Scientific publications
Research - Publications - 2009
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Publications by SIB Members from 2009. For other years, please click on the links below left.  


Peer-reviewed journal articles

  • Ahrne E, Masselot A, Binz P, Muller M, Lisacek F. A simple workflow to increase MS2 identification rate by subsequent spectral library search. Proteomics 2009;9(6):1731-6. (url)

  • Almeida LG, Sakabe NJ, deOliveira AR, Silva MC, Mundstein AS, Cohen T, Chen YT, Chua R, Gurung S, Gnjatic S, Jungbluth AA, Caballero OL, Bairoch A, Kiesler E, White SL, Simpson AJ, Old LJ, Camargo AA, Vasconcelos AT. CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res 2009;37(Database issue):D816-9. (url)

  • Altenhoff A, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 2009;5(1):e1000262. (url)

  • Altmann A, Daumer M, Beerenwinkel N, Peres Y, Schulter E, Buch J, Rhee SY, Sonnerborg A, Fessel WJ, Shafer RW, Zazzi M, Kaiser R, Lengauer T. Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. J Infect Dis 2009;199(7):999-1006. (url)

  • Anisimova M, Kosiol C. Investigating protein-coding sequence evolution with probabilistic codon substitution models. Mol Biol Evol 2009;26(2):255-71. (url)

  • Arnold K, Kiefer F, Kopp J, Battey J, Podvinec M, Westbrook J, Berman H, Bordoli L, Schwede T. The Protein Model Portal. J Struct Funct Genomics 2009;10(1):1-8. (url)

  • Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen EJ. Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biology 2009;10(7):R79. (url)

  • Becker M, Burkhardt K, Allal A, Dulguerov P, Ratib O, Becker C. [Pretherapeutic and posttherapeutic laryngeal imaging.]. Radiologe 2009;49(1):43-58. (url)

  • Beerenwinkel N, Sullivant S. Markov models for accumulating mutations. Biometrika 2009. (url)

  • Benazet J, Bischofberger M, Tiecke E, Goncalves A, Martin J, Zuniga A, Naef F, Zeller R. A self-regulatory system of interlinked signaling feedback loops controls mouse limb patterning. Science 2009;323(5917):1050-3. (url)

  • Bengtsson H, Wirapati P, Speed TP. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics 2009;25(17):2149-56. (url)

  • Benkert P, Schwede T, Tosatto SC. QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information. BMC Struct Biol 2009;9(1):35. (url)

  • Benkert P, Kunzli M, Schwede T. QMEAN server for protein model quality estimation. Nucleic Acids Res 2009;37(Web Server issue):W510-4. (url)

  • Benkert P, Tosatto S, Schwede T. Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins: Structure, Function, and Bioinformatics 2009;77(S9):173-180. (url)

  • Berman HM, Westbrook JD, Gabanyi MJ, Tao W, Shah R, Kouranov A, Schwede T, Arnold K, Kiefer F, Bordoli L, Kopp J, Podvinec M, Adams PD, Carter LG, Minor W, Nair R, La Baer J. The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res 2009;37(Database issue):D365-8. (url)

  • Berthonneche C, Peter B, Schupfer F, Hayoz P, Kutalik Z, Abriel H, Pedrazzini T, Beckmann JS, Bergmann S, Maurer F. Cardiovascular response to beta-adrenergic blockade or activation in 23 inbred mouse strains. PLoS One 2009;4(8):e6610. (url)

  • Besnard G, Muasya AM, Russier F, Roalson EH, Salamin N, Christin PA. Phylogenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence. Mol Biol Evol 2009;26(8):1909-19. (url)

  • Bizzini A, Entenza JM, Michielin O, Arnold I, Erni B, Moreillon P. A Single Mutation in the Enzyme I of the Sugar Phosphotransferase System Confers Penicillin Tolerance to Streptococcus gordonii. Antimicrob Agents Chemother 2009. (url)

  • Bordoli L, Kiefer F, Arnold K, Benkert P, Battey J, Schwede T. Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc 2009;4(1):1-13. (url)

  • Bouchenak-Khelladi Y, Verboom GA, Hodkinson TR, Salamin N, François O, Ni Chonghaile G, Savolainen V. The origins and diversification of C4 grasses and savanna-adapted ungulates. Global Change Biology 2009;15(10):2397 - 2417. (url)

  • Bragg J, Wagner A. Protein material costs: single atoms can make an evolutionary difference. Trends Genet 2009;25(1):5-8. (url)

  • Braaker S, Heckel G. Transalpine colonisation and partial phylogeographic erosion by dispersal in the common vole (Microtus arvalis). Mol Ecol 2009;18(11):2518-31. (url)

  • Bulliard Y, Turelli P, Rohrig UF, Zoete V, Mangeat B, Michielin O, Trono D. Functional Analysis and Structural Modeling of Human APOBEC3G Reveals the Role of Evolutionarily Conserved Elements in HIV-1 and Alu Inhibition. J Virol 2009. (url)

  • Caiazzo A, Falcone J-C, Chopard B, Hoekstra AG. Asymptotic analysis of Complex Automata models for reaction--diffusion systems. Applied Numerical Mathematics 2009;59(8):2023-2034. (url)

  • Calderon-Copete SP, Wigger G, Wunderlin C, Schmidheini T, Frey J, Quail MA, Falquet L. The Mycoplasma conjunctivae genome sequencing, annotation and analysis. BMC Bioinformatics 2009;10 Suppl 6:S7. (url)

  • Christin P, Salamin N, Kellogg E, Vicentini A, Besnard G. Integrating phylogeny into studies of C4 variation in the grasses. Plant Physiol 2009;149(1):82-7. (url)

  • Christin PA, Petitpierre B, Salamin N, Buchi L, Besnard G. Evolution of C(4) phosphoenolpyruvate carboxykinase in grasses, from genotype to phenotype. Mol Biol Evol 2009;26(2):357-65. (url)

  • Cockell MM, Lo Presti L, Cerutti L, Cano Del Rosario E, Hauser PM, Simanis V. Functional differentiation of tbf1 orthologues in fission and budding yeasts. Eukaryot Cell 2009;8(2):207-16. (url)

  • Cook AL, Chen W, Thurber AE, Smit DJ, Smith AG, Bladen TG, Brown DL, Duffy DL, Pastorino L, Bianchi-Scarra G, Leonard JH, Stow JL, Sturm RA. Analysis of cultured human melanocytes based on polymorphisms within the SLC45A2/MATP, SLC24A5/NCKX5, and OCA2/P loci. J Invest Dermatol 2009;129(2):392-405. (url)

  • Cruz F, Roux J, Robinson-Rechavi M. The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes. BMC Genomics 2009;10:619. (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 2009;73(4):769-77. (url)

