht 1 collaboration

Sabrina Lehmann 1 collaboration

Alice Montino 1 collaboration

Nico Posnien 1 collaboration

Daniela Gurska 1 collaboration

Thorsten Horn 1 collaboration

Jan Seibert 1 collaboration

Iris M Vargas Jentzsch 1 collaboration

Kristen A Panfilio 1 collaboration

Jianwei Li 1 collaboration

Ernst A Wimmer 1 collaboration

Dominik Stappert 1 collaboration

Siegfried Roth 1 collaboration

Reinhard Schröder 1 collaboration

Yoonseong Park 1 collaboration

Michael Schoppmeier 1 collaboration

Ho-Ryun Chung 1 collaboration

Martin Klingler 1 collaboration

Sebastian Kittelmann 1 collaboration

Markus Friedrich 1 collaboration

Rui Chen 1 collaboration

Boran Altincicek 1 collaboration

Andreas Vilcinskas 1 collaboration

Evgeny Zdobnov 1 collaboration

Sam Griffiths-Jones 1 collaboration

Matthew Ronshaugen 1 collaboration

Sue J Brown 1 collaboration

Gregor Bucher 1 collaboration

Alexandra Nagel 1 collaboration

Kai Nesemann 1 collaboration

Annalena M Höfer 1 collaboration

Emmanouil Bastakis 1 collaboration

Claire E Stanley 1 collaboration

Martina Stöckli 1 collaboration

Alexander Kaever 1 collaboration

Andrew J deMello 1 collaboration

Markus Künzler 1 collaboration

Cara H Haney 1 collaboration

Kristin Franke 1 collaboration

Isabell Karl 1 collaboration

Tonatiuh Pena Centeno 1 collaboration

Barbara Feldmeyer 1 collaboration

Christian Lassek 1 collaboration

Vicencio Oostra 1 collaboration

Katharina Riedel 1 collaboration

Christopher W Wheat 1 collaboration

Klaus Fischer 1 collaboration

Willy Bruhn 1 collaboration

Christine Koch 1 collaboration

Cornelia Bambey 1 collaboration

Natalie Filmann 1 collaboration

Marc Stanke 1 collaboration

Oliver Waidmann 1 collaboration

Gabriele Husmann 1 collaboration

Joerg Bojunga 1 collaboration

Darvin Mertsch 1 collaboration

Giovanna Migliorelli 1 collaboration

Paulo H R Amaral 1 collaboration

Leonardo G Diniz 1 collaboration

José R Mohallem 1 collaboration

Alexander Alijah 1 collaboration

Bertrand Fouks 1 collaboration

Philipp Brand 1 collaboration

Hung N Nguyen 1 collaboration

Jacob Herman 1 collaboration

Francisco Camara 1 collaboration

Daniel Ence 1 collaboration

Darren E Hagen 1 collaboration

Stefanie Nachweide 1 collaboration

Kimberly K O Walden 1 collaboration

Roderic Guigo 1 collaboration

Giuseppe Narzisi 1 collaboration

Mark Yandell 1 collaboration

Hugh M Robertson 1 collaboration

Nikolaus Koeniger 1 collaboration

Panuwan Chantawannakul 1 collaboration

Michael C Schatz 1 collaboration

Kim C Worley 1 collaboration

Gene E Robinson 1 collaboration

Christine G Elsik 1 collaboration

Olav Rueppell 1 collaboration

Anne K Schütz 1 collaboration

Verena Schöler 1 collaboration

E Tobias Krause 1 collaboration

Mareike Fischer 1 collaboration

Thomas Müller 1 collaboration

Conrad M Freuling 1 collaboration

Franz J Conraths 1 collaboration

Timo Homeier-Bachmann 1 collaboration

Hartmut H K Lentz 1 collaboration

Saeed Nasiri 1 collaboration

Sergiy Bubin 1 collaboration