Matthias Bernt

30 papers A 1B 3C 3Misc 1Journal 16Unranked 5
YearRankTypeTitle / Venue / Authors
2023 J jnl
Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs.
BMC Bioinform.
Lisa Fiedler, Matthias Bernt, Martin Middendorf, Peter F. Stadler
2022 J jnl
AI for predicting chemical-effect associations at the chemical universe level - <tt>deepFPlearn</tt>.
Briefings Bioinform.
Jana Schor, Patrick Scheibe, Matthias Bernt, Wibke Busch, Chih Lai, Jörg Hackermüller
2022 J jnl
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.
Nucleic Acids Res.
Enis Afgan, Anton Nekrutenko, Björn A. Grüning, Daniel J. Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis E. Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia D. Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier, Peter J. Briggs
2019 J jnl
An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tom Hartmann, Matthias Bernt, Martin Middendorf
2018 J jnl
Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tom Hartmann, An-Chiang Chu, Martin Middendorf, Matthias Bernt
2018 J jnl
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements.
BMC Bioinform.
Tom Hartmann, Matthias Bernt, Martin Middendorf
2018 J jnl
Genome Rearrangement with ILP.
IEEE ACM Trans. Comput. Biol. Bioinform.
Tom Hartmann, Nicolas Wieseke, Roded Sharan, Martin Middendorf, Matthias Bernt
2017 J jnl
Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements.
Algorithms Mol. Biol.
Marwa Al Arab, Matthias Bernt, Christian Höner zu Siederdissen, Kifah Tout, Peter F. Stadler
2016 B conf
A Property Preserving Method for Extending a Single-Objective Problem Instance to Multiple Objectives with Specific Correlations.
EvoCOP
Ruby L. V. Moritz, Enrico Reich, Matthias Bernt, Martin Middendorf
2015 J jnl
Cophylogenetic Reconciliation with ILP.
IEEE ACM Trans. Comput. Biol. Bioinform.
Nicolas Wieseke, Tom Hartmann, Matthias Bernt, Martin Middendorf
2015 J jnl
Refined ranking relations for selection of solutions in multi objective metaheuristics.
Eur. J. Oper. Res.
Ruby L. V. Moritz, Enrico Reich, Maik Schwarz, Matthias Bernt, Martin Middendorf
2014 B conf
The Influence of Correlated Objectives on Different Types of P-ACO Algorithms.
EvoCOP
Ruby L. V. Moritz, Enrico Reich, Matthias Bernt, Martin Middendorf
2013 — conf
A common interval guided ACO algorithm for permutation problems.
SIS
Martin Clauß, Matthias Bernt, Martin Middendorf
2013 — conf
On Weighting Schemes for Gene Order Analysis.
GCB
Matthias Bernt, Nicolas Wieseke, Martin Middendorf
2013 A conf
Refined ranking relations for multi objective optimization andapplication to P-ACO.
GECCO
Ruby L. V. Moritz, Enrico Reich, Maik Schwarz, Matthias Bernt, Martin Middendorf
2013 C conf
Unifying Parsimonious Tree Reconciliation.
WABI
Nicolas Wieseke, Matthias Bernt, Martin Middendorf
2012 C conf
Annotation guided local similarity search in multiple sequences and its application to mitochondrial genomes.
BIBE
Ruby L. V. Moritz, Matthias Bernt, Martin Middendorf
2012 C conf
Preserving Inversion Phylogeny Reconstruction.
WABI
Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier
2011 J jnl
A method for computing an inventory of metazoan mitochondrial gene order rearrangements.
BMC Bioinform.
Matthias Bernt, Martin Middendorf
2011 J jnl
Finding all sorting tandem duplication random loss operations.
J. Discrete Algorithms
Matthias Bernt, Kuan-Yu Chen, Ming-Chiang Chen, An-Chiang Chu, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf
2010 — —
Gene order rearrangement methods for the reconstruction of phylogeny
Matthias Bernt
2009 B conf
Finding All Sorting Tandem Duplication Random Loss Operations.
CPM
Matthias Bernt, Ming-Chiang Chen, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf
2008 — conf
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree.
RECOMB-CG
Matthias Bernt, Daniel Merkle, Martin Middendorf
2008 J jnl
Solving the Preserving Reversal Median Problem.
IEEE ACM Trans. Comput. Biol. Bioinform.
Matthias Bernt, Daniel Merkle, Martin Middendorf
2007 — conf
A Fast and Exact Algorithm for the Perfect Reversal Median Problem.
ISBRA
Matthias Bernt, Daniel Merkle, Martin Middendorf
2007 J jnl
CREx: inferring genomic rearrangements based on common intervals.
Bioinform.
Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf
2007 J jnl
Using median sets for inferring phylogenetic trees.
Bioinform.
Matthias Bernt, Daniel Merkle, Martin Middendorf
2006 J jnl
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals.
IEEE ACM Trans. Comput. Biol. Bioinform.
Matthias Bernt, Daniel Merkle, Martin Middendorf
2006 — conf
The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders.
CompLife
Matthias Bernt, Daniel Merkle, Martin Middendorf
2005 Misc conf
A Parallel Algorithm for Solving the Reversal Median Problem.
PPAM
Matthias Bernt, Daniel Merkle, Martin Middendorf