Publications by SIB Members for the year 2015

Peer-reviewed articles and conference proceedings

• Abate F, Todaro M, van der Krogt JA, Boi M, Landra I, Machiorlatti R, Tabbo F, Messana K, Abele C, Barreca A, Novero D, Gaudiano M, Aliberti S, Di Giacomo F, Tousseyn T, Lasorsa E, Crescenzo R, Bessone L, Ficarra E, Acquaviva A, Rinaldi A, Ponzoni M, Longo DL, Aime S, Cheng M, Ruggeri B, Piccaluga PP, Pileri S, Tiacci E, Falini B, Pera-Gresely B, Cerchietti L, Iqbal J, Chan WC, Shultz LD, Kwee I, Piva R, Wlodarska I, Rabadan R, Bertoni F, Inghirami G, European TcLSG. A novel patient-derived tumorgraft model with TRAF1-ALK anaplastic large-cell lymphoma translocation. Leukemia 2015;29(6):1390-401. (url)
• Abel J, Widmer A, John P, Stelling J. A Coupled Stochastic Model Explains Differences in Cry Knockout Behavior. IEEE Life Sciences Letters 2015;1(1):3 - 6 (url)
• Abriata LA, Dal Peraro M. Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding. Sci Rep 2015;5:10549. (url)
• Abriata LA, Palzkill T, Dal Peraro M. How structural and physicochemical determinants shape sequence constraints in a functional enzyme. PLoS One 2015;10(2):e0118684. (url)
• Aimo L, Liechti R, Hyka-Nouspikel N, Niknejad A, Gleizes A, Gotz L, Kuznetsov D, David FP, van der Goot FG, Riezman H, Bougueleret L, Xenarios I, Bridge A. The SwissLipids knowledgebase for lipid biology. Bioinformatics 2015. (url)
• Akyuz N, Georgieva ER, Zhou Z, Stolzenberg S, Cuendet MA, Khelashvili G, Altman RB, Terry DS, Freed JH, Weinstein H, Boudker O, Blanchard SC. Transport domain unlocking sets the uptake rate of an aspartate transporter. Nature 2015;518(7537):68-73. (url)
• Alajati A, Guccini I, Pinton S, Garcia-Escudero R, Bernasocchi T, Sarti M, Montani E, Rinaldi A, Montemurro F, Catapano C, Bertoni F, Alimonti A. Interaction of CDCP1 with HER2 enhances HER2-driven tumorigenesis and promotes trastuzumab resistance in breast cancer. Cell Rep 2015;11(4):564-76. (url)
• Alcala N, Jensen JD, Telenti A, Vuilleumier S. The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV. G3 (Bethesda) 2015;6(1):107-20. (url)
• Alfaiz AA, Muller V, Boutry-Kryza N, Ville D, Guex N, de Bellescize J, Rivier C, Labalme A, des Portes V, Edery P, Till M, Xenarios I, Sanlaville D, Herrmann JM, Lesca G, Reymond A. West syndrome caused by homozygous variant in the evolutionary conserved gene encoding the mitochondrial elongation factor GUF1. Eur J Hum Genet 2015. (url)
• Ali HS, Drewes S, Weber de Melo V, Schlegel M, Freise J, Groschup MH, Heckel G, Ulrich RG. Complete genome of a Puumala virus strain from Central Europe. Virus Genes 2015;50(2):292-8. (url)
• Allum F, Shao X, Guenard F, Simon MM, Busche S, Caron M, Lambourne J, Lessard J, Tandre K, Hedman AK, Kwan T, Ge B, Multiple Tissue Human Expression Resource C, Ronnblom L, McCarthy MI, Deloukas P, Richmond T, Burgess D, Spector TD, Tchernof A, Marceau S, Lathrop M, Vohl MC, Pastinen T, Grundberg E. Erratum: Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun 2015;6:8016. (url)
• Almeida AM, Bassols A, Bendixen E, Bhide M, Ceciliani F, Cristobal S, Eckersall PD, Hollung K, Lisacek F, Mazzucchelli G, McLaughlin M, Miller I, Nally JE, Plowman J, Renaut J, Rodrigues P, Roncada P, Staric J, Turk R. Animal board invited review: advances in proteomics for animal and food sciences. Animal 2015;9(1):1-17. (url)
