Publications
- Philine G D Feulner, Frédéric J J Chain, Mahesh Panchal, Christophe Eizaguirre, Martin Kalbe, Tobias L Lenz, Marvin Mundry, Irene Samonte-Padilla, Monika Stoll, Manfred Milinski, Thorsten B H Reusch, Erich Bornberg-Bauer
Genome-wide patterns of standing genetic variation in a natural marine population of three-spined sticklebacks.
Submitted, 2012
- Tobias Sikosek, Erich Bornberg-Bauer, Hue Sun Chan
Evolutionary dynamics on protein bi-stability landscapes have the potential to resolve adaptive conflicts.
Submitted, 2012
- Tobias Sikosek, Hue Sun Chan, Erich Bornberg-Bauer
Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness
Submitted, 2011
- Andrew D. Moore, Sonja Grath, Andreas Schüler, Ann K. Huylmans, and Erich Bornberg-Bauer
Rates, mechanisms and functional implications of modular protein rearrangements during 400 million years of Arthropod evolution
Submitted, 2011
- Wissler L, Godmann L, and E. Bornberg-Bauer
Genome-wide conservation of SSRs, Simple Sequence Repeats, across long evolutionary time scale in genus Drosophila
Submitted, 2012
- Jenny Gu, Katrin Weber, Elisabeth Klemp, Gidon Winters, Susanne U. Franssen, Isabell Wienpahl, Ann-Kathrin Huylmans, Karsten Zecher, Thorsten B.H. Reusch, Erich Bornberg-Bauer and Andreas P.M. Weber
Identifying core features of adaptive metabolomic mechanisms for chronic heat stress attenuation as a feature for systems robustness
Integrative Biology (2012), in press
- Marvin Mundry, Erich Bornberg-Bauer, Michael Sammeth, Philine G. D. Feulner
Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach
Plos One (2012) 7, e31410
[Online access]
- Anna R. Kersting, Erich Bornberg-Bauer, Andrew D. Moore, and Sonja Grath
Dynamics and adaptive bene fits of protein domain emergence and arrangements during plant genome evolution
Genome Biology and Evolution 4(3):316-329 (2012)
- Andrew D. Moore and Erich Bornberg-Bauer
The Dynamics and Evolutionary Potential of Domain Loss and Emergence
Molecular Biology and Evolution 29:787-796 (2012) [Online access]
- The Spider Mite Genome Consortium, including Lothar Wissler
The genome of Tetranychus urticae reveals herbivorous pest adaptations
Nature 479, 487-492 (2011) [Online access]
- Susanne U. Franssen, Jenny Gu, Nina Bergmann, Gidon Winters, Ulrich C.
Klostermeier, Philip Rosenstiel, Erich Bornberg-Bauer, and Thorsten
B.H. Reusch
Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species
PNAS 108(48):19276-8 (2011)
[Online access]
- Susanne U. Franssen, Roshan P. Shrestha, Andrea Bräutigam, Erich Bornberg-Bauer and Andreas P.M. Weber
Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
BMC Genomics 12:227 (2011) [Online access]
- A.R. Reineke, E. Bornberg-Bauer and J. Gu
Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes
Nucleic Acids research 39(14): 6029–6043 (2011)
[Online access]
- The Atta Genome Working Group
The Genome Sequence of the Leaf-cutter Ant Atta cephalotes Reveals Insights into its Obligate Symbiotic Lifestyle
PLoS Genetics 7(2): e1002007 (2011)
[S14] [S17]
[Online access][Cover picture Atta cephalotes]
- L. Wissler, F.C. Codoner, T.B.H. Reusch, J.L. Olsen, G. Procaccini and E. Bornberg-Bauer
Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life
BMC Evolutionary Biology 11:8 (2011) [Online access]
- A.M. Ernst, B. Ruping, S.B. Jekat, S. Nordzieke, A.R. Reineke, B. Müller , E. Bornberg-Bauer, D. Prüfer and G.A. Noll
The sieve element occlusion gene family in dicotyledonous plants
Plant Signaling & Behavior, V6 (2011)
- Bergmann, N; Winters, G; Rauch, G; Eizaguirre, C; Gu, J; Nelle, P; Fricke, B; Reusch, TBH
Population-specificity of heat stress gene induction in northern and southern eelgrass Zostera marina populations under simulated global warming.
