Publications


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.
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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.
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Hartmann, T., N. Wieseke, R. Sharan, M. Middendorf, and M. Bernt (2017).
“Genome Rearrangement with ILP.”
In: IEEE/ACM Transactions on Computational Biology and Bioinformatics PP.99, pp. 1–1.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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

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

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

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