Professor Dr. Erich Bornberg-Bauer

• 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

Akademische Ausbildung

06.1995

PhD in Theoretical Biochemistry (Institute for Theoratical Chemistry, University of Vienna, Austria)

1992

Diploma (equivalent to MSc) in Biochemistry, University of Vienna, Austria

1981 – 1991

Studies in Biochemistry, Physics and Mathematics, University of Vienna, Austria

Beruflicher Werdegang

seit 07.2013

Gastprofessur Université Lyon 1, Claude Bernard, Laboratoire de Biométrie et Biologie Évolutive

seit 2009

Gastwissenschaftler EBI, Thornton Group "The Spices", Cambridge

seit 09.2003

Full Professor of Molecular Evolution and Bioinformatics, University of Münster, Germany

04.2000 – 08.2003

Senior Lecturer in Bioinformatics, School of Biological Sciences, The University of Manchester, UK

10.1998 – 03.2000

Project Manager EML Ltd. (Heidelberg, Germany)

04.1996 – 09.1998

Postdoctoral Research Associate (Cancer Research Centre Heidelberg, Germany)

10.1994 – 03.1996

Assistant Professor in Mathematics (Univ. Ass., Institute for Mathematics, University of Vienna, Austria)

• Eenink, Berhard D. G., Holstein, Josephin M., Heberlein, Magdalena, Dilkaute, Carina, Jose, Joachim, Hollfelder, Florian, van Loo, Bert, Bornberg-Bauer, Erich, Kaminski, Tomasz S., und Lange, Andreas. 2025. „Studying the evolutionary potential of ancestral aryl sulfatases in the alkaline phosphatase family with droplet microfluidics.“ Preprint. bioRxiv doi: 10.1101/2024.12.10.627700.
• Aubel, Margaux, Eicholt, Lars, und Bornberg-Bauer, Erich. 2023. „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.
• Glaser-Schmitt, A, Lebherz, M, Saydam, E, Bornberg-Bauer, E, und Parsch, J. 2025. „Expression of De Novo Open Reading Frames in Natural Populations of Drosophila melanogaster.“ Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 344 (7): 415–427. doi: 10.1002/jez.b.23297.
• Coban, Abdulbaki, Bornberg-Bauer, Erich, und Kemena, Carsten. 2025. „Tracing the paths of modular evolution by quantifying rearrangement events of protein domains.“ BMC Ecology and Evolution 25 (1). doi: 10.1186/s12862-024-02347-7.
• Grandchamp, A, Berk, K, Dohmen, E, und Bornberg-Bauer, E. 2022. „New Genomic Signals Underlying the Emergence of Human Proto-Genes.“ Genes 13: 284–284. doi: 10.3390/genes13020284.
• Feldmeyer, Barbara, Bornberg-Bauer, Erich, Dohmen, Elias, Fouks, Bertrand, Heckenhauer, Jaqueline, Huylmans, Ann Kathrin, Jones, Alun, Stolle, Eckart, und Harrison, Mark C. 2024. „Comparative Evolutionary Genomics in Insects.“ In Comparative Genomics. Methods and Protocols, Methods in Molecular Biology, herausgegeben von João Carlos Setubal, Peter F. Stadler und Jens Stoye. New York: Springer Nature. doi: 10.1007/978-1-0716-3838-5_16.
• Aubel, Margaux, Buchel, Filip, Heames, Brennen, Jones, Alun, Honc, Ondrej, Bornberg-Bauer, Erich, und Houchova, Klara. 2024. „High-throughput Selection of Human de novo-emerged sORFs with High Folding Potential.“ Genome Biology and Evolution 16 (4) evae069. doi: 10.1093/gbe/evae069.
• 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., und Phillippy, Adam M. 2024. „The complete sequence and comparative analysis of ape sex chromosomes.“ Nature 630 (8015). doi: 10.1038/s41586-024-07473-2.
• Lebherz, Marie Kristin; Fouks, Bertrand; Schmidt, Julian; Bornberg-Bauer, Erich; Grandchamp, Anna. 2024. „DNA Transposons Favor De Novo Transcript Emergence Through Enrichment of Transcription Factor Binding Motifs.“ Genome Biology and Evolution 16 (7). doi: 10.1093/gbe/evae134.
• Iyengar, Bharat Ravi; Grandchamp, Anna; Bornberg-Bauer, Erich. 2024. „How antisense transcripts can evolve to encode novel proteins.“ Nature Communications 15 (1). doi: 10.1038/s41467-024-50550-3.
• Lebherz, Marie Kristin; Iyengar, Bharat Ravi; Bornberg-Bauer, Erich. 2024. „Modeling Length Changes in De Novo Open Reading Frames during Neutral Evolution.“ Genome Biology and Evolution 16 (7). doi: 10.1093/gbe/evae129.
• Grandchamp, Anna; Czuppon, Peter; Bornberg-Bauer, Erich. 2024. „Quantification and modeling of turnover dynamics of de novo transcripts in Drosophila melanogaster.“ Nucleic Acids Research 52 (1). doi: 10.1093/nar/gkad1079.
• Heames, Brennen, Buchel, Filip, Aubel, Margaux, Tretyachenko, Vyacheslav, Loginov, Dmitry, Novak, Petr, Lange, Andreas, Bornberg-Bauer, Erich, und Hlouchova, Klara. 2023. „Experimental characterization of de novo proteins and their unevolved random-sequence counterparts.“ Nature Ecology and Evolution 7 (4). doi: 10.1038/s41559-023-02010-2.
• Aubel, Margaux, und Bornberg-Bauer, Erich. 2023. „Introducing creative destruction as a mechanism in protein evolution.“ Proceedings of the National Academy of Sciences of the United States of America 120 (6). doi: 10.1073/pnas.2220460120.