• Almeida JM, Cisse OH, Fonseca A, Pagni M, Hauser PM. Comparative genomics suggests primary homothallism of Pneumocystis species. MBio 2015;6(1). (url)
• Alocci D, Mariethoz J, Horlacher O, Bolleman JT, Campbell MP, Lisacek F. Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search. PLoS One 2015;10(12):e0144578. (url)
• Altenhoff AM, Skunca N, Glover N, Train CM, Sueki A, Pilizota I, Gori K, Tomiczek B, Muller S, Redestig H, Gonnet GH, Dessimoz C. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res 2015;43(Database issue):D240-9. (url)
• Alwan H, Ehret G, Ponte B, Pruijm M, Ackermann D, Guessous I, Staessen JA, Asayama K, Kutalik Z, Vuistiner P, Paccaud F, Pechere-Bertschi A, Mohaupt M, Vogt B, Martin PY, Burnier M, Bochud M. Heritability of ambulatory and office blood pressure in the Swiss population. J Hypertens 2015;33(10):2061-7. (url)
• Amorim-Vaz S, Tran Vdu T, Pradervand S, Pagni M, Coste AT, Sanglard D. RNA Enrichment Method for Quantitative Transcriptional Analysis of Pathogens In Vivo Applied to the Fungus Candida albicans. MBio 2015;6(5):e00942-15. (url)
• Amorim CE, Daub JT, Salzano FM, Foll M, Excoffier L. Detection of convergent genome-wide signals of adaptation to tropical forests in humans. PLoS One 2015;10(4):e0121557. (url)
• Anisimova M, Pecerska J, Schaper E. Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. Front Bioeng Biotechnol 2015;3:31. (url)
• Anisimova M. Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry. BMC Evol Biol 2015;15:76. (url)
• Anstead CA, Korhonen PK, Young ND, Hall RS, Jex AR, Murali SC, Hughes DS, Lee SF, Perry T, Stroehlein AJ, Ansell BR, Breugelmans B, Hofmann A, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni HV, Worley KC, Muzny DM, Ioannidis P, Waterhouse RM, Zdobnov EM, James PJ, Bagnall NH, Kotze AC, Gibbs RA, Richards S, Batterham P, Gasser RB. Lucilia cuprina genome unlocks parasitic fly biology to underpin future interventions. Nat Commun 2015;6:7344. (url)
• Arous C, Ferreira PG, Dermitzakis ET, Halban PA. Short term exposure of beta cells to low concentrations of interleukin-1beta improves insulin secretion through focal adhesion and actin remodeling and regulation of gene expression. J Biol Chem 2015;290(23):14491. (url)
• Arribas AJ, Rinaldi A, Mensah AA, Kwee I, Cascione L, Robles EF, Martinez-Climent JA, Oscier D, Arcaini L, Baldini L, Marasca R, Thieblemont C, Briere J, Forconi F, Zamo A, Bonifacio M, Mollejo M, Facchetti F, Dirnhofer S, Ponzoni M, Bhagat G, Piris MA, Gaidano G, Zucca E, Rossi D, Bertoni F. DNA methylation profiling identifies two splenic marginal zone lymphoma subgroups with different clinical and genetic features. Blood 2015;125(12):1922-31. (url)
• Assefa K, Cannarozzi G, Girma D, Kamies R, Chanyalew S, Plaza-Wuthrich S, Blosch R, Rindisbacher A, Rafudeen S, Tadele Z. Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter]. Front Plant Sci 2015;6:177. (url)
• Ataman M, Hatzimanikatis V. Heading in the right direction: thermodynamics-based network analysis and pathway engineering. Curr Opin Biotechnol 2015;36:176-82. (url)
• Atger F, Gobet C, Marquis J, Martin E, Wang J, Weger B, Lefebvre G, Descombes P, Naef F, Gachon F. Circadian and feeding rhythms differentially affect rhythmic mRNA transcription and translation in mouse liver. Proc Natl Acad Sci U S A 2015;112(47):E6579-88. (url)
