Prof. Sonja Prohaska

Prof. Sonja Prohaska

PROJECT LEADER

Evolution and Development

sonja@bioinf.uni-leipzig.de

+49 (0) 341 - 97 16703

Room: 315

ACADEMIC CAREER

RESEARCH & EXPERIENCE
  • Juniorprofessor Computational EvoDevo, University of Leipzig, Germany - since Dec 2010 (Research topics range from the origin of regulation to modelling of chromatindynamics, and detection of protein-binding RNA motifs.Positive mid-term evalutation in summer 2013.
  • Research Assistant Bioinformatics, University of Leipzig, Germany, Oct 2008 – Nov 2010 (Functional role and evolutionary implications of chromatin regulation and thelink to structured RNAs. Initiation of a Working Group on “ComputationalEvoDevo”. Application for funding. Supervision of graduate and undergradu-ate students. Teaching.)
  • Researcher Theoretical Chemistry, University of Vienn, Austria, Jan 2008 – Sept 2008 (Involvment of RNAs and RNA structures in gene regulatory mechanisms.)
  • Research Fellow Evolutionary/Theoretical Biology, Santa Fe Institute, Santa Fe, NM, Jan 2008 – Jun 2008 (Examination and modelling of the evolution of gene regulation. Regulatorymechanisms, with focus on chromatin regulation, were traced back to theirevolutionary origin.)
  • Research Assistant Professional Biomedical Informatics, Arizona State University, Tempe, AZ Jan 2006 – Dec 2007 (Bioinformatics approaches to study gene regulation. Postdoctoral Research.Application for funding at NIH and NSF. Supervision of undergraduates. Sci-entific mentor: Sudhir Kumar.)
  • Research Assistant Bioinformatics, University of Leipzig, Germany, Jul 2003 – Dec 2005 (Investigation of phylogenetic footprints and their evolutionary changes. Research and dissertation. Supervision of undergraduates atbioinformatics courses.Supervisor: Peter Stadler)
EDUCATION
  • Postdoctoral research with Prof. Peter F. Stadler, Jul 2008 - Nov 2010, University of Leipzig,Germany
  • Postdoctoral research with Prof. David Krakauer, Jan -Jun 2008, Santa Fe Institute, Santa Fe, NM
  • Postdoctoral research with Prof. Sudhir Kumar, Jan 2006 - Dec 2007, Arizona State University, Tempe, AZ
  • PhD, Bioinformatics, graduated with honors, 12 Dec 2005  (Thesis: Evolution of Conserved Non-Coding Sequences, Supervisor: Prof. Peter F. StadlerAcademic degree: Doctor rerum naturalium, University of Leipzig, Germany)
  • MSc, Genetics, 2nd diploma with honors, Jul 2003 (Thesis:Picking Up the Trail of Phylogenetic Footprints, Supervisor: Prof. Peter F. Stadler, Academic degree: Magistra rerum naturaliumUniversity of Vienna, Austria)
  • Biology, 1st diploma with honors, Jun 2001, University of Vienna, Austria
  • Matura with honors, Jun 1998, High school, Horn, Austria
  • CSE with honors, Jun 1994

SCIENTIFIC INTERESTS

The AG Prohaska addresses research questions relating to the genotype phenotype map. This encompasses the fascinating diversity of gene regulatory mechanisms. In the past, a major subject of research was concerned with the evolution of Hox gene clusters and the regulation of Hox gene expression patterns along the anterior-posterior axis. Recent work of the group turned towards epigenetic regulation in the light of developmental and evolutionary constraints. Among the major achievements in the recent past is the proposal of an evolutionary scenario for the origin and evolution of epigenetic regulation. Her two main projects currently are:
  • Unusual RNA-polymerases: phylogenetic distribution and ancestral recomstruction of functional tRNA nucleotidyltransferases (CCA-adding enzymes)
  • Rule-based modelling of histone modification dynamics: chromatin state reconstruction in response to lossy replication during cell division

PUBLICATIONS

Google-Scholar

2020 (1)

  • L. Erber, P. Franz, H. Betat, S. Prohaska, M. Morl. Divergent Evolution of Eukaryotic CC- and A-Adding Enzymes. Int J Mol Sci. 2020. 21:

2018 (1)

  • M. D. Laubichler, S. J. Prohaska, P. F. Stadler. Toward a mechanistic explanation of phenotypic evolution: The need for a theory of theory integration. J Exp Zool B Mol Dev Evol. 2018. 330: 5-14.

