Erich Bornberg-Bauer - Publications

Affiliations: 
University of Munster, Münster, Nordrhein-Westfalen, Germany 
Area:
Molecular evolution, Biochemistry, Bioinformatics, Genomics

143 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Rivard EL, Ludwig AG, Patel PH, Grandchamp A, Arnold SE, Berger A, Scott EM, Kelly BJ, Mascha GC, Bornberg-Bauer E, Findlay GD. A putative de novo evolved gene required for spermatid chromatin condensation in Drosophila melanogaster. Plos Genetics. 17: e1009787. PMID 34478447 DOI: 10.1371/journal.pgen.1009787  1
2021 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. 1-7. PMID 34313541 DOI: 10.1080/15476286.2021.1952756  1
2021 Harrison MC, Jaimes Niño LM, Rodrigues MA, Ryll J, Flatt T, Oettler J, Bornberg-Bauer E. Gene co-expression network reveals highly conserved, well-regulated anti-ageing mechanisms in old ant queens. Genome Biology and Evolution. PMID 33944936 DOI: 10.1093/gbe/evab093  1
2021 Lange A, Patel PH, Heames B, Damry AM, Saenger T, Jackson CJ, Findlay GD, Bornberg-Bauer E. Structural and functional characterization of a putative de novo gene in Drosophila. Nature Communications. 12: 1667. PMID 33712569 DOI: 10.1038/s41467-021-21667-6  1
2021 Bornberg-Bauer E, Hlouchova K, Lange A. Structure and function of naturally evolved de novo proteins. Current Opinion in Structural Biology. 68: 175-183. PMID 33567396 DOI: 10.1016/j.sbi.2020.11.010  1
2020 Dowling D, Schmitz JF, Bornberg-Bauer E. Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage. Genome Biology and Evolution. 12: 2183-2195. PMID 33210146 DOI: 10.1093/gbe/evaa194  1
2020 Scharsack JP, Wieczorek B, Schmidt-Drewello A, Büscher J, Franke F, Moore A, Branca A, Witten A, Stoll M, Bornberg-Bauer E, Wicke S, Kurtz J. Climate change facilitates a parasite's host exploitation via temperature-mediated immunometabolic processes. Global Change Biology. PMID 33067869 DOI: 10.1111/gcb.15402  1
2020 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. PMID 32533134 DOI: 10.1038/S41589-020-0588-8  1
2020 Schmitz JF, Chain FJJ, Bornberg-Bauer E. Evolution of novel genes in three-spined stickleback populations. Heredity. PMID 32499660 DOI: 10.1038/S41437-020-0319-7  1
2020 Gstöttl C, Stoldt M, Jongepier E, Bornberg-Bauer E, Feldmeyer B, Heinze J, Foitzik S. Comparative analyses of caste, sex, and developmental stage-specific transcriptomes in two ants. Ecology and Evolution. 10: 4193-4203. PMID 32489589 DOI: 10.1002/Ece3.6187  1
2020 Oeyen JP, Baa-Puyoulet P, Benoit JB, Beukeboom LW, Bornberg-Bauer E, Buttstedt A, Calevro F, Cash EI, Chao H, Charles H, Chen MM, Childers C, Cridge AG, Dearden P, Dinh H, et al. Sawfly genomes reveal evolutionary acquisitions that fostered the mega-radiation of parasitoid and eusocial Hymenoptera. Genome Biology and Evolution. PMID 32442304 DOI: 10.1093/Gbe/Evaa106  1
2020 Heames B, Schmitz J, Bornberg-Bauer E. A Continuum of Evolving De Novo Genes Drives Protein-Coding Novelty in Drosophila. Journal of Molecular Evolution. PMID 32253450 DOI: 10.1007/S00239-020-09939-Z  1
2020 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: 30. PMID 32059645 DOI: 10.1186/S12862-020-1591-0  1
2020 Thomas GWC, Dohmen E, Hughes DST, Murali SC, Poelchau M, Glastad K, Anstead CA, Ayoub NA, Batterham P, Bellair M, Binford GJ, Chao H, Chen YH, Childers C, Dinh H, ... ... Bornberg-Bauer E, et al. Gene content evolution in the arthropods. Genome Biology. 21: 15. PMID 31969194 DOI: 10.1186/S13059-019-1925-7  1
