Andreas Wagner

Summary

Affiliation: University of Zurich
Country: Switzerland

Publications

  1. pmc Neutral network sizes of biological RNA molecules can be computed and are not atypically small
    Thomas Jörg
    Inria Saclay, Ile de France, INRIA, Parc Orsay Université 4, Orsay Cedex, France
    BMC Bioinformatics 9:464. 2008
  2. pmc A survey of bacterial insertion sequences using IScan
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 27 J 54, CH 8057 Zurich, Switzerland
    Nucleic Acids Res 35:5284-93. 2007
  3. pmc The evolvability of programmable hardware
    Karthik Raman
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
    J R Soc Interface 8:269-81. 2011
  4. doi request reprint Gene duplications, robustness and evolutionary innovations
    Andreas Wagner
    University of Zurich, Department of Biochemistry, Bldg Y27, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    Bioessays 30:367-73. 2008
  5. pmc From bit to it: how a complex metabolic network transforms information into living matter
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Building Y27, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    BMC Syst Biol 1:33. 2007
  6. pmc Rapid detection of positive selection in genes and genomes through variation clusters
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    Genetics 176:2451-63. 2007
  7. doi request reprint Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Bldg Y27, Winterthurerstrasse 190, 8057, Zurich, Switzerland
    Mol Genet Genomics 280:397-408. 2008
  8. pmc Robustness and evolvability: a paradox resolved
    Andreas Wagner
    Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
    Proc Biol Sci 275:91-100. 2008
  9. pmc Evolutionary constraints permeate large metabolic networks
    Andreas Wagner
    University of Zurich, Dept of Biochemistry, CH 8057 Zurich, Switzerland
    BMC Evol Biol 9:231. 2009
  10. doi request reprint Selection shapes the robustness of ligand-binding amino acids
    Tugce Bilgin
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    J Mol Evol 76:343-9. 2013

Detail Information

Publications88

  1. pmc Neutral network sizes of biological RNA molecules can be computed and are not atypically small
    Thomas Jörg
    Inria Saclay, Ile de France, INRIA, Parc Orsay Université 4, Orsay Cedex, France
    BMC Bioinformatics 9:464. 2008
    ..Unfortunately, any one neutral set contains generally only a tiny fraction of genotype space. Thus, current methods cannot measure neutral set sizes accurately, except in the smallest genotype spaces...
  2. pmc A survey of bacterial insertion sequences using IScan
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 27 J 54, CH 8057 Zurich, Switzerland
    Nucleic Acids Res 35:5284-93. 2007
    ..Applied to the thousands of genomes that will soon be available, IScan could be used for many purposes, such as mapping the evolutionary history and horizontal transfer patterns of different ISs...
  3. pmc The evolvability of programmable hardware
    Karthik Raman
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
    J R Soc Interface 8:269-81. 2011
    ..They also point to generic ways to generate fault-tolerant, adaptable and evolvable electronic circuitry...
  4. doi request reprint Gene duplications, robustness and evolutionary innovations
    Andreas Wagner
    University of Zurich, Department of Biochemistry, Bldg Y27, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    Bioessays 30:367-73. 2008
    ..These include the role of gene duplications in the vertebrate radiation, flowering plant evolution and heart development, which encompass some of the most striking innovations in the evolution of life...
  5. pmc From bit to it: how a complex metabolic network transforms information into living matter
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Building Y27, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    BMC Syst Biol 1:33. 2007
    ..A metabolic network transforms nutrients into biomass. The better it uses information on available nutrient availability, the faster it will allow a cell to divide...
  6. pmc Rapid detection of positive selection in genes and genomes through variation clusters
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    Genetics 176:2451-63. 2007
    ..I also identify multiple new human-chimpanzee orthologs subject to positive selection, among them genes that are involved in reproductive functions, immune defense, and the nervous system...
