2021

Buchholz, Patrick C. F.; van Loo, Bert; Eenink, Bernard D. G.; Bornberg-Bauer, Erich; Pleiss, Jürgen

Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation Journal Article Forthcoming

In: Forthcoming.

Abstract | Links | BibTeX

Eenink, Bernard D. G.; Kaminski, Thomasz S.; Bornberg-Bauer, Erich; Jose, Joachim; Hollfelder, Florian; van Loo, Bert

Vector Redesign and In-Droplet Cell-Growth Improves Enrichment and Recovery Journal Article Forthcoming

In: Forthcoming.

Abstract | Links | BibTeX

Harrison, Mark C.; Mallon, EB; Hammond, RL

Purged haploids - sheltered diploids: ploidy in uences selection efficacy in a haplodiploid bee. Journal Article Forthcoming

In: Forthcoming.

Abstract | Links | BibTeX

Scharsack, Jörn Peter; Wieczorek, Barth; Schmidt-Drewello, Alexander Manuel; Büscher, Janine; Franke, Frederik; Moore, Andrew; Branca, Antoine; Witten, Anika; Stoll, Monika; Bornberg-Bauer, Erich; Wicke, Susann; Kurtz, Joachim

Temperature variation shifts immune and metabolic activity in three-spined sticklebacks (Gasterosteus aculeatus) infected with the cestode Schistocephalus solidus Journal Article Forthcoming

In: Forthcoming.

Abstract | Links | BibTeX

Martens, Leonie; Rühle, Frank; Witten, Anika; Meder, Benjamin; Katus, Hugo A.; Arbustini, Eloisa; Hasenfuss, Gerd; Sinner, Moritz F.; Kaab, Stefan; Pankuweit, Sabine; Angermann, Christiane; Bornberg-Bauer, Erich; Stoll, Monika

A genetic variant alters the secondary structure of the lncRNA H19 and is associated with Dilated Cardiomyopathy Journal Article

In: RNA Biology, 2021.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; Hlouchova, Klara; Lange, Andreas

Structure and function of naturally evolved de novo proteins Journal Article

In: Current Opinion in Structural Biology, 68 , pp. 175-183, 2021.

Abstract | Links | BibTeX

Harrison, Mark C.; Niño, Luisa M. Jaimes; Rodrigues, Marisa Almeida; Ryll, Judith; Flatt, Thomas; Oettler, Jan; Bornberg-Bauer, Erich

Gene Coexpression Network Reveals Highly Conserved,Well- Regulated Anti-AgeingMechanisms in Old Ant Queens Journal Article

In: Genome Biology and Evolution, 13 (6), 2021.

Abstract | Links | BibTeX

Séguret, Alice; Stolle, Eckart; Fleites-Ayil, Fernando A; Quezada-Euán, José Javier G; Hartfelder, Klaus; Meusemann, Karen; Harrison, Mark C.; Soro, Antonella; Paxton, Robert J

Transcriptomic Signatures of Ageing Vary in Solitary and Social Forms of an Orchid Bee Journal Article

In: Genome Biology and Evolution, 13 (6), 2021.

Abstract | Links | BibTeX

Lange, Andreas; Patel, Prajal H.; Heames, Brennen; Damry, Adam M.; Saenger, Thorsten; Jackson, Colin J.; Findlay, Geoffrey D.; Bornberg-Bauer, Erich

Structural and functional characterization of a putative de novo gene in Drosophila Journal Article

In: Nature Communications, 12 (1667), 2021.

Abstract | Links | BibTeX

He, Shulin; Sieksmeyer, Thorben; Che, Yanli; Mora, M. Alejandra Esparza; Stiblik, Petr; Banasiak, Ronald; Harrison, Mark C.; Šobotník, Jan; Wang, Zongqing; Johnston, Paul R.; McMahon, Dino P.

Evidence for reduced immune gene diversity and activity during the evolution of termites Journal Article

In: Proceedings of the Royal Society B, 288 (1945), 2021.

Abstract | Links | BibTeX

2020

Harrison, Mark C.; Chernyshova, Anna M.; Thompson, Graham J.

No obvious transcriptome‐wide signature of indirect selection in termites Journal Article

In: Journal of Evolutionary Biology, 34 (2), pp. 403-415, 2020.

Abstract | Links | BibTeX

Scharsack, Jörn P.; Wieczorek, Bartholomäus; Schmidt‐Drewello, Alexander; Büscher, Janine; Franke, Frederik; Moore, Andrew D.; Branca, Antoine; Witten, Anika; Stoll, Monika; Bornberg-Bauer, Erich; Wicke, Susann; Kurtz, Joachim

Climate change facilitates a parasite’s host exploitation via temperature-mediated immunometabolic processes Journal Article

In: Global Change Biology, 27 (1), pp. 94-107, 2020.

Abstract | Links | BibTeX

Dowling, Daniel; Schmitz, Jonathan F.; Bornberg-Bauer, Erich

Stochastic Gain and Loss of Novel Transcribed Open Reading Frames in the Human Lineage Journal Article

In: Genome Biology and Evolution, 12 (11), pp. 2183–2195, 2020.

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Schmitz, Jonathan F.; Chain, Frédéric J. J.; Bornberg-Bauer, Erich

Evolution of novel genes in three-spined stickleback populations Journal Article

In: Heredity, 125 , pp. 50-59, 2020.

Abstract | Links | BibTeX

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; Dinh, Huyen; 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; Lesný, Peter; Lovegrove, Mackenzie; Martin, Sebastian; Martynov, Alexander G; Mayer, Christoph; Montagné, 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, Björn 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; Niehuis, Oliver

Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera Journal Article

In: Genome Biology and Evolution, 12 (7), pp. 1099–1188, 2020.

Abstract | Links | BibTeX

Heames, Brennen; Schmitz, Jonathan F.; Bornberg-Bauer, Erich

A Continuum of Evolving De Novo Genes Drives Protein‑Coding Novelty in Drosophila Journal Article

In: Journal of Molecular Evolution, 88 , pp. 382–398, 2020.

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Gstöttl, Claudia; Stoldt, Marah; Jongepier, Evelien; Bornberg-Bauer, Erich; Feldmeyer, Barbara; Heinze, Jürgen; Foitzik, Susanne

Comparative analyses of caste, sex, and developmental stage‐specific transcriptomes in two Temnothorax ants Journal Article

In: Ecology and Evolution, 10 (10), pp. 4193-4203, 2020.

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Dohmen, Elias; Klasberg, Steffen; Bornberg-Bauer, Erich; Perrey, Sören; Kemena, Carsten

The modular nature of protein evolution: domain rearrangement rates across eukaryotic life Journal Article

In: BMC Evolutionary Biology, 20 (30), 2020.

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Thomas, Gregg W. C.; Dohmen, Elias; Hughes, Daniel S. T.; Murali, Shwetha C.; Poelchau, Monica; Glastad, Karl; Anstead, Clare A.; Ayoub, Nadia A.; Batterham, Phillip; Bellair, Michelle; Binford, Gretta J.; Chao, Hsu; Chen, Yolanda H.; Childers, Christopher; Dinh, Huyen; Doddapaneni, HarshaVardhan; Duan, Jian J.; Dugan, Shannon; Esposito, Lauren A.; Friedrich, Markus; Garb, Jessica; Gasser, Robin B.; Goodisman, Michael A. D.; Gundersen-Rindal, Dawn E.; Han, Yi; Handler, Alfred M.; Hatakeyama, Masatsugu; Hering, Lars; Hunter, Wayne B.; Ioannidis, Panagiotis; Jayaseelan, Joy C.; Kalra, Divya; Khila, Abderrahman; Korhonen, Pasi K.; Lee, Carol Eunmi; Lee, Sandra L.; Li, Yiyuan; Lindsey, Amelia R. I.; Mayer, Georg; McGregor, Alistair P.; McKenna, Duane D.; Misof, Bernhard; Munidasa, Mala; Munoz-Torres, Monica; Muzny, Donna M.; Niehuis, Oliver; Osuji-Lacy, Nkechinyere; Palli, Subba R.; Panfilio, Kristen A.; Pechmann, Matthias; Perry, Trent; Peters, Ralph S.; Poynton, Helen C.; Prpic, Nikola-Michael; Qu, Jiaxin; Rotenberg, Dorith; Schal, Coby; Schoville, Sean D.; Scully, Erin D.; Skinner, Evette; Sloan, Daniel B.; Stouthamer, Richard; Strand, Michael R.; Szucsich, Nikolaus U.; Wijeratne, Asela; Young, Neil D.; Zattara, Eduardo E.; Benoit, Joshua B.; Zdobnov, Evgeny M.; Pfrender, Michael E.; Hackett, Kevin J.; Werren, John H.; Worley, Kim C.; Gibbs, Richard A.; Chipman, Ariel D.; Waterhouse, Robert M.; Bornberg-Bauer, Erich; Hahn, Matthew W.; Richards, Stephen

Gene content evolution in the arthropods Journal Article

In: Genome Biology, 21 (15), 2020.

