in press

  • 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 (in press) Molecular Profiling of Thymoma and Thymic Carcinoma: Genetic Differences and Potential Novel Therapeutic Targets. Pathol. Oncol. Res., in press. (DOI: 10.1007/s12253-016-0144-8, PMID: 27844328)
  • E. Klopf, H.A. Schmidt, S. Clauder-Münster, L.M. Steinmetz, and C. Schüller (in press) INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. Nucleic Acids Res., 45, in press. (DOI: 10.1093/nar/gkw1292, PMID: 28025392)
  • C. Prakash and A. von Haeseler (in press) 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, in press. (DOI: 10.1089/cmb.2016.0096, PMID: 27661099)


  • 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)


  • 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. 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, 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)
  • O. Chernomor, B.Q. Minh, F. Forest, S. Klaere, T. Ingram, M. Henzinger, and A. von Haeseler (2015) Split Diversity in Constrained Conservation Prioritization using Integer Linear Programming. Methods Ecol. Evol., 6, 83-91. (DOI: 10.1111/2041-210X.12299)
  • O. Chernomor, B.Q. Minh, and A. von Haeseler (2015) Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference. J. Comput. Biol., 22, 1129-1142. (DOI: 10.1089/cmb.2015.0146, PMID: 26448206)
  • D. Drecktrah, M. Lybecker, N. Popitsch, P. Rescheneder, L.S. Hall, and D.S. Samuels (2015) The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation. PLoS Pathog., 11, e1005160. (DOI: 10.1371/journal.ppat.1005160, PMID: 26371761)
  • C. Fieber, N. Gratz, T. Koestler, X.-D. Li, V. Castiglia, M. Janos, M. Aberle, M. Sauert, M. Wegner, L. Alexopoulou, C.J. Kirschning, Z.J. Chen, A. von Haeseler, and P. Kovarik (2015) Innate immune response to Streptococcus pyogenes depends on the combined activation of TLR13 and TLR2. PLoS ONE, 10, e0119727. (DOI: 10.1371/journal.pone.0119727, PMID: 25756897)
  • T. Flouri, F. Izquierdo-Carrasco, D. Darriba, A.J. Aberer, L.-T. Nguyen, B.Q. Minh, A. von Haeseler, and A. Stamatakis (2015) The phylogenetic Likelihood Library. Syst. Biol., 64, 356-362. (DOI: 10.1093/sysbio/syu084, PMID: 25358969, software)
  • M. Gallach (2015) 1.688 g/cm3 satellite-related repeats: a missing link to dosage compensation and speciation. Mol. Ecol., 24, 4340-4347. (DOI: 10.1111/mec.13335, PMID: 26224418)
  • M. Günther, C. Grumaz, S. Lorenz, P. Stevens, E. Lindemann, T. Hirth, K. Sohn, S. Zibek, and S. Rupp (2015) The transcriptomic profile of Pseudozyma aphidis during production of mannosylerythritol lipids. Appl. Microbiol. Biotechnol., 99, 1375-1388. (DOI: 10.1007/s00253-014-6359-2, PMID: 25586580)
  • D.T. Hai, N.D. Thanh, P.T.M. Trang, L.S. Quang, P.T.T. Hang, D.C. Cuong, H.K. Phuc, N.H. Duc, D.D. Dong, B.Q. Minh, P.B. Son, and L.S. Vinh (2015) Whole genome analysis of a Vietnamese trio. J. Biosci., 40, 113-124. (DOI: 10.1007/s12038-015-9501-0, PMID: 25740146)
  • 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)
  • H.A. Schmidt (2015) Round and Roundabout (Rundumadum). In RSCDS Book 49: 12 Scottish Country Dances, page 16, Royal Scottish Country Dance Society, Edinburgh. (ISBN 978-0-902997-30-1)
  • M. Smolka, P. Rescheneder, M. Schatz, A. von Haeseler, and F.J. Sedlazeck (2015) Teaser: Individualized benchmarking and optimization of read mapping results for NGS data. Genome Biol., 16, 235. (DOI: 10.1186/s13059-015-0803-1, PMID: 26494581, PMCID: PMC4618857, Teaser webpage)
  • 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)