2019 van Loo B, Heberlein M, Mair P, Zinchenko A, Schüürmann J, Eenink BDG, Holstein JM, Dilkaute C, Jose J, Hollfelder F, Bornberg-Bauer E. High-Throughput, Lysis-free Screening for Sulfatase Activity Using Autodisplay in Microdroplets. Acs Synthetic Biology. PMID 31738524 DOI: 10.1021/Acssynbio.9B00274  1
2019 Kleppe AS, Bornberg-Bauer E. Robustness by intrinsically disordered C-termini and translational readthrough. Nucleic Acids Research. PMID 31733061 DOI: 10.1093/nar/gkz1106  1
2019 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. PMID 31636435 DOI: 10.1038/S41589-019-0386-3  1
2019 Hartke J, Schell T, Jongepier E, Schmidt H, Sprenger PP, Paule J, Bornberg-Bauer E, Schmitt T, Menzel F, Pfenninger M, Feldmeyer B. Hybrid genome assembly of a neotropical mutualistic ant. Genome Biology and Evolution. PMID 31329228 DOI: 10.1093/Gbe/Evz159  1
2019 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. PMID 31298693 DOI: 10.1093/Gbe/Evz148  1
2019 Kemena C, Dohmen E, Bornberg-Bauer E. DOGMA: a web server for proteome and transcriptome quality assessment. Nucleic Acids Research. PMID 31076763 DOI: 10.1093/Nar/Gkz366  1
2019 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 of London. Series B, Biological Sciences. 374: 20180192. PMID 30967075 DOI: 10.1098/Rstb.2018.0192  1
2019 Bornberg-Bauer E, Heames B. Becoming a de novo gene. Nature Ecology & Evolution. PMID 30858587 DOI: 10.1038/S41559-019-0845-Y  1
2019 Kemena C, Bornberg-Bauer E. A Roadmap to Domain Based Proteomics. Methods in Molecular Biology (Clifton, N.J.). 1851: 287-300. PMID 30298404 DOI: 10.1007/978-1-4939-8736-8_16  1
2018 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. PMID 30597011 DOI: 10.1093/Gbe/Evy269  0.01
2018 Kleppe AS, Bornberg-Bauer E. Robustness by intrinsically disordered C-termini and translational readthrough. Nucleic Acids Research. PMID 30247639 DOI: 10.1093/Nar/Gky778  1
2018 Schmitz JF, Ullrich KK, Bornberg-Bauer E. Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover. Nature Ecology & Evolution. PMID 30201962 DOI: 10.1038/S41559-018-0639-7  1
2018 Bornberg-Bauer E, Harrison MC, Jongepier E. 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: 251-253. PMID 30168666 DOI: 10.1002/Jez.B.22826  1
2018 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. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. PMID 29998472 DOI: 10.1002/Jez.B.22824  1
2018 Kremer LPM, Korb J, Bornberg-Bauer E. Reconstructed evolution of insulin receptors in insects reveals duplications in early insects and cockroaches. Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution. PMID 29888542 DOI: 10.1002/Jez.B.22809  1
2018 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. PMID 29845724 DOI: 10.1002/Jez.B.22805  1
2018 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. PMID 29802682 DOI: 10.1111/febs.14504  1
2018 van Loo B, Schober M, Valkov E, Heberlein M, Bornberg-Bauer E, Faber K, Hyvönen M, Hollfelder F. Structural and Mechanistic Analysis of the Choline Sulfatase from Sinorhizobium melliloti: A Class I Sulfatase Specific for an Alkyl Sulfate Ester. Journal of Molecular Biology. PMID 29458126 DOI: 10.1016/J.Jmb.2018.02.010  1
2018 Lopez-Ezquerra A, Mitschke A, Bornberg-Bauer E, Joop G. Tribolium castaneum gene expression changes after Paranosema whitei infection. Journal of Invertebrate Pathology. PMID 29452083 DOI: 10.1016/J.Jip.2018.02.009  1
