A Parallel Algorithm for Solving the Reversal Median Problem. - Matthias Bernt; Daniel Merkle; Martin Middendorf (PPAM, 2005)

The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders. - Matthias Bernt; Daniel Merkle; Martin Middendorf (CompLife, 2006)

Genome Rearrangement Based on Reversals that Preserve Conserved Intervals. - Matthias Bernt; Daniel Merkle; Martin Middendorf (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

A Fast and Exact Algorithm for the Perfect Reversal Median Problem. - Matthias Bernt; Daniel Merkle; Martin Middendorf (ISBRA, 2007)

Using median sets for inferring phylogenetic trees. - Matthias Bernt; Daniel Merkle; Martin Middendorf (Bioinform., 2007)

CREx: inferring genomic rearrangements based on common intervals. - Matthias Bernt; Daniel Merkle; Kai Ramsch; Guido Fritzsch; Marleen Perseke; Detlef Bernhard; Martin Schlegel; Peter F. Stadler; Martin Middendorf (Bioinform., 2007)

An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. - Matthias Bernt; Daniel Merkle; Martin Middendorf (RECOMB-CG, 2008)

Solving the Preserving Reversal Median Problem. - Matthias Bernt; Daniel Merkle; Martin Middendorf (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Finding All Sorting Tandem Duplication Random Loss Operations. - Matthias Bernt; Ming-Chiang Chen; Daniel Merkle; Hung-Lung Wang; Kun-Mao Chao; Martin Middendorf (CPM, 2009)

Gene order rearrangement methods for the reconstruction of phylogeny - Matthias Bernt (2010)

A method for computing an inventory of metazoan mitochondrial gene order rearrangements. - Matthias Bernt; Martin Middendorf (BMC Bioinform., 2011)

Finding all sorting tandem duplication random loss operations. - Matthias Bernt; Kuan-Yu Chen 002; Ming-Chiang Chen; An-Chiang Chu; Daniel Merkle; Hung-Lung Wang; Kun-Mao Chao; Martin Middendorf (J. Discrete Algorithms, 2011)

Annotation guided local similarity search in multiple sequences and its application to mitochondrial genomes. - Ruby L. V. Moritz; Matthias Bernt; Martin Middendorf (BIBE, 2012)

Preserving Inversion Phylogeny Reconstruction. - Matthias Bernt; Kun-Mao Chao; Jyun-Wei Kao; Martin Middendorf; Eric Tannier (WABI, 2012)

On Weighting Schemes for Gene Order Analysis. - Matthias Bernt; Nicolas Wieseke; Martin Middendorf (GCB, 2013)

Refined ranking relations for multi objective optimization andapplication to P-ACO. - Ruby L. V. Moritz; Enrico Reich; Maik Schwarz; Matthias Bernt; Martin Middendorf (GECCO, 2013)

A common interval guided ACO algorithm for permutation problems. - Martin Clauß; Matthias Bernt; Martin Middendorf (SIS, 2013)

Unifying Parsimonious Tree Reconciliation. - Nicolas Wieseke; Matthias Bernt; Martin Middendorf (WABI, 2013)

The Influence of Correlated Objectives on Different Types of P-ACO Algorithms. - Ruby L. V. Moritz; Enrico Reich; Matthias Bernt; Martin Middendorf (EvoCOP, 2014)

Refined ranking relations for selection of solutions in multi objective metaheuristics. - Ruby L. V. Moritz; Enrico Reich; Maik Schwarz; Matthias Bernt; Martin Middendorf (Eur. J. Oper. Res., 2015)

Cophylogenetic Reconciliation with ILP. - Nicolas Wieseke; Tom Hartmann; Matthias Bernt; Martin Middendorf (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

A Property Preserving Method for Extending a Single-Objective Problem Instance to Multiple Objectives with Specific Correlations. - Ruby L. V. Moritz; Enrico Reich; Matthias Bernt; Martin Middendorf (EvoCOP, 2016)

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., 2017)

EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements. - Tom Hartmann; Matthias Bernt; Martin Middendorf (BMC Bioinform., 2018)

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., 2018)

Genome Rearrangement with ILP. - Tom Hartmann; Nicolas Wieseke; Roded Sharan; Martin Middendorf; Matthias Bernt (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements. - Tom Hartmann; Matthias Bernt; Martin Middendorf (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

AI for predicting chemical-effect associations at the chemical universe level - deepFPlearn. - Jana Schor; Patrick Scheibe; Matthias Bernt; Wibke Busch; Chih Lai; Jörg Hackermüller (Briefings Bioinform., 2022)

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. - 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; et al. (Nucleic Acids Res., 2022)

deepFPlearn +: enhancing toxicity prediction across the chemical universe using graph neural networks. - Kyriakos Soulios; Patrick Scheibe; Matthias Bernt; Jörg Hackermüller; Jana Schor (Bioinform., 2023)

Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs. - Lisa Fiedler; Matthias Bernt; Martin Middendorf; Peter F. Stadler (BMC Bioinform., 2023)