Publications

Articles

Books

Software

Data

Selected Publications

Bragg, J.G., Wagner, A. (2009) Protein material costs: single atoms can make an evolutionary difference. Trends in Genetics 25, 5-8. [reprint request]

Martin, O.C.M., Wagner, A. (2009) Effects of recombination on complex regulatory circuits. Genetics 183, 673-684. [reprint request]

Wagner, A. (2009) Evolutionary constraints permeate large metabolic networks. BMC Evolutionary Biology  9:231 [reprint request]

Rodrigues, J., Wagner, A. (2009) Evolutionary plasticity and innovations in complex metabolic reaction networks. PloS Computational Biology 5(12): e1000613. [reprint request]

Hafner, M., Koeppl, H., Hasler, M., Wagner, A. (2009) “Glocal” robustness analysis and model discrimination for circadian oscillators. PloS Computational Biology 5(10): e1000534. [reprint request]

de la Chaux, N., Wagner, A. (2009) Evolutionary dynamics of the LTR retrotransposon roo inferred from twelve complete Drosophila genomes. BMC Evolutionary Biology 9:205. [reprint request]

Wagner, A. (2009) Transposable elements as genomic diseases. Molecular Biosystems, 5 32. [reprint request]

Wagner, A. (2009) Networks in molecular evolution. In: Meyers, R.A. (ed.) Encyclopedia of Complexity and System Science. Springer, Heidelberg. [reprint request]

Hafner, M., Koeppl, H., Wagner, A. (2009) Evolution of feedback loops in oscillatory systems.  Proceedings of the Third International Conference on Foundations of Systems Biology in Engineering (FOSBE 2009), Denver, CO, August 9-12, 2009. [reprint request]

Wagner, A. (2008) Neutralism and selectionism: A network-based reconciliation. Nature Reviews Genetics 9, 965-974. [reprint request]

Wagner, A. (2008) Robustness and evolvability: A paradox resolved. Proc. Roy. Soc. London Series. B 275, 91-100. [reprint request]

Ferrada, E., Wagner, A. (2008) Protein robustness promotes evolutionary innovations
on large evolutionary time scales Proc. Roy. Soc. London Series. B 275:1595-602.
[reprint request]

Wright, J., Wagner, A. (2008) The systems biology research tool: Evolvable open-source software. BMC Systems Biology 2:55. [request reprint]

Martin, OC, Wagner, A. (2008) Multifunctionality and robustness tradeoffs in model genetic circuits. Biophysical Journal  94, 2927-2937. [request reprint]

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

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

Jörg, T., Martin, OC, Wagner, A. (2008) Neutral network sizes of biological RNA molecules can be computed and are atypically large. BMC Bioinformatics 9:464. [reprint request]

Wagner, A., de la Chaux, N. (2008) Distant horizontal gene transfer is rare for mobile prokaryotic DNA. Molecular Genetics and Genomics 280, 397-408. [reprint request]

Wright, J., Wagner, A. (2008) Exhaustive identification of steady state cycles in large stoichiometric networks. BMC Systems Biology, 2:61. [reprint request]

Fuller, M., Wagner, A. , Enquist, J. (2008) Using network analysis to characterize forest structure. Natural Resources Modeling 21, 225-247. [reprint request]

Ciliberti, S., Martin, OC, Wagner, A. (2007) Innovation and robustness in complex regulatory gene networks. Proc. Natl. Acad. Sci. U.S.A. 104, 13591-13596. [reprint request]

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

Wagner, A., Lewis, C., Bichsel, M. (2007) A survey of transposable elements using IScan. Nucleic Acids Research 35, 5284-5293. [reprint request]

Wagner, A. (2007) Rapid detection of positive selection in genes and genomes through variation clusters. Genetics 176: 2451–2463. [reprint request]

Bragg, JG, Wagner, A. (2007) Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes. Proc. Roy. Soc. London Series. B 274, 1063-1070. [reprint request]

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

Wagner, A. (2007) Energy costs constrain the evolution of gene expression. Journal of Experimental Zoology (Molecular and Developmental Evolution) 308B:322–324 [reprint request]

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

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

Sumedha, Martin, OC, Wagner, A. (2007) New structural variation in evolutionary searches of RNA neutral networks. Biosystems 90: 475-485. [reprint request]

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

Wagner, A . (2006) Periodic extinctions of transposable elements in bacterial lineages: Evidence from intragenomic variation in multiple genomes. Molecular Biology and Evolution 23, 723-733. [reprint request]

Vitkup, D, Kharchenko, P., Wagner, A. (2006) Influence of metabolic network structure and function on enzyme evolution. Genome Biology 7 (5):R39. [reprint request] 

Gilchrist, MA, Wagner, A. (2006) A model of protein translation including codon bias, nonsense errors,and ribosome recycling. Journal of Theoretical Biology239, 417-434. [reprint request]

Wagner, A. (2005) Circuit topology and the evolution of robustness in two-gene circadian oscillators. Proc. Natl. Acad. Sci. U.S.A. 102, 11775-11780 [reprint request]

Wagner, A. (2005) Robustness, Neutrality, and Evolvability. FEBS Letters 579: 1772–1778. [reprint request]

Wagner, A. (2005) Distributed robustness versus redundancy as causes of mutational robustness. Bioessays 27,176–188. [reprint request]

Wagner, A. (2005) Energy constraints on the evolution of gene expression. Molecular Biology and Evolution 22:1365–1374. [reprint request]

Conant, GC, Wagner, A. (2005) The rarity of gene shuffling in conserved genes. Genome Biology 6(6), R50 [reprint request]

