Professor Dr. Erich Bornberg-Bauer

Professor Dr. Erich Bornberg-Bauer

Hüfferstr. 1, Raum 100.16
48149 Münster

T: +49 251 83-21630
F: +49 251 83-24668

  • 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

    • Aubel, Margaux; Eicholt, Lars; Bornberg-Bauer, Erich. . ‘Assessing structure and disorder prediction tools for de novo emerged proteins in the age of machine learning .’ F1000Research eCollection 2023. doi: 10.12688/f1000research.130443.1.
    • Makova, Kateryna D.; Pickett, Brandon D.; Harris, Robert S.; Hartley, Gabrielle A.; Cechova, Monika; Pal, Karol; Nurk, Sergey; Yoo, Dongahn; Li, Qiuhui; Hebbar, Prajna; McGrath, Barbara C.; Antonacci, Francesca; Aubel, Margaux; Biddanda, Arjun; Borchers, Matthew; Bornberg-Bauer, Erich; Bouffard, Gerard G.; Brooks, Shelise Y.; Carbone, Lucia; Carrel, Laura; Carroll, Andrew; Chang, Pi-Chuan; Chin, Chen-Shan; Cook, Daniel E.; Craig, Sarah J. C.; de Gennaro, Luciana; Diekhans, Mark; Dutra, Amalia; Garcia, Gage H.; Grady, Patrick G. S.; Green, Richard E.; Haddad, Diana; Hallast, Pille; Harvey, William T.; Hickey, Glenn; Hillis, David A.; Hoyt, Savannah J.; Jeong, Hyeonsoo; Kamali, Kaivan; Pond, Sergei L. Kosakovsky; Lapolice, Troy M.; Lee, Charles; Lewis, Alexandra P.; Loh, Yong-Hwee E.; Masterson, Patrick; Mcgarvey, Kelly M.; Mccoy, Rajiv C.; Medvedev, Paul; Miga, Karen H.; Munson, Katherine M.; Pak, Evgenia; Paten, Benedict; Pinto, Brendan J.; Potapova, Tamara; Rhie, Arang; Rocha, Joana L.; Ryabov, Fedor; Ryder, Oliver A.; Sacco, Samuel; Shafin, Kishwar; Shepelev, Valery A.; Slon, Viviane; Solar, Steven J.; Storer, Jessica M.; Sudmant, Peter H.; Sweeten, Alex; Tassia, Michael G.; Thibaud-Nissen, Francoise; Ventura, Mario; Wilson, Melissa A.; Young, Alice C.; Zeng, Huiqing; Zhang, Xinru; Szpiech, Zachary A.; Huber, Christian D.; Gerton, Jennifer L.; Yi, Soojin V.; Schatz, Michael C.; Alexandrov, Ivan A.; Koren, Sergey; O'Neill, Rachel J.; Eichler, Evan E.; Phillippy, Adam M. . ‘The complete sequence and comparative analysis of ape sex chromosomes.’ Nature 630, Nr. 8015. doi: 10.1038/s41586-024-07473-2.
    • Lebherz, Marie Kristin; Fouks, Bertrand; Schmidt, Julian; Bornberg-Bauer, Erich; Grandchamp, Anna. . ‘DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs.’ Genome Biology and Evolution 16, Nr. 7. doi: 10.1093/gbe/evae134.
    • Iyengar, Bharat Ravi; Grandchamp, Anna; Bornberg-Bauer, Erich. . ‘How antisense transcripts can evolve to encode novel proteins.’ Nature Communications 15, Nr. 1. doi: 10.1038/s41467-024-50550-3.
    • Lebherz, Marie Kristin; Iyengar, Bharat Ravi; Bornberg-Bauer, Erich. . ‘Modeling Length Changes in De Novo Open Reading Frames during Neutral Evolution.’ Genome Biology and Evolution 16, Nr. 7. doi: 10.1093/gbe/evae129.
    • Grandchamp, Anna; Czuppon, Peter; Bornberg-Bauer, Erich. . ‘Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster.’ Nucleic Acids Research 52, Nr. 1. doi: 10.1093/nar/gkad1079.
    • Buchel, Filip; Heames, Brennen; Jones, Alun; Honc, Ondrej; Bornberg-Bauer, Erich; Houchova, Klara. . ‘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.
    • Heames, Brennen; Buchel, Filip; Aubel, Margaux; Tretyachenko, Vyacheslav; Loginov, Dmitry; Novak, Petr; Lange, Andreas; Bornberg-Bauer, Erich; Hlouchova, Klara. . ‘Experimental characterization of de novo proteins and their unevolved random-sequence counterparts.’ Nature Ecology and Evolution 7, Nr. 4. doi: 10.1038/s41559-023-02010-2.
    • Aubel, Margaux; Bornberg-Bauer, Erich. . ‘Introducing creative destruction as a mechanism in protein evolution.’ Proceedings of the National Academy of Sciences of the United States of America 120, Nr. 6. doi: 10.1073/pnas.2220460120.
    • Grandchamp Anna , Kühl Lucas , Lebherz Marie , Brüggemann Kathrin , Parsch John , Bornberg-Bauer Erich. . ‘Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster.’ Genome Research 33. doi: 10.1101/gr.277482.122.
    • Fouks, Bertrand; Harrison, Mark C.; Mikhailova, Alina A.; Marchal, Elisabeth; English, Sinead; Carruthers, Madeleine; Jennings, Emily C.; Chiamaka, Ezemuoka L.; Frigard, Ronja A.; Pippel, Martin; Attardo, Geoffrey M.; Benoit, Joshua B.; Bornberg-Bauer, Erich; Tobe, Stephen S. . ‘Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond.’ iScience 26, Nr. 10. doi: 10.1016/j.isci.2023.107832.
    • Thorburn, Doko-Miles J.; Sagonas, Kostas; Binzer-Panchal, Mahesh; Chain, Frederic J. J.; Feulner, Philine G. D.; Bornberg-Bauer, Erich; Reusch, Thorsten B. H.; Samonte-Padilla, Irene E.; Milinski, Manfred; Lenz, Tobias L.; Eizaguirre, Christophe. . ‘Origin matters: Using a local reference genome improves measures in population genomics.’ Molecular Ecology Resources 23, Nr. 7. doi: 10.1111/1755-0998.13838.
    • Iyengar, Bharat Ravi; Bornberg-Bauer, Erich. . ‘Neutral Models of De Novo Gene Emergence Suggest that Gene Evolution has a Preferred Trajectory.’ Molecular Biology and Evolution 40, Nr. 4. doi: 10.1093/molbev/msad079.
    • Eenink, Bernard D. G.; Kaminski, Tomasz S.; Bornberg-Bauer, Erich; Jose, Joachim; Hollfelder, Florian; van Loo, Bert. . ‘Vector Redesign and In-Droplet Cell-Growth Improves Enrichment and Recovery in live Escherichia coli.’ Microbial Biotechnology 15, Nr. 11. doi: 10.1111/1751-7915.14144.
