Submitted

  • Harrison, M.C., Jongepier, E., Robertson, H.M.,...Belles, X., Korb, J., Bornberg-Bauer, E.
    Cockroach and termite genomes elucidate evolutionary signatures of hemimetabolous eusociality
    Submitted, 2017
    [Abstract + Download]


  • van Loo B
    Misannotation of the Catalytic Function of Hydrolases in Plasmodium falciparum
    mBio, 2017
    [Abstract + Download]



    2017

  • Gubala AM, Schmitz JF, Kearns MJ, Vinh TT, Bornberg-Bauer E, Wolfner MF, Findlay GD
    The goddard and saturn genes are essential for Drosophila male fertility and may have arisen de novo
    Molecular Biology and Evolution, 2017
    [Abstract + Download]


  • Schmitz, JF and Bornberg-Bauer E Emergence Figure 2
    Fact or fiction: Updates on how protein coding genes might emerge de novo from previously non-coding DNA
    F1000Research, 2017
    [Online access] [Abstract + Download]


  • Lopez-Ezquerra A, Harrison MC, Bornberg-Bauer Erich
    Comparative analysis of lincRNAs in insect species.
    BMC Evolutionary Biology, 2017
    [Abstract + Download]


  • van Loo B and Bornberg-Bauer E
    Enzyme sub-functionalization driven by regulation
    EMBO reports, 2017
    [Abstract + Download]



    2016

  • Haase D*, Rieger JK*, Witten A, Stoll M, Bornberg-Bauer E, Kalbe M and Reusch TBH
    Immunity comes first: The effect of parasite genotypes to adaptive immunity and immunization in three-spined sticklebacks
    Development and Comparative Immunology, 2016
    [Abstract + Download]


  • Huang Y, Chain FJJ, Panchal M, Eizaguirre C, Kalbe M, Lenz TL, Samonte IE, Stoll M, Bornberg-Bauer E , Reusch TBH, Milinski M, Feulner PGD
    Habitat-specific gene expression in immune tissues between lake and river sticklebacks
    Molecular Ecology 25:943-958, 2016
    [Abstract + Download]


  • Olsen JL, Rouzé P, Verhelst B, Lin YC, Bayer T, Collen J, Dattolo E, De Paoli E, Dittami S, Maumus F, Michel G, Kersting A, Lauritano C, Lohaus R, Töpel M, Tonon T, Vanneste K, Amirebrahimi M, Brakel J, Boström C, Chovatia M, Grimwood J, Jenkins JW, Jüterbock A, Mraz A, Stam WT, Tice H, Bornberg-Bauer E, Green PJ, Pearson GA, Procaccini G, Duarte CM, Schmutz J, Reusch TBH, van de Peer Y Olsen Peer Genome Zostera Marina N 2016 Cover
    The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea
    Nature doi:10.1038/nature16548, 2016
    [Online access] [Abstract + Download]


  • Haase D, Rieger JK, Witten A, Stoll M, Bornberg-Bauer E , Kalbe M, Scharsack JP, Reusch TBH
    Comparative transcriptomics of stickleback immune gene responses upon infections by two helminth parasites, Diplostomum pseudospathaceum and Schistocephalus solidus
    Zoology, 2016
    [Abstract + Download]


  • Jueterbock A*, Franssen SU, Bergmann N, Gu J, Coyer JA, Reusch TBH, Bornberg-Bauer E , Olsen JL
    Phylogeographic differentiation versus transcriptomic adaptation to warm temperatures in Zostera marina, a globally important seagrass
    Molecular Ecology, 2016
    [Abstract + Download]


  • Greenwood J, Ezquerra A, Behrens S, Branca A, Mallet L
    Current analysis of next generation sequencing data with a focus on host-parasite interactions
    Zoology, 2016


  • Dohmen E, Kremer LPM, Bornberg-Bauer E and Kemena C
    DOGMA: Domain-based transcriptome and proteome quality assessment
    Bioinformatics, 2016
    [Online access] [Abstract + Download]


  • Schmitz JF, Zimmer F, Bornberg-Bauer E
    Mechanisms of transcription factor evolution in Metazoa
    Nucleic Acid Research, 2016
    [Online access] [Abstract + Download]


  • Elsner D, Kremer LPM, Arning N, Bornberg-Bauer E Elsner Ebb Comparative Genomics Molecular Traits Social Insects Cois 2016 Graphical Abstract
    Comparative genomic approaches to investigate molecular traits specific to social insects
    Current Opinion in Insect Science, 2016
    [Online access] [Abstract + Download]


  • Schüler A, Bornberg-Bauer E
    Evolution of Protein Domain Repeats in Metazoa
    Molecular Biology and Evolution, 2016
    [Online access] [Abstract + Download]


  • Klasberg S, Bitard-Feildel T, Mallet L
    Computational Identification of Novel Genes: Current and Future Perspectives
    Bioinformatics and Biology Insights, 2016
    [Online access] [Abstract + Download]



