Scientific publications
Research - Scientific Publications
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Publications by SIB Members for the year 2014. For older publications, please click on the date links below on the left.  


Peer-reviewed journal articles


  • Adrion JR, Kousathanas A, Pascual M, Burrack HJ, Haddad NM, Bergland AO, Machado H, Sackton TB, Schlenke TA, Watada M, Wegmann D, Singh ND. Drosophila suzukii: The Genetic Footprint of a Recent, Worldwide Invasion. Mol Biol Evol 2014. (url)

  • Aguilar-Bultet L, Calderon-Copete SP, Frey J, Falquet L. Draft Genome Sequence of the Virulent Avibacterium paragallinarum Serotype A Strain JF4211 and Identification of Two Toxins. Genome Announc 2013;1(4). (url)

  • Alcala N, Goudet J, Vuilleumier S. On the transition of genetic differentiation from isolation to panmixia: what we can learn from GST and D. Theor Popul Biol 2014;93:75-84. (url)

  • Alfaiz AA, Micale L, Mandriani B, Augello B, Pellico MT, Chrast J, Xenarios I, Zelante L, Merla G, Reymond A. TBC1D7 mutations are associated with intellectual disability, macrocrania, patellar dislocation, and celiac disease. Hum Mutat 2014;35(4):447-51. (url)

  • Ali HS, Drewes S, Sadowska ET, Mikowska M, Groschup MH, Heckel G, Koteja P, Ulrich RG. First molecular evidence for Puumala hantavirus in Poland. Viruses 2014;6(1):340-53. (url)

  • Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Paillerets BB, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurevic N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilas J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdic G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potocnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Soom AV, Vidakovic M, Widschwendter M. Relationship between genome and epigenome - challenges and requirements for future research. BMC Genomics 2014;15:487. (url)

  • Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jorgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Muller F, Forrest AR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature 2014;507(7493):455-61. (url)

  • Angelard C, Tanner CJ, Fontanillas P, Niculita-Hirzel H, Masclaux F, Sanders IR. Rapid genotypic change and plasticity in arbuscular mycorrhizal fungi is caused by a host shift and enhanced by segregation. ISME J 2014;8(2):284-94. (url)

  • Antoniazza S, Kanitz R, Neuenschwander S, Burri R, Gaigher A, Roulin A, Goudet J. Natural selection in a postglacial range expansion: the case of the colour cline in the European barn owl. Mol Ecol 2014;23(22):5508-23. (url)

  • Anzai H, Chopard B, Ohta M. Combinational Optimization of Strut Placement for Intracranial Stent Using a Realistic Aneurysm. Journal of Flow Control, Measurement & Visualization 2014;2:67-77. (url)

  • Arner E, Forrest AR, Ehrlund A, Mejhert N, Itoh M, Kawaji H, Lassmann T, Laurencikiene J, Ryden M, Arner P. Ceruloplasmin is a novel adipokine which is overexpressed in adipose tissue of obese subjects and in obesity-associated cancer cells. PLoS One 2014;9(3):e80274. (url)

  • Bachler M, Menshykau D, De Geyter C, Iber D. Species-specific differences in follicular antral sizes result from diffusion-based limitations on the thickness of the granulosa cell layer. Mol Hum Reprod 2014;20(3):208-21. (url)

  • Bachmann NL, Fraser TA, Bertelli C, Jelocnik M, Gillett A, Funnell O, Flanagan C, Myers GS, Timms P, Polkinghorne A. Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum. BMC Genomics 2014;15:667. (url)

  • Balwierz PJ, Pachkov M, Arnold P, Gruber AJ, Zavolan M, van Nimwegen E. ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs. Genome Res 2014;24(5):869-84. (url)

  • Bank C, Hietpas RT, Wong A, Bolon DN, Jensen JD. A Bayesian MCMC Approach To Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments. Genetics 2014. (url)

  • Bank C, Hietpas RT, Jensen JD, Bolon DN. A systematic survey of an intragenic epistatic landscape. Mol Biol Evol 2014. (url)

  • Baresic M, Salatino S, Kupr B, van Nimwegen E, Handschin C. Transcriptional Network Analysis in Muscle Reveals AP-1 as a Partner of PGC-1alpha in the Regulation of the Hypoxic Gene Program. Mol Cell Biol 2014;34(16):2996-3012. (url)

  • Barras D, Chevalier N, Zoete V, Dempsey R, Lapouge K, Olayioye MA, Michielin O, Widmann C. A WXW motif is required for the anticancer activity of the TAT-RasGAP317-326 peptide. J Biol Chem 2014;289(34):23701-11. (url)

  • Barreto-Hernandez E, Falquet L, Reguero MT, Mantilla JR, Valenzuela EM, Gonzalez E, Cepeda A, Escalante A. Draft Genome Sequences of Multidrug-Resistant Acinetobacter sp. Strains from Colombian Hospitals. Genome Announc 2013;1(6). (url)

  • Bartha I, McLaren PJ, Ciuffi A, Fellay J, Telenti A. GuavaH: a compendium of host genomic data in HIV biology and disease. Retrovirology 2014;11:6. (url)

  • Barve A, Hosseini SR, Martin OC, Wagner A. Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms. BMC Syst Biol 2014;8:48. (url)

  • Bashirova AA, Martin-Gayo E, Jones DC, Qi Y, Apps R, Gao X, Burke PS, Taylor CJ, Rogich J, Wolinsky S, Bream JH, Duggal P, Hussain S, Martinson J, Weintrob A, Kirk GD, Fellay J, Buchbinder SP, Goedert JJ, Deeks SG, Pereyra F, Trowsdale J, Lichterfeld M, Telenti A, Walker BD, Allen RL, Carrington M, Yu XG. LILRB2 interaction with HLA class I correlates with control of HIV-1 infection. PLoS Genet 2014;10(3):e1004196. (url)

  • Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F. Cancer evolution: mathematical models and computational inference. Syst Biol 2014. (url)

  • Beerenwinkel N, Beretta S, Bonizzoni P, Dondi R, Pirola Y. Covering Pairs in Directed Acyclic Graphs. Computer Science 2014(Data Structures and Algorithms). (url)

  • Benedetti F, Dorier J, Burnier Y, Stasiak A. Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes. Nucleic Acids Res 2014;42(5):2848-55. (url)

  • Benyamin B, Esko T, Ried JS, Radhakrishnan A, Vermeulen SH, Traglia M, Gogele M, Anderson D, Broer L, Podmore C, Luan J, Kutalik Z, Sanna S, van der Meer P, Tanaka T, Wang F, Westra HJ, Franke L, Mihailov E, Milani L, Haldin J, Winkelmann J, Meitinger T, Thiery J, Peters A, Waldenberger M, Rendon A, Jolley J, Sambrook J, Kiemeney LA, Sweep FC, Sala CF, Schwienbacher C, Pichler I, Hui J, Demirkan A, Isaacs A, Amin N, Steri M, Waeber G, Verweij N, Powell JE, Nyholt DR, Heath AC, Madden PA, Visscher PM, Wright MJ, Montgomery GW, Martin NG, Hernandez D, Bandinelli S, van der Harst P, Uda M, Vollenweider P, Scott RA, Langenberg C, Wareham NJ, InterAct C, van Duijn C, Beilby J, Pramstaller PP, Hicks AA, Ouwehand WH, Oexle K, Gieger C, Metspalu A, Camaschella C, Toniolo D, Swinkels DW, Whitfield JB. Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis. Nat Commun 2014;5:4926. (url)

  • Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M. Reconciliation of metabolites and biochemical reactions for metabolic networks. Brief Bioinform 2014;15(1):123-35. (url)

  • Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol 2014;31(5):1077-88. (url)

  • Beysard M, Heckel G. Structure and dynamics of hybrid zones at different stages of speciation in the common vole (Microtus arvalis). Mol Ecol 2014;23(3):673-87. (url)

  • Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, Bertoni M, Bordoli L, Schwede T. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 2014;42(Web Server issue):W252-8. (url)

  • Bieler J, Cannavo R, Gustafson K, Gobet C, Gatfield D, Naef F. Robust synchronization of coupled circadian and cell cycle oscillators in single mammalian cells. Mol Syst Biol 2014;10(7):739. (url)

  • Blaser O, Neuenschwander S, Perrin N. Sex-chromosome turnovers: the hot-potato model. Am Nat 2014;183(1):140-6. (url)

  • Bonafe L, Liang J, Gorna MW, Zhang Q, Ha-Vinh R, Campos-Xavier AB, Unger S, Beckmann JS, Le Bechec A, Stevenson B, Giedion A, Liu X, Superti-Furga G, Wang W, Spahr A, Superti-Furga A. MMP13 mutations are the cause of recessive metaphyseal dysplasia, Spahr type. Am J Med Genet A 2014;164A(5):1175-9. (url)

  • Bonhoure N, Bounova G, Bernasconi D, Praz V, Lammers F, Canella D, Willis IM, Herr W, Hernandez N, Delorenzi M. Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization. Genome Res 2014;24(7):1157-68. (url)

  • Borgdorff J, Ben Belgacem M, Bona-Casas C, Fazendeiro L, Groen D, Hoenen O, Mizeranschi A, Suter JL, Coster D, Coveney PV, Dubitzky W, Hoekstra AG, Strand P, Chopard B. Performance of distributed multiscale simulations. Philos Trans A Math Phys Eng Sci 2014;372(2021). (url)

  • Bryois J, Buil A, Evans DM, Kemp JP, Montgomery SB, Conrad DF, Ho KM, Ring S, Hurles M, Deloukas P, Davey Smith G, Dermitzakis ET. Cis and trans effects of human genomic variants on gene expression. PLoS Genet 2014;10(7):e1004461. (url)

  • Cai H, Kumar N, Ai N, Gupta S, Rath P, Baudis M. Progenetix: 12 years of oncogenomic data curation. Nucleic Acids Res 2014;42(Database issue):D1055-62. (url)

  • Cai H, Kumar N, Bagheri HC, von Mering C, Robinson MD, Baudis M. Chromothripsis-like patterns are recurring but heterogeneously distributed features in a survey of 22,347 cancer genome screens. BMC Genomics 2014;15:82. (url)

  • Cannarozzi G, Plaza-Wuthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blosch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z. Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 2014;15(1):581. (url)

  • Cerase A, Smeets D, Tang YA, Gdula M, Kraus F, Spivakov M, Moindrot B, Leleu M, Tattermusch A, Demmerle J, Nesterova TB, Green C, Otte AP, Schermelleh L, Brockdorff N. Spatial separation of Xist RNA and polycomb proteins revealed by superresolution microscopy. Proc Natl Acad Sci U S A 2014;111(6):2235-40. (url)

  • Charpilloz C, Veuthey AL, Chopard B, Falcone JL. Motifs tree: a new method for predicting post-translational modifications. Bioinformatics 2014;30(14):1974-82. (url)