Abstract | Links | BibTeX

2019

van Loo, Bert; Heberlein, Magdalena; Mair, Philip; Zinchenko, Anastasia; Schüürmann, Jan; Eenink, Bernard D. G.; Holstein, Josephin M.; Dilkaute, Carina; Jose, Joachim; Hollfelder, Florian; Bornberg-Bauer, Erich

High-Throughput, Lysis-Free Screening for Sulfatase Activity Using Escherichia coli Autodisplay in Microdroplets Journal Article

In: ACS synthetic biology, 8 (12), pp. 2690-2700, 2019.

Abstract | Links | BibTeX

Kleppe, April Snofrid; Bornberg-Bauer, Erich

Translational readthrough goes unseen by natural selection Journal Article Forthcoming

In: Forthcoming.

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Yang, Gloria; Anderson, Dave W; Baier, Florian; Dohmen, Elias; Hong, Nansook; Carr, Paul D; Kamerlin, Shina Caroline Lynn; Jackson, Colin J; Bornberg-Bauer, Erich; Tokuriki, Nobuhiko

Higher-order epistasis shapes the fitness landscape of a xenobiotic-degrading enzyme Journal Article

In: Nature Chemical Biology, 15 , pp. pages1120–1128, 2019.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; Heames, Brennen

Becoming a de Novo gene Journal Article

In: Nature Ecology & Evolution, 2019.

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Hartke, Juliane; Schell, Tilman; Jongepier, Evelien; Schmidt, Hanno; Sprenger, Philipp P; Paule, Juraj; Bornberg-Bauer, Erich; Schmitt, Thomas; Menzel, Florian; Pfenninger, Markus; Feldmeyer, Barbara

Hybrid genome assembly of a neotropical mutualistic ant Journal Article

In: Genome Biology and Evolution, 11 (8), pp. 2306–2311, 2019.

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Huang, Yun; Feulner, Philine G. D.; Eizaguirre, Christophe; Lenz, Tobias L; Bornberg-Bauer, Erich; Milinski, Manfred; Reusch, Thorsten B H; Chain, Frédéric J J

Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes Journal Article

In: Genome Biology and Evolution, 11 (8), pp. 2344–2359, 2019.

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Kemena, Carsten; Dohmen, Elias; Bornberg-Bauer, Erich

DOGMA: a web server for proteome and transcriptome quality assessment Journal Article

In: Nucleic Acids Research, 47 (W1), pp. W507–W510, 2019.

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Kaur, Rajbir; Stoldt, Marah; Jongepier, Evelien; Feldmeyer, Barbara; Menzel, Florian; Bornberg-Bauer, Erich; Foitzik, Susanne

Ant behaviour and brain gene expression of defending hosts depend on the ecological success of the intruding social parasite Journal Article

In: Philosophical Transactions of the Royal Society B, 374 (1769), 2019.

Abstract | Links | BibTeX

2018

Kurafeiski, Jasmin D; Pinto, Paulo; Bornberg-Bauer, Erich

Evolutionary Potential of Cis-Regulatory Mutations to Cause Rapid Changes in Transcription Factor Binding Journal Article

In: Genome Biology and Evolution, 11 (2), pp. 406–414, 2018.

Abstract | Links | BibTeX

Kleppe, April Snofrid; Bornberg-Bauer, Erich

Robustness by intrinsically disordered C-termini and translational readthrough Journal Article

In: Nucleic Acids Research, 46 (19), pp. 10184–10194, 2018.

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Schmitz, Jonathan F.; Ullrich , Kristian K.; Bornberg-Bauer, Erich

Incipient de novo genes can evolve from frozen accidents that escaped rapid transcript turnover Journal Article

In: Nature Ecology & Evolution, 2 , pp. 1626–1632, 2018.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; Harrison, Mark C.; Jongepier, Evelien

The first cockroach genome and its significance for understanding development and the evolution of insect eusociality Journal Article

In: Journal of Experimental Zoology Part B, 2018.

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Harrison, Mark C.; Arning, Nicolas; Kremer, Lukas P. M.; Ylla, Guillem; Belles, Xavier; Bornberg-Bauer, Erich; Huylmans, Ann Kathrin; Jongepier, Evelien; Piulachs, Maria‐Dolors; Richards, Stephen; Schal, Coby

Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest Journal Article

In: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 330 (5), pp. 254-264, 2018.

Abstract | Links | BibTeX

Kremer, Lukas P. M.; Korb, Judith; Bornberg-Bauer, Erich

Reconstructed evolution of insulin receptors in insects reveals duplications in early insects and cockroaches Journal Article

In: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 330 (5), pp. 305-311, 2018.

Abstract | Links | BibTeX

Jongepier, Evelien; Kemena, Carsten; Lopez-Ezquerra, Alberto; Belles, Xavier; Bornberg-Bauer, Erich; Korb, Judith

Remodeling of the juvenile hormone pathway through caste‐biased gene expression and positive selection along a gradient of termite eusociality Journal Article

In: Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 330 (5), pp. 296-304, 2018.

Abstract | Links | BibTeX

Klasberg, Steffen; Bitard-Feildel, Tristan; Callebaut, Isabelle; Bornberg-Bauer, Erich

Origins and structural properties of novel and de novo protein domains during insect evolution Journal Article

In: The FEBS journal, 285 (14), pp. 2605-2625, 2018.

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van Loo, Bert; Schober, Markus; Valkov, Eugene; Heberlein, Magdalena; Bornberg-Bauer, Erich; Faber, Kurt; Hyvönen, Marko; Hollfelder, Florian

Structural and Mechanistic Analysis of the Choline Sulfatase from Sinorhizobium melliloti: A Class I Sulfatase Specific for an Alkyl Sulfate Ester Journal Article

In: Journal of Molecular Biology, 430 (7), pp. 1004-1023, 2018.

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Lopez-Ezquerra, Alberto; Mitschke, Andreas; Bornberg-Bauer, Erich; Joop, Gerrit

Tribolium castaneum gene expression changes after Paranosema whitei infection Journal Article

In: Journal of Invertebrate Pathology, 153 , pp. 92-98, 2018.

Abstract | Links | BibTeX

Kemena, Carsten; Bornberg-Bauer, Erich

A roadmap to domain based proteomics Book Chapter

In: 2018.

Abstract | Links | BibTeX

Harrison, Mark C.; Jongepier, Evelien; Robertson, Hugh M.; Arning, Nicolas; Bitard-Feildel, Tristan; Chao, Hsu; Childers, Christopher P.; Dinh, Huyen; Doddapaneni, Harshavardhan; Dugan, Shannon; Gowin, Johannes; Greiner, Carolin; Han, Yi; Hu, Haofu; Hughes, Daniel S. T.; Huylmans, Ann-Kathrin; Kemena, Carsten; Kremer, Lukas P. M.; Lee, Sandra L.; Lopez-Ezquerra, Alberto; Mallet, Ludovic; Monroy-Kuhn, Jose M.; Moser, Annabell; Murali, Shwetha C.; Muzny, Donna M.; Otani, Saria; Piulachs, Maria-Dolors; Poelchau, Monica; Qu, Jiaxin; Schaub, Florentine; Wada-Katsumata, Ayako; Worley, Kim C.; Xie, Qiaolin; Ylla, Guillem; Poulsen, Michael; Gibbs, Richard A.; Schal, Coby; Richards, Stephen; Belles, Xavier; Korb, Judith; Bornberg-Bauer, Erich

Hemimetabolous genomes reveal molecular basis of termite eusociality Journal Article

In: Nature Ecology & Evolution, 2 , pp. 557–566, 2018.