    2015

  • Feulner PGD, Chain FJJ, Panchal M, Huang Y, Eizaguirre C, Kalbe M, Lenz TL, Samonte I, Stoll M, Bornberg‐Bauer E, Reusch TBH, Milinski M
    Genomics of Divergence along a Continuum of Parapatric Population Differentiation
    PLoS Genetics 11(2): e1004966. doi:10.1371/journal.pgen.1004966, 2015
    [Online access] [Abstract + Download]


  • Kersting A, Mizrachi E, Bornberg-Bauer E, Myburg AA
    Protein domain evolution is associated with reproductive diversification and adaptive radiation in the basal rosid Eucalyptus grandis
    New Phytologist 206:1328-1336, doi: 10.1111/nph.13211, 2015
    [Online access] [Abstract + Download]


  • Masri L*, Branca A*, Sheppard AE*, Papkou A, Laehnemann D, Günther PS, Prahl S, Saebelfeld M, Crain PR, Strauß J, Hollensteiner J, Liesegang H, Brzuszkiewicz E, Daniel R, Michiels NK, Schulte RD, Kurtz J, Rosenstiel P, Telschow A, Bornberg-Bauer E, Schulenburg H Plosbttoxins
    Host-Pathogen Coevolution: The Selective Advantage of Bacillus thuringiensis Virulence and Its Cry Toxin Genes
    PLoS Biology, 2015
    [Online access] [Abstract + Download]


  • Schüler A , Schmitz G, Reft A, Özbek S, Thurm U and Bornberg-Bauer E
    The rise and fall of TRP-N, an ancient family of mechanogated ion channels, in metazoan
    Genome Biology and Evolution, 2015
    [Online access] [Abstract + Download]


  • Kemena C, Bitard-Feildel T and Bornberg-Bauer E
    MDAT- Aligning multiple domain arrangements
    BMC Bioinformatics, 2015
    [Online access] [Abstract + Download]


  • Bitard-Feildel T, Kemena C, Greenwood JM, Bornberg-Bauer E
    Domain similarity based orthology detection
    BMC Bioinformatic, 2015
    [Online access] [Abstract + Download]


  • Sadd BM, ... Klasberg S, Bornberg-Bauer E, ... Worley K [134 authors] Bbfront
    The genomes of two key bumblebee species with primitive eusocial organization
    Genome Biology, 2015
    [Online access] [Abstract + Download]


  • Bitard-Feildel T, Heberlein M, Bornberg-Bauer E*, Callebaut I*
    Detection of Orphan Domains in Drosophila using "Hydrophobic clustering analysis"
    Biochimie, 2015
    [Online access] [Abstract + Download]


  • Smith CR, Helms Cahan S, Kemena C, Brady SG, Yang W, Bornberg-­Bauer E, Eriksson T, Gadau J, Helmkampf M, Gotzek D, Miyakawa MO, Suarez A, and Mikheyev A Mbe Cover Nov2015 0
    How do genomes create novel phenotypes? Insights from the loss of the worker caste in ant social parasites
    Mol Biol Evol, 2015
    [Online access] [Abstract + Download]


  • Bornberg-Bauer E, Schmitz J and Heberlein M
    Emergence of de novo proteins from "dark genomic matter" by "grow slow and moult"
    Biochem. Soc. Trans., 2015
    [Online access] [Abstract + Download]



    2014

  • Moore AD, Held A, Terrapon N, Weiner J and Bornberg-Bauer E
    DoMosaics: Software for domain arrangement visualization and domain-centric analysis of proteins.
    Bioinformatics, 2014 Jan 15;30(2):282-3. doi: 10.1093/bioinformatics/btt640. Epub 2013 Nov 12., 2014
    [Online access] [Abstract + Download]


  • Terrapon N*, Weiner J*, Grath S, Moore AD and Bornberg-Bauer E
    Rapid similarity search of proteins using alignments of domain arrangements
    Bioinformatics, 30, 274-281, 2014
    [Online access] [Abstract + Download]


  • Franssen SU*, Gu J* , Winters G, Huylmans AK, Wienpahl I, Sparwel M, Coyer JA, Olsen JL, Reusch TL and Bornberg-Bauer E
    Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types
    Marine Genomics 15:65 - 73., 2014
    [Online access] [Abstract + Download]


  • Behrens S, Peuß R, Milutinovic B, Eggert H, Esser D, Rosenstiel P, Schulenburg HS, Bornberg-Bauer E, Kurtz J
    Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis
    BMC Genomics 15: 445, 2014
    [Online access] [Abstract + Download]


  • Chain FJJ*, Feulner PGD*, Panchal M*, Eizaguirre C, Kalbe M, Lenz TL, Samonte-Padilla IE, Stoll M, Bornberg-Bauer E, Milinski M and Reusch TBH
    Extensive Copy-Number Variation of Young Genes across Stickleback Populations
    PLoS Genetics 10(12):e1004830, 2014
    [Online access] [Abstract + Download]