• Grandchamp, Anna Kühl Lucas, Lebherz, Marie Brüggemann Kathrin, und Parsch, John Bornberg-Bauer Erich. 2023. „Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in <i>Drosophila melanogaster</i>.“ 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.. 2023. „Live-bearing cockroach genome reveals convergent evolutionary mechanisms linked to viviparity in insects and beyond.“ iScience 26 (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., und Eizaguirre, Christophe. 2023. „Origin matters: Using a local reference genome improves measures in population genomics.“ Molecular Ecology Resources 23 (7). doi: 10.1111/1755-0998.13838.
• Iyengar, Bharat Ravi, und Bornberg-Bauer, Erich. 2023. „Neutral Models of De Novo Gene Emergence Suggest that Gene Evolution has a Preferred Trajectory.“ Molecular Biology and Evolution 40 (4). doi: 10.1093/molbev/msad079.
• Coban, Abdulbaki, Bornberg-Bauer, Erich, und Kemena, Carsten. 2022. „Domain Evolution of Vertebrate Blood Coagulation Cascade Proteins.“ Journal of Molecular Evolution 90: 418–428. doi: 10.1007/s00239-022-10071-3.
• Eenink, Bernard D. G., Kaminski, Tomasz S., Bornberg-Bauer, Erich, Jose, Joachim, Hollfelder, Florian, und van Loo, Bert. 2022. „Vector Redesign and In-Droplet Cell-Growth Improves Enrichment and Recovery in live Escherichia coli.“ Microbial Biotechnology 15 (11). doi: 10.1111/1751-7915.14144.
• Eicholt, Lars A., Aubel, Margaux, Berk, Katrin, Bornberg-Bauer, Erich, und Lange, Andreas. 2022. „Heterologous expression of naturally evolved putative <i>de novo</i> proteins with chaperones.“ Protein Science 31 (8). doi: 10.1002/pro.4371.
• Post, Frederik; Bornberg-Bauer, Erich; Vasseur-Cognet, Mireille; Harrison, Mark C.. 2022. „More effective transposon regulation in fertile, long-lived termite queens than in sterile workers.“ Molecular Ecology 32 (2). doi: 10.1111/mec.16753.
• Berger, Juliette, Legendre, Frederic, Zelosko, Kevin-Markus, Harrison, Mark C., Grandcolas, Philippe, Bornberg-Bauer, Erich, und Fouks, Bertrand. 2022. „Eusocial Transition in Blattodea: Transposable Elements and Shifts of Gene Expression.“ Genes 13 (11). doi: 10.3390/genes13111948.
• Feldmeyer, Barbara, Gstoettl, Claudia, Wallner, Jennifer, Jongepier, Evelien, Seguret, Alice, Grasso, Donato A., Bornberg-Bauer, Erich, Foitzik, Susanne, und Heinze, Jurgen. 2022. „Evidence for a conserved queen-worker genetic toolkit across slave-making ants and their ant hosts.“ Molecular Ecology 31 (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, und Vasseur-Cognet, Mireille. 2022. „Lifespan prolonging mechanisms and insulin upregulation without fat accumulation in long-lived reproductives of a higher termite.“ Communications biology 5 (44). doi: 10.1038/s42003-021-02974-6.
• 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, und Stoll, M. 2021. „A genetic variant alters the secondary structure of the lncRNA H19 and is associated with dilated cardiomyopathy.“ RNA Biology 18 (sup1): 409–415. doi: 10.1080/15476286.2021.1952756.
• Buchholz, Patrick C. F., van Loo, Bert, Eenink, Bernard D. G., Bornberg-Bauer, Erich, und Pleiss, Juergen. 2021. „Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation.“ Interface 18 (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, und Findlay, Geoffrey D. 2021. „A putative <i>de novo</i> evolved gene required for spermatid chromatin condensation in <i>Drosophila melanogaster</i>.“ PLOS Genetics 17 (9). doi: 10.1371/journal.pgen.1009787.
• Jongepier, Evelien, Seguret, Alice, Labutin, Anton, Feldmeyer, Barbara, Gstoettl, Claudia, Foitzik, Susanne, Heinze, Juergen, und Bornberg-Bauer, Erich. 2021. „Convergent Loss of Chemoreceptors across Independent Origins of Slave-Making in Ants.“ Molecular Biology and Evolution 39 (1). doi: 10.1093/molbev/msab305.
• Harrison, Mark C., Nino, Luisa M. Jaimes, Rodrigues, Marisa Almeida, Ryll, Judith, Flatt, Thomas, Oettler, Jan, und Bornberg-Bauer, Erich. 2021. „Gene Coexpression Network Reveals Highly Conserved, Well-Regulated Anti-Ageing Mechanisms in Old Ant Queens.“ Genome Biology and Evolution 13 (6). doi: 10.1093/gbe/evab093.
• Lange, Andreas, Patel, Prajal H., Heames, Brennen, Damry, Adam M., Saenger, Thorsten, Jackson, Colin J., Findlay, Geoffrey D., und Bornberg-Bauer, Erich. 2021. „Structural and functional characterization of a putative de novo gene in <i>Drosophila</i>.“ Nature Communications 12 (1). doi: 10.1038/s41467-021-21667-6.
• Bornberg-Bauer, Erich, Hlouchova, Klara, und Lange, Andreas. 2021. „Structure and function of naturally evolved de novo proteins.“ Current Opinion in Structural Biology 68. doi: 10.1016/j.sbi.2020.11.010.
• Yang G, Anderson DW, Baier F, Dohmen E, Hong N, Carr PD, Kamerlin SCL, Jackson CJ, Bornberg-Bauer E, Tokuriki N. 2020. „Author Correction: Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme.“ Nature Chemical Biology 16: 930–930. doi: 10.1038/s41589-020-0588-8.
• Scharsack, Jörn P., Wieczorek, Bartholomäus, Schmidt-Drewello, Alexander, Büscher, Janine, Franke, Frederik, Moore, Andrew, Branca, Antoine Witten Anika Stoll Monika, Bornberg-Bauer, Erich, Wicke, Susann, und Kurtz, Joachim. 2021. „Climate change facilitates a parasite’s host exploitation via temperature-mediated immunometabolic processes.“ Global Change Biology 27: 94–107. doi: 10.1111/gcb.15402.