Abstract | Links | BibTeX

2017

Lopez-Ezquerra, Alberto; Harrison, Mark C.; Bornberg-Bauer, Erich

Comparative analysis of lincRNA in insect species Journal Article

In: BMC Evolutionary Biology, 17 (1), pp. 1-11, 2017.

Abstract | Links | BibTeX

van Loo, Bert; Bornberg-Bauer, Erich

Enzyme sub‐functionalization driven by regulation Journal Article

In: EMBO Reports, 18 (7), pp. 1043-1045, 2017.

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Gubala, Anna M.; Schmitz, Jonathan F.; Kearns, Michael J.; Vinh, Tery T.; Bornberg-Bauer, Erich; Wolfner, Mariana F.; Findlay, Geoffrey D.

The Goddard and Saturn Genes Are Essential for Drosophila Male Fertility and May Have Arisen De Novo Journal Article

In: Molecular Biology and Evolution, 34 (5), pp. 1066–1082, 2017.

Abstract | Links | BibTeX

Schmitz, Jonathan F.; Bornberg-Bauer, Erich

Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA Journal Article

In: F1000 Research, 6 , 2017.

Abstract | Links | BibTeX

2016

Schüler, Andreas; Bornberg-Bauer, Erich

Evolution of Protein Domain Repeats in Metazoa Journal Article

In: Molecular Biology and Evolution, 33 (12), pp. 3170–3182, 2016.

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Jueterbock, A.; Franssen, Susanne U.; Bergmann, N.; Gu, Jenny; Coyer, J. A.; Reusch, T. B. H.; Bornberg-Bauer, Erich; Olsen, J. L.

Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass Journal Article

In: Molecular Ecology, 25 (21), pp. 5396-5411, 2016.

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Klasberg, Steffen; Bitard-Feildel, Tristan; Mallet, Ludovic

Computational Identification of Novel Genes: Current and Future Perspectives Journal Article

In: Bioinformatics and Biology Insights, 10 , 2016.

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Greenwood, Jenny M.; Lopez-Ezquerra, Alberto; Behrens, Sarah; Branca, Antoine; Mallet, Ludovic

Current analysis of next generation sequencing data with a focus on host-parasite interactions Journal Article

In: Zoology, 119 , pp. 298-306, 2016.

Abstract | Links | BibTeX

Schmitz, Jonathan F.; Zimmer, Fabian; Bornberg-Bauer, Erich

Mechanisms of transcription factor evolution in Metazoa Journal Article

In: Nucleic Acids Research, 44 (13), pp. 6287–6297, 2016.

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Elsner, Daniel; Kremer, Lukas P. M.; Arning, Nicolas; Bornberg-Bauer, Erich

Comparative genomic approaches to investigate molecular traits specific to social insects Journal Article

In: Current Opinion in Insect Science, 16 , pp. 87-94, 2016.

Abstract | Links | BibTeX

Haase, David; Rieger, Jenny K.; Witten, Anika; Stoll, Monika; Bornberg-Bauer, Erich; Kalbe, Martin; Schmidt-Drewello, Alexander; P.Scharsack, Jörn; Reusch, Thorsten B. H.

Comparative transcriptomics of stickleback immune gene responses upon infection by two helminth parasites, Diplostomum pseudospathaceum and Schistocephalus solidus Journal Article

In: Zoology, 119 (4), pp. 307-313, 2016.

Abstract | Links | BibTeX

Dohmen, Elias; Kremer, Lukas P. M.; Bornberg-Bauer, Erich; Kemena, Carsten

DOGMA: domain-based transcriptome and proteome quality assessment Journal Article

In: Bioinformatics, 32 (17), pp. 2577-2581, 2016.

Abstract | Links | BibTeX

Olsen, Jeanine L.; Rouzé, Pierre; Verhelst, Bram; Lin, Yao-Cheng; Bayer, Till; Collen, Jonas; Dattolo, Emanuela; Paoli, Emanuele De; Dittami, Simon; Maumus, Florian; Michel, Gurvan; Kersting, Anna R.; Lauritano, Chiara; Lohaus, Rolf; Töpel, Mats; Tonon, Thierry; Vanneste, Kevin; Amirebrahimi, Mojgan; Brakel, Janina; Boström, Christoffer; Chovatia, Mansi; Grimwood, Jane; Jenkins, Jerry W.; Jueterbock, Alexander; Mraz, Amy; Stam, Wytze T.; Tice, Hope; Bornberg-Bauer, Erich; Green, Pamela J.; Pearson, Gareth A.; Procaccini, Gabriele; Duarte, Carlos M.; Schmutz, Jeremy; Reusch, Thorsten B. H.; de Peer, Yves Van

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea Journal Article

In: Nature, 530 , pp. 331–335, 2016.

Abstract | Links | BibTeX

Huang, Yun; Chain, Frédéric J. J.; Panchal, Mahesh; Eizaguirre, Christophe; Kalbe, Martin; Lenz, Tobias L.; Samonte, Irene E.; Stoll, Monika; Bornberg-Bauer, Erich; Reusch, Thorsten B. H.; Milinski, Manfred; Feulner, Philine G. D.

Transcriptome profiling of immune tissues revealshabitat-specific gene expression between lake and riversticklebacks Journal Article

In: Molecular Ecology, 25 , pp. 943–958 , 2016.

Abstract | Links | BibTeX

2015

Bornberg-Bauer, Erich; Schmitz, Jonathan F.; Heberlein, Magdalena

Emergence of de novo proteins from "dark genomic matter" by "grow slow and moult" Journal Article

In: Biochemical Society Transactions, 43 (5), pp. 867–873, 2015.

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Haase, David; Rieger, Jennifer K.; Witten, Anika; Stoll, Monika; Bornberg-Bauer, Erich; Kalbe, Martin; Reusch, Thorsten B. H.

Immunity comes first: The effect of parasite genotypes on adaptive immunity and immunization in three-spined sticklebacks Journal Article

In: Developmental and Comparative Immunology, 54 (1), pp. 137-144, 2015.

Abstract | Links | BibTeX

Smith, Chris R.; Cahan, Sara Helms; Kemena, Carsten; Brady, Seán G.; Yang, Wei; Bornberg-Bauer, Erich; Eriksson, Ti; Gadau, Jürgen; Helmkampf, Martin; Gotzek, Dietrich; Miyakawa, Misato Okamoto; Suarez, Andrew V.; Mikheyev, Alexander

How Do Genomes Create Novel Phenotypes? Insights from the Loss of the Worker Caste in Ant Social Parasites Journal Article

In: Molecular Biology and Evolution, 32 (11), pp. 2919–2931, 2015.

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Schüler, Andreas; Schmitz, Gregor; Reft, Abigail; Özbek, Suat; Thurm, Ulrich; Bornberg-Bauer, Erich

The rise and fall of TRP-N, an ancient family of mechanogated ion channels, in metazoan Journal Article

In: Genome Biology and Evolution, 7 (6), pp. 1713–1727, 2015.

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Masri, Leila; Branca, Antoine; Sheppard, Anna E.; Papkou, Andrei; Laehnemann, David; Guenther, Patrick S.; Prahl, Swantje; Saebelfeld, Manja; Hollensteiner, Jacqueline; Liesegang, Heiko; Brzuszkiewicz, Elzbieta; Daniel, Rolf; Michiels, Nicolaas K.; Schulte, Rebecca D.; Kurtz, Joachim; Rosenstiel, Philip; Telschow, Arndt; Bornberg-Bauer, Erich; Schulenburg, Hinrich

Host-Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes Journal Article

In: PLOS Biology, 13 (6), 2015.

Abstract | Links | BibTeX

Bitard-Feildel, Tristan; Kemena, Carsten; Greenwood, Jenny M.; Bornberg-Bauer, Erich

Domain similarity based orthology detection Journal Article

In: BMC Bioinformatics, 16 (154), 2015.

