in press

  • S. Grampp, R. Krüger, V. Lauer, S. Uebel, K.X. Knaup, J. Naas, V. Höffken, T. Weide, N. Schiffer, S. Naas, and J. Schödel (in press) Hypoxia hits APOL1 in the kidney. Kidney Int., 103, in press. (DOI: 10.1016/j.kint.2023.03.035, PMID: 37098381)
  • A. Togkousidis, O. Chernomor, and A. Stamatakis (in press) Parallel Inference of Phylogenetic Stands with Gentrius. Proceedings of the 22nd IEEE International Workshop on High Performance Computational Biology -- HiCOMB 2023 (St. Petersburg, FL, USA), 139-148 (in press). IEEE Computer Society, Piscataway, NJ, USA. (DOI: 10.1109/IPDPSW59300.2023.00035)


  • O. Chernomor, C. Elgert, and A. von Haeseler (2023) Identifying equally scoring trees in phylogenomics with incomplete data using Gentrius. bioRxiv, 2022.03.11.483643 (DOI: 10.1101/2023.01.19.524678)
  • N. Durut, A.E. Kornienko, H.A. Schmidt, N. Lettner, M. Dona, M. Nordborg, and O. Mittelsten Scheid (2023) Long non-coding RNAs contribute to DNA damage resistance in Arabidopsis thaliana. bioRxiv, 2023.03.20.533408 (DOI: 10.1101/2023.03.20.533408)
  • S. Kattner, J. Müller, K. Glanz, M. Manoochehri, C. Sylvester, Y. Vainshtein, M.M. Berger, T. Brenner, and K. Sohn (2023) Identification of two early blood biomarkers ACHE and CLEC12A for improved risk stratification of critically ill COVID-19 patients. Sci. Rep., 13, 4388. (DOI: 10.1038/s41598-023-30158-1, PMID: 36928077, PMCID: PMC10019437)
  • R. Kleinova, V. Rajendra, A.F. Leuchtenberger, C.L. Giudice, C. Vesely, U. Kapoor, A. Tanzer, S. Derdak, E. Picardi, and M.F Jantsch (2023) The ADAR1 editome reveals drivers of editing-specificity for ADAR1-isoforms. Nucleic Acids Res., 51, 4191–4207. (DOI: 10.1093/nar/gkad265, PMID: 37026479)
  • L.F. Paulin, M. Raveendran, R.A. Harris, J. Rogers, A. von Haeseler und F.J. Sedlazeck (2023) SVhound: Detection of regions that harbor yet undetected Structural Variation. BMC Bioinform., 24, 23. (DOI: 10.1186/s12859-022-05046-6, PMID: 36670361, software)


  • C. Bangert, S. Villazala-Merino, M. Fahrenberger, T. Krausgruber, W.M. Bauer, V. Stanek, N.J. Campion, T. Bartosik, T. Quint, G. Regelsberger, V. Niederberger-Leppin, C. Bock, S. Schneider, and J. Eckl-Dorna (2022) Comprehensive Analysis of Nasal Polyps Reveals a More Pronounced Type 2 Transcriptomic Profile of Epithelial Cells and Mast Cells in Aspirin-Exacerbated Respiratory Disease. Front. Immunol., 13, 850494. (DOI: 10.3389/fimmu.2022.850494, PMID: 35418991, PMCID: PMC8996080)
  • S. Burgstaller-Muehlbacher, S.M. Crotty, H.A. Schmidt, T. Drucks, and A. von Haeseler (2022) ModelRevelator: Fast phylogenetic model estimation via deep learning. bioRxiv, 2021.12.22.473813 (DOI: 10.1101/2021.12.22.473813v2)
  • S.M. Crotty and B.R. Holland (2022) Comparing partitioned models to mixture models: Do information criteria apply? Syst. Biol., 71, 1541–1548. (DOI: 10.1093/sysbio/syac003, PMID: 35041002, PMCID: PMC9558833)
  • M.P.S. Dekens, B.M Fontinha, M. Gallach, S. Pflügler, and K. Tessmar-Raible (2022) Melanopsin elevates locomotor activity during the wake state of the diurnal zebrafish. EMBO Rep., 23, e51528. (DOI: 10.15252/embr.202051528, PMID: 35233929)
  • M. Huth, L. Santini, E. Galimberti, J. Ramesmayer, F. Titz-Teixeira, R. Sehlke, M. Oberhuemer, S. Stummer, V. Herzog, M. Garmhausen, M. Romeike, A. Chugunova, K.F. Leesch, L. Holcik, K. Weipoltshammer, A. Lackner, C. Schoefer, A. von Haeseler, C. Buecker, A. Pauli, S. Ameres, A. Smith, A. Beyer, and M. Leeb (2022) NMD is required for timely cell fate transitions by fine-tuning gene expression and regulating translation. Genes Dev., 36, 348-367. (DOI: 10.1101/gad.347690.120, PMID: 35241478)
  • J. Kaczanowskae, F. Ganglbergere, O. Chernomore, D. Kargl, B. Galik, A. Hess, Y. Moodley, A. von Haeseler, K. Bühler, and W. Haubensak (2022) Molecular archaeology of human cognitive traits. Cell Rep., 40, 111287. (DOI: 10.1016/j.celrep.2022.111287, PMID: 36044840)
    e contributed equally
  • M. Schwaigere, C. Andrikoue, R. Dnyansagare, P. Ferrer Murguia, P. Paganos, D. Voronov, B. Zimmermann, T. Lebedeva, H.A. Schmidt, G. Genikhovich, G. Benvenuto, M.I. Arnone, and U. Technau (2022) An ancestral Wnt-Brachyury feedback loop in axial patterning and recruitment of mesoderm-determining target genes. Nat. Ecol. Evol., 6, 1921–1939. (DOI: 10.1038/s41559-022-01905-w, PMID: 36396969)
    e contributed equally
  • S. Tiedeck, M.B. Heindl, P. Kramlinger, J. Naas, F. Brütting, N. Kirkwood, P. Mulvaney, and G. Herink (2022) Single-Pixel Fluorescence Spectroscopy Using Near-Field Dispersion for Single-Photon Counting and Single-Shot Acquisition. ACS Photonic, 9, 2931–2937. (DOI: 10.1021/acsphotonics.2c00710)
  • Á. Vértesy, O.L. Eichmueller, J. Naas, M. Novatchkova, C. Esk, M. Balmaña, S. Ladstaetter, C. Bock, A. von Haeseler, and J.A. Knoblich (2022) Gruffi: an algorithm for computational removal of stressed cells from brain organoid transcriptomic datasets. EMBO J., 41, e111118. (DOI: 10.15252/embj.2022111118, PMID: 35919947, software)
  • J. Voznica, A. Zhukova, V. Boskova, E. Saulnier, F. Lemoine, M. Moslonka-Lefebvre, and O. Gascuel (2022) Deep learning from phylogenies to uncover the epidemiological dynamics of outbreaks. Nat. Commun., 13, 3896. (DOI: 10.1038/s41467-022-31511-0, PMID: 35794110, PMCID: PMC9258765)


  • O. Chernomore, L. Peterse, J. Schneidewinde, A. Loeschcke, E. Knieps-Grünhagen, F. Schmitz, E. von Lieres, R.J. Kutta, V. Svensson, K.-E. Jaeger, T. Drepper, A. von Haeseler, and U. Krauss (2021) Complex evolution of light-dependent protochlorophyllide oxidoreductases in aerobic anoxygenic phototrophs: origin, phylogeny and function. Mol. Biol. Evol., 38, 819-837. (DOI: 10.1093/molbev/msaa234, PMID: 32931580)
    e contributed equally
  • I. Ferreira, S. Lepuschitz, S. Beisken, G. Fiume, K. Mrazek, B.J.H. Frank, S. Huber, M.A. Knoll, A. von Haeseler, A. Materna, J.G. Hofstaetter, A.E. Posch, and J. Weinberger (2021) Culture-Free Detection of Antibiotic Resistance Markers from Native Patient Samples by Hybridization Capture Sequencing. Microorganisms, 9, 1672. (DOI: 10.3390/microorganisms9081672, PMID: 34442751, PMCID: PMC8398375)
  • B.M. Fontinha, T. Zekoll, M. Al-Rawi, M. Gallach, F. Reithofer, A.J. Barker, M. Hofbauer, R.M. Fischer, A. von Haeseler, H. Baier, and K. Tessmar-Raible (2021) TMT-Opsins differentially modulate medaka brain function in a context-dependent manner. PLoS Biol., 19, e3001012. (DOI: 10.1371/journal.pbio.3001012, PMID: 33411725)
  • E.B. Hodcroft, N. De Maio, R. Lanfear, D.R. MacCannell, B.Q. Minh, H.A. Schmidt, A. Stamatakis, N. Goldman, and C. Dessimoz (2021) Want to track pandemic variants faster? Fix the bioinformatics bottleneck. Nature, 591, 30-33. (DOI: 10.1038/d41586-021-00525-x, PMID: 33649511)
  • T.S. Kaiser, A. von Haeseler, K. Tessmar-Raible, and D.G. Heckel (2021) Timing strains of the marine insect Clunio marinus evolved and persist in the face of gene flow. Mol. Ecol., 30, 1264-1280. (DOI: 10.1111/mec.15791, PMID: 33410230)
  • M.-T. Kurzbauer, M.P. Janisiw, L.F. Paulin, I. Prusén Mota, K. Tomanov, O. Krsicka, A. von Haeseler, V. Schubert, and Peter Schlögelhofer (2021) ATM controls meiotic DNA double-strand break formation and recombination and affects synaptonemal complex organization in plants. Plant Cell, 33, 1633-1656. (DOI: 10.1093/plcell/koab045, PMID: 33659989)
  • L. Lüftinger, I. Ferreira, B.J.H. Frank, S. Beisken, J. Weinberger, A. von Haeseler, T. Rattei, J.G. Hofstaetter, A.E. Posch, and A. Materna (2021) Predictive Antibiotic Susceptibility Testing by Next-Generation Sequencing for Periprosthetic Joint Infections: Potential & Limitations. Biomedicines, 9, 910. (DOI: 10.3390/biomedicines9080910, PMID: 34440114, PMCID: PMC8389688)
  • R. Revilla-i-Domingo, V.B. Veedin Rajan, M. Waldherr, G. Prohaczka, H. Musset, L. Orel, E. Gerrard, M. Smolka, A. Stockinger, M. Farlik, R.J. Lucas, F. Raible, and K. Tessmar-Raible (2021) Characterization of cephalic and non-cephalic sensory cell types provides insight into joint photo- and mechanoreceptor evolution. eLife, 10, e66144. (DOI: 10.7554/eLife.66144, PMID: 34350831, PMCID: PMC8367381)
  • J. Sims, F.A. Rabanal, C. Elgert, A. von Haeseler, and P. Schlögelhofer (2021) It's just a matter of time: Balancing Homologous Recombination and Non-Homologous End Joining at the rDNA Locus during Meiosis. Front. Plant Sci., 12, 773052. (DOI: 10.3389/fpls.2021.773052, PMID: 33452254, PMCID: PMC8580885)
  • J. Sims, G. Sestini, C. Elgert, A. von Haeseler, and P. Schlögelhofer (2021) Sequencing of the Arabidopsis NOR2 reveals its distinct organization and tissue-specific rRNA ribosomal variants. Nat. Commun., 12, 1-13. (DOI: 10.1038/s41467-020-20728-6, PMID: 33452254, PMCID: PMC7810690)


  • V. Boskova and T. Stadler (2020) PIQMEE: Bayesian phylodynamic method for analysis of large datasets with duplicate sequences. Mol. Biol. Evol., 37, 3061-3075. (DOI: 10.1093/molbev/msaa136, PMID: 32492139, software)
  • S.M. Crotty, B.Q. Minh, N.G. Bean, B.R. Holland, J. Tuke, L.S. Jermiin, and A. von Haeseler (2020) GHOST: Recovering Historical Signal from Heterotachously-evolved Sequence Alignments . Syst. Biol., 69, 249-264. (DOI: 10.1093/sysbio/syz051, PMID: 31364711, software)
  • C. Esk, D. Lindenhofer, S. Haendeler, R.A. Wester, F.G. Pflug, B. Schroeder, J.A. Bagley, U. Elling, J. Zuber, A. von Haeseler, and J.A. Knoblich (2020) A human tissue screen identifies a regulator of ER secretion as a brain size determinant. Science, 370, 935-941. (DOI: 10.1126/science.abb5390, PMID: 33122427)
  • I. Ferreira, S. Beisken, L. Lueftinger, T. Weinmaier, M. Klein, J. Bacher, R. Patel, A. von Haeseler, and A.E. Posch (2020) Species Identification and Antibiotic Resistance Prediction by Analysis of Whole Genome Sequence Data Using ARESdb: An Analysis of Isolates from the Unyvero Lower Respiratory Tract Infection Trial. J. Clin. Microbiol., 58, e00273-20. (DOI: 10.1128/JCM.00273-20, PMID: 32295890)
  • E. Janisiw, M. Raices, F. Balmir, L.F. Paulin, A. Baudrimont, A. von Haeseler, J. Yanowitz, V. Jantsch, and N. Silva (2020) Poly(ADP-ribose) glycohydrolase coordinates meiotic DNA double-strand break induction and repair independent of its catalytic activity. Nat. Commun., 11, 4869. (DOI: 10.1038/s41467-020-18693-1, PMID: 32978394)
  • A.F. Leuchtenbergere, S.M. Crottye, T. Drucks, H.A. Schmidt, S. Burgstaller-Muehlbacher, and A. von Haeseler (2020) Distinguishing Felsenstein Zone From Farris Zone Using Neural Networks. Mol. Biol. Evol., 37, 3632-3641. (free reprint, DOI: 10.1093/molbev/msaa164, PMID: 32637998, software)
    e contributed equally
  • S. Madritsch, S. Bomers, A. Posekany, A. Burg, R. Birke, F. Emerstorfer, R. Turetschek, S. Otte, H. Eigner, and E.M. Sehr (2020) Integrative transcriptomics reveals genotypic impact on sugar beet storability. Plant Mol. Biol., 104, 359–378. (DOI: 10.1007/s11103-020-01041-8, PMID: 32754876, PMCID: PMC7593311)
  • N. Mahfouz, I. Ferreira, S. Beisken, A. von Haeseler, A. Posch (2020) Large-Scale Assessment of Antimicrobial Resistance Marker Databases for Genetic Phenotype Prediction. J. Antimicrob. Chemother., 75, 3099–3108. (DOI: 10.1093/jac/dkaa257, PMID: 32658975)
  • C. Manuel and A. von Haeseler (2020) Structure of the space of taboo-free sequences. J. Math. Biol., 81, 1029-1057. (DOI: 10.1007/s00285-020-01535-5, PMID: 32940748, PMCID: PMC7560954)
  • C. Mavian, S. Kosakovsky Pond, S. Marini, B. Rife Magalis, A.-M. Vandamme, S. Dellicour, S.V. Scarpino, C. Houldcroft, J. Villabona-Arenas, T.K. Paisie, N.S. Trovao, C. Boucher, Y. Zhang, R.H. Scheuermann, O. Gascuel, T.T.-Y. Lam, M.A. Suchard, A. Abecasis, E. Wilkinson, T. de Oliveira, A.I. Bento, H.A. Schmidt, D. Martin, J. Hadfield, N. Faria, N.D. Grubaugh, R.A. Neher, G. Baele, P. Lemey, T. Stadler, J. Albert, K.A. Crandall, T, Leitner, A. Stamatakis, M. Prosperi and M. Salemi (2020) Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proc. Natl. Acad. Sci. USA, 117, 12522-12523. (DOI: 10.1073/pnas.2007295117, PMID: 32381734)
  • B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeselers, and R. Lanfears (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37, 1530-1534. (free reprint, DOI: 10.1093/molbev/msaa015, PMID: 32011700, software)
    s co-senior authors.
  • C. Missbach, H. Vogel, B.S. Hansson, E. Große-Wilde, A. Vilcinskas, and T.S. Kaiser (2020) Developmental and sexual divergence in the olfactory system of the marine insect Clunio marinus. Sci. Rep., 10, 2125. (DOI: 10.1038/s41598-020-59063-7, PMID: 32034235, PMCID: PMC7005812)
  • N. Popitsch, C.D. Huber, I. Buchumenski, E. Eisenberg, M. Jantsch, A. von Haeseler and M. Gallach (2020) A-to-I RNA editing uncovers hidden signals of adaptive genome evolution in animals. Genome Biol. Evol., 12, 345-357. (DOI: 10.1093/gbe/evaa046, PMID: 32145015)
  • C. Prakash, F.C. Trognitz, P. Venhuizen, A. von Haeseler, and Bodo Trognitz (2020) A Compendium of Genome-Wide Sequence Reads From NBS (Nucleotide Binding Site) Domains of Resistance Genes in the Common Potato. Sci. Rep., 10, 11392. (DOI: 10.1038/s41598-020-67848-z, PMID: 32647195)
  • R. Reinhardt, L. Truebestein, H.A. Schmidt, and T.A. Leonard (2020) It Takes Two to Tango: Activation of Protein Kinase D by Dimerization BioEssays, 42, 1900222. (DOI: 10.1002/bies.201900222, PMID: 31997382)
  • L. Riva, S. Yuan, X. Yin, L. Martin-Sancho, N. Matsunaga, L. Pache, S. Burgstaller-Muehlbacher, P.D. De Jesus, P. Teriete, M.V. Hull, M.W. Chang, J.F.-W. Chan, J. Cao, V.K.-M. Poon, K.M. Herbert, K. Cheng, T.-T.H. Nguyen, A. Rubanov, Y. Pu, C. Nguyen, A. Choi, R. Rathnasinghe, M. Schotsaert, L. Miorin, M. Dejosez, T.P. Zwaka, K.-Y. Sit, L. Martinez-Sobrido, W.-C. Liu, K.M. White, M.E. Chapman, E.K. Lendy, R.J. Glynne, R. Albrecht, E. Ruppin, A.D. Mesecar, J.R. Johnson, C. Benner, R. Sun, P.G. Schultz, A.I. Su, A. García-Sastre, A.K. Chatterjee, K.-Y. Yuen, and S.K. Chanda (2020) Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature, 586, 113-119. (DOI: 10.1038/s41586-020-2577-1, PMID: 32707573)
  • A. Waagmeester, G. Stupp, S. Burgstaller-Muehlbacher, B.M. Good, M. Griffith, O.L. Griffith, K. Hanspers, H. Hermjakob, T.S. Hudson, K. Hybiske, S.M. Keating, M. Manske, M. Mayers, D. Mietchen, E. Mitraka, A.R. Pico, T. Putman, A. Riutta, N. Queralt-Rosinach, L.M. Schriml, T. Shafee, D. Slenter, R. Stephan, K. Thornton, G. Tsueng, R. Tu, S. Ul-Hasan, E. Willighagen, C. Wu, and A.I. Su (2020) Wikidata as a knowledge graph for the life sciences. eLife, 9, e52614. (DOI: 10.7554/eLife.52614, PMID: 32180547, PMCID: PMC7077981)