2018 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, ... Bornberg-Bauer E, et al. Hemimetabolous genomes reveal molecular basis of termite eusociality. Nature Ecology & Evolution. PMID 29403074 DOI: 10.1038/S41559-017-0459-1  1
2017 Lopez-Ezquerra A, Harrison MC, Bornberg-Bauer E. Comparative analysis of lincRNA in insect species. Bmc Evolutionary Biology. 17: 155. PMID 28673235 DOI: 10.1186/S12862-017-0985-0  1
2017 van Loo B, Bornberg-Bauer E. Enzyme sub-functionalization driven by regulation. Embo Reports. PMID 28615289 DOI: 10.15252/embr.201744383  1
2017 Schmitz JF, Bornberg-Bauer E. Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA. F1000research. 6: 57. PMID 28163910 DOI: 10.12688/F1000Research.10079.1  1
2017 Gubala AM, Schmitz JF, Kearns MJ, Vinh TT, Bornberg-Bauer E, Wolfner MF, Findlay GD. The goddard and saturn genes are essential for Drosophila male fertility and may have arisen de novo. Molecular Biology and Evolution. PMID 28104747 DOI: 10.1093/Molbev/Msx057  1
2016 Elsner D, Kremer LP, Arning N, Bornberg-Bauer E. Chapter 6. Comparative genomic approaches to investigate molecular traits specific to social insects. Current Opinion in Insect Science. 16: 87-94. PMID 27720056 DOI: 10.1016/J.Cois.2016.05.016  1
2016 Schüler A, Bornberg-Bauer E. Evolution of Protein Domain Repeats in Metazoa. Molecular Biology and Evolution. PMID 27671125 DOI: 10.1093/Molbev/Msw194  1
2016 Jueterbock A, Franssen SU, Bergmann N, Gu J, Coyer JA, Reusch TB, Bornberg-Bauer E, Olsen JL. Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass. Molecular Ecology. PMID 27598849 DOI: 10.1111/Mec.13829  1
2016 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, Germany). PMID 27373340 DOI: 10.1016/J.Zool.2016.05.005  1
2016 Schmitz JF, Zimmer F, Bornberg-Bauer E. Mechanisms of transcription factor evolution in Metazoa. Nucleic Acids Research. PMID 27288445 DOI: 10.1093/Nar/Gkw492  1
2016 Dohmen E, Kremer LP, Bornberg-Bauer E, Kemena C. DOGMA: Domain-based transcriptome and proteome quality assessment. Bioinformatics (Oxford, England). PMID 27153665 DOI: 10.1093/Bioinformatics/Btw231  1
2016 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, ... Bornberg-Bauer E, et al. The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature. PMID 26814964 DOI: 10.1038/Nature16548  1
2016 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. PMID 26749022 DOI: 10.1111/Mec.13520  1
2016 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: 137-44. PMID 26400836 DOI: 10.1016/J.Dci.2015.09.008  1
2015 Bornberg-Bauer E, Schmitz J, Heberlein M. Emergence of de novo proteins from 'dark genomic matter' by 'grow slow and moult'. Biochemical Society Transactions. 43: 867-73. PMID 26517896 DOI: 10.1042/Bst20150089  1
2015 Smith CR, Helms Cahan S, Kemena C, Brady SG, Yang W, Bornberg-Bauer E, Eriksson T, Gadau J, Helmkampf M, Gotzek D, Okamoto Miyakawa M, Suarez AV, 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: 2919-31. PMID 26226984 DOI: 10.1093/Molbev/Msv165  1
2015 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. Correction: Genomics of Divergence along a Continuum of Parapatric Population Differentiation. Plos Genetics. 11: e1005414. PMID 26226517 DOI: 10.1371/Journal.Pgen.1005414  1