  • Chopard B, Borgdorff J, Hoekstra A. A framework for multi-scale modelling. Phil. Trans. R. Soc. A, 2014;372: 20130376. (url)

  • Choudhary V, Darwiche R, Gfeller D, Zoete V, Michielin O, Schneiter R. The caveolin-binding motif of the pathogen-related yeast protein Pry1, a member of the CAP protein superfamily, is required for in vivo export of cholesteryl acetate. J Lipid Res 2014;55(5):883-94. (url)

  • Christin PA, Spriggs E, Osborne CP, Stromberg CA, Salamin N, Edwards EJ. Molecular dating, evolutionary rates, and the age of the grasses. Syst Biol 2014;63(2):153-65. (url)

  • Cisse OH, Pagni M, Hauser PM. Comparative genomics suggests that the human pathogenic fungus Pneumocystis jirovecii acquired obligate biotrophy through gene loss. Genome Biol Evol 2014;6(8):1938-48. (url)

  • Claes F, Kuznetsov D, Liechti R, Von Dobschuetz S, Truong BD, Gleizes A, Conversa D, Colonna A, Demaio E, Ramazzotto S, Larfaoui F, Pinto J, Le Mercier P, Xenarios I, Dauphin G. The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses. Database (Oxford) 2014;2014:bau008. (url)

  • Constantinescu S, Hecht K, Sobotzki N, Erzinger MM, Bovet C, Shay JW, Wollscheid B, Sturla SJ, Marra G, Beerenwinkel N. Transcriptomic Responses of Cancerous and Noncancerous Human Colon Cells to Sulforaphane and Selenium. Chem Res Toxicol 2014. (url)

  • Cornelis G, Vernochet C, Malicorne S, Souquere S, Tzika AC, Goodman SM, Catzeflis F, Robinson TJ, Milinkovitch MC, Pierron G, Heidmann O, Dupressoir A, Heidmann T. Retroviral envelope syncytin capture in an ancestrally diverged mammalian clade for placentation in the primitive Afrotherian tenrecs. Proc Natl Acad Sci U S A 2014;111(41):E4332-41. (url)

  • Cortez D, Marin R, Toledo-Flores D, Froidevaux L, Liechti A, Waters PD, Grutzner F, Kaessmann H. Origins and functional evolution of Y chromosomes across mammals. Nature 2014;508(7497):488-93. (url)

  • Crouse J, Bedenikovic G, Wiesel M, Ibberson M, Xenarios I, Von Laer D, Kalinke U, Vivier E, Jonjic S, Oxenius A. Type I Interferons Protect T Cells against NK Cell Attack Mediated by the Activating Receptor NCR1. Immunity 2014;40(6):961-73. (url)

  • Cucchi T, Barnett R, Martinkova N, Renaud S, Renvoise E, Evin A, Sheridan A, Mainland I, Wickham-Jones C, Tougard C, Quere JP, Pascal M, Heckel G, O'Higgins P, Searle JB, Dobney KM. The Changing Pace of Insular Life: 5000 Years of Microevolution in the Orkney Vole (Microtus Arvalis Orcadensis). Evolution 2014. (url)

  • da Silveira Dos Santos AX, Riezman I, Aguilera-Romero MA, David F, Piccolis M, Loewith R, Schaad O, Riezman H. Systematic lipidomic analysis of yeast protein kinase and phosphatase mutants reveals novel insights into regulation of lipid homeostasis. Mol Biol Cell 2014;25(20):3234-46. (url)

  • Daubner GM, Brummer A, Tocchini C, Gerhardy S, Ciosk R, Zavolan M, Allain FH. Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Nucleic Acids Res 2014;42(12):8092-105. (url)

  • David FP, Delafontaine J, Carat S, Ross FJ, Lefebvre G, Jarosz Y, Sinclair L, Noordermeer D, Rougemont J, Leleu M. HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis. PLoS One 2014;9(1):e85879. (url)

  • Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution 2014;68(6):1775-91. (url)

  • Diepenbruck M, Waldmeier L, Ivanek R, Berninger P, Arnold P, van Nimwegen E, Christofori G. Tead2 expression levels control the subcellular distribution of Yap and Taz, zyxin expression and epithelial-mesenchymal transition. J Cell Sci 2014;127(Pt 7):1523-36. (url)

  • Dill MT, Makowska Z, Trincucci G, Gruber AJ, Vogt JE, Filipowicz M, Calabrese D, Krol I, Lau DT, Terracciano L, van Nimwegen E, Roth V, Heim MH. Pegylated IFN-alpha regulates hepatic gene expression through transient Jak/STAT activation. J Clin Invest 2014;124(4):1568-81. (url)

  • Dimopoulos S, Mayer CE, Rudolf F, Stelling J. Accurate cell segmentation in microscopy images using membrane patterns. Bioinformatics 2014. (url)

  • Drogemuller M, Jagannathan V, Becker D, Drogemuller C, Schelling C, Plassais J, Kaerle C, Dufaure de Citres C, Thomas A, Muller EJ, Welle MM, Roosje P, Leeb T. A mutation in the FAM83G gene in dogs with hereditary footpad hyperkeratosis (HFH). PLoS Genet 2014;10(5):e1004370. (url)

  • Dumcke S, Brauer J, Anchang B, Spang R, Beerenwinkel N, Tresch A. Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. Bioinformatics 2014;30(3):414-9. (url)

  • Dummer R, Goldinger SM, Turtschi CP, Eggmann NB, Michielin O, Mitchell L, Veronese L, Hilfiker PR, Felderer L, Rinderknecht JD. Vemurafenib in patients with BRAF(V600) mutation-positive melanoma with symptomatic brain metastases: final results of an open-label pilot study. Eur J Cancer 2014;50(3):611-21. (url)

  • Dussex N, Wegmann D, Robertson BC. Postglacial expansion and not human influence best explains the population structure in the endangered kea (Nestor notabilis). Mol Ecol 2014;23(9):2193-209. (url)

  • Engler R, Teplyakov V, Adams JM. An assessment of forest cover trends in South and North Korea, from 1980 to 2010. Environ Manage 2014;53(1):194-201. (url)

  • Erhard F, Haas J, Lieber D, Malterer G, Jaskiewicz L, Zavolan M, Dolken L, Zimmer R. Widespread context dependency of microRNA-mediated regulation. Genome Res 2014;24(6):906-19. (url)

  • Ettema TJ, Lindas AC, Hjort K, Poplawski AB, Kaessmann H, Grogan DW, Kelman Z, Andersson AF, Pelve EA, Lundgren M, Svard SG. Rolf Bernander (1956-2014): pioneer of the archaeal cell cycle. Mol Microbiol 2014;92(5):903-9. (url)

  • Ewing GB, Jensen JD. Distinguishing neutral from deleterious mutations in growing populations. Front Genet 2014;5:7. (url)

  • Falquet L, Calderon-Copete SP, Frey J. Draft Genome Sequence of the Virulent Clostridium chauvoei Reference Strain JF4335. Genome Announc 2013;1(4). (url)

  • Falquet L, Rossier G, Yael Maoz T. Report on the ALLBIO minisymposium and workshop: "Next Generation Sequencing (NGS) methods for identification of mutations and large structural variants”. EMBnet journal 2014;20. (url)

  • Feldberg K, Schneider H, Stadler T, Schafer-Verwimp A, Schmidt AR, Heinrichs J. Epiphytic leafy liverworts diversified in angiosperm-dominated forests. Sci Rep 2014;4:5974. (url)

  • Famiglietti ML, Estreicher A, Gos A, Bolleman J, Gehant S, Breuza L, Bridge A, Poux S, Redaschi N, Bougueleret L, Xenarios I. Genetic Variations and Diseases in UniProtKB/Swiss-Prot: The Ins and Outs of Expert Manual Curation. Hum Mutat 2014;35(8):927-35. (url)

  • Feldberg K, Schneider H, Stadler T, Schafer-Verwimp A, Schmidt AR, Heinrichs J. Epiphytic leafy liverworts diversified in angiosperm-dominated forests. Sci Rep 2014;4:5974. (url)

  • Felizzi F, Iber D. Integrin clustering as a result of local membrane deformations and local signaling feedbacks. Physica A 2014;408:198-211. (url)

  • Fengos G, Schmidt A, Martin K, Fluri E, Aebersold R, Iber D, Pertz O. Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome Sci 2014;12:23. (url)

  • Ferrer-Admetlla A, Liang M, Korneliussen T, Nielsen R. On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol Biol Evol 2014;31(5):1275-91. (url)

  • Fodor A, Segura V, Denis M, Neuenschwander S, Fournier-Level A, Chatelet P, Homa FA, Lacombe T, This P, Le Cunff L. Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine. PLoS One 2014;9(11):e110436. (url)

  • Foll M, Gaggiotti OE, Daub JT, Vatsiou A, Excoffier L. Widespread signals of convergent adaptation to high altitude in Asia and america. Am J Hum Genet 2014;95(4):394-407. (url)

  • Foll M, Shim H, Jensen JD. WFABC: a Wright-Fisher ABC-based approach for inferring effective population sizes and selection coefficients from time-sampled data. Mol Ecol Resour 2014. (url)

  • Foll M, Poh YP, Renzette N, Ferrer-Admetlla A, Bank C, Shim H, Malaspinas AS, Ewing G, Liu P, Wegmann D, Caffrey DR, Zeldovich KB, Bolon DN, Wang JP, Kowalik TF, Schiffer CA, Finberg RW, Jensen JD. Influenza virus drug resistance: a time-sampled population genetics perspective. PLoS Genet 2014;10(2):e1004185. (url)

  • Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Lassmann T, Itoh M, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y. A promoter-level mammalian expression atlas. Nature 2014;507(7493):462-70. (url)

  • Franceschini A, Meier R, Casanova A, Kreibich S, Daga N, Andritschke D, Dilling S, Ramo P, Emmenlauer M, Kaufmann A, Conde-Alvarez R, Low SH, Pelkmans L, Helenius A, Hardt WD, Dehio C, von Mering C. Specific inhibition of diverse pathogens in human cells by synthetic microRNA-like oligonucleotides inferred from RNAi screens. Proc Natl Acad Sci U S A 2014;111(12):4548-53. (url)

  • Fried P, Iber D. Dynamic scaling of morphogen gradients on growing domains. Nat Commun 2014;5:5077. (url)

  • Gallo Cassarino T, Bordoli L, Schwede T. Assessment of ligand binding site predictions in CASP10. Proteins 2014;82 Suppl 2:154-63. (url)

  • Ganter M, Kaltenbach HM, Stelling J. Predicting network functions with nested patterns. Nat Commun 2014;5:3006. (url)

  • Genolet R, Leignadier J, Osteras M, Farinelli L, Stevenson BJ, Luescher IF. Duality of the murine CD8 compartment. Proc Natl Acad Sci U S A 2014;111(11):E1007-15. (url)

  • Gfeller D, Grosdidier A, Wirth M, Daina A, Michielin O, Zoete V. SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Res 2014;42(Web Server issue):W32-8. (url)