Abstract | Links | BibTeX

Sadd, Ben M; Barribeau, Seth M; Bloch, Guy; de Graaf, Dirk C; Dearden, Peter; Elsik, Christine G; Gadau, Jürgen; Grimmelikhuijzen, Cornelis JP; Hasselmann, Martin; Lozier, Jeffrey D; Robertson, Hugh M; Smagghe, Guy; Stolle, Eckart; Vaerenbergh, Matthias Van; Waterhouse, Robert M; Bornberg-Bauer, Erich; Klasberg, Steffen; Bennett, Anna K; Câmara, Francisco; Guigó, Roderic; Hoff, Katharina; Mariotti, Marco; Munoz-Torres, Monica; Murphy, Terence; Santesmasses, Didac; Amdam, Gro V; Beckers, Matthew; Beye, Martin; Biewer, Matthias; Bitondi, Márcia MG; Blaxter, Mark L; Bourke, Andrew FG; Brown, Mark JF; Buechel, Severine D; Cameron, Rossanah; Cappelle, Kaat; Carolan, James C; Christiaens, Olivier; Ciborowski, Kate L; Clarke, David F; Colgan, Thomas J; Collins, David H; Cridge, Andrew G; Dalmay, Tamas; Dreier, Stephanie; du Plessis, Louis; Duncan, Elizabeth; Erler, Silvio; Evans, Jay; Falcon, Tiago; Flores, Kevin; Freitas, Flávia CP; Fuchikawa, Taro; Gempe, Tanja; Hartfelder, Klaus; Hauser, Frank; Helbing, Sophie; Humann, Fernanda C; Irvine, Frano; Jermiin, Lars S; Johnson, Claire E; Johnson, Reed M; Jones, Andrew K; Kadowaki, Tatsuhiko; Kidner, Jonathan H; Koch, Vasco; Köhler, Arian; Kraus, F Bernhard; Lattorff, H Michael G; Leask, Megan; Lockett, Gabrielle A; Mallon, Eamonn B; Antonio, David S Marco; Marxer, Monika; Meeus, Ivan; Moritz, Robin FA; Nair, Ajay; Näpflin, Kathrin; Nissen, Inga; Niu, Jinzhi; Nunes, Francis MF; Oakeshott, John G; Osborne, Amy; Otte, Marianne; Pinheiro, Daniel G; Rossié, Nina; Rueppell, Olav; Santos, Carolina G; Schmid-Hempel, Regula; Schmitt, Björn D; Schulte, Christina; Simões, Zilá LP; Soares, Michelle PM; Swevers, Luc; Winnebeck, Eva C; Wolschin, Florian; Yu, Na; Zdobnov, Evgeny M; Aqrawi, Peshtewani K; Blankenburg, Kerstin P; Coyle, Marcus; Francisco, Liezl; Hernandez, Alvaro G; Holder, Michael; Hudson, Matthew E; Jackson, LaRonda; Jayaseelan, Joy; Joshi, Vandita; Kovar, Christie; Lee, Sandra L; Mata, Robert; Mathew, Tittu; Newsham, Irene F; Ngo, Robin; Okwuonu, Geoffrey; Pham, Christopher; Pu, Ling-Ling; Saada, Nehad; Santibanez, Jireh; Simmons, DeNard; Thornton, Rebecca; Venkat, Aarti; Walden, Kimberly KO; Wu, Yuan-Qing; Debyser, Griet; Devreese, Bart; Asher, Claire; Blommaert, Julie; Chipman, Ariel D; Chittka, Lars; Fouks, Bertrand; Liu, Jisheng; O’Neill, Meaghan P; Sumner, Seirian; Puiu, Daniela; Qu, Jiaxin; Salzberg, Steven L; Scherer, Steven E; Muzny, Donna M; Richards, Stephen; Robinson, Gene E; Gibbs, Richard A; Schmid-Hempel, Paul; Worley, Kim C

The genomes of two key bumblebee species with primitive eusocial organization Journal Article

In: Genome Biology, 16 (76), 2015.

Abstract | Links | BibTeX

Bitard-Feildel, Tristan; Heberlein, Magdalena; Bornberg-Bauer, Erich; Callebaut, Isabelle

Detection of Orphan Domains in Drosophila using "Hydrophobic clustering analysis" Journal Article

In: Biochimie, 119 , pp. 244-253, 2015.

Abstract | Links | BibTeX

Feulner, Philine G. D.; Chain, Frédéric J. J.; Panchal, Mahesh; Huang, Yun; Eizaguirre, Christophe; Kalbe, Martin; Lenz, Tobias L.; Samonte, Irene E.; Stoll, Monika; Bornberg-Bauer, Erich; Reusch, Thorsten B. H.; Milinski, Manfred

Genomics of Divergence along a Continuum of Parapatric Population Differentiation Journal Article

In: PLOS Genetics, 11 (7), 2015.

Abstract | Links | BibTeX

Kemena, Carsten; Bitard-Feildel, Tristan; Bornberg-Bauer, Erich

MDAT- Aligning multiple domain arrangements Journal Article

In: BMC Bioinformatics, 16 (19), 2015.

Abstract | Links | BibTeX

2014

Schrader, Lukas; Kim, Jay W.; Ence, Daniel; Zimin, Aleksey; Klein, Antonia; Wyschetzki, Katharina; Weichselgartner, Tobias; Kemena, Carsten; Stökl, Johannes; Schultner, Eva; Wurm, Yannick; Smith, Christopher D.; Yandell, Mark; Heinze, Jürgen; Gadau, Jürgen; Oettler, Jan

Transposable element islands facilitate adaptation to novel environments in an invasive species Journal Article

In: Nature Communications, 5 (5495), 2014.

Abstract | Links | BibTeX

Kersting, Anna R.; Mizrachi, Eshchar; Bornberg-Bauer, Erich; Myburg, Alexander A.

Protein domain evolution is associated with reproductive diversification and adaptive radiation in the basal rosid Eucalyptus grandis Journal Article

In: New Phytologist, 206 (4), pp. 1328-1336, 2014.

Abstract | Links | BibTeX

Chain, Frédéric J. J.; Feulner, Philine G. D.; Panchal, Mahesh; Eizaguirre, Christophe; Samonte, Irene E.; Kalbe, Martin; Lenz, Tobias L.; Stoll, Monika; Bornberg-Bauer, Erich; Milinski, Manfred; Reusch, Thorsten B. H.

Extensive Copy-Number Variation of Young Genes across Stickleback Populations Journal Article

In: PLOS Genetics, 10 (12), 2014.

Abstract | Links | BibTeX

Haase, David; Rieger, Jennifer K.; Witten, Anika; Stoll, Monika; Bornberg-Bauer, Erich; Kalbe, Martin; Reusch, Thorsten B. H.

Specific Gene Expression Responses to Parasite Genotypes Reveal Redundancy of Innate Immunity in Vertebrates Journal Article

In: PLOS One, 9 (9), 2014.

Abstract | Links | BibTeX

Myburg, Alexander A.; Grattapaglia, Dario; Tuskan, Gerald A.; Hellsten, Uffe; Hayes, Richard D.; Grimwood, Jane; Jenkins, Jerry; Lindquist, Erika; Tice, Hope; Bauer, Diane; Goodstein, David M.; Dubchak, Inna; Poliakov, Alexandre; Mizrachi, Eshchar; Kullan, Anand R. K.; Hussey, Steven G.; Pinard, Desre; van der Merwe, Karen; Singh, Pooja; van Jaarsveld, Ida; Silva-Junior, Orzenil B.; Togawa, Roberto C.; Pappas, Marilia R.; Faria, Danielle A.; Sansaloni, Carolina P.; Petroli, Cesar D.; Yang, Xiaohan; Ranjan, Priya; Tschaplinski, Timothy J.; Ye, Chu-Yu; Li, Ting; Sterck, Lieven; Vanneste, Kevin; Murat, Florent; Soler, Marçal; Clemente, Hélène San; Saidi, Naijib; Cassan-Wang, Hua; Dunand, Christophe; Hefer, Charles A.; Bornberg-Bauer, Erich; Kersting, Anna R.; Vining, Kelly; Amarasinghe, Vindhya; Ranik, Martin; Naithani, Sushma; Elser, Justin; Boyd, Alexander E.; Liston, Aaron; Spatafora, Joseph W.; Dharmwardhana, Palitha; Raja, Rajani; Sullivan, Christopher; Romanel, Elisson; Alves-Ferreira, Marcio; Külheim, Carsten; Foley, William; Carocha, Victor; Paiva, Jorge; Kudrna, David; Brommonschenkel, Sergio H.; Pasquali, Giancarlo; Byrne, Margaret; Rigault, Philippe; Tibbits, Josquin; Spokevicius, Antanas; Jones, Rebecca C.; Steane, Dorothy A.; Vaillancourt, René E.; Potts, Brad M.; Joubert, Fourie; Barry, Kerrie; Pappas, Georgios J.; Strauss, Steven H.; Jaiswal, Pankaj; Grima-Pettenati, Jacqueline; Salse, Jérôme; de Peer, Yves Van; Rokhsar, Daniel S.; Schmutz, Jeremy

The genome of Eucalyptus grandis Journal Article

In: Nature, 510 , pp. 356–362, 2014.