• Babbitt PC, Bagos PG, Bairoch A, Bateman A, Chatonnet A, Chen MJ, Craik DJ, Finn RD, Gloriam D, Haft DH, Henrissat B, Holliday GL, Isberg V, Kaas Q, Landsman D, Lenfant N, Manning G, Nagano N, Srinivasan N, O'Donovan C, Pruitt KD, Sowdhamini R, Rawlings ND, Saier MH, Jr., Sharman JL, Spedding M, Tsirigos KD, Vastermark A, Vriend G. Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat. Database (Oxford) 2015;2015:bav063. (url)
• Baker EK, Taylor S, Gupte A, Chalk AM, Bhattacharya S, Green AC, Martin TJ, Strbenac D, Robinson MD, Purton LE, Walkley CR. Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma. Bone 2015;73:223-32. (url)
• Bank C, Hietpas RT, Jensen JD, Bolon DN. A systematic survey of an intragenic epistatic landscape. Mol Biol Evol 2015;32(1):229-38. (url)
• Barbier de Reuille P, Routier-Kierzkowska AL, Kierzkowski D, Bassel GW, Schupbach T, Tauriello G, Bajpai N, Strauss S, Weber A, Kiss A, Burian A, Hofhuis H, Sapala A, Lipowczan M, Heimlicher MB, Robinson S, Bayer EM, Basler K, Koumoutsakos P, Roeder AH, Aegerter-Wilmsen T, Nakayama N, Tsiantis M, Hay A, Kwiatkowska D, Xenarios I, Kuhlemeier C, Smith RS. MorphoGraphX: A platform for quantifying morphogenesis in 4D. Elife 2015;4:05864. (url)
• Barribeau SM, Sadd BM, du Plessis L, Brown MJ, Buechel SD, Cappelle K, Carolan JC, Christiaens O, Colgan TJ, Erler S, Evans J, Helbing S, Karaus E, Lattorff HM, Marxer M, Meeus I, Napflin K, Niu J, Schmid-Hempel R, Smagghe G, Waterhouse RM, Yu N, Zdobnov EM, Schmid-Hempel P. A depauperate immune repertoire precedes evolution of sociality in bees. Genome Biol 2015;16:83. (url)
• Bartesaghi L, Arnaud Gouttenoire E, Prunotto A, Medard JJ, Bergmann S, Chrast R. Sox4 participates in the modulation of Schwann cell myelination. Eur J Neurosci 2015. (url)
• Bartha I, Fellay J. Adaptation on a genomic scale. Elife 2015;4:e06193. (url)
• Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M. The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database (Oxford) 2015;2015:bav043. (url)
• Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F. Cancer evolution: mathematical models and computational inference. Syst Biol 2015;64(1):e1-25. (url)
• Ben Belgacem M, Chopard B. A hybrid HPC/cloud distributed infrastructure: Coupling EC2 cloud resources with HPC clusters to run large tightly coupled multiscale applications. Future Generation Computer Systems;42(January 2015):11-21. (url)
• Benedetti F, Japaridze A, Dorier J, Racko D, Kwapich R, Burnier Y, Dietler G, Stasiak A. Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling. Nucleic Acids Res 2015;43(4):2390-9. (url)
• Bergottini VM, Filippidou S, Junier T, Johnson S, Chain PS, Otegui MB, Zapata PD, Junier P. Genome Sequence of Kosakonia radicincitans Strain YD4, a Plant Growth-Promoting Rhizobacterium Isolated from Yerba Mate (Ilex paraguariensis St. Hill.). Genome Announc 2015;3(2). (url)
• Berman HM, Gabanyi MJ, Groom CR, Johnson JE, Murshudov GN, Nicholls RA, Reddy V, Schwede T, Zimmerman MD, Westbrook J, Minor W. Data to knowledge: how to get meaning from your result. IUCrJ 2015;2(Pt 1):45-58. (url)
• Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. Front Microbiol 2015;6:101. (url)