  7. doi request reprint Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Bldg Y27, Winterthurerstrasse 190, 8057, Zurich, Switzerland
    Mol Genet Genomics 280:397-408. 2008
    ..If true also for other, non-mobile DNA, the rarity of distant horizontal transfer increases the odds of reliable phylogenetic inference from sequence data...
  8. pmc Robustness and evolvability: a paradox resolved
    Andreas Wagner
    Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
    Proc Biol Sci 275:91-100. 2008
    ..My observations may apply to other genetic systems where many connected genotypes produce the same phenotypes...
  9. pmc Evolutionary constraints permeate large metabolic networks
    Andreas Wagner
    University of Zurich, Dept of Biochemistry, CH 8057 Zurich, Switzerland
    BMC Evol Biol 9:231. 2009
    ..These observations, together with the continual discovery of new microbial metabolic pathways and enzymes, raise the possibility that metabolic networks are only weakly constrained in changing their complement of enzymatic reactions...
  10. doi request reprint Selection shapes the robustness of ligand-binding amino acids
    Tugce Bilgin
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    J Mol Evol 76:343-9. 2013
    ..Our observations suggest that natural selection can affect the robustness of very small units of biological organization...
  11. pmc A comparison of genotype-phenotype maps for RNA and proteins
    Evandro Ferrada
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    Biophys J 102:1916-25. 2012
    ..We compare this property to evidence from natural RNA and protein molecules, and conclude that RNA genotype space may be more conducive to the evolution of new structure phenotypes...
  12. pmc Superessential reactions in metabolic networks
    Aditya Barve
    Institutes of Evolutionary Biology and Environmental Studies, University of Zurich, CH 8057 Zurich, Switzerland
    Proc Natl Acad Sci U S A 109:E1121-30. 2012
    ..Our work also shows how analyses of large network ensembles can help understand the evolution of complex and robust metabolic networks...
  13. pmc Evolutionary plasticity and innovations in complex metabolic reaction networks
    João F Matias Rodrigues
    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    PLoS Comput Biol 5:e1000613. 2009
    ..Our approach has broad implications for the evolution of metabolic networks, for our understanding of mutational robustness, for the design of antimetabolic drugs, and for metabolic engineering...
  14. pmc Topological augmentation to infer hidden processes in biological systems
    Mikael Sunnåker
    Department of Biosystems Science and Engineering Swiss Institute of Bioinformatics, ETH Zurich, 4058 Basel, Switzerland, Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, 8093 Zurich, Switzerland, Institute of Evolutionary Biology and Environmental Studies Swiss Institute of Bioinformatics, University of Zurich, 8057 Zurich, Switzerland, Institute for Molecular Systems Biology, 8093 Zurich, Switzerland and The Santa Fe Institute, Santa Fe, 87501 New Mexico, USA
    Bioinformatics 30:221-7. 2014
    ..Here we present a method called topological augmentation to infer this structure in a statistically rigorous and systematic way from prior knowledge and experimental data...
  15. pmc Genotype networks, innovation, and robustness in sulfur metabolism
    João F Matias Rodrigues
    Institute of Evolutionary Biology and Environmental Studies Bldg, Y27, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    BMC Syst Biol 5:39. 2011
    ..We here focus on the element sulfur. We study properties of the space of all possible metabolic genotypes in sulfur metabolism by analyzing random metabolic genotypes that are viable on different numbers of sulfur sources...
  16. pmc Evolutionary innovations and the organization of protein functions in genotype space
    Evandro Ferrada
    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    PLoS ONE 5:e14172. 2010
    ..Whether a protein with a given function can evolve specific new functions is thus determined by the protein's location in sequence space...
  17. pmc Efficient purging of deleterious mutations in plants with haploid selfing
    Péter Szövényi
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, SwitzerlandInstitute of Systematic Botany, University of Zurich, SwitzerlandSwiss Institute of Bioinformatics, Quartier Sorge Batiment Genopode, Lausanne, SwitzerlandMTA ELTE MTM Ecology Research Group, ELTE, Biological Institute, Hungary
    Genome Biol Evol 6:1238-52. 2014
    ..Our observations show that selfing need not impede but can even accelerate the removal of deleterious mutations, and do so on a genome-wide scale. ..