• Heames, Brennen, Schmitz, Jonathan, und Bornberg-Bauer, Erich. 2020. „A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in <i>Drosophila</i>.“ Preprint. Journal of Molecular Evolution 88 (4). doi: 10.1007/s00239-020-09939-z.
• Oeyen, Jan Philip, Baa-Puyoulet, Patrice, Benoit, Joshua B., Beukeboom, Leo W., Bornberg-Bauer, Erich, Buttstedt, Anja, Calevro, Federica, Cash, Elizabeth I, Chao, Hsu, Charles, Hubert, Chen, Mei-Ju May, Childers, Christopher, Cridge, Andrew G., Dearden, Peter, Huyen, Dinh, Doddapaneni, Harsha Vardhan, Dolan, Amanda, Donath, Alexander, Dowling, Daniel, Dugan, Shannon, Duncan, Elizabeth, Elpidina, Elena N., Friedrich, Markus, Geuverink, Elzemiek, Gibson, Joshua D., Grath, Sonja, Grimmelikhuijzen, Cornelis J. P., Grosse-Wilde, Ewald, Gudobba, Cameron, Han, Yi, Hansson, Bill S., Hauser, Frank, Hughes, Daniel S. T., Ioannidis, Panagiotis, Jacquin-Joly, Emmanuelle, Jennings, Emily C., Jones, Jeffery W., Klasberg, Steffen, Lee, Sandra L., Lesny, Peter, Lovegrove, Mackenzie, Martin, Sebastian, Martynov, Alexander G., Mayer, Christoph, Montagne, Nicolas, Moris, Victoria C., Munoz-Torres, Monica, Murali, Shwetha Canchi, Muzny, Donna M., Oppert, Brenda, Parisot, Nicolas, Pauli, Thomas, Peters, Ralph S., Petersen, Malte, Pick, Christian, Persyn, Emma, Podsiadlowski, Lars, Poelchau, Monica F., Provataris, Panagiotis, Qu, Jiaxin, Reijnders, Maarten J. M. F., von Reumont, Bjoern Marcus, Rosendale, Andrew J., Simao, Felipe A., Skelly, John, Sotiropoulos, Alexandros G., Stahl, Aaron L., Sumitani, Megumi, Szuter, Elise M., Tidswell, Olivia, Tsitlakidis, Evangelos, Vedder, Lucia, Waterhouse, Robert M., Werren, John H., Wilbrandt, Jeanne, Worley, Kim C., Yamamoto, Daisuke S., van de Zande, Louis, Zdobnov, Evgeny M., Ziesmann, Tanja, Gibbs, Richard A., Richards, Stephen, Hatakeyama, Masatsugu, Misof, Bernhard, und Niehuis, Oliver. 2020. „Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera.“ Preprint. Genome Biology and Evolution 12 (7). doi: 10.1093/gbe/evaa106.
• Dohmen, E, Klasberg, S, Bornberg-Bauer, E, Perrey, S, und Kemena, C. 2020. „The modular nature of protein evolution: domain rearrangement rates across eukaryotic life.“ BMC Evolutionary Biology 20 (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. 2020. „Gene content evolution in the arthropods.“ Genome Biology 21 (15). doi: 10.1186/s13059-019-1925-7.
• Dowling, Daniel, Schmitz, Jonathan F., und Bornberg-Bauer, Erich. 2020. „Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage.“ Genome Biology and Evolution 12 (11). doi: 10.1093/gbe/evaa194.
• Gstoettl, Claudia, Stoldt, Marah, Jongepier, Evelien, Bornberg-Bauer, Erich, Feldmeyer, Barbara, Heinze, Juergen, und Foitzik, Susanne. 2020. „Comparative analyses of caste, sex, and developmental stage-specific transcriptomes in two <i>Temnothorax</i> ants.“ Ecology and Evolution 10 (10). doi: 10.1002/ece3.6187.
• van Loo, Bert, Heberlein, Magdalena, Mair, Philip, Zinchenko, Anastasia, Schuurmann, Jan, Eenink, Bernard D. G., Holstein, Josephin M., Dilkaute, Carina, Jose, Joachim, Hollfelder, Florian, und Bornberg-Bauer, Erich. 2019. „High-Throughput, Lysis-Free Screening for Sulfatase Activity Using <i>Escherichia coli</i> Autodisplay in Microdroplets.“ Preprint. ACS Synthetic Biology 8 (12). doi: 10.1021/acssynbio.9b00274.
• Hartke, Juliane, Schell, Tilman, Jongepier, Evelien, Schmidt, Hanno, Sprenger, Philipp P., Paule, Juraj, Bornberg-Bauer, Erich, Schmitt, Thomas, Menzel, Florian, Pfenninger, Markus, und Feldmeyer, Barbara. 2019. „Hybrid Genome Assembly of a Neotropical Mutualistic Ant.“ Preprint. Genome Biology and Evolution 11 (8). doi: 10.1093/gbe/evz159.
• Bornberg-Bauer, E, und Heames, B. 2019. „Becoming a de novo gene.“ Nature Ecology and Evolution 3 (4): 524–525. doi: 10.1038.
• Kaur, R, Stoldt, M, Jongepier, E, Feldmeyer, B, Menzel, F, Bornberg-Bauer, E, und Foitzik, S. 2019. „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 (1769): 20180192.. doi: 10.1098/rstb.2018.0192.
• Huang, Y, Feulner, PGD, Eizaguirre, C, Lenz, TL, Bornberg-Bauer, E, Milinski, M, Reusch, TBH, und Chain, FJJ. 2019. „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, und Bornberg-Bauer, E. 2019. „A Roadmap to Domain Based Proteomics.“ In Computational Methods in Protein Evolution, herausgegeben von Tobias Sikosek. doi: 10.1007/978-1-4939-8736-8_16.
• Kemena, C, Dohmen, E, und Bornberg-Bauer, E. 2019. „DOGMA: a web server for proteome and transcriptome quality assessment.“ Nucleic Acids Research 47 (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. 2019. „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, und Tokuriki, Nobuhiko. 2019. „Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme (vol 51, pg 831, 2020).“ Nature Chemical Biology 16 (8). doi: 10.1038/s41589-020-0588-8.
• Klasberg, Steffen, Bitard-Feildel, Tristan, Callebaut, Isabelle, und Bornberg-Bauer, Erich. 2018. „Origins and structural properties of novel and <i>de novo</i> protein domains during insect evolution.“ Preprint. The FEBS Journal 285 (14). doi: 10.1111/febs.14504.
