Email: heiko.schmidt(AT)univie.ac.at
Phone: ++43 +1 / 4277 - 74321

Postal address:
Center for Integrative Bioinformatics Vienna (CIBIV)
Max Perutz Labs
Campus Vienna Biocenter 5 (VBC5)
A-1030 Wien, Austria

Publications:
Lists of publications are available via ORCID, Google Scholar, WoS ResearcherID

Research interests

• Phylogentics/Phylogenomics (methods, development and application; TREE-PUZZLE, IQ-Tree)
• Evolution on species and gene level
• Phylogenetic trees for large datasets
• Quality checks for alignments (phylogenetic information, quartet likelihood mapping)
• Parallel and grid computing in phylogenetics and bioinformatics
• Scientific workflows

Education

• 2003: Ph.D. in Computer Science (Dr. rer. nat.) at Düsseldorf University, Germany
  Advisor: Prof. Arndt von Haeseler
  Thesis: Phylogenetic Trees from Large Datasets
  (also accessible via URN:NBN-resolver:urn:nbn:de:hbz:061-20030730-000597-4 or the document service at Düsseldorf University)
• 1996: ‘M.Sc.’ in Biology (Diplom Biologe), Cologne University, Germany
  Advisors: Prof. Andreas Radbruch, Prof. Rainer Schrader
  Thesis: Parallelization of Phylogenetic Methods for the Analysis of the Crown Group Radiation (in German)
• 1989-1996: Studies at Cologne University: Biology
• 1991-1994: Studies at Bonn University: Computer Science
• 1979-1988: Beethoven-Gymnasium, Bonn

Professional Experience

• 2005-present: Postdoc at the Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs (formerly Max F. Perutz Laboratories, MFPL), University of Vienna, Vienna, Austria
• 2003-2005: Postdoc at the John-von-Neumann Institute for Computing (NIC), Research Center Jülich, Jülich
• 2001-2003: Staff scientist at the Computational Molecular Biology, MPI for Molecular Genetics, Berlin
• 1997-2001: Staff scientist at the Theoretical Bioinformatics, DKFZ, Heidelberg
• 1995-1997: Software engineer and system administrator at the Theoretical Bioinformatics, DKFZ, Heidelberg