  • R.G. Bayer, T. Köstler, A. Jain, S. Stael, I. Ebersberger, and M. Teige (2014) Higher plant proteins of cyanobacterial origin - are they or are they not preferentially targeted to chloroplasts? Mol. Plant, 7, 1797-1800. (DOI: 10.1093/mp/ssu095, PMID: 25178282, PMCID: PMC4261837)
  • I. Bilusic, N. Popitsch, P. Rescheneder, R. Schroeder, and M. Lybecker (2014) Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation. RNA Biol., 11, 641-654. (DOI: 10.4161/rna.29299, PMID: 24922322)
  • A.D. Chipman, D.E.K. Ferrier, C. Brena, J. Qu, D.S.T. Hughes, R. Schröder, M. Torres-Oliva, N. Znassi, H. Jiang, F.C. Almeida, C.R. Alonso, Z. Apostolou, P. Aqrawi, W. Arthur, J.C.J. Barna, K.P. Blankenburg, D. Brites, S. Capella-Gutierrez, M. Coyle, P.K. Dearden, L. Du Pasquier, E.J. Duncan, D. Ebert, C. Eibner, G. Erikson, P.D. Evans, C.G. Extavour, L. Francisco, T. Gabaldon, W.J. Gillis, E.A. Goodwin-Horn, J.E. Green, S. Griffiths-Jones, C.J.P. Grimmelikhuijzen, S. Gubbala, R. Guido, Y. Han, F. Hauser, P. Havlak, L. Hayden, S. Helbing, M. Holder, J.H.L. Hui, J.P. Hunn, V.S. Hunnekuhl, L. Jackson, M. Javaid, S.N. Jhangiani, F.M. Jiggins, T.E. Jones, T.S. Kaiser, D. Kalra, N.J. Kenny, V. Korchina, C.L. Kovar, F.B. Kraus, F. Lapraz, S.L. Lee, J. Lv, C. Mandapat, G. Manning, M. Mariotti, R. Mata, T. Mathew, T. Neumann, I. Newsham, D.N. Ngo, M. Ninova, G. Okwuonu, F. Ongeri, W.J. Palmer, S. Patil, P. Patraquim, C. Pham, L.-L. Pu, N.H. Putman, C. Rabouille, O. Mendivil Ramos, A.C. Rhodes, H.E. Robertson, H.M. Robertson, M. Ronshaugen, J. Rozas, N. Saada, A. Sanchez-Gracia, S.E. Scherer, A.M. Schurko, K.W. Siggens, D. Simmons, A. Stief, E. Stolle, M.J. Telford, K. Tessmar-Raible, R. Thornton, M. van der Zee, A. von Haeseler, J.M. Williams, J.H. Willis, Y. Wu, X. Zou, D. Lawson, D.M. Muzny, K.C. Worley, R.A. Gibbs, M. Akam, and S. Richards (2014) The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima. PLoS Biol., 12, e1002005. (DOI: 10.1371/journal.pbio.1002005, PMID: 25423365, PMCID: PMC4244043)
  • E. Dell'Ampioe, K. Meusemanne, N.U. Szucsiche, R.S. Peterse, B. Meyer, J. Borner, M. Petersen, A.J. Aberer, A. Stamatakis, M.G. Walzl, B.Q. Minh, A. von Haeseler, I. Ebersberger, G. Pass, and B. Misof (2014) Decisive Datasets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects. Mol. Biol. Evol., 31, 239-249. (DOI: 10.1093/molbev/mst196, PMID: 24140757)
    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)
  • S. Iantorno, K. Gori, N. Goldman, M. Gil, and C. Dessimoz (2014) Who Watches the Watchmen? An Appraisal of Benchmarks for Multiple Sequence Alignment. Methods Mol. Biol., 1079, 59-73. (DOI: 10.1007/978-1-62703-646-7_4, PMID: 24170395)
  • 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)
  • Y.K. Novozhilov, D.W. Mitchell, M.V. Okun, and O.N. Shchepin (2014) New species of Diderma from Vietnam. Mycosphere, 5, 554-564. (DOI: 10.5943/mycosphere/5/4/8, abstract, PDF)
  • 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)
  • N. Popitsch (2014) CODOC: Efficient Access, Analysis and Compression of Depth of Coverage Signals. Bioinformatics, 30, 2676-2677. (free reprint, DOI: 10.1093/bioinformatics/btu362, PMID: 24872424, software)
  • 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)
  • H. Watanabe, H.A. Schmidt, A. Kuhn, S. Özbek, S. Höger, Y. Kocagöz, N. Laumann-Lipp, and T. Holstein (2014) Nodal signalling determines biradial asymmetry in Hydra. Nature, 515, 112-115. (DOI: 10.1038/nature13666, PMID: 25156256) press release Heidelberg