• Kremer, Lukas Peter Maria, Korb, Judith, und Bornberg-Bauer, Erich. 2018. „Reconstructed evolution of insulin receptors in insects reveals duplications in early insects and cockroaches.“ Preprint. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (5). doi: 10.1002/jez.b.22809.
• van Loo, Bert, Schober, Markus, Valkov, Eugene, Heberlein, Magdalena, Bornberg-Bauer, Erich, Faber, Kurt, Hyvoenen, Marko, und Hollfelder, Florian. 2018. „Structural and Mechanistic Analysis of the Choline Sulfatase from &ITSinorhizobium melliloti&IT: A Class I Sulfatase Specific for an Alkyl Sulfate Ester.“ Preprint. Journal of Molecular Biology 430 (7). doi: 10.1016/j.jmb.2018.02.010.
• Lopez-Ezquerra, Alberto, Mitschke, Andreas, Bornberg-Bauer, Erich, und Joop, Gerrit. 2018. „<i>Tribolium castaneum</i> gene expression changes after <i>Paranosema whitei</i> infection.“ Preprint. Journal of Invertebrate Pathology 153. doi: 10.1016/j.jip.2018.02.009.
• Klasberg, S, Bitard-Feildel, T, Callebaut, I, und Bornberg-Bauer, E. 2018. „Origins and structural properties of novel and de novo protein domains during insect evolution.“ The FEBS Journal 285 (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, und Bornberg-Bauer, E. 2018. „Hemimetabolous genomes reveal molecular basis of termite eusociality.“ Nature Ecology and Evolution 2 (3): 557–566. doi: 10.1038/s41559-017-0459-1DO-10.1038/s41559-017-0459-1.
• Kurafeiski, JD, Pinto, P, und Bornberg-Bauer, E. 2018. „Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding.“ Genome Biology and Evolution 11 (2): 406–414. doi: 10.1093/gbe/evy269.
• Jongepier, E, Kemena, C, Lopez-Ezquerra, A, Belles, X, Bornberg-Bauer, E, und Korb, J. 2018. „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 (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, und Schal, C. 2018. „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 (5): 254–264. doi: 10.1002/jez.b.22824.
• Lopez-Ezquerra, Alberto; Mitschke, Andreas; Bornberg-Bauer, Erich; Joop, Gerrit. 2018. „<i>Tribolium castaneum</i> gene expression changes after <i>Paranosema whitei</i> infection.“ Journal of Invertebrate Pathology 153. doi: 10.1016/j.jip.2018.02.009.
• Bornberg-Bauer, Erich, Harrison, Mark C., und Jongepier, Evelien. 2018. „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 (5). doi: 10.1002/jez.b.22826.
• Gubala, A., Schmitz, J., Kearns, M., Vinh, T., Bornberg-Bauer, E., Wolfner, M., und Findlay, G. 2017. „The Goddard and Saturn Genes Are Essential for Drosophila Male Fertility and May Have Arisen de Novo.“ Molecular Biology and Evolution 34 (5): 1066–1082. doi: 10.1093/molbev/msx057.
• Bornberg-Bauer, E., und Schmitz, J. 2017. „Fact or fiction: Updates on how protein-coding genes might emerge de novo from previously non-coding DNA.“ F1000Research 6 (null). doi: 10.12688/f1000research.10079.1.
• Lopez-Ezquerra, A., Harrison, M., und Bornberg-Bauer, E. 2017. „Comparative analysis of lincRNA in insect species.“ BMC Evolutionary Biology 17 (1). doi: 10.1186/s12862-017-0985-0.
• van, Loo B and Bornberg-Bauer E. 2017. „Enzyme sub-functionalization driven by regulation.“ EMBO Reports 18: 1043–1045. doi: 10.15252/embr.201744383.
• Haase, D, Rieger, JK, Witten, A, Stoll, M, Bornberg-Bauer, E, Kalbe, M, Schmidt-Drewello, A, Scharsack, JP, und Reusch, TB. 2016. „Comparative transcriptomics of stickleback immune gene responses upon infection by two helminth parasites, Diplostomum pseudospathaceum and Schistocephalus solidus.“ Zoology (Jena) 2016 (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, und Feulner, PG. 2016. „Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks.“ Molecular Ecology 2016 (25(4)): 943–958. doi: 10.1111/mec.13520.
• Dohmen, E., Kremer, L., Bornberg-Bauer, E., und Kemena, C. 2016. „DOGMA: Domain-based transcriptome and proteome quality assessment.“ Bioinformatics 32 (17): 2577–2581. doi: 10.1093/bioinformatics/btw231.
• Elsner, D., Kremer, L., Arning, N., und Bornberg-Bauer, E. 2016. „Chapter 6. Comparative genomic approaches to investigate molecular traits specific to social insects.“ Current Opinion in Insect Science 16 (null): 87–94. doi: 10.1016/j.cois.2016.05.016.
• 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, und Van, de Peer Y. 2016. „The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.“ Nature doi: 10.1038/nature16548.
• Schüler, A, und Bornberg-Bauer, E. im Druck. „Evolution of Protein Domain Repeats in Metazoa.“ Molecular Biology and Evolution 33.
• Dohmen, E, Kremer, L, Bornberg-Bauer, E, und Kemena, C. 2016. „DOGMA: Domain-Based Transcriptome and Proteome Quality Assessment.“ Beitrag präsentiert auf der German Conference on Bioinformatics, Berlin
• Jueterbock, A., Franssen, S., Bergmann, N., Gu, J., Coyer, J., Reusch, T., Bornberg-Bauer, E., und Olsen, J. 2016. „Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass.“ Molecular Ecology 25 (21): 5396–5411. doi: 10.1111/mec.13829.
• Kemena, Carsten, Bitard-Feildel, Tristan, Terrapon, Nicolas, Moore, Andrew, und Bornberg-Bauer, Erich. 2016. „Domain World.“ Beitrag präsentiert auf der GCB 2016, Berlin, Deutschland
