Forschungsschwerpunkte
- Evolutionary molecular design: Escape from adaptative conflicts via multifunctionality in Proteins and RNA
- Modular evolution of proteins: Dynamics and adaptive benefits of domain rearrangements
- Genome evolution: Rearrangements and emergence of novel genes in development
- Regulatory network evolution: Molecular causes and phenotypic consequences for diseases
- Bioinformatics
Vita
Akademische Ausbildung
- PhD in Theoretical Biochemistry (Institute for Theoratical Chemistry, University of Vienna, Austria)
- Diploma (equivalent to MSc) in Biochemistry, University of Vienna, Austria
- Studies in Biochemistry, Physics and Mathematics, University of Vienna, Austria
Beruflicher Werdegang
- Gastprofessur Université Lyon 1, Claude Bernard, Laboratoire de Biométrie et Biologie Évolutive
- Gastwissenschaftler EBI, Thornton Group "The Spices", Cambridge
- Full Professor of Molecular Evolution and Bioinformatics, University of Münster, Germany
- Senior Lecturer in Bioinformatics, School of Biological Sciences, The University of Manchester, UK
- Project Manager EML Ltd. (Heidelberg, Germany)
- Postdoctoral Research Associate (Cancer Research Centre Heidelberg, Germany)
- Assistant Professor in Mathematics (Univ. Ass., Institute for Mathematics, University of Vienna, Austria)
Publikationen
- . . ‘High-throughput Selection of Human de novo-emerged sORFs with High Folding Potential.’ Genome Biology and Evolution 16, Nr. 4: evae069. doi: 10.1093/gbe/evae069.
- . . ‘Domain Evolution of Vertebrate Blood Coagulation Cascade Proteins.’ Journal of Molecular Evolution 90: 418–428. doi: 10.1007/s00239-022-10071-3.
- . . ‘A genetic variant alters the secondary structure of the lncRNA H19 and is associated with dilated cardiomyopathy.’ RNA Biology 18, Nr. sup1: 409–415. doi: 10.1080/15476286.2021.1952756.
- . . ‘The modular nature of protein evolution: domain rearrangement rates across eukaryotic life.’ BMC Evolutionary Biology 20, Nr. 1: 30. doi: 10.1186/s12862-020-1591-0.
- . . ‘Becoming a de novo gene.’ Nature Ecology and Evolution 3, Nr. 4: 524–525. doi: 10.1038.
- . . ‘Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite.’ Philosophical Transactions of the Royal Society B: Biological Sciences 374, Nr. 1769: 20180192. doi: 10.1098/rstb.2018.0192.
- . . ‘Genome-wide genotype-expression relationships reveal both copy number and single nucleotide differentiation contribute to differential gene expression between stickleback ecotypes.’ Genome Biology and Evolution n.a. doi: 10.1093/gbe/evz148.
- . . ‘A Roadmap to Domain Based Proteomics.’ In Computational Methods in Protein Evolution, edited by , 287–300. doi: 10.1007/978-1-4939-8736-8_16.
- . . ‘DOGMA: a web server for proteome and transcriptome quality assessment.’ Nucleic Acids Research 47, Nr. W1. doi: 10.1093/nar/gkz366.
- . . ‘Origins and structural properties of novel and de novo protein domains during insect evolution.’ The FEBS Journal 285, Nr. 14: 2605–2625. doi: 10.1111/febs.14504.
- . . ‘Hemimetabolous genomes reveal molecular basis of termite eusociality.’ Nature Ecology and Evolution 2, Nr. 3: 557–566. doi: 10.1038/s41559-017-0459-1DO-10.1038/s41559-017-0459-1.
- . . ‘Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding.’ Genome Biology and Evolution 11, Nr. 2: 406–414. doi: 10.1093/gbe/evy269.
- . . ‘Remodeling of the juvenile hormone pathway through caste-biased gene expression and positive selection along a gradient of termite eusociality.’ Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330, Nr. 5: 296–304. doi: 10.1002/jez.b.22805.
- . . ‘Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest.’ J. Exp. Zool. B Mol. Dev. Evol. 330, Nr. 5: 254–264. doi: 10.1002/jez.b.22824.
