Evolution and Development

Short Introduction

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.

Challenging the concept of a static “histone code”, Prof. Prohaska takes an adventurous turn in representing histone modification dynamics as a “Chromatin Computer” capable of performing complex computations.

Publications

2016 (2)

  • D. C. Krakauer, L. Muller, S. J. Prohaska, P. F. Stadler. Design specifications for cellular regulation. Theory Biosci. 2016. 135: 231-240.
  • 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.

2015 (3)

  • C. Zu Siederdissen, S. J. Prohaska, P. F. Stadler. Algebraic Dynamic Programming over general data structures. BMC Bioinformatics. 2015. 16 Suppl 19: S2.
  • M. D. Laubichler, P. F. Stadler, S. J. Prohaska, K. Nowick. The relativity of biological function. Theory Biosci. 2015. 134: 143-7.
  • 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.

2014 (5)

  • 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.
  • 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.
  • 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.
  • Parikesit A. A., Lydia Steiner, Peter F Stadler, Sonja 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)

  • 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.
  • C. Arnold, P. F. Stadler, S. J. Prohaska. Chromatin computation: epigenetic inheritance as a pattern reconstruction problem. J Theor Biol. 2013. 336: 61-74.

2012 (2)

  • 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.
  • 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.

2011 (6)

  • 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.
  • A. A. Parikesit, P. F. Stadler, S. J. Prohaska. Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions. Genes. 2011. 2: 912-924.
  • 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.
  • 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.
  • 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.

2010 (4)

  • 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.
  • 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.
  • 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.
  • 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.

2009 (4)

  • P. F. Stadler, S. J. Prohaska, C. V. Forst, D. C. Krakauer. Defining genes: a computational framework. Theory Biosci. 2009. 128: 165-70.
  • 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.
  • 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.
  • 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.

2008 (5)

  • Sonja J. Prohaska, Peter F. Stadler. Genes. Th. Biosci. 2008. 127: 215-221.
  • 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.
  • Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska. SynBlast: Assisting the Analysis of Conserved Synteny Information. BMC Bioinformatics. 2008. 9: 351.
  • 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.
  • 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.

2007 (2)

  • 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.
  • 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.

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