  • Ghiurcuta CG, Moret BM. Evaluating synteny for improved comparative studies. Bioinformatics 2014;30(12):i9-i18. (url)

  • Giallonardo FD, Topfer A, Rey M, Prabhakaran S, Duport Y, Leemann C, Schmutz S, Campbell NK, Joos B, Lecca MR, Patrignani A, Daumer M, Beisel C, Rusert P, Trkola A, Gunthard HF, Roth V, Beerenwinkel N, Metzner KJ. Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations. Nucleic Acids Res 2014. (url)

  • Giannuzzi G, Migliavacca E, Reymond A. Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures. Genome Res 2014;24(9):1455-68. (url)

  • Gilardi F, Migliavacca E, Naldi A, Baruchet M, Canella D, Le Martelot G, Guex N, Desvergne B. Genome-wide analysis of SREBP1 activity around the clock reveals its combined dependency on nutrient and circadian signals. PLoS Genet 2014;10(3):e1004155. (url)

  • Girma D, Assefa K, Chanyalew S, Cannarozzi G, Kuhlemeier C, Tadele Z. The origins and progress of genomics research on Tef (Eragrostis tef). Plant Biotechnol J 2014;12(5):534-40. (url)

  • Gopalakrishnan S, Montazeri H, Menz S, Beerenwinkel N, Huisinga W. Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data. PLoS Comput Biol 2014;10(11):e1003886. (url)

  • Gotz L, Abrahams JL, Mariethoz J, Rudd PM, Karlsson NG, Packer NH, Campbell MP, Lisacek F. GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination. Bioinformatics 2014;30(21):3131-3. (url)

  • Gray MM, Wegmann D, Haasl RJ, White MA, Gabriel SI, Searle JB, Cuthbert RJ, Ryan PG, Payseur BA. Demographic history of a recent invasion of house mice on the isolated Island of Gough. Mol Ecol 2014;23(8):1923-39. (url)

  • Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Perez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaino JA, Hermjakob H. The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience. Mol Cell Proteomics 2014;13(10):2765-75. (url)

  • Gruber AJ, Grandy WA, Balwierz PJ, Dimitrova YA, Pachkov M, Ciaudo C, Nimwegen E, Zavolan M. Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Res 2014;42(14):9313-26. (url)

  • Gu Y, Liu GH, Plongthongkum N, Benner C, Yi F, Qu J, Suzuki K, Yang J, Zhang W, Li M, Montserrat N, Crespo I, Del Sol A, Esteban CR, Zhang K, Izpisua Belmonte JC. Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. Protein Cell 2014;5(1):59-68. (url)

  • Hadadi N, Cher Soh K, Seijo M, Zisaki A, Guan X, Wenk MR, Hatzimanikatis V. A computational framework for integration of lipidomics data into metabolic pathways. Metab Eng 2014;23:1-8. (url)

  • Haendel MA, Balhoff JP, Bastian FB, Blackburn DC, Blake JA, Bradford Y, Comte A, Dahdul WM, Dececchi TA, Druzinsky RE, Hayamizu TF, Ibrahim N, Lewis SE, Mabee PM, Niknejad A, Robinson-Rechavi M, Sereno PC, Mungall CJ. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. J Biomed Semantics 2014;5:21. (url)

  • Hasegawa Y, Tang D, Takahashi N, Hayashizaki Y, Forrest AR, Consortium F, Suzuki H. CCL2 enhances pluripotency of human induced pluripotent stem cells by activating hypoxia related genes. Sci Rep 2014;4:5228. (url)

  • Hausser J, Zavolan M. Identification and consequences of miRNA-target interactions--beyond repression of gene expression. Nat Rev Genet 2014;15(9):599-612. (url)

  • Hauser PM, Bernard T, Greub G, Jaton K, Pagni M, Hafen GM. Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing. PLoS One 2014;9(3):e90934. (url)

  • Hayden EJ, Bratulic S, Koenig I, Ferrada E, Wagner A. The effects of stabilizing and directional selection on phenotypic and genotypic variation in a population of RNA enzymes. J Mol Evol 2014;78(2):101-8. (url)

  • Hersch M, Lorrain S, de Wit M, Trevisan M, Ljung K, Bergmann S, Fankhauser C. Light intensity modulates the regulatory network of the shade avoidance response in Arabidopsis. Proc Natl Acad Sci U S A 2014;111(17):6515-20. (url)

  • Hirschmann WD, Westendorf H, Mayer A, Cannarozzi G, Cramer P, Jansen RP. Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast. Nucleic Acids Res 2014;42(6):4043-55. (url)

  • Hoekstra A, Chopard B, Coveney P. Multiscale modelling and simulation: a position paper. Philos Trans A Math Phys Eng Sci 2014;372(2021). (url)

  • Hoffmann J, Symul L, Shostak A, Fischer T, Naef F, Brunner M. Non-circadian expression masking clock-driven weak transcription rhythms in U2OS cells. PLoS One 2014;9(7):e102238. (url)

  • Hoggart CJ, Venturini G, Mangino M, Gomez F, Ascari G, Zhao JH, Teumer A, Winkler TW, Tsernikova N, Luan J, Mihailov E, Ehret GB, Zhang W, Lamparter D, Esko T, Mace A, Rueger S, Bochud PY, Barcella M, Dauvilliers Y, Benyamin B, Evans DM, Hayward C, Lopez MF, Franke L, Russo A, Heid IM, Salvi E, Vendantam S, Arking DE, Boerwinkle E, Chambers JC, Fiorito G, Grallert H, Guarrera S, Homuth G, Huffman JE, Porteous D, Generation Scotland C, LifeLines Cohort s, Consortium G, Moradpour D, Iranzo A, Hebebrand J, Kemp JP, Lammers GJ, Aubert V, Heim MH, Martin NG, Montgomery GW, Peraita-Adrados R, Santamaria J, Negro F, Schmidt CO, Scott RA, Spector TD, Strauch K, Volzke H, Wareham NJ, Yuan W, Bell JT, Chakravarti A, Kooner JS, Peters A, Matullo G, Wallaschofski H, Whitfield JB, Paccaud F, Vollenweider P, Bergmann S, Beckmann JS, Tafti M, Hastie ND, Cusi D, Bochud M, Frayling TM, Metspalu A, Jarvelin MR, Scherag A, Smith GD, Borecki IB, Rousson V, Hirschhorn JN, Rivolta C, Loos RJ, Kutalik Z. Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index. PLoS Genet 2014;10(7):e1004508. (url)

  • Hohm T, Demarsy E, Quan C, Allenbach Petrolati L, Preuten T, Vernoux T, Bergmann S, Fankhauser C. Plasma membrane H(+) -ATPase regulation is required for auxin gradient formation preceding phototropic growth. Mol Syst Biol 2014;10:751. (url)

  • Huang W, Massouras A, Inoue Y, Peiffer J, Ramia M, Tarone AM, Turlapati L, Zichner T, Zhu D, Lyman RF, Magwire MM, Blankenburg K, Carbone MA, Chang K, Ellis LL, Fernandez S, Han Y, Highnam G, Hjelmen CE, Jack JR, Javaid M, Jayaseelan J, Kalra D, Lee S, Lewis L, Munidasa M, Ongeri F, Patel S, Perales L, Perez A, Pu L, Rollmann SM, Ruth R, Saada N, Warner C, Williams A, Wu YQ, Yamamoto A, Zhang Y, Zhu Y, Anholt RR, Korbel JO, Mittelman D, Muzny DM, Gibbs RA, Barbadilla A, Johnston JS, Stone EA, Richards S, Deplancke B, Mackay TF. Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines. Genome Res 2014;24(7):1193-208. (url)

  • Jacquemont S, Coe BP, Hersch M, Duyzend MH, Krumm N, Bergmann S, Beckmann JS, Rosenfeld JA, Eichler EE. A Higher Mutational Burden in Females Supports a "Female Protective Model" in Neurodevelopmental Disorders. Am J Hum Genet 2014. (url)

  • Jacquier N, Frandi A, Pillonel T, Viollier P, Greub G. Cell wall precursors are required to organize the chlamydial division septum. Nat Commun 2014;5:3578. (url)

  • Jensen JD. On the unfounded enthusiasm for soft selective sweeps. Nat Commun 2014;5:5281. (url)

  • Johne R, Dremsek P, Reetz J, Heckel G, Hess M, Ulrich RG. Hepeviridae: An expanding family of vertebrate viruses. Infect Genet Evol 2014. (url)

  • Jorjani H, Zavolan M. TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data. Bioinformatics 2014. (url)

  • Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kala M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lutteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics 2014;5(1):5. (url)

  • Kishore S, Piscuoglio S, Kovac MB, Gylling A, Wenzel F, Trapani F, Altermatt HJ, Mele V, Marra G, Peltomaki P, Terracciano L, Zavolan M, Heinimann K. 3'-UTR poly(T/U) tract deletions and altered expression of EWSR1 are a hallmark of mismatch repair-deficient cancers. Cancer Res 2014;74(1):224-34. (url)

  • Knight B, Kubik S, Ghosh B, Bruzzone MJ, Geertz M, Martin V, Denervaud N, Jacquet P, Ozkan B, Rougemont J, Maerkl SJ, Naef F, Shore D. Two distinct promoter architectures centered on dynamic nucleosomes control ribosomal protein gene transcription. Genes Dev 2014;28(15):1695-709. (url)

  • Kone M, Pullen TJ, Sun G, Ibberson M, Martinez-Sanchez A, Sayers S, Nguyen-Tu MS, Kantor C, Swisa A, Dor Y, Gorman T, Ferrer J, Thorens B, Reimann F, Gribble F, McGinty JA, Chen L, French PM, Birzele F, Hildebrandt T, Uphues I, Rutter GA. LKB1 and AMPK differentially regulate pancreatic beta-cell identity. FASEB J 2014;28(11):4972-85. (url)

  • Kryshtafovych A, Barbato A, Fidelis K, Monastyrskyy B, Schwede T, Tramontano A. Assessment of the assessment: Evaluation of the model quality estimates in CASP10. Proteins 2014;82 Suppl 2:112-26. (url)

  • Kryshtafovych A, Moult J, Bales P, Bazan JF, Biasini M, Burgin A, Chen C, Cochran FV, Craig TK, Das R, Fass D, Garcia-Doval C, Herzberg O, Lorimer D, Luecke H, Ma X, Nelson DC, van Raaij MJ, Rohwer F, Segall A, Seguritan V, Zeth K, Schwede T. Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins 2014;82 Suppl 2:26-42. (url)

  • Kryuchkova N, Robinson-Rechavi M. Determinants of protein evolutionary rates in light of ENCODE functional genomics. BMC Bioinformatics 2014;15((Suppl 3):A9). (url)

  • Kurics T, Menshykau D, Iber D. Feedback, receptor clustering, and receptor restriction to single cells yield large Turing spaces for ligand-receptor-based Turing models. Phys Rev E Stat Nonlin Soft Matter Phys 2014;90(2):022716. (url)