  • de la Chaux N, Wagner A. Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes. BMC Evol Biol 2009;9:205. (url)

  • Delmotte N, Knief C, Chaffron S, Innerebner G, Roschitzki B, Schlapbach R, Von Mering C, Vorholt JA. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. PNAS 2009;106(38):16428–16433. (url)

  • Dessimoz C, Gil M. Covariance of maximum likelihood evolutionary distances between sequences aligned pairwise. BMC Evol Biol 2008;8:179. (url)

  • Dibner C, Sage D, Unser M, Bauer C, d'Eysmond T, Naef F, Schibler U. Circadian gene expression is resilient to large fluctuations in overall transcription rates. EMBO J 2009;28(2):123-34. (url)

  • Dimisianos G, Stefanaki I, Nicolaou V, Sypsa V, Antoniou C, Poulou M, Papadopoulos O, Gogas H, Kanavakis E, Nicolaidou E, Katsambas AD, Stratigos AJ. A study of a single variant allele (rs1426654) of the pigmentation-related gene SLC24A5 in Greek subjects. Exp Dermatol 2009;18(2):175-7. (url)

  • Djojosubroto M, Bollotte F, Wirapati P, Radtke F, Stamenkovic I, Arsenijevic Y. Chromosomal number aberrations and transformation in adult mouse retinal stem cells in vitro. Invest Ophthalmol Vis Sci 2009. (url)

  • Duerig A, Abel S, Folcher M, Nicollier M, Schwede T, Amiot N, Giese B, Jenal U. Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. Genes Dev 2009;23(1):93-104. (url)

  • Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Hakkinen J, Levander F, Aebersold R, Vandekerckhove J, Dunn MJ, Lisacek F, Siepen JA, Hubbard SJ, Binz PA, Bluggel M, Thiele H, Cottrell J, Meyer HE, Apweiler R, Stephan C. Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics 2009;9(15):3928-33. (url)

  • Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, Adelson DL, Eichler EE, Elnitski L, Guigo R, Hamernik DL, Kappes SM, Lewin HA, Lynn DJ, Nicholas FW, Reymond A, Rijnkels M, Skow LC, Zdobnov EM, Schook L, Womack J, Alioto T, Antonarakis SE, Astashyn A, Chapple CE, Chen HC, Chrast J, Camara F, Ermolaeva O, Henrichsen CN, Hlavina W, Kapustin Y, Kiryutin B, Kitts P, Kokocinski F, Landrum M, Maglott D, Pruitt K, Sapojnikov V, Searle SM, Solovyev V, Souvorov A, Ucla C, Wyss C, Anzola JM, Gerlach D, Elhaik E, Graur D, Reese JT, Edgar RC, McEwan JC, Payne GM, Raison JM, Junier T, Kriventseva EV, Eyras E, Plass M, Donthu R, Larkin DM, Reecy J, Yang MQ, Chen L, Cheng Z, Chitko-McKown CG, Liu GE, Matukumalli LK, Song J, Zhu B, Bradley DG, Brinkman FS, Lau LP, Whiteside MD, Walker A, Wheeler TT, Casey T, German JB, Lemay DG, Maqbool NJ, Molenaar AJ, Seo S, Stothard P, Baldwin CL, Baxter R, Brinkmeyer-Langford CL, Brown WC, Childers CP, Connelley T, Ellis SA, Fritz K, Glass EJ, Herzig CT, Iivanainen A, Lahmers KK, Bennett AK, Dickens CM, Gilbert JG, Hagen DE, Salih H, Aerts J, Caetano AR, Dalrymple B, Garcia JF, Gill CA, Hiendleder SG, Memili E, Spurlock D, Williams JL, Alexander L, Brownstein MJ, Guan L, Holt RA, Jones SJ, Marra MA, Moore R, Moore SS, Roberts A, Taniguchi M, Waterman RC, Chacko J, Chandrabose MM, Cree A, Dao MD, Dinh HH, Gabisi RA, Hines S, Hume J, Jhangiani SN, Joshi V, Kovar CL, Lewis LR, Liu YS, Lopez J, Morgan MB, Nguyen NB, Okwuonu GO, Ruiz SJ, Santibanez J, Wright RA, Buhay C, Ding Y, Dugan-Rocha S, Herdandez J, Holder M, Sabo A, Egan A, Goodell J, Wilczek-Boney K, Fowler GR, Hitchens ME, Lozado RJ, Moen C, Steffen D, Warren JT, Zhang J, Chiu R, Schein JE, Durbin KJ, Havlak P, Jiang H, Liu Y, Qin X, Ren Y, Shen Y, Song H, Bell SN, Davis C, Johnson AJ, Lee S, Nazareth LV, Patel BM, Pu LL, Vattathil S, Williams RL, Jr., Curry S, Hamilton C, Sodergren E, Wheeler DA, Barris W, Bennett GL, Eggen A, Green RD, Harhay GP, Hobbs M, Jann O, Keele JW, Kent MP, Lien S, McKay SD, McWilliam S, Ratnakumar A, Schnabel RD, Smith T, Snelling WM, Sonstegard TS, Stone RT, Sugimoto Y, Takasuga A, Taylor JF, Van Tassell CP, Macneil MD, Abatepaulo AR, Abbey CA, Ahola V, Almeida IG, Amadio AF, Anatriello E, Bahadue SM, Biase FH, Boldt CR, Carroll JA, Carvalho WA, Cervelatti EP, Chacko E, Chapin JE, Cheng Y, Choi J, Colley AJ, de Campos TA, De Donato M, Santos IK, de Oliveira CJ, Deobald H, Devinoy E, Donohue KE, Dovc P, Eberlein A, Fitzsimmons CJ, Franzin AM, Garcia GR, Genini S, Gladney CJ, Grant JR, Greaser ML, Green JA, Hadsell DL, Hakimov HA, Halgren R, Harrow JL, Hart EA, Hastings N, Hernandez M, Hu ZL, Ingham A, Iso-Touru T, Jamis C, Jensen K, Kapetis D, Kerr T, Khalil SS, Khatib H, Kolbehdari D, Kumar CG, Kumar D, Leach R, Lee JC, Li C, Logan KM, Malinverni R, Marques E, Martin WF, Martins NF, Maruyama SR, Mazza R, McLean KL, Medrano JF, Moreno BT, More DD, Muntean CT, Nandakumar HP, Nogueira MF, Olsaker I, Pant SD, Panzitta F, Pastor RC, Poli MA, Poslusny N, Rachagani S, Ranganathan S, Razpet A, Riggs PK, Rincon G, Rodriguez-Osorio N, Rodriguez-Zas SL, Romero NE, Rosenwald A, Sando L, Schmutz SM, Shen L, Sherman L, Southey BR, Lutzow YS, Sweedler JV, Tammen I, Telugu BP, Urbanski JM, Utsunomiya YT, Verschoor CP, Waardenberg AJ, Wang Z, Ward R, Weikard R, Welsh TH, Jr., White SN, Wilming LG, Wunderlich KR, Yang J, Zhao FQ. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science 2009;324(5926):522-8. (url)

  • Emamzadah S, Petty TJ, De Almeida V, Nishimura T, Joly J, Ferrer JL, Halazonetis TD. Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction. Acta Crystallogr D Biol Crystallogr 2009;65(Pt 9):913-20. (url)

  • Excoffier L, Hofer T, Foll M. Detecting loci under selection in a hierarchically structured population. Heredity 2009. (url)

  • Excoffier L, Foll M, Petit RJ. Genetic Consequences of Range Expansions. Annual Review of Ecology, Evolution, and Systematics 2009;40. (url)

  • Fantom Consortium SH, Riken Omics Science Center AT. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. 2009;41(5):553-562.