  18. doi request reprint The robustness and evolvability of transcription factor binding sites
    Joshua L Payne
    University of Zurich, Institute of Evolutionary Biology and Environmental Studies, Zurich, Switzerland
    Science 343:875-7. 2014
    ..We show that the binding sites of larger genotype networks are not only more robust, but the sequences adjacent to such networks can also bind more transcription factors, thus demonstrating that robustness can facilitate evolvability. ..
  19. doi request reprint Estimating the fitness effect of an insertion sequence
    Manuel Bichsel
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zuerich, Switzerland
    J Math Biol 66:95-114. 2013
    ..Occasional beneficial effects may thus have played an important role in the fast spreading of insertion sequences like IS5...
  20. doi request reprint Metabolic networks and their evolution
    Andreas Wagner
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    Adv Exp Med Biol 751:29-52. 2012
    ..Reaction addition also provides a window into the evolution of metabolic innovations, the ability of a metabolism to sustain life on new sources of energy and of chemical elements...
  21. doi request reprint Evolvability and robustness in a complex signalling circuit
    Karthik Raman
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
    Mol Biosyst 7:1081-92. 2011
    ..Our approach points a way towards mapping genotype spaces in complex circuitry, and it exposes some challenges such mapping faces...
  22. doi request reprint A latent capacity for evolutionary innovation through exaptation in metabolic systems
    Aditya Barve
    Institute of Evolutionary Biology and Environmental Sciences, Building Y27, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    Nature 500:203-6. 2013
    ..Our observations suggest that many more metabolic traits may have non-adaptive origins than is appreciated at present. They also challenge our ability to distinguish adaptive from non-adaptive traits. ..
  23. ncbi request reprint Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication
    Baocheng Guo
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    Mol Biol Evol 29:3005-22. 2012
    ..Our observations are consistent across all five fish species. Taken together, they suggest a general pattern of duplicate gene evolution in which indels are important driving forces of evolutionary change...
  24. pmc Environmental change exposes beneficial epistatic interactions in a catalytic RNA
    Eric J Hayden
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
    Proc Biol Sci 279:3418-25. 2012
    ..Our results suggest that such change can facilitate adaptive evolution by exposing new peaks of a fitness landscape. They highlight a prominent role for genotype-environment interactions in doing so...
  25. pmc Exhaustive identification of steady state cycles in large stoichiometric networks
    Jeremiah Wright
    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    BMC Syst Biol 2:61. 2008
    ..Unfortunately, our ability to identify cycles in stoichiometric networks, such as signal transduction and genome-scale metabolic networks, has been hampered by the computational complexity of the methods currently used...
  26. pmc Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes
    Nicole de la Chaux
    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    BMC Evol Biol 9:205. 2009
    ..We here study the phylogenetic distribution and evolution of roo, and its highly diverged relative rooA in 12 completely sequenced genomes of the genus Drosophila...
  27. pmc Efficient characterization of high-dimensional parameter spaces for systems biology
    Elías Zamora-Sillero
    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    BMC Syst Biol 5:142. 2011
    ..This hampers explorations of the viable space based on "brute force" or Gaussian sampling...
  28. pmc BEL/Pao retrotransposons in metazoan genomes
    Nicole de la Chaux
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
    BMC Evol Biol 11:154. 2011
    ..No comprehensive characterization of these elements is available so far. The aim of this study was to describe all BEL/Pao elements in a set of 62 sequenced metazoan genomes, and to analyze their phylogenetic relationship...
  29. doi request reprint The low cost of recombination in creating novel phenotypes: Recombination can create new phenotypes while disrupting well-adapted phenotypes much less than mutation
    Andreas Wagner
    Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Zurich, Switzerland
    Bioessays 33:636-46. 2011
    ..A better understanding might shed light on the evolution of recombination and help improve evolutionary strategies in biochemical engineering...