  • Larson EL, White TA, Ross CL, Harrison RG. Gene flow and the maintenance of species boundaries. Mol Ecol 2014;23(7):1668-78. (url)

  • Latreille M, Hausser J, Stutzer I, Zhang Q, Hastoy B, Gargani S, Kerr-Conte J, Pattou F, Zavolan M, Esguerra JL, Eliasson L, Rulicke T, Rorsman P, Stoffel M. MicroRNA-7a regulates pancreatic beta cell function. J Clin Invest 2014;124(6):2722-35. (url)

  • Ledda M, Kutalik Z, Souza Destito MC, Souza MM, Cirillo CA, Zamboni A, Martin N, Morya E, Sameshima K, Beckmann JS, le Coutre J, Bergmann S, Genick UK. GWAS of human bitter taste perception identifies new loci and reveals additional complexity of bitter taste genetics. Hum Mol Genet 2014;23(1):259-67. (url)

  • Letourneau A, Santoni FA, Bonilla X, Sailani MR, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Garieri M, Popadin K, Falconnet E, Gagnebin M, Gehrig C, Vannier A, Guipponi M, Farinelli L, Robyr D, Migliavacca E, Borel C, Deutsch S, Feki A, Stamatoyannopoulos JA, Herault Y, van Steensel B, Guigo R, Antonarakis SE. Domains of genome-wide gene expression dysregulation in Down's syndrome. Nature 2014;508(7496):345-50. (url)

  • Lischer HE, Excoffier L, Heckel G. Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles. Mol Biol Evol 2014. (url)

  • Litsios G, Wuest RO, Kostikova A, Forest F, Lexer C, Linder HP, Pearman PB, Zimmermann NE, Salamin N. Effects of a fire response trait on diversification in replicated radiations. Evolution 2014;68(2):453-65. (url)

  • Liu Y, Gunawan R. Parameter estimation of dynamic biological network models using integrated fluxes. BMC Syst Biol 2014;8(1):127. (url)

  • Lopez-Rios J, Duchesne A, Speziale D, Andrey G, Peterson KA, Germann P, Unal E, Liu J, Floriot S, Barbey S, Gallard Y, Muller-Gerbl M, Courtney AD, Klopp C, Rodriguez S, Ivanek R, Beisel C, Wicking C, Iber D, Robert B, McMahon AP, Duboule D, Zeller R. Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature 2014;511(7507):46-51. (url)

  • Luisier R, Unterberger EB, Goodman JI, Schwarz M, Moggs J, Terranova R, van Nimwegen E. Computational modeling identifies key gene regulatory interactions underlying phenobarbital-mediated tumor promotion. Nucleic Acids Res 2014. (url)

  • Maier L, Vyas R, Cordova CD, Lindsay H, Schmidt TS, Brugiroux S, Periaswamy B, Bauer R, Sturm A, Schreiber F, von Mering C, Robinson MD, Stecher B, Hardt WD. Microbiota-derived hydrogen fuels Salmonella typhimurium invasion of the gut ecosystem. Cell Host Microbe 2014;14(6):641-51. (url)

  • Maillard AM, Ruef A, Pizzagalli F, Migliavacca E, Hippolyte L, Adaszewski S, Dukart J, Ferrari C, Conus P, Mannik K, Zazhytska M, Siffredi V, Maeder P, Kutalik Z, Kherif F, Hadjikhani N, p11.2 European C, Beckmann JS, Reymond A, Draganski B, Jacquemont S. The 16p11.2 locus modulates brain structures common to autism, schizophrenia and obesity. Mol Psychiatry 2014. (url)

  • Marti-Solano M, Birney E, Bril A, Della Pasqua O, Kitano H, Mons B, Xenarios I, Sanz F. Integrative knowledge management to enhance pharmaceutical R&D. Nat Rev Drug Discov 2014;13(4):239-40. (url)

  • Martinez-Garcia R, Juan D, Rausell A, Munoz M, Banos N, Menendez C, Lopez-Casas PP, Rico D, Valencia A, Hidalgo M. Transcriptional dissection of pancreatic tumors engrafted in mice. Genome Med 2014;6(4):27. (url)

  • Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Topfer A. Challenges in RNA Virus Bioinformatics. Bioinformatics 2014. (url)

  • Masclaux FG, Hotz P, Gashi D, Savova-Bianchi D, Oppliger A. Assessment of airborne virus contamination in wastewater treatment plants. Environ Res 2014;133:260-5. (url)

  • Masson P, Hulo C, de Castro E, Foulger R, Poux S, Bridge A, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. An integrated ontology resource to explore and study host-virus relationships. PLoS One 2014;9(9):e108075. (url)

  • Matias Rodrigues JF, von Mering C. HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. Bioinformatics 2014;30(2):287-8. (url)

  • Mauvoisin D, Wang J, Jouffe C, Martin E, Atger F, Waridel P, Quadroni M, Gachon F, Naef F. Circadian clock-dependent and -independent rhythmic proteomes implement distinct diurnal functions in mouse liver. Proc Natl Acad Sci U S A 2014;111(1):167-72. (url)

  • Meier R, Franceschini A, Horvath P, Tetard M, Mancini R, von Mering C, Helenius A, Lozach PY. Genome-Wide Small Interfering RNA Screens Reveal VAMP3 as a Novel Host Factor Required for Uukuniemi Virus Late Penetration. J Virol 2014;88(15):8565-8578. (url)

  • Menshykau D, Blanc P, Unal E, Sapin V, Iber D. An interplay of geometry and signaling enables robust lung branching morphogenesis. Development 2014;141(23):4526-36. (url)

  • Meyer C, Cagnon L, Costa-Nunes CM, Baumgaertner P, Montandon N, Leyvraz L, Michielin O, Romano E, Speiser DE. Frequencies of circulating MDSC correlate with clinical outcome of melanoma patients treated with ipilimumab. Cancer Immunol Immunother 2014;63(3):247-57. (url)

  • Mittal N, Zavolan M. Seq and CLIP through the miRNA world. Genome Biol 2014;15(1):202. (url)

  • Miyazaki R, Bertelli C, Benaglio P, Canton J, De Coi N, Gharib WH, Gjoksi B, Goesmann A, Greub G, Harshman K, Linke B, Mikulic J, Mueller L, Nicolas D, Robinson-Rechavi M, Rivolta C, Roggo C, Roy S, Sentchilo V, Siebenthal AV, Falquet L, van der Meer JR. Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environ Microbiol 2014. (url)

  • Mohammadi P, di Iulio J, Munoz M, Martinez R, Bartha I, Cavassini M, Thorball C, Fellay J, Beerenwinkel N, Ciuffi A, Telenti A. Dynamics of HIV latency and reactivation in a primary CD4+ T cell model. PLoS Pathog 2014;10(5):e1004156. (url)

  • Mona S, Ray N, Arenas M, Excoffier L. Genetic consequences of habitat fragmentation during a range expansion. Heredity (Edinb) 2014;112(3):291-9. (url)

  • Montagner A, Delgado MB, Tallichet-Blanc C, Chan JS, Sng MK, Mottaz H, Degueurce G, Lippi Y, Moret C, Baruchet M, Antsiferova M, Werner S, Hohl D, Saati TA, Farmer PJ, Tan NS, Michalik L, Wahli W. Src is activated by the nuclear receptor peroxisome proliferator-activated receptor beta/delta in ultraviolet radiation-induced skin cancer. EMBO Mol Med 2014;6(1):80-98. (url)

  • Montandon SA, Tzika AC, Martins A, Chopard B, Milinkovitch M. Two Waves of Anisotropic Growth Generate Enlarged Follicles in the Spiny Mouse. EvoDevo 2014;5. (url)

  • Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M. Selectome update: quality control and computational improvements to a database of positive selection. Nucleic Acids Res 2014;42(Database issue):D917-21. (url)

  • Morikawa H, Ohkura N, Vandenbon A, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Standley DM, Date H, Sakaguchi S. Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proc Natl Acad Sci U S A 2014;111(14):5289-94. (url)

  • Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP) - round x. Proteins 2014;82 Suppl 2:1-6. (url)

  • Murgiano L, Jagannathan V, Benazzi C, Bolcato M, Brunetti B, Muscatello LV, Dittmer K, Piffer C, Gentile A, Drogemuller C. Deletion in the EVC2 gene causes chondrodysplastic dwarfism in Tyrolean Grey cattle. PLoS One 2014;9(4):e94861. (url)

  • Nair NU, Kumar S, Moret BM, Bucher P. Probabilistic partitioning methods to find significant patterns in ChIP-Seq data. Bioinformatics 2014;30(17):2406-13. (url)

  • Nair NU, Lin Y, Manasovska A, Antic J, Grnarova P, Sahu AD, Bucher P, Moret BM. Study of cell differentiation by phylogenetic analysis using histone modification data. BMC Bioinformatics 2014;15:269. (url)

  • Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grutzner F, Kaessmann H. The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature 2014;505(7485):635-40. (url)

  • Nikolayeva O, Robinson MD. edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology. Methods Mol Biol 2014;1150:45-79. (url)

  • Noordermeer D, Leleu M, Schorderet P, Joye E, Chabaud F, Duboule D. Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci. Elife (Cambridge) 2014;3:e02557. (url)

  • Olden M, Corre T, Hayward C, Toniolo D, Ulivi S, Gasparini P, Pistis G, Hwang SJ, Bergmann S, Campbell H, Cocca M, Gandin I, Girotto G, Glaudemans B, Hastie ND, Loffing J, Polasek O, Rampoldi L, Rudan I, Sala C, Traglia M, Vollenweider P, Vuckovic D, Youhanna S, Weber J, Wright AF, Kutalik Z, Bochud M, Fox CS, Devuyst O. Common Variants in UMOD Associate with Urinary Uromodulin Levels: A Meta-Analysis. J Am Soc Nephrol 2014. (url)

  • O'Shea D, Widmer LA, Stelling J, Egli A. Changing face of vaccination in immunocompromised hosts. Curr Infect Dis Rep 2014;16(9):420. (url)

  • Ounzain S, Pezzuto I, Micheletti R, Burdet F, Sheta R, Nemir M, Gonzales C, Sarre A, Alexanian M, Blow MJ, May D, Johnson R, Dauvillier J, Pennacchio LA, Pedrazzini T. Functional importance of cardiac enhancer-associated noncoding RNAs in heart development and disease. J Mol Cell Cardiol 2014;76C:55-70. (url)

  • Ounzain S, Micheletti R, Beckmann T, Schroen B, Alexanian M, Pezzuto I, Crippa S, Nemir M, Sarre A, Johnson R, Dauvillier J, Burdet F, Ibberson M, Guigo R, Xenarios I, Heymans S, Pedrazzini T. Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs. Eur Heart J 2014. (url)