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

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

Evangelisti, A, Wagner, A. (2004) Molecular evolution in the transcriptional regulation network of yeast. Journal of Experimental Zoology Part B – Molecular and Developmental Evolution 302B, 392-411. [reprint request]

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

Hahn, M., Conant, G.C., Wagner, A. (2004) Evolution in large genetic networks: does connectivity equal importance? Journal of Molecular Evolution 58, 203-211. [reprint request]

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

Tringe, SG, Wagner, A., Ruby, S.W. (2004) Enriching for direct regulatory targets in perturbed gene expression profiles. Genome Biology 5, 109 [reprint request]

Wagner, A. (2004) Reconstructing pathways in large genetic networks from genetic perturbations. Journal of Computational Biology 11, 53-60. [reprint request]

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

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

Conant, G.C. Wagner, A. (2003) Convergent evolution in gene circuits. Nature Genetics 34, 264-266 [reprint request]

Wagner, A. Does natural selection mold molecular networks? (2003) Science STKE, pe 41-43. [reprint request]

Wagner, A. (2003) How large protein interaction networks evolve. Proc. R. Soc. Lond. B 270, 457-466 [reprint request]

Conant, G.C., Wagner, A. (2003) Asymmetric sequence divergence of duplicate genes. Genome Research 13, 2052-2058 [reprint request]

Wagner, A. (2003) Risk management in biological evolution. Journal of Theoretical Biology 225, 45-47. [reprint request]

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., and Whitlock, M.C. Evolution and detection of genetic robustness. (2003) Evolution 57, 1959-1972. [reprint request]

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

Conant, G.C., Wagner, A. (2002) GenomeHistory: a software tool and its application to fully sequenced genomes. Nucleic Acids Research  30, 1-10. [reprint request] [Supplement]

Wagner, A. (2002) Estimating coarse gene network structure from large-scale gene perturbation data. Genome Research 12, 309-315. [reprint request]

Wagner, A. (2002) Selection after gene duplication: a view from the genome. Genome Biology 3, reviews 1012.1-1012.3 [reprint request]

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

Wagner, A. (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Molecular Biology and Evolution 18, 1283-1292. [reprint request]

Wagner, A. (2001) How to reconstruct a large genetic network from n gene perturbation in n^2 easy steps. Bioinformatics 17, 1183-1197. [reprint request]

Wagner, A. (2001) Birth and death of redundant duplicate genes. Trends in Genetics 17, 237-239.  [reprint request]

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

Wagner, A. (2001) Neutralist view. In Encyclopedia of the Human Genome. David Cooper (ed.) Nature Publishing Group, London. In press.   [reprint request]

Wagner, A. (2001) Selectionist view. In Encyclopedia of the Human Genome. David Cooper (ed.) Nature Publishing Group, London. In press.   [reprint request]

Wagner, A. (2000) Mutational robustness in genetic networks of yeast. Nature Genetics 24, 355 - 361.  [reprint request]

Fell, D., Wagner, A. (2000) The small world of metabolism. Nature Biotechnology 18, 1121-1122.  [reprint request]

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

Wagner, A. (2000) Decoupled evolution of coding region and expression patterns after gene duplications: implications for the neutralist-selectionist debate. Proc. Natl. Acad. Sci. U.S.A.97, 6579-6584.  [reprint request]

Wagner, A. (2000) Inferring life style from gene expression patterns. Molecular Biology and Evolution 17, 1985-1987  [reprint request]

Wagner, A., Stadler, P. (1999) Viral RNA and evolved mutational robustness. Journal of Experimental Zoology 285, 119-127 [reprint request]

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

Wagner, A.  (1999) Redundant gene functions and natural selection.  Journal of Evolutionary Biology 12, 1-16 [reprint request]

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

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

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

Wagner, A. (1998) The fate of duplicated genes: loss or new function? BioEssays 20, 785-788   [reprint request]

Lavorgna, G., Boncinelli, E., Wagner, A. and T. Werner (1998) Detection of potential target genes in silico? Trends in Genetics 14, 375-376   [reprint request]

Wagner, A. (1998) 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 on Biocomputing 1998,  264-278.   [reprint request]

Wagner, A., Dudgeon, S., Vaisnys, R., and L.W. Buss. (1998) Non-linear oscillations in polyps of the colonial hydroid Podocoryne carnea. Naturwissenschaften 85, 117-120.   [reprint request]

Wagner, A. (1997) A computational genomics approach to the identification of gene networks. Nucleic Acids Research 25, 3594-3604. [reprint request]

Wagner, A. (1997) Models in the biological sciences. In: Dialektik 1997 (1) Falkenburg, B.; Hauser, S. (Eds.),  43-57. Felix Meiner, Hamburg. [reprint request]

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

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

Wagner, A. (1996) Genetic redundancy caused by gene duplications and its evolution in networks of transcriptional regulators. Biological Cybernetics 74, 557-567.   [reprint request]

Wagner, A. (1995) Reductionism in Evolutionary Biology: A Perceptional Artifact? in 1993 Lectures in Complex Systems, eds. D. Stein and L. Nadel, Santa Fe Institute Studies in the Sciences of Complexity, Lect. Vol. VI, Reading, MA:Addison-Wesley, 603-611.  [reprint request]

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

Wagner, A. (1994) Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. Proc. Natl. Acad. Sci. USA. 91, 4387-4391.  [reprint request]

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

Belazzi, T., Wagner, A., Wieser, R., Schanz, M., Adam, G., Hartig, A. and H. Ruis. (1991) 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.  [reprint request]

Wieser, R., Adam, G., Wagner, A., Schueller, C., Marchler, G., Ruis, H., Krawiec, Z. and T. Bilinski. (1991) 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.  [reprint request]