    • Eicholt, Lars A.; Aubel, Margaux; Berk, Katrin; Bornberg-Bauer, Erich; Lange, Andreas. . ‘Heterologous expression of naturally evolved putative de novo proteins with chaperones.’ Protein Science 31, Nr. 8. doi: 10.1002/pro.4371.
    • Post, Frederik; Bornberg-Bauer, Erich; Vasseur-Cognet, Mireille; Harrison, Mark C. . ‘More effective transposon regulation in fertile, long-lived termite queens than in sterile workers.’ Molecular Ecology 32, Nr. 2. doi: 10.1111/mec.16753.
    • Berger, Juliette; Legendre, Frederic; Zelosko, Kevin-Markus; Harrison, Mark C.; Grandcolas, Philippe; Bornberg-Bauer, Erich; Fouks, Bertrand. . ‘Eusocial Transition in Blattodea: Transposable Elements and Shifts of Gene Expression.’ Genes 13, Nr. 11. doi: 10.3390/genes13111948.
    • Feldmeyer, Barbara; Gstoettl, Claudia; Wallner, Jennifer; Jongepier, Evelien; Seguret, Alice; Grasso, Donato A.; Bornberg-Bauer, Erich; Foitzik, Susanne; Heinze, Jurgen. . ‘Evidence for a conserved queen-worker genetic toolkit across slave-making ants and their ant hosts.’ Molecular Ecology 31, Nr. 19. doi: 10.1111/mec.16639.
    • Seite, Sarah; Harrison, Mark C.; Sillam-Dusses, David; Lupoli, Roland; van Dooren, Tom J. M.; Robert, Alain; Poissonnier, Laure-Anne; Lemainque, Arnaud; Renault, David; Acket, Sebastien; Andrieu, Muriel; Viscarra, Jose; Sul, Hei Sook; de Beer, Z. Wilhelm; Bornberg-Bauer, Erich; Vasseur-Cognet, Mireille. . ‘Lifespan prolonging mechanisms and insulin upregulation without fat accumulation in long-lived reproductives of a higher termite.’ Communications biology 5, Nr. 44. doi: 10.1038/s42003-021-02974-6.
    • Coban, Abdulbaki; Bornberg-Bauer, Erich; Kemena, Carsten. . ‘Domain Evolution of Vertebrate Blood Coagulation Cascade Proteins.’ Journal of Molecular Evolution 90: 418–428. doi: 10.1007/s00239-022-10071-3.
    • Buchholz, Patrick C. F.; van Loo, Bert; Eenink, Bernard D. G.; Bornberg-Bauer, Erich; Pleiss, Juergen. . ‘Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation.’ Interface 18, Nr. 184. doi: 10.1098/rsif.2021.0389.
    • Rivard, Emily L.; Ludwig, Andrew G.; Patel, Prajal H.; Grandchamp, Anna; Arnold, Sarah E.; Berger, Alina; Scott, Emilie M.; Kelly, Brendan J.; Mascha, Grace C.; Bornberg-Bauer, Erich; Findlay, Geoffrey D. . ‘A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster.’ PLOS GENETICS 17, Nr. 9. doi: 10.1371/journal.pgen.1009787.
    • Jongepier, Evelien; Seguret, Alice; Labutin, Anton; Feldmeyer, Barbara; Gstoettl, Claudia; Foitzik, Susanne; Heinze, Juergen; Bornberg-Bauer, Erich. . ‘Convergent Loss of Chemoreceptors across Independent Origins of Slave-Making in Ants.’ Molecular Biology and Evolution 39, Nr. 1. doi: 10.1093/molbev/msab305.
    • Harrison, Mark C.; Nino, Luisa M. Jaimes; Rodrigues, Marisa Almeida; Ryll, Judith; Flatt, Thomas; Oettler, Jan; Bornberg-Bauer, Erich. . ‘Gene Coexpression Network Reveals Highly Conserved, Well-Regulated Anti-Ageing Mechanisms in Old Ant Queens.’ Genome Biology and Evolution 13, Nr. 6. doi: 10.1093/gbe/evab093.
    • Lange, Andreas; Patel, Prajal H.; Heames, Brennen; Damry, Adam M.; Saenger, Thorsten; Jackson, Colin J.; Findlay, Geoffrey D.; Bornberg-Bauer, Erich. . ‘Structural and functional characterization of a putative de novo gene in Drosophila.’ Nature Communications 12, Nr. 1. doi: 10.1038/s41467-021-21667-6.
    • Bornberg-Bauer, Erich; Hlouchova, Klara; Lange, Andreas. . ‘Structure and function of naturally evolved de novo proteins.’ Current Opinion in Structural Biology 68. doi: 10.1016/j.sbi.2020.11.010.
    • Martens L, Rühle F, Witten A, Meder B, Katus HA, Arbustini E, Hasenfuß G, Sinner MF, Kääb S, Pankuweit S, Angermann C, Bornberg-Bauer E, Stoll M. . ‘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.
    • Yang G, Anderson DW, Baier F, Dohmen E, Hong N, Carr PD, Kamerlin SCL, Jackson CJ, Bornberg-Bauer E, Tokuriki N. . ‘Author Correction: Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme.’ Nature Chemical Biology 16: 930. doi: 10.1038/s41589-020-0588-8.
    • Dohmen E, Klasberg S, Bornberg-Bauer E, Perrey S, Kemena C. . ‘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.
    • Thomas, Gregg W. C.; Dohmen, Elias; Hughes, Daniel S. T.; Murali, Shwetha C.; Poelchau, Monica; Glastad, Karl; Anstead, Clare A.; Ayoub, Nadia A.; Batterham, Phillip; Bellair, Michelle; Binford, Gretta J.; Chao, Hsu; Chen, Yolanda H.; Childers, Christopher; Dinh, Huyen; Doddapaneni, HarshaVardhan; Duan, Jian J.; Dugan, Shannon; Esposito, Lauren A.; Friedrich, Markus; Garb, Jessica; Gasser, Robin B.; Goodisman, Michael A. D.; Gundersen-Rindal, Dawn E.; Han, Yi; Handler, Alfred M.; Hatakeyama, Masatsugu; Hering, Lars; Hunter, Wayne B.; Ioannidis, Panagiotis; Jayaseelan, Joy C.; Kalra, Divya; Khila, Abderrahman; Korhonen, Pasi K.; Lee, Carol Eunmi; Lee, Sandra L.; Li, Yiyuan; Lindsey, Amelia R. I.; Mayer, Georg; McGregor, Alistair P.; McKenna, Duane D.; Misof, Bernhard; Munidasa, Mala; Munoz-Torres, Monica; Muzny, Donna M.; Niehuis, Oliver; Osuji-Lacy, Nkechinyere; Palli, Subba R.; Panfilio, Kristen A.; Pechmann, Matthias; Perry, Trent; Peters, Ralph S.; Poynton, Helen C.; Prpic, Nikola-Michael; Qu, Jiaxin; Rotenberg, Dorith; Schal, Coby; Schoville, Sean D.; Scully, Erin D.; Skinner, Evette; Sloan, Daniel B.; Stouthamer, Richard; Strand, Michael R.; Szucsich, Nikolaus U.; Wijeratne, Asela; Young, Neil D.; Zattara, Eduardo E.; Benoit, Joshua B.; Zdobnov, Evgeny M.; Pfrender, Michael E.; Hackett, Kevin J.; Werren, John H.; Worley, Kim C.; Gibbs, Richard A.; Chipman, Ariel D.; Waterhouse, Robert M.; Bornberg-Bauer, Erich; Hahn, Matthew W.; Richards, Stephen. . ‘Gene content evolution in the arthropods.’ Genome Biology 21, Nr. 15. doi: 10.1186/s13059-019-1925-7.
    • Dowling, Daniel; Schmitz, Jonathan F.; Bornberg-Bauer, Erich. . ‘Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage.’ Genome Biology and Evolution 12, Nr. 11. doi: 10.1093/gbe/evaa194.
    • Gstoettl, Claudia; Stoldt, Marah; Jongepier, Evelien; Bornberg-Bauer, Erich; Feldmeyer, Barbara; Heinze, Juergen; Foitzik, Susanne. . ‘Comparative analyses of caste, sex, and developmental stage-specific transcriptomes in two Temnothorax ants.’ Ecology and Evolution 10, Nr. 10. doi: 10.1002/ece3.6187.
    • Bornberg-Bauer E, Heames B. . ‘Becoming a de novo gene.’ Nature Ecology and Evolution 3, Nr. 4: 524–525. doi: 10.1038.
    • Kaur R, Stoldt M, Jongepier E, Feldmeyer B, Menzel F, Bornberg-Bauer E, Foitzik S. . ‘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.
    • Huang Y, Feulner PGD, Eizaguirre C, Lenz TL, Bornberg-Bauer E, Milinski M, Reusch TBH, Chain FJJ. . ‘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.
    • Kemena C, Bornberg-Bauer E. . ‘A Roadmap to Domain Based Proteomics.’ In Computational Methods in Protein Evolution, edited by Sikosek, Tobias, 287–300. doi: 10.1007/978-1-4939-8736-8_16.
    • Kemena C, Dohmen E, Bornberg-Bauer E. . ‘DOGMA: a web server for proteome and transcriptome quality assessment.’ Nucleic Acids Research 47, Nr. W1. doi: 10.1093/nar/gkz366.
    • Yang G, Anderson DW, Baier F, Dohmen E, Hong N, Carr PD, Kamerlin SCL, Jackson CJ, Bornberg-Bauer E, Tokuriki N. . ‘Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme.’ Nature Chemical Biology 15: 1120–1128. doi: 10.1038/s41589-019-0386-3.
    • Yang, Gloria; Anderson, Dave W.; Baier, Florian; Dohmen, Elias; Hong, Nansook; Carr, Paul D.; Kamerlin, Shina Caroline Lynn; Jackson, Colin J.; Bornberg-Bauer, Erich; Tokuriki, Nobuhiko. . ‘Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme (vol 51, pg 831, 2020).’ Nature Chemical Biology 16, Nr. 8. doi: 10.1038/s41589-020-0588-8.
    • Bornberg-Bauer, Erich; Harrison, Mark C.; Jongepier, Evelien. . ‘The first cockroach genome and its significance for understanding development and the evolution of insect eusociality.’ Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330, Nr. 5. doi: 10.1002/jez.b.22826.
    • Klasberg S, Bitard-Feildel T, Callebaut I, Bornberg-Bauer E. . ‘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.
    • Harrison MC, Jongepier E, Robertson HM, Arning N, Bitard-Feildel T, Chao H, Childers CP, Dinh H, Doddapaneni H, Dugan S, Gowin J, Greiner C, Han Y, Hu H, Hughes DST, Huylmans A, Kemena C, Kremer LPM, Lee SL, Lopez-Ezquerra A, Mallet L, Monroy-Kuhn JM, Moser A, Murali SC, Muzny DM, Otani S, Piulachs M, Poelchau M, Qu J, Schaub F, Wada-Katsumata A, Worley KC, Xie Q, Ylla G, Poulsen M, Gibbs RA, Schal C, Richards S, Belles X, Korb J, Bornberg-Bauer E. . ‘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.
    • Kurafeiski JD, Pinto P, Bornberg-Bauer E. . ‘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.
    • Jongepier E, Kemena C, Lopez-Ezquerra A, Belles X, Bornberg-Bauer E, Korb J. . ‘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.
    • Harrison MC, Arning N, Kremer LPM, Ylla G, Belles X, Bornberg-Bauer E, Huylmans AK, Jongepier E, Piulachs MD, Richards S, Schal C. . ‘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.
    • Lopez-Ezquerra, Alberto; Mitschke, Andreas; Bornberg-Bauer, Erich; Joop, Gerrit. . ‘Tribolium castaneum gene expression changes after Paranosema whitei infection.’ Journal of Invertebrate Pathology 153. doi: 10.1016/j.jip.2018.02.009.
    • Gubala A., Schmitz J., Kearns M., Vinh T., Bornberg-Bauer E., Wolfner M., Findlay G. . ‘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: 10.1093/molbev/msx057.
    • Bornberg-Bauer E., Schmitz J. . ‘Fact or fiction: Updates on how protein-coding genes might emerge de novo from previously non-coding DNA.’ F1000Research 6, Nr. null. doi: 10.12688/f1000research.10079.1.
    • Lopez-Ezquerra A., Harrison M., Bornberg-Bauer E. . ‘Comparative analysis of lincRNA in insect species.’ BMC Evolutionary Biology 17, Nr. 1. doi: 10.1186/s12862-017-0985-0.
    • van Loo B and Bornberg-Bauer E. . ‘Enzyme sub-functionalization driven by regulation.’ EMBO Reports 18: 1043–1045. doi: 10.15252/embr.201744383.
    • Olsen JL, Rouzé P, Verhelst B, Lin YC, Bayer T, Collen J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, Töpel M, Tonon T, Vanneste K, Amirebrahimi M, Brakel J, Boström C, Chovatia M, Grimwood J, Jenkins JW, Jueterbock A, Mraz A, Stam WT, Tice H, Bornberg-Bauer E, Green PJ, Pearson GA, Procaccini G, Duarte CM, Schmutz J, Reusch TB, Van de Peer Y. . ‘The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.’ Nature doi: 10.1038/nature16548.
    • Schüler A, Bornberg-Bauer E. . ‘Evolution of Protein Domain Repeats in Metazoa.’ Molecular Biology and Evolution 33. [accepted / in Press (not yet published)]
    • Dohmen E, Kremer L, Bornberg-Bauer E, Kemena C. „DOGMA: Domain-Based Transcriptome and Proteome Quality Assessment.“ contributed to the German Conference on Bioinformatics, Berlin, .
    • Jueterbock A., Franssen S., Bergmann N., Gu J., Coyer J., Reusch T., Bornberg-Bauer E., Olsen J. . ‘Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass.’ Molecular Ecology 25, Nr. 21: 5396–5411. doi: 10.1111/mec.13829.
    • Kemena Carsten, Bitard-Feildel Tristan, Terrapon Nicolas, Moore Andrew, Bornberg-Bauer Erich. „Domain World.“ contributed to the GCB 2016, Berlin, Deutschland, .
    • Schmitz J., Zimmer F., Bornberg-Bauer E. . ‘Mechanisms of transcription factor evolution in Metazoa.’ Nucleic Acids Research 44, Nr. 13: 6287–6297. doi: 10.1093/nar/gkw492.
    • Dohmen E., Kremer L., Bornberg-Bauer E., Kemena C. . ‘DOGMA: Domain-based transcriptome and proteome quality assessment.’ Bioinformatics 32, Nr. 17: 2577–2581. doi: 10.1093/bioinformatics/btw231.
    • Elsner D., Kremer L., Arning N., Bornberg-Bauer E. . ‘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.cois.2016.05.016.
    • Haase D, Rieger JK, Witten A, Stoll M, Bornberg-Bauer E, Kalbe M, Schmidt-Drewello A, Scharsack JP, Reusch TB. . ‘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: 10.1016/j.zool.2016.05.005.
    • Huang Y, Chain FJ, Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E, Reusch TB, Milinski M, Feulner PG. . ‘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.
    • Haase D, Rieger JK, Witten A, Stoll M, Bornberg-Bauer E, Kalbe M, Reusch TB. . ‘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: 10.1016/j.dci.2015.09.008.
    • Bitard-Feildel T, Heberlein M, Bornberg-Bauer E, Callebaut I. . ‘Detection of orphan domains in Drosophila using "hydrophobic cluster analysis".’ Biochimie 119: 244–253. doi: 10.1016/j.biochi.2015.02.019.
    • Kersting AR, Mizrachi E, Bornberg-Bauer E, Myburg AA. . ‘Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.’ New Phytologist 206: 1328–1336. doi: 10.1111/nph.13211.
    • Sadd BM, Barribeau SM, Bloch G, de Graaf DC, Dearden P, Elsik CG, Gadau J, Grimmelikhuijzen CJ, Hasselmann M, Lozier JD, Robertson HM, Smagghe G, Stolle E, Van Vaerenbergh M, Waterhouse RM, Bornberg-Bauer E, Klasberg S, Bennett AK, Câmara F, Guigó R, Hoff K, Mariotti M, Munoz-Torres M, Murphy T, Santesmasses D, Amdam GV, Beckers M, Beye M, Biewer M, Bitondi MM, Blaxter ML, Bourke AF, Brown MJ, Buechel SD, Cameron R, Cappelle K, Carolan JC, Christiaens O, Ciborowski KL, Clarke DF, Colgan TJ, Collins DH, Cridge AG, Dalmay T, Dreier S, du Plessis L, Duncan E, Erler S, Evans J, Falcon T, Flores K, Freitas FC, Fuchikawa T, Gempe T, Hartfelder K, Hauser F, Helbing S, Humann FC, Irvine F, Jermiin LS, Johnson CE, Johnson RM, Jones AK, Kadowaki T, Kidner JH, Koch V, Köhler A, Kraus FB, Lattorff HM, Leask M, Lockett GA, Mallon EB, Antonio DS, Marxer M, Meeus I, Moritz RF, Nair A, Näpflin K, Nissen I, Niu J, Nunes FM, Oakeshott JG, Osborne A, Otte M, Pinheiro DG, Rossié N, Rueppell O, Santos CG, Schmid-Hempel R, Schmitt BD, Schulte C, Simões ZL, Soares MP, Swevers L, Winnebeck EC, Wolschin F, Yu N, Zdobnov EM, Aqrawi PK, Blankenburg KP, Coyle M, Francisco L, Hernandez AG, Holder M, Hudson ME, Jackson L, Jayaseelan J, Joshi V, Kovar C, Lee SL, Mata R, Mathew T, Newsham IF, Ngo R, Okwuonu G, Pham C, Pu LL, Saada N, Santibanez J, Simmons D, Thornton R, Venkat A, Walden KK, Wu YQ, Debyser G, Devreese B, Asher C, Blommaert J, Chipman AD, Chittka L, Fouks B, Liu J, O'Neill MP, Sumner S, Puiu D, Qu J, Salzberg SL, Scherer SE, Muzny DM, Richards S, Robinson GE, Gibbs RA, Schmid-Hempel P, Worley KC. . ‘The genomes of two key bumblebee species with primitive eusocial organization.’ Genome Biol. 16. doi: 10.1186/s13059-015-0623-3.
    • Smith C., Helms Cahan S., Kemena C., Brady S., Yang W., Bornberg-Bauer E., Eriksson T., Gadau J., Helmkampf M., Gotzek D., Okamoto Miyakawa M., Suarez A., Mikheyev A. . ‘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: 10.1093/molbev/msv165.
    • Bitard-Feildel T., Kemena C., Greenwood J., Bornberg-Bauer E. . ‘Domain similarity based orthology detection.’ BMC Bioinformatics 16, Nr. 1. doi: 10.1186/s12859-015-0570-8.
    • Schüler A, Schmitz G, Reft A, Özbek S, Thurm U, Bornberg-Bauer E,. . ‘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.
    • Kemena C, Bitard-Feildel T, Bornberg-Bauer E. . ‘MDAT - Aligning multiple domain arrangements.’ BMC Bioinformatics 16. doi: 10.1186/s12859-014-0442-7.
    • Heberlein M, van Loo B, Hollfelder F, Bornberg-Bauer E. „Evolution of enzyme specificity in the alkaline phosphatase superfamily.“ contributed to the SMBE, Vienna, Austria, . [accepted / in Press (not yet published)]
    • van Loo B, Heberlein M, Bornberg-Bauer E. „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)]
    • van Loo B, Heberlein M, Dohmen E, Hollfelder F, Bornberg-Bauer E. „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)]
    • Greenwood J., Bitard-Feildel T., Kemena C., Terrapon N., Schaub F., Bornberg-Bauer E., Korb J. „Detecting convergent molecular evolution in eusocial insects.“ contributed to the Society of Molecular Biology and Evolution, Wien, .
    • Bitard-Feildel, Tristan; Heberlein, Magdalena; Bornberg-Bauer, Erich; Callebaut, Isabelle. . ‘Detection of orphan domains in Drosophila using "hydrophobic cluster analysis".’ Biochimie 119. doi: 10.1016/j.biochi.2015.02.019.
    • Bornberg-Bauer E, Schmitz J, Heberlein M. . ‘Emergence of de novo proteins from 'dark genomic matter' by 'grow slow and moult'.’ Biochem Soc Trans. 43(5): 867–873. doi: 10.1042/BST20150089.
    • Feulner PG, Chain FJ, Panchal M, Huang Y, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E, Reusch TB, Milinski M. . ‘Genomics of Divergence along a Continuum of Parapatric Population Differentiation.’ PLoS Genetics 2015. doi: 10.1371/journal.pgen.1004966.
    • Masri L, Branca A, Sheppard AE, Papkou A, Laehnemann D, Guenther PS, Prahl S, Saebelfeld M, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels NK, Schulte RD, Kurtz J, Rosenstiel P, Telschow A, Bornberg-Bauer E, Schulenburg H. . ‘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.
    • Behrens, Sarah; Peuss, Robert; Milutinovic, Barbara; Eggert, Hendrik; Esser, Daniela; Rosenstiel, Philip; Schulenburg, Hinrich; Bornberg-Bauer, Erich; Kurtz, Joachim. . ‘Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis.’ BMC Genomics 15. doi: 10.1186/1471-2164-15-445.
    • Guo B, Chain FJ, Bornberg-Bauer E , Leder EH and Merilä J. . ‘Genomic divergence between nine- and three -spined sticklebacks .’ BMC Genomics 14.
    • Terrapon N , Li C, Robertson HM, Ji L, Meng X, Booth W, Chen Z, Childers CP, Glastad KM, Gokhale K, Gowin J, Gronenberg W, Hermansen RA, Hu H, Hunt BG, Huylmans AK, Khalil SMS, Mitchell RD, Munoz-Torres MC, Mustard JA, Pan H, Reese JT, Scharf ME, Sun F, Vogel H, Xiao J, Yang W, Yang Z, Yang Z, Zhou J, Zhu J, Brent CS, Elsik CG, Goodisman MAD, Liberles DA, Roe RM, Vargo EL, Vilcinskas A, Wang J, Bornberg-Bauer E, Korb J, Zhang G, Liebig J. . ‘Molecular traces of alternative social organization in a termite genome .’ Nature Communications 5.
    • Behrens S, Peuß R, Milutinović B, Eggert H, Esser D, Rosenstiel P, Schulenburg H, Bornberg-Bauer E, Kurtz J. . ‘Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis.’ BMC Genomics 16, Nr. 1: 445.
    • Haase, David D., Rieger, Jennifer K. J.K., Witten, Anika A., Stoll, Monika M., Bornberg-Bauer, Erich G. E.G., Kalbe, Martin M., Reusch, Thorsten Bh H T.B.H.,. . ‘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.
    • Myburg, Alexander Andrew A.A., Grattapaglia, Dário D., Tuskan, Gerald A. G.A., Hellsten, Uffe U., Hayes, Richard D. R.D., Grimwood, Jane J., Jenkins, Jerry J. J.J., Lindquist, Erika A. E.A., Tice, Hope N. H.N., Bauer, Diane D., Goodstein, David M. D.M., Dubchak, Inna L. I.L., Poliakov, Alexander V. A.V., Mizrachi, Eshchar E., Kullan, Anand Raj Kumar A.R.K., Hussey, Steven G. S.G., Pinard, Desre D., Van Der Merwe, Karen K., Singh, Pooja P., Van Jaarsveld, Ida I., Silva-Junior, Orzenil Bonfim O.B., Togawa, Robertocoiti R., Pappas, Marilia R. M.R., Faria, Danielle Assis De D.A.D., Sansaloni, Carolina P. C.P., Petroli, César Daniel C.D., Yang, Xiaohan X., Ranjan, Priya P., Tschaplinski, Timothy J. T.J., Ye, Chuyu C., Li, Ting T., Sterck, Lieven L., Vanneste, Kevin K., Murat, Florent F., Soler, Marçal M., Clemente, Hélène San H.S., Saidi, Naijib N., Cassan-Wang, Hua H., Dunand, Christophe C., Hefer, Charles A. C.A., Bornberg-Bauer, Erich G. E.G., Kersting, Anna R. A.R., Vining, Kelly J. K.J., Amarasinghe, Vindhya V., Ranik, Martin M., Naithani, Sushma S., Elser, Justin J., Boyd, Alexander E. A.E., Liston, Aaron A., Spatafora, Joseph W. J.W., Dharmwardhana, Palitha P., Raja, Rajani R., Sullivan, Christopher M. C.M., Romanel, Elisson A C E.A.C., Alves-Ferreira, Márcio M., Külheim, Carsten C., Foley, William J. W.J., Carocha, Víctor J. V.J., Paiva, Jorge Ap Pinto J.A.P., Kudrna, Dave D., Brommonschenkel, Sérgio Hermínio S.H., Pasquali, Giancarlo G., Byrne, Margaret M., Rigault, Philippe P., Tibbits, Josquin F G J.F.G., Spokevicius, Antanas V. A.V., Jones, Rebecca C. R.C., Steane, Dorothy A. D.A., Vaillancourt, René E. R.E., Potts, B. M. B.M., Joubert, Fourie F., Barry, Kerrie W. K.W., Pappas, Georgios Joanis Oannis G.J.O., Strauss, Steven H. S.H., Jaiswal, Pankaj P., Grima-Pettenati, Jacqueline J., Salse, Jérôme J., Van de Peer, Yves Y., Rokhsar, Daniel S. D.S., Schmutz, Jeremy J.,. . ‘The genome of Eucalyptus grandis.’ Nature 510, Nr. 7505: 362. doi: 10.1038/nature13308.
    • Terrapon, Nicolas N., Weiner, January J., Grath, Sonja S., Moore, Andrew D. A.D., Bornberg-Bauer, Erich G. E.G.,. . ‘Rapid similarity search of proteins using alignments of domain arrangements.’ Bioinformatics 30, Nr. 2: 281. doi: 10.1093/bioinformatics/btt379.
    • Terrapon, Nicolas N., Moore, Andrew D. A.D., Bornberg-Bauer, Erich G. E.G.,. . ‘Protein family analysis at the domain-level.’ Lecture Notes in Informatics (LNI), Proceedings - Series of the Gesellschaft fur Informatik (GI) P-235: 26.
    • Franssen, Susanne U. S.U., Gu, Jenny J., Winters, Gidon G., Huylmans, Ann Kathrin A.K., Wienpahl, Isabell I., Sparwel, Maximiliane M., Coyer, James A. J.A., Olsen, Jeanine L. J.L., Reusch, Thorsten Bh H T.B.H., Bornberg-Bauer, Erich G. E.G.,. . ‘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.
    • Moore, Andrew D. A.D., Heldy, Andreas A., Terrapon, Nicolas N., Weiner, January J., Bornberg-Bauer, Erich G. E.G.,. . ‘DoMosaics: Software for domain arrangement visualization and domain-centric analysis of proteins.’ Bioinformatics 30, Nr. 2: 283. doi: 10.1093/bioinformatics/btt640.
    • Chain, Frédéric J J F.J.J., Feulner, Philine G D P.G.D., Panchal, Mahesh M., Eizaguirre, Christophe C., Samonte, Irene E. I.E., Kalbe, Martin M., Lenz, Tobias L. T.L., Stoll, Monika M., Bornberg-Bauer, Erich G. E.G., Milinski, Manfred M., Reusch, Thorsten Bh H T.B.H.,. . ‘Extensive Copy-Number Variation of Young Genes across Stickleback Populations.’ PLoS Genetics 10, Nr. 12. doi: 10.1371/journal.pgen.1004830.
    • Wissler L, Gadau J, Simola DF, Helmkampf M, Bornberg-Bauer E. . ‘Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes.’ Genome Biology and Evolution 5, Nr. 2: 439–455. doi: 10.1093/gbe/evt009.
    • Moore A., Grath S., Schüler A., Huylmans A., Bornberg-Bauer E. . ‘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: 10.1016/j.bbapap.2013.01.007.
    • Simola, D.F., Wissler, L., Donahue, G., Waterhouse, R.M., Helmkampf, M., Roux, J., Nygaard, S., Glastad, K.M., Hagen, D.E., Viljakainen, L., Reese, J.T., Hunt, B.G., Graur, D., Elhaik, E., Kriventseva, E.V., Wen, J., Parker, B.J., Cash, E., Privman, E., Childers, C.P., Munoz-Torres, M.C., Boomsma, J.J., Bornberg-Bauer, E., Currie, C.R., Elsik, C.G., Suen, G., Goodisman, M.A.D., Keller, L., Liebig, J., Rawls, A., Reinberg, D., Smith, C.D., Smith, C.R., Tsutsui, N., Wurm, Y., Zdobnov, E.M., Berger, S.L., Gadau, J.,. . ‘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.
    • Bornberg-Bauer E, Albà MM. . ‘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.
    • Feulner, Philine G D P.G.D., Chain, Frédéric J J F.J.J., Panchal, Mahesh M., Eizaguirre, Christophe C., Kalbe, Martin M., Lenz, Tobias L. T.L., Mundry, Marvin M., Samonte, Irene E. I.E., Stoll, Monika M., Milinski, Manfred M., Reusch, Thorsten Bh H T.B.H., Bornberg-Bauer, Erich G. E.G.,. . ‘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.
    • Mundry M, Bornberg-Bauer E, Sammeth M, Feulner PG. . ‘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.
    • Kersting AR, Bornberg-Bauer E, Moore AD, Grath S. . ‘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.
    • Balasubramanian, Prakash G.; Beckmann, Anna; Warnken, Uwe; Schnoelzer, Martina; Schueler, Andreas; Bornberg-Bauer, Erich; Holstein, Thomas W.; Oezbek, Suat. . ‘Proteome of Hydra Nematocyst.’ Journal of Biological Chemistry 287, Nr. 13. doi: 10.1074/jbc.M111.328203.
    • Moore A.D., Bornberg-Bauer E. . ‘The dynamics and evolutionary potential of domain loss and emergence.’ Molecular Biology and Evolution 29, Nr. 2: 787–796. doi: 10.1093/molbev/msr250.
    • Wissler L, Godmann L, Bornberg-Bauer E. . ‘Evolutionary dynamics of simple sequence repeats across long evolutionary time in genus Drosphila.’ Trends in Evolutionary Biology 4, Nr. 1.
    • Terrapon N, Grath S, Weiner J, Moore A, Bornberg-Bauer E. . ‘Fast Homology Search Using Domain-Architecture Alignment.’ JOBIM, Conference proceedings 1.
    • Sikosek T, Bornberg-Bauer E, Chan HS. . ‘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.
    • Sikosek T, Chan HS, Bornberg-Bauer E. . ‘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 109, Nr. 37. doi: 10.1073/pnas.1115620109.
    • Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S. . ‘The interface of protein structure, protein biophysics, and molecular evolution.’ Protein Science 21, Nr. 6: 769. doi: 10.1002/pro.2071.
    • Niehuis O, Hartig G, Grath S, Pohl H, Lehmann J, Tafer H, Donath A, Krauss V, Eisenhardt C, Hertel J, Petersen M, Mayer C, Meusemann K, Peters RS, Stadler PF, Beutel RG, Bornberg-Bauer E, McKenna DD, Misof B. . ‘Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera.’ Current biology 22, Nr. 14: 1309–1313. doi: 10.1016/j.cub.2012.05.018.
    • Gu J, Weber K, Klemp E, Winters G, Franssen SU, Wienpahl I, Huylmans AK, Zecher K, Reusch TB, Bornberg-Bauer E, Weber AP. . ‘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.
    • Balasubramanian PG, Beckmann A, Warnken U, Schnölzer M, Schüler A, Bornberg-Bauer E, Holstein TW, Ozbek S. . ‘Proteome of Hydra nematocyst.’ Journal of Biological Chemistry 287, Nr. 13: 9672. doi: 10.1074/jbc.M111.328203.
    • Suen G, Teiling C, Li L, Holt C, Abouheif E, Bornberg-Bauer E, Bouffard P, Caldera EJ, Cash E, Cavanaugh A, Denas O, Elhaik E, Favé MJ, Gadau J, Gibson JD, Graur D, Grubbs KJ, Hagen DE, Harkins TT, Helmkampf M, Hu H, Johnson BR, Kim J, Marsh SE, Moeller JA, Muñoz-Torres MC, Murphy MC, Naughton MC, Nigam S, Overson R, Rajakumar R, Reese JT, Scott JJ, Smith CR, Tao S, Tsutsui ND, Viljakainen L, Wissler L, Yandell MD, Zimmer F, Taylor J, Slater SC, Clifton SW, Warren WC, Elsik CG, Smith CD, Weinstock GM, Gerardo NM, Currie CR. . ‘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.
    • Wissler L, Codoñer FM, Gu J, Reusch TB, Olsen JL, Procaccini G, Bornberg-Bauer E. . ‘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.
    • Schüler A, Bornberg-Bauer E. . ‘The evolution of protein interaction networks.’ Methods in Molecular Biology 696: 273. doi: 10.1007/978-1-60761-987-1_17.
    • Franssen SU, Gu J, Bergmann N, Winters G, Klostermeier UC, Rosenstiel P, Bornberg-Bauer E, Reusch TB. . ‘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 108, Nr. 48: –81. doi: 10.1073/pnas.1107680108.
    • Franssen SU, Shrestha RP, Brautigam A, Bornberg-Bauer E, Weber AP. . ‘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.
    • Reineke AR, Bornberg-Bauer E, Gu J. . ‘Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes.’ Nucleic Acids Research . doi: 10.1093/nar/gkr179.
    • Ernst AM, Rüping B, Jekat SB, Nordzieke S, Reineke AR, Müller B, Bornberg-Bauer E, Prüfer D, Noll GA. . ‘The sieve element occlusion gene family in dicotyledonous plants.’ Plant Signaling and Behavior 6, Nr. 1: 151. doi: 10.4161/psb.6.1.14308.
    • Bornberg-Bauer E. . ‘Signals: tinkering with domains.’ Science Signaling 3, Nr. 139: pe31. doi: 10.1126/scisignal.3139pe31.
    • Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJP, Kitts P, Lynch JA, Murphy T, Oliveira DCSG, Smith CD, Van Zande LD, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MMG, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi J-H, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, De Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter Iv HC, Hurst GDD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon Jr. JM, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FMF, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu L-L, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Hugh M Robertson II, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZLP, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Vattathil CTS, Eveline C Verhulst II, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA. . ‘Functional and evolutionary insights from the genomes of three parasitoid nasonia species.’ Science 327, Nr. 5963: 343–348. doi: 10.1126/science.1178028.
    • Bornberg-Bauer, Erich; Huylmans, Ann-Kathrin; Sikosek, Tobias. . ‘How do new proteins arise?’ Current Opinion in Structural Biology 20, Nr. 3. doi: 10.1016/j.sbi.2010.02.005.
    • Chen T., Vernazobres D., Yomo T., Bornberg-Bauer E., Chan H. . ‘EvoIvability and single-genotype fluctuation in phenotypic properties: A simple heteropolymer model.’ Biophysical Journal 98, Nr. 11: 2487–2496. doi: 10.1016/j.bpj.2010.02.046.
    • Sikosek T, Bornberg-Bauer E. . ‘Evolution after and before gene duplication?’ In Evolution after Gene Duplication, edited by Liberles D, Dittmar K, e. New York City: John Wiley & Sons. doi: 10.1002/9780470619902.ch6.
    • Rüping B, Ernst AM, Jekat SB, Nordzieke S, Reineke AR, Müller B, Bornberg-Bauer E, Prüfer D, Noll GA. . ‘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.
    • Caetano-Anollés G, Moore AD, Bornberg-Bauer E. . ‘Protein Domains as Evolutionary Units.’ In Evolutionary Genomics and System Biology, edited by Bioinformatics Laboratory, Dep of Crop Sciences, University of Illinois, USA, 213–230. N/A: unbekannt / n.a. / unknown. doi: 10.1002/9780470570418.ch12.
    • Bornberg-Bauer E, Huylmans AK, Sikosek T. . ‘How do new proteins arise?’ Current Opinion in Structural Biology 20, Nr. 3: 390. doi: 10.1016/j.sbi.2010.02.005.
    • Bornberg-Bauer E, Kramer L. . ‘Robustness versus evolvability: a paradigm revisited.’ HFSP Journal 4, Nr. 3-4: 105. doi: 10.2976/1.3404403.
    • Chen T, Vernazobres D, Yomo T, Bornberg-Bauer E, Chan HS. . ‘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.
    • Wissler L, Dattolo E, Moore AD, Reusch TB, Olsen JL, Migliaccio M, Bornberg-Bauer E, Procaccini G. . ‘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.
    • Weiner J, Moore AD, Bornberg-Bauer E. . ‘Just how versatile are domains?’ BMC Evolutionary Biology 8: 285. doi: 10.1186/1471-2148-8-285.
    • Schulenburg H, Hoeppner MP, Weiner J, Bornberg-Bauer E. . ‘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.
    • Whitehead DJ, Wilke CO, Vernazobres D, Bornberg-Bauer E. . ‘The look-ahead effect of phenotypic mutations.’ Biology Direct 3: 18. doi: 10.1186/1745-6150-3-18.
    • Friedrichs F, Henckaerts L, Vermeire S, Kucharzik T, Seehafer T, Moller-Krull M, Bornberg-Bauer E, Stoll M, {Weiner 3rd} J. . ‘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.
    • Falb M., Müller K., Königsmaier L., Oberwinkler T., Horn P., Von Gronau S., Gonzalez O., Pfeiffer F., Bornberg-Bauer E., Oesterhelt D. . ‘Metabolism of halophilic archaea.’ Extremophiles 12, Nr. 2: 177–196. doi: 10.1007/s00792-008-0138-x.
    • Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A. . ‘Arrangements in the modular evolution of proteins.’ Trends in Biochemical Sciences 33, Nr. 9: 444. doi: 10.1016/j.tibs.2008.05.008.
    • Reusch TB, Veron AS, Preuss C, Weiner J, Wissler L, Beck A, Klages S, Kube M, Reinhardt R, Bornberg-Bauer E. . ‘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.
    • Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, Robinson-Rechavi M, Bornberg-Bauer E, Robertson DL, Oliver SG. . ‘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.
    • Wroe R, Chan HS, Bornberg-Bauer E. . ‘A structural model of latent evolutionary potentials underlying neutral networks in proteins.’ HFSP J. 1: 79–87.
    • Beaussart F, Weiner J, Bornberg-Bauer E. . ‘Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN).’ Bioinformatics 23, Nr. 14: 1834. doi: 10.1093/bioinformatics/btm240.
    • Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bornberg-Bauer E, Kudla J, Harter K. . ‘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.
    • Veron AS, Kaufmann K, Bornberg-Bauer E. . ‘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.
    • Amoutzias GD, Veron AS, Weiner J, Robinson-Rechavi M, Bornberg-Bauer E, Oliver SG, Robertson DL. . ‘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.
    • Amoutzias GD, Bornberg-Bauer E, Oliver SG, Robertson DL. . ‘Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network.’ BMC Genomics 7: 107. doi: 10.1186/1471-2164-7-107.
    • Gerke M, Bornberg-Bauer E, Jiang X, Fuellen G. . ‘Finding common protein interaction patterns across organisms.’ Evolutionary Bioinformatics 2: 45–52.
    • Weiner J, Beaussart F, Bornberg-Bauer E. . ‘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.
    • Weiner J, Bornberg-Bauer E. . ‘Evolution of circular permutations in multidomain proteins.’ Molecular Biology and Evolution 23, Nr. 4: 734. doi: 10.1093/molbev/msj091.
    • Teichmann SA, Bornberg-Bauer E, Luscombe NM. . Transcriptional networking. 6. Aufl. . doi: 10.1186/gb-2005-6-9-344.
    • Malonek S, Boemke C, Bornberg-Bauer E, Rojas MC, Hedden P, Hopkins P, Tudzynski B. . ‘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.
    • Weiner J, Thomas G, Bornberg-Bauer E. . ‘Rapid motif-based prediction of circular permutations in multi-domain proteins.’ Bioinformatics 21, Nr. 7: 932. doi: 10.1093/bioinformatics/bti085.
    • Amoutzias GD, Weiner J, Bornberg-Bauer E. . ‘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.
    • Bornberg-Bauer E, Beaussart F, Kummerfeld SK, Teichmann SA, Weiner J. . ‘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.
    • Wroe R, Bornberg-Bauer E, Chan HS. . ‘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.
    • Amoutzias GD, Robertson DL, Bornberg-Bauer E. . ‘The evolution of protein interaction networks in regulatory proteins.’ Comparative and Functional Genomics 5, Nr. 1: 79–84. doi: 10.1002/cfg.365.
    • Do J.H., Anderson M.J., Denning D.W., Bornberg-Bauer E. . ‘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.
    • Amoutzias GD, Robertson DL, Oliver SG, Bornberg-Bauer E. . ‘Convergent evolution of gene networks by single-gene duplications in higher eukaryotes.’ EMBO Reports 5, Nr. 3: 274. doi: 10.1038/sj.embor.7400096.
    • Mabey JE, Anderson MJ, Giles PF, Miller CJ, Attwood TK, Paton NW, Bornberg-Bauer E, Robson GD, Oliver SG, Denning DW. . ‘CADRE: the Central Aspergillus Data REpository.’ Nucleic Acids Research 32, Nr. Database issue: –5. doi: 10.1093/nar/gkh009.
    • Bornberg-Bauer E, Weiner J. . A putative transcription factor inducing mobility in Mycoplasma pneumoniae..
    • Sirava M, Schäfer T, Eiglsperger M, Kaufmann M, Kohlbacher O, Bornberg-Bauer E, Lenhof HP. . ‘BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.’ Bioinformatics 18 Suppl 2: –30. doi: 10.1093/bioinformatics/18.suppl_2.S219.
    • Chan HS, Bornberg-Bauer E. . ‘Perspectives on protein evolution from simple exact models.’ Applied Bioinformatics 1, Nr. 3: 121.
    • Cui Y, Wong H, Bornberg-Bauer E, Chan HS. . ‘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.
    • Bornberg-Bauer E, Paton NW. . ‘Conceptual data modelling for bioinformatics.’ Briefings in Bioinformatics 3, Nr. 2: 166. doi: 10.1093/bib/3.2.166.
    • Rost U, Bornberg-Bauer E. . ‘TreeWiz: interactive exploration of huge trees.’ Bioinformatics 18, Nr. 1: 109. doi: 10.1093/bioinformatics/18.1.109.
    • Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G. . ‘Switching from simple to complex oscillations in calcium signaling.’ Biophysical Journal 79, Nr. 3: 1188. doi: 10.1016/S0006-3495(00)76373-9.
    • Bornberg-Bauer E, Chan HS. . ‘Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space.’ Proceedings of the National Academy of Sciences of the United States of America 96, Nr. 19: 10689. doi: 10.1073/pnas.96.19.10689.
    • Backofen R, Will S, Bornberg-Bauer E. . ‘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.
    • Krause A, Nicodème P, Bornberg-Bauer E, Rehmsmeier M, Vingron M. . ‘WWW access to the SYSTERS protein sequence cluster set.’ Bioinformatics 15, Nr. 3: 262. doi: 10.1093/bioinformatics/15.3.262.
    • Bornberg-Bauer E, Rivals E, Vingron M. . ‘Computational approaches to identify leucine zippers.’ Nucleic Acids Res. 26, Nr. 11: 2740–2746. doi: 10.1093/nar/26.11.2740.
    • Renner A, Bornberg-Bauer E. . ‘Exploring the fitness landscapes of lattice proteins.’ Pacific Symposium on Biocomputing : 361.
    • Bornberg-Bauer E. . ‘How are model protein structures distributed in sequence space?’ Biophysical Journal 73, Nr. 5: 2393. doi: 10.1016/S0006-3495(97)78268-7.
    • Bornberg-Bauer E. . ‘Structure formation of biopolymers is complex, their evolution may be simple.’ Pacific Symposium on Biocomputing : 97–108.
    • Fontana W, Stadler PF, Bornberg-Bauer EG, Griesmacher T, Hofacker IL, Tacker M, Tarazona P, Weinberger ED, Schuster P. . ‘RNA folding and combinatory landscapes.’ Physical Review E - Statistical, nonlinear, and soft matter physics 47, Nr. 3: 2083–2099.

  • Betreute Arbeiten

    Promotionen

    Contribution of non-coding RNAs to the pathogenesis of cardiovascular diseases
    Genomische und evolutionäre Untersuchung des Sekundärmetaboliten Colibactin in Enterobacteriaceae
    Gandhi, ShreyIncRNAs as a novel epigenetic layer in the genetic predisposition to heart failure
    Analysis of non-coding RNA sequence, structure and function using comparative transcriptomics and biophysics approaches
    Investigation of non-coding RNA in the cardiovascular system
    Ancestral reconstruction and experimental test of long- and short term evolvability using the AP-superfamily as a model system
    Reconstructing de novo gene emergence
    Wiechers, SarahEntwicklung von Softwarekomponenten für und Analyse von DNA Barcoding Daten der deutschen Flora
    Epistasis, robustness and evolvability in biomolecules
    Benefits and hazards of novel protein coding genes
    The role of the NMDA receptor subunit 2B (NR2B) in the regulation of autoimmune neuroinflammation
    Cryptic Mutations in Protein Evolution
    Properties in de novo genes in vertebrates
    Modular protein evolution in insects: On the emergence of novel domains and domain arrangements
    Next-generation sequencing-based genome and transcriptome studies of unicellular Apicomplexa and Kinetoplastida parasites
    Evolution of Substrate Specificity in the Alkaline Phosphatase Superfamily
    Evolution of Protein Domain Repeats in Metazoa
    Mona RiemenschneiderOn the evolution of modularity in gene regulatory networks affecting complex traits / diseases
    Coevolution between the red flour beetle and Bacillus thuringiensis bacteria
    Poos, KathrinThe pathogenesis of Osteosarcoma - systems biological approaches to explain cancer development and progression
    Hiersche, MilanMultifaktorielle Assoziationsmuster con SNP/CNV Daten zu kardiovaskulären Phänotypen
    Phyletic distribution and evolution of ancient globin genes
    Computational Analysis of Genome Evolution in Holmetabolous Insects (Endopterygota)
    RNA-seq in non-model organisms: Microevolutionary and ecological insights from gene expression of seagrasses under global warming
    The resolution of adaptive conflicts in protein evolution through shifts in thermodynamic stability and gene duplication
    Conserved Motifs in Plant Genome Evolution
    On the evolution of complex genetic diseases
    Mechanisms of Modular Protein Evolution
    Specht, MichaelNovel strategies for high-throughput data analysis in computational proteomics and proteogenesis
    Characterization of the "sieve element occlusion" gene family with special emphasis on gene expression
    Friedrichs, FraukeEpidemiological, statistical and molecular biology approaches to assess the role of inflammatory genes in the pathogenesis of complex diseases
    Veron, AmélieAdaptive Evolution of Networks
    Spitzer, MichaelAutomating the Analysis of Protein Family Evolution

    Habilitation

    Weiner, JanuaryDomain-wise evolution of proteins