Publications since 2006

Prakash, C. and A. von Haeseler (2017). An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Non-uniformity of the Expected Fragment Starting Point and Coverage Profile. J COMPUT BIOL;24(3):200-212. PMID: 27661099
Enkner, Franz; Pichlhöfer, Bettina; Zaharie, Alexandru Teodor; Krunic, Milica; Holper, Tina Maria; Janik, Stefan; Moser, Bernhard; Schlangen, Karin; Neudert, Barbara; Walter, Karin; Migschitz, Brigitte; Müllauer, Leonhard (2017). Molecular Profiling of Thymoma and Thymic Carcinoma: Genetic Differences and Potential Novel Therapeutic Targets. Pathology oncology research : POR.;23(3):551-564. PMID: 27844328
Popitsch, Niko; Bilusic, Ivana; Rescheneder, Philipp; Schroeder, Renée; Lybecker, Meghan (2017). Temperature-dependent sRNA transcriptome of the Lyme disease spirochete. BMC GENOMICS;18(1):28. PMID: 28056764
Klopf, Eva; Schmidt, Heiko A; Clauder-Münster, Sandra; Steinmetz, Lars M; Schüller, Christoph (2017). INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. NUCLEIC ACIDS RES;7(45):3752-3766. PMID: 28025392
Kühbacher, Andreas; Henkel, Helena; Stevens, Philip; Grumaz, Christian; Finkelmeier, Doris; Burger-Kentischer, Anke; Sohn, Kai; Rupp, Steffen (2017). Dermal Fibroblasts Play a Central Role in Skin Model Protection against C. albicans Invasion. J INFECT DIS;215(11):1742-1752. PMID: 28368492
Kalyaanamoorthy, Subha; Minh, Bui Quang; Wong, Thomas K F; von Haeseler, Arndt; Jermiin, Lars S (2017). ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods;14(6):587-589. PMID: 28481363
Sedlyarova, Nadezda; Rescheneder, Philipp; Magán, Andrés; Popitsch, Niko; Rziha, Natascha; Bilusic, Ivana; Epshtein, Vitaly; Zimmermann, Bob; Lybecker, Meghan; Sedlyarov, Vitaly; Schroeder, Renée; Nudler, Evgeny (2017). Natural RNA Polymerase Aptamers Regulate Transcription in E. coli. MOL CELL;67(1):30-43.e6. PMID: 28648779
Ratmann, Oliver; Wymant, Chris; Colijn, Caroline; Danaviah, Siva; Essex, M; Frost, Simon D W; Gall, Astrid; Gaiseitsiwe, Simani; Grabowski, Mary; Gray, Ronald; Guindon, Stephane; von Haeseler, Arndt; Kaleebu, Pontiano; Kendall, Michelle; Kozlov, Alexey; Manasa, Justen; Minh, Bui Quang; Moyo, Sikhulile; Novitsky, Vladimir; Nsubuga, Rebecca; Pillay, Sureshnee; Quinn, Thomas C; Serwadda, David; Ssemwanga, Deogratius; Stamatakis, Alexandros; Trifinopoulos, Jana; Wawer, Maria; Leigh Brown, Andrew; de Oliveira, Tulio; Kellam, Paul; Pillay, Deenan; Fraser, Christophe (2017). HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. AIDS research and human retroviruses.. PMID: 28540766
Chernomor, Olga; von Haeseler, Arndt; Minh, Bui Quang (2016). Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. SYST BIOL. PMID: 27121966
Jagut, Marlène; Hamminger, Patricia; Woglar, Alexander; Millonigg, Sophia; Paulin, Luis; Mikl, Martin; Dello Stritto, Maria Rosaria; Tang, Lois; Habacher, Cornelia; Tam, Angela; Gallach, Miguel; von Haeseler, Arndt; Villeneuve, Anne M; Jantsch, Verena (2016). Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance. PLOS BIOLOGY;14(3):e1002412. PMID: 27011106
Burki, Fabien; Kaplan, Maia; Tikhonenkov, Denis V; Zlatogursky, Vasily; Minh, Bui Quang; Radaykina, Liudmila V; Smirnov, Alexey; Mylnikov, Alexander P; Keeling, Patrick J (2016). Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. Proceedings. Biological sciences;283(1823). PMID: 26817772
Chernomor O., Klaere S., von Haeseler A., and B.Q. Minh (2016). Split diversity: measuring and optimizing biodiversity using phylogenetic split networks. Topics in Biodiversity and Conservation;14:173-195.
Gesson, Kevin; Rescheneder, Philipp; Skoruppa, Michael P; von Haeseler, Arndt; Dechat, Thomas; Foisner, Roland (2016). A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha. GENOME RES;26(4):462-73. PMID: 26798136
Holthaus, Karin Brigit; Strasser, Bettina; Sipos, Wolfgang; Schmidt, Heiko A; Mlitz, Veronika; Sukseree, Supawadee; Weissenbacher, Anton; Tschachler, Erwin; Alibardi, Lorenzo; Eckhart, Leopold (2016). Comparative Genomics Identifies Epidermal Proteins Associated with the Evolution of the Turtle Shell. MOL BIOL EVOL;33(3):726-37. PMID: 26601937
Gallach, Miguel; Betrán, Esther (2016). Dosage Compensation and the Distribution of Sex-Biased Gene Expression in Drosophila: Considerations and Genomic Constraints. J MOL EVOL;82(4-5):199-206. PMID: 27059220
Trifinopoulos J., Nguyen L.-T., von Haeseler A., and B.Q. Minh (2016). W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. NUCLEIC ACIDS RES. PMID: 27084950
Grumaz, Silke; Stevens, Philip; Grumaz, Christian; Decker, Sebastian O; Weigand, Markus A; Hofer, Stefan; Brenner, Thorsten; von Haeseler, Arndt; Sohn, Kai (2016). Next-generation sequencing diagnostics of bacteremia in septic patients. Genome medicine;8(1):73. PMID: 27368373
Schrempf, Dominik; Minh, Bui Quang; De Maio, Nicola; von Haeseler, Arndt; Kosiol, Carolin (2016). Reversible polymorphism-aware phylogenetic models and their application to tree inference. Journal of theoretical biology.;407:362-70. PMID: 27480613
Kaiser, Tobias S; Poehn, Birgit; Szkiba, David; Preussner, Marco; Sedlazeck, Fritz J; Zrim, Alexander; Neumann, Tobias; Nguyen, Lam-Tung; Betancourt, Andrea J; Hummel, Thomas; Vogel, Heiko; Dorner, Silke; Heyd, Florian; von Haeseler, Arndt; Tessmar-Raible, Kristin (2016). The genomic basis of circadian and circalunar timing adaptations in a midge. NATURE. PMID: 27871090
Nguyen, Lam-Tung; Schmidt, Heiko A; von Haeseler, Arndt; Minh, Bui Quang (2015). IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. MOL BIOL EVOL;32(1):268-74. PMID: 25371430