  • Farmer P, Bonnefoi H, Anderle P, Cameron D, Wirapati P, Becette V, Andre S, Piccart M, Campone M, Brain E, Macgrogan G, Petit T, Jassem J, Bibeau F, Blot E, Bogaerts J, Aguet M, Bergh J, Iggo R, Delorenzi M. A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancer. Nat Med 2009;15(1):68-74. (url)

  • Fulton DC, Stettler M, Mettler T, Vaughan CK, Li J, Francisco P, Gil M, Reinhold H, Eicke S, Messerli G, Dorken G, Halliday K, Smith AM, Smith SM, Zeeman SC. Beta-AMYLASE4, a noncatalytic protein required for starch breakdown, acts upstream of three active beta-amylases in Arabidopsis chloroplasts. Plant Cell 2008;20(4):1040-58. (url)

  • Gaggiotti OE, Bekkevold D, Jorgensen HB, Foll M, Carvalho GR, Andre C, Ruzzante DE. Disentangling the effects of evolutionary, demographic, and environmental factors influencing genetic structure of natural populations: Atlantic herring as a case study. Evolution 2009;63(11):2939-51. (url)

  • Garg A, Mohanram K, Di Cara A, De Micheli G, Xenarios I. Modeling stochasticity and robustness in gene regulatory networks. Bioinformatics 2009;25(12):i101-9. (url)

  • Gatfield D, Le Martelot G, Vejnar C, Gerlach D, Schaad O, Ruskeepää A, Oresic M, Esau C, Zdobnov E, Schibler U. Integration of microRNA miR-122 in hepatic circadian gene expression. Genes & Development 2009. (url)

  • Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J. The Microbe browser for comparative genomics. Nucleic Acids Res 2009;37(Web Server issue):W296-9. (url)

  • Gattiker A, Hermida L, Liechti R, Xenarios I, Collin O, Rougemont J, Primig M. MIMAS 3.0 is a Multiomics Information Management and Annotation System. BMC Bioinformatics 2009;10(1):151. (url)

  • Gerlach D, Kriventseva EV, Rahman N, Vejnar CE, Zdobnov EM. miROrtho: computational survey of microRNA genes. Nucleic Acids Res 2009;37(Database issue):D111-7. (url)

  • Gerstung M, Baudis M, Moch H, Beerenwinkel N. Quantifying cancer progression with conjunctive Bayesian networks. Bioinformatics 2009;25(21):2809-15. (url)

  • Gevers M, Bazanella AS, Bombois X, Miskovic L. Identification and the information matrix: how to get just sufficiently rich? IEEE Transactions on Automatic Control 2009;54(12):2828 - 2840 (url)

  • Griffon N, Jin W, Petty TJ, Millar J, Badellino KO, Saven JG, Marchadier DH, Kempner ES, Billheimer J, Glick JM, Rader DJ. Identification of the active form of endothelial lipase, a homodimer in a head-to-tail conformation. J Biol Chem 2009;284(35):23322-30. (url)

  • Grosdidier A, Zoete V, Michielin O. Blind docking of 260 protein-ligand complexes with EADock 2.0. J Comput Chem 2009. (url)

  • Guex N, Peitsch MC, Schwede T. Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis 2009;30 Suppl 1:S162-73. (url)

  • Guillot G, Foll M. Correcting for ascertainment bias in the inference of population structure. Bioinformatics 2009;25(4):552-4. (url)

  • Hafner M, Koeppl H, Hasler M, Wagner A. 'Glocal' robustness analysis and model discrimination for circadian oscillators. PLoS Comput Biol 2009;5(10):e1000534. (url)

  • Hainard A, Tiberti N, Robin X, Lejon V, Ngoyi DM, Matovu E, Enyaru JC, Fouda C, Ndung'u JM, Lisacek F, Muller M, Turck N, Sanchez JC. A Combined CXCL10, CXCL8 and H-FABP Panel for the Staging of Human African Trypanosomiasis Patients. PLoS Negl Trop Dis 2009;3(6):e459. (url)

  • Hausmann G, von Mering C, Basler K. The hedgehog signaling pathway: where did it come from? PLoS Biol 2009;7(6):e1000146. (url)

  • Hausser J, Berninger P, Rodak C, Jantscher Y, Wirth S, Zavolan M. MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Res 2009;37(Web Server issue):W266-72. (url)

  • Hazen S, Naef F, Quisel T, Gendron J, Chen H, Ecker J, Borevitz J, Kay S. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol 2009;10(2):R17. (url)

  • Helmuth JA, Burckhardt CJ, Greber UF, Sbalzarini IF. Shape reconstruction of subcellular structures from live cell fluorescence microscopy images. J Struct Biol 2009;167(1):1-10. (url)

  • Hofer T, Ray N, Wegmann D, Excoffier L. Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Ann Hum Genet 2009;73(1):95-108. (url)

  • Hornitschek P, Lorrain S, Zoete V, Michielin O, Fankhauser C. Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers. EMBO J 2009. (url)

  • Hunter S, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn R, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn A, Selengut J, Sigrist C, Thimma M, Thomas P, Valentin F, Wilson D, Wu C, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res 2009;37(Database issue):D211-5. (url)

  • Hutzinger R, Feederle R, Mrazek J, Schiefermeier N, Balwierz PJ, Zavolan M, Polacek N, Delecluse HJ, Huttenhofer A. Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS Pathog 2009;5(8):e1000547. (url)

  • Iwema T, Chaumot A, Studer R, Robinson-Rechavi M, Billas I, Moras D, Laudet V, Bonneton F. Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects. Mol Biol Evol 2009;26(4):753-68. (url)

  • Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, Suzek BE, Martin MJ, McGarvey P, Gasteiger E. Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 2009;10:136. (url)

  • Jensen L, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009;37(Database issue):D412-6. (url)