  30. pmc Specialization can drive the evolution of modularity
    Carlos Espinosa-Soto
    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    PLoS Comput Biol 6:e1000719. 2010
    ..We also show how modularity can facilitate co-option, the utilization of existing gene activity to build new gene activity patterns, a frequent feature of evolutionary innovations...
  31. doi request reprint The molecular origins of evolutionary innovations
    Andreas Wagner
    University of Zurich Institute of Evolutionary Biology and Environmental Studies, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    Trends Genet 27:397-410. 2011
    ..Both features emerge from a common cause, the robustness of phenotypes to perturbations, whose origins are linked to life in changing environments...
  32. pmc Cooperation is fleeting in the world of transposable elements
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    PLoS Comput Biol 2:e162. 2006
    ..Because such cooperation does not pay in the long run, the vehicles of such survival will eventually disappear again. My analysis demonstrates that game theory can help explain behavioral strategies even for mobile DNA...
  33. ncbi request reprint Energy costs constrain the evolution of gene expression
    Andreas Wagner
    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    J Exp Zool B Mol Dev Evol 308:322-4. 2007
    ..In small organisms with large effective population sizes, the evolution of transcription and translation rates are thus not evolutionarily neutral processes...
  34. pmc Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms
    Aditya Barve
    Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Bldg, Y27, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    BMC Syst Biol 8:48. 2014
    ....
  35. pmc Constraint and contingency in multifunctional gene regulatory circuits
    Joshua L Payne
    University of Zurich, Institute of Evolutionary Biology and Environmental Studies, Zurich, Switzerland
    PLoS Comput Biol 9:e1003071. 2013
    ..Circuits with many functions also become increasingly brittle and sensitive to mutation. These observations are generic properties of a broad class of circuits and independent of any one circuit genotype or phenotype...
  36. pmc Design constraints on a synthetic metabolism
    Tugce Bilgin
    Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Zurich, Switzerland
    PLoS ONE 7:e39903. 2012
    ..The constraints we identify prescribe broad boundary conditions that can help to guide synthetic metabolism design...
  37. pmc Differences in cell division rates drive the evolution of terminal differentiation in microbes
    João F Matias Rodrigues
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    PLoS Comput Biol 8:e1002468. 2012
    ..This may explain why plants engage in symbiotic interactions with diazotrophic bacteria...
  38. ncbi request reprint Genotype networks shed light on evolutionary constraints
    Andreas Wagner
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Y27 J 54, Winterthurerstrasse 190, CH 8057 Zurich, Switzerland
    Trends Ecol Evol 26:577-84. 2011
    ..Furthermore, they can explain important consequences of constraints, such as punctuated stasis and canalization...
  39. pmc The Systems Biology Research Tool: evolvable open-source software
    Jeremiah Wright
    Department of Biochemistry, University of Zurich, Zurich, Switzerland
    BMC Syst Biol 2:55. 2008
    ..Software must also be used to implement mathematical models and algorithms required for simulation and theoretical predictions on the system-level...
  40. pmc Protein robustness promotes evolutionary innovations on large evolutionary time-scales
    Evandro Ferrada
    Department of Biochemistry, University of Zurich, Building Y27, Winterthurerstrasse 190, 8057 Zurich, Switzerland
    Proc Biol Sci 275:1595-602. 2008
    ..Significant associations among structural designability, folding rate and intrinsic disorder also exist, underlining the complex relationship of the structural factors that affect protein evolution...
  41. doi request reprint Transposable elements as genomic diseases
    Andreas Wagner
    University of Zurich, Dept of Biochemistry, Bldg Y27, Winterthurerstrasse 190, CH 8057, Zurich, Switzerland
    Mol Biosyst 5:32-5. 2009
    ....
  42. doi request reprint Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme
    Eric J Hayden
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
    Nature 474:92-5. 2011
    ..Our observations show that cryptic variation contains new genotypes pre-adapted to a changed environment. Our results highlight the positive role that robustness and epistasis can have in adaptive evolution...
