submitted

Hartmann, T., M. Bannach, P.F. Stadler, N. Wieseke and M. Hellmuth
Complete Edge-Colored Permutation Graphs
submitted
Link

2021

Schaller D., M. Lafond, P.F. Stadler, N. Wieseke and M. Hellmuth (2021)
“Indirect identification of horizontal gene transfer.”
Journal of Mathematical Biology, 83(1), 1-73.
Link

2020

Moreira-Soto, A., F. Arroyo-Murillo, A.L. Sander, A. Rasche, V. Corman, B. Tegtmeyer, B., E. Steinmann, E. Corrales-Aguilar, N. Wieseke, J. Avey-Arroyo and J.F. Drexler (2020).
“Cross-order host switches of hepatitis C-related viruses illustrated by a novel hepacivirus from sloths.”
Virus evolution, 6(2), veaa033.
Link

Hellmuth, M., A. Fritz, P.F. Stadler and N. Wieseke (2020).
“Cograph Editing: Merging Modules is equivalent to Editing P4s.”
The Art of Discrete and Applied Mathematics, 3(2), P2-01.
Link

2019

Kahnt, B., W.N. Hattingh, P. Theodorou, N. Wieseke, M. Kuhlmann, K.L. Glennon, T. van der Niet, R. Paxton, and G.V. Cron (2019)
“Should I stay or should I go? Pollinator shifts rather than cospeciation dominate the evolutionary history of South African Rediviva bees and their Diascia host plants.”
Molecular ecology, 28(17), 4118-4133.
Link

Käfer, S., S. Paraskevopoulou, F. Zirkel, N. Wieseke, A. Donath, M. Petersen, T.C.. Jones, S. Liu, X. Zhou, M. Middendorf, S. Junglen, B. Misof and C. Drosten (2019)
“Re-assessing the diversity of negative strand RNA viruses in insects.”
PLoS Pathogens, 15(12).
Link

2018

Nøjgaard, N., M. Geiss, D. Merkle, P.F. Stadler, N. Wieseke, and M. Hellmuth (2018).
“Time-consistent reconciliation maps and forbidden time travel.”
Algorithms for Molecular Biology, 13(1), 2.
Link

Geiß, M., J. Anders, P.F. Stadler, N. Wieseke, and M. Hellmuth (2018)
“Reconstructing gene trees from Fitch’s xenology relation.”
Journal of mathematical biology, 77(5), 1459-1491.
Link

Nøjgaard, N., N. El-Mabrouk, D. Merkle, N. Wieseke, and M. Hellmuth (2018).
“Partial Homology Relations - Satisfiability in Terms of Di-Cographs.”
International Computing and Combinatorics Conference (pp. 403-415). Springer, Cham.
Link

Hellmuth, M. and N. Wieseke (2018).
“On Tree Representations of Relations and Graphs: Symbolic Ultrametrics and Cograph Edge Decompositions.”
Journal of Combinatorial Optimization, 36(2), 591-616.
Link

Hartmann, T., N. Wieseke, R. Sharan, M. Middendorf, and M. Bernt (2018).
“Genome Rearrangement with ILP.”
In: IEEE/ACM Transactions on Computational Biology and Bioinformatics PP.99, pp. 1–1.
Link

Middendorf, M. and N. Wieseke (2018).
“A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees.”
PloS one, 13(9), e0204907.
Link

de Oliveira Carneiro, I., A.L. Sander, N. Silva, A. Moreira-Soto, A. Normann, B. Flehmig, A.N. Lukashev, A. Dotzauer, N. Wieseke, C.R. Franke, and J.F. Drexler (2018).
“A novel marsupial hepatitis A virus corroborates complex evolutionary patterns shaping the genus Hepatovirus.”
Journal of virology, 92(13), e00082-18.
Link

2017

Hellmuth, M. and N. Wieseke (2017).
“On Tree Representations of Relations and Graphs: Symbolic Ultrametrics and Cograph Edge Decompositions.”
In: Journal of Combinatorial Optimization (JOCO), pp. 1–26.
Link

Nøjgaard, N., M. Geiß, D. Merkle, P.F. Stadler, N. Wieseke, and M. Hellmuth (2017).
“Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps.”
In: 17th Inter- national Workshop on Algorithms in Bioinformatics (WABI 2017). Vol. 88. Leibniz International Proceedings in Informatics (LIPIcs), 17:1–17:12.
Link

2016

Indrischek, H., N. Wieseke, P.F. Stadler, and S.J. Prohaska (2016).
“The Paralog-to-Contig Assignment Problem: High quality gene models from fragmented assemblies.”
In: Algorithms for Molecular Biology (ALMOB) 11.1.
Link

Hellmuth, M., P.F. Stadler, and N. Wieseke (2016).
“The Mathematics of Xenology: Di-cographs, Symbolic Ultrametrics, 2-structures and Tree-representable Systems of Binary Relations.”
In: Journal of Mathematical Biology (JOMB), pp. 1–39.
Link

Gomard, Y., M. Dietrich, N. Wieseke, B. Ramasindrazana, E. Lagadec, S.M. Goodman, K. Dellagi, and P. Tortosa (2016).
“Malagasy bats shelter a considerable diversity of pathogenic Leptospira displaying a strong host-specificity pattern.”
In: FEMS Microbiology Ecology 92.4.
Link

