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

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

Forthcoming.

Abstract | Links | BibTeX

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

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

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

Forthcoming.

Abstract | Links | BibTeX

Martens, Leonie; Rühle, Frank; Witten, Anika; Meder, Benjamin; Katus, Hugo A; Arbustini, Eloisa; Hasenfu, 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

RNA Biology, 2021.

Abstract | Links | BibTeX

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

Structure and function of naturally evolved de novo proteins Journal Article

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

Abstract | Links | BibTeX

Harrison, Mark C; Niño, Luisa Jaimes M; 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

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

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

Nature Communications, 12 (1667), 2021.

Abstract | Links | BibTeX

He, Shulin; Sieksmeyer, Thorben; Che, Yanli; Mora, Alejandra Esparza M; 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

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

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

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

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

Abstract | Links | BibTeX

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

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

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

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

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

BMC Evolutionary Biology, 20 (30), 2020.

Abstract | Links | BibTeX

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

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

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

Forthcoming.

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

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

Abstract | Links | BibTeX

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

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

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

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

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

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

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

Kemena, Carsten; Bornberg-Bauer, Erich

A roadmap to domain based proteomics Book Chapter

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

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

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

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

Abstract | Links | BibTeX

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

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

F1000 Research, 6 , 2017.

Abstract | Links | BibTeX

2016

Schüler, Andreas; Bornberg-Bauer, Erich

Evolution of Protein Domain Repeats in Metazoa Journal Article

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

Bioinformatics and Biology Insights, 10 , 2016.

Abstract | Links | BibTeX

Greenwood, Jenny M; Ezquerra, Alberto L´opez; Behrens, Sarah; Branca, Antoine; Mallet, Ludovic

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

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

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

Abstract | Links | BibTeX

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

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

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

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

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

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

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

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

Abstract | Links | BibTeX

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

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

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

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, Bernhard F; Lattorff, Michael H G; Leask, Megan; Lockett, Gabrielle A; Mallon, Eamonn B; Antonio, David Marco S; 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

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

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

PLOS Genetics, 11 (7), 2015.

Abstract | Links | BibTeX

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

MDAT- Aligning multiple domain arrangements Journal Article

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

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

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

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

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

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

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, Michael R; 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

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

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

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

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

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

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

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; Albà, Mar M

Dynamics and Adaptive Benefits of Modular Protein Evolution Journal Article

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

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

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

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

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

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

Abstract | Links | BibTeX

FEULNER, PHILINE G D; CHAIN, FRÉDÉRIC 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

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

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, Jason A P; 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

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

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

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

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

Genome Biology and Evolution, 4 (3), pp. 316–329, 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, Ryan T; 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

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

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

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Moore, Andrew D; Bornberg-Bauer, Erich

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

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

Abstract | Links | BibTeX

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

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

Zitteliana, pp. 30-32, 2011.

Links | BibTeX

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

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

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

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

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

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

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

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-Fabaceaeplants Journal Article

BMC Plant Biology , 10 (219), 2010.

Abstract | Links | BibTeX

Sikosek, Tobias; Bornberg-Bauer, Erich

Evolution after and before gene duplication? Journal Article

2010.

Abstract | Links | BibTeX

Bornberg-Bauer, Erich

Signals: Tinkering with Domains Journal Article

Science Signaling, 14 (3), 2010.

Abstract | Links | BibTeX

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

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

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

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; Kramer, Linus

Robustness versus evolvability: a paradigm revisited Journal Article

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

Abstract | Links | BibTeX

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

How do new proteins arise? Journal Article

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

Abstract | Links | BibTeX

Moore, Andrew D; Bornberg-Bauer, Erich

Protein Domains as Evolutionary Units Journal Article

Evolutionary Genomics and Systems Biology, 2010.

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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

Database, 2009 , 2009.

Abstract | Links | BibTeX

2008

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

Just how versatile are domains? Journal Article

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

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

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

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

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

Abstract | Links | BibTeX

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

BMC Systems Biology, 1 (34), 2007.

Abstract | Links | BibTeX

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

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

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

Abstract | Links | BibTeX

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

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

HFSP Journal, 1 (1), pp. 79–87, 2007.

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

BMC Genomics, 7 (107), 2006.

Abstract | Links | BibTeX

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

Domain deletions and substitutions in the modular protein evolution Journal Article

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

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

Abstract | Links | BibTeX

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

Finding Common Protein Interaction Patterns Across Organisms Journal Article

Evolutionary Bioinformatics, 2006.

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2005

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

Transcriptional networking Journal Article

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

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

Abstract | Links | BibTeX

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

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

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

Abstract | Links | BibTeX

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

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

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

Genetics, Genomics, Proteomics and Bioinformatics, 2005.

Abstract | Links | BibTeX

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

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

Abstract | Links | BibTeX

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

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

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

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

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

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

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

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

Abstract | Links | BibTeX

Bornberg-Bauer, Erich; Paton, Norman W

Conceptual data modelling for bioinformatics Journal Article

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

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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

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

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Bornberg-Bauer, Erich

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

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

2002.

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HS, Chan; Bornberg-Bauer, Erich

Perspectives on protein evolution from simple exact models. Journal Article

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

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Rost, Ursula; Bornberg-Bauer, Erich

TreeWiz: interactive exploration of huge trees Journal Article

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

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

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

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

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

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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

Proceeding of SSGRR, 2000.

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1999

Bornberg-Bauer, Erich; Chan, Hue Sun

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

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

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

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

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

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

WWW access to the SYSTERS protein sequence cluster set Journal Article

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

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Rojas-Mujica, Isabel; Bornberg-Bauer, Erich

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

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

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1998

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

Computational Approaches to Identify Leucine Zippers Journal Article

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

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1997

Bornberg-Bauer, Erich

Chain growth algorithms for HP type lattice proteins Journal Article

RECOMB Proceedings, pp. 47-55, 1997.

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Bornberg-Bauer, Erich

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

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

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Renner, A; Bornberg-Bauer, Erich

Exploring the fitness landscapes of lattice proteins. Journal Article

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

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1996

Bornberg-Bauer, Erich

Simple folding model for HP lattice proteins Journal Article

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

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

Algorithm independent properties of RNA secondary structure predictions Journal Article

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

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Bornberg-Bauer, Erich

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

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

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

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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

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

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