2017 (3)

  • H. Indrischek, S. J. Prohaska, V. V. Gurevich, E. V. Gurevich, P. F. Stadler. Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes. BMC Evol Biol. 2017. 17: 163.
  • S. J. Prohaska, S. J. Berkemer, F. Gartner, T. Gatter, N. Retzlaff, C. Honer Zu Siederdissen, P. F. Stadler. Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem. J Math Biol. 2017.
  • C. L. Richards, C. Alonso, C. Becker, O. Bossdorf, E. Bucher, M. Colome-Tatche, W. Durka, J. Engelhardt, B. Gaspar, A. Gogol-Doring, I. Grosse, T. P. van Gurp, K. Heer, I. Kronholm, C. Lampei, V. Latzel, M. Mirouze, L. Opgenoorth, O. Paun, S. J. Prohaska, S. A. Rensing, P. F. Stadler, E. Trucchi, K. Ullrich, K. J. F. Verhoeven. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward. Ecol Lett. 2017. 20: 1576-1590.

2016 (2)

  • H. Indrischek, N. Wieseke, P. F. Stadler, S. J. Prohaska. The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies. Algorithms Mol Biol. 2016. 11: 1.
  • D. C. Krakauer, L. Mueller, S. J. Prohaska, P. F. Stadler. Design specifications for cellular regulation. Theory Biosci. 2016. 135: 231-240.

2015 (3)

  • H. Betat, T. Mede, S. Tretbar, L. Steiner, P. F. Stadler, M. Mörl, S. J. Prohaska. The ancestor of modern Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer. Nucleic Acids Res. 2015. 43: 6739-46.
  • M. D. Laubichler, P. F. Stadler, S. J. Prohaska, K. Nowick. The relativity of biological function. Theory Biosci. 2015. 134: 143-7.
  • C. Zu Siederdissen, S. J. Prohaska, P. F. Stadler. Algebraic Dynamic Programming over general data structures. BMC Bioinformatics. 2015. 16 Suppl 19: S2.

2014 (5)

  • Christian Höner zu Siederdissen, SonjaJ Prohaska, PeterF Stadler. Dynamic Programming for Set Data Types. In: Advances in Bioinformatics and Computational Biology, Springer International Publishing 2014. 8826: 57-64. Ed: Campos, Sérgio.
  • M. Lechner, M. Hernandez-Rosales, D. Dörr, N. Wieseke, A. Thevenin, J. Stoye, R. K. Hartmann, S. J. Prohaska, P. F. Stadler. Orthology detection combining clustering and synteny for very large datasets. PLoS One. 2014. 9: e105015.
  • G. A. Müller, A. Wintsche, K. Stangner, S. J. Prohaska, P. F. Stadler, K. Engeland. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. Nucleic Acids Res. 2014. 42: 10331-50.
  • G. A. Müller, A. Wintsche, K. Stangner, S. J. Prohaska, P. F. Stadler, K. Engeland. The CHR site: definition and genome-wide identification of a cell cycle transcriptional element. Nucleic Acids Res. 2014. 42: 10331-50.
  • A.A. Parikesit, L. Steiner, P.F. Stadler, S.J. Prohaska. Pitfalls of Ascertainment Biases in Genome Annotations —Computing Comparable Protein Domain Distributions in Eukarya. Malaysian Journal of Fundamental and Applied Sciences. 2014. 10, No. 2: 13-033.

2013 (2)

  • C. Arnold, P. F. Stadler, S. J. Prohaska. Chromatin computation: epigenetic inheritance as a pattern reconstruction problem. J Theor Biol. 2013. 336: 61-74.
  • H. Binder, L. Steiner, J. Przybilla, T. Rohlf, S. Prohaska, J. Galle. Transcriptional regulation by histone modifications: towards a theory of chromatin re-organization during stem cell differentiation. Phys Biol. 2013. 10: 026006.

2012 (2)

  • T. Rohlf, L. Steiner, J. Przybilla, S. Prohaska, H. Binder, J. Galle. Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin. Epigenomics. 2012. 4: 205-19.
  • L. Steiner, L. Hopp, H. Wirth, J. Galle, H. Binder, S. J. Prohaska, T. Rohlf. A global genome segmentation method for exploration of epigenetic patterns. PLoS One. 2012. 7: e46811.

2011 (6)

  • S. Findeiss, J. Engelhardt, S. J. Prohaska, P. F. Stadler. Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids. Biochimie. 2011. 93: 2019-23.
  • M. Lechner, S. Findeiss, L. Steiner, M. Marz, P. F. Stadler, S. J. Prohaska. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics. 2011. 12: 124.
  • I. Lozada-Chavez, P. F. Stadler, S. J. Prohaska. "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity. Orig Life Evol Biosph. 2011. 41: 587-607.
  • A. A. Parikesit, P. F. Stadler, S. J. Prohaska. Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions. Genes. 2011. 2: 912-924.
  • S. J. Prohaska, P. F. Stadler. The use and abuse of -omes. Methods Mol Biol. 2011. 719: 173-96.
  • J. D. Raincrow, K. Dewar, C. Stocsits, S. J. Prohaska, C. T. Amemiya, P. F. Stadler, C. H. Chiu. Hox clusters of the bichir (Actinopterygii, Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny. J Exp Zool B Mol Dev Evol. 2011. 316: 451-64.