  • R.J.E. Alves, M. Kerou, A. Zappe, R. Bittner, S.S. Abby, H.A. Schmidt, K. Pfeifer, and C. Schleper (2019) Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures. Front. Microbiol., 10, 1571. (DOI: 10.3389/fmicb.2019.01571, PMID: 31379764, PMCID: PMC6657660)
  • P. Breitling, A. Stamatakis, O. Chernomor, B. Bettisworth, and L. Reszczynski (2019) Empirical Analysis of Phylogenetic Quasi-Terraces bioRxiv, 810309. (DOI: 10.1101/810309)
  • A. Jain, D. Perisa, F. Fliedner, A. von Haeseler, and I. Ebersberger (2019) The evolutionary traceability of a protein. Genome Biol. Evol., 11, 531–545. (DOI: 10.1093/gbe/evz008, PMID: 30649284)
  • M. Krunic, P. Venhuizen, L. Müllauer, B. Kaserer and A. von Haeseler (2019) VARIFI – Web-based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data. J. Pers. Med., 9, 10. (DOI: 10.3390/jpm9010010, PMID: 30717290
  • S. Madritsch, E. Wischnitzki, P. Kotrade, A. Ashoub, A. Burg, S. Fluch, W. Brüggemann, and E.M. Sehr (2019) Elucidating Drought Stress Tolerance in European Oaks Through Cross-Species Transcriptomics. G3-Genes Genomes Genet., 9, 3181-3199. (DOI: 10.1534/g3.119.400456, PMID: 31395652, PMCID: PMC6778798)
  • T. Neumann, V.A. Herzog, M. Muhar, A. von Haeseler, J. Zuber; S.L. Ameres, and P. Rescheneder (2019) Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets. BMC Bioinform., 20, 258. (DOI: 10.1186/s12859-019-2849-7, PMID: 31109287)
  • S. Schenk, S. Bannister, F.J. Sedlazeck, D. Anrather, B.Q. Minh, A. Bileck, M. Hartl, A. von Haeseler, C. Gerner, F. Raible, and K. Tessmar-Raible (2019) Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase. eLife, 8, e41556. (DOI: 10.7554/eLife.41556.001, PMID: 30767890)
  • D. Schrempf, B.Q. Minh, A. von Haeseler, and C. Kosiol (2019) Polymorphism-aware species trees with advanced mutation models, bootstrap and rate heterogeneity. Mol. Biol. Evol., 35, 1294–1301. (free reprint, DOI: 10.1093/molbev/msz043, PMID: 30825307)
  • S. Uhse, F.G. Pflug, A. von Haeseler, and A. Djamei (2019) Insertion pool sequencing for insertional mutant analysis in complex host-microbe interactions. Current Protocols in Plant Biology, 4, e20086. (DOI: 10.1002/cppb.20097, PMID: 31479207)


  • R. Alves, B.Q. Minh, T. Urich, A. von Haeseler, and C. Schleper (2018) Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat. Commun., 9, 1517. (DOI: 10.1038/s41467-018-03861-1, PMID: 29666365, PMCID: PMC5904100)
  • D. Drecktrah, L.S. Hall, P. Rescheneder, M. Lybecker, and D.S. Samuels1,4 (2018) The Stringent Response-Regulated sRNA Transcriptome of Borrelia burgdorferi. Front. Cell. Infect. Microbiol., 8, 231. (DOI: 10.3389/fcimb.2018.00231, PMID: 30027068, PMCID: PMC6041397)
  • R. Finsterwalder, M. Karthika Ganesan, H. Leb, A. Habertheuer, J. Basílio, I. Lang, M. Krunic, D. Wiedemann, and P. Petzelbauer (2018) Hypoxia/reperfusion predisposes to atherosclerosis. PLoS ONE, 13, e0205067. (DOI: 10.1371/journal.pone.0205067, PMID: 30289932)
  • D.T. Hoange, O. Chernomore, A. von Haeseler, B.Q. Minhc, and L.S. Vinhc (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Mol. Biol. Evol., 35, 518-522. (free reprint, DOI: 10.1093/molbev/msx281, PMID: 29077904, software)
    e contributed equally, c corresponding authors.
  • D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeselerc, and B.Q. Minhc (2018) MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation. BMC Evol. Biol., 18, 11. (DOI: 10.1186/s12862-018-1131-3, PMID: 29390973, software)
    c corresponding authors.
  • M. Muhar, A. Ebert, T. Neumann, C. Umkehrer, J. Jude, C. Wieshofer, P. Rescheneder, J.J. Lipp, V.A. Herzog, B. Reichholf, D.A. Cisneros, T. Hoffmann, M.F. Schlapansky, P. Bhat, A. von Haeseler, T. Köcher, A.C. Obenauf, J. Popow, S.L. Ameres, and J. Zuber (2018) SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science, 360, 800-805. (DOI: 10.1126/science.aao2793, PMID: 29622725)
  • C. Müller, M. Krunic, J. Wendt, A. von Haeseler, and I. Okamoto (2018) Germline variants in the POT1-gene in high-risk melanoma patients in Austria. G3-Genes Genomes Genet., 8, 1475-1480. (DOI: 10.1534/g3.117.300394, PMID: 29523635)
  • M. Nattestad, S. Goodwin, K. Ng, T. Baslan, F. Sedlazeck, P. Rescheneder, T. Garvin, H. Fang, J. Gurtowski, E. Hutton, E. Tseng, J. Chin, T. Beck, Y. Sundaravadanam, M. Kramer, E. Antoniou, J. McPherson, J. Hicks, W.R. McCombie, and M.C Schatz (2018) Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res., 28, 1126-1135. (DOI: 10.1101/gr.231100.117, PMID: 29954844)
  • L.-T. Nguyen, A. von Haeseler, and B.Q. Minh (2018) Complex models of sequence evolution require accurate estimators as exemplified with the invariable site plus Gamma model. Syst. Biol., 67, 552-558. (DOI: 10.1093/sysbio/syx092, PMID: 29186593, software)
  • F.G. Pflug and A. von Haeseler (2018) TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers. Bioinformatics, 34, 3137-3144. (DOI: 10.1093/bioinformatics/bty283, PMID: 29672674, software)
  • F.J. Sedlazecke, P. Reschenedere, M. Smolka, H. Fang, M. Nattestad, A. von Haeseler, and M.C. Schatz (2018) Accurate detection of complex structural variations using single molecule sequencing. Nat. Meth., 15, 461-468. (DOI: 10.1038/s41592-018-0001-7, PMID: 29713083)
    e contributed equally
  • S. Uhse, F.G. Pflug, A. Stirnberg, K. Ehrlinger, A. von Haeseler, and A. Djamei (2018) In vivo Insertion Pool Sequencing identifies Virulence Factors in a complex Fungal-Host Interaction. PLoS Biol., 16, e2005129. (DOI: 10.1371/journal.pbio.2005129, PMID: 29684023)
  • H.C. Wange, B.Q. Minhe, S. Susko, and A.J. Roger (2018) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Syst. Biol., 67, 216-235. (DOI: 10.1093/sysbio/syx068, PMID: 28950365, software)
    e contributed equally


  • F. Enkner, B. Pichlhöfer, A.T. Zaharie, M. Krunic, T.M. Holper, S. Janik, B. Moser, K. Schlangen, B. Neudert, K. Walter, B. Migschitz, and L. Müllauer (2017) Molecular Profiling of Thymoma and Thymic Carcinoma: Genetic Differences and Potential Novel Therapeutic Targets. Pathol. Oncol. Res., 23, 551–564. (DOI: 10.1007/s12253-016-0144-8, PMID: 27844328)
  • V.A. Herzog, B. Reichholf, T. Neumann, P. Rescheneder, P. Bhat, T.R. Burkard, W. Wlotzka, A. von Haeseler, J. Zuber, and S.L. Ameres (2017) Thiol-linked alkylation for the metabolic sequencing of RNA. Nat. Methods, 14, 1198-1204. (DOI: 10.1038/nMeth.4435, PMID: 28945705)
  • S. Kalyaanamoorthye, B.Q. Minhe, T.K.F. Wonge, A. von Haeseler, and L.S. Jermiin (2017) ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates. Nat. Methods, 14, 587-589. (DOI: 10.1038/nmeth.4285, PMID: 28481363) PMCID: PMC5453245) software) press release by MFPL
    e contributed equally
  • E. Klopf, H.A. Schmidt, S. Clauder-Münster, L.M. Steinmetz, and C. Schüller (2017) INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. Nucleic Acids Res., 45, 3752-3766. (DOI: 10.1093/nar/gkw1292, PMID: 28025392)
  • A. Kühbacher, H. Henkel, P. Stevens, C. Grumaz, D. Finkelmeier, A. Burger-Kentischer, K. Sohn, and S. Rupp (2017) Dermal Fibroblasts Play a Central Role in Skin Model Protection against C. albicans Invasion. J. Infect. Dis., 215, 1742–1752. (DOI: 10.1093/infdis/jix153, PMID: 28368492)
  • D. Mailänder-Sénchez, C. Braunsdorf, C. Grumaz, C. Müller, S. Lorenz, P. Stevens, J. Wagener, B. Hebecker, B. Hube, F. Bracher, K. Sohn, and M. Schaller (2017) Antifungal defense of probiotic Lactobacillus rhamnosus GG is mediated by blocking adhesion and nutrient depletion. PLoS, 12, e0184438. (DOI: 10.1371/journal.pone.0184438, PMID: 29023454, PMCID: PMC5638248)
  • N. Popitsch, I. Bilusic, P. Rescheneder, R. Schroeder, and M. Lybecker (2017) Temperature-dependent sRNA transcriptome of the Lyme disease spirochete. BMC Genomics, 18, 28. (DOI: 10.1186/s12864-016-3398-3, PMID: 28056764)
  • C. Prakash 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, 200-212. (DOI: 10.1089/cmb.2016.0096, PMID: 27661099)
  • O. Ratmann, C. Wymant, C. Colijn, S. Danaviah, M. Essex, S.D.W. Frost, A. Gall, S. Gaiseitsiwe, M. Grabowski, R. Gray, S. Guindon, A. von Haeseler, P. Kaleebu, M. Kendall, A. Kozlov, J. Manasa, B.Q. Minh, S. Moyo, V. Novitsky, R. Nsubuga, S. Pillay, T.C. Quinn, D. Serwadda, D. Ssemwanga, A. Stamatakis, J. Trifinopoulos, M. Wawer, A. Leigh Brown, T. de Oliveira, P. Kellam, D. Pillay, and C. Fraser (2017) HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences. AIDS Res. Hum. Retrovir., 33, 1083-1098. (DOI: 10.1089/AID.2017.0061, PMID: 28540766)
  • N. Sedlyarova, P. Rescheneder, A. Magán, N. Popitsch, N. Rziha, I. Bilusic, V. Epshtein, B. Zimmermann, M. Lybecker, V. Sedlyarov, R. Schroeder, and E. Nudler (2017) Natural RNA polymerase aptamers regulate transcription in E. coli. Mol. Cell, 67, 30-43. (DOI: 10.1016/j.molcel.2017.05.025, PMID: 28648779, PMCID: PMC5535762)