Molecular Ecology, 2010(19), 2870-2883. [Online access ]
- N. Yamamura, A. Telschow, K. Uchii and Z. Kawabata
A basic equation for population dynamics with destruction of breeding habitats and its application to outbreak of cyprinid herpesvirus 3 (CyHV-3)
Ecological Research (2010) [Online access]
- A. Schueler and E. Bornberg-Bauer
The Evolution of Protein Interaction Networks
in:Data Mining in Proteomics (Ed: Martin Eisenacher, Michael Hamacher and Christian Stephan), SpringerLink (2010)
[Online access][Request reprint]
- B. Ruping, A.M. Ernst, S.B. Jekat, S. Nordzieke, A.R. Reineke, B. Müller , E. Bornberg-Bauer, D. Prüfer and G.A. Noll
Molecular and phylogenetic characterization of the sieve element occlusion gene family in Fabaceae and non-Fabaceae plants
BMC Plant Biology,10:219 (2010)
[Online access]
- E. Bornberg-Bauer
Signals: Tinkering with Domains
Science Signaling, 3:139 (2010)
[Online access][Request reprint]
- E. Bornberg-Bauer and L. Kramer
Robustness Versus Evolvability: A Paradigm Revisited.
HFSP Journal 4(3) (2010)
- T. Chen, D. Vernazobres, T. Yomo, E. Bornberg-Bauer and H. S. Chan
Evolvability and Single-Genotype Fluctuation in Phenotypic Properties: A Simple Heteropolymer Model
Biophysical Journal,98:2487-2496 (2010) [Online access] [Request reprint]
- A. D. Moore and E. Bornberg-Bauer
Protein domains as evolutionary units
in: Evolutionary Genomics and Systems Biology, Ed. G. Caetano-Anollés (2010)
John Wiley & Sons
[Online access][Request reprint]
- A. Kobayashi and A. Telschow
The Concept of Effective Recombination Rate and Its Application in Speciation Theory
Evolution (2010)
[Online access ][Request reprint]
- Gu J; Hilser VJ.
Predicting the energetics of conformational fluctuations in proteins from sequence: a strategy for profiling the proteome.
Structure, 16:1627-1637 (2008)
[Online access][Request reprint]
- J. Weiner 3rd, A. D. Moore, E. Bornberg-Bauer
Just how versatile are domains?
