Matthias Bernt

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 10

Top Topics

Genome Rearrangements

Multi Objective

Engineering Design Problems

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Lisa Fiedler, Matthias Bernt, Martin Middendorf, Peter F. Stadler
Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs. BMC Bioinform. 24 (1) (2023)
Kyriakos Soulios, Patrick Scheibe, Matthias Bernt, Jörg Hackermüller, Jana Schor
+: enhancing toxicity prediction across the chemical universe using graph neural networks. Bioinform. 39 (12) (2023)
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 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 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
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 50 (W1) (2022)
Jana Schor, Patrick Scheibe, Matthias Bernt, Wibke Busch, Chih Lai, Jörg Hackermüller
AI for predicting chemical-effect associations at the chemical universe level - deepFPlearn. Briefings Bioinform. 23 (5) (2022)
Tom Hartmann, Matthias Bernt, Martin Middendorf
An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (1) (2019)
Tom Hartmann, An-Chiang Chu, Martin Middendorf, Matthias Bernt
Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (1) (2018)
Tom Hartmann, Nicolas Wieseke, Roded Sharan, Martin Middendorf, Matthias Bernt
Genome Rearrangement with ILP. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (5) (2018)
Tom Hartmann, Matthias Bernt, Martin Middendorf
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements. BMC Bioinform. 19 (1) (2018)
Marwa Al Arab, Matthias Bernt, Christian Höner zu Siederdissen, Kifah Tout, Peter F. Stadler
Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements. Algorithms Mol. Biol. 12 (1) (2017)
Ruby L. V. Moritz, Enrico Reich, Matthias Bernt, Martin Middendorf
A Property Preserving Method for Extending a Single-Objective Problem Instance to Multiple Objectives with Specific Correlations. EvoCOP (2016)
Ruby L. V. Moritz, Enrico Reich, Maik Schwarz, Matthias Bernt, Martin Middendorf
Refined ranking relations for selection of solutions in multi objective metaheuristics. Eur. J. Oper. Res. 243 (2) (2015)
Nicolas Wieseke, Tom Hartmann, Matthias Bernt, Martin Middendorf
Cophylogenetic Reconciliation with ILP. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
Ruby L. V. Moritz, Enrico Reich, Matthias Bernt, Martin Middendorf
The Influence of Correlated Objectives on Different Types of P-ACO Algorithms. EvoCOP (2014)
Nicolas Wieseke, Matthias Bernt, Martin Middendorf
Unifying Parsimonious Tree Reconciliation. WABI (2013)
Martin Clauß, Matthias Bernt, Martin Middendorf
A common interval guided ACO algorithm for permutation problems. SIS (2013)
Ruby L. V. Moritz, Enrico Reich, Maik Schwarz, Matthias Bernt, Martin Middendorf
Refined ranking relations for multi objective optimization andapplication to P-ACO. GECCO (2013)
Matthias Bernt, Nicolas Wieseke, Martin Middendorf
On Weighting Schemes for Gene Order Analysis. GCB (2013)
Ruby L. V. Moritz, Matthias Bernt, Martin Middendorf
Annotation guided local similarity search in multiple sequences and its application to mitochondrial genomes. BIBE (2012)
Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier
Preserving Inversion Phylogeny Reconstruction. WABI (2012)
Matthias Bernt, Kuan-Yu Chen, Ming-Chiang Chen, An-Chiang Chu, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf
Finding all sorting tandem duplication random loss operations. J. Discrete Algorithms 9 (1) (2011)
Matthias Bernt, Martin Middendorf
A method for computing an inventory of metazoan mitochondrial gene order rearrangements. BMC Bioinform. 12 (S-9) (2011)
Matthias Bernt, Ming-Chiang Chen, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf
Finding All Sorting Tandem Duplication Random Loss Operations. CPM (2009)
Matthias Bernt, Daniel Merkle, Martin Middendorf
Solving the Preserving Reversal Median Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (3) (2008)
Matthias Bernt, Daniel Merkle, Martin Middendorf
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. RECOMB-CG (2008)
Matthias Bernt, Daniel Merkle, Martin Middendorf
A Fast and Exact Algorithm for the Perfect Reversal Median Problem. ISBRA (2007)
Matthias Bernt, Daniel Merkle, Martin Middendorf
Using median sets for inferring phylogenetic trees. Bioinform. 23 (2) (2007)
Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf
CREx: inferring genomic rearrangements based on common intervals. Bioinform. 23 (21) (2007)
Matthias Bernt, Daniel Merkle, Martin Middendorf
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (3) (2006)
Matthias Bernt, Daniel Merkle, Martin Middendorf
The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders. CompLife (2006)
Matthias Bernt, Daniel Merkle, Martin Middendorf
A Parallel Algorithm for Solving the Reversal Median Problem. PPAM (2005)