  • F. Burki, M. Kaplan, D.V. Tikhonekov, V. Zlatogursky, B.Q. Minh, L.V. Radaykina, A. Smirnov, A.P. Mylnikov, and P.J. Keeling (2016) Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta, and Cryptista. Proc. R. Soc. B, 283, 20152802. (free reprint, DOI: 10.1098/rspb.2015.2802, PMID: 26817772)
  • O. Chernomor, A. von Haeseler, and B.Q. Minh (2016) Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices. Syst. Biol., 65, 997-1008. (free reprint, DOI: 10.1093/sysbio/syw037, PMID: 27121966, software)
  • O. Chernomor, S. Klaere, A. von Haeseler, and B.Q. Minh (2016) Split diversity: measuring and optimizing biodiversity using phylogenetic split networks. In R. Pellens and P. Grandcolas (eds.) Biodiversity Conservation and Phylogenetic Systematics (Series: Topics in Biodiversity and Conservation, Vol. 14), 173-195, Springer, Heidelberg/New York. (DOI: 10.1007/978-3-319-22461-9_9, book-DOI: 10.1007/978-3-319-22461-9_9, eISBN: 978-3-319-22461-9, ISBN: 978-3-319-22460-2)
  • M. Gallach and E. Betran (2016) Dosage compensation and the distribution of sex-biased gene expression in Drosophila: considerations and genomic constraints. J. Mol. Evol., 82, 199-206. (DOI: 10.1007/s00239-016-9735-y, PMID: 27059220)
  • K. Gessone, P. Reschenedere, M.P. Skoruppa, A. von Haeseler, T. Dechat, and R. Foisner (2016) A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2alpha. Genome Res., 26, 462-473. (DOI: 10.1101/gr.196220.115, PMID: 26798136)
    e contributed equally
  • S. Grumaze, P. Stevense, C. Grumaz, S. Decker, M. Weigand, S. Hofer, T. Brenner, A. von Haeseler, and K. Sohn (2016) Next-generation sequencing diagnostics of bacteremia in septic patients. Genome Med., 8:73. (DOI: 10.1186/s13073-016-0326-8, PMID: 27368373)
    e contributed equally
  • D.T. Hoang, L.S. Vinh, T. Flouri, A. Stamatakis, A. von Haeseler, and B.Q. Minh (2016) A new phylogenetic tree sampling method for maximum parsimony bootstrapping and proof-of-concept implementation. Proceedings of the 8th International Conference on Knowledge and Systems Engeneering - KSE-2016 (Hanoi, Vietnam), 1-6, IEEE Computer Society, Piscataway, NJ, USA. (DOI: 10.1109/KSE.2016.7758020)
  • K.B. Holthaus, B. Strasser, W. Sipos, H.A. Schmidt, V. Mlitz, S. Sukseree, A. Weissenbacher, E. Tschachler, L. Alibardi, and L. Eckhart (2016) Comparative genomics identifies epidermal proteins associated with the evolution of the turtle shell. Mol. Biol. Evol., 33, 726-737. (DOI: 10.1093/molbev/msv265, PMID: 26601937) , press releases by MBE, MFPL (German version), Medical University of Vienna (German version)
  • M. Jagut, P. Hamminger, A. Woglar, S. Millonigg, L.F. Paulin, M. Mikl, M.R. Dello Stritto, L. Tang, C. Habacher, A. Tam, M. Gallach, A. von Haeseler, A.M. Villeneuve, V. Jantsch (2016) Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance. PLoS Biol., 14, e1002412. (DOI: 10.1371/journal.pbio.1002412) PMID: 27011106, PMCID: PMC4807110)
  • T.S. Kaiser, B. Poehn, D. Szkiba, M. Preussner, F.J. Sedlazeck, A. Zrim, T. Neumann, L.-T. Nguyen, A.J. Betancourt, T. Hummel, H. Vogel, S. Dorner, F. Heyd, A. von Haeseler, and K. Tessmar-Raible (2016) The genomic basis of circadian and circalunar timing adaptations in a midge. Nature, 540, 69-73. (DOI: 10.1038/nature20151, PMID: 27871090, PMCID: PMC5133387, ClunioBase)
  • D. Schrempf, B.Q. Minh, N. De Maio, A. von Haeseler, and C. Kosiol (2016) Reversible polymorphism-aware phylogenetic models and their application to tree inference. J. Theor. Biol., 407, 362-370. (DOI: 10.1016/j.jtbi.2016.07.042, PMID: 27480613, software, bioRxiv-preprint-DOI:10.1101/048496)
  • J. Trifinopoulos, L.-T. Nguyen, A. von Haeseler, and B.Q. Minh (2016) W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res., 44, W232-W235. (free reprint, DOI: 10.1093/nar/gkw256, PMID: 27084950, W-IQ-TREE webserver)


  • J. Cheng, F. Sedlazek, J. Altmüller, and A. Nolte (2015) Ectodysplasin signalling genes and typic evolution in sculpins (Cottus). Proc. R. Soc. B, 282, 20150746. (DOI: 10.1098/rspb.2015.0746, PMID: 26354934)
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  • M. Krunice, R. Ertle, B. Hagen, F.J. Sedlazeck, R. Hofmann-Lehmann, A. von Haeseler and D. Klein (2015) Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study. BMC Vet. Res., 11, 90. (DOI: 10.1186/s12917-015-0378-9, PMID: 25879730)
    e contributed equally
  • D.T. Nguyen, T.M.T. Pham, T.H. Dang, H.A.T. Nguyen, S.Q. Le, B.Q. Minh, Q.M. Dao, B.S Pham, and L.S. Vinh (2015) Building population-specific reference genomes: A case study of Vietnamese reference genome. Proceedings of the 7th International Conference on Knowledge and Systems Engeneering - KSE-2015 (Ho Chi Minh City, Vietnam), 97-102, IEEE Computer Society, Los Alamitos, CA, USA. (DOI: 10.1109/KSE.2015.49)
  • L.-T. Nguyen, H.A. Schmidt, A. von Haeseler, and B.Q. Minh (2015) IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. Mol. Biol. Evol., 32, 268-274. (free reprint, DOI: 10.1093/molbev/msu300, PMID: 25371430, PMCID: PMC4271533, software)
  • M. Preusser, A.S. Berghoff, R. Koller, C.C. Zielinski, J.A. Hainfellner, S. Liebmann-Reindl, N. Popitsch, C.B. Geier, B. Streubel, and P. Birner (2015) Spectrum of gene mutations detected by next generation exome sequencing in brain metastases of lung adenocarcinoma. Eur. J. Cancer, 51, 1803-1811. (DOI: 10.1016/j.ejca.2015.06.107, PMID: 26164066)
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  • M. Tscherner, F. Zwolanek, S. Jenull, F.J. Sedlazeck, A. Petryshyn, I.E. Frohner, J. Mavrianos, N. Chauhan, A. von Haeseler, and K. Kuchler (2015) The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways. PLoS Pathog., 11, e1005218. (DOI: 10.1371/journal.ppat.1005218, PMID: 26473952)
  • K. Wagner, J. Linde, K. Krause, M. Gube, T. Koestler, D. Sammer, O. Kniemeyer, and E. Kothe (2015) Tricholoma vaccinum host communication during ectomycorrhiza formation. FEMS Microbiol. Ecol., 91, fiv120. (DOI: 10.1093/femsec/fiv120, PMID: 26449385)


