Center for Integrative Bioinformatics Vienna
Max F. Perutz Laboratories
Dr. Bohr Gasse 9
A-1030 Vienna, Austria

Arndt von HAESELER

Arndt von Haeseler

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Addresses

Center for Integrative Bioinformatics Vienna (CIBIV)
(CIBIV is a joint institute of Vienna University and Medical University, Vienna, Austria)
Max F. Perutz Laboratories (MFPL)
Campus Vienna Biocenter 5 (VBC5), Ebene 1
A-1030 Wien, Austria
Phone: ++43 +1 / 4277 - 74307
Email: arndt.von.haeseler(AT)univie.ac.at

Postal Address:

Center for Integrative Bioinformatics Vienna (CIBIV)
Max F. Perutz Laboratories (MFPL)
Dr. Bohr Gasse 9
A-1030 Wien, Austria

Research Interests:

Alignment
Sequence evolution
Gene trees
Population genetics
Complex patterns of evolution

Short Vita:

Education:

1994: University of Munich, State doctorate (Habilitation) in Zoology
1988: University of Bielefeld, Ph. D. in Mathematics
1984: Philipps University Marburg, State examination (1. Staatsexamen) for biology, mathematics, education science

Professional Experience:

since 2017: Dean of the Center of Molecular Biology at the University of Vienna; Head of the Center for Medical Biochemistry at the Medical University of Vienna; Scientific Director of the Max F. Perutz Laboratories
since October 2010: Full Professor for Bioinformatics at the Center for Molecular Biology and Department for Computer Sciences (University of Vienna) and at the Department for Medical Biochemistry (Medical University of Vienna), Austria
since 2005: Scientific Director of the Center for Integrative Bioinformatics Vienna (CIBIV).
Sept 2005 - Sept 2011: WWTF Science Chair for Bioinformatics and Full Professor at the Medical University Vienna, the University Vienna, University of Veterinary Medicine, Austria
2002 - Aug 2005: Chairman of Computer Sciences, Heinrich Heine University, Düsseldorf, Germany
2001 - Aug 2005: Full Professor (C4) for Bioinformatics, Heinrich Heine University, Düsseldorf, Germany
2001-2004: Group Leader of the Bioinformatics Group at the Neumann Institute for Computing, Research Center Jülich, Germany
1998-2001: Group Leader (C3) of the Theoretical Biology Group, Max Planck Institute for evolutionary Anthropology, Leipzig, Germany
1995-1998: Senior Scientific Lecturer (Hochschulassistent, C2), Biology Dept., Ludwig Maximilians University, Munich, Germany
1991-1995: Scientific Lecturer (Hochschulassistent, C1), Biology Dept., Ludwig Maximilians University, Munich, Germany
1990-1991: Visiting Assistant Professor, Mathematics Dept., University of Southern California, Los Angeles, USA
1989-1990: Postdoc, Mathematics Dept., University of Southern California, Los Angeles, USA
1988-1989: Postdoc, Mathematics Dept., University of Bielefeld, Germany

Awards and Honors:

since April 2012: Visiting Professor at Division of theoretical Genetics, National Institute of Genetics, Mishima, Japan
2005: Award of the WWTF Science Chairs, Vienna, Austria
since 1999: Honorary Professor for Theoretical Biology, University of Leipzig, Germany
1985-1988: PhD scholarship, Studienstiftung des Deutschen Volkes, Germany

Publications

in press

A. Jain, D. Perisa, F. Fliedner, A. von Haeseler, and I. Ebersberger (2019) The evolutionary traceability of a protein. Genome Biol. Evol., 11, in press. (DOI: 10.1093/gbe/evz008, PMID: 30649284)
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, accepted.