BMC Evolutionary Biology, 8:285, 2008
[Free online access]
- A. D. Moore*, A. K. Bjoerklund*, D. Ekman, E. Bornberg-Bauer and A. Elofsson
Arrangements in the modular evolution of proteins
Trends in Biochemical Sciences, 33:09 (2008)
* these authors contributed equally to this work
[Free online access]
- Kobayashi, Y; Hammerstein, P; Telschow, A
The neutral effective migration rate in a mainland-island context
Theoretical Population Biology, 74:84-92 (2008)
[Online access][Request reprint]
- D. Whitehead, C. Wilke, D. Vernazobres, E. Bornberg-Bauer
The look-ahead effect of phenotypic mutations
Biology Direct, 3:18 (2008)
[Online access][Request reprint]
- F. Friedrichs, L. Henckaerts, S. Vermaire, T. Kucharzik, T. Seehafer, M. Krull, E. Bornberg-Bauer, M. Stoll, J. Weiner
Discovery of a caspase recruitment domain in the Crohn's disease susceptibility gene DLG5 by sequence comparison and phylogenies
Journal of Molecular Medicine 86(4):423-32 (2008)
[online access][Request reprint]
- Falb Michaela, Mueller Kerstin, Koenigsmaier Lisa, Oberwinkler Tanja, Horn Patrick, Gronau Susanne von, Orland Gonzales, Pfeiffer Friedhelm, Bornberg-Bauer Erich, Oesterhelt Dieter
Metabolism of Halophilic Archaea
Extremophiles, 12:177-196 (2008)
[online access][Request reprint]
- H. Schulenburg, M. Hoeppner, J. Weiner III, E. Bornberg-Bauer
Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans
Immunobiology 213(3-4):237-50 (2008)
[online access][Request reprint]
- Thorsten BH Reusch*, Amelie S Veron*, Christoph Sapper, January Weiner, Lothar Wissler, Alfred Beck, Sven Klages, Michael Kube, Richard Reinhardt and Erich Bornberg-Bauer
Comparative analysis of expressed sequence tag libraries in the seagrass Zostera marina subjected to temperature stress
Marine Biotechnology, 10(3):297-309 (2008)
[ Online access] [Request reprint]
* these authors contributed equally to this work
- Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, Robinson-Rechavi M, Bornberg-Bauer E, Robertson DL, Oliver SG
A protein interaction atlas for the nuclear receptors: Properties and quality of a hub-based dimerisation network.
BMC Systems Biology, 1:34 (2007)
[Online access]]
- Francois Beaussart, January Weiner 3rd, Erich Bornberg-Bauer
Automated Improvement of Domain ANnotations using context analysis of Domain Arrangements (AIDAN)
Supplementary material
Bioinformatics, 23:1834-1836 (2007)
[Online access][Request reprint]
- R. Wroe, H.S. Chan and E. Bornberg-Bauer
A Structural Model of Latent Evolutionary Potentials Underlying Neutral Networks in Proteins
HFSP Journal 1:79 (2007) [See the cover of this issue]
Supplementary Material
- J. Kilian, D. Whitehead, J. Horak, D. Wanke, S. Weinl, O. Batistic, C. D'Angelo, E. Bornberg-Bauer, J. Kudla and K. Harter
The AtGenExpress global stress expression data set: Protocols, evoluation and model data analysis of UV-B light, drought and cold stress responses
Plant Journal, Apr;50(2):347-63 (2007)
[Online access][Request reprint]
- A. Veron, K. Kaufmann, E. Bornberg-Bauer
Evidence of interaction network evolution by whole genome duplications: a case-study in MADS-box proteins
Molecular Biology and Evolution, 24:670-678 (2007)
[Online access][Request reprint]
- G. Amoutzias, A. Veron, J. Weiner, M. Robinson-Rechavi, E. Bornberg-Bauer, S. Oliver, D. Robertson
One billion years of bZIP transcription factor evolution: conservation and change in dimerization and DNA-binding site specificity
Molecular Biology and Evolution, 24:827-835 (2007)
[Online access][Request reprint]
- A. Veron and D. Whitehead and E. Bornberg-Bauer
Studying the evolution of regulatory networks
in: Biological Networks, Ed. F. Kepes, World Scientific (invited) (2007)
[Request reprint]
- Farwick A, Jordan U, Fuellen G, Huchon D, Catzeflis F, Brosius J, Schmitz J.
Automated Scanning for Phylogenetically Informative Transposed Elements in Rodents
Systematical Biology, 55:936-948 (2006)
[ Free online access ]
- Amoutzias G.D., Bornberg-Bauer E., Oliver S.G. and Robertson D.L.
Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network
BMC Genomics, 7:107 (2006)
[ Free online access ]
- Gerke M, X Jiang, E Bornberg-Bauer and G. Fuellen
Finding Common Protein Interaction Patterns Across Organisms
Evolutinary Bioinformatics Online, 2:45-52 (2006)
[ Free online access ]
- J. Weiner, F. Beaussart, E. Bornberg-Bauer
Domain Deletions and Substitutions in the Modular Protein Evolution
FEBS Journal, 273:2037-2047 (2006)
[Online access][Request reprint]
- Spitzer M, Lorkowski S, Cullen P, Sczyrba A, Fuellen G.