• Schmitz, J., Zimmer, F., und Bornberg-Bauer, E. 2016. „Mechanisms of transcription factor evolution in Metazoa.“ Nucleic Acids Research 44 (13): 6287–6297. doi: 10.1093/nar/gkw492.
• Haase, D, Rieger, JK, Witten, A, Stoll, M, Bornberg-Bauer, E, Kalbe, M, und Reusch, TB. 2016. „Immunity comes first: the effect of parasite genotypes on adaptive immunity and immunization in three-spined sticklebacks.“ Developmental and Comparative Immunology 54 (1): 137–144. doi: 10.1016/j.dci.2015.09.008.
• Bornberg-Bauer, E, Schmitz, J, und Heberlein, M. 2015. „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, und Milinski, M. 2015. „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, und Schulenburg, H. 2015. „Host-Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes.“ PLoS Biology 13 (6): e1002169.. doi: 10.1371/journal.pbio.1002169.
• Heberlein, M, van, Loo B, Hollfelder, F, und Bornberg-Bauer, E. im Druck. „Evolution of enzyme specificity in the alkaline phosphatase superfamily.“ Beitrag präsentiert auf der SMBE, Vienna, Austria
• van, Loo B, Heberlein, M, und Bornberg-Bauer, E. im Druck. „The Origins of Life's Molecular Diversity: Does Modularity Epitomize the Evolvability of Early Functional Units.“ Beitrag präsentiert auf der Volkswagen Stiftung Kick-off Conference: Life? - A New Funding Initiative Introduces Itself, Schloss Herrenhausen, Hannover, Germany
• van, Loo B, Heberlein, M, Dohmen, E, Hollfelder, F, und Bornberg-Bauer, E. im Druck. „Functional Transitions in Enzyme Evolution: Balancing Stability, Folding and Catalytic Specificity.“ Beitrag präsentiert auf der The annual meeting of the Society for Molecular Biology and Evolution, Hofburg Palace, Vienna, Austria
• Greenwood, J., Bitard-Feildel, T., Kemena, C., Terrapon, N., Schaub, F., Bornberg-Bauer, E., und Korb, J. 2015. „Detecting convergent molecular evolution in eusocial insects.“ Beitrag präsentiert auf der Society of Molecular Biology and Evolution, Wien
• Bitard-Feildel, Tristan, Heberlein, Magdalena, Bornberg-Bauer, Erich, und Callebaut, Isabelle. 2015. „Detection of orphan domains in <i>Drosophila</i> using "hydrophobic cluster analysis".“ Biochimie 119. doi: 10.1016/j.biochi.2015.02.019.
• Bitard-Feildel, T, Heberlein, M, Bornberg-Bauer, E, und Callebaut, I. 2015. „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, und Myburg, AA. 2015. „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, und Worley, KC. 2015. „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., und Mikheyev, A. 2015. „How do genomes create novel phenotypes Insights from the loss of the worker caste in ant social parasites.“ Molecular Biology and Evolution 32 (11): 2919–2931. doi: 10.1093/molbev/msv165.
• Bitard-Feildel, T., Kemena, C., Greenwood, J., und Bornberg-Bauer, E. 2015. „Domain similarity based orthology detection.“ BMC Bioinformatics 16 (1). doi: 10.1186/s12859-015-0570-8.
• Schüler, A, Schmitz, G, Reft, A, Özbek, S, Thurm, U, und Bornberg-Bauer, E. 2015. „The Rise and Fall of TRP-N, an Ancient Family of Mechanogated Ion Channels, in Metazoa.“ Genome Biol. Evol. 7 (6): 1713–1727. doi: 10.1093/gbe/evv091.
• Kemena, C, Bitard-Feildel, T, und Bornberg-Bauer, E. 2015. „MDAT - Aligning multiple domain arrangements.“ BMC Bioinformatics 16. doi: 10.1186/s12859-014-0442-7.
• Haase, David D., Rieger, Jennifer K. J.K., Witten, Anika A., Stoll, Monika M., Bornberg-Bauer, Erich G. E.G., Kalbe, Martin M., und Reusch, Thorsten Bh H T.B.H. 2014. „Specific gene expression responses to parasite genotypes reveal redundancy of innate immunity in vertebrates.“ PloS one 9 (9). doi: 10.1371/journal.pone.0108001.
• Behrens, S, Peuß, R, Milutinović, B, Eggert, H, Esser, D, Rosenstiel, P, Schulenburg, H, Bornberg-Bauer, E, und Kurtz, J. 2014. „Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis.“ BMC Genomics 16 (1): 445.
• Behrens, Sarah, Peuss, Robert, Milutinovic, Barbara, Eggert, Hendrik, Esser, Daniela, Rosenstiel, Philip, Schulenburg, Hinrich, Bornberg-Bauer, Erich, und Kurtz, Joachim. 2014. „Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen <i>Bacillus thuringiensis</i>.“ BMC Genomics 15. doi: 10.1186/1471-2164-15-445.
• Guo, B, Chain, FJ, Bornberg-Bauer, E, und Leder, EHand Merilä J. 2014. „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, und Liebig, J. 2014. „Molecular traces of alternative social organization in a termite genome.“ Nature Communications 5.
• 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., und Schmutz, Jeremy J. 2014. „The genome of Eucalyptus grandis.“ Nature 510 (7505): 362. doi: 10.1038/nature13308.
• Terrapon, Nicolas N., Weiner, January J., Grath, Sonja S., Moore, Andrew D. A.D., und Bornberg-Bauer, Erich G. E.G. 2014. „Rapid similarity search of proteins using alignments of domain arrangements.“ Bioinformatics 30 (2): 281. doi: 10.1093/bioinformatics/btt379.