Abstract | Links | BibTeX

Behrens, Sarah; Peuß, Robert; Milutinović, Barbara; Eggert, Hendrik; Esser, Daniela; Rosenstiel, Philip; Schulenburg, Hinrich; Bornberg-Bauer, Erich; Kurtz, Joachim

Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis Journal Article

In: BMC Genomics, 15 (445), 2014.

Abstract | Links | BibTeX

Terrapon, Nicolas; Li, Cai; Robertson, Hugh M.; Ji, Lu; Meng, Xuehong; Booth, Warren; Chen, Zhensheng; Childers, Christopher P.; Glastad, Karl M.; Gokhale, Kaustubh; Gowin, Johannes; Gronenberg, Wulfila; Hermansen, Russell A.; Hu, Haofu; Hunt, Brendan G.; Huylmans, Ann Kathrin; Khalil, Sayed M. S.; Mitchell, Robert D.; Munoz-Torres, Monica C.; Mustard, Julie A.; Pan, Hailin; Reese, Justin T.; Scharf, Michael E.; Sun, Fengming; Vogel, Heiko; Xiao, Jin; Yang, Wei; Yang, Zhikai; Yang, Zuoquan; Zhou, Jiajian; Zhu, Jiwei; Brent, Colin S.; Elsik, Christine G.; Goodisman, Michael A. D.; Liberles, David A.; Roe, R. Michael; Vargo, Edward L.; Vilcinskas, Andreas; Wang, Jun; Bornberg-Bauer, Erich; Korb, Judith; Zhang, Guojie; Liebig, Jürgen

Molecular traces of alternative social organization in a termite genome Journal Article

In: Nature Communications, 5 (3636), 2014.

Abstract | Links | BibTeX

Franssen, Susanne U.; Gu, Jenny; Winters, Gidon; Huylmans, Ann-Kathrin; Wienpahl, Isabell; Sparwel, Maximiliane; Coyer, James A.; Olsen, Jeanine L.; Reusch, Thorsten B. H.; Bornberg-Bauer, Erich

Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types Journal Article

In: Marine Genomics, 15 , pp. 65-73, 2014.

Abstract | Links | BibTeX

Moore, Andrew D.; Held, Andreas; Terrapon, Nicolas; Weiner, January; Bornberg-Bauer, Erich

DoMosaics: Software for domain arrangement visualization and domain-centric analysis of proteins. Journal Article

In: Bioinformatics, 30 (2), pp. 282–283, 2014.

Abstract | Links | BibTeX

Terrapon, Nicolas; Weiner, January; Grath, Sonja; Moore, Andrew D.; Bornberg-Bauer, Erich

Rapid similarity search of proteins using alignments of domain arrangements Journal Article

In: Bioinformatics, 30 (2), pp. 274–281, 2014.

Abstract | Links | BibTeX

2013

Guo, Baocheng; Chain, Frédéric JJ; Bornberg-Bauer, Erich; Leder, Erica H; Merilä, Juha

Genomic divergence between nine- and three-spined sticklebacks Journal Article

In: BMC Genomics, 6 (756 ), 2013.

Abstract | Links | BibTeX

Simola, Daniel F.; Wissler, Lothar; Donahue, Greg; Waterhouse, Robert M.; Helmkampf, Martin; Roux, Julien; Nygaard, Sanne; Glastad, Karl M.; Hagen, Darren E.; Viljakainen, Lumi; Reese, Justin T.; Hunt, Brendan G.; Graur, Dan; Elhaik, Eran; Kriventseva, Evgenia V.; Wen, Jiayu; Parker, Brian J.; Cash, Elizabeth; Privman, Eyal; Childers, Christopher P.; Muñoz-Torres, Monica C.; Boomsma, Jacobus J.; Bornberg-Bauer, Erich; Currie, Cameron R.; Elsik, Christine G.; Suen, Garret; Goodisman, Michael A. D.; Keller, Laurent; Liebig, Jürgen; Rawls, Alan; Reinberg, Danny; Smith, Chris D.; Smith, Chris R.; Tsutsui, Neil; Wurm, Yannick; Zdobnov, Evgeny M.; Berger, Shelley L.; Gadau, Jürgen

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality Journal Article

In: Genome Research, 23 , pp. 1235-1247, 2013.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; Albà, M Mar

Dynamics and Adaptive Benefits of Modular Protein Evolution Journal Article

In: Current Opinion in Structural Biology, 23 (3), pp. 459-466, 2013.

Abstract | Links | BibTeX

Moore, Andrew D.; Grath, Sonja; Schüler, Andreas; Huylmans, Ann K.; Bornberg-Bauer, Erich

Quantification and Functional Analysis of Modular Protein Evolution in a Dense Phylogenetic Tree Journal Article

In: Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 1834 (5), pp. 898-907, 2013.

Abstract | Links | BibTeX

Wissler, Lothar; Gadau, Jürgen; Simola, Daniel F.; Helmkampf, Martin; Bornberg-Bauer, Erich

Mechanisms and dynamics of orphan gene emergence in insect genomes Journal Article

In: Genome Biology and Evolution, 5 (2), pp. 439–455, 2013.

Abstract | Links | BibTeX

2012

Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts Journal Article

In: PLOS Computational Biology, 8 (9), 2012.

Abstract | Links | BibTeX

Sikosek, Tobias; Chan, Hue Sun; Bornberg-Bauer, Erich

Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness Journal Article

In: PNAS, 109 (37), pp. 14888-14893, 2012.

Abstract | Links | BibTeX

Niehuis, Oliver; Hartig, Gerrit; Grath, Sonja; Pohl, Hans; Lehmann, Jörg; Tafer, Hakim; Donath, Alexander; Krauss, Veiko; Eisenhardt, Carina; Hertel, Jana; Petersen, Malte; Mayer, Christoph; Meusemann, Karen; Peters, Ralph S.; Stadler, Peter F.; Beutel, Rolf G.; Bornberg-Bauer, Erich; McKenna, Duane D.; Misof, Bernhard

Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera Journal Article

In: Current Biology, 22 (14), pp. 1309-1313, 2012.

Abstract | Links | BibTeX

Feulner, Philine G. D.; Chain, Frederic J. J.; Panchal, Mahesh; Eizaguirre, Christophe; Kalbe, Martin; Lenz, Tobias L.; Mundry, Marvin; Samonte, Irene E.; Stoll, Monika; Milinski, Manfred; Reusch, Thorsten B. H.; Bornberg-Bauer, Erich

Genome‐wide patterns of standing genetic variation in a marine population of three‐spined sticklebacks Journal Article

In: Molecular Ecology, 22 (3), pp. 635-649, 2012.

Abstract | Links | BibTeX

Wissler, Lothar; Godmann, Lars; Bornberg-Bauer, Erich

Evolutionary dynamics of simple sequence repeats across long evolutionary time in genus Drosophila Journal Article

In: Trends in Evolutionary Biology, 4 (7), 2012.

Abstract | Links | BibTeX

Liberles, David A.; Teichmann, Sarah A.; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J.; de Koning, A. P. Jason; Dokholyan, Nikolay V.; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L.; Goldstein, Richard A.; Grahnen, Johan A.; Holder, Mark T.; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C.; Naylor, Gavin; Perica, Tina; Pollock, David D.; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I.; Thorne, Jeffrey L.; Thornton, Joseph W.; Weinreich, Daniel M.; Whelan, Simon

The interface of protein structure, protein biophysics, and molecular evolution Journal Article

In: Protein Science, 21 (6), pp. 769-785, 2012.