2015 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 Biology and Evolution. PMID 26100409 DOI: 10.1093/Gbe/Evv091  1
2015 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, ... Bornberg-Bauer E, et al. Host-Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes. Plos Biology. 13: e1002169. PMID 26042786 DOI: 10.1371/Journal.Pbio.1002169  1
2015 Bitard-Feildel T, Kemena C, Greenwood JM, Bornberg-Bauer E. Domain similarity based orthology detection. Bmc Bioinformatics. 16: 154. PMID 25968113 DOI: 10.1186/S12859-015-0570-8  1
2015 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, et al. The genomes of two key bumblebee species with primitive eusocial organization. Genome Biology. 16: 76. PMID 25908251 DOI: 10.1186/S13059-015-0623-3  1
2015 Bitard-Feildel T, Heberlein M, Bornberg-Bauer E, Callebaut I. Detection of orphan domains in Drosophila using "hydrophobic cluster analysis". Biochimie. PMID 25736992 DOI: 10.1016/J.Biochi.2015.02.019  1
2015 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. 11: e1004966. PMID 25679225 DOI: 10.1371/Journal.Pgen.1004966  1
2015 Kemena C, Bitard-Feildel T, Bornberg-Bauer E. MDAT- Aligning multiple domain arrangements. Bmc Bioinformatics. 16: 19. PMID 25626688 DOI: 10.1186/S12859-014-0442-7  1
2015 Kersting AR, Mizrachi E, Bornberg-Bauer E, Myburg AA. Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus. The New Phytologist. 206: 1328-36. PMID 25494981 DOI: 10.1111/Nph.13211  1
2014 Chain FJ, Feulner PG, Panchal M, Eizaguirre C, Samonte IE, Kalbe M, Lenz TL, Stoll M, Bornberg-Bauer E, Milinski M, Reusch TB. Extensive copy-number variation of young genes across stickleback populations. Plos Genetics. 10: e1004830. PMID 25474574 DOI: 10.1371/Journal.Pgen.1004830  1
2014 Haase D, Rieger JK, Witten A, Stoll M, Bornberg-Bauer E, Kalbe M, Reusch TB. Specific gene expression responses to parasite genotypes reveal redundancy of innate immunity in vertebrates. Plos One. 9: e108001. PMID 25254967 DOI: 10.1371/Journal.Pone.0108001  1
2014 Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, Hayes RD, Grimwood J, Jenkins J, Lindquist E, Tice H, Bauer D, Goodstein DM, Dubchak I, Poliakov A, Mizrachi E, Kullan AR, ... Bornberg-Bauer E, et al. The genome of Eucalyptus grandis. Nature. 510: 356-62. PMID 24919147 DOI: 10.1038/Nature13308  1
2014 Behrens S, Peuß R, Milutinovi? 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. 15: 445. PMID 24908078 DOI: 10.1186/1471-2164-15-445  1
2014 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, ... Bornberg-Bauer E, et al. Molecular traces of alternative social organization in a termite genome. Nature Communications. 5: 3636. PMID 24845553 DOI: 10.1038/Ncomms4636  1
2014 Franssen SU, Gu J, Winters G, Huylmans AK, Wienpahl I, Sparwel M, Coyer JA, Olsen JL, Reusch TB, Bornberg-Bauer E. Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types. Marine Genomics. 15: 65-73. PMID 24703884 DOI: 10.1016/J.Margen.2014.03.004  1
2014 Moore AD, Held A, Terrapon N, Weiner J, Bornberg-Bauer E. DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins. Bioinformatics (Oxford, England). 30: 282-3. PMID 24222210 DOI: 10.1093/Bioinformatics/Btt640  1
2014 Terrapon N, Weiner J, Grath S, Moore AD, Bornberg-Bauer E. Rapid similarity search of proteins using alignments of domain arrangements. Bioinformatics (Oxford, England). 30: 274-81. PMID 23828785 DOI: 10.1093/Bioinformatics/Btt379  1