• Terrapon, Nicolas N., Moore, Andrew D. A.D., und Bornberg-Bauer, Erich G. E.G. 2014. „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., und Bornberg-Bauer, Erich G. E.G. 2014. „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., und Bornberg-Bauer, Erich G. E.G. 2014. „DoMosaics: Software for domain arrangement visualization and domain-centric analysis of proteins.“ Bioinformatics 30 (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., und Reusch, Thorsten Bh H T.B.H. 2014. „Extensive Copy-Number Variation of Young Genes across Stickleback Populations.“ PLOS Genetics 10 (12). doi: 10.1371/journal.pgen.1004830.
• Wissler, L, Gadau, J, Simola, DF, Helmkampf, M, und Bornberg-Bauer, E. 2013. „Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes.“ Genome Biology and Evolution 5 (2): 439–455. doi: 10.1093/gbe/evt009.
• 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., und Gadau, J. 2013. „Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.“ Genome Research 23 (8): 1247. doi: 10.1101/gr.155408.113.
• Bornberg-Bauer, E, und Albà, MM. 2013. „Dynamics and adaptive benefits of modular protein evolution.“ Current Opinion in Structural Biology 23 (3): 459–66. 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., und Bornberg-Bauer, Erich G. E.G. 2013. „Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks.“ Molecular Ecology 22 (3): 649. doi: 10.1111/j.1365-294X.2012.05680.x.
• Moore, A., Grath, S., Schüler, A., Huylmans, A., und Bornberg-Bauer, E. 2013. „Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree.“ BBA - Proteins and Proteomics 1834 (5): 898–907. doi: 10.1016/j.bbapap.2013.01.007.
• Mundry, M, Bornberg-Bauer, E, Sammeth, M, und Feulner, PG. 2012. „Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.“ PloS one 7 (2): e31410.. doi: 10.1371/journal.pone.0031410.
• Kersting, AR, Bornberg-Bauer, E, Moore, AD, und Grath, S. 2012. „Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution.“ Genome Biology and Evolution 4 (3): 316–29. doi: 10.1093/gbe/evs004.
• Sikosek, T, Bornberg-Bauer, E, und Chan, HS. 2012. „Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts.“ PLoS Computational Biology 8 (9): e1002659.. doi: 10.1371/journal.pcbi.1002659.
• Sikosek, T, Chan, HS, und Bornberg-Bauer, E. 2012. „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 (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, und Whelan, S. 2012. „The interface of protein structure, protein biophysics, and molecular evolution.“ Protein Science 21 (6): 769–85. 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, und Misof, B. 2012. „Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera.“ Current biology 22 (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, und Weber, AP. 2012. „Identifying core features of adaptive metabolic mechanisms for chronic heat stress attenuation contributing to systems robustness.“ Integrative Biology 4 (5): 480–93. doi: 10.1039/c2ib00109h.
• Balasubramanian, PG, Beckmann, A, Warnken, U, Schnölzer, M, Schüler, A, Bornberg-Bauer, E, Holstein, TW, und Ozbek, S. 2012. „Proteome of Hydra nematocyst.“ Journal of Biological Chemistry 287 (13): 9672–81. doi: 10.1074/jbc.M111.328203.
• Balasubramanian, Prakash G., Beckmann, Anna, Warnken, Uwe, Schnoelzer, Martina, Schueler, Andreas, Bornberg-Bauer, Erich, Holstein, Thomas W., und Oezbek, Suat. 2012. „Proteome of <i>Hydra</i> Nematocyst.“ Journal of Biological Chemistry 287 (13). doi: 10.1074/jbc.M111.328203.
• Moore, A.D., und Bornberg-Bauer, E. 2012. „The dynamics and evolutionary potential of domain loss and emergence.“ Molecular Biology and Evolution 29 (2): 787–796. doi: 10.1093/molbev/msr250.
• Wissler, L, Godmann, L, und Bornberg-Bauer, E. 2012. „Evolutionary dynamics of simple sequence repeats across long evolutionary time in genus Drosphila.“ Trends in Evolutionary Biology 4 (1).
• Terrapon, N, Grath, S, Weiner, J, Moore, A, und Bornberg-Bauer, E. 2012. „Fast Homology Search Using Domain-Architecture Alignment.“ JOBIM, Conference proceedings 1.
• 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, und Currie, CR. 2011. „The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle.“ PLOS Genetics 7 (2): e1002007.. doi: 10.1371/journal.pgen.1002007.
• Wissler, L, Codoñer, FM, Gu, J, Reusch, TB, Olsen, JL, Procaccini, G, und Bornberg-Bauer, E. 2011. „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, und Bornberg-Bauer, E. 2011. „The evolution of protein interaction networks.“ Methods in Molecular Biology 696: 273–89. doi: 10.1007/978-1-60761-987-1_17.
• Franssen, SU, Gu, J, Bergmann, N, Winters, G, Klostermeier, UC, Rosenstiel, P, Bornberg-Bauer, E, und Reusch, TB. 2011. „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 (48): 81. doi: 10.1073/pnas.1107680108.
• Franssen, SU, Shrestha, RP, Brautigam, A, Bornberg-Bauer, E, und Weber, AP. 2011. „Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing.“ BMC Genomics 12 (1): 227.. doi: 10.1186/1471-2164-12-227.
• Reineke, AR, Bornberg-Bauer, E, und Gu, J. 2011. „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, und Noll, GA. 2011. „The sieve element occlusion gene family in dicotyledonous plants.“ Plant Signaling and Behavior 6 (1): 151–3. doi: 10.4161/psb.6.1.14308.