Abstract | Links | BibTeX

Balasubramanian, Prakash G.; Beckmann, Anna; Warnken, Uwe; Schnölzer, Martina; Schüler, Andreas; Bornberg-Bauer, Erich; Holstein, Thomas W.; SuatÖzbek,

Proteome of Hydra Nematocyst Journal Article

In: Journal of Biological Chemistry, 287 (13), pp. 9672-9681, 2012.

Abstract | Links | BibTeX

Gu, Jenny; Weber, Katrin; Klemp, Elisabeth; Winters, Gidon; Franssen, Susanne U.; Wienpahl, Isabell; Huylmans, Ann-Kathrin; Zecher, Karsten; Reusch, Thorsten B. H.; Bornberg-Bauer, Erich; Weber, Andreas P. M.

Identifying core features of adaptive metabolic mechanisms for chronic heat stress attenuation contributing to systems robustness Journal Article

In: Integrative Biology, 4 (5), pp. 480-493, 2012.

Abstract | Links | BibTeX

Mundry, Marvin; Bornberg-Bauer, Erich; Sammeth, Michael; Feulner, Philine G. D.

Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach Journal Article

In: PLOS One, 7 (2), 2012.

Abstract | Links | BibTeX

Kersting, Anna R.; Bornberg-Bauer, Erich; Moore, Andrew D.; Grath, Sonja

Dynamics and Adaptive Benefits of Protein Domain Emergence and Arrangements during Plant Genome Evolution Journal Article

In: Genome Biology and Evolution, 4 (3), pp. 316–329, 2012.

Abstract | Links | BibTeX

TERRAPON, Nicolas; GRATH, Sonja; WEINER, January; MOORE, Andrew D.; Bornberg-Bauer, Erich

Fast Homology Search Using Domain-Architecture Alignment Proceeding

2012.

Abstract | Links | BibTeX

2011

Grbić, Miodrag; Leeuwen, Thomas Van; Clark, Richard M.; Rombauts, Stephane; Rouzé, Pierre; Grbić, Vojislava; Osborne, Edward J.; Dermauw, Wannes; Ngoc, Phuong Cao Thi; Ortego, Félix; Hernández-Crespo, Pedro; Diaz, Isabel; Martinez, Manuel; Navajas, Maria; Sucena, Élio; Magalhães, Sara; Nagy, Lisa; Pace, Ryan M.; Djuranović, Sergej; Smagghe, Guy; Iga, Masatoshi; Christiaens, Olivier; Veenstra, Jan A.; Ewer, John; Villalobos, Rodrigo Mancilla; Hutter, Jeffrey L.; Hudson, Stephen D.; Velez, Marisela; Yi, Soojin V.; Zeng, Jia; Pires-daSilva, Andre; Roch, Fernando; Cazaux, Marc; Navarro, Marie; Zhurov, Vladimir; Acevedo, Gustavo; Bjelica, Anica; Fawcett, Jeffrey A.; Bonnet, Eric; Martens, Cindy; Baele, Guy; Wissler, Lothar; Sanchez-Rodriguez, Aminael; Tirry, Luc; Blais, Catherine; Demeestere, Kristof; Henz, Stefan R.; Gregory, T. Ryan; Mathieu, Johannes; Verdon, Lou; Farinelli, Laurent; Schmutz, Jeremy; Lindquist, Erika; Feyereisen, René; de Peer, Yves Van

The genome of Tetranychus urticae reveals herbivorous pest adaptations Journal Article

In: Nature, 479 , pp. 487–492, 2011.

Abstract | Links | BibTeX

Franssen, Susanne U.; Gu, Jenny; Bergmann, Nina; Winters, Gidon; Klostermeier, Ulrich C.; Rosenstiel, Philip; Bornberg-Bauer, Erich; Reusch, Thorsten B. H.

Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species Journal Article

In: Proceedings of the National Academy of Sciences, (48), pp. 19276-8, 2011.

Abstract | Links | BibTeX

Moore, Andrew D.; Bornberg-Bauer, Erich

The Dynamics and Evolutionary Potential of Domain Loss and Emergence Journal Article

In: Molecular Biology and Evolution, 29 (2), pp. 787–796, 2011.

Abstract | Links | BibTeX

Hartig, G; Niehuis, O; Grath, Sonja; Pohl, H; Donath, A; Eisenhart, C; Hertel, J; Krauss, V; Lehmann, J; Mayer, C; Tafer, H; Meusemann, K; Peters, RS; Beutel, RG; Stadler, P; Bornberg-Bauer, Erich; Misof, B

The first genome of a twisted wing parasite (Insectae: strepsiptera) and its phylogenetic implications Journal Article

In: Zitteliana, pp. 30-32, 2011.

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Reineke, Anna R.; Bornberg-Bauer, Erich; Gu, Jenny

Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes Journal Article

In: Nucleic Acids Research, 39 (14), pp. 6029–6043, 2011.

Abstract | Links | BibTeX

Franssen, Susanne U.; Shrestha, Roshan P; Bräutigam, Andrea; Bornberg-Bauer, Erich; Weber, Andreas P M

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing Journal Article

In: BMC Genomics, 12 (227), 2011.

Abstract | Links | BibTeX

Suen, Garret; Teiling, Clotilde; Li, Lewyn; Holt, Carson; Abouheif, Ehab; Bornberg-Bauer, Erich; Bouffard, Pascal; Caldera, Eric J.; Cash, Elizabeth; Cavanaugh, Amy; Denas, Olgert; Elhaik, Eran; Favé, Marie-Julie; Gadau, Jürgen; Gibson, Joshua D.; Graur, Dan; Grubbs, Kirk J.; Hagen, Darren E.; Harkins, Timothy T.; Helmkampf, Martin; Hu, Hao; Johnson, Brian R.; Kim, Jay; Marsh, Sarah E.; Moeller, Joseph A.; Muñoz-Torres, Mónica C.; Murphy, Marguerite C.; Naughton, Meredith C.; Nigam, Surabhi; Overson, Rick; Rajakumar, Rajendhran; Reese, Justin T.; Scott, Jarrod J.; Smith, Chris R.; Tao, Shu; Tsutsui, Neil D.; Viljakainen, Lumi; Wissler, Lothar; Yandell, Mark D.; Zimmer, Fabian; Taylor, James; Slater, Steven C.; Clifton, Sandra W.; Warren, Wesley C.; Elsik, Christine G.; Smith, Christopher D.; Weinstock, George M.; Gerardo, Nicole M.; Currie, Cameron R.

The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle Journal Article

In: PLOS Genetics, 2011.

Abstract | Links | BibTeX

Wissler, Lothar; Codoñer, Francisco M; Gu, Jenny; Reusch, Thorsten BH; Olsen, Jeanine L; Procaccini, Gabriele; Bornberg-Bauer, Erich

Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life Journal Article

In: BMC Evolutionary Biology, 11 (8), 2011.

Abstract | Links | BibTeX

Ernst, Antonia M; Rüping, Boris; Jekat, Stephan B; Nordzieke, Steffen; Reineke, Anna R; Müller, Boje; Bornberg-Bauer, Erich; Prüfer, Dirk; Noll, Gundula A

The sieve element occlusion gene family in dicotyledonous plants Journal Article

In: Plant Signal Behaviour, 6 (19), pp. 151-3, 2011.

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2010

Schüler, Andreas; Bornberg-Bauer, Erich

The Evolution of Protein Interaction Networks Journal Article

In: Data Mining in Proteomics, pp. 273-289, 2010.

Abstract | Links | BibTeX

Rüping, Boris; Ernst, Antonia M; Jekat, Stephan B; Nordzieke, Steffen; Reineke, Anna R; Müller, Boje; Bornberg-Bauer, Erich; Prüfer, Dirk

Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants Journal Article

In: BMC Plant Biology , 10 (219), pp. 1-14, 2010.