  • Joosten R, Salzemann J, Bloch V, Stockinger H, Berglund A-C, Blanchet C, Bongcam-Rudloff E, Combet C, Da Costa A, Deleage G, Diarena M, Fabbretti R, Fettahi G, Flegel V, Gisel A, Kasam V, Kervinen T, Korpelainen E, Mattila K, Pagni M, Reichstadt M, Breton V, Tickle I, Vriend G. PDB_REDO: automated re-refinement of X-ray structure models in the PDB. Applied Crystallography 2009(42):376–384. (url)

  • Junier P, Kim O-S, Junier T, Ahn T-S, Imhoff JF, Witzel K-P. Community analysis of betaproteobacterial ammonia-oxidizing bacteria using the amoCAB operon. Applied Microbiology and Biotechnology 2009;83(1):175-188. (url)

  • Kaltenbach HM, Dimopoulos S, Stelling J. Systems analysis of cellular networks under uncertainty. FEBS Lett 2009;583(24):3923-30. (url)

  • Kaltenbach HM, Dimopoulos S, Stelling J. Systems analysis of cellular networks under uncertainty. FEBS Lett 2009;583(24):3923-30. (url)

  • Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T. The SWISS-MODEL Repository and associated resources. Nucleic Acids Res 2009;37(Database issue):D387-92. (url)

  • Kolz M, Johnson T, Sanna S, Teumer A, Vitart V, Perola M, Mangino M, Albrecht E, Wallace C, Farrall M, Johansson A, Nyholt DR, Aulchenko Y, Beckmann JS, Bergmann S, Bochud M, Brown M, Campbell H, Connell J, Dominiczak A, Homuth G, Lamina C, McCarthy MI, Meitinger T, Mooser V, Munroe P, Nauck M, Peden J, Prokisch H, Salo P, Salomaa V, Samani NJ, Schlessinger D, Uda M, Volker U, Waeber G, Waterworth D, Wang-Sattler R, Wright AF, Adamski J, Whitfield JB, Gyllensten U, Wilson JF, Rudan I, Pramstaller P, Watkins H, Doering A, Wichmann HE, Spector TD, Peltonen L, Volzke H, Nagaraja R, Vollenweider P, Caulfield M, Illig T, Gieger C. Meta-analysis of 28,141 individuals identifies common variants within five new loci that influence uric acid concentrations. PLoS Genet 2009;5(6):e1000504. (url)

  • Koua D, Cerutti L, Falquet L, Sigrist CJ, Theiler G, Hulo N, Dunand C. PeroxiBase: a database with new tools for peroxidase family classification. Nucleic Acids Res 2009;37(Database issue):D261-6. (url)

  • Leimgruber E, Seguin-Estevez Q, Dunand-Sauthier I, Rybtsova N, Schmid CD, Ambrosini G, Bucher P, Reith W. Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site. Nucleic Acids Res 2009. (url)

  • Lemay DG, Lynn DJ, Martin WF, Neville MC, Casey TM, Rincon G, Kriventseva EV, Barris WC, Hinrichs AS, Molenaar AJ, Pollard KS, Maqbool NJ, Singh K, Murney R, Zdobnov EM, Tellam RL, Medrano JF, German JB, Rijnkels M. The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biol 2009;10(4):R43. (url)

  • Liebl A, Prager R, Binz K, Kaiser M, Bergenstal R, Gallwitz B. Comparison of insulin analogue regimens in people with type 2 diabetes mellitus in the PREFER Study: a randomized controlled trial. Diabetes Obes Metab 2009;11(1):45-52. (url)

  • Lima T, Auchincloss AH, Coudert E, Keller G, Michoud K, Rivoire C, Bulliard V, de Castro E, Lachaize C, Baratin D, Phan I, Bougueleret L, Bairoch A. HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot. Nucleic Acids Res 2009;37(Database issue):D471-8. (url)

  • Makrythanasis P, Kapranov P, Bartoloni L, Reymond A, Deutsch S, Guigó R, Denoeud F, Drenkow J, Rossier C, Ariani F, ., Capra V, Excoffier L, Renieri A, ., Gingeras TR, Antonarakis SE. Variation in novel exons (RACEfrags) of the MECP2 gene in Rett syndrome patients and controls. Human Mutation 2009;30(9):E866 - E879. (url)

  • Marchisio MA, Stelling J. Computational design tools for synthetic biology. Curr Opin Biotechnol 2009;20(4):479-85. (url)

  • Martin O, Valsesia A, Telenti A, Xenarios I, Stevenson BJ. AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. Bioinformatics 2009;25(5):662-3. (url)

  • Martin OC, Wagner A. Effects of recombination on complex regulatory circuits. Genetics 2009;183(2):673-84, 1SI-8SI. (url)

  • Matias Rodrigues JF, Wagner A. Evolutionary plasticity and innovations in complex metabolic reaction networks. PLoS Comput Biol 2009;5(12):e1000613. (url)

  • Matsui T, Yamamoto T, Wyder S, Zdobnov E, Kadowaki T. Expression profiles of urbilaterian genes uniquely shared between honey bee and vertebrates. BMC Genomics 2009;10:17. (url)

  • Mayoral RJ, Pipkin ME, Pachkov M, van Nimwegen E, Rao A, Monticelli S. MicroRNA-221-222 regulate the cell cycle in mast cells. J Immunol 2009;182(1):433-45. (url)

  • Meier P, Antonov J, Zbinden R, Kuhn A, Zbinden S, Gloekler S, Delorenzi M, Jaggi R, Seiler C. Non-invasive gene-expression-based detection of well-developed collateral function in individuals with and without coronary artery disease. Heart 2009;95(11):900-8. (url)

  • Molina N, van Nimwegen E. Scaling laws in functional genome content across prokaryotic clades and lifestyles. Trends in Genetics : TIG 2009;25(6):243-247. (url)

  • Monot M, Honore N, Garnier T, Zidane N, Sherafi D, Paniz-Mondolfi A, Matsuoka M, Taylor GM, Donoghue HD, Bouwman A, Mays S, Watson C, Lockwood D, Khamispour A, Dowlati Y, Jianping S, Rea TH, Vera-Cabrera L, Stefani MM, Banu S, Macdonald M, Sapkota BR, Spencer JS, Thomas J, Harshman K, Singh P, Busso P, Gattiker A, Rougemont J, Brennan PJ, Cole ST. Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet 2009. (url)

  • Muller CL, Sbalzarini IF, van Gunsteren WF, Zagrovic B, Hunenberger PH. In the eye of the beholder: Inhomogeneous distribution of high-resolution shapes within the random-walk ensemble. J Chem Phys 2009;130(21):214904. (url)

  • Muller D, Stelling J. Precise regulation of gene expression dynamics favors complex promoter architectures. PLoS Comput Biol 2009;5(1):e1000279. (url)