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    e contributed equally
  • L. Demmel, K. Schmidt, L. Lucast, K. Havlicek, A. Zankel, T. Koestler, V. Reithofer, P. de Camilli, and G. Warren (2014) The endocytic activity of the flagellar pocket in Trypanosoma brucei is regulated by an adjacent phosphatidylinositol phosphate kinase. J. Cell Sci., 127, 2351-2364. (DOI: 10.1242/jcs.146894, PMID: 24639465)
  • I. Ebersberger and A. von Haeseler (2014) Exploring phylogenomic data. In J.W. Waegele, T. Bartholomaeus (eds.) Deep Metazoan Phylogeny: The Backbone of the Tree of Life., 595-617, De Gruyter, Berlin. (DOI: 10.1515/9783110277524.595, eISBN: 9783110277524)
  • I. Ebersberger, S. Simm, M. Leisegang, P. Schmitzberger, O. Mirus, A. von Haeseler, M. Bohnsack, and E. Schleiff (2014) The evolution of the ribosome biogenesis pathway from a yeast perspective. Nucleic Acids Res., 42, 1509-1523. (DOI: 10.1093/nar/gkt1137, PMID: 24234440)
  • M. Gallach (2014) Recurrent turnover of chromosome-specific satellites in Drosophila. Genome Biol. Evol., 6, 1279-1286. (DOI: 10.1093/gbe/evu104, PMID: 24846631)
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  • M. Kaschner, A. Loeschcke, J. Krause, B.Q. Minh, A. Heck, S. Endres, V. Svensson, A. Wirtz, A. von Haeseler K.-E. Jaeger, T. Drepper, and U. Krauss (2014) Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria. Mol. Microbiol., 93, 1066-1078. (DOI: 10.1111/mmi.12719, PMID: 25039543)
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  • D.D. Pollak, B.Q. Minh, A. Cicvaric, and F.J. Monje (2014) A novel Fibroblast Growth Factor Receptor family member promotes neuronal outgrowth and synaptic plasticity in Aplysia. Amino Acids, 2477-2488. (DOI: 10.1007/s00726-014-1803-2, PMID: 25059541)
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  • G. Sengoelge, W. Winnicki, A. Kupczok, A. von Haeseler, M. Schuster, W. Pfaller, P. Jennings, A. Weltermann, S. Blake, and G. Sunder-Plassmann (2014) A SAGE based approach to human glomerular endothelium: defining the transcriptome, finding a novel molecule and highlighting endothelial diversity. BMC Genomics, 15, 725. (DOI: 10.1186/1471-2164-15-725, PMID: 25163811, PMCID: PMC4156628)
  • M. Sorourian, M. M. Kunte, S. Domingues, M. Gallach, F. Özdil, J. Rio and E. Betran (2014) Relocation Facilitates the Acquisition of Short Cis-Regulatory Regions that Drive the Expression of Retrogenes during Spermatogenesis in Drosophila. Mol. Biol. Evol., 31, 2170-2180. (DOI: 10.1093/molbev/msu168, PMID: 24855141)
  • D. Szkiba, M. Kapun, A. von Haeseler, and M. Gallach (2014) SNP2GO: functional analysis of genome-wide association studies. Genetics, 197, 285-289. (DOI: 10.1534/genetics.113.160341, PMID: 24561481, software)
  • C. Vesely, S. Tauber, F. Sedlazeck, M. Tajaddod, A. von Haeseler, and M. Jantsch (2014) ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain. Nucleic Acids Res., 42, 2155-12168. (DOI: 10.1093/nar/gku844, PMID: 25260591)
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  • M. Anisimova, D.A. Liberles, H. Philippe, J. Provan, T. Pupko, and A. von Haeseler (2013) State-of the art methodologies dictate new standards for phylogenetic analysis. BMC Evol. Biol., 13, 161. (DOI: 10.1186/1471-2148-13-161, PMID: 23914788, PMCID: PMC3751533)
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    e contributed equally
  • E. Giannoulatou, G. McVean, I.B. Taylor, S.J. McGowan, G.J. Maher, Z. Iqbal, S.P. Pfeifer, I. Turner, E.M.M. Burkitt Wright, J. Shorto, A. Itani, K. Turner, L. Gregory, D. Buck, E. Rajpert-De Meyts, L.H.J. Looijenga, B. Kerr, A.O.M. Wilkie, and Anne Goriely (2013) Contributions of intrinsic mutation rate and selfish selection to levels of de novo HRAS mutations in the paternal germline. Proc. Natl. Acad. Sci. USA, 110, 20152-20157. (DOI: 10.1073/pnas.1311381110) PMID: 24259709, PMCID: PMC3864328)
  • M. Gil, M.S. Zanetti, S. Zoller, and M. Anisimova (2013) CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models. Mol. Biol. Evol., 30, 1270-1280. (DOI: 10.1093/molbev/mst034, PMID: 23436912, PMCID: PMC3649670)
  • J.E. Heraud-Farlow, T. Sharangdhar, X. Li, P. Pfeifer, S. Tauber, D. Orozco, A. Hörmann, S. Thomas, A. Bakosova, A.R. Farlow, D. Edbauer, H.D. Lipshitz, Q.D. Morris, M. Bilban, M. Doyle, M.A. Kiebler (2013) Staufen2 Regulates Neuronal Target RNAs. Cell Rep., 5, 1511-1518. (DOI: 10.1016/j.celrep.2013.11.039) PMID: 24360961)
  • S. Jünemann, F.J. Sedlazeck, K. Prior, A. Albersmeier, U. John, J. Kalinowski, A. Mellmann, A. Goesmann, A. von Haeseler, J. Stoye and D. Harmsen (2013) Updating benchtop sequencing performance comparison. Nat. Biotechnol., 31, 294-296. (DOI: 10.1038/nbt.2522, PMID: 23563421)
  • B.Q. Minh, M.A.T. Nguyen, and A. von Haeseler (2013) Ultra-Fast Approximation for Phylogenetic Bootstrap. Mol. Biol. Evol., 30, 1188-1195. (free reprint, DOI: 10.1093/molbev/mst024, PMID: 23418397, software)
  • Y.K. Novozhilov, M.V. Okun, D.A. Erastova, N. Shchepin, I.V. Zemlyanskaya, E. Garcia-Carvajal and M. Schnittler (2013) Description, culture and phylogenetic position of a new xerotolerant species of Physarum. Mycologia, 105, 1535-1546. (DOI: 10.3852/12-284, PMID: 23921236)
  • Y.K. Novozhilov, M. Schnittler, D.A. Erastova, M.V. Okun, N. Shchepin, and E. Heinrich (2013) Diversity of nivicolous myxomycetes of the Teberda State Biosphere Reserve (Northwestern Caucasus, Russia). Fungal Divers., 59, 109-130. (DOI: 10.1007/s13225-012-0199-0)
  • N. Popitsch and A. von Haeseler (2013) NGC: Lossless and Lossy Compression of Aligned High-throughput Sequencing Data. Nucleic Acids Res., 41, e27. (free reprint, DOI: 10.1093/nar/gks939, PMID: 23066097, software)
  • E. Porpaczy, S. Tauber, M. Bilban, G. Kostner, M. Gruber, S. Eder, D. Heintel, T. Le, K. Fleiss, C. Skrabs, M. Shehata, U. Jäger, and K. Vanura (2013) Lipoprotein lipase in chronic lymphocytic leukaemia - Strong biomarker with lack of functional significance. Leuk. Res., 37, 631-636. (DOI: 10.1016/j.leukres.2013.02.008, PMID: 23478142)
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  • F.J. Sedlazecke, P. Reschenedere, and A. von Haeseler (2013) NextGenMap: Fast and accurate read mapping in highly polymorphic genomes. Bioinformatics, 29, 2790-2791. (DOI: 10.1093/bioinformatics/btt468, PMID: 23975764, software)
    e contributed equally
  • F.J. Sedlazeck, P. Talloji, A. von Haeseler, and A. Bachmair (2013) Benefit-of-doubt (BOD) scoring: a sequencing-based method for SNP candidate assessment from high to medium read number data sets. Genomics, 101, 204-209. (DOI: 10.1016/j.ygeno.2012.12.001, PMID: 23246509)
  • S. Tauber and A. von Haeseler (2013) Exploring the sampling universe of RNA-seq. Stat. Appl. Genet. Mol. Biol. (SAGMB), 12, 175-188. (DOI: 10.1515/sagmb-2012-0049, PMID: 23629158)


  • C. Dessimoz, T. Gabaldon, D.S. Roos, E. Sonnhammer, J. Herrero, and the Quest for Orthologs Consortium* (2012) Toward Community Standards in the Quest for Orthologs. Bioinformatics, 29, 900-904. (DOI: 10.1093/bioinformatics/bts050, PMID: 22332236)
    * Members of the Quest for Orthologs Consortium: A. Altenhoff, R. Apweiler, J. Blake, B. Boeckmann, A. Bridge, E. Bruford, M. Cherry, M. Conte, D. Durand, R. Datta, J.-B. Domelevo Entfellner, I. Ebersberger, M. Galperin, J. Joseph, T. Koestler, E. Kriventseva, O. Lecompte, J. Leunissen, S. Lewis, B. Linard, M.S. Livstone, H.-C. Lu, M. Martin, R. Mazumder, V. Miele, M. Muffato, G. Perriere, M. Punta, M. Rouard, T. Schmitt, F. Schreiber, A. Silva, K. Sjolander, N. Skunca, E. Stanley, R. Szklarczyk, P. Thomas, I. Uchiyama, M. Van Bel, K. Vandepoele, A.J. Vilella, A. Yates, and E. Zdobnov.
  • D.D. Duc, H.Q. Dinh, T.H. Dang, K. Laukens and X.H. Hoang (2012) AcoSeeD: An Ant Colony Optimization for Finding Optimal Spaced Seeds in Biological Sequence Search. LNCS, 7461 (Proceedings of the 8th Intl. Conf. on Swarm Intelligence, ANTS 2012), 204-211. (DOI: 10.1007/978-3-642-32650-9_19)
  • H.Q. Dinh, M. Dubine, F.J. Sedlazecke, N. Lettner, O. Mittelsten Scheid, and A. von Haeseler (2012) Advanced Methylome Analysis after Bisulfite Deep Sequencing: an Example in Arabidopsis. PLoS ONE, 7, e41528. (DOI: 10.1371/journal.pone.0041528, PMID: 22911809, PMCID: PMC3401099)
    e contributed equally
  • I. Ebersberger, R. de Matos Simoes, A. Kupczok, M. Gube, E. Kothe, K. Voigt, and A. von Haeseler (2012) A Consistent Backbone for the Fungi. Mol. Biol. Evol., 29, 1319-1334. (DOI: 10.1093/molbev/msr285, PMID: 22114356)
  • M. Fischer (2012) Non-hereditary maximum parsimony trees. J. Math. Biol., 65, 293-308. (DOI: 10.1007/s00285-011-0458-9, PMID: 21842167)
  • M. Fischer, S. Klaere, M.A.T. Nguyen and A. von Haeseler (2012) On the group theoretical background of assigning stepwise mutations onto phylogenies. Algoritms Mol. Biol., 7, 36. (DOI: 10.1186/1748-7188-7-36, PMID: 23241267)
  • A. von Haeseler (2012) Do we still need supertrees? BMC Biol., 10, 13. (DOI: 10.1186/1741-7007-10-13, PMID: 22369571)
  • M. Kalyna, C.G. Simpson, N.H. Syed, D. Lewandowska, Y. Marquez, B. Kusenda, J. Marshall, J. Fuller, L. Cardle, J. McNicol, H.Q. Dinh, A. Barta, and J.W.S. Brown (2012) Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res., 40, 2454-2469. (DOI: 10.1093/nar/gkr932, PMID: 22127866)
  • T. Köstler, A. von Haeseler, and I. Ebersberger (2012) REvolver: Modeling sequence evolution under domain constraints. Mol. Biol. Evol., 29, 2133-2145. (DOI: 10.1093/molbev/mss078, PMID: 2383532)
  • T. Laubach, A. von Haeseler, and M.J. Lercher (2012) TreeSnatcher plus: capturing phylogenetic trees from images. BMC Bioinform., 13, 110. (DOI: 10.1186/1471-2105-13-110, PMID: 22624611)
  • J. Loidl, A. Lukaszewicz, R. Howard-Till, and T. Koestler (2012) The Tetrahymena meiotic chromosome bouquet is organized by centromeres and promotes interhomolog recombination. J. Cell Sci., 125, 5873-5880. (DOI: 10.1242/jcs.112664, PMID: 22976299)
  • M.A.T. Nguyen, T. Gesell, and A. von Haeseler (2012) ImOSM: Intermittent Evolution and Robustness of Phylogenetic Methods. Mol. Biol. Evol., 29, 663-673. (free reprint, DOI: 10.1093/molbev/msr220, PMID: 21940641)
  • H. Niederleithner, M. Heinz, S. Tauber, M. Bilban, H. Pehamberger, S. Sonderegger, M. Knoefler, A. Bracher, W. Berger, R. Loewe, and P. Petzelbauer (2012) Wnt1 Is Anti-Lymphangiogenic in a Melanoma Mouse Model. J. Invest. Dermatol., 132, 2235-2244. (DOI: 10.1038/jid.2012.138, PMID: 22572818)
  • S. Reitter-Pfoertner, A. von Haeseler B. Horvath, R. Sunder-Plassmann, V. Tiedje, I. Pabinger, and C. Mannhalter (2012) Identification of an ancient haemophilia A splice site mutation. Thromb. Res., 130, 445-450. (DOI: 10.1016/j.thromres.2012.02.008, PMID: 22401796)
  • P. Rescheneder, A. von Haeseler, and F.J. Sedlazeck (2012) MASon: Million Alignments In Seconds - A Platform Independent Pairwise Sequence Alignment Library for Next Generation Sequencing Data. Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2012), 195-201, SciTePress, Setubal, Portugal. (DOI: 10.5220/0003775701950201)
  • B.M. von Reumont, R.A. Jenner, M.A. Wills, E. DellAmpio, G. Pass, I. Ebersberger, B. Meyer, S. Koenemann, T.M. Iliffe, A. Stamatakis, O. Niehuis, K. Meusemann and B. Misof (2012) Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda. Mol. Biol. Evol., 29, 1031-1045. (free reprint, DOI: 10.1093/molbev/msr270, PMID: 22049065)
  • K.D. Scharf, T. Berberich, I. Ebersberger, and L. Nover (2012) The plant heat stress transcription factor (Hsf) family: structure, function and evolution. Biochim. Biophys. Acta-Gene Regul. Mech., 1819, 104-119. (DOI: 10.1016/j.bbagrm.2011.10.002, PMID: 22033015)
  • A. Swoboda, O. Schanab, S. Tauber, M. Bilban, W. Berger, P. Petzelbauer, M. Mikula (2012) MET expression in melanoma correlates with a lymphangiogenic phenotype. Hum. Mol. Genet., 21, 3387-2296. (DOI: 10.1093/hmg/dds171, PMID: 22570180)
  • T. Tschager and H.A. Schmidt (2012) DAGwoman: enabling DAGman-like workflows on non-Condor platforms. Proceedings of the 1st ACM SIGMOD Workshop on Scalable Workflow Execution Engines and Technologies (SWEET 2012), article 3. (DOI: 10.1145/2443416.2443419, early preprint at workshop page, software)
  • C. Veselye, S. Taubere, F.J. Sedlazeck, A. von Haeseler, and M.F. Jantsch (2012) Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs. Genome Res., 22, 1468-1476. (DOI: 10.1101/gr.133025.111, PMID: 22310477)
    e contributed equally
  • J.O. Yanez-Cuna, H.Q. Dinh, E.Z. Kvon, D. Shlyueva, and A. Stark (2012) Uncovering cis-regulatory sequence requirements for context specific transcription factor binding. Genome Res., 22, 2018-2030. (DOI: 10.1101/gr.132811.111, PMID: 22534400)



  • T. Baubec, H.Q. Dinh, A. Pecinka, B. Rakic, W. Rozhon, B. Wohlrab, A. von Haeseler and O. Mittelsten Scheid (2010) Cooperation of Multiple Chromatin Modifications Can Generate Unanticipated Stability of Epigenetic States in Arabidopsis. Plant Cell, 22, 34-47. (DOI: 10.1105/tpc.109.072819, PMID: 20097869)
  • H.Q. Dinh, B.Q. Minh, H.X. Huan and A. von Haeseler (2010) ACOPHY: A simple and general ant colony optimization approach for phylogenetic tree reconstruction. LNCS, 6234 (Proceedings of the 7th Intl. Conf. on Swarm Intelligence, ANTS 2010), 360-367. (DOI: 10.1007/978-3-642-15461-4_32)
  • K.A. Gurley, S.A. Elliot, O. Simakov, H.A. Schmidt, T.W. Holstein and A. Sánchez Alvarado (2010) Expression of secreted Wnt pathway components reveals unexpected complexity of the planarian amputation response. Dev. Biol., 347, 24-39. (DOI: 10.1016/j.ydbio.2010.08.007, PMID: 20707997)
  • J. Hofmann, K. Frenzel, B.Q. Minh, A. von Haeseler, A. Edelmann, R.S. Ross, D.H. Krueger, H. Meisel (2010) Quantitative detection and typing of Hepatitis D virus in human serum by real-time PCR and melting curve analysis. Diagn. Microbiol. Infect. Dis., 67, 172-179. (DOI: 10.1016/j.diagmicrobio.2010.02.003, PMID: 20466196)
  • T. Köstler, A. von Haeseler, and I. Ebersberger (2010) FACT: Functional annotation transfer between proteins with similar feature architecture. BMC Bioinform., 11, 417. (DOI: 10.1186/1471-2105-11-417, PMID: 20696036)
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  • C. Lorenz, T. Gesell, B. Zimmermann, U. Schoeberl, I. Bilusic, L. Rajkowitsch, C. Waldsich, A. von Haeseler and R. Schroeder (2010) Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res., 38, 3794-3808. (DOI: 10.1093/nar/gkq032, PMID: 20348540)
  • K. Meusemann, B.M. von Reumont, S. Simon, F. Roeding, S. Strauss, P. Kück, I. Ebersberger, M. Walzl, G. Pass, S. Breuers, V. Achter, A. von Haeseler, T. Burmester, H. Hadrys, W.W. Wägele and B. Misof (2010) A phylogenomic approach to resolve the arthropod tree of life. Mol. Biol. Evol., 27, 2451-2464. (DOI: 10.1093/molbev/msq130, PMID: 20534705)
  • B.Q. Minh, S. Klaere, and A. von Haeseler (2010) SDA*: A Simple and Unifying Solution to Recent Bioinformatic Chaallenges for Conservation Genetics. Proceedings of the 2nd International Conference on Knowledge and Systems Engeneering - KSE-2010 (Hanoi, Vietnam), 33-37, IEEE Computer Society, Los Alamitos, CA, USA. (DOI: 10.1109/KSE.2010.24, ISBN: 978-0-7695-4213-3)
  • A. Pecinka, H.Q. Dinh, T. Baubec, M. Rosa, N. Lettner, and O. Mittelsten Scheid (2010) Epigenetic regulation of repetitive elements is attenuated by prolonged heat stress in Arabidopsis. Plant Cell, 22, 3118-3129. (DOI: 10.1105/tpc.110.078493, PMID: 20876829)
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    e contributed equally


  • F. Catalanotti, G. Reyes, V. Jesenberger, G. Galabova-Kovacs, R. de Matos Simoes, O. Carugo, M. Baccarini (2009) A Mek1-Mek2 heterodimer determines the strength and duration of the Erk signal. Nat. Struct. Mol. Biol., 16, 294-303. (DOI: 10.1038/nsmb.1564, PMID: 19219045)
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  • R. Hanada, A. Leibbrandt, T. Hanada, S. Kitaoka, T. Furuyashiki, H. Fujihara, J. Trichereau, M. Paolino, F. Qadri, R. Plehm, S. Klaere, V. Komnenovic, H. Mimata, H. Yoshimatsu, N. Takahashi, A. von Haeseler, M. Bader, S. Sebnem Kilic, Y. Ueta, C. Pifl, S. Narumiya and J.M. Penninger (2009) Central control of fever and female body temperature by RANKL/RANK. Nature, 462, 505-509. (DOI: 10.1038/nature08596, PMID: 19940926)
  • U. Krausse, B.Q. Minhe, A. Losi, W. Gaertner, T. Eggert, A. von Haeselerc, and K.E. Jaeger (2009) Distribution and phylogeny of light-oxygen-voltage-blue-light-signaling proteins in the three kingdoms of life. J. Bacteriol., 191, 7234-7242. (DOI: 10.1128/JB.00923-09, PMID: 19783626)
    e contributed equally, c corresponding author
  • A. Kupczok and A. von Haeseler (2009) Comment on: A congruency index for testing topological similarity between trees. Bioinformatics, 25, 147-149. (DOI: 10.1093/bioinformatics/btn539, PMID: 18922807)
  • M. Knapp, N. Rohland, J. Weinstock, G. Baryshnikov, A. Sher, D. Nagel, G. Rabeder, R. Pinhasi, H.A. Schmidt, and M. Hofreiter (2009) First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns. Mol. Ecol., 18, 1225-1238. (DOI: 10.1111/j.1365-294X.2009.04088.x, PMID: 19226321)
  • T. Lengfeld, H. Watanabe, O. Simakov, D. Lindgens, L. Gee, L. Law, H.A. Schmidt, S. Ozbek, H. Bode, and T.W. Holstein (2009) Multiple Wnts are involved in Hydra organizer formation and regeneration. Dev. Biol., 330, 186-199. (DOI: 10.1016/j.ydbio.2009.02.004, PMID: 19217898)
  • B.Q. Minh, S. Klaere, and A. von Haeseler (2009) Taxon Selection under Split Diversity. Syst. Biol., 57, 586-594. (DOI: 10.1093/sysbio/syp058)
  • B.Q. Minh, F. Pardi, S. Klaere, and A. von Haeseler (2009) Budgeted Phylogenetic Diversity on Circular Split Systems. IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 22-29. (DOI: 10.1109/TCBB.2008.54, PMID: 19179696)
  • O. Mirus, T. Bionda, A. von Haeseler, and E. Schleiff (2009) Evolutionarily evolved discriminators in the TPR domain of the Toc64 family involved in protein translocation at the outer membrane of chloroplasts and mitochondria. J. Mol. Mod., 15, 971-982. (DOI: 10.1007/s00894-008-0449-y, PMID: 19198901)
  • O. Miruse, S. Strausse, K. Nicolaisen, A. von Haeseler, E. Schleiff (2009) TonB-dependent transporters and their occurrence in cyanobacteria. BMC Biol., 7, 68. (DOI: 10.1186/1741-7007-7-68, PMID: 19821963)
    e contributed equally
  • H.A. Schmidt (2009) Testing Tree Topologies. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 381-404, Cambridge University Press, Cambridge. (DOI: 10.1017/CBO9780511819049.014, ISBN: paperback: 9780521730716, hardcover: 9780521877107, book webpage)
  • H.A. Schmidt and A. von Haeseler (2009) Phylogenetic Inference Using Maximum Likelihood Methods. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 181-209, Cambridge University Press, Cambridge. (DOI: 10.1017/CBO9780511819049.008, ISBN: paperback: 9780521730716, hardcover: 9780521877107, book webpage)
  • S. Simon, S. Strauss, A. von Haeseler, and H. Hadrys (2009) A phylogenomic approach to resolve the basal pterygote divergence. Mol. Biol. Evol., 26, 2719-2730. (DOI: 10.1093/molbev/msp191, PMID: 19713325)
  • K. Strimmer and A. von Haeseler (2009) Nucleotide Substitition Models. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 111-141, Cambridge University Press, Cambridge. (ISBN: paperback: 9780521730716, hardcover: 9780521877107, book webpage)
  • M. Tillich, L.S. Vinh, K. Schulerowitz, A. von Haeseler, U.G. Maier and C. Schmitz-Linneweber (2009) Loss of MatK RNA Editing in Seed Plant Chloroplasts. BMC Evol. Biol., 9, 201. (DOI: 10.1186/1471-2148-9-201) PMID: 19678945)
  • C. Weber, A. Pickl-Herk, S. Strauss, O. Carugo and D. Blaas (2009) Predictive bioinformatic identification of minor receptor group human rhinoviruses. FEBS Lett., 583, 2547-2551. (DOI: 10.1016/j.febslet.2009.07.015, PMID: 19615999)
  • A. Witek, H. Herlyn, I. Ebersberger, D.B.M. Welch and T. Hankeln (2009) Support for the Monophyletic Origin of Gnathifera from Phylogenomics. Mol. Phylogenet. Evol., 53, 1037-1041. (DOI: 10.1016/j.ympev.2009.07.031, PMID: 19654049)