2013 Guo B, Chain FJ, Bornberg-Bauer E, Leder EH, Merilä J. Genomic divergence between nine- and three-spined sticklebacks. Bmc Genomics. 14: 756. PMID 24188282 DOI: 10.1186/1471-2164-14-756  1
2013 Simola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, Viljakainen L, Reese JT, Hunt BG, Graur D, Elhaik E, Kriventseva EV, ... Bornberg-Bauer E, et al. Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Research. 23: 1235-47. PMID 23636946 DOI: 10.1101/Gr.155408.113  1
2013 Bornberg-Bauer E, Albà MM. Dynamics and adaptive benefits of modular protein evolution. Current Opinion in Structural Biology. 23: 459-66. PMID 23562500 DOI: 10.1016/J.Sbi.2013.02.012  1
2013 Moore AD, Grath S, Schüler A, Huylmans AK, Bornberg-Bauer E. Quantification and functional analysis of modular protein evolution in a dense phylogenetic tree. Biochimica Et Biophysica Acta. 1834: 898-907. PMID 23376183 DOI: 10.1016/J.Bbapap.2013.01.007  1
2013 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: 439-55. PMID 23348040 DOI: 10.1093/Gbe/Evt009  1
2013 Feulner PG, Chain FJ, Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Mundry M, Samonte IE, Stoll M, Milinski M, Reusch TB, Bornberg-Bauer E. Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks. Molecular Ecology. 22: 635-49. PMID 22747593 DOI: 10.1111/J.1365-294X.2012.05680.X  1
2012 Sikosek T, Bornberg-Bauer E, Chan HS. Evolutionary dynamics on protein bi-stability landscapes can potentially resolve adaptive conflicts. Plos Computational Biology. 8: e1002659. PMID 23028272 DOI: 10.1371/Journal.Pcbi.1002659  1
2012 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: 14888-93. PMID 22927372 DOI: 10.1073/Pnas.1115620109  1
2012 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, ... Bornberg-Bauer E, et al. Genomic and morphological evidence converge to resolve the enigma of Strepsiptera. Current Biology : Cb. 22: 1309-13. PMID 22704986 DOI: 10.1016/J.Cub.2012.05.018  1
2012 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, et al. The interface of protein structure, protein biophysics, and molecular evolution. Protein Science : a Publication of the Protein Society. 21: 769-85. PMID 22528593 DOI: 10.1002/Pro.2071  1
2012 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 : Quantitative Biosciences From Nano to Macro. 4: 480-93. PMID 22402787 DOI: 10.1039/C2Ib00109H  1
2012 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: e31410. PMID 22384018 DOI: 10.1371/Journal.Pone.0031410  1
2012 Balasubramanian PG, Beckmann A, Warnken U, Schnölzer M, Schüler A, Bornberg-Bauer E, Holstein TW, Ozbek S. Proteome of Hydra nematocyst. The Journal of Biological Chemistry. 287: 9672-81. PMID 22291027 DOI: 10.1074/Jbc.M111.328203  1
2012 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: 316-29. PMID 22250127 DOI: 10.1093/Gbe/Evs004  1
2012 Moore AD, Bornberg-Bauer E. The dynamics and evolutionary potential of domain loss and emergence. Molecular Biology and Evolution. 29: 787-96. PMID 22016574 DOI: 10.1093/Molbev/Msr250  1
2012 Chain FJJ, Feulner PGD, Panchal M, Eizaguirre C, Kalbe M, Stoll M, Reusch TBH, Bornberg-Bauer E, Milinski M. Sex chromosome differentiation across stickleback populations F1000research. 3. DOI: 10.7490/F1000Research.1092195.1  1
2012 Wissler L, Godmann L, Bornberg-Bauer E. Evolutionary dynamics of simple sequence repeats across long evolutionary time scale in genus Drosophila Trends in Evolutionary Biology. 4: 34-44. DOI: 10.4081/Eb.2012.E7  1
