Publications by authors named "Matthias Bernt"

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Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.
Engy Nasr, Nikos Pechlivanis, Nikolaos Strepis, Pierre Amato, Matthias Bernt

bioRxiv· September 2025

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High-content screening (HCS) workflows for FAIR image data management with OMERO.
Riccardo Massei, Wibke Busch, Beatriz Serrano-Solano, Matthias Bernt, Stefan Scholz

Sci Rep· May 2025

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Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution.
Iuliia Ozerova, Jörg Fallmann, Mario Mörl, Matthias Bernt, Sonja J Prohaska

Genome Biol Evol· November 2024

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DeGeCI 1.1: a web platform for gene annotation of mitochondrial genomes.
Lisa Fiedler, Matthias Bernt, Martin Middendorf

Bioinform Adv· May 2024

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Genome Rearrangement Analysis : Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches.
Tom Hartmann, Martin Middendorf, Matthias Bernt

Methods Mol Biol· May 2024

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OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data.
Julianus Pfeuffer, Chris Bielow, Samuel Wein, Kyowon Jeong, Eugen Netz, Matthias Bernt

Nat Methods· March 2024

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deepFPlearn +: enhancing toxicity prediction across the chemical universe using graph neural networks.
Kyriakos Soulios, Patrick Scheibe, Matthias Bernt, Jörg Hackermüller, Jana Schor

Bioinformatics· December 2023

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A Galaxy of informatics resources for MS-based proteomics.
Subina Mehta, Matthias Bernt, Matthew Chambers, Matthias Fahrner, Melanie Christine Föll

Expert Rev Proteomics· November 2023

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Fully automated annotation of mitochondrial genomes using a cluster-based approach with de Bruijn graphs.
Lisa Fiedler, Martin Middendorf, Matthias Bernt

Front Genet· August 2023

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Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs.
Lisa Fiedler, Matthias Bernt, Martin Middendorf, Peter F Stadler

BMC Bioinformatics· June 2023

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The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond.
Simon Bray, John Chilton, Matthias Bernt, Nicola Soranzo, Marius van den Beek

Genome Res· February 2023

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AI for predicting chemical-effect associations at the chemical universe level-deepFPlearn.
Jana Schor, Patrick Scheibe, Matthias Bernt, Wibke Busch, Chih Lai

Brief Bioinform· September 2022

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Expanding the Galaxy's reference data.
Nagampalli VijayKrishna, Jayadev Joshi, Nate Coraor, Jennifer Hillman-Jackson, Dave Bouvier, Matthias Bernt

Bioinform Adv· April 2022

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Democratizing data-independent acquisition proteomics analysis on public cloud infrastructures via the Galaxy framework.
Matthias Fahrner, Melanie Christine Föll, Björn Andreas Grüning, Matthias Bernt, Hannes Röst

Gigascience· February 2022

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Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes.
Alexander Donath, Frank Jühling, Marwa Al-Arab, Stephan H Bernhart, Franziska Reinhardt, Matthias Bernt

Nucleic Acids Res· November 2019

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An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements.
Tom Hartmann, Matthias Bernt, Martin Middendorf

IEEE/ACM Trans Comput Biol Bioinform· August 2019

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Genome Rearrangement with ILP.
Tom Hartmann, Nicolas Wieseke, Roded Sharan, Martin Middendorf, Matthias Bernt

IEEE/ACM Trans Comput Biol Bioinform· June 2019

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Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes.
Tom Hartmann, An-Chiang Chu, Martin Middendorf, Matthias Bernt

IEEE/ACM Trans Comput Biol Bioinform· January 2019

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Mitogenomics Reveals a Novel Genetic Code in Hemichordata.
Yuanning Li, Kevin M Kocot, Michael G Tassia, Johanna T Cannon, Matthias Bernt

Genome Biol Evol· January 2019

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Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches.
Tom Hartmann, Martin Middendorf, Matthias Bernt

Methods Mol Biol· December 2018

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EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements.
Tom Hartmann, Matthias Bernt, Martin Middendorf

BMC Bioinformatics· May 2018

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Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements.
Marwa Al Arab, Matthias Bernt, Christian Höner Zu Siederdissen, Kifah Tout, Peter F Stadler

Algorithms Mol Biol· August 2017

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Accurate annotation of protein-coding genes in mitochondrial genomes.
Marwa Al Arab, Christian Höner Zu Siederdissen, Kifah Tout, Abdullah H Sahyoun, Peter F Stadler, Matthias Bernt

Mol Phylogenet Evol· January 2017

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Cophylogenetic Reconciliation with ILP.
Nicolas Wieseke, Tom Hartmann, Matthias Bernt, Martin Middendorf

IEEE/ACM Trans Comput Biol Bioinform· September 2016

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Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes.
Abdullah H Sahyoun, Martin Hölzer, Frank Jühling, Christian Höner zu Siederdissen, Marwa Al-Arab, Matthias Bernt

Nucleic Acids Res· September 2015

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