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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

  • Ahrne E, Muller M, Lisacek F. Unrestricted identification of modified proteins using MS/MS. Proteomics;10(4):671-86. (url)

  • Antonov J, Popovici V, Delorenzi M, Wirapati P, Baltzer A, Oberli A, Thurlimann B, Giobbie-Hurder A, Viale G, Altermatt HJ, Aebi S, Jaggi R. Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue. BMC Cancer;10:37. (url)

  • 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)

  • Awile O, Krisko A, Sbalzarini IF, Zagrovic B. Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans. PLoS Comput Biol 2010;6(7):e1000854. (url)

  • Bazanella AS, Gevers M, L. M. Closed-loop identication of MIMO systems: a new look at identifiability and experiment design. European Journal of Control 2010;16(3). (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)

  • Bergdorf M, Sbalzarini IF, Koumoutsakos P. A Lagrangian particle method for reaction-diffusion systems on deforming surfaces. J Math Biol 2009. (url)

  • Berardini TZ, Li D, Huala E, Bridges S, Burgess S, McCarthy F, Carbon S, Lewis SE, Mungall CJ, Abdulla A, Wood V, Feltrin E, Valle G, Chisholm RL, Fey P, Gaudet P, Kibbe W, Basu S, Bushmanova Y, Eilbeck K, Siegele DA, McIntosh B, Renfro D, Zweifel A, Hu JC, Ashburner M, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Bairoch A, Barrell D, Binns D, Blatter MC, Bougueleret L, Boutet E, Breuza L, Bridge A, Browne P, Chan WM, Coudert E, Daugherty L, Dimmer E, Eberhardt R, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Foulger R, Gruaz-Gumowski N, Hinz U, Huntley R, Jimenez S, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, O'Donovan C, Pedruzzi I, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stanley E, Stutz A, Sundaram S, Tognolli M, Xenarios I, Harris MA, Deegan JI, Ireland A, Lomax J, Jaiswal P, Chibucos M, Giglio MG, Wortman J, Hannick L, Madupu R, Botstein D, Dolinski K, Livstone MS, Oughtred R, Blake JA, Bult C, Diehl AD, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Sitnikov D, Collmer C, Torto-Alalibo T, Laulederkind S, Shimoyama M, Twigger S, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Christie KR, Costanzo MC, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Aslett M, Chan J, Kishore R, Sternberg P, Van Auke K, Khodiyar VK, Lovering RC, Talmud PJ, Howe D, Westerfield M. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 2010;38(Database issue):D331-5. (url)

  • Bittner D, Excoffier L, Largiader CR. Patterns of morphological changes and hybridization between sympatric whitefish morphs (Coregonus spp.) in a Swiss lake: a role for eutrophication? Mol Ecol 2010;19(10):2152-67. (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)

  • Bryant B, Ungerer MC, Liu Q, Waterhouse RM, Clem RJ. A caspase-like decoy molecule enhances the activity of a paralogous caspase in the yellow fever mosquito, Aedes aegypti. Insect Biochem Mol Biol. (url)

  • Burger L, van Nimwegen E. Disentangling direct from indirect co-evolution of residues in protein alignments. PLoS Computational Biology 2010;6(1):e1000633 (url)

  • Cannarozzi G, Schraudolph NN, Faty M, von Rohr P, Friberg MT, Roth AC, Gonnet P, Gonnet G, Barral Y. A role for codon order in translation dynamics. Cell 2010;141(2):355-67. (url)

  • Chaffron S, Rehrauer H, Pernthaler J, von Mering C. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res 2010;20(7):947-959. (url)

  • Comte A, Roux J, Robinson-Rechavi M. Molecular signaling in zebrafish development and the vertebrate phylotypic period. Evol Dev;12(2):144-56. (url)

  • Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, Aerts J, Andrews TD, Barnes C, Campbell P, Fitzgerald T, Hu M, Ihm CH, Kristiansson K, Macarthur DG, Macdonald JR, Onyiah I, Pang AW, Robson S, Stirrups K, Valsesia A, Walter K, Wei J, Tyler-Smith C, Carter NP, Lee C, Scherer SW, Hurles ME. Origins and functional impact of copy number variation in the human genome. Nature;464(7289):704-12. (url)