2010 (4)

  • C. T. Amemiya, T. P. Powers, S. J. Prohaska, J. Grimwood, J. Schmutz, M. Dickson, T. Miyake, M. A. Schoenborn, R. M. Myers, F. H. Ruddle, P. F. Stadler. Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome. Proc Natl Acad Sci U S A. 2010. 107: 3622-7.
  • C. Bermudez-Santana, C. S. Attolini, T. Kirsten, J. Engelhardt, S. J. Prohaska, S. Steigele, P. F. Stadler. Genomic organization of eukaryotic tRNAs. BMC Genomics. 2010. 11: 270.
  • A. A. Parikesit, P. F. Stadler, S. J. Prohaska. Quantitative Comparison of Genomic-Wide Protein Domain Distributions. In: German Conference on Bioinformatics, Gesellschaft für Informatik 2010. P-173: 93-102. Ed: Schomburg, D. and Grote, A.
  • S. J. Prohaska, P. F. Stadler, D. C. Krakauer. Innovation in gene regulation: the case of chromatin computation. J Theor Biol. 2010. 265: 27-44.

2009 (4)

  • M. Hiller, S. Findeiss, S. Lein, M. Marz, C. Nickel, D. Rose, C. Schulz, R. Backofen, S. J. Prohaska, G. Reuter, P. F. Stadler. Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Res. 2009. 19: 1289-300.
  • A. Mosig, T. BIyIkoglu, S.J. Prohaska, P.F. Stadler. Discovering cis-regulatory modules by optimizing barbecues. Discrete Applied Mathematics Networks in Computational Biology. 2009. 157: 2458-2468.
  • P. F. Stadler, J. J. Chen, J. Hackermüller, S. Hoffmann, F. Horn, P. Khaitovich, A. K. Kretzschmar, A. Mosig, S. J. Prohaska, X. Qi, K. Schutt, K. Ullmann. Evolution of vault RNAs. Mol Biol Evol. 2009. 26: 1975-91.
  • P. F. Stadler, S. J. Prohaska, C. V. Forst, D. C. Krakauer. Defining genes: a computational framework. Theory Biosci. 2009. 128: 165-70.

2008 (5)

  • Andreas W.M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grunewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler. Noisy: identification of problematic columns in multiple sequence alignments. Algorithms Mol Biol. 2008. 3: 7.
  • A. Heffel, P. F. Stadler, S. J. Prohaska, G. Kauer, J. P. Kuska. Process Flow for Classification and Clustering of Fruit Fly Gene Expression Patterns. In: Proc Int Conf Image Proc 2008. 1: 721-724.
  • Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska. SynBlast: Assisting the Analysis of Conserved Synteny Information. BMC Bioinformatics. 2008. 9: 351.
  • Sonja J. Prohaska, Guido Fritzsch, Peter F. Stadler. Rate Variations, Phylogenetics, and Partial Orders. In: Fifth International Workshop on Computational Systems Biology, WCSB 2008, TU Tampere 2008. 133-136. Ed: Ahdesmäki, Miika and Strimmer, Korbinian and Radde, Nicole and Rahnenführer, Jörg and Klemm, Konstantin and Lähdesmäki, Harri and Yli-Harja, Olli.
  • Sonja J. Prohaska, Peter F. Stadler. Genes. Th. Biosci. 2008. 127: 215-221.

2007 (2)

  • Athanasius F. Bompfünewerer, Rolf Backofen, Christoph Flamm, Claudia Fried, Guido Fritzsch, Joerg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Domininc Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will. RNAs Everywhere: Genome-Wide Annotation of Structured RNAs. J. Exp.Zool.B: Mol. Dev. Evol. 2007. 308B: 1-25.
  • The Athanasius F. Bompfünewerer RNA Consortium, Rolf Backofen, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Will Sebastian. RNAs Everywhere: Genome-Wide Annotation of Structured RNAs. J. Exp. Zool. B: Mol. Dev. Evol. 2007. 308B: 1-25.

2005 (1)

  • Athanasius F. Bompfuenewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M. R. Stadler, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Christina Witwer. Evolutionary Patterns of Non-Coding RNAs. Th. Biosci. 2005. 123: 301-369.

MISCELLANEOUS

  • since 2017 External Faculty at the Santa Fe Institut (SFI), Santa Fe, New Mexico, U.S.
  • since 2019 External Faculty at the Complexity Science Hub (CSH), Vienna, Austria