Journal Publications


T Hartmann, N Wieseke, R Sharan, M Middendorf, and M Bernt
Genome Rearrangement with ILP
IEEE/ACM Transactions on Computational Biology and Bioinformatics
accepted

M. Al Arab, C. Höner zu Siederdissen, K. Tout, A. H. Sahyoun, P. F. Stadler, M. Bernt
Accurate Annotation of Protein-Coding Genes in Mitochondrial Genomes
accepted for Molecular Phylogenetics and Evolution
Link

T. Hartmann, A.-C. Chu, M. Middendorf, and M. Bernt
Combinatorics of Tandem Duplication Random Loss Mutations on Circular Genomes
accepted at IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics

A. Sahyoun, M. Hölzer, F. Jühling, C. Hoener zu Siederdissen, M. Al-Arab, K. Tout, M. Marz, M. Middendorf, P. Stadler, and M. Bernt
Towards a Comprehensive Picture of Alloacceptor tRNA Remolding in Metazoan Mitochondrial Genomes
Nucleic Acids Research
Link

N. Wieseke, T. Hartmann, M. Bernt, M. Middendorf
Cophylogenetic Reconciliation with ILP
accepted for IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics
Link

R. L.V. Moritz, E. Reich, M. Schwarz, M. Bernt, and M. Middendorf
Refined Ranking Relations for Selection of Solutions in Multi Objective Metaheuristics
European Journal of Operational Research 2015, 243(2):454-464
Link

A. H. Sahyoun, M. Bernt, P. F. Stadler, K. Tout
GC Skew and Mitochondrial Origins of Replication
Mitochondrion 2014, 17:56-66
Link

R. L.V. Moritz, M. Bernt, and M. Middendorf
Local Similarity Search to Find Gene Indicators in Mitochondrial Genomes
Biology 2014, 3(1), 220-242
Special Issue: Developments in Bioinformatic Algorithms
Link

H. J. Osigus, M. Eitel, M. Bernt, A. Donath, B. Schierwater
Mitogenomics at the base of Metazoa
Molecular Phylogenetics and Evolution 2013, 69(2):339-351
link

M. Bernt, C. Bleidorn, A. Braband, J. Dambach, A. Donath, G. Fritzsch, A. Golombek, H. Hadrys, F. Jühling, K. Meusemann, M. Middendorf, B. Misof, , M. Perseke, L. Podsiadlowski, B. v. Reumont, B. Schierwater, M. Schlegel, M. Schrödl, S. Simon, P. F. Stadler, I. Stöger, T. H. Struck
A comprehensive analysis of bilaterian mitochondrial genomes and animal phylogeny
Molecular Phylogenetics and Evolution 2013, 69(2):352-364
link

M. Bernt, A. Braband, B. Schierwater, P. F. Stadler
Genetic aspects of mitochondrial genome evolution
Molecular Phylogenetics and Evolution 2013, 69(2):328-338
link

M. Bernt, A. Braband, M. Middendorf, B. Misof, O. Rota-Stabelli, P. F. Stadler
Bioinformatics Methods for the Comparative Analysis of Metazoan Mitochondrial Genome Sequences
Molecular Phylogenetics and Evolution 2013, 69(2):320-327
link

M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz, G. Fritzsch, J. Pütz, M. Middendorf, and P. F. Stadler
MITOS: Improved de novo Metazoan Mitochondrial Genome Annotation
Molecular Phylogenetics and Evolution 2013, 69(2):313-319
link

A. Duò, R. Bruggmann, S. Zoller, M. Bernt, and C. R. Gruenig
Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex
BMC Genomics 2012, 13:166
link

F. Jühling, J. Pütz, M. Bernt, A. Donath, M. Middendorf, C. Florentz, and P. F. Stadler
Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements
Nucleic Acids Research, 2012, 40(7):2833-2845
link

M. Bernt and M. Middendorf
A Method for Computing an Inventory of Metazoan Mitochondrial Gene Order Rearrangements
BMC Bioinformatics 2011, 12(Suppl 9):S6
Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics
link

M. Perseke, J. Hetmank, M. Bernt, P. F. Stadler, M. Schlegel, and D. Bernhard
The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria
BMC Evolutionary Biology 2011, 11:134
link

M. Bernt, K.-Y. Chen, M.-C. Chen, A.-C. Chu, D. Merkle, H.-L. Wang, K.-M. Chao, and M. Middendorf
Finding All Sorting Tandem Duplication Random Loss Operations
Journal of Discrete Algorithms 2011, 9(1):32–48
link

M. Bernt, D. Merkle, M. Middendorf
Solving the Preserving Reversal Median Problem
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2008, 5(3):332-347
link