  • Pajkovic M, Lappe S, Barman R, Parisod C, Neuenschwander S, Goudet J, Alvarez N, Guadagnuolo R, Felber F, Arrigo N. Wheat alleles introgress into selfing wild relatives: empirical estimates from approximate Bayesian computation in Aegilops triuncialis. Mol Ecol 2014;23(20):5089-101. (url)

  • Pasche E, Gobeill J, Kreim O, Oezdemir-Zaech F, Vachon T, Lovis C, Ruch P. Development and tuning of an original search engine for patent libraries in medicinal chemistry. BMC Bioinformatics 2014;15 Suppl 1:S15. (url)

  • Payne JL, Wagner A. The robustness and evolvability of transcription factor binding sites. Science 2014;343(6173):875-7. (url)

  • Payne JL, Wagner A. Latent phenotypes pervade gene regulatory circuits. BMC Syst Biol 2014;8:64. (url)

  • Pedersen BP, Ifrim G, Liboriussen P, Axelsen KB, Palmgren MG, Nissen P, Wiuf C, Pedersen CN. Large scale identification and categorization of protein sequences using structured logistic regression. PLoS One 2014;9(1):e85139. (url)

  • Pellissier L, Niculita-Hirzel H, Dubuis A, Pagni M, Guex N, Ndiribe C, Salamin N, Xenarios I, Goudet J, Sanders IR, Guisan A. Soil fungal communities of grasslands are environmentally structured at a regional scale in the Alps. Mol Ecol 2014;23(17):4274-90. (url)

  • Perry GH, Foll M, Grenier JC, Patin E, Nedelec Y, Pacis A, Barakatt M, Gravel S, Zhou X, Nsobya SL, Excoffier L, Quintana-Murci L, Dominy NJ, Barreiro LB. Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers. Proc Natl Acad Sci U S A 2014;111(35):E3596-603. (url)

  • Perry JR, Day F, Elks CE, Sulem P, Thompson DJ, Ferreira T, He C, Chasman DI, Esko T, Thorleifsson G, Albrecht E, Ang WQ, Corre T, Cousminer DL, Feenstra B, Franceschini N, Ganna A, Johnson AD, Kjellqvist S, Lunetta KL, McMahon G, Nolte IM, Paternoster L, Porcu E, Smith AV, Stolk L, Teumer A, Tsernikova N, Tikkanen E, Ulivi S, Wagner EK, Amin N, Bierut LJ, Byrne EM, Hottenga JJ, Koller DL, Mangino M, Pers TH, Yerges-Armstrong LM, Hua Zhao J, Andrulis IL, Anton-Culver H, Atsma F, Bandinelli S, Beckmann MW, Benitez J, Blomqvist C, Bojesen SE, Bolla MK, Bonanni B, Brauch H, Brenner H, Buring JE, Chang-Claude J, Chanock S, Chen J, Chenevix-Trench G, Collee JM, Couch FJ, Couper D, Coviello AD, Cox A, Czene K, D'Adamo A P, Davey Smith G, De Vivo I, Demerath EW, Dennis J, Devilee P, Dieffenbach AK, Dunning AM, Eiriksdottir G, Eriksson JG, Fasching PA, Ferrucci L, Flesch-Janys D, Flyger H, Foroud T, Franke L, Garcia ME, Garcia-Closas M, Geller F, de Geus EE, Giles GG, Gudbjartsson DF, Gudnason V, Guenel P, Guo S, Hall P, Hamann U, Haring R, Hartman CA, Heath AC, Hofman A, Hooning MJ, Hopper JL, Hu FB, Hunter DJ, Karasik D, Kiel DP, Knight JA, Kosma VM, Kutalik Z, Lai S, Lambrechts D, Lindblom A, Magi R, Magnusson PK, Mannermaa A, Martin NG, Masson G, McArdle PF, McArdle WL, Melbye M, Michailidou K, Mihailov E, Milani L, Milne RL, Nevanlinna H, Neven P, Nohr EA, Oldehinkel AJ, Oostra BA, Palotie A, Peacock M, Pedersen NL, Peterlongo P, Peto J, Pharoah PD, Postma DS, Pouta A, Pylkas K, Radice P, Ring S, Rivadeneira F, Robino A, Rose LM, Rudolph A, Salomaa V, Sanna S, Schlessinger D, Schmidt MK, Southey MC, Sovio U, Stampfer MJ, Stockl D, Storniolo AM, Timpson NJ, Tyrer J, Visser JA, Vollenweider P, Volzke H, Waeber G, Waldenberger M, Wallaschofski H, Wang Q, Willemsen G, Winqvist R, Wolffenbuttel BH, Wright MJ, Australian Ovarian Cancer S, Network G, kConFab, LifeLines Cohort S, InterAct C, Early Growth Genetics C, Boomsma DI, Econs MJ, Khaw KT, Loos RJ, McCarthy MI, Montgomery GW, Rice JP, Streeten EA, Thorsteinsdottir U, van Duijn CM, Alizadeh BZ, Bergmann S, Boerwinkle E, Boyd HA, Crisponi L, Gasparini P, Gieger C, Harris TB, Ingelsson E, Jarvelin MR, Kraft P, Lawlor D, Metspalu A, Pennell CE, Ridker PM, Snieder H, Sorensen TI, Spector TD, Strachan DP, Uitterlinden AG, Wareham NJ, Widen E, Zygmunt M, Murray A, Easton DF, Stefansson K, Murabito JM, Ong KK. Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. Nature 2014;514(7520):92-7. (url)

  • Peters S, Bouchaab H, Zimmerman S, Bucher M, Gaide O, Letovanec I, Homicsko K, Michielin O. Dramatic response of vemurafenib-induced cutaneous lesions upon switch to dual BRAF/MEK inhibition in a metastatic melanoma patient. Melanoma Res 2014;24(5):496-500. (url)

  • Poh YP, Domingues VS, Hoekstra HE, Jensen JD. On the prospect of identifying adaptive Loci in recently bottlenecked populations. PLoS One 2014;9(11):e110579. (url)

  • Poux S, Magrane M, Arighi CN, Bridge A, O'Donovan C, Laiho K. Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. Database (Oxford) 2014;2014:bau016. (url)

  • Prabhakaran S, Rey M, Zagordi O, Beerenwinkel N, Roth V. HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model. IEEE/ACM Trans Comput Biol Bioinform 2014. (url)

  • Quinodoz M, Gobet C, Naef F, Gustafson K. Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. Genome Biology 2014;15:R85. (url)

  • Ramundo S, Casero D, Muhlhaus T, Hemme D, Sommer F, Crevecoeur M, Rahire M, Schroda M, Rusch J, Goodenough U, Pellegrini M, Perez-Perez ME, Crespo JL, Schaad O, Civic N, Rochaix JD. Conditional Depletion of the Chlamydomonas Chloroplast ClpP Protease Activates Nuclear Genes Involved in Autophagy and Plastid Protein Quality Control. Plant Cell 2014;26(5):2201-2222. (url)

  • Rausell A, Mohammadi P, McLaren PJ, Bartha I, Xenarios I, Fellay J, Telenti A. Analysis of stop-gain and frameshift variants in human innate immunity genes. PLoS Comput Biol 2014;10(7):e1003757. (url)

  • Rausell A, Telenti A. Genomics of host-pathogen interactions. Curr Opin Immunol 2014;30C:32-38. (url)

  • Regoes RR, McLaren PJ, Battegay M, Bernasconi E, Calmy A, Gunthard HF, Hoffmann M, Rauch A, Telenti A, Fellay J, Swiss HIVCS. Disentangling human tolerance and resistance against HIV. PLoS Biol 2014;12(9):e1001951. (url)

  • Renaud M, Praz V, Vieu E, Florens L, Washburn MP, l'Hote P, Hernandez N. Gene duplication and neofunctionalization: POLR3G and POLR3GL. Genome Res 2014;24(1):37-51. (url)

  • Renzette N, Caffrey DR, Zeldovich KB, Liu P, Gallagher GR, Aiello D, Porter AJ, Kurt-Jones EA, Bolon DN, Poh YP, Jensen JD, Schiffer CA, Kowalik TF, Finberg RW, Wang JP. Evolution of the influenza A virus genome during development of oseltamivir resistance in vitro. J Virol 2014;88(1):272-81. (url)

  • Renzette N, Somasundaran M, Brewster F, Coderre J, Weiss ER, McManus M, Greenough T, Tabak B, Garber M, Kowalik TF, Luzuriaga K. Epstein-Barr virus latent membrane protein 1 genetic variability in peripheral blood B cells and oropharyngeal fluids. J Virol 2014;88(7):3744-55. (url)

  • Renzette N, Gibson L, Jensen JD, Kowalik TF. Human cytomegalovirus intrahost evolution-a new avenue for understanding and controlling herpesvirus infections. Curr Opin Virol 2014;8C:109-115. (url)

  • Rezaei M, Andrieu T, Neuenschwander S, Bruggmann R, Mordasini D, Frey FJ, Vogt B, Frey BM. Regulation of 11beta-Hydroxysteroid Dehydrogenase Type 2 by MicroRNA. Hypertension 2014. (url)

  • Riebler A, Menigatti M, Song JZ, Statham AL, Stirzaker C, Mahmud N, Mein CA, Clark SJ, Robinson MD. BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach. Genome Biol 2014;15(2):R35. (url)

  • Rohrig UF, Majjigapu SR, Chambon M, Bron S, Pilotte L, Colau D, Van den Eynde BJ, Turcatti G, Vogel P, Zoete V, Michielin O. Detailed analysis and follow-up studies of a high-throughput screening for indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors. Eur J Med Chem 2014;84:284-301. (url)

  • Romano E, Michielin O. Successes and limitations of targeted cancer therapy in melanoma. Prog Tumor Res 2014;41:78-88. (url)

  • Romano E, Michielin O, Voelter V, Laurent J, Bichat H, Stravodimou A, Romero P, Speiser DE, Triebel F, Leyvraz S, Harari A. MART-1 peptide vaccination plus IMP321 (LAG-3Ig fusion protein) in patients receiving autologous PBMCs after lymphodepletion: results of a Phase I trial. J Transl Med 2014;12:97. (url)

  • Roppolo D, Boeckmann B, Pfister A, Boutet E, Rubio MC, Denervaud-Tendon V, Vermeer JE, Gheyselinck J, Xenarios I, Geldner N. Functional and evolutionary analysis of the CASPARIAN STRIP MEMBRANE DOMAIN PROTEIN family. Plant Physiol 2014. (url)

  • Rosikiewicz M, Robinson-Rechavi M. IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinformatics 2014;30(10):1392-9. (url)

  • Roux J, Privman E, Moretti S, Daub JT, Robinson-Rechavi M, Keller L. Patterns of positive selection in seven ant genomes. Mol Biol Evol 2014;31(7):1661-85. (url)

  • Rueedi R, Ledda M, Nicholls AW, Salek RM, Marques-Vidal P, Morya E, Sameshima K, Montoliu I, Da Silva L, Collino S, Martin FP, Rezzi S, Steinbeck C, Waterworth DM, Waeber G, Vollenweider P, Beckmann JS, Le Coutre J, Mooser V, Bergmann S, Genick UK, Kutalik Z. Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links. PLoS Genet 2014;10(2):e1004132. (url)

  • Rueger S, Bochud PY, Dufour JF, Mullhaupt B, Semela D, Heim MH, Moradpour D, Cerny A, Malinverni R, Booth DR, Suppiah V, George J, Argiro L, Halfon P, Bourliere M, Talal AH, Jacobson IM, Patin E, Nalpas B, Poynard T, Pol S, Abel L, Kutalik Z, Negro F. Impact of common risk factors of fibrosis progression in chronic hepatitis C. Gut 2014. (url)

  • Sankar M, Nieminen K, Ragni L, Xenarios I, Hardtke CS. Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth. Elife 2014;3:e01567. (url)

  • Schaper E, Gascuel O, Anisimova M. Deep conservation of human protein tandem repeats within the eukaryotes. Mol Biol Evol 2014;31(5):1132-48. (url)

  • Schmidt TS, Matias Rodrigues JF, von Mering C. Limits to robustness and reproducibility in the demarcation of operational taxonomic units. Environ Microbiol 2014. (url)

  • Schmidt S, Essbauer SS, Mayer-Scholl A, Poppert S, Schmidt-Chanasit J, Klempa B, Henning K, Schares G, Groschup MH, Spitzenberger F, Richter D, Heckel G, Ulrich RG. Multiple infections of rodents with zoonotic pathogens in austria. Vector Borne Zoonotic Dis 2014;14(7):467-75. (url)

  • Schmidt T, Bergner A, Schwede T. Modelling three-dimensional protein structures for applications in drug design. Drug Discov Today 2014;19(7):890-897. (url)

  • Schmidt T, Schwede T, Meuwly M. Computational analysis of methyl transfer reactions in dengue virus methyltransferase. J Phys Chem B 2014;118(22):5882-90. (url)

  • Schmidt TS, Matias Rodrigues JF, von Mering C. Ecological consistency of SSU rRNA-based operational taxonomic units at a global scale. PLoS Comput Biol 2014;10(4):e1003594. (url)

  • Schonemann L, Kuhn U, Martin G, Schafer P, Gruber AR, Keller W, Zavolan M, Wahle E. Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33. Genes Dev 2014;28(21):2381-93. (url)

  • Seehausen O, Butlin RK, Keller I, Wagner CE, Boughman JW, Hohenlohe PA, Peichel CL, Saetre GP, Bank C, Brannstrom A, Brelsford A, Clarkson CS, Eroukhmanoff F, Feder JL, Fischer MC, Foote AD, Franchini P, Jiggins CD, Jones FC, Lindholm AK, Lucek K, Maan ME, Marques DA, Martin SH, Matthews B, Meier JI, Most M, Nachman MW, Nonaka E, Rennison DJ, Schwarzer J, Watson ET, Westram AM, Widmer A. Genomics and the origin of species. Nat Rev Genet 2014;15(3):176-92. (url)

  • Seguin-Estevez Q, Dunand-Sauthier I, Lemeille S, Iseli C, Ibberson M, Ioannidis V, Schmid CD, Rousseau P, Barras E, Geinoz A, Xenarios I, Acha-Orbea H, Reith W. Extensive remodeling of DC function by rapid maturation-induced transcriptional silencing. Nucleic Acids Res 2014;42(15):9641-55. (url)

  • Seifert D, Di Giallonardo F, Metzner KJ, Gunthard HF, Beerenwinkel N. A Framework for Inferring Fitness Landscapes of Patient-Derived Viruses Using Quasispecies Theory. Genetics 2014. (url)

  • Shao M, Lin Y, Moret BM. An Exact Algorithm to Compute the DCJ Distance for Genomes with Duplicate Genes. Springer 2014;8394(Lecture Notes in Computer Science):280-292 (url)

  • Shao M, Moret BM. On the DCJ Median Problem. Springer 2014;8486(Lecture Notes in Computer Science):273-282 (url)

  • Silvestro D, Zizka G, Schulte K. Disentangling the effects of key innovations on the diversification of Bromelioideae (bromeliaceae). Evolution 2014;68(1):163-75. (url)

  • Simino J, Shi G, Bis JC, Chasman DI, Ehret GB, Gu X, Guo X, Hwang SJ, Sijbrands E, Smith AV, Verwoert GC, Bragg-Gresham JL, Cadby G, Chen P, Cheng CY, Corre T, de Boer RA, Goel A, Johnson T, Khor CC, Lluis-Ganella C, Luan J, Lyytikainen LP, Nolte IM, Sim X, Sober S, van der Most PJ, Verweij N, Zhao JH, Amin N, Boerwinkle E, Bouchard C, Dehghan A, Eiriksdottir G, Elosua R, Franco OH, Gieger C, Harris TB, Hercberg S, Hofman A, James AL, Johnson AD, Kahonen M, Khaw KT, Kutalik Z, Larson MG, Launer LJ, Li G, Liu J, Liu K, Morrison AC, Navis G, Ong RT, Papanicolau GJ, Penninx BW, Psaty BM, Raffel LJ, Raitakari OT, Rice K, Rivadeneira F, Rose LM, Sanna S, Scott RA, Siscovick DS, Stolk RP, Uitterlinden AG, Vaidya D, van der Klauw MM, Vasan RS, Vithana EN, Volker U, Volzke H, Watkins H, Young TL, Aung T, Bochud M, Farrall M, Hartman CA, Laan M, Lakatta EG, Lehtimaki T, Loos RJ, Lucas G, Meneton P, Palmer LJ, Rettig R, Snieder H, Tai ES, Teo YY, van der Harst P, Wareham NJ, Wijmenga C, Wong TY, Fornage M, Gudnason V, Levy D, Palmas W, Ridker PM, Rotter JI, van Duijn CM, Witteman JC, Chakravarti A, Rao DC. Gene-Age Interactions in Blood Pressure Regulation: A Large-Scale Investigation with the CHARGE, Global BPgen, and ICBP Consortia. Am J Hum Genet 2014;95(1):24-38. (url)

  • Simkin AT, Bailey JA, Gao FB, Jensen JD. Inferring the Evolutionary History of Primate microRNA Binding Sites: Overcoming Motif Counting Biases. Mol Biol Evol 2014;31(7):1894-901. (url)

  • Singh P, Benjak A, Carat S, Kai M, Busso P, Avanzi C, Paniz-Mondolfi A, Peter C, Harshman K, Rougemont J, Matsuoka M, Cole ST. Genome-wide re-sequencing of multidrug-resistant Mycobacterium leprae Airaku-3. Clin Microbiol Infect 2014. (url)

  • Solans L, Gonzalo-Asensio J, Sala C, Benjak A, Uplekar S, Rougemont J, Guilhot C, Malaga W, Martin C, Cole ST. The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis. PLoS Pathog 2014;10(5):e1004183. (url)

  • Sonnhammer EL, Gabaldon T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C, Quest for Orthologs c. Big data and other challenges in the quest for orthologs. Bioinformatics 2014;30(21):2993-8. (url)

  • Soste M, Hrabakova R, Wanka S, Melnik A, Boersema P, Maiolica A, Wernas T, Tognetti M, von Mering C, Picotti P. A sentinel protein assay for simultaneously quantifying cellular processes. Nat Methods 2014;11(10):1045-8. (url)

  • Sousa V, Peischl S, Excoffier L. Impact of range expansions on current human genomic diversity. Curr Opin Genet Dev 2014;29C:22-30. (url)

  • Spitzer J, Hafner M, Landthaler M, Ascano M, Farazi T, Wardle G, Nusbaum J, Khorshid M, Burger L, Zavolan M, Tuschl T. PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins. Methods Enzymol 2014;539:113-61. (url)

  • Stadler T, Rabosky DL, Ricklefs RE, Bokma F. On age and species richness of higher taxa. Am Nat 2014;184(4):447-55. (url)

  • Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Mercier PL, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, Mering C, Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD. Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Res 2014;42(Web Server issue):W436-41. (url)

  • Sunnaker M, Zamora-Sillero E, Lopez Garcia de Lomana A, Rudroff F, Sauer U, Stelling J, Wagner A. Topological augmentation to infer hidden processes in biological systems. Bioinformatics 2014;30(2):221-7. (url)

  • Szczurek E, Beerenwinkel N. Modeling mutual exclusivity of cancer mutations. PLoS Comput Biol 2014;10(3):e1003503. (url)

  • Szklarczyk D, Franceschini A, Wyder S, Forslund K, Heller D, Huerta-Cepas J, Simonovic M, Roth A, Santos A, Tsafou KP, Kuhn M, Bork P, Jensen LJ, von Mering C. STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 2014. (url)

  • Szovenyi P, Devos N, Weston DJ, Yang X, Hock Z, Shaw JA, Shimizu KK, McDaniel SF, Wagner A. Efficient purging of deleterious mutations in plants with haploid selfing. Genome Biol Evol 2014;6(5):1238-52. (url)

  • Tafti M, Hor H, Dauvilliers Y, Lammers GJ, Overeem S, Mayer G, Javidi S, Iranzo A, Santamaria J, Peraita-Adrados R, Vicario JL, Arnulf I, Plazzi G, Bayard S, Poli F, Pizza F, Geisler P, Wierzbicka A, Bassetti CL, Mathis J, Lecendreux M, Donjacour CE, van der Heide A, Heinzer R, Haba-Rubio J, Feketeova E, Hogl B, Frauscher B, Beneto A, Khatami R, Canellas F, Pfister C, Scholz S, Billiard M, Baumann CR, Ercilla G, Verduijn W, Claas FH, Dubois V, Nowak J, Eberhard HP, Pradervand S, Hor CN, Testi M, Tiercy JM, Kutalik Z. DQB1 locus alone explains most of the risk and protection in narcolepsy with cataplexy in Europe. Sleep 2014;37(1):19-25. (url)

  • Tattikota SG, Rathjen T, McAnulty SJ, Wessels HH, Akerman I, van de Bunt M, Hausser J, Esguerra JL, Musahl A, Pandey AK, You X, Chen W, Herrera PL, Johnson PR, O'Carroll D, Eliasson L, Zavolan M, Gloyn AL, Ferrer J, Shalom-Feuerstein R, Aberdam D, Poy MN. Argonaute2 mediates compensatory expansion of the pancreatic beta cell. Cell Metab 2014;19(1):122-34. (url)