  • 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)
  • A. Bracher, A. Soler, S. Tauber, A.M. Fink, A. Steiner, H. Pehamberger, H. Niederleithner, P. Petzelbauer, M. Groeger, and R. Loewe (2013) Epidermal growth factor facilitates melanoma lymph node metastasis by influencing tumor lymphangiogenesis. J. Invest. Dermatol., 133, 230-238. (DOI: 10.1038/jid.2012.272, PMID: 22951723)
  • D.A. Erastova, M.V. Okun, A.M. Fiore-Donno, Y.K. Novozhilov, and M. Schnittler (2013) Phylogenetic position of the enigmatic myxomycete genus Kelleromyxa revealed by SSU rDNA sequences. Mycol. Prog., 12, 599-608. (DOI: 10.1007/s11557-013-0892-8)
  • C.A. Gebeshuber, C. Kornauth, L. Dong, R. Sierig, J. Seibler, M. Reiss, S. Tauber, M. Bilban, S. Wang, R. Kain, G.A. Bömig, M.J. Moeller, H.-J. Gröne, C. Englert, J. Martineze, and D. Kerjaschkie (2013) Focal segmental glomerulosclerosis is induced by microRNA-193a and its downregulation of WT1. Nat. Med., 19, 481-487. (DOI: 10.1038/nm.3142, PMID: 23502960)
    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)
  • S.F. Schoppmann, U. Vinatzer, N. Popitsch, G. Jomrich, B. Streubel and P. Birner (2013) Novel Clinically relevant genes in gastrointestinal stromal tumors identified by exome sequencing. Clin. Cancer Res., 19, 5329-5339. (DOI: 10.1158/1078-0432.CCR-12-3863, PMID: 23942094)
  • 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)
  • A. Kupczok, H.A. Schmidt, and A. von Haeseler (2010) Accuracy of phylogeny reconstruction methods combining overlapping gene data sets. Algorithms Mol. Biol., 5, 37. (DOI: 10.1186/1748-7188-5-37, PMID: 21134245)
  • 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)
  • S. Washietl and T. Gesell (2010) Graph Representations and Algorithms in Computational Biology of RNA Secondary Structure. In M. Dehmer (ed.) Structural Analysis of Complex Networks., 421-437, Birkhäuser, Boston, USA. (ISBN: 978-0-8176-4788-9)
  • B. Zimmermanne, T. Geselle, D. Chen, C. Lorenz and R. Schroeder (2010) Monitoring Genomic Sequences during SELEX Using High-Throughput Sequencing: Neutral SELEX. PLoS ONE, 5, e9169. (DOI: 10.1371/journal.pone.0009169, PMID: 20161784)
    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)
  • S.J.F. Cronin, N.T. Nehme, S. Limmer, S. Liegeois, J.A. Pospisilik, D. Schramek, A. Leibbrandt, R. de Matos Simoes, S. Gruber, U. Puc, I. Ebersberger, T. Zoranovic, G.G. Neely, A. von Haeseler, D. Ferrandon and J.M. Penninger (2009) A genome-wide in vivo RNAi screen on innate immunity to intestinal pathogenic infections. Science, 325, 340-343. (DOI: 10.1126/science.1173164, PMID: 19520911)
  • I. Ebersberger, S. Strauss, and A. von Haeseler (2009) HaMStR: Profile Hidden Markov Model Based Search for Orthologs in ESTs. BMC Evol. Biol., 9, 157. (DOI: 10.1186/1471-2148-9-157, PMID: 19586527)
  • 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. (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. (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)
  • I. Bruns, Ingmar and U. Steidl, Ulrich and J.C. Fischer, A. Czibere, G. Kobbe, S. Raschke, R. Singh, R. Fenk, M. Rosskopf, S. Pechtel, A. von Haeseler, P. Wernet, D. Tenen, R. Haas, and R. Kronenwett (2008) Pegylated G-CSF mobilizes CD34+ cells with different stem and progenitor subsets and distinct functional properties in comparison with unconjugated G-CSF. Haematologica, 93, 347-355. (DOI: 10.3324/haematol.12081, PMID: 18268278)
  • 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. (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, 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. (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.
  • 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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