2011 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: 19276-81. PMID 22084086 DOI: 10.1073/Pnas.1107680108  1
2011 Franssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E, Weber AP. Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing. Bmc Genomics. 12: 227. PMID 21569327 DOI: 10.1186/1471-2164-12-227  1
2011 Reineke AR, Bornberg-Bauer E, Gu J. Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes. Nucleic Acids Research. 39: 6029-43. PMID 21470961 DOI: 10.1093/Nar/Gkr179  1
2011 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 & Behavior. 6: 151-3. PMID 21422825 DOI: 10.4161/Psb.6.1.14308  1
2011 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, et al. The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. Plos Genetics. 7: e1002007. PMID 21347285 DOI: 10.1371/Journal.Pgen.1002007  1
2011 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. PMID 21226908 DOI: 10.1186/1471-2148-11-8  1
2011 Schüler A, Bornberg-Bauer E. The evolution of protein interaction networks. Methods in Molecular Biology (Clifton, N.J.). 696: 273-89. PMID 21063954 DOI: 10.1007/978-1-60761-987-1_17  1
2011 Sikosek T, Bornberg-Bauer E. Evolution After and Before Gene Duplication? Evolution After Gene Duplication. 105-131. DOI: 10.1002/9780470619902.ch6  1
2010 Bornberg-Bauer E, Kramer L. Robustness versus evolvability: a paradigm revisited. Hfsp Journal. 4: 105-8. PMID 21119763 DOI: 10.2976/1.3404403  1
2010 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: 219. PMID 20932300 DOI: 10.1186/1471-2229-10-219  1
2010 Bornberg-Bauer E. Signals: tinkering with domains. Science Signaling. 3: pe31. PMID 20841566 DOI: 10.1126/Scisignal.3139Pe31  1
2010 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: 2487-96. PMID 20513392 DOI: 10.1016/J.Bpj.2010.02.046  1
2010 Bornberg-Bauer E, Huylmans AK, Sikosek T. How do new proteins arise? Current Opinion in Structural Biology. 20: 390-6. PMID 20347587 DOI: 10.1016/J.Sbi.2010.02.005  1
2010 Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, ... Bornberg-Bauer E, et al. Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (New York, N.Y.). 327: 343-8. PMID 20075255 DOI: 10.1126/Science.1178028  1
2010 Moore AD, Bornberg-Bauer E. Protein Domains as Evolutionary Units Evolutionary Genomics and Systems Biology. 213-230. DOI: 10.1002/9780470570418.ch12  1
2009 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. PMID 20157482 DOI: 10.1093/Database/Bap009  1
2008 Weiner J, Moore AD, Bornberg-Bauer E. Just how versatile are domains? Bmc Evolutionary Biology. 8: 285. PMID 18854028 DOI: 10.1186/1471-2148-8-285  1
2008 Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A. Arrangements in the modular evolution of proteins. Trends in Biochemical Sciences. 33: 444-51. PMID 18656364 DOI: 10.1016/J.Tibs.2008.05.008  1
2008 Whitehead DJ, Wilke CO, Vernazobres D, Bornberg-Bauer E. The look-ahead effect of phenotypic mutations. Biology Direct. 3: 18. PMID 18479505 DOI: 10.1186/1745-6150-3-18  1
2008 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: 237-50. PMID 18406370 DOI: 10.1016/J.Imbio.2007.12.004  1
2008 Friedrichs F, Henckaerts L, Vermeire S, Kucharzik T, Seehafer T, Möller-Krull M, Bornberg-Bauer E, Stoll M, Weiner J. The Crohn's disease susceptibility gene DLG5 as a member of the CARD interaction network. Journal of Molecular Medicine (Berlin, Germany). 86: 423-32. PMID 18335190 DOI: 10.1007/S00109-008-0307-5  1