• Bornberg-Bauer, E. 2010. „Signals: tinkering with domains.“ Science Signaling 3 (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, IvHC, 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, MRobertson 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, CVerhulst 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, und Gibbs, RA. 2010. „Functional and evolutionary insights from the genomes of three parasitoid nasonia species.“ Science 327 (5963): 343–348. doi: 10.1126/science.1178028.
• Rüping, B, Ernst, AM, Jekat, SB, Nordzieke, S, Reineke, AR, Müller, B, Bornberg-Bauer, E, Prüfer, D, und Noll, GA. 2010. „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, und Bornberg-Bauer, E. 2010. „Protein Domains as Evolutionary Units.“ In Evolutionary Genomics and System Biology, herausgegeben von Dep of Crop Sciences Bioinformatics Laboratory und USA University of Illinois. unbekannt / n.a. / unknown. doi: 10.1002/9780470570418.ch12.
• Bornberg-Bauer, E, Huylmans, AK, und Sikosek, T. 2010. „How do new proteins arise?“ Current Opinion in Structural Biology 20 (3): 390–6. doi: 10.1016/j.sbi.2010.02.005.
• Bornberg-Bauer, E, und Kramer, L. 2010. „Robustness versus evolvability: a paradigm revisited.“ HFSP Journal 4 (3-4): 105–8. doi: 10.2976/1.3404403.
• Chen, T, Vernazobres, D, Yomo, T, Bornberg-Bauer, E, und Chan, HS. 2010. „Evolvability and single-genotype fluctuation in phenotypic properties: a simple heteropolymer model.“ Biophysical Journal 98 (11): 2487–96. doi: 10.1016/j.bpj.2010.02.046.
• Bornberg-Bauer, Erich, Huylmans, Ann-Kathrin, und Sikosek, Tobias. 2010. „How do new proteins arise?“ Current Opinion in Structural Biology 20 (3). doi: 10.1016/j.sbi.2010.02.005.
• Chen, T., Vernazobres, D., Yomo, T., Bornberg-Bauer, E., und Chan, H. 2010. „EvoIvability and single-genotype fluctuation in phenotypic properties: A simple heteropolymer model.“ Biophysical Journal 98 (11): 2487–2496. doi: 10.1016/j.bpj.2010.02.046.
• Sikosek, T, und Bornberg-Bauer, E. 2010. „Evolution after and before gene duplication?“ In Evolution after Gene Duplication, herausgegeben von D Liberles und K Dittmar. Hoboken, NJ, USA: John Wiley & Sons. doi: 10.1002/9780470619902.ch6.
• Wissler, L, Dattolo, E, Moore, AD, Reusch, TB, Olsen, JL, Migliaccio, M, Bornberg-Bauer, E, und Procaccini, G. 2009. „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, und Bornberg-Bauer, E. 2008. „Just how versatile are domains?“ BMC Evolutionary Biology 8: 285.. doi: 10.1186/1471-2148-8-285.
• Schulenburg, H, Hoeppner, MP, Weiner, J, und Bornberg-Bauer, E. 2008. „Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans.“ Immunobiology 213 (3-4): 237–50. doi: 10.1016/j.imbio.2007.12.004.
• Whitehead, DJ, Wilke, CO, Vernazobres, D, und Bornberg-Bauer, E. 2008. „The look-ahead effect of phenotypic mutations.“ Biology Direct 3: 18.. doi: 10.1186/1745-6150-3-18.
• Moore, AD, Björklund, AK, Ekman, D, Bornberg-Bauer, E, und Elofsson, A. 2008. „Arrangements in the modular evolution of proteins.“ Trends in Biochemical Sciences 33 (9): 444–51. 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, und Bornberg-Bauer, E. 2008. „Comparative analysis of expressed sequence tag (EST) libraries in the seagrass Zostera marina subjected to temperature stress.“ Marine Biotechnology 10 (3): 297–309. doi: 10.1007/s10126-007-9065-6.
• Friedrichs, F, Henckaerts, L, Vermeire, S, Kucharzik, T, Seehafer, T, Moller-Krull, M, Bornberg-Bauer, E, Stoll, M, und {Weiner, 3rd} J. 2008. „The Crohn's disease susceptibility gene DLG5 as a member of the CARD interaction network.“ Journal of Molecular Medicine 86 (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., und Oesterhelt, D. 2008. „Metabolism of halophilic archaea.“ Extremophiles 12 (2): 177–196. doi: 10.1007/s00792-008-0138-x.
• Amoutzias, GD, Pichler, EE, Mian, N, De, Graaf D, Imsiridou, A, Robinson-Rechavi, M, Bornberg-Bauer, E, Robertson, DL, und Oliver, SG. 2007. „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.
• Beaussart, F, Weiner, J, und Bornberg-Bauer, E. 2007. „Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN).“ Bioinformatics 23 (14): 1834–6. 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, und Harter, K. 2007. „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 (2): 347–63. doi: 10.1111/j.1365-313X.2007.03052.x.
• Veron, AS, Kaufmann, K, und Bornberg-Bauer, E. 2007. „Evidence of interaction network evolution by whole-genome duplications: a case study in MADS-box proteins.“ Molecular Biology and Evolution 24 (3): 670–8. doi: 10.1093/molbev/msl197.
• Amoutzias, GD, Veron, AS, Weiner, J, Robinson-Rechavi, M, Bornberg-Bauer, E, Oliver, SG, und Robertson, DL. 2007. „One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity.“ Molecular Biology and Evolution 24 (3): 827–35. doi: 10.1093/molbev/msl211.
• Wroe, R, Chan, HS, und Bornberg-Bauer, E. 2007. „A structural model of latent evolutionary potentials underlying neutral networks in proteins.“ HFSP J. 1: 79–87.
• Amoutzias, GD, Bornberg-Bauer, E, Oliver, SG, und Robertson, DL. 2006. „Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network.“ BMC Genomics 7: 107–107. doi: 10.1186/1471-2164-7-107.