  • Murat A, Migliavacca E, Hussain S, Heimberger A, Desbaillets I, Hamou M, Rüegg C, Stupp R, Delorenzi M, Hegi M. Modulation of angiogenic and inflammatory response in glioblastoma by hypoxia. PLoS One 2009. (url)

  • Mylonas R, Mauron Y, Masselot A, Binz PA, Budin N, Fathi M, Viette V, Hochstrasser DF, Lisacek F. X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry. Anal Chem 2009;81(18):7604-10. (url)

  • Newton-Cheh C, Johnson T, Gateva V, Tobin MD, Bochud M, Coin L, Najjar SS, Zhao JH, Heath SC, Eyheramendy S, Papadakis K, Voight BF, Scott LJ, Zhang F, Farrall M, Tanaka T, Wallace C, Chambers JC, Khaw KT, Nilsson P, van der Harst P, Polidoro S, Grobbee DE, Onland-Moret NC, Bots ML, Wain LV, Elliott KS, Teumer A, Luan J, Lucas G, Kuusisto J, Burton PR, Hadley D, McArdle WL, Brown M, Dominiczak A, Newhouse SJ, Samani NJ, Webster J, Zeggini E, Beckmann JS, Bergmann S, Lim N, Song K, Vollenweider P, Waeber G, Waterworth DM, Yuan X, Groop L, Orho-Melander M, Allione A, Di Gregorio A, Guarrera S, Panico S, Ricceri F, Romanazzi V, Sacerdote C, Vineis P, Barroso I, Sandhu MS, Luben RN, Crawford GJ, Jousilahti P, Perola M, Boehnke M, Bonnycastle LL, Collins FS, Jackson AU, Mohlke KL, Stringham HM, Valle TT, Willer CJ, Bergman RN, Morken MA, Doring A, Gieger C, Illig T, Meitinger T, Org E, Pfeufer A, Wichmann HE, Kathiresan S, Marrugat J, O'Donnell CJ, Schwartz SM, Siscovick DS, Subirana I, Freimer NB, Hartikainen AL, McCarthy MI, O'Reilly PF, Peltonen L, Pouta A, de Jong PE, Snieder H, van Gilst WH, Clarke R, Goel A, Hamsten A, Peden JF, Seedorf U, Syvanen AC, Tognoni G, Lakatta EG, Sanna S, Scheet P, Schlessinger D, Scuteri A, Dorr M, Ernst F, Felix SB, Homuth G, Lorbeer R, Reffelmann T, Rettig R, Volker U, Galan P, Gut IG, Hercberg S, Lathrop GM, Zelenika D, Deloukas P, Soranzo N, Williams FM, Zhai G, Salomaa V, Laakso M, Elosua R, Forouhi NG, Volzke H, Uiterwaal CS, van der Schouw YT, Numans ME, Matullo G, Navis G, Berglund G, Bingham SA, Kooner JS, Connell JM, Bandinelli S, Ferrucci L, Watkins H, Spector TD, Tuomilehto J, Altshuler D, Strachan DP, Laan M, Meneton P, Wareham NJ, Uda M, Jarvelin MR, Mooser V, Melander O, Loos RJ, Elliott P, Abecasis GR, Caulfield M, Munroe PB. Genome-wide association study identifies eight loci associated with blood pressure. Nat Genet 2009. (url)

  • Nikolaev SI, Iseli C, Sharp AJ, Robyr D, Rougemont J, Gehrig C, Farinelli L, Antonarakis SE. Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing. PLoS One 2009;4(8):e6659. (url)

  • Norrmén C, Ivanov K, Cheng J, Zangger N, Delorenzi M, Jaquet M, Miura N, Puolakkainen P, Horsley V, Hu J, Augustin H, Ylä-Herttuala S, Alitalo K, Petrova P. FOXC2 controls formation and maturation of lymphatic collecting vessels through cooperation with NFATc1. J Cell Biol 2009:439-57. (url)

  • Ortiz M, Guex N, Patin E, Martin O, Xenarios I, Ciuffi A, Quintana-Murci L, Telenti A. Evolutionary trajectories of primate genes involved in HIV pathogenesis. Mol Biol Evol 2009;26(12):2865-75. (url)

  • Palagi PM, Lisacek F, Appel RD. Database interrogation algorithms for identification of proteins in proteomic separations. Methods Mol Biol 2009;519:515-31. (url)

  • Papaioannou M, Pitetti J, Ro S, Park C, Aubry F, Schaad O, Vejnar C, Kuhne F, Descombes P, Zdobnov E, McManus M, Guillou F, Harfe B, Yan W, Jegou B, Nef S. Sertoli cell Dicer is essential for spermatogenesis in mice. Dev Biol 2009;326(1):250-9. (url)

  • Parisi F, Sonderegger B, Wirapati P, Delorenzi M, Naef F. Relationship between estrogen receptor alpha location and gene induction reveals the importance of downstream sites and cofactors. BMC Genomics 2009;10:381. (url)

  • Parisi F, Koeppl H, Naef F. Network inference by combining biologically motivated regulatory constraints with penalized regression. Ann N Y Acad Sci 2009;1158:114-24. (url)

  • Parmigiani A, Chopard B, Latt J, Huber C, Bachmann O. Application of the multi distribution function lattice Boltzmann approach to thermal flows. Special Topics 2009;171:37-43. (url)

  • Pathare S, Schaffer AA, Beerenwinkel N, Mahimkar M. Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression. Int J Cancer 2009;124(12):2864-71. (url)

  • Pena JT, Sohn-Lee C, Rouhanifard SH, Ludwig J, Hafner M, Mihailovic A, Lim C, Holoch D, Berninger P, Zavolan M, Tuschl T. miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nat Methods 2009;6(2):139-41. (url)

  • Petit RJ, Excoffier L. Gene flow and species delimitation. Trends Ecol Evol 2009. (url)

  • Pick H, Etter S, Baud O, Schmauder R, Bordoli L, Schwede T, Vogel H. Dual activities of odorants on olfactory and nuclear hormone receptors. J Biol Chem 2009;284(44):30547-55. (url)

  • Pinto SB, Lombardo F, Koutsos AC, Waterhouse RM, McKay K, An C, Ramakrishnan C, Kafatos FC, Michel K. Discovery of Plasmodium modulators by genome-wide analysis of circulating hemocytes in Anopheles gambiae. Proc Natl Acad Sci U S A 2009;106(50):21270-5. (url)

  • Poloni ES, Naciri Y, Bucho R, Niba R, Kervaire B, Excoffier L, Langaney A, Sanchez-Mazas A. Genetic evidence for complexity in ethnic differentiation and history in East Africa. Ann Hum Genet 2009;73(Pt 6):582-600. (url)

  • Popovici V, Goldstein DR, Antonov J, Jaggi R, Delorenzi M, Wirapati P. Selecting control genes for RT-QPCR using public microarray data. BMC Bioinformatics 2009;10:42. (url)

  • Poy MN, Hausser J, Trajkovski M, Braun M, Collins S, Rorsman P, Zavolan M, Stoffel M. miR-375 maintains normal pancreatic alpha- and beta-cell mass. Proc Natl Acad Sci U S A 2009;106(14):5813-8. (url)

  • Pradervand S, Weber J, Thomas J, Bueno M, Wirapati P, Lefort K, Dotto GP, Harshman K. Impact of normalization on miRNA microarray expression profiling. RNA 2009;15(3):493-501. (url)

  • Praz V, Bucher P. CleanEx: new data extraction and merging tools based on MeSH term annotation. Nucleic Acids Res 2009;37(Database issue):D880-4. (url)

  • Priego-Capote F, Scherl A, Mu Ller M, Waridel P, Lisacek F, Sanchez JC. Glycation isotopic labelling (GIL) with 13C-reducing sugars for quantitative analysis of glycated proteins in human plasma. Mol Cell Proteomics 2009. (url)

  • Prior JO, Montemurro M, Orcurto MV, Michielin O, Luthi F, Benhattar J, Guillou L, Elsig V, Stupp R, Delaloye AB, Leyvraz S. Early prediction of response to sunitinib after imatinib failure by 18F-fluorodeoxyglucose positron emission tomography in patients with gastrointestinal stromal tumor. J Clin Oncol 2009;27(3):439-45. (url)

  • Proux E, Studer RA, Moretti S, Robinson-Rechavi M. Selectome: a database of positive selection. Nucleic Acids Res 2009;37(Database issue):D404-7. (url)

  • Quandt A, Masselot A, Hernandez P, Hernandez C, Maffioletti S, Appel RD, Lisacek F. SwissPIT: An workflow-based platform for analyzing tandem-MS spectra using the Grid. Proteomics 2009;9(10):2648-55. (url)

  • Ramaswamy R, Gonzalez-Segredo N, Sbalzarini IF. A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks. J Chem Phys 2009;130(24):244104. (url)

  • Robin X, Turck N, Hainard A, Lisacek F, Sanchez JC, Muller M. Bioinformatics for protein biomarker panel classification: what is needed to bring biomarker panels into in vitro diagnostics? Expert Rev Proteomics 2009;6(6):675-89. (url)

  • Rohrig UF, Grosdidier A, Zoete V, Michielin O. Docking to heme proteins. J Comput Chem 2009. (url)

  • Roulin A, Wink M, Salamin N. Selection on a eumelanic ornament is stronger in the tropics than in temperate zones in the worldwide-distributed barn owl. J Evol Biol 2009;22(2):345-54. (url)

  • Schiess R, Mueller LN, Schmidt A, Mueller M, Wollscheid B, Aebersold R. Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Mol Cell Proteomics 2009;8(4):624-38. (url)

  • Schneider A, Souvorov A, Sabath N, Landan G, and GG, D G. Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biology and Evolution 2009;2009:114. (url)

  • Schneider A, Cannarozzi GM. Support patterns from different outgroups provide a strong phylogenetic signal. Mol Biol Evol 2009;26(6):1259-72. (url)

  • Schneider M, Lane L, Boutet E, Lieberherr D, Tognolli M, Bougueleret L, Bairoch A. The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program. J Proteomics 2009;72(3):567-73. (url)

  • Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmstrom J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE, Aebersold R, von Mering C, Hengartner MO. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol 2009;7(3):e48. (url)

  • Schupbach T, Zoete V, Tsakam-Sotche B, Michielin O. Fourier transform convolution integrals applied to generalized Born molecular volume. J Comput Chem 2009. (url)

  • Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Jr., Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Jr., Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure 2009;17(2):151-9. (url)

  • Severin J, Waterhouse AM, Kawaji H, Lassmann T, van Nimwegen E, Balwierz PJ, de Hoon MJ, Hume DA, Carninci P, Hayashizaki Y, Suzuki H, Daub CO, Forrest AR. FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biology 2009;10(4):R39. (url)

  • Sevin M, Kutalik Z, Bergmann S, Vercelletto M, Renou P, Lamy E, Vingerhoets F, Di-Virgilio G, Boisseau P, Bezieau S, Pasquier L, Rival JM, Beckmann J, Damier P, Jacquemont S. The penetrance of marked cognitive impairment in older male carriers of the FMR1 Gene Premutation. J Med Genet 2009. (url)

  • Steiner C, Vees H, Zaidi H, Wissmeyer M, Berrebi O, Kossovsky MP, Khan HG, Miralbell R, Ratib O, Buchegger F. Three-phase 18F-fluorocholine PET/CT in the evaluation of prostate cancer recurrence. Nuklearmedizin 2009;48(1):1-9; quiz N2-3. (url)

  • Stelling J, Kholodenko BN. Signaling cascades as cellular devices for spatial computations. J Math Biol 2009;58(1-2):35-55. (url)

  • Studer RA, Robinson-Rechavi M. How confident can we be that orthologs are similar, but paralogs differ? Trends Genet 2009;25(5):210-6. (url)

  • Studer RA, Robinson-Rechavi M. Evidence for an episodic model of protein sequence evolution. Biochem Soc Trans 2009;37(Pt 4):783-6. (url)

  • Sungkaew S, Stapleton CM, Salamin N, Hodkinson TR. Non-monophyly of the woody bamboos (Bambuseae; Poaceae): a multi-gene region phylogenetic analysis of Bambusoideae s.s. J Plant Res 2009;122(1):95-108. (url)

  • Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Bjorkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engstrom PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hornquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schonbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegner J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 2009;41(5):553-62. (url)

  • Swenson KM, Lin Y, Rajan V, Moret BM. Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results. J Comput Biol 2009. (url)

  • Swenson KM, Moret BM. Inversion-based genomic signatures. BMC Bioinformatics 2009;10 Suppl 1:S7. (url)

  • Swenson KM, To Y, Tang J, Moret BM. Maximum independent sets of commuting and noninterfering inversions. BMC Bioinformatics 2009;10 Suppl 1:S6. (url)

  • Szklarczyk O, Zuberek J, Antosiewicz JM. Poisson-Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E. Biophys Chem 2009;140(1-3):16-23. (url)

  • Taddei A, Van Houwe G, Nagai S, Erb I, van Nimwegen E, Gasser SM. The functional importance of telomere clustering: Global changes in gene expression result from SIR factor dispersion. Genome Res 2009;19(4):611-25. (url)

  • Tapparel C, Junier T, Gerlach D, Van-Belle S, Turin L, Cordey S, Muhlemann K, Regamey N, Aubert JD, Soccal PM, Eigenmann P, Zdobnov E, Kaiser L. New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses. Emerg Infect Dis 2009;15(5):719-26. (url)

  • Terzer M, Maynard ND, Covert MW, Stelling J. Genome-scale metabolic networks. Wiley Interdisciplinary Reviews 2009;Systems Biology and Medicine. (url)

  • Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M. A tunable synthetic mammalian oscillator. Nature 2009;457(7227):309-12. (url)

  • Turck N, Vutskits L, Sanchez-Pena P, Robin X, Hainard A, Gex-Fabry M, Fouda C, Bassem H, Mueller M, Lisacek F, Puybasset L, Sanchez JC. A multiparameter panel method for outcome prediction following aneurysmal subarachnoid hemorrhage. Intensive Care Med 2009;36(1):107-15. (url)

  • Ulrich RG, Heckel G, Pelz HJ, Wieler LH, Nordhoff M, Dobler G, Freise J, Matuschka FR, Jacob J, Schmidt-Chanasit J, Gerstengarbe FW, Jakel T, Suss J, Ehlers B, Nitsche A, Kallies R, Johne R, Gunther S, Henning K, Grunow R, Wenk M, Maul LC, Hunfeld KP, Wolfel R, Schares G, Scholz HC, Brockmann SO, Pfeffer M, Essbauer SS. [Rodents and rodent associated disease vectors: the network of "rodent carrying pathogens" introduces itself]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2009;52(3):352-69. (url)

  • Van Der Loo B, Naef F, Spring S, Rousson V, Amann-Vesti B, Koppensteiner R. Lack of major gender-related differences in patients undergoing elective endovascular or surgical repair of abdominal aortic aneurysm. Int Angiol 2009;28(1):50-5. (url)

  • Vees H, Senthamizhchelvan S, Miralbell R, Weber DC, Ratib O, Zaidi H. Assessment of various strategies for 18F-FET PET-guided delineation of target volumes in high-grade glioma patients. Eur J Nucl Med Mol Imaging 2009;36(2):182-93. (url)

  • Vonlanthen P, Roy D, Hudson AG, Largiader CR, Bittner D, Seehausen O. Divergence along a steep ecological gradient in lake whitefish (Coregonus sp.). J Evol Biol 2009;22(3):498-514. (url)

  • Vuilleumier S, Chistoserdova L, Lee MC, Bringel F, Lajus A, Zhou Y, Gourion B, Barbe V, Chang J, Cruveiller S, Dossat C, Gillett W, Gruffaz C, Haugen E, Hourcade E, Levy R, Mangenot S, Muller E, Nadalig T, Pagni M, Penny C, Peyraud R, Robinson DG, Roche D, Rouy Z, Saenampechek C, Salvignol G, Vallenet D, Wu Z, Marx CJ, Vorholt JA, Olson MV, Kaul R, Weissenbach J, Medigue C, Lidstrom ME. Methylobacterium genome sequences: a reference blueprint to investigate microbial metabolism of C1 compounds from natural and industrial sources. PLoS One 2009;4(5):e5584. (url)

  • Wagner A. Transposable elements as genomic diseases. Mol Biosyst 2009;5(1):32-5. (url)

  • Wagner A. Evolutionary constraints permeate large metabolic networks. BMC Evol Biol 2009;9:231. (url)

  • Wagner A. Networks in molecular evolution. Encyclopedia of Complexity and System Science 2009. (url)

  • Walther JH, Sbalzarini IF. Large-scale parallel discrete element simulations of granular flow. Engineering Computations 2009;26(6):688-697. (url)

  • Wang N, Liu Y, Zhang Z-W. Characterization of nine microsatellite loci for a globally vulnerable species, Reeves’s Pheasant (Syrmaticus reevesii) Conservation Genetics 2009;10(5):1511-1514. (url)

  • Wegmann D, Leuenberger C, Excoffier L. Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood. Genetics 2009;182(4):1207-18. (url)

  • Wurm Y, Uva P, Ricci F, Wang J, Jemielity S, Iseli C, Falquet L, Keller L. Fourmidable: a database for ant genomics. BMC Genomics 2009;10:5. (url)

  • Yerly S, Junier T, Gayet-Ageron A, Amari EB, von Wyl V, Gunthard HF, Hirschel B, Zdobnov E, Kaiser L. The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection. AIDS 2009;23(11):1415-23. (url)

  • Zambrano HA, Walther JH, Koumoutsakos P, Sbalzarini IF. Thermophoretic motion of water nanodroplets confined inside carbon nanotubes. Nano Lett 2009;9(1):66-71. (url)

  • Zoete V, Grosdidier A, Michielin O. Docking, virtual high throughput screening and in silico fragment-based drug design. J Cell Mol Med 2009;13(2):238-48. (url)

Books

  • Baillie Gerritsen V., Tales from a Small World, SIB, September 2009.

  • Baillie Gerritsen V, Déthiollaz S. Globine et Poïétine sur la piste de la moelle rouge: Swiss-Prot group, SIB; 2009.

  • Appel RD, Feytmans E. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009. (url)

  • Sbalzarini IF. Analysis, Modeling & Simulation of Diffusion Processes in Cell Biology: VDM Publishing; 2009.

Book Chapters

  • Bairoch A, Lane L. UniProtKB/Swiss-Prot Manual and Automated Annotation of Complete Proteomes: The Dictyostelium discoideum Case Study. Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Bergmann S. From Modules to Models: Advanced Analysis Methods for Large Scale Data Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Bittar GJ, Sonderegger BP. An Introduction to Phylogenetics and Its Molecular Aspects Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Bucher P. Methods for Discovery and Characterization of DNA Sequence Motifs Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Chopard B. Cellular Automata Modeling of Physical Systems. Meyers RA, editor. Springer Encyclopedia of Complex systems: Springer; 2009. p. 865-892. (url)

  • Gil M, Gonnet GH. Phylogenetic Tree Building Methods Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Hoogland C, Mostaguir K, Appel RD. Creating 2-DE Databases for the World Wide Web. Sheehan D, editor. Methods in Molecular Biology - Two Dimensional Electrophoresis Protocols: Humana Press; 2009. p. 533-539.

  • Palagi PM, Lisacek F. Analytical bioinformatics for proteomics. Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Palagi PM, Lisacek F, Appel RD. Database interrogation algorithms for identification of proteins in proteomic separations. Press H, editor. Two-Dimensional Electrophoresis Protocols; 2009. p. 515-531. (url)

  • Pattengale ND, Alipour M, Bininda-Edmonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Batzoglou S, editor. Research in Computational Molecular Biology: Springer Verlag; 2009. p. 184-200.