  • Terrapon N*, Li C*, Robertson HM, Ji L, Meng X, Booth W, Chen Z, Childers CP, Glastad KM, Gokhale K, Gowin J, Gronenberg W, Hermansen RA, Hu H, Hunt BG, Huylmans AK, Khalil SMS, Mitchell RD, Munoz-Torres MC, Mustard JA, Pan H, Reese JT, Scharf ME, Sun F, Vogel H, Xiao J, Yang W, Yang Z, Yang Z, Zhou J, Zhu J, Brent CS, Elsik CG, Goodisman MAD, Liberles DA, Roe RM, Vargo EL, Vilcinskas A, Wang J, Bornberg-Bauer E, Korb J, Zhang G, Liebig J
    Molecular traces of alternative social organization in a termite genome
    Nature Communications 5:3636. doi: 10.1038/ncomms4636, 2014
    [Online access] [Abstract + Download]


  • Haase D, Rieger JK, Witten A, Stoll M, Bornberg-Bauer E, Kalbe M and Reusch TBH
    Specific Gene Expression Responses to Parasite Genotypes Reveal Redundancy of Innate Immunity in Vertebrates
    PLoS One, 9 (9) e108001, 2014
    [Online access] [Abstract + Download]


  • Myburg AA, ... Bornberg-Bauer E, Kersting AR ... Van de Peer Y, Rokhsar DS, Schmutz J (80 authors)
    Genome sequence of Eucalyptus grandis
    Nature 510(7505):356-62, 2014
    [Online access] [Abstract + Download]


  • Schrader L, Kim JW, Ence D, Zimin A, Klein A, Wyschetzki K, Weichselgartner T, Kemena C, Stökl J, Schultner E, Wurm Y, Smith CD, Yandell M, Heinze J, Gadau J & Oettler J
    Transposable element islands facilitate adaptation to novel environments in an invasive species
    Nature Communications, 2014
    [Online access] [Abstract + Download]



    2013

  • Moore AD, Grath S, Schüler A, Huylmans AK and Bornberg-Bauer E
    Quantification and Functional Analysis of Modular Protein Evolution in a Dense Phylogenetic Tree
    Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1834, (5): 898–907, 2013
    [Online access] [Abstract + Download]


  • Wissler L, Gadau J, Simola DF, Helmkampf M, Bornberg-Bauer E
    Mechanisms and dynamics of orphan gene emergence in insect genomes
    Genome Biology and Evolution 5(2): 439-55, 2013
    [Online access] [Abstract + Download]


  • Simola DF, Wissler L, Donahue G, Waterhouse RM, Helmkampf M, Roux J, Nygaard S, Glastad KM, Hagen DE, Viljakainen L, Reese JT, Hunt BG, Graur D, Elhaik E, Kriventseva EV, Wen J, Parker BJ, Cash E, Privman E, Childers CP, Munoz-Torres MC, Berger SL, Boomsma JJ, Bornberg-Bauer E, Currie C, Elsik CG, Suen G, Goodisman MAD, Keller L, Liebig J, Rawls A, Reinberg D, Smith CD, Smith CR, Tsustui N, Wurm Y, Zdobnov EM, Gadau J
    Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality.
    Genome Research, 23:1235-1247, 2013
    [Online access] [Abstract + Download]


  • Bornberg-Bauer E and Alba MM
    Dynamics and Adaptive Benefits of Modular Protein Evolution
    Current Opinion in Structural Biology 23(3): 459-66, 2013
    [Online access] [Abstract + Download]


  • Feulner PGD*, Chain FJJ*, Panchal M*, Eizaguirre C, Kalbe M, Lenz TL, Mundry M, Samonte-Padilla I, Stoll M, Milinski M, Reusch TBH, Bornberg-Bauer E
    Genome-wide patterns of standing genetic variation in a natural marine population of three-spined sticklebacks
    Molecular Ecology 22(3): 635-49, 2013
    [Online access] [Abstract + Download]


  • Guo B, Chain FJ, Bornberg-Bauer E , Leder EH and Merilä J
    Genomic divergence between nine- and three -spined sticklebacks
    BMC Genomics, 2013
    [Online access] [Abstract + Download]



    2012

  • Sikosek T, Bornberg-Bauer E, Chan HS
    Evolutionary dynamics on protein bi-stability landscapes have the potential to resolve adaptive conflicts
    PLoS Comput Biol 8(9):e1002659, 2012
    [Online access] [Abstract + Download]


  • Wissler L, Godmann L and Bornberg-Bauer E
    Evolutionary dynamics of simple sequence repeats across long evolutionary time in genus Drosophila
    Trends in Evolutionary Biology 4:1, 2012
    [Online access] [Abstract + Download]


  • Sikosek T, Chan HS, Bornberg-Bauer E
    Escape from Adaptive Conflict follows from weak functional trade-offs and mutational robustness
    Proc. Natl. Acad. Sci., USA, 109(37):14888-14893, 2012
    [Online access] [Abstract + Download]


  • Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhanovich E, Sjölander K, Sunyaev S, Teufel AJ, Thorne JL, Thornton JW, Weinreich DM, Whelan S
    The interface of protein structure, protein biophysic, and molecular evolution (R)
    Protein Science 21(6): 769-85, 2012
    [Online access] [Abstract + Download]


  • Terrapon N, Grath S, Weiner J, Moore AD and Bornberg-Bauer E
    Fast Homology Search Using Domain-Architecture Alignment
    JOBIM, Conference proceedings, 2012
    [Abstract + Download]


  • Gu J, Weber K, Klemp E, Winters G, Franssen SU, Wienpahl I, Huylmans AK, Zecher K, Reusch TBH, Bornberg-Bauer E and Weber APM Integrativebiologyv4
    Identifying core features of adaptive metabolomic mechanisms for chronic heat stress attenuation as a feature for systems robustness
    Integrative Biology 4:480 - 493, 2012
    [Online access] [Abstract + Download]


  • Balasubramanian PG, Beckmann A, Warnken U, Schnölzer M, Schüler A, Bornberg-Bauer E, Holstein TW, Ozbek S
    Proteome of Hydra Nematocyst
    Journal of Biological Chemistry 287(13):9672-81, 2012
    [Online access] [Abstract + Download]


  • Mundry M, Bornberg-Bauer E, Sammeth M, Feulner PGD
    Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach
    Plos One 7, e31410, 2012
    [Online access] [Abstract + Download]


  • Kersting A, Bornberg-Bauer E, Moore AD and Grath S
    Dynamics and adaptive benefits of protein domain emergence and arrangements during plant genome evolution
    Genome Biology and Evolution 4(3):316-329, 2012
    [Online access] [Abstract + Download]


  • Moore AD and Bornberg-Bauer E
    The Dynamics and Evolutionary Potential of Domain Loss and Emergence
    Molecular Biology and Evolution 29(2): 787-796, 2012
    [Online access] [Abstract + Download]


  • Niehuis O, Hartig G, Grath S, Pohl H, Lehmann J, Tafer H, Donath A, Krauss V, Eisenhardt C, Hertel J, Petersen M, Mayer C, Meusemann K, Peters RS, Stadler PF, Beutel RG, Bornberg-Bauer E, McKenna DD, Misof B
    Genomic and Morphological Evidence Converge to Resolve the Enigma of Strepsiptera
    Current Biology 22(14):1309-13, 2012
    [Online access] [Abstract + Download]



    2011

  • Franssen SU, Gu J, Bergmann N, Winters G, Klostermeier UC, Rosenstiel P, Bornberg-Bauer E and Reusch TBH
    Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species
    Proc Nat Acad Sci USA 108(48):19276-8, 2011
    [Online access] [Abstract + Download]


  • Franssen SU, Shrestha RP, Bräutigam A, Bornberg-Bauer E and Weber APM
    Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing
    BMC Genomics 12:227, 2011
    [Online access] [Abstract + Download]


  • Reineke AR, Bornberg-Bauer E and Gu J 14.Cover
    Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes
    Nucleic Acids Research 39(14): 6029–6043, 2011
    [Online access] [Abstract + Download]


  • Wissler L, Codoner FC, Gu J, Reusch TBH, Olsen JL, Procaccini G and Bornberg-Bauer E
    Back to the sea twice: identifying candidate plant genes for molecular evolution to marine life
    BMC Evolutionary Biology 11:8, 2011
    [Online access] [Abstract + Download]


  • Ernst AM, Ruping B, Jekat SB, Nordzieke S, Reineke AR, Müller B , Bornberg-Bauer E, Prüfer D and Noll GA
    The sieve element occlusion gene family in dicotyledonous plants (#)
    Plant Signaling & Behavior, 6(1): 151-3, 2011
    [Online access] [Abstract + Download]


  • Schueler A and Bornberg-Bauer E
    The Evolution of Protein Interaction Networks (#R)
    Data Mining in Proteomics (Ed: Martin Eisenacher, Michael Hamacher and Christian Stephan), SpringerLink, #R, 2011
    [Online access] [Abstract + Download]


  • The Atta Genome Working Group, including Zimmer F, Wissler L, Bornberg-Bauer E Ant
    The Genome Sequence of the Leaf-cutter Ant Atta cephalotes Reveals Insights into its Obligate Symbiotic Lifestyle
    PLoS Genetics 7(2): e1002007, 2011
    [Online access] [Abstract + Download]


  • Hartig G, Niehuis O , Grath S , 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 E , Misof B
    The first genome of a twisted wing parasite (Insectae: strepsiptera) and its phylogenetic implications
    Zitteliana B 30:22, 2011
    [Online access]


  • Grbić M, Van Leeuwen T, Clark RM, Rombauts S, Rouze P, Grbić V, Osborne EJ, Dermauw W, Ngoc PC, Ortego F, Hernandez-Crespo P, Diaz I, Martinez M, Navajas M, Sucena E, Magalhaes S, Nagy L, Pace RM, Djuranović S, Smagghe G, Iga M, Christiaens O, Veenstra JA, Ewer J, Villalobos RM, Hutter JL, Hudson SD, Velez M, Yi SV, Zeng J, Pires-daSilva A, Roch F, Cazaux M, Navarro M, Zhurov V, Acevedo G, Bjelica A, Fawcett JA, Bonnet E, Martens C, Baele G, Wissler L, Sanchez-Rodriguez A, Tirry L, Blais C, Demeestere K, Henz SR, Gregory TR, Mathieu J, Verdon L, Farinelli L, Schmutz J, Lindquist E, Feyereisen R, Van de Peer Y
    The genome of Tetranychus urticae reveals herbivorous pest adaptations
    Nature, 2011
    [Online access]



    2010

  • Rüping B, Ernst AM, Jekat SB, Nordzieke S, Reineke AR, Müller B , Bornberg-Bauer E, Prüfer D and Noll GA
    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] [Abstract + Download]


  • Bornberg-Bauer E Cover Expansion
    Signals: Tinkering with Domains (#R)
    Science Signaling, 3:139, 2010
    [Online access] [Abstract + Download]


  • Bornberg-Bauer E and Kramer L
    Robustness Versus Evolvability: A Paradigm Revisited. (#R)
    HFSP Journal 4(3), 2010
    [Online access] [Abstract + Download]


  • Chen T, Vernazobres D, Yomo T, Bornberg-Bauer E and Chan HS
    Evolvability and Single-Genotype Fluctuation in Phenotypic Properties: A Simple Heteropolymer Model
    Biophysical Journal,98:2487-2496, 2010
    [Online access] [Abstract + Download]


  • Moore AD and Bornberg-Bauer E
    Protein domains as evolutionary units (#R)
    Evolutionary Genomics and Systems Biology, Ed. G. Caetano-Anollés; John Wiley & Sons, 2010
    [Online access] [Abstract + Download]


  • Bornberg-Bauer E, Huylmans AK and Sikosek T
    How do new proteins arise? (R)
    Current Opinion in Structural Biology. 20:1-7, 2010
    [Online access] [Abstract + Download]


  • Sikosek T and Bornberg-Bauer E
    Evolution after and before gene duplication? (#R)
    Evolution after gene duplication (Ed. D. Liberles and K. Dittmar), Wiley-Blackwell, 2010
    [Online access] [Abstract + Download]


  • Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK; Nasonia Genome Working Group, Werren JH, Richards S, Desjardins CA, Niehuis O, Gadau J, Colbourne JK, Beukeboom LW, Desplan C, Elsik CG, Grimmelikhuijzen CJ, Kitts P, Lynch JA, Murphy T, Oliveira DC, Smith CD, van de Zande L, Worley KC, Zdobnov EM, Aerts M, Albert S, Anaya VH, Anzola JM, Barchuk AR, Behura SK, Bera AN, Berenbaum MR, Bertossa RC, Bitondi MM, Bordenstein SR, Bork P, Bornberg-Bauer E, Brunain M, Cazzamali G, Chaboub L, Chacko J, Chavez D, Childers CP, Choi JH, Clark ME, Claudianos C, Clinton RA, Cree AG, Cristino AS, Dang PM, Darby AC, de Graaf DC, Devreese B, Dinh HH, Edwards R, Elango N, Elhaik E, Ermolaeva O, Evans JD, Foret S, Fowler GR, Gerlach D, Gibson JD, Gilbert DG, Graur D, Gründer S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HC 4th, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, Kim J, Kim J, Kiryutin B, Koevoets T, Kovar CL, Kriventseva EV, Kucharski R, Lee H, Lee SL, Lees K, Lewis LR, Loehlin DW, Logsdon JM Jr, Lopez JA, Lozado RJ, Maglott D, Maleszka R, Mayampurath A, Mazur DJ, McClure MA, Moore AD, Morgan MB, Muller J, Munoz-Torres MC, Muzny DM, Nazareth LV, Neupert S, Nguyen NB, Nunes FM, Oakeshott JG, Okwuonu GO, Pannebakker BA, Pejaver VR, Peng Z, Pratt SC, Predel R, Pu LL, Ranson H, Raychoudhury R, Rechtsteiner A, Reese JT, Reid JG, Riddle M, Robertson HM, Romero-Severson J, Rosenberg M, Sackton TB, Sattelle DB, Schlüns H, Schmitt T, Schneider M, Schüler A, Schurko AM, Shuker DM, Simões ZL, Sinha S, Smith Z, Solovyev V, Souvorov A, Springauf A, Stafflinger E, Stage DE, Stanke M, Tanaka Y, Telschow A, Trent C, Vattathil S, Verhulst EC, Viljakainen L, Wanner KW, Waterhouse RM, Whitfield JB, Wilkes TE, Williamson M, Willis JH, Wolschin F, Wyder S, Yamada T, Yi SV, Zecher CN, Zhang L, Gibbs RA
    Functional and evolutionary insights from the genomes of three parasitoid Nasonia species
    Science, 5963:327-342, 2010
    [Online access] [Abstract + Download]



    2009

  • Wissler L, Dattolo E, Moore AD, Reusch THB, Olsen JL, Migliaccio M, Bornberg-Bauer E, Procaccini G
    Dr. Zompo: an online data repository for Zostera marina and Posidonia oceanica ESTs
    Database 2009: bap 009, 2009
    [Online access] [Abstract + Download]



    2008

  • Weiner J 3rd, Moore AD, Bornberg-Bauer E
    Just how versatile are domains?
    BMC Evolutionary Biology, 8:285, 2008
    [Online access] [Abstract + Download]


  • Moore AD*, Bjoerklund AK*, Ekman D, Bornberg-Bauer E and Elofsson A.
    Arrangements in the modular evolution of proteins
    Trends in Biochemical Sciences, 33(09): 444-51, 2008
    [Online access] [Abstract + Download]


  • Whitehead D, Wilke C, Vernazobres D, Bornberg-Bauer E
    The look-ahead effect of phenotypic mutations
    Biology Direct, 3:18, 2008
    [Online access] [Abstract + Download]


  • Friedrichs, Henckaerts L, Vermaire S, Kucharzik T, Seehafer T, Krull M, Bornberg-Bauer E, Stoll M, Weiner J
    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] [Abstract + Download]


  • Falb M, Mueller K, Koenigsmaier L, Oberwinkler T, Horn P, Gronau S, Orland G, Pfeiffer F, Bornberg-Bauer E, Oesterhelt D
    Metabolism of Halophilic Archaea
    Extremophiles, 12:177-196, 2008
    [Online access] [Abstract + Download]


  • Schulenburg H, Hoeppner M, Weiner J III, Bornberg-Bauer E
    Specificity of the innate immune system and diversity of C-type lectin domain (CTLD) proteins in the nematode Caenorhabditis elegans
    Immunobiology 213(3-4):237-50, 2008
    [Online access] [Abstract + Download]


  • Reusch TBH*, Veron AS*, Sapper C, Weiner J, Wissler L, Beck A, Klages S, Kube M, Reinhardt R and Bornberg-Bauer E
    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] [Abstract + Download]



    2007

  • Amoutzias GD, Pichler EE, Mian N, De Graaf D, Imsiridou A, Robinson-Rechavi M, Bornberg-Bauer E, Robertson DL, Oliver SG
    A protein interaction atlas for the nuclear receptors: Properties and quality of a hub-based dimerisation network
    BMC Systems Biology, 1:34, 2007
    [Online access] [Abstract + Download]


  • Beaussart F, Weiner J 3rd, Bornberg-Bauer E
    Automated Improvement of Domain ANnotations using context analysis of Domain Arrangements (AIDAN)
    Bioinformatics, 23:1834-1836, 2007
    [Online access] [Abstract + Download]


  • Wroe R, Chan HS and Bornberg-Bauer E Hfsp Cover
    A Structural Model of Latent Evolutionary Potentials Underlying Neutral Networks in Proteins
    HFSP Journal 1:79, 2007
    [Online access] [Abstract + Download]


  • Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, Angelo CD, Bornberg-Bauer E, Kudla J and Harter K
    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] [Abstract + Download]


  • Veron A, Kaufmann K, Bornberg-Bauer E
    Evidence of interaction network evolution by whole genome duplications: a case-study in MADS-box proteins
    Molecular Biology and Evolution, 24:670-678, 2007
    [Online access] [Abstract + Download]


  • Amoutzias G, Veron A, Weiner J, Robinson-Rechavi M, Bornberg-Bauer E, Oliver S, Robertson D
    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] [Abstract + Download]


  • Veron A, Whitehead D and Bornberg-Bauer E
    Studying the evolution of regulatory networks (#R)
    Biological Networks, Ed. F. Kepes, World Scientific, 2007
    [Abstract + Download]



    2006

  • Amoutzias GD, Bornberg-Bauer E, Oliver SG and Robertson DL
    Reduction/oxidation-phosphorylation control of DNA binding in the bZIP dimerization network
    BMC Genomics, 7:107, 2006
    [Online access] [Abstract + Download]


  • Gerke M, Jiang X, Bornberg-Bauer E and Fuellen G
    Finding Common Protein Interaction Patterns Across Organisms
    Evolutinary Bioinformatics Online, 2:45-52, 2006
    [Online access] [Abstract + Download]


  • Weiner J, Beaussart F, Bornberg-Bauer E
    Domain Deletions and Substitutions in the Modular Protein Evolution
    FEBS Journal, 273:2037-2047, 2006
    [Online access] [Abstract + Download]


  • Weiner J and Bornberg-Bauer E
    Evolution of Circular Permutations in Multi-Domain Proteins
    Molecular Biology and Evolution 23(4):734-743, 2006
    [Online access] [Abstract + Download]



    2005

  • Bornberg-Bauer E and Veron Amelie
    Evolution of regulatory networks (#R)
    Genetics, Genomics, Proteomics and Bioinformatics John Wiley & Sons, 2005
    [Abstract + Download]


  • Teichmann SA, Teichmann SA, Bornberg-Bauer E, Luscombe NM
    Transcriptional Networking (#)
    Genome Biology 6(9):344, 2005
    [Online access] [Abstract + Download]


  • Wroe R, Bornberg-Bauer E, Chan HS
    Comparing folding codes in simple heteropolymer models of protein evolutionary landscapes: robustness of the superfunnel paradigm
    Biophysical Journal, 88(1):118-31, 2005
    [Online access] [Abstract + Download]


  • Weiner J, Thomas G and Bornberg-Bauer E
    Rapid Motif-Based Prediction of Circular Permutations in Multi-Domain Proteins
    Bioinformatics, 21(7):932-7, 2005
    [Online access] [Abstract + Download]


  • Bornberg-Bauer E, Beaussart F, Kummerfeld S, Teichmann S and Weiner J
    The Evolution of Domain Arrangements in Proteins and Interaction Networks (Review)
    CMLS, 62(4):435-45, 2005
    [Online access] [Abstract + Download]


  • 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] [Abstract + Download]


  • Amoutzias G, Weiner J and Bornberg-Bauer E
    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] [Abstract + Download]



    2004

  • Amoutzias G, Robertson DL, Oliver SG and Bornberg-Bauer E
    Convergent evolution of gene networks by single-gene duplications in higher eurkaryotes
    EMBO Reports, 5(3):274-279, 2004
    [Online access] [Abstract + Download]


  • Mabey JE, Anderson MJ, Giles PF, Miller CJ, Attwood TK, Paton NW, Bornberg-Bauer E, Robson GD, Oliver SG and Denning DW
    CADRE: The Central Aspergillus Data REpository
    Nucleic Acids Research, 32:D401-D405, 2004
    [Online access] [Abstract + Download]


  • Amoutzias GD, Robertson DL and Bornberg-Bauer E
    The evolution of protein interaction networks in regulatory proteins.
    Comparative and Functional Genomics, 5(1): 79–84, 2004
    [Online access] [Abstract + Download]


  • Do, J.H., Anderson, M.J., Denning, D.W., Bornberg-Bauer, E.
    Inference of Aspergillus fumigatus pathways by computational genome analysis: Tricarboxylic acic cycle (TCA) and glyoxylate shunt
    Journal of Microbiology and Biotechnology, Volume 14, Issue 1, Pages 74-80, 2004
    [Online access] [Abstract + Download]



    2003

  • Gerrard DG and Bornberg-Bauer E
    doMosaic: Analysis of the mosaic-like domain architecture in proteins
    Informatica; 27: 15-20, 2003
    [Abstract + Download]



    2002

  • Bornberg-Bauer E
    Randomness, Structural Uniqueness, Modularity, and Neutral Evolution in Sequence Space of Model Proteins.
    Zeitschrift für physikalische Chemie 216: 139-154, 2002
    [Abstract + Download]


  • Cui Y., Wong WH, Bornberg-Bauer E, and Chan HS
    Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes
    PNAS, 99: 809-814, 2002
    [Online access] [Abstract + Download]


  • Sirava M, Schäfer T, Eigelsperger M, Kauffman M, Kohlbacher O, Bornberg-Bauer E and Lenhof HP
    BioMiner - Modeling, Analyzing and Visualizing Biochemical Pathways and Networks
    Bioinformatics; 18(S):219-230, 2002
    [Online access] [Abstract + Download]


  • Bornberg-Bauer E and Paton N
    Conceptual data modelling for bioinformatics (R)
    Briefings in Bioinformatics, 3(2): 166-180, 2002
    [Online access] [Abstract + Download]


  • Rojas-Mujica I and Bornberg-Bauer E
    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 HS and Bornberg-Bauer E
    Perspectives on Protein Evolution from simple exact models (R)
    Applied Bioinformatics; 1:121-144, 2002
    [Abstract + Download]


  • Bornberg-Bauer E, and Weiner J 3rd
    A putative trancription factor inducing mobility in Mycoplasma Pneumoniae (comment)
    Microbiology, 148(Pt 12):3764-5, 2002
    [Online access] [Abstract + Download]


  • Rost U and Bornberg-Bauer E
    TreeWiz: Interactive exploration of huge trees
    Bioinformatics, 18(1): 109-114, 2002
    [Online access] [Abstract + Download]