• Bernasconi E, Gaudio E, Kwee I, Rinaldi A, Cascione L, Tarantelli C, Mensah AA, Stathis A, Zucca E, Vesci L, Giannini G, Bertoni F. The novel atypical retinoid ST5589 down-regulates Aurora Kinase A and has anti-tumour activity in lymphoma pre-clinical models. Br J Haematol 2015;171(3):378-86. (url)
• Bertelli C, Pillonel T, Torregrossa A, Prod'hom G, Fischer CJ, Greub G, Giannoni E. Bifidobacterium longum Bacteremia in Preterm Infants Receiving Probiotics. Clin Infect Dis 2015;60(6):924-7. (url)
• Bhuiyan T, Waridel P, Kapuria V, Zoete V, Herr W. Distinct OGT-Binding Sites Promote HCF-1 Cleavage. PLoS One 2015;10(8):e0136636. (url)
• Biass D, Violette A, Hulo N, Lisacek F, Favreau P, Stocklin R. Uncovering intense protein diversification in a cone snail venom gland using an integrative venomics approach. J Proteome Res 2015;14(2):628-38. (url)
• Bignucolo O, Leung HT, Grzesiek S, Berneche S. Backbone hydration determines the folding signature of amino acid residues. J Am Chem Soc 2015;137(13):4300-3. (url)
• Bilbao A, Varesio E, Luban J, Strambio-De-Castillia C, Hopfgartner G, Muller M, Lisacek F. Processing strategies and software solutions for data-independent acquisition in mass spectrometry. Proteomics 2015;15(5-6):964-80. (url)
• Bilbao A, Zhang Y, Varesio E, Luban J, Strambio-De-Castillia C, Lisacek F, Hopfgartner G. Ranking Fragment Ions Based on Outlier Detection for Improved Label-Free Quantification in Data-Independent Acquisition LC-MS/MS. J Proteome Res 2015;14(11):4581-93. (url)
• Bilgin Sonay T, Carvalho T, Robinson MD, Greminger MP, Krutzen M, Comas D, Highnam G, Mittelman D, Sharp A, Marques-Bonet T, Wagner A. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. Genome Res 2015;25(11):1591-9. (url)
• Bilgin Sonay T, Carvalho T, Robinson MD, Greminger MP, Krutzen M, Comas D, Highnam G, Mittelman D, Sharp A, Marques-Bonet T, Wagner A. Tandem repeat variation in human and great ape populations and its impact on gene expression divergence. Genome Res 2015;25(11):1591-9. (url)
• Blanc M, David F, Abrami L, Migliozzi D, Armand F, Burgi J, van der Goot FG. SwissPalm: Protein Palmitoylation database. F1000Res 2015;4:261. (url)
• Blanchoud S, Busso C, Naef F, Gonczy P. Quantitative analysis and modeling probe polarity establishment in C. elegans embryos. Biophys J 2015;108(4):799-809. (url)
• Blanchoud S, Nicolas D, Zoller B, Tidin O, Naef F. CAST: An automated segmentation and tracking tool for the analysis of transcriptional kinetics from single-cell time-lapse recordings. Methods 2015;85:3-11. (url)
• Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldon T, Quest for Orthologs Species Tree Working G. Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream. Genome Biol Evol 2015;7(7):1988-99. (url)
• Boi M, Gaudio E, Bonetti P, Kwee I, Bernasconi E, Tarantelli C, Rinaldi A, Testoni M, Cascione L, Ponzoni M, Mensah AA, Stathis A, Stussi G, Riveiro ME, Herait P, Inghirami G, Cvitkovic E, Zucca E, Bertoni F. The BET Bromodomain inhibitor OTX015 affects pathogenetic pathways in pre-clinical B-cell tumor models and synergizes with targeted drugs. Clin Cancer Res 2015. (url)
• Bonhoure N, Byrnes A, Moir RD, Hodroj W, Preitner F, Praz V, Marcelin G, Chua SC, Jr., Martinez-Lopez N, Singh R, Moullan N, Auwerx J, Willemin G, Shah H, Hartil K, Vaitheesvaran B, Kurland I, Hernandez N, Willis IM. Loss of the RNA polymerase III repressor MAF1 confers obesity resistance. Genes Dev 2015;29(9):934-47. (url)