  43. pmc Phenotypic plasticity can facilitate adaptive evolution in gene regulatory circuits
    Carlos Espinosa-Soto
    University of Zurich, Dept of Biochemistry, Zurich, Switzerland
    BMC Evol Biol 11:5. 2011
    ..Phenotypic plasticity allows a genotype to produce different - alternative - phenotypes after non-genetic perturbations that include gene expression noise, environmental change, or epigenetic modification...
  44. doi request reprint The early phase of a bacterial insertion sequence infection
    Manuel Bichsel
    Department of Biochemistry, University of Zurich, CH 8057 Zurich, Switzerland
    Theor Popul Biol 78:278-88. 2010
    ..We conclude that horizontal gene transfer is strong enough to allow the persistence of insertion sequences, although infection is an erratic and slow process...
  45. ncbi request reprint Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes
    Riddhiman Dhar
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH 8057 Zurich, Switzerland The Swiss Institute of Bioinformatics, CH 1015 Lausanne, Switzerland Centre for Genomic Regulation CRG, C Dr Aiguader 88, 08003 Barcelona, Spain
    Evolution 68:1775-91. 2014
    ..Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region. ..
  46. pmc Latent phenotypes pervade gene regulatory circuits
    Joshua L Payne
    University of Zurich, Zurich, Switzerland
    BMC Syst Biol 8:64. 2014
    ..We know little about their prevalence in the gene expression phenotypes of regulatory circuits, important sources of evolutionary innovations...
  47. doi request reprint Yeast adapts to a changing stressful environment by evolving cross-protection and anticipatory gene regulation
    Riddhiman Dhar
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    Mol Biol Evol 30:573-88. 2013
    ..Our study shows that highly complex physiological states that are adaptive in future environments can evolve on very short evolutionary time scales...
  48. ncbi request reprint Selection is no more efficient in haploid than in diploid life stages of an angiosperm and a moss
    Péter Szövényi
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    Mol Biol Evol 30:1929-39. 2013
    ..Our observations have implications for the role of haploid life stages in the purging of deleterious mutations, as well as for the evolution of ploidy. ..
  49. pmc Evolution of viral proteins originated de novo by overprinting
    Niv Sabath
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    Mol Biol Evol 29:3767-80. 2012
    ..Some of the oldest de novo genes evolve under stronger selection pressure than the ancestral gene they overlap, suggesting an evolutionary tug of war between the ancestral and the de novo gene...
  50. pmc The role of robustness in phenotypic adaptation and innovation
    Andreas Wagner
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Y27 J 54 Winterthurerstrasse 190, 8057 Zurich, Switzerland
    Proc Biol Sci 279:1249-58. 2012
    ..In addition, robustness can help avoid an important evolutionary conflict between the interests of individuals and populations-a conflict that can impede evolutionary adaptation...
  51. pmc Hsp90 is important for fecundity, longevity, and buffering of cryptic deleterious variation in wild fly populations
    Bing Chen
    Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
    BMC Evol Biol 12:25. 2012
    ..It is unknown whether observations from such laboratory experiments are relevant in the wild...
  52. pmc The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata
    Nicole de la Chaux
    Molecular Evolution and Evolutionary Systems Biology, Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
    Mob DNA 3:2. 2012
    ..abstract:..
  53. ncbi request reprint Asymmetric functional divergence of duplicate genes in yeast
    Andreas Wagner
    Department of Biology, University of New Mexico, Albuquerque, USA
    Mol Biol Evol 19:1760-8. 2002
    ..I propose a model that can explain this divergence pattern if asymmetrically diverging duplicate gene pairs show increased robustness to deleterious mutations...
  54. ncbi request reprint Reconstructing pathways in large genetic networks from genetic perturbations
    Andreas Wagner
    University of New Mexico, Department of Biology, Albuquerque, NM 817131 1091, USA
    J Comput Biol 11:53-60. 2004
    ..The algorithm is able to distinguish a large fraction of direct regulatory interactions from indirect interactions, even if the accuracy of its input data is substantially compromised...