Publications

• S. Burgstaller-Muehlbacher, S.M. Crotty, H.A. Schmidt, F. Reden, T. Drucks, and A. von Haeseler (2023) ModelRevelator: Fast phylogenetic model estimation via deep learning. Mol. Phylogenet. Evol., 188, 107905. (DOI: 10.1016/j.ympev.2023.107905, PMID: 37595933)
• N. Durut, A.E. Kornienko, H.A. Schmidt, N. Lettner, M. Dona, M. Nordborg, and O. Mittelsten Scheid (2023) Long noncoding RNAs contribute to DNA damage resistance in Arabidopsis thaliana. Genetics, 225, iyad135. (DOI: 10.1093/genetics/iyad135, PMID: 37467473, PMCID: PMC10471225)
• M. Schwaiger^e, C. Andrikou^e, R. Dnyansagar^e, P. Ferrer Murguia, P. Paganos, D. Voronov, B. Zimmermann, T. Lebedeva, H.A. Schmidt, G. Genikhovich, G. Benvenuto, M.I. Arnone, and U. Technau (2022) An ancestral Wnt-Brachyury feedback loop in axial patterning and recruitment of mesoderm-determining target genes. Nat. Ecol. Evol., 6, 1921–1939. (DOI: 10.1038/s41559-022-01905-w, PMID: 36396969)
  ^e contributed equally
• E.B. Hodcroft, N. De Maio, R. Lanfear, D.R. MacCannell, B.Q. Minh, H.A. Schmidt, A. Stamatakis, N. Goldman, and C. Dessimoz (2021) Want to track pandemic variants faster? Fix the bioinformatics bottleneck. Nature, 591, 30-33. (DOI: 10.1038/d41586-021-00525-x, PMID: 33649511)
• A.F. Leuchtenberger^e, S.M. Crotty^e, T. Drucks, H.A. Schmidt, S. Burgstaller-Muehlbacher, and A. von Haeseler (2020) Distinguishing Felsenstein Zone From Farris Zone Using Neural Networks. Mol. Biol. Evol., 37, 3632-3641. (free reprint, DOI: 10.1093/molbev/msaa164, PMID: 32637998, software)
  ^e contributed equally
• C. Mavian, S. Kosakovsky Pond, S. Marini, B. Rife Magalis, A.-M. Vandamme, S. Dellicour, S.V. Scarpino, C. Houldcroft, J. Villabona-Arenas, T.K. Paisie, N.S. Trovao, C. Boucher, Y. Zhang, R.H. Scheuermann, O. Gascuel, T.T.-Y. Lam, M.A. Suchard, A. Abecasis, E. Wilkinson, T. de Oliveira, A.I. Bento, H.A. Schmidt, D. Martin, J. Hadfield, N. Faria, N.D. Grubaugh, R.A. Neher, G. Baele, P. Lemey, T. Stadler, J. Albert, K.A. Crandall, T, Leitner, A. Stamatakis, M. Prosperi and M. Salemi (2020) Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable. Proc. Natl. Acad. Sci. USA, 117, 12522-12523. (DOI: 10.1073/pnas.2007295117, PMID: 32381734)
• B.Q. Minh, H.A. Schmidt, O. Chernomor, D. Schrempf, M.D. Woodhams, A. von Haeseler^s, and R. Lanfear^s (2020) IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol., 37, 1530-1534. (free reprint, DOI: 10.1093/molbev/msaa015, PMID: 32011700, software)
  ^s co-senior authors.
• R. Reinhardt, L. Truebestein, H.A. Schmidt, and T.A. Leonard (2020) It Takes Two to Tango: Activation of Protein Kinase D by Dimerization BioEssays, 42, 1900222. (DOI: 10.1002/bies.201900222, PMID: 31997382)
• R.J.E. Alves, M. Kerou, A. Zappe, R. Bittner, S.S. Abby, H.A. Schmidt, K. Pfeifer, and C. Schleper (2019) Ammonia Oxidation by the Arctic Terrestrial Thaumarchaeote Candidatus Nitrosocosmicus arcticus Is Stimulated by Increasing Temperatures. Front. Microbiol., 10, 1571. (DOI: 10.3389/fmicb.2019.01571, PMID: 31379764, PMCID: PMC6657660)
• E. Klopf, H.A. Schmidt, S. Clauder-Münster, L.M. Steinmetz, and C. Schüller (2017) INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. Nucleic Acids Res., 45, 3752-3766. (DOI: 10.1093/nar/gkw1292, PMID: 28025392)
• 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)
• 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)
• 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)
• 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
• 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)
• 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)
• 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)
• 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)
• H.A. Schmidt (2009) Testing Tree Topologies. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 381-404, Cambridge University Press, Cambridge. (DOI: 10.1017/CBO9780511819049.014, ISBN: paperback: 9780521730716, hardcover: 9780521877107, book webpage)
• H.A. Schmidt and A. von Haeseler (2009) Phylogenetic Inference Using Maximum Likelihood Methods. In P. Lemey, M. Salemi, A.M. Vandamme (eds.)The Phylogenetic Handbook: a Practical Approach to Phylogenetic Analysis and Hypothesis Testing., 2nd Edition, 181-209, Cambridge University Press, Cambridge. (DOI: 10.1017/CBO9780511819049.008, ISBN: paperback: 9780521730716, hardcover: 9780521877107, book webpage)