  • Cordey S, Junier T, Gerlach D, Gobbini F, Farinelli L, Zdobnov EM, Winther B, Tapparel C, Kaiser L. Rhinovirus genome evolution during experimental human infection. PLoS One 2010;5(5):e10588. (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)

  • Craddock N, Hurles ME, Cardin N, Pearson RD, Plagnol V, Robson S, Vukcevic D, Barnes C, Conrad DF, Giannoulatou E, Holmes C, Marchini JL, Stirrups K, Tobin MD, Wain LV, Yau C, Aerts J, Ahmad T, Andrews TD, Arbury H, Attwood A, Auton A, Ball SG, Balmforth AJ, Barrett JC, Barroso I, Barton A, Bennett AJ, Bhaskar S, Blaszczyk K, Bowes J, Brand OJ, Braund PS, Bredin F, Breen G, Brown MJ, Bruce IN, Bull J, Burren OS, Burton J, Byrnes J, Caesar S, Clee CM, Coffey AJ, Connell JM, Cooper JD, Dominiczak AF, Downes K, Drummond HE, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans DM, Evans G, Eyre S, Farmer A, Ferrier IN, Feuk L, Fitzgerald T, Flynn E, Forbes A, Forty L, Franklyn JA, Freathy RM, Gibbs P, Gilbert P, Gokumen O, Gordon-Smith K, Gray E, Green E, Groves CJ, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman GA, Hocking L, Howard E, Howard P, Howson JM, Hughes D, Hunt S, Isaacs JD, Jain M, Jewell DP, Johnson T, Jolley JD, Jones IR, Jones LA, Kirov G, Langford CF, Lango-Allen H, Lathrop GM, Lee J, Lee KL, Lees C, Lewis K, Lindgren CM, Maisuria-Armer M, Maller J, Mansfield J, Martin P, Massey DC, McArdle WL, McGuffin P, McLay KE, Mentzer A, Mimmack ML, Morgan AE, Morris AP, Mowat C, Myers S, Newman W, Nimmo ER, O'Donovan MC, Onipinla A, Onyiah I, Ovington NR, Owen MJ, Palin K, Parnell K, Pernet D, Perry JR, Phillips A, Pinto D, Prescott NJ, Prokopenko I, Quail MA, Rafelt S, Rayner NW, Redon R, Reid DM, Renwick, Ring SM, Robertson N, Russell E, St Clair D, Sambrook JG, Sanderson JD, Schuilenburg H, Scott CE, Scott R, Seal S, Shaw-Hawkins S, Shields BM, Simmonds MJ, Smyth DJ, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens HE, Stone MA, Su Z, Symmons DP, Thompson JR, Thomson W, Travers ME, Turnbull C, Valsesia A, Walker M, Walker NM, Wallace C, Warren-Perry M, Watkins NA, Webster J, Weedon MN, Wilson AG, Woodburn M, Wordsworth BP, Young AH, Zeggini E, Carter NP, Frayling TM, Lee C, McVean G, Munroe PB, Palotie A, Sawcer SJ, Scherer SW, Strachan DP, Tyler-Smith C, Brown MA, Burton PR, Caulfield MJ, Compston A, Farrall M, Gough SC, Hall AS, Hattersley AT, Hill AV, Mathew CG, Pembrey M, Satsangi J, Stratton MR, Worthington J, Deloukas P, Duncanson A, Kwiatkowski DP, McCarthy MI, Ouwehand W, Parkes M, Rahman N, Todd JA, Samani NJ, Donnelly P. Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. Nature;464(7289):713-20. (url)

  • Csardi G, Kutalik Z, Bergmann S. Modular analysis of gene expression data with R. Bioinformatics 2010;26(10):1376-7. (url)

  • Dayon L, Pasquarello C, Hoogland C, Sanchez JC, Scherl A. Combining low- and high-energy tandem mass spectra for optimized peptide quantification with isobaric tags. J Proteomics;73(4):769-77. (url)