- 10.1093/molbev/msx057. . ‘The Goddard and Saturn Genes Are Essential for Drosophila Male Fertility and May Have Arisen de Novo.’ Molecular Biology and Evolution 34, Nr. 5: 1066–1082. doi:
- 10.12688/f1000research.10079.1. . ‘Fact or fiction: Updates on how protein-coding genes might emerge de novo from previously non-coding DNA.’ F1000Research 6, Nr. null. doi:
- 10.1186/s12862-017-0985-0. . ‘Comparative analysis of lincRNA in insect species.’ BMC Evolutionary Biology 17, Nr. 1. doi:
- . . ‘Enzyme sub-functionalization driven by regulation.’ EMBO Reports 18: 1043–1045. doi: 10.15252/embr.201744383.
- 10.1016/j.zool.2016.05.005. . ‘Comparative transcriptomics of stickleback immune gene responses upon infection by two helminth parasites, Diplostomum pseudospathaceum and Schistocephalus solidus.’ Zoology (Jena) 2016, Nr. 119(4): 307–313. doi:
- . . ‘Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks.’ Molecular Ecology 2016, Nr. 25(4): 943–958. doi: 10.1111/mec.13520.
- . ‘The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.’ Nature doi: 10.1038/nature16548.
- . „DOGMA: Domain-Based Transcriptome and Proteome Quality Assessment.“ contributed to the German Conference on Bioinformatics, Berlin, .
- 10.1111/mec.13829. . ‘Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass.’ Molecular Ecology 25, Nr. 21: 5396–5411. doi:
- . „Domain World.“ contributed to the GCB 2016, Berlin, Deutschland, .
- 10.1093/nar/gkw492. . ‘Mechanisms of transcription factor evolution in Metazoa.’ Nucleic Acids Research 44, Nr. 13: 6287–6297. doi:
- 10.1093/bioinformatics/btw231. . ‘DOGMA: Domain-based transcriptome and proteome quality assessment.’ Bioinformatics 32, Nr. 17: 2577–2581. doi:
- 10.1016/j.cois.2016.05.016. . ‘Chapter 6. Comparative genomic approaches to investigate molecular traits specific to social insects.’ Current Opinion in Insect Science 16, Nr. null: 87–94. doi:
- 10.1016/j.dci.2015.09.008. . ‘Immunity comes first: the effect of parasite genotypes on adaptive immunity and immunization in three-spined sticklebacks.’ Developmental and Comparative Immunology 54, Nr. 1: 137–144. doi:
- . . ‘Emergence of de novo proteins from 'dark genomic matter' by 'grow slow and moult'.’ Biochem Soc Trans. 43(5): 867–73. doi: 10.1042/BST20150089.
- 10.1371/journal.pgen.1004966. . ‘Genomics of Divergence along a Continuum of Parapatric Population Differentiation.’ PLoS Genetics 2015. doi:
- . . ‘Host-Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes.’ PLoS Biology 13, Nr. 6: e1002169. doi: 10.1371/journal.pbio.1002169.
- 10.1016/j.biochi.2015.02.019. . ‘Detection of orphan domains in Drosophila using "hydrophobic cluster analysis".’ Biochimie 119: 244–53. doi:
- 10.1111/nph.13211. . ‘Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.’ New Phytologist 206: 1328–36. doi:
- 10.1186/s13059-015-0623-3. . ‘The genomes of two key bumblebee species with primitive eusocial organization.’ Genome Biol. 16. doi:
- 10.1093/molbev/msv165. . ‘How do genomes create novel phenotypes Insights from the loss of the worker caste in ant social parasites.’ Molecular Biology and Evolution 32, Nr. 11: 2919–2931. doi:
- 10.1186/s12859-015-0570-8. . ‘Domain similarity based orthology detection.’ BMC Bioinformatics 16, Nr. 1. doi:
- . . ‘The Rise and Fall of TRP-N, an Ancient Family of Mechanogated Ion Channels, in Metazoa.’ Genome Biol. Evol. 7, Nr. 6: 1713–1727. doi: 10.1093/gbe/evv091.
- . . ‘MDAT - Aligning multiple domain arrangements.’ BMC Bioinformatics 16. doi: 10.1186/s12859-014-0442-7.
- . „Evolution of enzyme specificity in the alkaline phosphatase superfamily.“ contributed to the SMBE, Vienna, Austria, . [accepted / in Press (not yet published)]
- . „The Origins of Life's Molecular Diversity: Does Modularity Epitomize the Evolvability of Early Functional Units .“ contributed to the Volkswagen Stiftung Kick-off Conference: Life? - A New Funding Initiative Introduces Itself, Schloss Herrenhausen, Hannover, Germany, . [accepted / in Press (not yet published)]
- . „Functional Transitions in Enzyme Evolution: Balancing Stability, Folding and Catalytic Specificity.“ contributed to the The annual meeting of the Society for Molecular Biology and Evolution, Hofburg Palace, Vienna, Austria, . [accepted / in Press (not yet published)]
- contributed to the Society of Molecular Biology and Evolution, Wien, . „Detecting convergent molecular evolution in eusocial insects.“
- . . ‘Specific gene expression responses to parasite genotypes reveal redundancy of innate immunity in vertebrates.’ PloS one 9, Nr. 9. doi: 10.1371/journal.pone.0108001.
- . . ‘The genome of Eucalyptus grandis.’ Nature 510, Nr. 7505: 362. doi: 10.1038/nature13308.
- . . ‘Rapid similarity search of proteins using alignments of domain arrangements.’ Bioinformatics 30, Nr. 2: 281. doi: 10.1093/bioinformatics/btt379.
- . . ‘Protein family analysis at the domain-level.’ Lecture Notes in Informatics (LNI), Proceedings - Series of the Gesellschaft fur Informatik (GI) P-235: 26.
- . . ‘Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types.’ Marine Genomics 15: 73. doi: 10.1016/j.margen.2014.03.004.
- . . ‘DoMosaics: Software for domain arrangement visualization and domain-centric analysis of proteins.’ Bioinformatics 30, Nr. 2: 283. doi: 10.1093/bioinformatics/btt640.
- . . ‘Extensive Copy-Number Variation of Young Genes across Stickleback Populations.’ PLoS Genetics 10, Nr. 12. doi: 10.1371/journal.pgen.1004830.
- . . ‘Genomic divergence between nine- and three -spined sticklebacks .’ BMC Genomics 14.
- . . ‘Molecular traces of alternative social organization in a termite genome .’ Nature Communications 5.
- . . ‘Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis.’ BMC Genomics 16, Nr. 1: 445.
- . . ‘Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes.’ Genome Biology and Evolution 5, Nr. 2: 439–455. doi: 10.1093/gbe/evt009.
- . . ‘Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.’ Genome Research 23, Nr. 8: 1247. doi: 10.1101/gr.155408.113.
- . . ‘Dynamics and adaptive benefits of modular protein evolution.’ Current Opinion in Structural Biology 23, Nr. 3: 459. doi: 10.1016/j.sbi.2013.02.012.
- . . ‘Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree.’ BBA - Biochimica et Biophysica Acta 1834, Nr. 5: 898–907. doi: 10.1016/j.bbapap.2013.01.007.
- . . ‘Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks.’ Molecular Ecology 22, Nr. 3: 649. doi: 10.1111/j.1365-294X.2012.05680.x.
- 10.1016/j.bbapap.2013.01.007. . ‘Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree.’ Biochimica et Biophysica Acta - Proteins and Proteomics 1834, Nr. 5: 898–907. doi:
- 10.1186/1471-2164-14-756. . ‘Genomic divergence between nine- and three-spined sticklebacks.’ BMC Genomics 14, Nr. 1. doi:
- . . ‘Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.’ PloS one 7, Nr. 2: e31410. doi: 10.1371/journal.pone.0031410.
- . . ‘Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution.’ Genome Biology and Evolution 4, Nr. 3: 316. doi: 10.1093/gbe/evs004.
- . . ‘Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts.’ PLoS Computational Biology 8, Nr. 9: e1002659. doi: 10.1371/journal.pcbi.1002659.
- . . ‘Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness.’ Proceedings of the National Academy of Sciences of the United States of America (PNAS) 109, Nr. 37. doi: 10.1073/pnas.1115620109.
- . . ‘The interface of protein structure, protein biophysics, and molecular evolution.’ Protein Science 21, Nr. 6: 769. doi: 10.1002/pro.2071.
- . . ‘Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera.’ Current biology 22, Nr. 14: 1309–13. doi: 10.1016/j.cub.2012.05.018.
- . . ‘Identifying core features of adaptive metabolic mechanisms for chronic heat stress attenuation contributing to systems robustness.’ Integrative Biology 4, Nr. 5: 480. doi: 10.1039/c2ib00109h.
- . . ‘Proteome of Hydra nematocyst.’ Journal of Biological Chemistry 287, Nr. 13: 9672. doi: 10.1074/jbc.M111.328203.
- 10.1093/molbev/msr250. . ‘The dynamics and evolutionary potential of domain loss and emergence.’ Molecular Biology and Evolution 29, Nr. 2: 787–796. doi:
- . . ‘Evolutionary dynamics of simple sequence repeats across long evolutionary time in genus Drosphila.’ Trends in Evolutionary Biology 4, Nr. 1.
- . . ‘Fast Homology Search Using Domain-Architecture Alignment.’ JOBIM, Conference proceedings 1.
- . . ‘The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.’ PLoS Genetics 7, Nr. 2: e1002007. doi: 10.1371/journal.pgen.1002007.
- . . ‘Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life.’ BMC Evolutionary Biology 11: 8. doi: 10.1186/1471-2148-11-8.
- . . ‘The evolution of protein interaction networks.’ Methods in Molecular Biology 696: 273. doi: 10.1007/978-1-60761-987-1_17.
- . . ‘Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species.’ Proceedings of the National Academy of Sciences of the United States of America (PNAS) 108, Nr. 48: –81. doi: 10.1073/pnas.1107680108.
- . . ‘Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing.’ BMC Genomics 12, Nr. 1: 227. doi: 10.1186/1471-2164-12-227.
- . . ‘Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.’ Nucleic Acids Research . doi: 10.1093/nar/gkr179.
- . . ‘The sieve element occlusion gene family in dicotyledonous plants.’ Plant Signaling and Behavior 6, Nr. 1: 151. doi: 10.4161/psb.6.1.14308.
- . . ‘Signals: tinkering with domains.’ Science Signaling 3, Nr. 139: pe31. doi: 10.1126/scisignal.3139pe31.
- . . ‘Functional and evolutionary insights from the genomes of three parasitoid nasonia species.’ Science 327, Nr. 5963: 343–348. doi: 10.1126/science.1178028.
- . . ‘Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants.’ BMC Plant Biology 10. doi: 10.1186/1471-2229-10-219.
- . . ‘Protein Domains as Evolutionary Units.’ In Evolutionary Genomics and System Biology, edited by , 213–230. unbekannt / n.a. / unknown. doi: 10.1002/9780470570418.ch12.
- . . ‘How do new proteins arise?’ Current Opinion in Structural Biology 20, Nr. 3: 390. doi: 10.1016/j.sbi.2010.02.005.
- . . ‘Robustness versus evolvability: a paradigm revisited.’ HFSP Journal 4, Nr. 3-4: 105. doi: 10.2976/1.3404403.
- . . ‘Evolvability and single-genotype fluctuation in phenotypic properties: a simple heteropolymer model.’ Biophysical Journal 98, Nr. 11: 2487. doi: 10.1016/j.bpj.2010.02.046.
- 10.1016/j.bpj.2010.02.046. . ‘EvoIvability and single-genotype fluctuation in phenotypic properties: A simple heteropolymer model.’ Biophysical Journal 98, Nr. 11: 2487–2496. doi:
- . . ‘Evolution after and before gene duplication?’ In Evolution after Gene Duplication, edited by , e. Hoboken, NJ, USA: John Wiley & Sons. doi: 10.1002/9780470619902.ch6.
- . . ‘Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs.’ Database: The Journal of Biological Databases and Curation 2009: bap009. doi: 10.1093/database/bap009.
- . . ‘Just how versatile are domains?’ BMC Evolutionary Biology 8: 285. doi: 10.1186/1471-2148-8-285.
- . . ‘Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans.’ Immunobiology 213, Nr. 3-4: 237. doi: 10.1016/j.imbio.2007.12.004.
- . . ‘The look-ahead effect of phenotypic mutations.’ Biology Direct 3: 18. doi: 10.1186/1745-6150-3-18.
- . . ‘Arrangements in the modular evolution of proteins.’ Trends in Biochemical Sciences 33, Nr. 9: 444. doi: 10.1016/j.tibs.2008.05.008.
- . . ‘Comparative analysis of expressed sequence tag (EST) libraries in the seagrass Zostera marina subjected to temperature stress.’ Marine Biotechnology 10, Nr. 3: 297–309. doi: 10.1007/s10126-007-9065-6.
- . . ‘The Crohn's disease susceptibility gene DLG5 as a member of the CARD interaction network.’ Journal of Molecular Medicine 86, Nr. 4: 423––432. doi: 10.1007/s00109-008-0307-5.
- 10.1007/s00792-008-0138-x. . ‘Metabolism of halophilic archaea.’ Extremophiles 12, Nr. 2: 177–196. doi:
- . . ‘A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network.’ BMC Systems Biology 1: 34. doi: 10.1186/1752-0509-1-34.
- . . ‘Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN).’ Bioinformatics 23, Nr. 14: 1834. doi: 10.1093/bioinformatics/btm240.
- . . ‘The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses.’ The Plant journal 50, Nr. 2: 347. doi: 10.1111/j.1365-313X.2007.03052.x.
- . . ‘Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins.’ Molecular Biology and Evolution 24, Nr. 3: 670. doi: 10.1093/molbev/msl197.
- . . ‘One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity.’ Molecular Biology and Evolution 24, Nr. 3: 827. doi: 10.1093/molbev/msl211.
- . . ‘A structural model of latent evolutionary potentials underlying neutral networks in proteins.’ HFSP J. 1: 79–87.
- . . ‘Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network.’ BMC Genomics 7: 107. doi: 10.1186/1471-2164-7-107.
- . . ‘Domain deletions and substitutions in the modular protein evolution.’ The FEBS Journal 273, Nr. 9: 2037. doi: 10.1111/j.1742-4658.2006.05220.x.
- . . ‘Evolution of circular permutations in multidomain proteins.’ Molecular Biology and Evolution 23, Nr. 4: 734. doi: 10.1093/molbev/msj091.
- . . ‘Finding common protein interaction patterns across organisms.’ Evolutionary Bioinformatics 2: 45–52.
- . . Transcriptional networking. 6. Aufl. . doi: 10.1186/gb-2005-6-9-344.
- . . ‘Distribution of gibberellin biosynthetic genes and gibberellin production in the Gibberella fujikuroi species complex.’ Phytochemistry 66, Nr. 11: 1296–1311. doi: 10.1016/j.phytochem.2005.04.012.
- . . ‘Rapid motif-based prediction of circular permutations in multi-domain proteins.’ Bioinformatics 21, Nr. 7: 932. doi: 10.1093/bioinformatics/bti085.
- . . ‘Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs.’ Gene 347, Nr. 2: 247–253. doi: 10.1016/j.gene.2004.12.031.
- . . ‘The evolution of domain arrangements in proteins and interaction networks.’ Cellular and Molecular Life Sciences 62, Nr. 4: 435. doi: 10.1007/s00018-004-4416-1.
- . . ‘Comparing folding codes in simple heteropolymer models of protein evolutionary landscape: robustness of the superfunnel paradigm.’ Biophysical Journal 88, Nr. 1: 118–131. doi: 10.1529/biophysj.104.050369.
- . . ‘The evolution of protein interaction networks in regulatory proteins.’ Comparative and Functional Genomics 5, Nr. 1: 79–84. doi: 10.1002/cfg.365.
- . . ‘Convergent evolution of gene networks by single-gene duplications in higher eukaryotes.’ EMBO Reports 5, Nr. 3: 274. doi: 10.1038/sj.embor.7400096.
- . . ‘CADRE: the Central Aspergillus Data REpository.’ Nucleic Acids Research 32, Nr. Database issue: –5. doi: 10.1093/nar/gkh009.
- . ‘Inference of Aspergillus fumigatus pathways by computational genome analysis: Tricarboxylic acic cycle (TCA) and glyoxylate shunt.’ Journal of microbiology and biotechnology 14, Nr. 1: 74–80.
- . . A putative transcription factor inducing mobility in Mycoplasma pneumoniae..
- . . ‘BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.’ Bioinformatics 18 Suppl 2: –30. doi: 10.1093/bioinformatics/18.suppl_2.S219.
- . . ‘Perspectives on protein evolution from simple exact models.’ Applied Bioinformatics 1, Nr. 3: 121.
- . . ‘Conceptual data modelling for bioinformatics.’ Briefings in Bioinformatics 3, Nr. 2: 166. doi: 10.1093/bib/3.2.166.
- . . ‘TreeWiz: interactive exploration of huge trees.’ Bioinformatics 18, Nr. 1: 109. doi: 10.1093/bioinformatics/18.1.109.
- . . ‘Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes.’ Proc. Natl. Acad. Sci. 99: 809–814. doi: 10.1073/pnas.022240299.
- . . ‘Switching from simple to complex oscillations in calcium signaling.’ Biophysical Journal 79, Nr. 3: 1188. doi: 10.1016/S0006-3495(00)76373-9.
- . . ‘Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space.’ Proceedings of the National Academy of Sciences of the United States of America (PNAS) 96, Nr. 19: 10689. doi: 10.1073/pnas.96.19.10689.