Abstract | Links | BibTeX

Sikosek, Tobias; Bornberg-Bauer, Erich

Evolution after and before gene duplication? Journal Article

In: 2010.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich

Signals: Tinkering with Domains Journal Article

In: Science Signaling, 14 (3), 2010.

Abstract | Links | BibTeX

Chen, Tao; Vernazobres, David; Yomo, Tetsuya; Bornberg-Bauer, Erich; Chan, Hue Sun

Evolvability and Single-Genotype Fluctuation in Phenotypic Properties: A Simple Heteropolymer Model Journal Article

In: Biophysical Journal, 98 (11), pp. 2487-2496, 2010.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; Kramer, Linus

Robustness versus evolvability: a paradigm revisited Journal Article

In: HFSP Journal, 4 (3-4), pp. 105-108, 2010.

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Bornberg-Bauer, Erich; Huylmans, Ann-Kathrin; Sikosek, Tobias

How do new proteins arise? Journal Article

In: Current Opinion in Structural Biology, 20 (344), pp. 390-396, 2010.

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Moore, Andrew D.; Bornberg-Bauer, Erich

Protein Domains as Evolutionary Units Journal Article

In: Evolutionary Genomics and Systems Biology, 2010.

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Werren, John H.; Richards, Stephen; [....],; Bornberg-Bauer, Erich; [....],; Yamada, Takuji; Yi, Soojin V.; Zecher, Courtney N.; Zhang, Lan; Gibbs, Richard A.

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species Journal Article

In: Science, 327 (5963), pp. 343-348, 2010.

Abstract | Links | BibTeX

2009

Wissler, Lothar; Dattolo, E.; Moore, Andrew D.; Reusch, T. B. H.; Olsen, J. L.; Migliaccio, M.; Bornberg-Bauer, Erich; Procaccini, G.

Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs Journal Article

In: Database, 2009 , 2009.

Abstract | Links | BibTeX

2008

Weiner, January; Moore, Andrew D.; Bornberg-Bauer, Erich

Just how versatile are domains? Journal Article

In: BMC Evolutionary Biology, 8 (285), 2008.

Abstract | Links | BibTeX

Moore, Andrew D.; Björklund, Åsa K.; Ekman, Diana; Bornberg-Bauer, Erich; Elofsson, Arne

Arrangements in the modular evolution of proteins Journal Article

In: Trends in Biomedical Science, 33 (9), pp. 444-451, 2008.

Abstract | Links | BibTeX

Whitehead, Dion; Wilke, Claus O; Vernazobres, David; Bornberg-Bauer, Erich

The look-ahead effect of phenotypic mutations Journal Article

In: Biology Direct, 3 (18), 2008.

Abstract | Links | BibTeX

Schulenburg, Hinrich; Hoeppner, Marc P.; Weiner, January; Bornberg-Bauer, Erich

Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans Journal Article

In: Immunobiology , 213 (3-4), pp. 237-250, 2008.

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Friedrichs, Frauke; Henckaerts, Liesbet; Vermeire, Severine; Kucharzik, Torsten; Seehafer, Tanja; Möller-Krull, Maren; Bornberg-Bauer, Erich; Stoll, Monika; Weiner, January

The Crohn’s disease susceptibility gene DLG5 as a member of the CARD interaction network Journal Article

In: Journal of Molecular Medicine , 86 , pp. 423-432, 2008.

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Falb, Michaela; Müller, Kerstin; Königsmaier, Lisa; Oberwinkler, Tanja; Horn, Patrick; von Gronau, Susanne; Gonzalez, Orland; Pfeiffer, Friedhelm; Bornberg-Bauer, Erich; Oesterhelt, Dieter

Metabolism of halophilic archaea Journal Article

In: Extremophiles , 12 , pp. 177–196, 2008.

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Reusch, Thorsten B. H.; Veron, Amelie S.; Preuss, Christoph; Weiner, January; Wissler, Lothar; Beck, Alfred; Klages, Sven; Kube, Michael; Reinhardt, Richard; Bornberg-Bauer, Erich

Comparative Analysis of Expressed Sequence Tag (EST) Libraries in the Seagrass Zostera marina Subjected to Temperature Stress Journal Article

In: Marine Biotechnology, 10 , pp. 297–309, 2008.

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2007

Amoutzias, Gregory D.; Pichler, Elgar E; Mian, Nina; Graaf, David De; Imsiridou, Anastasia; Robinson-Rechavi, Marc; Bornberg-Bauer, Erich; Robertson, David L; Oliver, Stephen G

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network Journal Article

In: BMC Systems Biology, 1 (34), 2007.

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Beaussart, Francois; Weiner, January; Bornberg-Bauer, Erich

Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN) Journal Article

In: Bioinformatics, 23 (14), pp. 1834–1836, 2007.

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Wroe, Richard; Chan, Hue Sun; Bornberg-Bauer, Erich

A structural model of latent evolutionary potentials underlying neutral networks in proteins Journal Article

In: HFSP Journal, 1 (1), pp. 79–87, 2007.

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Kilian, Joachim; Whitehead, Dion; Horak, Jakub; Wanke, Dierk; Weinl, Stefan; Batistic, Oliver; D’Angelo, Cecilia; Bornberg-Bauer, Erich; Kudla, Jörg; Harter, Klaus

The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV‐B light, drought and cold stress responses Journal Article

In: The Plant Journal, 50 (2), pp. 347-363, 2007.

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2006

Amoutzias, Gregory D.; Veron, Amelie S.; Weiner, January; Robinson-Rechavi, M; Bornberg-Bauer, Erich; Oliver, SG; Robertson, DL

One Billion Years of bZIP Transcription Factor Evolution: Conservation and Change in Dimerization and DNA-Binding Site Specificity Journal Article

In: Molecular Biology and Evolution, 24 (3), pp. 827–835, 2006.

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Veron, Amelie S.; Kaufmann, Kerstin; Bornberg-Bauer, Erich

Evidence of Interaction Network Evolution by Whole-Genome Duplications: A Case Study in MADS-Box Proteins Journal Article

In: Molecular Biology and Evolution, 24 (3), pp. 670-678, 2006.

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Amoutzias, Gregory D.; Bornberg-Bauer, Erich; Oliver, Stephen G; Robertson, David L

Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network Journal Article

In: BMC Genomics, 7 (107), 2006.

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Weiner, January; Beaussart, Francois; Bornberg-Bauer, Erich

Domain deletions and substitutions in the modular protein evolution Journal Article

In: The FEBS journal, 273 , pp. 2037-2047, 2006.

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Weiner, January; Bornberg-Bauer, Erich

Evolution of Circular Permutations in Multidomain Proteins Journal Article

In: Molecular Biology and Evolution, 23 (4), pp. 734–743, 2006.

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Gerke, Mirco; Bornberg-Bauer, Erich; Jiang, Xiaoyi; Fuellen, Georg

Finding Common Protein Interaction Patterns Across Organisms Journal Article

In: Evolutionary Bioinformatics, 2006.

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2005

Teichmann, Sarah A; Bornberg-Bauer, Erich; Luscombe, Nicholas M

Transcriptional networking Journal Article

In: Genome Biology, 6 (344), 2005.

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Malonek, Stefan; Bömke, Christiane; Bornberg-Bauer, Erich; C.Rojas, María; Hedden, Peter; Hopkins, Paul; Tudzynski, Bettina

Distribution of gibberellin biosynthetic genes and gibberellin production in the Gibberella fujikuroi species complex Journal Article

In: Phytochemistry, 66 (11), pp. 1296-1311, 2005.

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Weiner, January; Thomas, Geraint; Bornberg-Bauer, Erich

Rapid motif-based prediction of circular permutations in multi-domain proteins Journal Article

In: Bioinformatics, 21 (7), pp. 932–937, 2005.

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Bornberg-Bauer, Erich; Beaussart, Francois; Kummerfeld, S. K.; Teichmann, S. A.; Weiner, January

The evolution of domain arrangements in proteins and interaction networks Journal Article

In: Cellular and Molecular Life Sciences CMLS, 62 , pp. 435–445, 2005.

Abstract | Links | BibTeX

Amoutzias, Gregory D.; Weiner, January; Bornberg-Bauer, Erich

Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs Journal Article

In: Gene Volume, 347 (2), pp. 247-253, 2005.