M. Perseke, G. Fritzsch, K. Ramsch, M. Bernt, D. Merkle, M. Middendorf, D. Bernhard, P. F.Stadler and M. Schlegel
Evolution of Mitochondrial Gene Orders in Echinoderms
Molecular Phylogenetics and Evolution 2008, 47(2):855-864
link

M. Bernt, D. Merkle, K. Ramsch, G. Fritzsch, M. Perseke, D. Bernhard, M. Schlegel, P. F. Stadler, and M. Middendorf
CREx: inferring genomic rearrangements based on common intervals
Bioinformatics 2007, 23(21): 2957-2958
link

M. Bernt, D. Merkle, and M. Middendorf
Using Median Sets for Inferring Phylogenetic Trees
Bioinformatics 2007, 23(2):e129-e135 (special issue of ECCB 2006)
This paper won the 3rd prize in the Best Paper Competition of the 5th European Conference on Computational Biology (ECCB), Eilat, Israel, January 21-24, 2007
link

M. Bernt, D. Merkle, and M. Middendorf
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals
IEEE/ACM Transactions on Computational Biology and Bioinformatics 2006, 3(3):275-288
link

Book Chapters


T. Hartmann, M. Middendorf, M. Bernt
Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches
"Comparative Genomics" in the Springer Series "Methods in Molecular Biology" (eds. J.C. Setubal J. Stoye P. Stadler)
accepted

M. Bernt, D. Merkle, M. Middendorf, B. Schierwater, M. Schlegel, and P. F. Stadler
Computational methods for the analysis of mitochondrial genome rearrangements
In: Deep Metazoan Phylogeny: The backbone of the Tree of Life. Wägele J.W.; Bartholomäus T.; Misof B.; Vogt L. (Hrsg.). De Gruyter.
In press
Link

M. Bernt, R. Machne, A. H. Sahyoun, M. Middendorf, P. F. Stadler
Mitochondrial genome evolution
eLS (formerly Encyclopedia of Life Sciences), Advanced Article, Wiley, 2013
Paper
Link

Conference and Workshop Proceedings


T. Hartmann, N. Wieseke, R. Sharan, M. Middendorf, and Matthias Bernt
Genome Rearrangement with ILP
accepted for the Fifteenth Asia Pacific Bioinformatics Conference (APBC2017)

R. L. V. Moritz, E. Reich, M. Bernt, M. Middendorf
A Property Preserving Method for Extending a Single-objective Problem Instance to Multiple Objectives with Specific Correlations
EvoCOP 2016, LNCS 9595, pp 18-33

N. Wieseke, T. Hartmann, M. Bernt, M. Middendorf
Cophylogenetic Reconciliation with ILP
accepted for Thirteenth Asia-Pacific Bioinformatics Conference (APBC 2015), Hsinchu, Taiwan

R. L.V. Moritz, E. Reich, M. Bernt, M. Middendorf
The Influence of Correlated Objectives on Different Types of P-ACO Algorithms
EvoCOP 2014, LNCS 8600, pp. 230--241
Link

M. Bernt, N. Wieseke, and M. Middendorf
On Weighting Schemes for Gene Order Analysis
German Conference on Bioinformatics 2013, OASIcs Vol. 34, 14-23
link

N. Wieseke, M. Bernt, M. Middendorf
Unifying Parsimonious Tree Reconciliation
WABI 2013, LNBI 8126, pp. 200-214
link

R. L. V. Moritz, E. Reich, M. Schwarz, M. Bernt, and M. Middendorf
Refined Ranking Relations for Multi Objective Optimization and Application to P-ACO
Proceeding of the fifteenth annual conference on Genetic and evolutionary computation conference, GECCO '13, 65-72
link

M. Clauß, M. Bernt. M. Middendorf
A Common Interval Guided ACO Algorithm for Permutation Problems
IEEE Symposium on Swarm Intelligence (SIS), 2013, pp. 64 - 71
Link

R. L. V. Moritz, M. Bernt, and M. Middendorf
Annotation Guided Local Similarity Search in Multiple Sequences and its Application to Mitochondrial Genomes
Bioinformatics & Bioengineering (BIBE), 2012 IEEE 12th International Conference on, pp.157-162
Link

M. Bernt, K.-M. Chao, J.-W. Kao, M. Middendorf, E. Tannier
Preserving Inversion Phylogeny Reconstruction
Algorithms in Bioinformatics 2012, Lecture Notes in Computer Science, Vol. 7534, Springer, pp. 1-13
appendix
link