2008 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 : Life Under Extreme Conditions. 12: 177-96. PMID 18278431 DOI: 10.1007/S00792-008-0138-X  1
2008 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 (New York, N.Y.). 10: 297-309. PMID 18239962 DOI: 10.1007/S10126-007-9065-6  1
2007 Wroe R, Chan HS, Bornberg-Bauer E. A structural model of latent evolutionary potentials underlying neutral networks in proteins. Hfsp Journal. 1: 79-87. PMID 19404462 DOI: 10.2976/1.2739116/10.2976/1  1
2007 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. PMID 17672894 DOI: 10.1186/1752-0509-1-34  1
2007 Beaussart F, Weiner J, Bornberg-Bauer E. Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN). Bioinformatics (Oxford, England). 23: 1834-6. PMID 17483506 DOI: 10.1093/Bioinformatics/Btm240  1
2007 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 : For Cell and Molecular Biology. 50: 347-63. PMID 17376166 DOI: 10.1111/J.1365-313X.2007.03052.X  1
2007 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: 827-35. PMID 17194801 DOI: 10.1093/Molbev/Msl211  1
2007 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: 670-8. PMID 17175526 DOI: 10.1093/Molbev/Msl197  1
2006 Gerke M, Bornberg-Bauer E, Jiang X, Fuellen G. Finding common protein interaction patterns across organisms. Evolutionary Bioinformatics Online. 2: 45-52. PMID 19455201 DOI: 10.4137/Ebo.S0  0.01
2006 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. PMID 16674813 DOI: 10.1186/1471-2164-7-107  1
2006 Weiner J, Beaussart F, Bornberg-Bauer E. Domain deletions and substitutions in the modular protein evolution. The Febs Journal. 273: 2037-47. PMID 16640566 DOI: 10.1111/j.1742-4658.2006.05220.x  1
2006 Weiner J, Bornberg-Bauer E. Evolution of circular permutations in multidomain proteins. Molecular Biology and Evolution. 23: 734-43. PMID 16431849 DOI: 10.1093/Molbev/Msj091  1
2005 Teichmann SA, Bornberg-Bauer E, Luscombe NM. Transcriptional networking. Genome Biology. 6: 344. PMID 16168097 DOI: 10.1186/gb-2005-6-9-344  1
2005 Malonek S, Bömke 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: 1296-311. PMID 15925394 DOI: 10.1016/J.Phytochem.2005.04.012  1
2005 Weiner J, Thomas G, Bornberg-Bauer E. Rapid motif-based prediction of circular permutations in multi-domain proteins. Bioinformatics (Oxford, England). 21: 932-7. PMID 15788783 DOI: 10.1093/Bioinformatics/Bti085  1
2005 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: 247-53. PMID 15777629 DOI: 10.1016/J.Gene.2004.12.031  1
2005 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 : Cmls. 62: 435-45. PMID 15719170 DOI: 10.1007/S00018-004-4416-1  1
2005 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: 118-31. PMID 15501948 DOI: 10.1529/Biophysj.104.050369  1
2004 Amoutzias GD, Robertson DL, Bornberg-Bauer E. The evolution of protein interaction networks in regulatory proteins. Comparative and Functional Genomics. 5: 79-84. PMID 18629034 DOI: 10.1002/Cfg.365  1
2004 Amoutzias GD, Robertson DL, Oliver SG, Bornberg-Bauer E. Convergent evolution of gene networks by single-gene duplications in higher eukaryotes. Embo Reports. 5: 274-9. PMID 14968135 DOI: 10.1038/sj.embor.7400096  1
2004 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: D401-5. PMID 14681443 DOI: 10.1093/nar/gkh009  1
