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ORCIDMatthias Bernt
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2020 – today
- 2023
[j17]Kyriakos Soulios
, Patrick Scheibe, Matthias Bernt, Jörg Hackermüller, Jana Schor:
deepFPlearn +: enhancing toxicity prediction across the chemical universe using graph neural networks. Bioinform. 39(12) (2023)- [j16]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): 235 (2023) - 2022
- [j15]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) - [j14]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:
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 50(W1): 345-351 (2022)
2010 – 2019
- 2019
- [j13]Tom Hartmann, Matthias Bernt, Martin Middendorf:
An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements. IEEE ACM Trans. Comput. Biol. Bioinform. 16(1): 52-62 (2019) - 2018
- [j12]Tom Hartmann, Matthias Bernt, Martin Middendorf:
EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements. BMC Bioinform. 19(1): 192:1-192:10 (2018) - [j11]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): 83-95 (2018) - [j10]Tom Hartmann, Nicolas Wieseke, Roded Sharan, Martin Middendorf, Matthias Bernt:
Genome Rearrangement with ILP. IEEE ACM Trans. Comput. Biol. Bioinform. 15(5): 1585-1593 (2018) - 2017
- [j9]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): 22:1-22:11 (2017) - 2016
- [c13]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: 18-33 - 2015
- [j8]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): 454-464 (2015) - [j7]Nicolas Wieseke, Tom Hartmann, Matthias Bernt, Martin Middendorf:
Cophylogenetic Reconciliation with ILP. IEEE ACM Trans. Comput. Biol. Bioinform. 12(6): 1227-1235 (2015) - 2014
- [c12]Ruby L. V. Moritz, Enrico Reich, Matthias Bernt, Martin Middendorf:
The Influence of Correlated Objectives on Different Types of P-ACO Algorithms. EvoCOP 2014: 230-241 - 2013
- [c11]Matthias Bernt, Nicolas Wieseke, Martin Middendorf:
On Weighting Schemes for Gene Order Analysis. GCB 2013: 14-23 - [c10]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: 65-72 - [c9]Martin Clauß, Matthias Bernt, Martin Middendorf:
A common interval guided ACO algorithm for permutation problems. SIS 2013: 64-71 - [c8]Nicolas Wieseke, Matthias Bernt, Martin Middendorf:
Unifying Parsimonious Tree Reconciliation. WABI 2013: 200-214 - 2012
- [c7]Ruby L. V. Moritz, Matthias Bernt, Martin Middendorf:
Annotation guided local similarity search in multiple sequences and its application to mitochondrial genomes. BIBE 2012: 157-162 - [c6]Matthias Bernt, Kun-Mao Chao, Jyun-Wei Kao, Martin Middendorf, Eric Tannier:
Preserving Inversion Phylogeny Reconstruction. WABI 2012: 1-13 - 2011
- [j6]Matthias Bernt, Martin Middendorf:
A method for computing an inventory of metazoan mitochondrial gene order rearrangements. BMC Bioinform. 12(S-9): S6 (2011) - [j5]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): 32-48 (2011) - 2010
- [b1]Matthias Bernt:
Gene order rearrangement methods for the reconstruction of phylogeny. Leipzig University, Germany, 2010
2000 – 2009
- 2009
- [c5]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: 301-313 - 2008
- [j4]Matthias Bernt, Daniel Merkle, Martin Middendorf:
Solving the Preserving Reversal Median Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 5(3): 332-347 (2008) - [c4]Matthias Bernt, Daniel Merkle, Martin Middendorf:
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. RECOMB-CG 2008: 143-157 - 2007
- [j3]Matthias Bernt, Daniel Merkle, Martin Middendorf:
Using median sets for inferring phylogenetic trees. Bioinform. 23(2): 129-135 (2007) - [j2]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): 2957-2958 (2007) - [c3]Matthias Bernt, Daniel Merkle, Martin Middendorf:
A Fast and Exact Algorithm for the Perfect Reversal Median Problem. ISBRA 2007: 305-316 - 2006
- [j1]Matthias Bernt, Daniel Merkle, Martin Middendorf:
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals. IEEE ACM Trans. Comput. Biol. Bioinform. 3(3): 275-288 (2006) - [c2]Matthias Bernt, Daniel Merkle, Martin Middendorf:
The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders. CompLife 2006: 52-63 - 2005
- [c1]Matthias Bernt, Daniel Merkle, Martin Middendorf:
A Parallel Algorithm for Solving the Reversal Median Problem. PPAM 2005: 1089-1096
Coauthor Index
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