Heiko A. Schmidt

Research Interests:

• Phylogeny (methods, development and application)
• Evolution on species and gene level
• Parallel and grid computing in phylogenetics
• Quartet methods for phylogeny (TREE-PUZZLE)
• Phylogenetic trees for large datasets

Short Vita:

Education:

• 2003: Ph.D. at Düsseldorf University: Computer Science
• 1991-1994: Studies at Bonn University: Computer Science
• 1989-1996: Studies at Cologne University: Biology
• 1979-1988: Beethoven-Gymnasium, Bonn

Degrees:

• 'Ph.D.' in Computer Science (Dr. rer. nat.), Düsseldorf, Germany, in 2003
  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)
• 'M.Sc.' in Biology (Diplom Biologe), Cologne, Germany, in 1996
  Advisors: Prof. Andreas Radbruch, Prof. Rainer Schrader
  Thesis: Parallelization of Phylogenetic Methods for the Analysis of the Crown Group Radiation (in German)

Professional Experience:

• 2005-present: Postdoc at the Center for Integrative Bioinformatics Vienna (CIBIV), Max F. Perutz Laboratories (MFPL), 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 / Conference Contributions

• E. Klopf, H.A. Schmidt, S. Clauder-Münster, L.M. Steinmetz, C. Schüller (2017) INO80 represses osmostress induced gene expression by resetting promoter proximal nucleosomes. Nucleic Acids Res., 45, in press. (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. (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)
• 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. (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, 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)
• 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. (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 the 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 (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. (ISBN-13: 978-3-540-25677-9)
• 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, 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)
• 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)
• 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, (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, (DOI: 10.1007/978-3-7091-6542-3_7, ISBN 978-3-211-83035-2)

Conference Posters

• H.A. Schmidt and A. von Haeseler (2005) A Novel Way for Combined Phylogenetic Analysis between Supertrees and Supermatrices. Poster at Conference on the Mathematics of Evolution and Phylogeny (MEP 2005), June 17-21, 2005, Paris, France.
• H.A. Schmidt, K. Strimmer, M. Vingron, and A. von Haeseler (2000) TREE-PUZZLE 5.0: Maximum Likelihood Phylogenetic Analysis Using Quartets and Parallel Computing. Poster at The 15th German Conference on Bioinformatics (GCB 2000), October 5-7, 2000, Heidelberg, Germany. (PS)
• H.A. Schmidt, K. Strimmer, A. von Haeseler, and M. Vingron (1999) PUZZLE/PPUZZLE: Using Parallel Computing for Maximum Likelihood Phylogenetic Analysis. Poster at The 7th International Conference on Intelligent Systems for Molecular Biology (ISMB 1999), August 6 - 10, 1999, Heidelberg, Germany. (PS)
• H.A. Schmidt and M. Vingron (1998) pfastDNAml: Using Parallel Computing for Maximum Likelihood Phylogenetic Analysis. Poster at The 13th German Conference on Bioinformatics (GCB 1998), October 7-10, 1998, Bergisch-Gladbach near Cologne, Gemany. (PS)

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Addresses

Postal Address: