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Department of Biochemistry

Publications of the Wagner Group, until 2010

Bichsel, M., Barbour, AD. & Wagner, A. The early phase of a bacterial insertion sequence infection. Theor Popul Biol. 78, 278-288 (2010).

Bragg, JG. & Wagner, A. The evolution of protein material costs. In: Caetano-Anolles, G. Evolutionary genomics and systems biology. New York , 203-211 (2010).

Espinosa-Soto, C. & Wagner, A. Specialization can drive the evolution of modularity. PLoS Comput. Biol. 6, e1000719 (2010).

Ferrada, E. & Wagner, A. Evolutionary innovations and the organization of protein functions in genotype space. PLoS One. 5(11):e14172 (2010). 

Rankin, DJ., Bichsel, M. & Wagner, A. Mobile DNA can drive lineage extinction in prokaryotic populations. J Evol Biol. 23, 2422-2431 (2010).

Samal, A., Matias Rodrigues JF., Jost J., Martin OC. & Wagner A. Genotype networks in metabolic reaction spaces. BMC Syst Biol. 4, 30 (2010) 

Sulc, P., Wagner, A. & Martin, OC. Quantifying slow evolutionary dynamics in RNA fitness landscapes. J Bioinform Comput Biol. 8, 1027-1040 (2010).

Bragg, JG. & Wagner, A. Protein material costs: single atoms can make an evolutionary difference. Trends Genet. 25, 5-8 (2009).

de la Chaux, N. & Wagner, A. Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes. BMC Evol Biol. 9, 205 (2009). 

Hafner, M., Koeppl, H., Hasler, M. & Wagner, A. "Glocal" robustness analysis and model discrimination for circadian oscillators. PLoS Computational Biol. 5: e1000534 (2009). 

Hafner, M., Koeppl, H. & Wagner, A. Evolution of feedback loops in oscillatory systems. In: Proceedings of the Third International Conference on Foundations of Systems Biology in Engineering (FOSBE 2009). Denver, CO / USA, 157-160.

Martin, OC. & Wagner, A. Effects of recombination on complex regulatory circuits. Genetics 183, 673-684 (2009). 

Matias Rodrigues, JF., & Wagner, A. Evolutionary plasticity and innovations in compex metabolic reaction networks. PLoS Comput. Biol. 5, e1000613 (2009). 

Wagner A. Transposable elements as genomic diseases. Mol. Biosyst. 5, 32-35 (2009).

Wagner A. Evolutionary constraints permeate large metabolic networks. BMC Evol Biol 9, 231 (2009). 

Wagner, A. Networks in molecular evolution. In: Meyers, RA. (ed.), Encyclopedia of complexity and systems science, Part 13. New York, NY, USA, Springer, 5655-5667 (2009). 

Wagner, A. Andreas Wagner. In: Oftedal, G. et al (ed.), Evolutionary Theory: 5 questions. Automatic Press/ VIP , ? (2009).

Felix, M. & Wagner, A. Robustness and evolution: concepts, insights and challenges from a developmental model system. Heredity 100, 132-140 (2008). 

Ferrada, E. & Wagner, A. Protein robustness promotes evolutionary innovations in large evolutionary time-scales. Proceedings. Biological Sciences/ Royal Society 275, 1595-1602 (2008).

Fuller, A., Wagner, A. & Enquist, J. Using network analysis to chracterize forest structure. Natural Resources Modeling 21, 225-247 (2008).

Jorg, T., Martin, OC. & Wagner, A. Neutral network sizes of biological RNA molecules can be computed and are not atypically small. BMC Bioinformatics 9, 464 (2008).

Martin, OC. & Wagner, A. Multifunctionality and robustness trade-offs in model genetic circuits. Biophys J. 94, 2927-2937 (2008).

Wagner, A. Neutralism and selectionism: a network-based reconciliation. Nat. Rev. Genet. 9, 965 -974 (2008). 

Wagner, A. Robustness and evolvability: a paradox resolved. Proc Biol Sci. 275, 91-100 (2008).

Wagner, A. Gene duplications, robustness and evolutionary innovations. Bioessays 30, 367-373 (2008).

Wagner, A. & de la Chaux. N. Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences. Mol Genet Genomics 280, 397-408 (2008).  

Wright, J. & Wagner, A. The Systems Biology Research Tool: evolvable open-source software. BMC Syst Biol. 2, 55 (2008). 

Wright, J. & Wagner, A. Exhaustive identification of steady state cycles in large stochiometric networks. BMC Syst Biol. 2, 61 (2008).

Bragg, J.G. &  Wagner A. Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes. Proc. Biol. Sci. 274, 1063-70 (2007).

Ciliberti, S, Martin, OC & Wagner, A. Innovation and robustness in complex regulatory gene networks. PNAS U.S.A. 104, 13591-13596 (2007).

Ciliberti, S, Martin, OC & Wagner, A. Robustness can evolve gradually in complex regulatory networks with varying topology. PLoS Computational Biology 3(2), e15 (2007).

Sumedha, M., Martin, OC. & Wagner, A. New structural variaton in evolutionary searches of RNA neutral networks. Biosystems 90, 475-485 (2007).

Wagner A. From bit to it: the transformation of information into living matter by metabolic networks. BMC Systems Biology 1, 33 (2007).

Wagner A. Rapid detection of positive selection in genes and genomes through variation clusters. Genetics 176, 2451-2463 (2007).

Wagner A. Energy costs constrain the evolution of gene expression. J. Exp. Zoolog. B. Mol. Dev. Evol. 308B, 322-324 (2007).

Wagner, A. Robustness and evolvability: A paradox resolved. Proc. Roy. Soc. London Series B  275, 91-100 (2007).

Wagner, A. & Wright, J Alternative routes and mutational robustness in complex regulatory networks. Biosystems 88, 163-172 (2007).

Wagner, A. Gene networks and natural selection: Is there a network biology? (In: Pagel, M. Pomiankowski, A. (eds.) Evolutionary Genomics and Proteomics, Sinauer Associates, Sunderland, MA, 2007).

Gilchrist, MA. & Wagner, A. A model of protein translation including codon bias, nonsense errors,and ribosome recycling. J. Theor. Biol. 239, 417-434 (2006).

Vitkup, D., Kharchenko, P. & Wagner, A. Influence of metabolic network structure and function on enzyme evolution. Genome Biol. 7, R39 (2006).

Wagner, A. Periodic extinctions of transposable elements in bacterial lineages: Evidence from intragenomic variation in multiple genomes. Mol. Biol. Evol. 23, 723-733(2006).

Wagner, A. Cooperation is Fleeting in the World of Transposable Elements. PLoS Computational Biology 2(12): e162 (2006).

Conant, G.C. & Wagner, A. The rarity of gene shuffling in conserved genes. Genome Biology 6, R50 (2005).

Wagner, A. Robustness and Evolvability in Living Systems (Princeton University Press, 2005)

Wagner, A. Circuit topology and the evolution of robustness in two-gene circadian oscillators. PNAS U.S.A. 102, 11775-11780 (2005).

Wagner, A. Energy constraints on the evolution of gene expression. Mol. Biol. Evol. 22, 1365-1374 (2005).

Wagner, A. Distributed robustness and redundancy as causes of mutational robustness. Bioessays 27, 176-188 (2005).

Wagner, A. Robustness, Neutrality, and Evolvability. FEBS Lett. 579, 1772-1778 (2005).

Wagner, A. The structure of large genetic networks: design, history, or (mere) chemistry? In: Koonin, EV (ed.) Power laws, scale-free networks and genome biology. (Landes Bioscience, Georgetown, TX, 2005)

Wagner, A. & Wright, J. Compactness and cycles in signal transduction and transcriptional regulation networks: a signature of natural selection? Advances in Complex Systems 7, 419-432 (2005).

Wagner, A. Lessons from a genetic network about the evolution of dominance. In: Veitia R. (ed.) The biology of genetic dominance. (Landes Bioscience, Georgetown, TX, 2005)

Berg, J. Lässig, M. & Wagner, A. Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplication. BMC Evolutionary Biology 4, 51 (2004).

Conant, G.C. & Wagner, A. Duplicate genes and robustness to transient gene knockouts in Caenorhabditis elegans Proc. Roy. Soc. Lond. Series. B 271, 89-96 (2004).

Conant, G.C. & Wagner, A. A fast algorithm for determining the longest combination of local alignments to a query sequence. BMC Bioinformatics 5, 62 (2004).

Evangelisti, A & Wagner, A. Molecular evolution in the transcriptional regulation network of yeast. J. Exp. Zool. 302B, 392-411 (2004).

Gilchrist, M.A., Salter, L.A., Wagner, A. Gilchrist, MA, Salter, L. & Wagner, A. A statistical framework for combining and interpreting proteomic datasets. Bioinformatics 20, 689-700 (2004).

Hahn, M., Conant, G.C., & Wagner, A. Evolution in large genetic networks: connectivity does not equal importance. J. Mol. Evol. 58, 203-211 (2004).

Tringe, SG, Wagner, A. & Ruby, S.W. Enriching for direct regulatory targets in perturbed gene expression profiles. Genome Biol. 5, 109 (2004).

Wagner, A. Reconstructing pathways in large genetic networks from genetic perturbations. J. Comput. Biol. 11, 53-60 (2004).

Conant, G.C. & Wagner, A. Convergent evolution in gene circuits. Nat. Genet. 34, 264-266 (2003).

Conant, G.C. & Wagner, A. Asymmetric sequence divergence of duplicate genes. Genome Res. 13, 2052-2058 (2003).

Conant, G.C., Plimpton, S.J. Old, W., Wagner, A., Fain, P.R., Pacheco, T.R. & Heffelfinger, G. Parallel Genehunter: Implementation of a Linkage Analysis Package for Distributed-Memory Architectures, J. Parallel and Distributed Comput. 63, 674-682 (2003).

de Visser, J.A.G.M, Hermisson, J., Wagner, G.P., Ancel, L.W., Bagheri, H., Blanchard, J.L., Chao, L., Cheverud, J.M., Elena, S.F., Fontana, W., Gibson, G., Hansen, T., Krakauer, D., Lewontin, R.C., Ofria, C., Rice, S.H., von Dassow, G., Wagner, A. & Whitlock, M.C. Evolution and detection of genetic robustness. Evolution 57, 1959-1972 (2003).

Wagner, A. Protein networks. In Complex Systems Science in Biomedicine. Deisboeck, TS, Kresh, JY, Kepler, TB (eds.) (Kluwer, New York, 2003)

Conant, G.C. & Wagner, A. GenomeHistory: a software tool and its application to fully sequenced genomes. Nucleic Acids Res. 30, 1-10 (2002).

Wagner, A. Asymmetric functional divergence of duplicate genes. Mol. Biol. Evol. 19, 1760-1768 (2002).

Wagner, A. Estimating coarse gene network structure from large-scale gene perturbation data. Genome Res. 12, 309-315 (2002).

Wagner, A. Selection after gene duplication: a view from the genome. Genome Biol. 3, 1012.1-1012.3 (2002).

Wagner, A. The large-scale structure of metabolic networks: a glimpse at life's origin? Complexity 8, 15-19 (2002).

Wagner, A.Gene duplications and gene redundancy. In: Encyclopedia of Life Sciences. (Nature Publishing Group: London, UK. (, 2002)

Conant, G., Plimpton, S., Old, W., Wagner, A., Fain, P., and Heffelfinger, G. Pa (2001).rallel Genehunter: Implementation of a Linkage Analysis Package for Distributed-Memory Architectures, Proceedings of the First IEEE Workshop on High Performance Computational Biology. (, (2001)

Gleiss, P.M., Stadler, P.F., Wagner, A., Fell, D.A. Relevant cycles in chemical reaction networks. Advances in Complex Systems 4, 207-226 (2001)

Wagner, A., Fell, D. The small world inside large metabolic networks. Proc. Roy. Soc. Lond. Series B, 268, 1803-1810 (2001)

Wagner, A. How to reconstruct a large genetic network from n gene perturbation in n2 easy steps. Bioinformatics 17, 1183-1197 (2001)

Wagner, A. The yeast protein interaction network evolves rapidly and has few redundant duplicate genes. Mol. Biol. Evol. 18, 1283-1292 (2001)

Wagner, A. Birth and death of duplicate genes in fully sequenced eukaryotes. Trends Genet. 17, 237-239 (2001)

Fell, D., Wagner, A. The small world of metabolism. Nat. Biotechnol. 18, 1121-1122 (2000)

Fell, D.A. and Wagner, A. Structural properties of metabolic networks: implications for evolution and modelling of metabolism. In: J.-H. S. Hofmeyr, J. M. Rohwer and J. L. Snoep (eds) Animating the cellular map. (Stellenbosch University Press, Stellenbosch. pp. 79-85, 2000)

Wagner, A. Mutational robustness in genetic networks of yeast. Nat. Genet. 24, 355-361 (2000)

Wagner, A. The role of pleiotropy, population size fluctuations, and fitness effects of mutations in the evolution of redundant gene functions. Genetics 154, 1389-1401 (2000)

Wagner, A.Decoupled evolution of coding region and expression patterns after gene duplications: implications for the neutralist-selectionist debate. Proc. Natl. Acad. Sci. USA97, 6579-6584 (2000)

Wagner, A.Inferring life style from gene expression patterns. Mol. Biol. Evol. 17, 1985-1987 (2000)

Dudgeon, S., Wagner, A., Vaisnys, J.R., Buss, L.W. Dynamics of gastrovascular circulation in the hydrozoan Podocoryne carnea: the one-polyp case. Biological Bulletin 196, 1-17 (1999)

Wagner, A. Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes. Bioinformatics 15, 776-784 (1999)

Wagner, A., Stadler, P. Viral RNA and evolved mutational robustness. J. Exp. Zool. 285, 119-127 (1999)

Wagner, A. Redundant gene functions and natural selection. J. Evol. Biol. 12 , 1-16 (1999)

Wagner, A. Causality in complex systems. Biology and Philosophy 14, 83-101 (1999)

Lavorgna, G., Boncinelli, E., Wagner, A. and Werner, T. Detection of potential target genes in silico? Trends Genet. 375-376 (1998)

Wagner, A. A computational "genome walk" technique to identify regulatory interactions in gene networks. In: Altman, R.B., Dunker, K.A., Hunter, L., Klein, T.E. (eds.), Proceedings of the Pacific Symposium for Biocomputing, 264-278 (1998)

Wagner, A., Dudgeon, S., Vaisnys, R., and Buss, L.W. No Buss.n-linear oscillations in the marine invertebrate Podocoryne carnea. Naturwissenschaften 85, 117-120 (1998)

Wagner, A. Distribution of transcription factor binding sites in the yeast genome suggests abundance of coordinately regulated genes. Genomics 50, 293-295 (1998)

Wagner, A. The fate of duplicated genes: loss or diversification? Bioessays 20, 785-788 (1998)

Wagner, A. Models in the biological sciences. In Falkenburg, B., Hauser, S. (eds.) Dialektik , 1997/1, (Felix Meiner, Hamburg, 1997)

Wagner, A. A computational genomics approach to the identification of gene networks. Nucleic Acids Res. 25, 3594-3604 (1997)

Wagner, A. Does evolutionary plasticity evolve? Evolution 50, 1008-1023 (1996)

Wagner, A. Can nonlinear epigenetic interactions obscure causal relations between genotype and phenotype? Nonlinearity 9, 607-629 (1996)

Wagner, A. Genetic redundancy and its evolution in networks of transcriptional regulators. Biological Cybernetics 74, 559-569 (1996)

Wagner, A., Blackstone, N., Cartwright, P., Dick, M., Misof, B., Snow, P., Wagner, G.P., Bartels, J., Murtha, M. and Pendleton, J. Surveys of gene families using polymerase chain reaction: PCR selection and PCR drift. Syst. Biol. 43, 250-261 (1994)

Wagner, A. Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. Proc. Natl. Acad. Sci. USA91, 4387-4391 (1994)

Wagner, A. Reductionism in Evolutionary Biology: A Perceptional Artifact? in 1993 Lectures in Complex Systems, eds. D. Stein and L. Nagel, Santa Fe Institute Studies in the Sciences of Complexity, Lect. Vol. X, Reading, (MA:Addison-Wesley, 1994)

Wagner, A., Wagner, G.P. and Similon, P. Epistasis can facilitate the evolution of reproductive isolation by peak shifts: a two-locus two-allele model. Genetics 138, 533-545 (1994)

Belazzi, T., Wagner, A., Wieser, R., Schanz, M., Adam, G., Hartig, A. and H. Ruis. Negative regulation of transcription of the Saccharomyces cerevisiae catalase T (CTT1) gene by cAMP is mediated by a positive control element. EMBO J. 10, 585-592 (1991)

Wieser, R., Adam, G., Wagner, A., Schueller, C., Marchler, G., Ruis, H., Krawiec, Z. and T. Bilinski. Heat shock factor-independent heat control of transcription of the CTT1 gene encoding the cytosolic catalase T of Saccharomyces cerevisiae. J. Biol. Chem. 19, 12406-12411 (1991)