Publications since 2006

Nguyen, Lam-Tung; von Haeseler, Arndt; Minh, Bui Quang (2018). Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site plus Gamma Model. SYST BIOL;67(3):552-558. PMID: 29186593
Wang, Huai-Chun; Minh, Bui Quang; Susko, Edward; Roger, Andrew J (2018). Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation. SYST BIOL;67(2):216-235. PMID: 28950365
Hoang, Diep Thi; Chernomor, Olga; von Haeseler, Arndt; Minh, Bui Quang; Le, Sy Vinh (2018). UFBoot2: Improving the Ultrafast Bootstrap Approximation. MOL BIOL EVOL;35(2):518-522. PMID: 29077904
Alves, Ricardo J Eloy; Minh, Bui Quang; Urich, Tim; von Haeseler, Arndt; Schleper, Christa (2018). Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. NAT COMMUN;9(1):1517. PMID: 29666365
Hoang, Diep Thi; Vinh, Le Sy; Flouri, Tomá?; Stamatakis, Alexandros; von Haeseler, Arndt; Minh, Bui Quang (2018). MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC EVOL BIOL;18(1):11. PMID: 29390973
Uhse, Simon; Pflug, Florian G; Stirnberg, Alexandra; Ehrlinger, Klaus; von Haeseler, Arndt; Djamei, Armin (2018). In vivo insertion pool sequencing identifies virulence factors in a complex fungal-host interaction. PLOS BIOLOGY;16(4):e2005129. PMID: 29684023
Muhar, Matthias; Ebert, Anja; Neumann, Tobias; Umkehrer, Christian; Jude, Julian; Wieshofer, Corinna; Rescheneder, Philipp; Lipp, Jesse J; Herzog, Veronika A; Reichholf, Brian; Cisneros, David A; Hoffmann, Thomas; Schlapansky, Moritz F; Bhat, Pooja; von Haeseler, Arndt; Köcher, Thomas; Obenauf, Anna C; Popow, Johannes; Ameres, Stefan L; Zuber, Johannes (2018). SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. SCIENCE. PMID: 29622725
Pflug, Florian G; von Haeseler, Arndt (2018). TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers. BIOINFORMATICS. PMID: 29672674
Müller, Christoph; Krunic, Milica; Wendt, Judith; von Haeseler, Arndt; Okamoto, Ichiro (2018). Germline Variants in the POT1-Gene in High-Risk Melanoma Patients in Austria. G3-Genes Genomes Genetics;8:1475-1480. PMID: 29523635
Drecktrah, Dan; Hall, Laura S; Rescheneder, Philipp; Lybecker, Meghan; Samuels, D Scott (2018). The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi Frontiers in cellular and infection microbiology;8:231. PMID: 30027068
Nattestad, Maria; Goodwin, Sara; Ng, Karen; Baslan, Timour; Sedlazeck, Fritz J; Rescheneder, Philipp; Garvin, Tyler; Fang, Han; Gurtowski, James; Hutton, Elizabeth; Tseng, Elizabeth; Chin, Chen-Shan; Beck, Timothy; Sundaravadanam, Yogi; Kramer, Melissa; Antoniou, Eric; McPherson, John D; Hicks, James; McCombie, W Richard; Schatz, Michael C (2018). Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. GENOME RES;28(8):1126-1135. PMID: 29954844
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
Herzog, Veronika A; Reichholf, Brian; Neumann, Tobias; Rescheneder, Philipp; Bhat, Pooja; Burkard, Thomas R; Wlotzka, Wiebke; von Haeseler, Arndt; Zuber, Johannes; Ameres, Stefan L (2017). Thiol-linked alkylation of RNA to assess expression dynamics. Nature Methods;14(12):1198-1204. PMID: 28945705
Niemiec, Maria J; Grumaz, Christian; Ermert, David; Desel, Christiane; Shankar, Madhu; Lopes, José Pedro; Mills, Ian G; Stevens, Philip; Sohn, Kai; Urban, Constantin F (2017). Correction to: Dual transcriptome of the immediate neutrophil and Candida albicans interplay. BMC GENOMICS;18(1):863. PMID: 29132295