  • de Lachapelle AM, Bergmann S. Precision and scaling in morphogen gradient read-out. Mol Syst Biol 2010;6:351. (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)

  • Dessimoz C, Gil M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol 2010;11(4):R37. (url)

  • Dominiczak AF, Herget-Rosenthal S, Delles C, Fliser D, Fournier I, Graber A, Girolami M, Holmes E, Lang F, Molina F, Nicholson J, Remuzzi G, Rossing P, Rudolph KL, Wolkenhauer O, Xenarios I, Zubarev R, Zubov D, Vlahou A, Schanstra JP. Systems biology to battle vascular disease. Nephrol Dial Transplant;25(4):1019-22. (url)

  • Dupuis J, Langenberg C, Prokopenko I, Saxena R, Soranzo N, Jackson AU, Wheeler E, Glazer NL, Bouatia-Naji N, Gloyn AL, Lindgren CM, Magi R, Morris AP, Randall J, Johnson T, Elliott P, Rybin D, Thorleifsson G, Steinthorsdottir V, Henneman P, Grallert H, Dehghan A, Hottenga JJ, Franklin CS, Navarro P, Song K, Goel A, Perry JR, Egan JM, Lajunen T, Grarup N, Sparso T, Doney A, Voight BF, Stringham HM, Li M, Kanoni S, Shrader P, Cavalcanti-Proenca C, Kumari M, Qi L, Timpson NJ, Gieger C, Zabena C, Rocheleau G, Ingelsson E, An P, O'Connell J, Luan J, Elliott A, McCarroll SA, Payne F, Roccasecca RM, Pattou F, Sethupathy P, Ardlie K, Ariyurek Y, Balkau B, Barter P, Beilby JP, Ben-Shlomo Y, Benediktsson R, Bennett AJ, Bergmann S, Bochud M, Boerwinkle E, Bonnefond A, Bonnycastle LL, Borch-Johnsen K, Bottcher Y, Brunner E, Bumpstead SJ, Charpentier G, Chen YD, Chines P, Clarke R, Coin LJ, Cooper MN, Cornelis M, Crawford G, Crisponi L, Day IN, de Geus EJ, Delplanque J, Dina C, Erdos MR, Fedson AC, Fischer-Rosinsky A, Forouhi NG, Fox CS, Frants R, Franzosi MG, Galan P, Goodarzi MO, Graessler J, Groves CJ, Grundy S, Gwilliam R, Gyllensten U, Hadjadj S, Hallmans G, Hammond N, Han X, Hartikainen AL, Hassanali N, Hayward C, Heath SC, Hercberg S, Herder C, Hicks AA, Hillman DR, Hingorani AD, Hofman A, Hui J, Hung J, Isomaa B, Johnson PR, Jorgensen T, Jula A, Kaakinen M, Kaprio J, Kesaniemi YA, Kivimaki M, Knight B, Koskinen S, Kovacs P, Kyvik KO, Lathrop GM, Lawlor DA, Le Bacquer O, Lecoeur C, Li Y, Lyssenko V, Mahley R, Mangino M, Manning AK, Martinez-Larrad MT, McAteer JB, McCulloch LJ, McPherson R, Meisinger C, Melzer D, Meyre D, Mitchell BD, Morken MA, Mukherjee S, Naitza S, Narisu N, Neville MJ, Oostra BA, Orru M, Pakyz R, Palmer CN, Paolisso G, Pattaro C, Pearson D, Peden JF, Pedersen NL, Perola M, Pfeiffer AF, Pichler I, Polasek O, Posthuma D, Potter SC, Pouta A, Province MA, Psaty BM, Rathmann W, Rayner NW, Rice K, Ripatti S, Rivadeneira F, Roden M, Rolandsson O, Sandbaek A, Sandhu M, Sanna S, Sayer AA, Scheet P, Scott LJ, Seedorf U, Sharp SJ, Shields B, Sigurethsson G, Sijbrands EJ, Silveira A, Simpson L, Singleton A, Smith NL, Sovio U, Swift A, Syddall H, Syvanen AC, Tanaka T, Thorand B, Tichet J, Tonjes A, Tuomi T, Uitterlinden AG, van Dijk KW, van Hoek M, Varma D, Visvikis-Siest S, Vitart V, Vogelzangs N, Waeber G, Wagner PJ, Walley A, Walters GB, Ward KL, Watkins H, Weedon MN, Wild SH, Willemsen G, Witteman JC, Yarnell JW, Zeggini E, Zelenika D, Zethelius B, Zhai G, Zhao JH, Zillikens MC, Borecki IB, Loos RJ, Meneton P, Magnusson PK, Nathan DM, Williams GH, Hattersley AT, Silander K, Salomaa V, Smith GD, Bornstein SR, Schwarz P, Spranger J, Karpe F, Shuldiner AR, Cooper C, Dedoussis GV, Serrano-Rios M, Morris AD, Lind L, Palmer LJ, Hu FB, Franks PW, Ebrahim S, Marmot M, Kao WH, Pankow JS, Sampson MJ, Kuusisto J, Laakso M, Hansen T, Pedersen O, Pramstaller PP, Wichmann HE, Illig T, Rudan I, Wright AF, Stumvoll M, Campbell H, Wilson JF, Bergman RN, Buchanan TA, Collins FS, Mohlke KL, Tuomilehto J, Valle TT, Altshuler D, Rotter JI, Siscovick DS, Penninx BW, Boomsma DI, Deloukas P, Spector TD, Frayling TM, Ferrucci L, Kong A, Thorsteinsdottir U, Stefansson K, van Duijn CM, Aulchenko YS, Cao A, Scuteri A, Schlessinger D, Uda M, Ruokonen A, Jarvelin MR, Waterworth DM, Vollenweider P, Peltonen L, Mooser V, Abecasis GR, Wareham NJ, Sladek R, Froguel P, Watanabe RM, Meigs JB, Groop L, Boehnke M, McCarthy MI, Florez JC, Barroso I. New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk. Nat Genet;42(2):105-16. (url)