  • Bornberg-Bauer E, Harvey M and McMeekin A
    Bioinformatics education: skills shortage or fundamental shift in skill creation and demand (#)
    European Biopharmaceutical Review 5: 104-110, 2002
    [Online access] [Abstract + Download]



    2000

  • Kummer U, Olsen LF, Dixon CJ, Green AK, Bornberg-Bauer E, Baier G
    Switching from simple to complex oscillations in calcium signaling
    Biophys J. 79(3):1188-1195, 2000
    [Online access] [Abstract + Download]


  • Butler G, Bornberg-Bauer E, Grahne G, Kurfess Lam FC, Paquet J, Rojas I, Shinghal R, Tao L and Tsang A
    The BioIT Projects: Internet, Database and Software Technology Applied to Bioinformatics (#)
    Proceeding of SSGRR'2000, IEEE - International conference on advances in infrastructure Rome, Italy, 2000



    1999

  • Bornberg-Bauer E and Chan HS
    Modeling Evolutionary Landscapes: Mutational Stability, Topology and Superfunnels in Sequence Space
    Proc. Natl. Acad. Sci., USA, track 2, 96(19): 10689-10694, 1999
    [Online access] [Abstract + Download]


  • Backofen R, Will S and Bornberg-Bauer E
    Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets
    Bioinformatics, 15(3): 234-242, 1999
    [Online access] [Abstract + Download]


  • Krause A, Nicodeme P, Bornberg-Bauer E, Rehmsmeier M and Vingron M
    WWW-access to the SYSTERS Protein Sequence Cluster Set
    Bioinformatics., 15(3): 262-263, 1999
    [Online access] [Abstract + Download]


  • Rojas-Mujica I and Bornberg-Bauer
    A Comprehensible Database Model for the Computation of Biochemical Pathways (#)
    In Proceedings of the Workshop on Computation of Biochemical Pathways and Genetic Networks 95-100, Logos, Berlin, 1999



    1998

  • Bornberg-Bauer E, Rivals E and Vingron M
    Computational Approaches to Identify Leucine Zippers
    Nucleic Acids Res., 26(11):2740-2746, 1998
    [Online access] [Abstract + Download]



    1997

  • Bornberg-Bauer E
    Simple folding model for HP lattice proteins
    In German Conference on Bioinformatics Hofestaedt, R., T. Lengauer, T. Loeffler and D Schomburg, editors, Lecture Notes in Computer Science, vol. 1278:125-136, Springer, Berlin, 1997


  • Bornberg-Bauer E
    How are model protein structures distributed in sequence space?
    Biophys.J., 73(5):2393-2403, 1997
    [Online access] [Abstract + Download]


  • Renner A and Bornberg-Bauer E
    Exploring the fitness landscapes of lattice proteins
    In Proceedings of the 1997 Pacific Symposium on Biocomputing (Altman, R., K. Dunker, L. Hunter and T. Klein, editors), 361-373, World Scientific, London, 1997
    [Online access] [Abstract + Download]


  • Bornberg-Bauer E
    Chain growth algorithms for HP type lattice proteins
    In RECOMB Proceedings 47-55, ACM press, New York, 1997
    [Online access] [Abstract + Download]



    1996

  • Bornberg-Bauer E
    A simple folding model for HP-type lattice proteins
    In Computer Science and Biology: Proceedings of German Conference on Bioinformatics (Hofestaedt, R., T. Lengauer, M Loeffler and D. Schomburg, editors, vol. IMISE Report No. 1, 72-77, University Leipzig, 1996


  • Bornberg-Bauer E
    Random Structures and Evolution of Biopolymers: A Computational Case Study on RNA Secondary Structures
    Pharm. Acta Helv., 71:79-85, 1996
    [Online access] [Abstract + Download]


  • Bornberg-Bauer E
    Structure formation of biopolymers is complex, their evolution may be simple
    In Proceedings of the 1996 Pacific Symposium on Biocomputing (Hunter, L. and T. Klein, editors), pp 97-108, World Scientific, London, 1996
    [Online access] [Abstract + Download]


  • Tacker M, Stadler PF, Bornberg-Bauer E, Hofacker IL and Schuster P
    Algorithm independent properties of RNA secondary structure predictions
    Eur. Biophys. J. 25:115-130, 1996
    [Online access] [Abstract + Download]



    1993

  • Fontana W, Stadler PF, Bornberg-Bauer E, Griesmacher T, Hofacker IL, Tacker M, Tarazona P, Weinberger ED and Schuster P
    RNA folding and combinatorial landscapes
    Phys. Rev. E 47:2083-2099, 1993
    [Online access] [Abstract + Download]



    Footnote


  • * indicates authors which deserve recognition as equal first authors
    # indicates a paper which has not been peer reviewed following the usual standards
    R indicates a review or commentary
    [Names in bold] indicate the authors have contributed to this work under the supervision of Erich Bornberg-Bauer
    _ underlined names indicate PIs that supervised a paper