• 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)
• 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)
• 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)
• I. Ebersberger, A. von Haeseler, and H.A. Schmidt (2007) Phylogeny Reconstruction. In T. Lengauer (ed.) Bioinformatics: From Genomes to Therapies 83-128, Wiley-VCH, Weinheim. (DOI: 10.1002/9783527619368.ch4, ISBN 978-3-527-31278-8)
• H.A. Schmidt and A. von Haeseler (2007) Maximum Likelihood Analysis using TREE-PUZZLE. (revised version) In A.D. Baxevanis, D.B. Davison, R.D.M. Page, G. Stormo, and L. Stein (eds.) Current Protocols in Bioinformatics, 17, Unit 6.6, pages 6.6.1-6.6.23, Wiley and Sons, New York. (DOI: 10.1002/0471250953.bi0606s17, PMID: 18428792, ISBN 0-471-25093-7, CP online)
• H.A. Schmidt, A. von Haeseler, and J. Buschbom (2007) pIPHULA - Parallel Inference of Population Parameters Using a Likelihood Approach. Bioinformatics, 23, 2636-2637. (free reprint, DOI: 10.1093/bioinformatics/btm391, PMID: 17698495)
• 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.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)
• E. Petzold, D. Merkle, M. Middendorf, A. von Haeseler, and H.A. Schmidt (2006) Phylogenetic Parameter Estimation on COWs. In A.Y. Zomaya (ed.) Parallel Computing for Bioinformatics and Computational Biology 347-368, Wiley and Sons, New York. (DOI: 10.1002/0471756504.ch15, ISBN 0-471-71848-3)
• 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
• 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)
• L.S. Vinh, H.A. Schmidt, and A. von Haeseler (2005) PhyNav: A novel approach to reconstruct large phylogenies. In C. Weihs and W. Gaul (eds.) Classification, the Ubiquitous Challenge Series Studies in Classification, Data Analysis, and Knowledge Organization, 386-393, Springer, Heidelberg/New York. (DOI: 10.1007/3-540-28084-7_44)
• B. Klempa, R. Ulrich, H. Meisel, D.H. Krüger, H.A. Schmidt, S. Kaluz, M. Labuda, and B. Hjelle (2003) Letter to the Editor: Genetic Interaction between Dobrava and Saaremaa Hantaviruses: Now or Millions of Years Ago? (Authors' Reply). J. Virol., 77, 7157-7158. (DOI: 10.1128/JVI.77.12.7156-7158.2003)
• B. Klempa, H.A. Schmidt, R. Ulrich, S. Kaluz, M. Labuda, H. Meisel, B. Hjelle, and D.H. Krüger (2003) Genetic Interaction between Distinct Dobrava Hantavirus Subtypes in Apodemus agrarius and A. flavicollis in Nature. J. Virol., 77, 804-809. (DOI: 10.1128/JVI.77.1.804-809.2003, PMID: 12477889)
• 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, 1, Unit 6.6, pages 6.6.1-6.6.23, Wiley and Sons, New York. (DOI: 10.1002/0471250953.bi0606s01, 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)
• D. Liebers, H.A. Schmidt, M. Vingron, and A. von Haeseler (2002) Computer assisted phylogenetic analysis of large genomic datasets. In J. Wadzack, A. Haese, and B. Löhmer (eds.) Progress Report 1999 - 2002: German Human Genome Project (DHGP). 68-69, Druckhaus Schmergow, Berlin. (ISBN: 978-3-00-010097-0)
• 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 H.-H. 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)
• 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)
• N. Pollet, H.A. Schmidt, V. Gawantka, M. Vingron, and C. Niehrs (2000) Axeldb: a Xenopus laevis database focusing on gene expression. Nucleic Acids Res., 28, 139-140. (DOI: 10.1093/nar/28.1.139, PMID: 10592204)
• N. Pollet, H.A. Schmidt, V. Gawantka, C. Niehrs, M. Vingron (2000) In Silico Analysis of Gene Expression Patterns During Early Development of Xenopus laevis. Proceedings of the 5th Pacific Symposium on Biocomputing (PSB2000), Hawaii, 440-451, (PMID: 10902192, PDF)
• Bhattacharya, D., Friedl, T., and Schmidt, H.A. (1999) The Phylogeny of Thermophiles and Hyperthermophiles and the Three Domains of Life. The Phylogeny of Thermophiles. In Seckbach, J. (ed.) Enigmatic Microorganisms and Life in Extreme Environments, 291-304, Kluwer Academic Publishers, Dordrecht, Netherlands, (DOI: 10.1007/978-94-011-4838-2_23, (ISBN 978-0-7923-5492-5)
• Bhattacharya, D. and Schmidt, H.A. (1997) Division Glaucocystophyta. In Bhattacharya, D.(ed.) The Origin of Algae and their Plastids, (Plant Syst. Evol., Suppl. 11, 139-148) Springer Verlag, Vienna, Austria (DOI: 10.1007/978-3-7091-6542-3_7, ISBN 978-3-211-83035-2)