  • I. Barinaga-Rementeria Ramirez, C.L. de Graffenried, I. Ebersberger, J. Yelinek, C.Y. He, A. Price, and G. Warren (2008) TbG63, a golgin involved in Golgi architecture in Trypanosoma brucei. J. Cell Sci., 121, 1538-1546. (DOI: 10.1242/jcs.014324, PMID: 18411253)
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  • M. Dehmer, F. Emmert-Streib, and T. Gesell (2008) A comparative analysis of multidimensional features of objects resembling sets of graphs. Appl. Math. Comput., 196, 221-235. (DOI: 10.1016/j.amc.2007.05.058)
  • G.B. Ewing, I. Ebersberger, H.A. Schmidt, and A. von Haeseler (2008) Rooted Triple Consensus and Anomalous Gene Trees. BMC Evol. Biol., 8, 118. (DOI: 10.1186/1471-2148-8-118, PMID: 18439266)
  • T. Gesell and S. Washietl (2008) Dinucleotide Controlled Null Models for Comparative RNA Gene Prediction. BMC Bioinform., 9, 248. (DOI: 10.1186/1471-2105-9-248, PMID: 18505553)
  • S. Klaere, T. Gesell, and A. von Haeseler (2008) The impact of single substitutions on multiple sequence alignments. Phil. Trans. R. Soc. Lond. B, 363, 4041-4047. (DOI: 10.1098/rstb.2008.0140, PMID: 18852110)
  • A. Kupczok, A. von Haeseler, and S. Klaere (2008) An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. J. Comput. Biol., 15, 577-591. (DOI: 10.1089/cmb.2008.0068, PMID: 18631022)
  • G. Magiorkinis, D. Paraskevis, H.A. Schmidt, and A. Hatzakis (2008) The phylogenetic information profile of HIV-1 and the degradation effect of recombination. Infect. Genet. Evol., 8, 139-145. (DOI: 10.1016/j.meegid.2007.11.002, PMID: 18093883)
  • D. Mainz, I. Paulsen, I. Mainz, K. Weller, J. Kohl, and A. von Haeseler (2008) Knowledge Acquisition Focused Cooperative Development of Bio-Ontologies - A Case Study with BIO2Me. In M. Elloumi, J. Küng, M. Linial, R.F. Murphy, K. Schneider, T. Cristian (eds.) Bioinformatics Research and Development., 258-272, Springer, Berlin. (ISBN 978-3-540-70598-7)
  • I. Mainz, K. Weller, I. Paulsen, D. Mainz, J. Kohl, and A. von Haeseler (2008) Ontoverse: Collaborative Ontology Engineering for the Life Sciences. Inform. Wiss. Praxis, 2, 91-99. (online access)
  • A. Rohrbeck, J. Neukirchen, M. Rosskopf, G.G. Pardillos, H. Geddert, A. Schwalen, H.E. Gabbert, A. von Haeseler, G. Pitschke, M. Schott, R. Kronenwett, R. Haas, Rainer U.-P. Rohr (2008) Gene expression profiling for molecular discrimination and characterization of laser captured primary lung cancers. J. Translat. Med., 6, 69. (DOI: 10.1186/1479-5876-6-69)
  • H. Schabauer, J. Zottl, A. von Haeseler, W.N. Gansterer, and H.A. Schmidt (2008) Phylogenetic Quality Assessment for Campus Grids. In J. Küng, K. Schneider, R. Wagner (eds.) BIRD'08 -- 2nd International Conference on Bioinformatics and Development (Articles on Poster Presentations)., Schriftenreihe Informatik, 109-114, Trauner Verlag, Linz. (ISBN 978-3-85499-422-0)
  • J. Shi, J. Franklin, J. Yelinek, I. Ebersberger, G. Warren, and C.Y. He (2008) Centrin4 coordinates cell and nuclear division in Trypanosoma brucei. J. Cell Sci., 121, 3062-3070. (DOI: 10.1242/jcs.030643, PMID: 18768932)
  • L.S. Vinh and A. von Haeseler (2008) Bookreview on "Computational Molecular Evolution by Ziheng Yang, 2006, Oxford University Press, Oxford". Syst. Biol., 56, 1024-1026. (DOI: 10.1080/10635150701752532, PMID: 18066933)


  • R. Bredemeier, T. Schlegel, F. Ertel, A. Vojita, L. Borissenko, M.T. Bohnsack, M. Groll, A. von Haeseler, and E. Schleiff (2007) Functional and phylogenetic properties of the pore forming β-barrel transporter of the Omp85 family. J. Biol. Chem., 282, 1882-1890. (DOI: 10.1074/jbc.M609598200, PMID: 17088246)
  • M. Dehmer and F. Emmert-Streib (2007) Comparing large graphs efficiently by margins of feature vectors. Appl. Math. Comput., 188, 1699-1710. (DOI: 10.1016/j.amc.2006.11.185)
  • M. Dehmer and F. Emmert-Streib (2007) Structural similarity of directed universal hierarchical graphs: A low computational complexity approach. Appl. Math. Comput., 194, 7-20. (DOI: 10.1016/j.amc.2007.04.006)
  • E. Diaz-Blanco, I. Bruns, F. Neumann, J.C. Fischer, T. Graef, M. Rosskopf, B. Brors, S. Pechtel, S. Bork, A. Koch, A. Baer, U.-P. Rohr, G. Kobbe, A. von Haeseler, N. Gattermann, and R. Kronenwett (2007) Molecular signature of CD34+ hematopoietic stem and progenitor cells of patients with CML in chronic phase. Leukemia, 21, 494-504. (DOI: 10.1038/sj.leu.2404549, PMID: 17252012)
  • I. Ebersberger, P. Galgoczy, S. Taudien, S. Taenzer, M. Platzer, and A. von Haeseler (2007) Mapping human genetic ancestry. Mol. Biol. Evol., 24, 2266-2276. (DOI: 10.1093/molbev/msm156, PMID: 17660505)
  • I. Ebersberger, A. von Haeseler, and H.A. Schmidt (2007) Phylogeny Reconstruction. In T. Lengauer (ed.) Bioinformatics: From Genomes to Therapies 83-128, Wiley-VCH, Weinheim. (DOI: 10.1002/9783527619368.ch4, ISBN 978-3-527-31278-8)
  • M.R. Eckert, T. Gesell, M. Grabner, A. Gruber, K. Gonzales, I.L. Hofacker, A. von Haeseler, and E. Charpentier (2007) A bioinformatic screen reveals novel small noncoding RNAs in Streptococcus pyogenes FEBS J., 274, 189. (DOI: 10.1111/j.0014-2956.2007.05861.x)
  • F. Emmert-Streib and M. Dehmer (2007) Information theoretic measures of UHG graphs with low computational complexity. Appl. Math. Comput., 190, 1783-1794. (DOI: 10.1016/j.amc.2007.02.095)
  • W. Glaser, T. Schwarzmüller, K. Kuchler, and M. Grabner (2007) Automated generation of PCR primers for a genomewide knock-out in Candida glabrata FEBS J., 274, 246. (DOI: 10.1111/j.0014-2956.2007.05861_5.x)
  • T. Laubach and A. von Haeseler (2007) TreeSnatcher: Coding trees from images. Bioinformatics, 23, 3384-3385. (DOI: 10.1093/bioinformatics/btm438, PMID: 17893085)
  • S. Linz, A. Radtke, A. von Haeseler (2007) A maximum likelihood framework to measure horizontal gene transfer. Mol. Biol. Evol., 24, 1312-1319. (DOI: 10.1093/molbev/msm052, PMID: 17374878)
  • W. Löffelhardt, A. von Haeseler, E. Schleiff (2007) The β-barrel shaped polypeptide transporter, an old concept for precursor protein transfer across membranes. Symbiosis, 44, 33-42.
  • S. Piskacek, M. Gregor, M. Nemethova, M. Grabner, P. Kovarik and M. Piskacek (2007) Nine-amino-acid transactivation domain: Establishment and prediction utilities. Genomics, 89, 756-768. (DOI: 10.1016/j.ygeno.2007.02.003, PMID: 17467953)
  • J.A. Pospisilik, C. Knauf, N. Joza, P. Benit, M. Orthofer, P.D. Cani, I. Ebersberger, T. Nakashima, R. Sarao, G. Neely, H. Esterbauer, A. Kozlov, C.R. Kahn, G. Kroemer, P. Rustin, R. Burcelin, and J.M. Penninger (2007) Targeted deletion of AIF decreases mitochondrial oxidative phosphorylation and protects from obesity and diabetes. Cell, 131, 476-491. (DOI: 10.1016/j.cell.2007.08.047, PMID: 17981116)
  • F. Roeding, S. Hagner-Holler, H. Ruhberg, I. Ebersberger, A. von Haeseler, M. Kube, R. Reinhardt, and Burmester, T. (2007) EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol. Phylogenet. Evol., 45, 942-951. (DOI: 10.1016/j.ympev.2007.09.002, PMID: 17933557)
  • U. Schauer, C. Lorenz, T. Gesell, C. Waldsich, A. von Haeseler, and R. Schroeder (2007) Characterization of high affinity Hfq binding sites FEBS J., 274, 86. (DOI: 10.1111/j.0014-2956.2007.05861_1.x)
  • T. Schlegel, O. Mirus, A. von Haeseler and E. Schleiff (2007) The tetratricopeptide repeats of receptors involved in protein translocation across membranes. Mol. Biol. Evol., 24, 2763-2774. (DOI: 10.1093/molbev/msm211, PMID: 17905998)
  • H.A. Schmidt and A. von Haeseler (2007) Maximum Likelihood Analysis using TREE-PUZZLE. (revised version) In A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, and L. Stein (eds.) Current Protocols in Bioinformatics, 17, Unit 6.6, pages 6.6.1-6.6.23, Wiley and Sons, New York. (DOI: 10.1002/0471250953.bi0606s17, PMID: 18428792, ISBN 0-471-25093-7, CP online)
  • H.A. Schmidt, A. von Haeseler, and J. Buschbom (2007) pIPHULA - Parallel Inference of Population Parameters Using a Likelihood Approach. Bioinformatics, 23, 2636-2637. (free reprint, DOI: 10.1093/bioinformatics/btm391, PMID: 17698495)