2018

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.T. Hoang^e, O. Chernomor^e, A. von Haeseler, B.Q. Minh^c, and L.S. Vinh^c (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 Haeseler^c, and B.Q. Minh^c (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)
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. 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. Sedlazeck^e, P. Rescheneder^e, 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, 15, 461-468. (DOI: 10.1038/s41592-018-0001-7, PMID: 29713083)
^e contributed equally
S. Uhse, F. 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)

2017

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 (in press) Thiol-linked alkylation for the metabolic sequencing of RNA. Nat. Methods, 14, 1198-1204. (DOI: 10.1038/nMeth.4435, PMID: 28945705)
S. Kalyaanamoorthy^e, B.Q. Minh^e, T.K.F. Wong^e, 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, abstract, software) press release by MFPL
^e contributed equally
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)

2016

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)
K. Gesson^e, P. Rescheneder^e, 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. Grumaz, P. Stevens^e, 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)
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)

2015

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)
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. Krunic^e, R. Ertl^e, 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
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. 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)

2014

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'Ampio^e, K. Meusemann^e, N.U. Szucsich^e, R.S. Peters^e, 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
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. 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)
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)
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)

2013

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)
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 (2012) 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)
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)
F.J. Sedlazeck^e, P. Rescheneder^e, 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)

2012

H.Q. Dinh, M. Dubin^e, F. Sedlazeck^e, 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, 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)
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)
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)
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)
C. Vesely^e, S. Tauber^e, 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

2011

M. A. T. Nguyen, S. Klaere, and A. von Haeseler (2011) MISFITS: Evaluating the goodness of fit between a phylogenetic model and an alignment. Mol. Biol. Evol., 28, 143-152. (free copy, DOI: 10.1093/molbev/msq180, PMID: 20643866)
W. Salzburger, G. Ewing, and A. von Haeseler (2011) The performance of phylogenetic algorithms in estimating haplotype genealogies with migration. Mol. Ecol., 20, 1952-1963. (DOI: 10.1111/j.1365-294X.2011.05066.x, PMID: 21457168)
L.S. Vinh, A. Fuehrer, and A. von Haeseler (2011) Random Tree-Puzzle leads to the Yule-Harding Distribution. Mol. Biol. Evol., 28, 873-877. (DOI: 10.1093/molbev/msq212, PMID: 20705907)

2010

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)
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)

2009

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. Krauss^e, B.Q. Minh^e, A. Losi, W. Gaertner, T. Eggert, A. von Haeseler^c, 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
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)
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)
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. Mirus^e, S. Strauss^e, 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 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 Substitution 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)

2008

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)
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)
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)
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)
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)

2007

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)
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)
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.
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, Supplement 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)

2006

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)
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)
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., 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)

2005

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)
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)
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)
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 (Proceedings of the 28th Annual Conference of the GfKl 2004), 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 Bioinformatics, 6, 92. (DOI: 10.1186/1471-2105-6-92, PMID: 15819989)

2004

G. Jobb, A. von Haeseler, and K. Strimmer (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol., 4:18. (DOI: 10.1186/1471-2148-4-18, PMID: 15222900)
D. Metzler, R. Fleißner, A. Wakolbinger, and A. von Haeseler (2004) Assessing Variability by Joint Sampling of Alignments and Mutation Rates. J. Mol. Evol., 53, 660-669. (DOI: 10.1007/s002390010253, PMID: 11677626)
J. Partecke, A. von Haeseler, and M. Wikelski (2004) Territory establishment in lekking marine iguanas, Amblyrhynchus cristatus: support for the hotshot mechanism. Behav. Ecol. Sociobiol., 51, 579-587. (DOI: 10.1007/s00265-002-0469-z)
L.S. Vinh and A. von Haeseler (2004) IQPNNI: Moving Fast Through Tree Space and Stopping in Time. Mol. Biol. Evol., 21, 1565-1571. (free reprint, DOI: 10.1093/molbev/msh176, PMID: 15163768)