- . . ‘Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets.’ Bioinformatics 15, Nr. 3: 234. doi: 10.1093/bioinformatics/15.3.234.
- . . ‘WWW access to the SYSTERS protein sequence cluster set.’ Bioinformatics 15, Nr. 3: 262. doi: 10.1093/bioinformatics/15.3.262.
- . . ‘Computational approaches to identify leucine zippers.’ Nucleic Acids Res. 26, Nr. 11: 2740–2746. doi: 10.1093/nar/26.11.2740.
- . . ‘Exploring the fitness landscapes of lattice proteins.’ Pacific Symposium on Biocomputing : 361.
- . . ‘How are model protein structures distributed in sequence space?’ Biophysical Journal 73, Nr. 5: 2393. doi: 10.1016/S0006-3495(97)78268-7.
- . . ‘Structure formation of biopolymers is complex, their evolution may be simple.’ Pacific Symposium on Biocomputing : 97–108.
- . . ‘RNA folding and combinatory landscapes.’ Physical Review E - Statistical, nonlinear, and soft matter physics 47, Nr. 3: 2083–2099.
Betreute Arbeiten
Promotionen
Ghalawinji, Amer (MHD) Contribution of non-coding RNAs to the pathogenesis of cardiovascular diseases Wami, Haleluya Tesfaye Genomische und evolutionäre Untersuchung des Sekundärmetaboliten Colibactin in Enterobacteriaceae Gandhi, Shrey IncRNAs as a novel epigenetic layer in the genetic predisposition to heart failure López Ezquerra, Alberto Analysis of non-coding RNA sequence, structure and function using comparative transcriptomics and biophysics approaches Martens, Leonie Chiara Investigation of non-coding RNA in the cardiovascular system Eenink, Bernard Derk Gertjan Ancestral reconstruction and experimental test of long- and short term evolvability using the AP-superfamily as a model system Heames, Brennen Reconstructing de novo gene emergence Wiechers, Sarah Entwicklung von Softwarekomponenten für und Analyse von DNA Barcoding Daten der deutschen Flora Kurafeiski, Jasmin Epistasis, robustness and evolvability in biomolecules Dowling, Daniel Benefits and hazards of novel protein coding genes Glumm, Sarah The role of the NMDA receptor subunit 2B (NR2B) in the regulation of autoimmune neuroinflammation Kleppe, April Snofrid Cryptic Mutations in Protein Evolution Schmitz, Jonathan Properties in de novo genes in vertebrates Klasberg, Steffen Modular protein evolution in insects: On the emergence of novel domains and domain arrangements Jąkalski, Marcin Next-generation sequencing-based genome and transcriptome studies of unicellular Apicomplexa and Kinetoplastida parasites Heberlein, Magdalena Evolution of Substrate Specificity in the Alkaline Phosphatase Superfamily Schüler, Andreas Evolution of Protein Domain Repeats in Metazoa Mona Riemenschneider On the evolution of modularity in gene regulatory networks affecting complex traits / diseases Milutinovic, Barbara Coevolution between the red flour beetle and Bacillus thuringiensis bacteria Poos, Kathrin The pathogenesis of Osteosarcoma - systems biological approaches to explain cancer development and progression Hiersche, Milan Multifaktorielle Assoziationsmuster con SNP/CNV Daten zu kardiovaskulären Phänotypen Dröge, Jasmin Sybille Phyletic distribution and evolution of ancient globin genes Wissler, Lothar Computational Analysis of Genome Evolution in Holmetabolous Insects (Endopterygota) Franssen, Susanne RNA-seq in non-model organisms: Microevolutionary and ecological insights from gene expression of seagrasses under global warming Sikosek, Tobias The resolution of adaptive conflicts in protein evolution through shifts in thermodynamic stability and gene duplication Kersting, Anna Conserved Motifs in Plant Genome Evolution Preuss, Christoph On the evolution of complex genetic diseases Moore, Andrew Mechanisms of Modular Protein Evolution Specht, Michael Novel strategies for high-throughput data analysis in computational proteomics and proteogenesis Rüping, Boris Characterization of the "sieve element occlusion" gene family with special emphasis on gene expression Friedrichs, Frauke Epidemiological, statistical and molecular biology approaches to assess the role of inflammatory genes in the pathogenesis of complex diseases Veron, Amélie Adaptive Evolution of Networks Spitzer, Michael Automating the Analysis of Protein Family Evolution Habilitation
Weiner, January Domain-wise evolution of proteins