  • The Coffee Caffeine Genetics Consortium, Cornelis MC, Byrne EM, Esko T, Nalls MA, Ganna A, Paynter N, Monda KL, Amin N, Fischer K, Renstrom F, Ngwa JS, Huikari V, Cavadino A, Nolte IM, Teumer A, Yu K, Marques-Vidal P, Rawal R, Manichaikul A, Wojczynski MK, Vink JM, Zhao JH, Burlutsky G, Lahti J, Mikkila V, Lemaitre RN, Eriksson J, Musani SK, Tanaka T, Geller F, Luan J, Hui J, Magi R, Dimitriou M, Garcia ME, Ho WK, Wright MJ, Rose LM, Magnusson PK, Pedersen NL, Couper D, Oostra BA, Hofman A, Ikram MA, Tiemeier HW, Uitterlinden AG, van Rooij FJ, Barroso I, Johansson I, Xue L, Kaakinen M, Milani L, Power C, Snieder H, Stolk RP, Baumeister SE, Biffar R, Gu F, Bastardot F, Kutalik Z, Jacobs DR, Jr., Forouhi NG, Mihailov E, Lind L, Lindgren C, Michaelsson K, Morris A, Jensen M, Khaw KT, Luben RN, Wang JJ, Mannisto S, Perala MM, Kahonen M, Lehtimaki T, Viikari J, Mozaffarian D, Mukamal K, Psaty BM, Doring A, Heath AC, Montgomery GW, Dahmen N, Carithers T, Tucker KL, Ferrucci L, Boyd HA, Melbye M, Treur JL, Mellstrom D, Hottenga JJ, Prokopenko I, Tonjes A, Deloukas P, Kanoni S, Lorentzon M, Houston DK, Liu Y, Danesh J, Rasheed A, Mason MA, Zonderman AB, Franke L, Kristal BS, International Parkinson's Disease Genomics C, North American Brain Expression C, Consortium UKBE, Karjalainen J, Reed DR, Westra HJ, Evans MK, Saleheen D, Harris TB, Dedoussis G, Curhan G, Stumvoll M, Beilby J, Pasquale LR, Feenstra B, Bandinelli S, Ordovas JM, Chan AT, Peters U, Ohlsson C, Gieger C, Martin NG, Waldenberger M, Siscovick DS, Raitakari O, Eriksson JG, Mitchell P, Hunter DJ, Kraft P, Rimm EB, Boomsma DI, Borecki IB, Loos RJ, Wareham NJ, Vollenweider P, Caporaso N, Grabe HJ, Neuhouser ML, Wolffenbuttel BH, Hu FB, Hypponen E, Jarvelin MR, Cupples LA, Franks PW, Ridker PM, van Duijn CM, Heiss G, Metspalu A, North KE, Ingelsson E, Nettleton JA, van Dam RM, Chasman DI. Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption. Mol Psychiatry 2014. (url)

  • Thomson AS, Heer FT, Smith FJ, Hendron E, Berneche S, Rothberg BS. Initial steps of inactivation at the K+ channel selectivity filter. Proc Natl Acad Sci U S A 2014;111(17):E1713-22. (url)

  • Tisserant E, Malbreil M, Kuo A, Kohler A, Symeonidi A, Balestrini R, Charron P, Duensing N, Frei dit Frey N, Gianinazzi-Pearson V, Gilbert LB, Handa Y, Herr JR, Hijri M, Koul R, Kawaguchi M, Krajinski F, Lammers PJ, Masclaux FG, Murat C, Morin E, Ndikumana S, Pagni M, Petitpierre D, Requena N, Rosikiewicz P, Riley R, Saito K, San Clemente H, Shapiro H, van Tuinen D, Becard G, Bonfante P, Paszkowski U, Shachar-Hill YY, Tuskan GA, Young JP, Sanders IR, Henrissat B, Rensing SA, Grigoriev IV, Corradi N, Roux C, Martin F. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A 2014;110(50):20117-22. (url)

  • Tokonami N, Mordasini D, Pradervand S, Centeno G, Jouffe C, Maillard M, Bonny O, Gachon F, Gomez RA, Sequeira-Lopez ML, Firsov D. Local Renal Circadian Clocks Control Fluid-Electrolyte Homeostasis and BP. J Am Soc Nephrol 2014;25(7):1430-1439. (url)

  • Topfer A, Marschall T, Bull RA, Luciani F, Schonhuth A, Beerenwinkel N. Viral quasispecies assembly via maximal clique enumeration. PLoS Comput Biol 2014;10(3):e1003515. (url)

  • Trachana K, Forslund K, Larsson T, Powell S, Doerks T, von Mering C, Bork P. A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PLoS One 2014;9(11):e111122. (url)

  • Tsunematsu K, Chopard B, Falcone J, Bonadonna C. A numerical model of ballistic transport with collisions in a volcanic setting. Computers & Geosciences 2014;63:62–69. (url)

  • Ud-Dean SM, Gunawan R. Ensemble inference and inferability of gene regulatory networks. PLoS One 2014;9(8):e103812. (url)

  • Valle M, Schabauer H, Pacher C, Stockinger H, Stamatakis A, Robinson-Rechavi M, Salamin N. Optimization strategies for fast detection of positive selection on phylogenetic trees. Bioinformatics 2014. (url)

  • Vallois D, Niederhauser G, Ibberson M, Nagaray V, Marselli L, Marchetti P, Chatton JY, Thorens B. Gluco-incretins regulate beta-cell glucose competence by epigenetic silencing of Fxyd3 expression. PLoS One 2014;9(7):e103277. (url)

  • Vigano MA, Ivanek R, Balwierz P, Berninger P, van Nimwegen E, Karjalainen K, Rolink A. An epigenetic profile of early T-cell development from multipotent progenitors to committed T-cell descendants. Eur J Immunol 2014;44(4):1181-93. (url)

  • Vince N, Bashirova AA, Lied A, Gao X, Dorrell L, McLaren PJ, Fellay J, Carrington M. HLA class I and KIR genes do not protect against HIV type 1 infection in highly exposed uninfected individuals with hemophilia A. J Infect Dis 2014;210(7):1047-51. (url)

  • Vishnyakova D, Bottone S, Pasche E, Lovis C. Practical implementation of a bridge between legacy EHR system and a clinical research environment. Stud Health Technol Inform 2014;197:29-33. (url)

  • Vizcaino JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Rios D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolome S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H. ProteomeXchange provides globally coordinated proteomics data submission and dissemination. Nat Biotechnol 2014;32(3):223-6. (url)

  • Wagner A. A genotype network reveals homoplastic cycles of convergent evolution in influenza A (H3N2) haemagglutinin. Proc Biol Sci 2014;281(1786). (url)

  • Wagner A. Mutational robustness accelerates the origin of novel RNA phenotypes through phenotypic plasticity. Biophys J 2014;106(4):955-65. (url)

  • Wagner A, Andriasyan V, Barve A. The organization of metabolic genotype space facilitates adaptive evolution in nitrogen metabolism. Journal of Molecular Biochemistry 2014;3: 2-13. (url)

  • Wagner A, Rosen W. Spaces of the possible: universal Darwinism and the wall between technological and biological innovation. J R Soc Interface 2014;11(97):20131190. (url)

  • Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-Garcia DC, Eppler E, Seiler R, Hansen LH, Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM, Jr., Collins MJ, Gilbert MT, Ruhli F, Cappellini E. Pathogens and host immunity in the ancient human oral cavity. Nat Genet 2014;46(4):336-44. (url)

  • Warinner C, Rodrigues JF, Vyas R, Trachsel C, Shved N, Grossmann J, Radini A, Hancock Y, Tito RY, Fiddyment S, Speller C, Hendy J, Charlton S, Luder HU, Salazar-Garcia DC, Eppler E, Seiler R, Hansen LH, Castruita JA, Barkow-Oesterreicher S, Teoh KY, Kelstrup CD, Olsen JV, Nanni P, Kawai T, Willerslev E, von Mering C, Lewis CM, Jr., Collins MJ, Gilbert MT, Ruhli F, Cappellini E. Pathogens and host immunity in the ancient human oral cavity. Nat Genet 2014. (url)

  • Warnefors M, Liechti A, Halbert J, Valloton D, Kaessmann H. Conserved microRNA editing in mammalian evolution, development and disease. Genome Biol 2014;15(6):R83. (url)

  • Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. Bioinformatics 2014;30(2):165-71. (url)

  • Wegmann D, Currat M. Recipient of the 2013 Molecular Ecology Prize: Laurent Excoffier. Mol Ecol 2014;23(1):16-9. (url)

  • Wiedemar N, Tetens J, Jagannathan V, Menoud A, Neuenschwander S, Bruggmann R, Thaller G, Drogemuller C. Independent polled mutations leading to complex gene expression differences in cattle. PLoS One 2014;9(3):e93435. (url)

  • Williams EG, Mouchiroud L, Frochaux M, Pandey A, Andreux PA, Deplancke B, Auwerx J. An evolutionarily conserved role for the aryl hydrocarbon receptor in the regulation of movement. PLoS Genet 2014;10(9):e1004673. (url)

  • Winkler TW, Kutalik Z, Gorski M, Lottaz C, Kronenberg F, Heid IM. EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data. Bioinformatics 2014. (url)

  • Winkler TW, Day FR, Croteau-Chonka DC, Wood AR, Locke AE, Magi R, Ferreira T, Fall T, Graff M, Justice AE, Luan J, Gustafsson S, Randall JC, Vedantam S, Workalemahu T, Kilpelainen TO, Scherag A, Esko T, Kutalik Z, Heid IM, Loos RJ. Quality control and conduct of genome-wide association meta-analyses. Nat Protoc 2014;9(5):1192-212. (url)

  • Wojtowicz A, Gresnigt MS, Lecompte T, Bibert S, Manuel O, Joosten LA, Rueger S, Berger C, Boggian K, Cusini A, Garzoni C, Hirsch HH, Weisser M, Mueller NJ, Meylan PR, Steiger J, Kutalik Z, Pascual M, van Delden C, van de Veerdonk FL, Bochud PY, the Swiss Transplant Cohort S. IL1B and DEFB1 Polymorphisms Increase Susceptibility to Invasive Mold Infection After Solid Organ Transplantation. J Infect Dis 2014. (url)

  • Woltering JM, Noordermeer D, Leleu M, Duboule D. Conservation and divergence of regulatory strategies at Hox Loci and the origin of tetrapod digits. PLoS Biol 2014;12(1):e1001773. (url)

  • Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, Chu AY, Estrada K, Luan J, Kutalik Z, Amin N, Buchkovich ML, Croteau-Chonka DC, Day FR, Duan Y, Fall T, Fehrmann R, Ferreira T, Jackson AU, Karjalainen J, Lo KS, Locke AE, Magi R, Mihailov E, Porcu E, Randall JC, Scherag A, Vinkhuyzen AA, Westra HJ, Winkler TW, Workalemahu T, Zhao JH, Absher D, Albrecht E, Anderson D, Baron J, Beekman M, Demirkan A, Ehret GB, Feenstra B, Feitosa MF, Fischer K, Fraser RM, Goel A, Gong J, Justice AE, Kanoni S, Kleber ME, Kristiansson K, Lim U, Lotay V, Lui JC, Mangino M, Mateo Leach I, Medina-Gomez C, Nalls MA, Nyholt DR, Palmer CD, Pasko D, Pechlivanis S, Prokopenko I, Ried JS, Ripke S, Shungin D, Stancakova A, Strawbridge RJ, Sung YJ, Tanaka T, Teumer A, Trompet S, van der Laan SW, van Setten J, Van Vliet-Ostaptchouk JV, Wang Z, Yengo L, Zhang W, Afzal U, Arnlov J, Arscott GM, Bandinelli S, Barrett A, Bellis C, Bennett AJ, Berne C, Bluher M, Bolton JL, Bottcher Y, Boyd HA, Bruinenberg M, Buckley BM, Buyske S, Caspersen IH, Chines PS, Clarke R, Claudi-Boehm S, Cooper M, Daw EW, De Jong PA, Deelen J, Delgado G, Denny JC, Dhonukshe-Rutten R, Dimitriou M, Doney AS, Dorr M, Eklund N, Eury E, Folkersen L, Garcia ME, Geller F, Giedraitis V, Go AS, Grallert H, Grammer TB, Grassler J, Gronberg H, de Groot LC, Groves CJ, Haessler J, Hall P, Haller T, Hallmans G, Hannemann A, Hartman CA, Hassinen M, Hayward C, Heard-Costa NL, Helmer Q, Hemani G, Henders AK, Hillege HL, Hlatky MA, Hoffmann W, Hoffmann P, Holmen O, Houwing-Duistermaat JJ, Illig T, Isaacs A, James AL, Jeff J, Johansen B, Johansson A, Jolley J, Juliusdottir T, Junttila J, Kho AN, Kinnunen L, Klopp N, Kocher T, Kratzer W, Lichtner P, Lind L, Lindstrom J, Lobbens S, Lorentzon M, Lu Y, Lyssenko V, Magnusson PK, Mahajan A, Maillard M, McArdle WL, McKenzie CA, McLachlan S, McLaren PJ, Menni C, Merger S, Milani L, Moayyeri A, Monda KL, Morken MA, Muller G, Muller-Nurasyid M, Musk AW, Narisu N, Nauck M, Nolte IM, Nothen MM, Oozageer L, Pilz S, Rayner NW, Renstrom F, Robertson NR, Rose LM, Roussel R, Sanna S, Scharnagl H, Scholtens S, Schumacher FR, Schunkert H, Scott RA, Sehmi J, Seufferlein T, Shi J, Silventoinen K, Smit JH, Smith AV, Smolonska J, Stanton AV, Stirrups K, Stott DJ, Stringham HM, Sundstrom J, Swertz MA, Syvanen AC, Tayo BO, Thorleifsson G, Tyrer JP, van Dijk S, van Schoor NM, van der Velde N, van Heemst D, van Oort FV, Vermeulen SH, Verweij N, Vonk JM, Waite LL, Waldenberger M, Wennauer R, Wilkens LR, Willenborg C, Wilsgaard T, Wojczynski MK, Wong A, Wright AF, Zhang Q, Arveiler D, Bakker SJ, Beilby J, Bergman RN, Bergmann S, Biffar R, Blangero J, Boomsma DI, Bornstein SR, Bovet P, Brambilla P, Brown MJ, Campbell H, Caulfield MJ, Chakravarti A, Collins R, Collins FS, Crawford DC, Cupples LA, Danesh J, de Faire U, den Ruijter HM, Erbel R, Erdmann J, Eriksson JG, Farrall M, Ferrannini E, Ferrieres J, Ford I, Forouhi NG, Forrester T, Gansevoort RT, Gejman PV, Gieger C, Golay A, Gottesman O, Gudnason V, Gyllensten U, Haas DW, Hall AS, Harris TB, Hattersley AT, Heath AC, Hengstenberg C, Hicks AA, Hindorff LA, Hingorani AD, Hofman A, Hovingh GK, Humphries SE, Hunt SC, Hypponen E, Jacobs KB, Jarvelin MR, Jousilahti P, Jula AM, Kaprio J, Kastelein JJ, Kayser M, Kee F, Keinanen-Kiukaanniemi SM, Kiemeney LA, Kooner JS, Kooperberg C, Koskinen S, Kovacs P, Kraja AT, Kumari M, Kuusisto J, Lakka TA, Langenberg C, Le Marchand L, Lehtimaki T, Lupoli S, Madden PA, Mannisto S, Manunta P, Marette A, Matise TC, McKnight B, Meitinger T, Moll FL, Montgomery GW, Morris AD, Morris AP, Murray JC, Nelis M, Ohlsson C, Oldehinkel AJ, Ong KK, Ouwehand WH, Pasterkamp G, Peters A, Pramstaller PP, Price JF, Qi L, Raitakari OT, Rankinen T, Rao DC, Rice TK, Ritchie M, Rudan I, Salomaa V, Samani NJ, Saramies J, Sarzynski MA, Schwarz PE, Sebert S, Sever P, Shuldiner AR, Sinisalo J, Steinthorsdottir V, Stolk RP, Tardif JC, Tonjes A, Tremblay A, Tremoli E, Virtamo J, Vohl MC, Amouyel P, Asselbergs FW, Assimes TL, Bochud M, Boehm BO, Boerwinkle E, Bottinger EP, Bouchard C, Cauchi S, Chambers JC, Chanock SJ, Cooper RS, de Bakker PI, Dedoussis G, Ferrucci L, Franks PW, Froguel P, Groop LC, Haiman CA, Hamsten A, Hayes MG, Hui J, Hunter DJ, Hveem K, Jukema JW, Kaplan RC, Kivimaki M, Kuh D, Laakso M, Liu Y, Martin NG, Marz W, Melbye M, Moebus S, Munroe PB, Njolstad I, Oostra BA, Palmer CN, Pedersen NL, Perola M, Perusse L, Peters U, Powell JE, Power C, Quertermous T, Rauramaa R, Reinmaa E, Ridker PM, Rivadeneira F, Rotter JI, Saaristo TE, Saleheen D, Schlessinger D, Slagboom PE, Snieder H, Spector TD, Strauch K, Stumvoll M, Tuomilehto J, Uusitupa M, van der Harst P, Volzke H, Walker M, Wareham NJ, Watkins H, Wichmann HE, Wilson JF, Zanen P, Deloukas P, Heid IM, Lindgren CM, Mohlke KL, Speliotes EK, Thorsteinsdottir U, Barroso I, Fox CS, North KE, Strachan DP, Beckmann JS, Berndt SI, Boehnke M, Borecki IB, McCarthy MI, Metspalu A, Stefansson K, Uitterlinden AG, van Duijn CM, Franke L, Willer CJ, Price AL, Lettre G, Loos RJ, Weedon MN, Ingelsson E, O'Connell JR, Abecasis GR, Chasman DI, Goddard ME, Visscher PM, Hirschhorn JN, Frayling TM. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat Genet 2014;46(11):1173-86. (url)

  • Woods DP, Ream TS, Amasino RM. Memory of the vernalized state in plants including the model grass Brachypodium distachyon. Front Plant Sci 2014;5:99. (url)

  • Wu Y, Williams EG, Dubuis S, Mottis A, Jovaisaite V, Houten SM, Argmann CA, Faridi P, Wolski W, Kutalik Z, Zamboni N, Auwerx J, Aebersold R. Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. Cell 2014;158(6):1415-30. (url)

  • Wu H, Fujiwara T, Yamamoto Y, Bolleman J, Yamaguchi A. BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. Journal of Biomedical Semantics 2014;5:32. (url)

  • Wunderlin T, Junier T, Roussel-Delif L, Jeanneret N, Junier P. Stage 0 sporulation gene A as a molecular marker to study diversity of endospore-forming Firmicutes. Environ Microbiol Rep 2013;5(6):911-24. (url)

  • Xing Y, Onstein RE, Carter RJ, Stadler T, Peter Linder H. Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity, and turnover rates are disconnected. Evolution 2014;68(10):2821-32. (url)

  • Zawistowski M, Reppell M, Wegmann D, St Jean PL, Ehm MG, Nelson MR, Novembre J, Zollner S. Analysis of rare variant population structure in Europeans explains differential stratification of gene-based tests. Eur J Hum Genet 2014. (url)

  • Zhou X, Lindsay H, Robinson MD. Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Res 2014;42(11):e91. (url)

  • Zimmermann C, Romero Y, Warnefors M, Bilican A, Borel C, Smith LB, Kotaja N, Kaessmann H, Nef S. Germ cell-specific targeting of DICER or DGCR8 reveals a novel role for endo-siRNAs in the progression of mammalian spermatogenesis and male fertility. PLoS One 2014;9(9):e107023. (url)

Conference proceedings


  • Chliamovitch G, Chopard B, Dupuis A. On the Dynamics of Multi-information in Cellular Automata. Cellular Automata LNiCS, editor. ACRI 2014; 2014; Krakow, Poland; 2014. p. 87-95. (url)

  • Karimaddini Z, Ünal E, Menshykau D, Iber D. Simulating Organogenesis in COMSOL: Image-based Modeling. COMSOL; 2014; Cambridge, UK; 2014. (url)

  • Shao M, Lin Y, Moret BME. An exact algorithm to compute the DCJ distance for genomes with duplicate genes. Science LNiC, editor. RECOMB'14; 2014; Pittsburgh, Pennsylvania, USA: Springer; 2014. p. 280-292. (url)

  • Velten B, Ünal E, Iber D. Image-based Parameter Inference for Spatio-temporal models of Organogenesis. NOLTA 2014; 2014; Luzern; 2014. (url)

  • Zhang M, Anzai H, Chopard B, Ohta M. An Optimization Method of FD Stent for Cerebral Aneurysm facing tne Stent Design and Manufacturing Needs. JSB2014; 2014; Shima, Japan; 2014. (url)

Book chapters


  • Iber D, Tanaka S, Fried P, Germann G, Menshykau D. Simulating Tissue Morphogenesis and Signaling. Nelson C, editor. Tissue Morphogenesis: Methods and Protocols: Springer Book Series: Methods in Molecular Biology; 2014. (url)

Other articles


  • Baillie Gerritsen V. a pain soothed. Protein Spotlight 2014 (157). (url)

  • Baillie Gerritsen V. a gut's tale. Protein Spotlight 2014 (158). (url)

  • Baillie Gerritsen V. On the garden pea. Protein Spotlight 2014 (159) (url)

  • Baillie Gerritsen V. An unusual chemistry. Protein Spotlight 2014 (160) (url)

  • Baillie Gerritsen V. The senses confused. Protein Spotlight 2014 (161) (url)

  • Baillie Gerritsen V. It did it its way. Protein Spotlight 2014 (162) (url)

  • Baillie Gerritsen V. Two's company. Protein Spotlight 2014 (163) (url)

  • Baillie Gerritsen V. Moving forward. Protein Spotlight 2014 (164) (url)

  • Baillie Gerritsen V. The heart of things. Protein Spotlight 2014 (165) (url)

 

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