IsoSVM--distinguishing isoforms and paralogs on the protein level.
BMC Bioinformatics, 7:110 (2006)
[Free online access]
- J. Weiner and E. Bornberg-Bauer
Evolution of Circular Permutations in Multi-Domain Proteins
Molecular Biology and Evolution 23(4):734-743 (2006)
[Online access][Request reprint]
- Shahid M, Alam I, Fuellen G.
Biotool2Web: creating simple Web interfaces for bioinformatics applications
Applied Bioinformatics 5(1):63-6.(2006)
[ Online access ][Request reprint]
- E. Bornberg-Bauer and Amelie Veron
Evolution of regulatory networks
Genetics, Genomics, Proteomics and Bioinformatics John Wiley & Sons (invited) (2005)
- Stolle K, Schnoor M, Fuellen G, Spitzer M, Engel T, Spener F, Cullen P, Lorkowski S
Cloning, cellular localization, genomic organization, and tissue-specific expression of the TGFbeta1-inducible SMAP-5 gene
Gene. 351:199-30 (2005)
[Online access][Request reprint]
- Teichmann SA, Bornberg-Bauer E, Luscombe NM
Transcriptional Networking
Genome Biology 6(9):344 (2005)
[Online access ][Request reprint]
- Fuellen G, Spitzer M, Cullen P, Lorkowski S
Correspondance of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets
Proteins. 61(4):888-99 (2005)
[Online access]
- Wroe R, E. Bornberg-Bauer and HS Chan
Comparing folding codes in simple heteropolymer models of protein evolutionary landscapes: How robust is the superfunnel paradigm?
Biophysical Journal, 88(1):118-31 (2005)
[ Free online access ]
- Weiner J, G. Thomas and E. Bornberg-Bauer
Rapid Motif-Based Prediction of Circular Permutations in Multi-Domain Proteins
Bioinformatics, 21(7):932-7 (2005)
[Online access][Request reprint]
- E. Bornberg-Bauer, F Beaussart, S Kummerfeld, S Teichmann and J Weiner
The Evolution of Domain Arrangements in Proteins and Interaction Networks (Review)
CMLS, 62(4):435-45 (2005)
[Online access][Request reprint]
- Malonek S, Bomke C, Bornberg-Bauer E, Rojas MC, Hedden P, Hopkins P, Tudzynski B.
Distribution of gibberellin biosynthetic genes and gibberellin production in the Gibberella fujikuroi species complex
Phytochemistry, 66(11):1296-1311 (2005)
[Online access][Request reprint]
- Amoutzias G, J Weiner and E. Bornberg-Bauer
Phylogenetic profiling of protein interaction networks in eukaryotic transcription factors reveals focal proteins being ancestral to hubs
Gene, 347(2):247-253 (2005)
[Online access][Request reprint]
- Fuellen G, Nacken W, Sorg C, Kerkhoff C
Computational searches for missing orthologs: the case of S100A12 in mice
OMICS, 8(4):334-40 (2004)
[Online access ][Request reprint]
- Alam I, Dress A, Rehmsmeier M, Fuellen G
Comparative homology agreement search: an effective combination of homology-search methods
PNAS, 101(38):13814-9. (2004)
[Free online access ]
- Amoutzias G, DL Robertson, SG Oliver and E. Bornberg-Bauer;
Convergent Evolution of Gene Networks by single-gene duplication in higher eukaryotes
EMBO Reports, 5:274-279, (2004)
[Free online access ]
- Amoutzias G and E. Bornberg-Bauer
Evolution of protein-protein interaction networks in homo- and heterodimerising eukaryotic transcription factors
Comparative and Functional Genomics, 5:79 - 84, (2004)
[ Online access ][Request reprint]
- Mabey JE, MJ Anderson, PF Giles, CJ Miller, TK Attwood, NW Paton, E. Bornberg-Bauer, GD Robson, SG Oliver and DW Denning
CADRE: The Central Aspergillus Data REpository
Nucleic Acids Research, 32:D401-D405; (2004)
[ Free online access ]
- Spitzer M, Fuellen G, Cullen P, Lorkowski S
VisCoSe: visualization and comparison of consensus sequences
Bioinformatics, 20(3):433-5 (2004)
[Online access ][Request reprint]
- Klenk HP, Spitzer M, Ochsenreiter T, Fuellen G
Phylogenomics of hyperthermophilic Archaea and Bacteria.