2003

A. von Haeseler and D. Liebers (2003) Molekulare Evolution., Fischer-Verlag, Frankfurt, Germany. (ISBN: 3-596-15365-4)
A. von Haeseler and K. Strimmer (2003) Phylogenetic inference based on maximum likelihood methods with TREE-PUZZLE. In M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook., 137-159, Cambridge University Press, Cambridge. (ISBN: 052180390X)
J. Hofmann, M. Renz, S. Meyer, A. von Haeseler, and G. Liebert (2003) Complete genome sequences of two Rubella virus isolates and identification of a variable region within the gene coding for nonstructural protein NSP1. Virus Res., 96, 123-128. (DOI: 10.1016/S0168-1702(03)00180-1)
S. Meyer and A. von Haeseler (2003) Identifying site specific substitution rates. Mol. Biol. Evol., 20, 182-189. (DOI: 10.1093/molbev/msg019, PMID: 12598684)
H.A. Schmidt and A. von Haeseler (2003) Maximum Likelihood Analysis using TREE-PUZZLE. In A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, and L. Stein (eds.) Current Protocols in Bioinformatics, Supplement 1, Unit 6.6, pages 6.6.1-6.6.23, Wiley and Sons, New York. (ISBN: 0-471-25093-7, CP online)
H.A. Schmidt, E. Petzold, M. Vingron, and A. von Haeseler (2003) Molecular Phylogenetics: Parallelized Parameter Estimation and Quartet Puzzling. J. Parallel Distrib. Comput., 63, 719-727. (DOI: 10.1016/S0743-7315(03)00129-1)
K. Strimmer and A. von Haeseler (2003) Nucleotide Substitution Models. In M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook., 72-87, Cambridge University Press, Cambridge. (ISBN: 052180390X)
G. Weiss and A. von Haeseler (2003) Testing substitution models within a phylogenetic tree. Mol. Biol. Evol., 20, 572-578. (DOI: 10.1093/molbev/msg073, PMID: 12679552)

2002

J. Partecke, A. von Haeseler, and M. Wikelski (2002) Territory establishment in lekking marine iguanas, Amblyrhynchus cristatus: Support for the hotshot mechanism. Behav. Ecol. Sociobiol., 51, 579-587. (DOI: 10.1007/s00265-002-0469-z)
H.A. Schmidt, K. Strimmer, M. Vingron, and A. von Haeseler (2002) TREE-PUZZLE: Maximum Likelihood Phylogenetic Analysis Using Quartets and Parallel Computing. Bioinformatics, 18, 502-504. (DOI: 10.1093/bioinformatics/18.3.502, PMID: 11934758)
H.A. Schmidt and A. von Haeseler (2002) Quartet Trees as a Tool to Reconstruct Large Trees from Sequences. In K. Jajuga, A. Sokolowsky, and Bock (eds.) Data Analysis, Classification, and Related Methods (Proceedings of the 9th Conference of the International Federation of Classification Societies - IFCS-2002, Krakow), 379-388, Springer, Heidelberg/New York. (DOI: 10.1007/978-3-642-56181-8_42)
S. Zöllner and A. von Haeseler (2002) Population history and linkage disequilibrium. Encyclopedia of the Human Genome., Nature Publishing Group, New York, USA. (ISBN: 0-333-80386-8)

2001

M. Hofreiter, V. Jaenicke, D. Serre, A. von Haeseler, and S. Pääbo (2001) DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res., 29, 4793-4799. (DOI: 10.1093/nar/29.23.4793, PMID: 11726688)
H. Kaessmann, F. Heissig, V. Wiebe, A. von Haeseler, and S. Pääbo (2001) Resume: DNA sequence variation on the X chromosome of humans and great apes. Pathol. Biol.., 49, 394. (DOI: 10.1016/S0369-8114(01)00185-7)
K. Nieselt-Struwe and A. von Haeseler (2001) Quartet-Mapping, a Generalization of the Likelihood-Mapping Procedure. Mol. Biol. Evol., 18, 1204-1219. (PMID: 11420361)

