Research Topics
Genomes and GenesSpecies | Andreas WagnerSummaryAffiliation: University of New Mexico Country: USA Publications
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Publications
The rarity of gene shuffling in conserved genesGavin 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...- Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplicationsJohannes 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... - How the global structure of protein interaction networks evolvesAndreas Wagner
Department of Biology, University of New Mexico, 167A Castetter Hall, Albuquerque, NM 817131 1091, USA
Proc Biol Sci 270:457-66. 2003.... - Alternative routes and mutational robustness in complex regulatory networksAndreas 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... - Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomesAndreas 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... - Circuit topology and the evolution of robustness in two-gene circadian oscillatorsAndreas 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... - 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... - Risk management in biological evolutionAndreas Wagner
Department of Biology, University of New Mexico, 167A Castetter Hall, Albuquerque, NM 817131 1091, USA
J Theor Biol 225:45-57. 2003.... - Robustness, evolvability, and neutralityAndreas Wagner
Department of Biology, 167 Castetter Hall, The University of New Mexico, Albuquerque, NM 87131, USA
FEBS Lett 579:1772-8. 2005.... - Energy constraints on the evolution of gene expressionAndreas 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... - Reconstructing pathways in large genetic networks from genetic perturbationsAndreas 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... - Asymmetric functional divergence of duplicate genes in yeastAndreas 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... - Distributed robustness versus redundancy as causes of mutational robustnessAndreas 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... - Viral RNA and evolved mutational robustnessA Wagner
Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131 1091, USA
J Exp Zool 285:119-27. 1999..We provide evidence that mutational robustness of the genome of RNA viruses to mutational changes in secondary structure has evolved. J. Exp. Zool. ( Mol. Dev. Evol.) 285:119-127, 1999... - Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomesA Wagner
Department of Biology, University of New Mexico, Albuquerque, USA
Bioinformatics 15:776-84. 1999.... - Robustness against mutations in genetic networks of yeastA Wagner
Department of Biology, University of New Mexico, and The Santa Fe Institute, Albuquerque, NM, USA
Nat Genet 24:355-61. 2000..My results demonstrate that interactions among unrelated genes are the major cause of robustness against mutations. This type of robustness is probably an evolved response of genetic networks to stabilizing selection... - The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functionsA Wagner
Department of Biology, University of New Mexico, Albuquerque, New Mexico 87131 1091, USA
Genetics 154:1389-401. 2000..These results are discussed with respect to experimental evidence on redundant genes in organismal development... - Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debateA Wagner
The Santa Fe Institute, University of New Mexico, Department of Biology, 167A Castetter Hall, Albuquerque, NM 87131 1091, USA
Proc Natl Acad Sci U S A 97:6579-84. 2000..Implications of this finding for the neutralist-selectionist debate are discussed... - Birth and death of duplicated genes in completely sequenced eukaryotesA Wagner
University of New Mexico, Dept of Biology, 167A Castetter Hall, Albuquerque, NM 817131 1091, USA
Trends Genet 17:237-9. 2001..They conclude that although the rate of gene duplications is high, so is the rate of gene loss, and they argue that gene duplications could be a major factor in speciation... - The yeast protein interaction network evolves rapidly and contains few redundant duplicate genesA Wagner
Department of Biology, University of New Mexico, Albequerque, New Mexico 87131 1091, USA
Mol Biol Evol 18:1283-92. 2001..2 x 10(-3)/Myr. New interactions are estimated to evolve at a rate that is approximately three orders of magnitude smaller. Every 300 Myr, as many as half of all interactions may be replaced by new interactions... - How to reconstruct a large genetic network from n gene perturbations in fewer than n(2) easy stepsA Wagner
The Santa Fe Institute, Department of Biology, University of New Mexico, 167A Castetter Hall, Albuquerque, NM 817131 1091, USA
Bioinformatics 17:1183-97. 2001..However, such experiments cannot distinguish between direct and indirect effects of a genetic perturbation... - Estimating coarse gene network structure from large-scale gene perturbation dataAndreas 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... - Selection and gene duplication: a view from the genomeAndreas Wagner
Department of Biology, University of New Mexico, 167A Castetter Hall, Albuquerque, NM 817131 1091, USA
Genome Biol 3:reviews1012. 2002.... - Convergent evolution of gene circuitsGavin 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... - Asymmetric sequence divergence of duplicate genesGavin 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... - Enriching for direct regulatory targets in perturbed gene-expression profilesSusannah 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... - Molecular evolution in the yeast transcriptional regulation networkAnnette M Evangelisti
Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
J Exp Zoolog 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... - A fast algorithm for determining the best combination of local alignments to a query sequenceGavin 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... - Protein material costs: single atoms can make an evolutionary differenceJason G Bragg
Biology Department, University of New Mexico, Albuquerque, NM 87131, USA
Trends Genet 25:5-8. 2009..We find that mutations causing small increases in expression and even single amino acid replacements can be subject to natural selection on the basis of their material costs... - GenomeHistory: a software tool and its application to fully sequenced genomesGavin 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... - Duplicate genes and robustness to transient gene knock-downs in Caenorhabditis elegansGavin 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... - Protein carbon content evolves in response to carbon availability and may influence the fate of duplicated genesJason 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... - A statistical framework for combining and interpreting proteomic datasetsMichael A Gilchrist
Department of Biology, University of New Mexico, Albuquerque 87106, USA
Bioinformatics 20:689-700. 2004..AVAILABILITY: A suite of simple programs to accomplish some of the above tasks is available at www.unm.edu/~compbio/software/DatasetAssess.. - A computational genomics approach to the identification of gene networksA Wagner
The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
Nucleic Acids Res 25:3594-604. 1997..The technique may aid in the discovery of interactions between genes of known function, and the assignment of biological functions to putative open reading frames... - Gene duplications, robustness and evolutionary innovationsAndreas 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... - Robustness and evolvability: a paradox resolvedAndreas 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... - Exhaustive identification of steady state cycles in large stoichiometric networksJeremiah 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... - Multifunctionality and robustness trade-offs in model genetic circuitsOlivier 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... - Rapid detection of positive selection in genes and genomes through variation clustersAndreas 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... - 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... - Robustness can evolve gradually in complex regulatory gene networks with varying topologyStefano 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... - Energy costs constrain the evolution of gene expressionAndreas 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... - A survey of bacterial insertion sequences using IScanAndreas 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... - Cooperation is fleeting in the world of transposable elementsAndreas 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... - 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... - Influence of metabolic network structure and function on enzyme evolutionDennis 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... - Perspective: Evolution and detection of genetic robustnessJ Arjan G M de Visser
Department of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
Evolution 57:1959-72. 2003.... - A model of protein translation including codon bias, nonsense errors, and ribosome recyclingMichael 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... - The Systems Biology Research Tool: evolvable open-source softwareJeremiah 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... - Protein robustness promotes evolutionary innovations on large evolutionary time-scalesEvandro 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... - [Effects of a computer-assisted system for nursing care documentation on quality and quantity of nursing care documentation]Cornelia Mahler
Projektleitung PIK, , 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... - Direct time-of-flight for quantitative, real-time in-beam PET: a concept and feasibility studyPaulo 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... - Experimental design for in vitro skin penetration study of liposomal superoxide dismutaseEdith 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... - From bit to it: how a complex metabolic network transforms information into living matterAndreas 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... - Identification of HLA-A*0201-presented T cell epitopes derived from the oncofetal antigen-immature laminin receptor protein in patients with hematological malignanciesSandra Siegel
General Hospital St Georg, Department of Hematology, Hamburg, Germany
J Immunol 176:6935-44. 2006..The identification of OFA-iLR-derived peptide epitopes provides a basis for tumor immunological studies and therapeutic vaccination strategies in patients with OFA-iLR-expressing malignancies... - Enhanced protein loading into liposomes by the multiple crossflow injection techniqueAndreas 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... - Trimeric membrane-anchored gp41 inhibits HIV membrane fusionOliver 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...
Research Grants
- Characterization of a large protein interaction networkAndreas Wagner; Fiscal Year: 2005..The proposed work will put this speculation to an end for a key genetic network, some of whose conserved components are also involved in the etiology of human disease. ..