  55. pmc Enriching for direct regulatory targets in perturbed gene-expression profiles
    Susannah G Tringe
    Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
    Genome Biol 5:R29. 2004
    ..When applied to experimental data the reconstruction procedure preferentially retains direct transcription factor-target relationships...
  56. ncbi request reprint Molecular evolution in large genetic networks: does connectivity equal constraint?
    Matthew W Hahn
    Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA mwhahn ucdavis edu
    J Mol Evol 58:203-11. 2004
    ..The finding that highly connected proteins can tolerate just as many amino acid substitutions as other proteins leads us to conclude that power-laws in cellular networks do not reflect selection for mutational robustness...
  57. ncbi request reprint A statistical framework for combining and interpreting proteomic datasets
    Michael A Gilchrist
    Department of Biology, University of New Mexico, Albuquerque 87106, USA
    Bioinformatics 20:689-700. 2004
    ..In order to illustrate our approach we apply it to two protein complex purification datasets...
  58. pmc Asymmetric sequence divergence of duplicate genes
    Gavin C Conant
    Department of Biology, The University of New Mexico, Albuquerque, New Mexico 87131, USA
    Genome Res 13:2052-8. 2003
    ..The method is also more sensitive in detecting positive selection (Ka/Ks > 1) than models relying only on pairwise gene comparisons...
  59. ncbi request reprint Energy constraints on the evolution of gene expression
    Andreas Wagner
    Department of Biology, The University of New Mexico, NM, USA
    Mol Biol Evol 22:1365-74. 2005
    ..They are under active selection opposing them. My estimates are based on genome-scale information of gene expression in the yeast S. cerevisiae as well as information on the energy cost of biosynthesizing amino acids and nucleotides...
  60. pmc GenomeHistory: a software tool and its application to fully sequenced genomes
    Gavin C Conant
    Department of Biology, 167 Castetter Hall, The University of New Mexico, Albuquerque, NM 87131, USA
    Nucleic Acids Res 30:3378-86. 2002
    ..In contrast, a weakly negative such correlation is seen in multicellular eukaryotes...
  61. ncbi request reprint Convergent evolution of gene circuits
    Gavin C Conant
    Department of Biology, 167 Castetter Hall, The University of New Mexico, Albuquerque, New Mexico 87131, USA
    Nat Genet 34:264-6. 2003
    ..Specifically, we show that multiple types of transcriptional regulation circuitry in Escherichia coli and the yeast Saccharomyces cerevisiae have evolved independently and not by duplication of one or a few ancestral circuits...
  62. pmc How the global structure of protein interaction networks evolves
    Andreas Wagner
    Department of Biology, University of New Mexico, 167A Castetter Hall, Albuquerque, NM 817131 1091, USA
    Proc Biol Sci 270:457-66. 2003
    ....
  63. ncbi request reprint Alternative routes and mutational robustness in complex regulatory networks
    Andreas Wagner
    Department of Biology, MSC03 2020, The University of New Mexico, Albuquerque, NM 87131 0001, USA
    Biosystems 88:163-72. 2007
    ..Our results underscore the importance of systems biology approaches to understand functional and evolutionary constraints on genes and proteins...
  64. pmc A fast algorithm for determining the best combination of local alignments to a query sequence
    Gavin C Conant
    Department of Biology, The University of New Mexico, Albuquerque, NM, USA
    BMC Bioinformatics 5:62. 2004
    ..Recombination perturbs this order. An algorithm that can reconstruct sequence similarity despite rearrangement would be helpful for reconstructing the evolutionary history of recombined sequences...
  65. ncbi request reprint Molecular evolution in the yeast transcriptional regulation network
    Annette M Evangelisti
    Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
    J Exp Zool B Mol Dev Evol 302:392-411. 2004
    ..On the other hand, the number of transcription factors that bind to highly diverged duplicates is significantly greater than would be expected if loss of binding played the only role in the divergence of duplicate genes...