M. Bernt, M.-C. Chen, D. Merkle, H.-L. Wang, K.-M. Chao, and M. Middendorf
Finding All Sorting Tandem Duplication Random Loss Operations
Combinatorial Pattern Matching 2009, Lille (France), Lecture Notes in Computer Science, Vol. 5577, Springer, pp. 301-313
link

M. Bernt, D. Merkle, and M. Middendorf
An Algorithm for Inferring Mitochondrial Genome Rearrangements in a Phylogenetic Tree
Comparative Genomics International Workshop, RECOMB-CG 2008, 5267 Lecture Notes in Bioinformatics (LNBI), 143-157, 2008
Link

M. Bernt, D. Merkle, and M. Middendorf
A Fast and Exact Algorithm for the Perfect Reversal Median Problem
Bioinformatics Research and Applications, 4463 Lecture Notes in Bioinformatics (LNBI), 305-316, 2007
link

M. Bernt, D. Merkle, and M. Middendorf
The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders
Computational Life Sciences II: Second International Symposium CompLife 2006, Cambridge (UK), Sept. 2006, Lecture Notes in Bioinformatics, M.R. Berthold, R. Glen, I. Fischer (eds.), Vol. 4216, Springer, pp. 52-63, 2006
link

M. Bernt, D. Merkle, and M. Middendorf
A Parallel Algorithm for Solving the Reversal Median Problem
Proc. Parallel Processing and Applied Mathematics - Bio-Computing Workshop (PBC'5), LNCS 3911, 1089-1096, 2005
link

Phd Thesis


M. Bernt
Gene order rearrangement methods for the reconstruction of phylogeny

Paper
link

Other


R Kolora, I Riemsdijk, M Bernt, K Nowick, PF Stadler
Identification of genomic rearrangements with de novo assemblies and read-based pipelines
ISMB 2016
Poster

M. Bernt
Characteristics and Evolution of Mitochondrial Genomes
Workshop "Evolution of Non-recombining Chromosomes and Genomes" Lübeck 2014

A. H. Sahyoun, M. Bernt, P. F. Stadler, and K. Tout
Analysis of the relation of replication mechanism and nucleotide composition in metazoan mitogenomes
German Conference on Bioinformatics 2012
Poster

M. Bernt and M. Middendorf
Rearrangement analysis for large sets of gene orders: Towards reconstructing the evolution of metazoan gene orders
Zitteliana B30
Deep Metazoan Phylogeny 2011 New data, new challenges
link

M. Bernt
Inferring Genome Rearrangements in a Phylogenetic Tree
Abstracts of 2010 Information and Management of Application and Innovation Forum, Hwa Hsia Institute of Technology, Taipei, Taiwan

A. Donath, F. Externbrink, F. Jühling, M. Bernt, G. Fritzsch, M. Middendorf, and P. F. Stadler
Improved Automatic Annotation of Metazoan Mitochondrial Genomes
Poster at GCB '09 Halle (Saale), Germany; September 28-30, 2009

M. Bernt, D. Merkle, and M. Middendorf
A method for Solving the Preserving Reversal Median Problem
Abstracts of Saxon Biotechnology Symposium 2007, Biotechnolgy Center, Technische Universität Dresden, 116, 2007

M. Bernt, D. Merkle, K. Ramsch, G. Fritzsch, M. Perseke, D. Bernhard, M. Schlegel, P. F. Stadler, and M. Middendorf
Crex - a tool for analyzing genomic rearrangement operations based on common intervals
Abstracts of Saxon Biotechnology Symposium 2007, Biotechnolgy Center, Technische Universität Dresden; page 15; 2007

M. Bernt, D. Merkle, and M. Middendorf
From genome rearrangements to phylogenies
Abstracts of 5th Biotechnolgy Symposium 2006, Center of Biotechnolgy and Biomedicine, University of Leipzig, 59, 2006

M. Bernt, D. Merkle, and M. Middendorf
Heuristics for the Reversal Median Problem: How to select good reversals?
Proc. of the 20th Dubrovnik International Course and Conference on the Interfaces Among Mathematics, Chemistry and Computer Sciences, Inter-University Centre Dubrovnik, 3, 2005
link

M. Bernt, D. Merkle, and M. Middendorf
Multiple Genome Rearrangement with conserved intervals
Abstracts of 4th Biotechnolgy Symposium 2005, Center of Biotechnolgy and Biomedicine, University of Leipzig, 202, 2005

M. Bernt, D. Merkle, and M. Middendorf
Solving the Multiple Genome Rearrangement Problem with Common Intervals
Proc. of the 19th Dubrovnik International Course and Conference on the Interfaces Among Mathematics, Chemistry and Computer Sciences, Inter-University Centre Dubrovnik, 6, 2004
link