• Weiner, J, Beaussart, F, und Bornberg-Bauer, E. 2006. „Domain deletions and substitutions in the modular protein evolution.“ The FEBS Journal 273 (9): 2037–47. doi: 10.1111/j.1742-4658.2006.05220.x.
• Weiner, J, und Bornberg-Bauer, E. 2006. „Evolution of circular permutations in multidomain proteins.“ Molecular Biology and Evolution 23 (4): 734–43. doi: 10.1093/molbev/msj091.
• Gerke, M, Bornberg-Bauer, E, Jiang, X, und Fuellen, G. 2006. „Finding common protein interaction patterns across organisms.“ Evolutionary Bioinformatics 2: 45–52.
• Teichmann, SA, Bornberg-Bauer, E, und Luscombe, NM. 2005. 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, und Tudzynski, B. 2005. „Distribution of gibberellin biosynthetic genes and gibberellin production in the Gibberella fujikuroi species complex.“ Phytochemistry 66 (11): 1296–1311. doi: 10.1016/j.phytochem.2005.04.012.
• Weiner, J, Thomas, G, und Bornberg-Bauer, E. 2005. „Rapid motif-based prediction of circular permutations in multi-domain proteins.“ Bioinformatics 21 (7): 932–7. doi: 10.1093/bioinformatics/bti085.
• Amoutzias, GD, Weiner, J, und Bornberg-Bauer, E. 2005. „Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs.“ Gene 347 (2): 247–253. doi: 10.1016/j.gene.2004.12.031.
• Bornberg-Bauer, E, Beaussart, F, Kummerfeld, SK, Teichmann, SA, und Weiner, J. 2005. „The evolution of domain arrangements in proteins and interaction networks.“ Cellular and Molecular Life Sciences 62 (4): 435–45. doi: 10.1007/s00018-004-4416-1.
• Wroe, R, Bornberg-Bauer, E, und Chan, HS. 2005. „Comparing folding codes in simple heteropolymer models of protein evolutionary landscape: robustness of the superfunnel paradigm.“ Biophysical Journal 88 (1): 118–131. doi: 10.1529/biophysj.104.050369.
• Amoutzias, GD, Robertson, DL, und Bornberg-Bauer, E. 2004. „The evolution of protein interaction networks in regulatory proteins.“ Comparative and Functional Genomics 5 (1): 79–84. doi: 10.1002/cfg.365.
• Amoutzias, GD, Robertson, DL, Oliver, SG, und Bornberg-Bauer, E. 2004. „Convergent evolution of gene networks by single-gene duplications in higher eukaryotes.“ EMBO Reports 5 (3): 274–9. doi: 10.1038/sj.embor.7400096.
• Do, J.H., Anderson, M.J., Denning, D.W., und Bornberg-Bauer, E. 2004. „Inference of Aspergillus fumigatus pathways by computational genome analysis: Tricarboxylic acic cycle (TCA) and glyoxylate shunt.“ Journal of microbiology and biotechnology 14 (1): 74–80.
• Mabey, JE, Anderson, MJ, Giles, PF, Miller, CJ, Attwood, TK, Paton, NW, Bornberg-Bauer, E, Robson, GD, Oliver, SG, und Denning, DW. 2004. „CADRE: the Central Aspergillus Data REpository.“ Nucleic Acids Research 32 (Database issue): 5. doi: 10.1093/nar/gkh009.
• Bornberg-Bauer, E, und Weiner, J. 2002. A putative transcription factor inducing mobility in Mycoplasma pneumoniae.
• Sirava, M, Schäfer, T, Eiglsperger, M, Kaufmann, M, Kohlbacher, O, Bornberg-Bauer, E, und Lenhof, HP. 2002. „BioMiner--modeling, analyzing, and visualizing biochemical pathways and networks.“ Bioinformatics 18 Suppl 2: 30. doi: 10.1093/bioinformatics/18.suppl_2.S219.
• Chan, HS, und Bornberg-Bauer, E. 2002. „Perspectives on protein evolution from simple exact models.“ Applied Bioinformatics 1 (3): 121–44.
• Bornberg-Bauer, E, und Paton, NW. 2002. „Conceptual data modelling for bioinformatics.“ Briefings in Bioinformatics 3 (2): 166–80. doi: 10.1093/bib/3.2.166.
• Rost, U, und Bornberg-Bauer, E. 2002. „TreeWiz: interactive exploration of huge trees.“ Bioinformatics 18 (1): 109–14. doi: 10.1093/bioinformatics/18.1.109.
• Cui, Y, Wong, H, Bornberg-Bauer, E, und Chan, HS. 2002. „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.
• Kummer, U, Olsen, LF, Dixon, CJ, Green, AK, Bornberg-Bauer, E, und Baier, G. 2000. „Switching from simple to complex oscillations in calcium signaling.“ Biophysical Journal 79 (3): 1188–95. doi: 10.1016/S0006-3495(00)76373-9.
• Bornberg-Bauer, E, und Chan, HS. 1999. „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 (19): 10689–94. doi: 10.1073/pnas.96.19.10689.
• Backofen, R, Will, S, und Bornberg-Bauer, E. 1999. „Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets.“ Bioinformatics 15 (3): 234–42. doi: 10.1093/bioinformatics/15.3.234.
• Krause, A, Nicodème, P, Bornberg-Bauer, E, Rehmsmeier, M, und Vingron, M. 1999. „WWW access to the SYSTERS protein sequence cluster set.“ Bioinformatics 15 (3): 262–3. doi: 10.1093/bioinformatics/15.3.262.
• Bornberg-Bauer, E, Rivals, E, und Vingron, M. 1998. „Computational approaches to identify leucine zippers.“ Nucleic Acids Res. 26 (11): 2740–2746. doi: 10.1093/nar/26.11.2740.
• Renner, A, und Bornberg-Bauer, E. 1997. „Exploring the fitness landscapes of lattice proteins.“ Pacific Symposium on Biocomputing: 361–72.
• Bornberg-Bauer, E. 1997. „How are model protein structures distributed in sequence space?“ Biophysical Journal 73 (5): 2393–403. doi: 10.1016/S0006-3495(97)78268-7.
• Bornberg-Bauer, E. 1996. „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, und Schuster, P. 1993. „RNA folding and combinatory landscapes.“ Physical Review E - Statistical, nonlinear, and soft matter physics 47 (3): 2083–2099.