2004 Amoutzias GD, Robertson DL, Bornberg-Bauer E. The evolution of protein interaction networks in regulatory proteins: Conference Reviews Comparative and Functional Genomics. 5: 79-84. DOI: 10.1002/Cfg.V5:1  1
2002 Chan HS, Bornberg-Bauer E. Perspectives on protein evolution from simple exact models. Applied Bioinformatics. 1: 121-44. PMID 15130840  1
2002 Bornberg-Bauer E, Weiner J. A putative transcription factor inducing mobility in Mycoplasma pneumoniae. Microbiology (Reading, England). 148: 3764-5. PMID 12480880 DOI: 10.1099/00221287-148-12-3764  1
2002 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 (Oxford, England). 18: S219-30. PMID 12386006 DOI: 10.1093/BIOINFORMATICS/18.SUPPL_2.S219  1
2002 Bornberg-Bauer E, Paton NW. Conceptual data modelling for bioinformatics. Briefings in Bioinformatics. 3: 166-80. PMID 12139436 DOI: 10.1093/Bib/3.2.166  1
2002 Rost U, Bornberg-Bauer E. TreeWiz: interactive exploration of huge trees. Bioinformatics (Oxford, England). 18: 109-14. PMID 11836218 DOI: 10.1093/Bioinformatics/18.1.109  1
2002 Cui Y, Wong WH, Bornberg-Bauer E, Chan HS. Recombinatoric exploration of novel folded structures: a heteropolymer-based model of protein evolutionary landscapes. Proceedings of the National Academy of Sciences of the United States of America. 99: 809-14. PMID 11805332 DOI: 10.1073/Pnas.022240299  1
2002 Bornberg-Bauer E. Randomness, Structural Uniqueness, Modularity and Neutral Evolution in Sequence Space of Model Proteins Zeitschrift FüR Physikalische Chemie. 216. DOI: 10.1524/zpch.2002.216.2.139  0.01
2002 Bornberg-Bauer E. Randomness, structural uniqueness, modularity and neutral evolution in sequence space of model proteins Zeitschrift Fur Physikalische Chemie. 216: 139-154. DOI: 10.1524/Zpch.2002.216.2.139  1
2000 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: 1188-95. PMID 10968983 DOI: 10.1016/S0006-3495(00)76373-9  1
1999 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: 10689-94. PMID 10485887 DOI: 10.1073/Pnas.96.19.10689  1
1999 Krause A, Nicodème P, Bornberg-Bauer E, Rehmsmeier M, Vingron M. WWW access to the SYSTERS protein sequence cluster set. Bioinformatics (Oxford, England). 15: 262-3. PMID 10222416 DOI: 10.1093/bioinformatics/15.3.262  1
1999 Backofen R, Will S, Bornberg-Bauer E. Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets. Bioinformatics (Oxford, England). 15: 234-42. PMID 10222411 DOI: 10.1093/bioinformatics/15.3.234  1
1998 Bornberg-Bauer E, Rivals E, Vingron M. Computational approaches to identify leucine zippers. Nucleic Acids Research. 26: 2740-6. PMID 9592163 DOI: 10.1093/Nar/26.11.2740  1
1997 Bornberg-Bauer E. How are model protein structures distributed in sequence space? Biophysical Journal. 73: 2393-403. PMID 9370433 DOI: 10.1016/S0006-3495(97)78268-7  1
1996 Bornberg-Bauer E. Random structures and evolution of biopolymers: A computational case study on RNA secondary structures Pharmaceutica Acta Helvetiae. 71: 79-85. DOI: 10.1016/0031-6865(95)00053-4  1
1996 Tacker M, Stadler PF, Bornberg-Bauer EG, Hofacker IL, Schuster P. Algorithm independent properties of RNA secondary structure predictions European Biophysics Journal. 25: 115-130. DOI: 10.1007/S002490050023  1
1994 Bornberg-Bauer EG, Stadler PF. Random structures and evolution of biopolymers Berichte Der Bunsengesellschaft FüR Physikalische Chemie. 98: 1128-1128. DOI: 10.1002/bbpc.19940980910  0.2
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