  • Edwards EJ, Osborne CP, Stromberg CA, Smith SA, Bond WJ, Christin PA, Cousins AB, Duvall MR, Fox DL, Freckleton RP, Ghannoum O, Hartwell J, Huang Y, Janis CM, Keeley JE, Kellogg EA, Knapp AK, Leakey AD, Nelson DM, Saarela JM, Sage RF, Sala OE, Salamin N, Still CJ, Tipple B. The origins of C4 grasslands: integrating evolutionary and ecosystem science. Science;328(5978):587-91. (url)

  • Egri-Nagy A, Galliot B, Naef F, Nehaniv CL. Information Processing in Cells and Tissues (IPCAT'2009): From Small Scale Dynamics to Understanding Systems Behavior. Biosystems 2010. (url)

  • Excoffier L, E. LH. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Wiley 2010;10(3):564 - 567. (url)

  • Francois O, Currat M, Ray N, Han E, Excoffier L, Novembre J. Principal Component Analysis under Population Genetic Models of Range Expansion and Admixture. Mol Biol Evol. (url)

  • Gerstung M, Beerenwinkel N. Waiting Time Models of Cancer Progression Mathematical Population Studies 2010;17(3):115-135. (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)

  • Guex N, Migliavacca E, Xenarios I. Multiple imputations applied to the DREAM3 phosphoproteomics challenge: a winning strategy. PLoS One;5(1):e8012. (url)

  • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010;59(3):307-21. (url)

  • Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano MJ, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 2010;141(1):129-141 (url)

  • Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M, Ulrich A, Wardle GS, Dewell S, Zavolan M, Tuschl T. PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins. J Vis Exp 2010(41). (url)

  • Helmuth JA, Paul G, Sbalzarini IF. Beyond co-localization: inferring spatial interactions between sub-cellular structures from microscopy images. BMC Bioinformatics 2010;11:372. (url)

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

  • Hoogland C, O'Gorman M, Bogard P, Gibson F, Berth M, Cockell SJ, Ekefjard A, Forsstrom-Olsson O, Kapferer A, Nilsson M, Martinez-Bartolome S, Albar JP, Echevarria-Zomeno S, Martinez-Gomariz M, Joets J, Binz PA, Taylor CF, Dowsey A, Jones AR. Guidelines for reporting the use of gel image informatics in proteomics. Nat Biotechnol 2010;28(7):655-6. (url)

  • Hor H, Kutalik Z, Dauvilliers Y, Valsesia A, Lammers GJ, Donjacour CE, Iranzo A, Santamaria J, Peraita Adrados R, Vicario JL, Overeem S, Arnulf I, Theodorou I, Jennum P, Knudsen S, Bassetti C, Mathis J, Lecendreux M, Mayer G, Geisler P, Beneto A, Petit B, Pfister C, Burki JV, Didelot G, Billiard M, Ercilla G, Verduijn W, Claas FH, Vollenwider P, Waeber G, Waterworth DM, Mooser V, Heinzer R, Beckmann JS, Bergmann S, Tafti M. Genome-wide association study identifies new HLA class II haplotypes strongly protective against narcolepsy. Nat Genet 2010. (url)

  • Hovatta O, Jaconi M, Tohonen V, Bena F, Gimelli S, Bosman A, Holm F, Wyder S, Zdobnov EM, Irion O, Andrews PW, Antonarakis SE, Zucchelli M, Kere J, Feki A. A teratocarcinoma-like human embryonic stem cell (hESC) line and four hESC lines reveal potentially oncogenic genomic changes. PLoS One;5(4):e10263. (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)

  • Jungo F, A. E, Bairoch A, Bougueleret L, Xenarios I. Animal Toxins: How is Complexity Reprensented in Databases? Toxins 2010*:262.282. (url)

  • Junier T, Zdobnov EM. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 2010;26(13):1669-70. (url)

  • Kapur K, Johnson T, Beckmann ND, Sehmi J, Tanaka T, Kutalik Z, Styrkarsdottir U, Zhang W, Marek D, Gudbjartsson DF, Milaneschi Y, Holm H, Diiorio A, Waterworth D, Li Y, Singleton AB, Bjornsdottir US, Sigurdsson G, Hernandez DG, Desilva R, Elliott P, Eyjolfsson GI, Guralnik JM, Scott J, Thorsteinsdottir U, Bandinelli S, Chambers J, Stefansson K, Waeber G, Ferrucci L, Kooner JS, Mooser V, Vollenweider P, Beckmann JS, Bochud M, Bergmann S. Genome-wide meta-analysis for serum calcium identifies significantly associated SNPs near the calcium-sensing receptor (CASR) gene. PLoS Genet 2010;6(7):e1001035. (url)

  • Kemmer C, Gitzinger M, Daoud-El Baba M, Djonov V, Stelling J, Fussenegger M. Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat Biotechnol. (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)

  • Kirkness EF, Haas BJ, Sun W, Braig HR, Perotti MA, Clark JM, Lee SH, Robertson HM, Kennedy RC, Elhaik E, Gerlach D, Kriventseva EV, Elsik CG, Graur D, Hill CA, Veenstra JA, Walenz B, Tubio JM, Ribeiro JM, Rozas J, Johnston JS, Reese JT, Popadic A, Tojo M, Raoult D, Reed DL, Tomoyasu Y, Krause E, Mittapalli O, Margam VM, Li HM, Meyer JM, Johnson RM, Romero-Severson J, Vanzee JP, Alvarez-Ponce D, Vieira FG, Aguade M, Guirao-Rico S, Anzola JM, Yoon KS, Strycharz JP, Unger MF, Christley S, Lobo NF, Seufferheld MJ, Wang N, Dasch GA, Struchiner CJ, Madey G, Hannick LI, Bidwell S, Joardar V, Caler E, Shao R, Barker SC, Cameron S, Bruggner RV, Regier A, Johnson J, Viswanathan L, Utterback TR, Sutton GG, Lawson D, Waterhouse RM, Venter JC, Strausberg RL, Berenbaum MR, Collins FH, Zdobnov EM, Pittendrigh BR. Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle. Proc Natl Acad Sci U S A 2010. (url)