Hellmuth, M. and N. Wieseke (2016).
“From Sequence Data incl. Orthologs, Paralogs, and Xenologs to Gene and Species Trees.”
In: Evolutionary Biology: Convergent Evolution, Evolution of Complex Traits, Concepts and Methods. Ed. by Pierre Pontarotti. Springer International Publishing, pp. 373–392.
Link

Mélade, J., N. Wieseke, B. Ramazindrasana, O. Flores, E. Lagadec, Y. Gommard, S.M. Goodman, K. Dellagi, and H. Pascalis (2016).
“An eco-epidemiological study of Morbilli-related paramyxovirus infection in Madagascar bats reveals host-switching as the dominant macro-evolutionary mechanism.”
In: Scientific Reports 6.23752.
Link

2015

Hellmuth, M., N. Wieseke, M. Lechner, H.P. Lenhof, M. Middendorf, and P.F. Stadler (2015).
“Phylogenomics with paralogs.”
In: Proceedings of the National Academy of Sciences of the United States of America (PNAS) 112.7, pp. 2058–2063.
Link

Hellmuth, M. and N. Wieseke (2015).
“On Symbolic Ultrametrics, Cotree Representations, and Cograph Edge Decompositions and Partitions.”
In: Computing and Combinatorics. Vol. 9198. Lecture Notes in Computer Science (LNCS), pp. 609–623.
Link

Wieseke, N., T. Hartmann, M. Bernt, and M. Middendorf (2015).
“Cophylogenetic Reconciliation with ILP.”
In: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 12.6, pp. 1227–1235.
Link

2014

Hernandez-Rosales, M., N. Wieseke, M. Hellmuth, and P.F. Stadler (2014).
“Simulation of gene family histories.”
In: BMC Bioinformatics 15.Suppl 3, A8.
Link

Lechner, M., M. Hernandez-Rosales, D. Doerr, N. Wieseke, A. Thévenin, J. Stoye, R.K. Hartmann, S.J. Prohaska, and P.F. Stadler (2014).
“Orthology detection combining clustering and synteny for very large datasets.”
In: PLoS ONE 9.8, e105015.
Link

Lechner, M., A. Nickel, S. Wehner, K. Riege, N. Wieseke, B. Beckmann, R.K. Hartmann, and M. Marz (2014).
“Genomewide comparison and novel ncRNAs of Aquificales.”
In: BMC Genomics 15.1, p. 522.
Link

2013

Wieseke, Nicolas, Matthias Bernt, and Martin Middendorf (2013).
“Unifying Parsimonious Tree Reconciliation.”
In: Algorithms in Bioinformatics. Vol. 8126. Lecture Notes in Computer Science (LNCS), pp. 200–214.
Link

Wieseke, N., M. Lechner, M. Ludwig, and M. Marz (2013).
“POMAGO: Multiple Genome-Wide Alignment Tool for Bacteria.”
In: Bioinformatics Re- search and Applications. Vol. 7875. Lecture Notes in Computer Science (LNCS), pp. 249–260.
Link

Hellmuth, M., M. Hernandez-Rosales, K.T. Huber, V. Moulton, P.F. Stadler, and N. Wieseke (2013).
“Orthology relations, symbolic ultrametrics, and cographs.”
In: Journal of Mathematical Biology (JOMB) 66.1-2, pp. 399–420.
Link

Bernt, M., N. Wieseke, and M. Middendorf (2013).
“On Weighting Schemes for Gene Order Analysis.”
In: German Conference on Bioinformatics 2013. Vol. 34. OpenAccess Series in Informatics (OASIcs), pp. 14–23.
Link

2012

Dilcher, M., L. Hasib, M. Lechner, N. Wieseke, M. Middendorf, M. Marz, A. Koch, M. Spiegel, G. Dobler, F.T. Hufert, and M. Weidmann (2012).
“Genetic characterization of Tribec virus and Kemerovo virus, two tick-transmitted human-pathogenic Orbiviruses.”
In: Virology 423.1, pp. 68– 76.
Link

Hernandez-Rosales, M., M. Hellmuth, N. Wieseke, K.T. Huber, V. Moulton, and P.F. Stadler (2012).
“From event-labeled gene trees to species trees.”
In: BMC Bioinformatics 13.Suppl 19, S6.
Link

2011

Hernandez-Rosales, M., N. Wieseke, M. Hellmuth, and P.F. Stadler (2011).
Simulation of gene family histories.
Tech. rep. Research Report Nr. 12-017. Department of Computer Science, University Leipzig.
Link

Keller-Schmidt, S., N. Wieseke, K. Klemm, and M. Middendorf (2011).
Evaluation of Host Parasite Reconciliation Methods using a new Approach for Cophylogeny Generation.
Tech. rep. Research Report Nr. 11-013. Department of Computer Science, University Leipzig.
Link

2010

Merkle, D., M. Middendorf, and N. Wieseke (2010).
“A parameter-adaptive dynamic programming approach for inferring cophylogenies.”
In: BMC Bioinformatics 11.Suppl 1, S60.
Link

Theses

Wieseke, N. (2017).
“From Homologous Genes to Phylogenetic Species Trees.”
PhD thesis (Dissertation). Germany: Leipzig University.
Link

Wieseke, N. (2008).
“Algorithmen zur Rekonstruktion kophylogenetischer Ereignisse.”
Masters thesis (Diplomarbeit). Germany: Leipzig University.
Link