  • I. Bruns, U. Steidl, J.C. Fischer, S. Raschke, G. Kobbe, R. Fenk, M. Rosskopf, S. Pechtel, U.-P. Rohr, A. von Haeseler, P. Wernet, D. Tenen, R. Haas, and R. Kronenwett (2006) Meeting Abstract: Pegylated G-CSF Mobilizes CD34+ Cells with Different Stem and Progenitor Cell Subsets and Distinct Functional Properties in Comparison with Unconjugated G-CSF. Blood, 108, 3382. (Journal site)
  • F. Emmert-Streib and M. Dehmer (2006) Topological Mappings between Graphs, Trees and Generalized Trees. Appl. Math. Comput., 186, 1326-1333. (DOI: 10.1016/j.amc.2006.07.162)
  • F. Emmert-Streib, M. Dehmer, and C. Seidel (2006) Influence of Prior Information on the Reconstruction of the Yeast Cell Cycle from Microarray Data. Proceedings of the Workshop 'Gene Networks: Theory and Application' at the 2006 International Conference on Bioinformatics and Computational Biology (BIOCOMP'06). 477-482. (PDF)
  • F. Emmert-Streib and M. Dehmer (2006) Theoretical Bounds for the Number of inferable Edges in sparse Random Networks. Proceedings of the Workshop 'Gene Networks: Theory and Application' at the 2006 International Conference on Bioinformatics and Computational Biology (BIOCOMP'06). 477-482. (PDF)
  • T. Gesell and A. von Haeseler (2006) In silico sequence evolution with site-specific interactions along phylogenetic trees. Bioinformatics, 22, 716-722. (DOI: 10.1093/bioinformatics/bti812, PMID: 16332711)
  • C. Guder, S. Pinho, T.G. Nacak, H.A. Schmidt, B. Hobmayer, C. Niehrs, and T.W. Holstein (2006) An ancient Wnt-Dickkopf antagonism in Hydra. Development, 133, 901-911. (DOI: 10.1242/dev.02265, PMID: 16452091)
  • B. Kilian, H. Özkan, J. Kohl, A. von Haeseler, O. Deusch, A. Brandolini, C. Yucel, W. Martin, and F. Salamini (2006) Haplotype structure at seven barley genes: relevance to gene pool bottlenecks, phylogeny of ear type and site of barley domestication. Mol. Genet. Genomics, 275, 230-241. (DOI: 10.1007/s00438-006-0136-6, PMID: 16758198)
  • J. Kohl, I. Paulsen, T. Laubach, A. Radtke, and A. von Haeseler (2006) HvrBase++: A phylogenetic database for primate species. Nucleic Acids Res., 34, D700-D704. (DOI: 10.1093/nar/gkj030, PMID: 16381963)
  • J. Krause, P.H. Dear, J.L. Pollack, M. Slatkin, H. Spriggs, I. Barnes, A. Lister, I. Ebersberger, S. Pääbo, and M. Hofreiter (2006) Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature, 439, 724-727. (DOI: 10.1038/nature04432)
  • B.Q. Minh, S. Klaere, and A. von Haeseler (2006) Phylogenetic Diversity within Seconds. Syst. Biol., 55, 769-773. (DOI: 10.1080/10635150600981604)
  • B.Q. Minh, L.S. Vinh, H.A. Schmidt, and A. von Haeseler (2006) Large Maximum Likelihood Trees. Proceedings of the NIC Symposium 2006. 357-365, Forschungszentrum Jülich, Germany. (free reprint, ISBN 3-00-017351-X)
  • I. Paulsen and A. von Haeseler (2006) INVHOGEN: A database of homologous invertebrate genes. Nucleic Acids Res., 34, D349-D353. (DOI: 10.1093/nar/gkj100, PMID: 16381884)
  • E. Petzold, D. Merkle, M. Middendorf, A. von Haeseler, and H.A. Schmidt (2006) Phylogenetic Parameter Estimation on COWs. In A.Y. Zomaya (ed.) Parallel Computing for Bioinformatics and Computational Biology 347-368, Wiley and Sons, New York. (DOI: 10.1002/0471756504.ch15, ISBN 0-471-71848-3)
  • S. Taudien, I. Ebersberger, Gernot Glöckner, and Mattias Platzer (2006) Should the draft chimpanzee sequence be finished? Trends Genet., 22, 122-125. (DOI: 10.1016/j.tig.2005.12.007, PMID: 16406850)


  • J. Buschbom and A. von Haeseler (2005) Introduction to applications of the likelihood function in molecular evolution. In R. Nielsen (ed.) Statistical Methods in Molecular Evolution 25-44, Springer, New York. (ISBN: 0-387-22333-9)
  • I. Ebersberger, J. Knobloch, and W. Kunz (2005) Cracks in the shell: zooming in on eggshell formation in the human parasite Schistosoma mansoni. Dev. Genes Evol., 215, 261-267. (DOI: 10.1007/s00427-005-0467-z, PMID: 15747129)
  • I. Ebersberger and M. Meyer (2005) A genomic region evolving toward different GC contents in humans and chimpanzees indicates a recent and regionally limited shift in the mutation pattern. Mol. Biol. Evol., 22, 1240-1245. (DOI: 10.1093/molbev/msi109, PMID: 15703238)
  • R. Fleißner, D. Metzler, and A. von Haeseler (2005) Simultaneous statistical multiple alignment and phylogeny reconstruction. Syst. Biol., 54, 548-561. (DOI: 10.1080/10635150590950371, PMID: 16085574)
  • P. Khaitovich, S. Pääbo, and G. Weiss (2005) Toward a Neutral Evolutionary Model of Gene Expression. Genetics, 170, 929-939. (DOI: 10.1534/genetics.104.037135, PMID: 15834146)
  • J. Kohl and A. von Haeseler (2005) Bookreview on "Perl Programming for Biologists by D.C. Jamison. Wiley-Liss, Chichester, 2003". Biometrics, 61, 316. (DOI: 10.1111/j.0006-341X.2005.20050217-2_6.x)
  • A. Kusserow, K. Pang, C. Sturm, M. Hrouda, J. Lentfer, H.A. Schmidt, U. Technau, A. von Haeseler, B. Hobmayer, M.Q. Martindale, and T.W. Holstein (2005) Unexpected complexity of Wnt gene family in a sea anemone. Nature, 433, 156-160. (DOI: 10.1038/nature03158, PMID: 15650739) , press releases by FZ Jülich (follow-ups: Bionity, Google search), Heidelberg University
  • D. Metzler, R. Fleißner, A. Wakolbinger, and A. von Haeseler (2005) Stochastic insertion-deletion processes and statistical sequence alignment. In A. Greven and D. Deuschel (eds.) Interacting Stochastic Systems, 247-267, Springer, Heidelberg/Berlin. (ISBN: 3-540-23033-5)
  • B.Q. Minh, L.S. Vinh, A. von Haeseler, and H.A. Schmidt (2005) pIQPNNI -- Parallel Reconstruction of Large Maximum Likelihood Phylogenies. Bioinformatics, 21:3794-3796. (free reprint, DOI: 10.1093/bioinformatics/bti594, PMID: 16046495)
  • S. Moslavac, O. Mirus, R. Bredemeier, J. Soll, A. von Haeseler, and E. Schleiff (2005) Conserved pore-forming regions in polypeptide-transporting proteins. FEBS J., 272, 1367-1378. (DOI: 10.1111/j.1742-4658.2005.04569.x, PMID: 15752354)
  • H. Oota, B. Pakendorf, G. Weiss, A. von Haeseler, S. Pookajorn, W. Settheetham-Ishida, D. Tiwawech, T. Ishida, and M. Stoneking (2005) Recent Origin and Cultural Reversion of a Hunter-Gatherer Group. PLoS Biol., 3, e71. (DOI: 10.1371/journal.pbio.0030071, PMID: 15736978)
  • L.S. Vinh, H.A. Schmidt, and A. von Haeseler (2005) PhyNav: A novel approach to reconstruct large phylogenies. In C. Weihs and W. Gaul (eds.) Classification, the Ubiquitous Challenge Series Studies in Classification, Data Analysis, and Knowledge Organization, 386-393, Springer, Heidelberg/New York. (DOI: 10.1007/3-540-28084-7_44)
  • L.S. Vinh and A. von Haeseler (2005) Shortest triplet clustering: reconstructing large phylogenies using representative sets. BMC Bioinform., 6, 92. (DOI: 10.1186/1471-2105-6-92, PMID: 15819989)


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