  • Kishore S, Khanna A, Zhang Z, Hui J, Balwierz PJ, Stefan M, Beach C, Nicholls RD, Zavolan M, Stamm S. The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Human Molecular Genetics 2010 (url)

  • Kraut A, Moretti S, Robinson-Rechavi M, Stockinger H, Flanders D. Phylogenetic Code in the Cloud - Can it Meet the Expectations? Stud Health Technol Inform 2010;159:55-63. (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)

  • Kutalik Z, Johnson T, Bochud M, Mooser V, Vollenweider P, Waeber G, Waterworth D, Beckmann JS, Bergmann S. Methods for testing association between uncertain genotypes and quantitative traits. Biostatistics 2010. (url)

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

  • Liechti R, Gleizes A, Kuznetsov D, Bougueleret L, Lemercier P, Bairoch A, Xenarios I. OpenFluDB, a database for human and animal influenza virus. Database 2010*;2010. (url)

  • Liechti LA, Berneche S, Bargeton B, Iwaszkiewicz J, Roy S, Michielin O, Kellenberger S. A combined computational and functional approach identifies new residues involved in pH-dependent gating of ASIC1a. The Journal of Biological Chemistry 2010 (url)

  • LopezJimenez N, Gerber S, Popovici V, Mirza S, Copren K, Ta L, Shaw GM, Trueb B, Slavotinek AM. Examination of FGFRL1 as a candidate gene for diaphragmatic defects at chromosome 4p16.3 shows that Fgfrl1 null mice have reduced expression of Tpm3, sarcomere genes and Lrtm1 in the diaphragm. Hum Genet 2010;127(3):325-36. (url)

  • Luscher A, Csardi G, de Lachapelle AM, Kutalik Z, Peter B, Bergmann S. ExpressionView--an interactive viewer for modules identified in gene expression data. Bioinformatics 2010;26(16):2062-3. (url)

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Books

  • Duret L, Bataillon T, Bierne N, Daubin V, Dutheil J, Gautier C, Glemin S, Gouy M, Heyer E, Marais G, Mouchiroud D, Pontarotti P, Quintana-Murci L, Robinson-Rechavi M, Galtier N. Evolution moléculaire: de boeck; 2010.
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Book Sections

  • Comte A, Roux J, M. R-R. Molecular signaling in zebrafish development and the vertebrate phylotypic period. Evolution & Development: Wiley; 2010. p. 144 - 156. (url)

  • Hoekstra AG, Caiazzo A, Lorenz E, Falcone JC, B C. Complex Automata: multi-scale Modeling with coupled Cellular Automat, in Modelling Complex Systems by Cellular Automata. Verlag S, editor.; 2010

Conference proceedings

  • Aberer A, Pattengale N, Stamatakis A. Parallel computation of phylogenetic consensus trees. ScienceDirect, editor. ICCS 2010; 2010 May 2010; Amsterdam , The Netherlands: Elsevier B.V. ; 2010. p. 1059-1067 (url)

  • Hirabayashi M, Ohta M, Kojima H, Oiwa K, Rufenacht DA, B. C. Jet-fluids effects on the stented-flow structure in the cavity of cerebral aneurysm. Journal B, editor. Biophysical Society 54th Annual Meeting; 2010 Feb 20-24; San Francisco, USA; 2010. p. 407a (url)

  • 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)

  • Pattengale ND, Swenson KM, Moret BME. Uncovering hidden phylogenetic consensus. Berlin S, editor. ISBRA'10; 2010; Storrs, Connecticut, USA; 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)

  • Baillie Gerritsen V. sickly smell. Protein Spotlight 2010(114). (url)

  • Baillie Gerritsen V. love at first smell. Protein Spotlight 2010(115). (url)

  • Baillie Gerritsen V. a complicated affair. Protein Spotlight 2010(116). (url)

  • Baillie Gerritsen V. a short story. Protein Spotlight (117). (url)

  • Baillie Gerritsen V. a mind astray. Protein Spotlight (118). (url)

  • Baillie Gerritsen V. a tail of protection. Protein Spotlight 2010(119). (url)

 

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