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Publications by SIB Members for the year 2010. For older publications, please click on the date links below on the left.  


Peer-reviewed journal articles

  • Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H. The IntAct molecular interaction database in 2010. Nucleic Acids Res 2010;38(Database issue):D525-31. (url)

  • Beaumont MA, Nielsen R, Robert C, Hey J, Gaggiotti O, Knowles L, Estoup A, Panchal M, Corander J, Hickerson M, Sisson SA, Fagundes N, Chikhi L, Beerli P, Vitalis R, Cornuet JM, Huelsenbeck J, Foll M, Yang Z, Rousset F, Balding D, Excoffier L. In defence of model-based inference in phylogeography. Mol Ecol. (url)

  • Bizzini A, Entenza JM, Michielin O, Arnold I, Erni B, Moreillon P. A single mutation in enzyme I of the sugar phosphotransferase system confers penicillin tolerance to Streptococcus gordonii. Antimicrob Agents Chemother;54(1):259-66. (url)

  • Consortium TU. The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Research 2010;38(Database issue):D142-D148. (url)

  • Coute Y, Brunner Y, Schvartz D, Hernandez C, Masselot A, Lisacek F, Wollheim CB, Sanchez JC. Early activation of the fatty acid metabolism pathway by chronic high glucose exposure in rat insulin secretory beta-cells. Proteomics;10(1):59-71. (url)

  • Derre L, Rivals JP, Jandus C, Pastor S, Rimoldi D, Romero P, Michielin O, Olive D, Speiser DE. BTLA mediates inhibition of human tumor-specific CD8+ T cells that can be partially reversed by vaccination. J Clin Invest 2010;120(1):157-67. (url)

  • Group NGW, 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, Grunder S, Hagen DE, Han Y, Hauser F, Hultmark D, Hunter HCt, Hurst GD, Jhangian SN, Jiang H, Johnson RM, Jones AK, Junier T, Kadowaki T, Kamping A, Kapustin Y, Kechavarzi B, 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, Schluns H, Schmitt T, Schneider M, Schuler A, Schurko AM, Shuker DM, Simoes 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 2010;327(5963):343-8. (url)

  • Hinz U, Consortium TU. From protein sequences to 3D-structures and beyond: the example of the UniProt Knowledgebase. Cell Mol Life Sci. (url)

  • Hunt BG, Wyder S, Elango N, Werren JH, Zdobnov EM, Yi SV, Goodisman MA. Sociality is linked to rates of protein evolution in a highly social insect. Mol Biol Evol. (url)

  • Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha S. Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances. PLoS Comput Biol;6(1):e1000652. (url)

  • Kuhn M, Szklarczyk D, Franceschini A, Campillos M, von Mering C, Jensen LJ, Beyer A, P B. STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Research 2010;38. (url)

  • Leuenberger C, Wegmann D. Bayesian computation and model selection without likelihoods. Genetics;184(1):243-52. (url)

  • Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res;38(Database issue):D190-5. (url)

  • Ramaswamy R, Sbalzarini IF. A partial-propensity variant of the composition-rejection stochastic simulation algorithm for chemical reaction networks. J Chem Phys;132(4):044102. (url)

  • Ray N, Wegmann D, Fagundes NJ, Wang S, Ruiz-Linares A, Excoffier L. A statistical evaluation of models for the initial settlement of the american continent emphasizes the importance of gene flow with Asia. Mol Biol Evol;27(2):337-45. (url)

  • Rohrig UF, Awad L, Grosdidier A, Larrieu P, Stroobant V, Colau D, Cerundolo V, Simpson AJ, Vogel P, Van den Eynde BJ, Zoete V, Michielin O. Rational Design of Indoleamine 2,3-Dioxygenase Inhibitors. J Med Chem 2010. (url)

  • Rowe HM, Jakobsson J, Mesnard D, Rougemont J, Reynard S, Aktas T, Maillard PV, Layard-Liesching H, Verp S, Marquis J, Spitz F, Constam DB, Trono D. KAP1 controls endogenous retroviruses in embryonic stem cells. Nature;463(7278):237-40. (url)

  • Schmidt-Chanasit J, Essbauer S, Petraityte R, Yoshimatsu K, Tackmann K, Conraths FJ, Sasnauskas K, Arikawa J, Thomas A, Pfeffer M, Scharninghausen JJ, Splettstoesser W, Wenk M, Heckel G, Ulrich RG. Extensive host sharing of central European Tula virus. J Virol;84(1):459-74. (url)

  • Schupbach T, Zoete V, Tsakam-Sotche B, Michielin O. Fourier transform convolution integrals applied to generalized Born molecular volume. J Comput Chem;31(3):649-59. (url)

  • Sigrist C.-J., Cerutti L., De Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N. PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Research 2010;Vol. 38(Database issue):D161-D166. (url)

  • Stecher B, Chaffron S, Kappeli R, Hapfelmeier S, Freedrich S, Weber TC, Kirundi J, Suar M, McCoy KD, von Mering C, Macpherson AJ, Hardt WD. Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria. PLoS Pathog;6(1):e1000711. (url)

  • Zoete V, Grosdidier A, Cuendet M, Michielin O. Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock. J Mol Recognit 2010. (url)

Conference proceedings

  • Lin Y, Rajan V, Swenson KM, Moret BME. Estimating true evolutionary distances under rearrangements, duplications, and losses. APBC'10 18-21 January 2010; Bangalore, India. (url)

  • Müller CL, Sbalzarini IF. Gaussian adaptation revisited — an entropic view on covariance matrix adaptation. EvoStar April 2010; Istanbul, Turkey: Lecture Notes in Computer Science 2010. (url)

  • Rajan V, Xu AW, Lin Y, Swenson KM, Moret BME. Heuristics for the inversion median problem. APBC'10 18-21 January 2010; Bangalore, India. (url)

Other articles

  • Baillie Gerritsen V. mint condition. Protein Spotlight 2010(113). (url)
 

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