2000

M. Eppard, W.E. Krumbein, A. von Haeseler, and E. Riehl (2000) Characterization of fcp4 and fcp12, Two Additional Genes Encoding Light Harvesting Proteins of Cyclotella cryptica (Bacillariophyceae) and Phylogenetic Analysis of this Complex Gene Family. Plant Biol., 2, 283-289. (DOI: 10.1055/s-2000-3702)
N.C. Grassly, A. von Haeseler, and D.C. Krakauer (2000) Error, Population Structure and the Origin of Diverse Sign Systems. J. Theor. Biol., 206, 369-378. (DOI: 10.1006/jtbi.2000.2133 , PMID: 10988022)
A. von Haeseler (2000) Maximum likelihood tree reconstruction. Zoology - Analysis of Complex Systems., 106, 101-110.
M. Krings, C. Capelli, F. Tschentscher, H. Geisert, S. Meyer, A. von Haeseler, K. Grossschmidt, G. Possnert, M. Paunovic, and S. Pääbo (2000) A view of Neandertal genetic diversity. Nat. Genet., 26, 144-146. (DOI: 10.1038/79855, PMID: 11017066)
J. Saas, K. Ziegelbauer, A. von Haeseler, B. Fast, and M. Boshart (2000) A Developmentally Regulated Aconitase Related to Iron-regulatory Protein-1 Is Localized in the Cytoplasm and in the Mitochondrion of Trypanosoma brucei. J. Biol. Chem., 4, 2745-2755. (PMID: 10644738)
S. Zöllner and A. von Haeseler (2000) A Coalescent Approach to Study Linkage Disequilibrium between Single-Nucleotide Polymorphisms. Am. J. Hum. Genet., 66, 615-628. (PMID: 10677321)

1999

E. Baake and A. von Haeseler (1999) Distance Measures in Terms of Substitution Processes. Theor. Popul. Biol., 55, 166-175. (DOI: 10.1006/tpbi.1998.1395, PMID: 10329516)
F. Burckhardt, A. von Haeseler, and S. Meyer (1999) HvrBase: compilation of mtDNA control region sequences from primates. Nucleic Acids Res., 27, 138-142. (DOI: 10.1093/nar/27.1.138, PMID: 9847159)
T. Fujino, N. Navaratnam, A. Jarmuz, A. von Haeseler, and J. Scott (1999) C->U editing of apolipoprotein B mRNA in marsupials: identification and characterisation of APOBEC-1 from the American opossum Monodelphus domestica. Nucleic Acids Res., 27, 2662-2671. (DOI: 10.1093/nar/27.13.2662, PMID: 10373583)
H. Kaessmann, F. Heißig, A. von Haeseler, and S. Pääbo (2001) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat. Genet. , 22, 78-81. (DOI: 10.1038/8785, PMID: 10319866)
S. Meyer, G. Weiss, and A. von Haeseler (1999) Pattern of Nucleotide Substitution and Rate Heterogeneity in the Hypervariable Regions I and II of Human mtDNA. Genetics, 152, 1103-1110. (PMID: 10388828)
M. Schöniger and A. von Haeseler (1999) Toward Assigning Helical Regions in Alignments of Ribosomal RNA and Testing the Appropriateness of Evolutionary Models. J. Mol. Evol., 49, 691-698. (DOI: 10.1007/PL00006590, PMID: 10552050)

1998

M. Allen, A.-S. Engstrom, S. Meyers, O. Handt, T. Saldeen, A. von Haeseler, S. Pääbo, and U. Gyllensten (1998) Mitochondrial DNA sequencing of shed hairs and saliva on robbery caps: sensitivity and matching probabilities. J. Forensic Sci., 43, 453-464. (PMID: 9608683)
A. von Haeseler and M. Schöniger (1998) Evolution of DNA or amino acid sequences with dependent sites. J. Comput. Biol., 5, 149-163. (PMID: 9541878)
O. Handt, S. Meyer, and A. von Haeseler (1998) Compilation of human mtDNA control region sequences. Nucleic Acids Res., 26, 126-129. (DOI: 10.1093/nar/26.1.126, PMID: 9399816)
G. Weiss and A. von Haeseler (1998) Inference of Population History Using a Likelihood Approach. Genetics, 149, 1539-1546. (PMID: 9649540)

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