Biochemical Society Transactions, 32(Pt 2):175-8.(2004)
[Online access ][Request reprint]
- Do JH, MJ Anderson, DW Denning and E. Bornberg-Bauer
Computational identification of TCA and glyoxylate cycle in Aspergillus fumigatus
Journal of Microbiology and Biotechnology ; 14:74-80 (2004)
- Gerrard DG and E. Bornberg-Bauer
doMosaic: Analysis of the mosaic-like domain architecture in proteins
Informatica; 27: 15-20; (2003)
[Request reprint]
- Fuellen G, Spitzer M, Cullen P, Lorkowski S
BLASTing proteomes, yielding phylogenies
In Silico Biology 3(3):313-9 (2003)
[Online access ][Request reprint]
- Bornberg-Bauer E.;
Randomness, Structural Uniqueness, Modularity, and Neutral Evolution in Sequence Space of Model Proteins.
Zeitschrift für physikalische Chemie 216: 139 -- 154, (2002)
[Request reprint]
- Cui Y., W.H. Wong, E. Bornberg-Bauer, and H.S. Chan;
Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes
PNAS, 99: 809 -- 814, (2002)
[Online access ][Request reprint]
- Sirava M, T Schäfer, M Eigelsperger, M Kauffman, O Kohlbacher, E. Bornberg-Bauer and HP Lenhof;
BioMiner - Modeling, Analyzing and Visualizing Biochemical Pathways and Networks
Bioinformatics; 18(S):219-230; (2002) [ECCB Proceedings Issue]
[Online access ][Request reprint]
- Bornberg-Bauer E. and N. Paton;
Conceptual data modelling for bioinformatics (Review);
Briefings in Bioinformatics, 3(2): 166 -- 180, (2002)
[Online access][Request reprint]
- Rojas-Mujica I. and E. Bornberg-Bauer
Database systems for the analysis of biochemical pathways (invited)
In Molecular Biology and Pathogenicity of Mycoplasmas, 201--220; (S. Razin and R. Herrmann, editors),
Kluver Academic/Plenum Publishers (KAPP), New York; (2002)
- Chan H.S. and E. Bornberg-Bauer;
Perspectives on Protein Evolution from simple exact models (Review)
Applied Bioinformatics; 1:121-144; (2002)
- E. Bornberg-Bauer and January Weiner III
Computational identification of a putative trancription factor responsible for mobility in Mycoplasma Pneumoniae (comment)
Microbiology UK, 148:10-11; (2002)
[Online access ][Request reprint]
- Rost U. and E. Bornberg-Bauer
TreeWiz: Interactive exploration of huge trees
Bioinformatics, 18(1): 109 -- 114, (2002)
[Online access ][Request reprint]
- E. Bornberg-Bauer Mark Harvey and Andrew McMeekin
Bioinformatics education: skills shortage or fundamental shift in skill creation and demand (invited)
European Biopharmaceutical Review 5: 104 -- 110; (2002)
[Free online access (free registration required) ] [Request reprint]
for earlier publications, please refer to people / Erich Bornberg-Bauer
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