  • Quandt A, Maffioletti S, Pautasso C, Stockinger H, Lisacek F, Kunzst P. High-throughput Data Analysis of Proteomic Mass Spectra on the SwissBioGrid. Cannataro M, editor. Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare: IGI Publishing: Hershey; 2009. (url)

  • Robinson-Rechavi M. Bioinformatics for Evolutionary Developmental Biology Appel R, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific Publishing; 2009.

  • Saeed F, Khokhar A, Zagordi O, Beerenwinkel N. Multiple Sequence Alignment System for Pyrosequencing Reads. Bioinformatics and Computational Biology: Springer Berlin / Heidelberg; 2009. p. 362-375. (url)

  • Sbalzarini IF. Spatiotemporal Modeling and Simulation in Biology Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Schwede T, Peitsch M. Protein Structure Modeling and Docking at the Swiss Institute of Bioinformatics. Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Studer RA, Robinson-Rechavi M. Large-Scale Analyses of Positive Selection Using Codon Models. Evolutionary Biology: Springer Berlin Heidelberg; 2009. p. 217-235. (url)

  • Swenson KM, Rajan V, Lin Y, Moret BME. Sorting signed permutations by inversions in O(nlogn) time. Batzoglou S, editor. Research in Computational Molecular Biology: Springer Verlag; 2009. p. 386-399.

  • von Mering C. Protein-Protein Interaction Networks: Assembly and Analysis Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Waterhouse RM, Kriventseva EV, Zdobnov EM. Comparative Genome Analysis Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Wirapati P, Goldstein DR, Delorenzi M. Integrated Analysis of Gene Expression Profiling Studies - Examples in Breast Cancer Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Zagordi O, Geyrhofer L, Roth V, Beerenwinkel N. Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction. Research in Computational Molecular Biology: Springer Berlin / Heidelberg; 2009. p. 271-284. (url)

  • Zavolan M, Jaskiewicz L. Computational Biology of Small Regulatory RNAs Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

  • Zoete V, Cuendet M, Röhrig UF, Grosdidier A, Michielin O. Molecular Modeling of Proteins: From Simulations to Drug Design Applications Appel RD, Feytmans E, editors. Bioinformatics: A Swiss Perspective. Singapore: World Scientific; 2009.

Conference proceedings

  • Cardinale J, Rauch A, Barral Y, Székely G, Sbalzarini IF. Bayesian image analysis with on-line confidence estimates and its application to microtubule tracking. In Proc. IEEE Intl. Symposium Biomedical Imaging (ISBI); 2009 June; Boston, USA; 2009. p. 1091-1094. (url)

  • Hafner M, Koeppl H, Wagner A. Evolution of feedback loops in oscillatory systems. FOSBE 2009 August 9-12, 2009; Denver, CO, USA. (url)

  • Helmuth JA, Sbalzarini IF. Deconvolving Active Contours for Fluorescence Microscopy Images. Sc LNC, editor. ISVC December 2009; Las Vegas, USA. p. 544-553. (url)

  • Hirabayashi M, Ohta M, Rufenacht DA, Chopard B. Computational studies on characteristic uid behavior in the stented cerebral aneurysm. APS meeting March 16-20, 2009; Pittsburg, Pennsylvania, USA. (url)

  • Hoogland C, Ehrler F, Palagi PM, Sanchez JC, Lisacek F, Ruch P. Turning a set of binary classifiers into a single ranker to help digestion of proteomics literature. 3rd EuPA Congress; 2009; Stockholm, Sweden; 2009. (url)

  • Marchisio MA, J. S. Synthetic gene network computational design. ISCAS 2009; 2009 May 24-27, 2009; Taipei, Taiwan; 2009. p. 309-312. (url)

  • Müller CL, Baumgartner B, Sbalzarini IF. Particle swarm CMA evolution strategy for the optimization of multi-funnel landscapes. In Proc. IEEE Congress on Evolutionary Computation (CEC); 2009 May Trondheim, Norway; 2009. p. 2685-2692. (url)

  • Müller CL, Baumgartner B, Ofenbeck G, Schrader B, Sbalzarini IF. pCMALib: a parallel FORTRAN 90 library for the evolution strategy with covariance matrix adaptation. ACM Genetic and Evolutionary Computation Conference (GECCO’09); 2009 July 2009; Montreal, Canada; 2009. (url)

  • Müller CL, Sbalzarini IF. A Tunable Real-World Multi-Funnel Benchmark. Problem For Evolutionary Optimization. And Why Parallel Island Models Might Remedy the Failure of CMA-ES on It. ICEC 2009 October 5-7, 2009; Madeira, Portugal (url)

  • Nikitin F, Mauron Y, Tuloup M, Palagi PM, Masselot A, Mueller M, Lisacek F. JPL - A JAVA framework for proteomics software development. In: 3rd EuPA Congress. Stockholm, Sweden; 2009. (url)

  • Ouared R, Chopard B, Rufenacht D. Thrombosis Engi-neering in Intracranial Aneurysms using a Lattice Boltzmann Numerical Method. Medical Physics and Biomedical Engineering World Congress WC2009 September 7-12, 2009; Munich, Germany. (url)

  • Palagi PM, Hernandez P, Quandt A, Maffioletti S, Pautasso C, Masselot A, Appel RD, Lisacek F. Grid-based analysis of high-throughput ms/ms data. 3rd EuPA Congress; 2009; Stockholm, Sweden; 2009. (url)

  • Pattengale ND, Alipour M, Bininda-Edmonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Recomb 2009; 2009 May 18-21 Tucson, US: Springer-Verlag; 2009. (url)

  • Philippi PC, Chopard B. Focus on Recent Advances in Particle Methods for Fluid Dynamics. Mechanics JoS, editor. DSFD 2008; 2008; Florianópolis, Brazil; 2008. (url)

  • Swenson KM, Moret BM. Inversion-based genomic signatures. APBC 2009; 2009 January 13-16; Beijing, China; 2009. (url)

  • Swenson KM, Rajan V, Lin Y, Moret BME. Sorting signed permutations by inversions in O(nlogn) time. Recomb 2009 May 18-21; Tucson, USA. (url)

  • Swenson KM, To Y, Tang J, Moret BM. Maximum independent sets of commuting and noninterfering inversions. APBC 2009 January 13-16; Beijing, China. (url)

  • Terzer M, Stelling J. Parallel Extreme Ray and Pathway Computation. PPAM 2009 September 13-16, 2009; Wroclaw, Poland. (url)

  • Uhr M, Kaltenbach HM, Conradi C, Stelling J. Analysis of Degenerate Chemical Reaction Networks. POSTA 09 September 2-4, 2009; Valencia, Spain. (url)

  • Zhang X, Moret B. Improving inference of transcriptional regulatory networks based on network evolutionary models. Proc. 9th Workshop on Algs. in Bioinformatics WABI'09 September 12-13, 2009; Philadelphia, USA: Springer Verlag. p. 412-425. (url)

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