  66. pmc Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genes
    Jason G Bragg
    Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
    Proc Biol Sci 274:1063-70. 2007
    ..Taken together, our results contribute to the emerging view that protein atomic composition influences genome and transcriptome evolution...
  67. ncbi request reprint Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes
    Andreas Wagner
    Department of Biology, The University of New Mexico, USA
    Mol Biol Evol 23:723-33. 2006
    ..This is also suggested by the highly skewed and patchy distribution of insertion sequences among genomes. In sum, one can think of insertion sequences as slow-acting infectious diseases of cell lineages...
  68. pmc Influence of metabolic network structure and function on enzyme evolution
    Dennis Vitkup
    Center for Computational Biology and Bioinformatics, Department of Biomedical Informatics, Columbia University, Russ Berrie Pavilion, St Nicholas Avenue, New York, NY 10032, USA
    Genome Biol 7:R39. 2006
    ..The ability to consider fluxes in a metabolic network allows us to relate the functional role of each enzyme in a network to its rate of evolution...
  69. pmc Robustness can evolve gradually in complex regulatory gene networks with varying topology
    Stefano Ciliberti
    Laboratoire de Physique Théoique et Modèles Statistiques, Universite Paris Sud, Orsay, France
    PLoS Comput Biol 3:e15. 2007
    ..In addition, it exists also for RNA and protein structures, and may thus be a general organizational principle of all biological systems...
  70. ncbi request reprint New structural variation in evolutionary searches of RNA neutral networks
    - Sumedha
    Univ Paris Sud, LPTMS, UMR8626, CNRS, Orsay F 91405, France
    Biosystems 90:475-85. 2007
    ..Our findings underscore the role of neutral networks in evolutionary innovation, and the role that high robustness can play in diminishing the potential for such innovation...
  71. ncbi request reprint Robustness, evolvability, and neutrality
    Andreas Wagner
    Department of Biology, 167 Castetter Hall, The University of New Mexico, Albuquerque, NM 87131, USA
    FEBS Lett 579:1772-8. 2005
    ....
  72. pmc Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegans
    Gavin C Conant
    Department of Biology, 167 Castetter Hall, The University of New Mexico, Albuquerque, NM 87131, USA
    Proc Biol Sci 271:89-96. 2004
    ..We discuss the different causes of mutational robustness in single-copy and duplicate genes, as well as its evolutionary origin...
  73. pmc Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications
    Johannes Berg
    Institut fur Theoretische Physik, Universitat zu Koln, Zülpicherstr, 77, 50937 Koln, Germany
    BMC Evol Biol 4:51. 2004
    ..Understanding the underlying evolutionary dynamics is crucial for discerning random parts of the network from biologically important properties shaped by natural selection...
  74. ncbi request reprint Direct time-of-flight for quantitative, real-time in-beam PET: a concept and feasibility study
    Paulo Crespo
    Forschungszentrum Dresden Rossendorf, Institute of Radiation Physics, Bautzner Landstr 128, PO Box 510119, 01314 Dresden, Germany
    Phys Med Biol 52:6795-811. 2007
    ..The latter greatly alleviates the installation of in-beam PET at radiotherapeutic sites...
  75. pmc Selection and gene duplication: a view from the genome
    Andreas Wagner
    Department of Biology, University of New Mexico, 167A Castetter Hall, Albuquerque, NM 817131 1091, USA
    Genome Biol 3:reviews1012. 2002
    ....
  76. pmc Multifunctionality and robustness trade-offs in model genetic circuits
    Olivier C Martin
    Univ Paris Sud, UMR8120, Laboratoire de Genetique Vegetale du Moulon, INRA, and CNRS, Gif sur Yvette, F 91190, France
    Biophys J 94:2927-37. 2008
    ..As long as there are many alternative network structures, each of which can fulfill all required functions, multiple functions may acquire high robustness through gradual Darwinian evolution...
  77. ncbi request reprint [Effects of a computer-assisted system for nursing care documentation on quality and quantity of nursing care documentation]
    Cornelia Mahler
    Projektleitung PIK, Universitatsklinikum Heidelberg, Vossstrasse 2, D 69115 Heidelberg
    Pflege 16:144-52. 2003
    ..The content of the documentation as well as the individualization of the nursing care plan still need to be improved...