Abstract | Links | BibTeX

Veron, Amelie S.; Whitehead, Dion; Bornberg-Bauer, Erich

Evolution of regulatory networks Journal Article

In: Genetics, Genomics, Proteomics and Bioinformatics, 2005.

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Wroe, Richard; Bornberg-Bauer, Erich; Chan, Hue Sun

Comparing Folding Codes in Simple Heteropolymer Models of Protein Evolutionary Landscape: Robustness of the Superfunnel Paradigm Journal Article

In: Biophysical Journal, 88 (1), pp. 118–131, 2005.

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2004

Amoutzias, Gregory D.; Robertson, David L; Oliver, Stephen G; Bornberg-Bauer, Erich

Convergent evolution of gene networks by single‐gene duplications in higher eukaryotes Journal Article

In: EMBO Reports, 5 (3), pp. 274-279, 2004.

Abstract | Links | BibTeX

Amoutzias, Gregory D.; Robertson, David L.; Bornberg-Bauer, Erich

The evolution of protein interaction networks in regulatory proteins Journal Article

In: Comparative and Functional Genomics, 5 (1), pp. 79-84, 2004.

Abstract | Links | BibTeX

Do, Jin-Hwan; Anderson, Michael-J.; Denning, David-W.; Bornberg-Bauer, Erich

Inference of Aspergillus fumigatus Pathways by Computational Genome Analysis: Tricarboxylic Acid Cycle (TCA) and Glyoxylate Shunt Journal Article

In: Journal of Microbiology and Biotechnology, 14 (1), pp. 74-80, 2004.

Abstract | Links | BibTeX

Mabey, J. E.; Anderson, M. J.; Giles, P. F.; Miller, C. J.; Attwood, T. K.; Paton, N. W.; Bornberg-Bauer, Erich; Robson, G. D.; Oliver, S. G.; Denning, D. W.

C A DRE: the Central Aspergillus Data REpository Journal Article

In: Nucleic Acids Research, 32 (1), pp. 401-405, 2004.

Abstract | Links | BibTeX

2003

Gerrard, David T.; Bornberg-Bauer, Erich

DoMosaic - Analysis of the Mosaic-like Domain Arrangements in Proteins Journal Article

In: Informatica, 27 , pp. 15-20, 2003.

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2002

Bornberg-Bauer, Erich; Weiner, January

A putative transcription factor inducing mobility in Mycoplasma pneumoniae Journal Article

In: Microbiology, 148 , 2002.

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Šırava, M.; Schäfer, T.; Eiglsperger, M.; Kaufmann, M.; Kohlbacher, O.; Bornberg-Bauer, Erich; Lenhof, H. P.

BioMiner—modeling, analyzing, and visualizing biochemical pathways and networks Journal Article

In: Bioinformatics, 18 (2), pp. 219–S230, 2002.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; Paton, Norman W.

Conceptual data modelling for bioinformatics Journal Article

In: Briefings in Bioinformatics, 3 (2), pp. 166–180, 2002.

Abstract | Links | BibTeX

Cui, Yan; Wong, Wing Hung; Bornberg-Bauer, Erich; Chan, Hue Sun

Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes Journal Article

In: Proceedings of the National Academy of Sciences, 99 (2), pp. 809-814, 2002.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich

Randomness, Structural Uniqueness, Modularity and Neutral Evolution in Sequence Space of Model Proteins Journal Article

In: Zeitschrift für physikalische, 216 , pp. 139-154, 2002.

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Rojas-Mujica, Isabel; Bornberg-Bauer, Erich

Database Systems for the Analysis of Biochemical Pathways Journal Article

In: 2002.

Abstract | BibTeX

HS, Chan; Bornberg-Bauer, Erich

Perspectives on protein evolution from simple exact models. Journal Article

In: Applied Bioinformatics, 1 (3), pp. 121-144, 2002.

Abstract | Links | BibTeX

Rost, Ursula; Bornberg-Bauer, Erich

TreeWiz: interactive exploration of huge trees Journal Article

In: Bioinformatics, 18 (1), pp. 109-114, 2002.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; M, Harvey; A, McMeekin

Bioinformatics education: skills shortage or fundamental shift in skill creation and demand Journal Article

In: European Biopharmaceutical Review, 5 , pp. 104-110, 2002.

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2000

Kummer, U.; Olsen, L. F.; Dixon, C. J.; Green, A. K.; Bornberg-Bauer, Erich; Baier, G.

Switching from Simple to Complex Oscillations in Calcium Signaling Journal Article

In: Biophysical Journal, 79 (3), pp. 1188-1195, 2000.

Abstract | Links | BibTeX

G, Butler; Bornberg-Bauer, Erich; G, Grahne; FC, Kurfess Lam; J, Paquet; Rojas-Mujica, Isabel; R, Shinghal; L, Tao; A, Tsang

The BioIT Projects: Internet, Database and Software Technology Applied to Bioinformatics Journal Article

In: Proceeding of SSGRR, 2000.

BibTeX

1999

Bornberg-Bauer, Erich; Chan, Hue Sun

Modeling evolutionary landscapes: Mutational stability, topology, and superfunnels in sequence space Journal Article

In: Proceedings of the National Academy of Sciences, 96 (19), pp. 10689-10694, 1999.

Abstract | Links | BibTeX

Backofen, R; Will, S; Bornberg-Bauer, Erich

Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets Journal Article

In: Bioinformatics, 15 (3), pp. 234–242, 1999.

Abstract | Links | BibTeX

Krause, A; Nicodème, P; Bornberg-Bauer, Erich; Rehmsmeier, M; Vingron, M

WWW access to the SYSTERS protein sequence cluster set Journal Article

In: Bioinformatics, 15 (3), pp. 262–263, 1999.

Abstract | Links | BibTeX

Rojas-Mujica, Isabel; Bornberg-Bauer, Erich

A Comprehensible Database Model for the Computation of Biochemical Pathways Journal Article

In: Proceedings of the Workshop on Computation of Biochemical Pathways and Genetic Networks, pp. 95-100, 1999.

BibTeX

1998

Bornberg-Bauer, Erich; Rivals, Eric; Vingron, Martin

Computational Approaches to Identify Leucine Zippers Journal Article

In: Nucleic Acids Research, 26 (11), pp. 2740–2746, 1998.

Abstract | Links | BibTeX

1997

Bornberg-Bauer, Erich

Chain growth algorithms for HP type lattice proteins Journal Article

In: RECOMB Proceedings, pp. 47-55, 1997.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich

How are model protein structures distributed in sequence space? Journal Article

In: Biophysical Journal, 73 (5), pp. 2393-2403, 1997.

Abstract | Links | BibTeX

Renner, A; Bornberg-Bauer, Erich

Exploring the fitness landscapes of lattice proteins. Journal Article

In: Pacific Symposium on Biocomputing, pp. 361-372, 1997.

Abstract | Links | BibTeX

1996

Bornberg-Bauer, Erich

Simple folding model for HP lattice proteins Journal Article

In: German Conference on Bioinformatics, pp. 125-136, 1996.

Abstract | Links | BibTeX

Tacker, Manfred; Stadler, Peter F.; Bornberg-Bauer, Erich; Hofacker, Ivo L.; Schuster, Peter

Algorithm independent properties of RNA secondary structure predictions Journal Article

In: European Biophysics Journal, 25 (2), pp. 115-130, 1996.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich

Structure formation of biopolymers is complex, their evolution may be simple Journal Article

In: Proceedings of the Pacific Symposium on Biocomputing, pp. 97-108, 1996.

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1995

Bornberg-Bauer, Erich

Random structures and evolution of biopolymers: A computational case study on RNA secondary structures Journal Article

In: Pharmaceutica Acta Helvetiae, 71 (1), pp. 79-85, 1995.

Abstract | Links | BibTeX

1993

Fontana, Walter; Stadler, Peter F.; Bornberg-Bauer, Erich; Griesmacher, Thomas; Hofacker, Ivo L.; Tacker, Manfred; Tarazona, Pedro; Weinberger, Edward D.; Schuster, Peter

RNA folding and combinatory landscapes Journal Article

In: Physical Review, 47 (3), pp. 2083, 1993.

Abstract | Links | BibTeX