  78. ncbi request reprint Experimental design for in vitro skin penetration study of liposomal superoxide dismutase
    Edith Braun
    Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A 1190 Vienna, Austria
    J Pharm Biomed Anal 40:1187-97. 2006
    ..Analysis of variance showed that the size and the cholesterol content of liposomes as well as the duration of the penetration studies have a statistically significant influence on the amount of protein found in deeper skin layers...
  79. ncbi request reprint A model of protein translation including codon bias, nonsense errors, and ribosome recycling
    Michael A Gilchrist
    Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, 37996, USA
    J Theor Biol 239:417-34. 2006
    ..These results indirectly validate our underlying model assumptions and confirm that nonsense errors can play an important role in shaping codon usage bias...
  80. ncbi request reprint Distributed robustness versus redundancy as causes of mutational robustness
    Andreas Wagner
    Department of Biology, University of New Mexico, 167A Castetter Hall, Albuquerque, NM 87131 1091, USA
    Bioessays 27:176-88. 2005
    ..I also ask whether one can quantify the extent to which redundancy or distributed robustness contribute to mutational robustness...
  81. pmc Estimating coarse gene network structure from large-scale gene perturbation data
    Andreas Wagner
    University of New Mexico and The Santa Fe Institute, University of New Mexico, Department of Biology, Albuquerque, New Mexico 87131 1091, USA
    Genome Res 12:309-15. 2002
    ..The network comprises >100 independent subnetworks...
  82. pmc The rarity of gene shuffling in conserved genes
    Gavin C Conant
    Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland
    Genome Biol 6:R50. 2005
    ..However, surprisingly little is known about its incidence on a genome-wide scale...
  83. ncbi request reprint Trimeric membrane-anchored gp41 inhibits HIV membrane fusion
    Oliver Lenz
    European Molecular Biology Laboratory EMBL, 6, rue Jules Horowitz, 38042 Grenoble, France
    J Biol Chem 280:4095-101. 2005
    ..Our data suggest that liposome-anchored gp41ctm exerts its inhibitory action outside of the initial fusion contact site, and its implications for the fusion reaction are discussed...
  84. ncbi request reprint Risk management in biological evolution
    Andreas Wagner
    Department of Biology, University of New Mexico, 167A Castetter Hall, Albuquerque, NM 817131 1091, USA
    J Theor Biol 225:45-57. 2003
    ....
  85. ncbi request reprint Does selection mold molecular networks?
    Andreas Wagner
    University of New Mexico, Department of Biology, 167A Castetter Hall, Albuquerque, NM 817131 1091, USA
    Sci STKE 2003:PE41. 2003
    ..I illustrate the importance of thorough studies of network evolution with two recent examples, one from genome-scale networks, the other from small transcriptional regulation circuits...
  86. pmc Circuit topology and the evolution of robustness in two-gene circadian oscillators
    Andreas Wagner
    Department of Biology, University of New Mexico, 167A Castetter Hall, Albuquerque, NM 87131 1091, USA
    Proc Natl Acad Sci U S A 102:11775-80. 2005
    ..The regulatory interlocking of several oscillating gene products in biological circadian oscillators may exist because it provides robustness...
  87. ncbi request reprint Perspective: Evolution and detection of genetic robustness
    J Arjan G M de Visser
    Department of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
    Evolution 57:1959-72. 2003
    ....
  88. ncbi request reprint Enhanced protein loading into liposomes by the multiple crossflow injection technique
    Andreas Wagner
    Institute of Applied Microbiology, University of Agricultural Sciences, A 1190 Vienna, Austria
    J Liposome Res 12:271-83. 2002
    ..Vesicle size distribution and encapsulation efficiency remain constant. Furthermore, special attention is paid on reproducibility of prepared liposomes, scale-up and on long term stability of the lipid vesicles...