• Bornet P, Clivaz C, Durisch Gauthier N, Honoré E. L'homme augmenté. Vital-IT-DH/Swiss Institute of Bioinformatics 2015. (url)
• Bou Sleiman MS, Osman D, Massouras A, Hoffmann AA, Lemaitre B, Deplancke B. Genetic, molecular and physiological basis of variation in Drosophila gut immunocompetence. Nat Commun 2015;6:7829. (url)
• Bovigny C, Tamo G, Lemmin T, Maino N, Dal Peraro M. LipidBuilder: A Framework To Build Realistic Models for Biological Membranes. J Chem Inf Model 2015;55(12):2491-9. (url)
• Brambilla L, Genini D, Laurini E, Merulla J, Perez L, Fermeglia M, Carbone GM, Pricl S, Catapano CV. Hitting the right spot: Mechanism of action of OPB-31121, a novel and potent inhibitor of the Signal Transducer and Activator of Transcription 3 (STAT3). Mol Oncol 2015;9(6):1194-206. (url)
• Brandenberg OF, Magnus C, Regoes RR, Trkola A. The HIV-1 Entry Process: A Stoichiometric View. Trends Microbiol 2015;23(12):763-74. (url)
• Brandt DY, Aguiar VR, Bitarello BD, Nunes K, Goudet J, Meyer D. Mapping Bias Overestimates Reference Allele Frequencies at the HLA Genes in the 1000 Genomes Project Phase I Data. G3 (Bethesda) 2015;5(5):931-41. (url)
• Bratulic S, Gerber F, Wagner A. Mistranslation drives the evolution of robustness in TEM-1 beta-lactamase. Proc Natl Acad Sci U S A 2015;112(41):12758-63. (url)
• Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M. Quantifying the strength of miRNA-target interactions. Methods 2015;85:90-9. (url)
• Bruford EA, Lane L, Harrow J. Devising a Consensus Framework for Validation of Novel Human Coding Loci. J Proteome Res 2015;14(12):4945-8. (url)
• Bruford MW, Ginja C, Hoffmann I, Joost S, Orozco-terWengel P, Alberto FJ, Amaral AJ, Barbato M, Biscarini F, Colli L, Costa M, Curik I, Duruz S, Ferencakovic M, Fischer D, Fitak R, Groeneveld LF, Hall SJ, Hanotte O, Hassan FU, Helsen P, Iacolina L, Kantanen J, Leempoel K, Lenstra JA, Ajmone-Marsan P, Masembe C, Megens HJ, Miele M, Neuditschko M, Nicolazzi EL, Pompanon F, Roosen J, Sevane N, Smetko A, Stambuk A, Streeter I, Stucki S, Supakorn C, Telo Da Gama L, Tixier-Boichard M, Wegmann D, Zhan X. Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025. Front Genet 2015;6:314. (url)
• Calcott B, Levy A, Siegal ML, Soyer OS, Wagner A. Engineering and Biology: Counsel for a Continued Relationship. Biol Theory 2015;10(1):50-59. (url)
• Carapito C, Lane L, Benama M, Opsomer A, Mouton-Barbosa E, Garrigues L, Gonzalez de Peredo A, Burel A, Bruley C, Gateau A, Bouyssie D, Jaquinod M, Cianferani S, Burlet-Schiltz O, Van Dorsselaer A, Garin J, Vandenbrouck Y. Computational and Mass-Spectrometry-Based Workflow for the Discovery and Validation of Missing Human Proteins: Application to Chromosomes 2 and 14. J Proteome Res 2015;14(9):3621-34. (url)
• Cebrian J, Kadomatsu-Hermosa MJ, Castan A, Martinez V, Parra C, Fernandez-Nestosa MJ, Schaerer C, Martinez-Robles ML, Hernandez P, Krimer DB, Stasiak A, Schvartzman JB. Electrophoretic mobility of supercoiled, catenated and knotted DNA molecules. Nucleic Acids Res 2015;43(4):e24. (url)
• Chasapi A, Wachowicz P, Niknejad A, Collin P, Krapp A, Cano E, Simanis V, Xenarios I. An Extended, Boolean Model of the Septation Initiation Network in S.Pombe Provides Insights into Its Regulation. PLoS One 2015;10(8):e0134214. (url)
• Chichester C, Karch O, Gaudet P, Lane L, Mons B, Bairoch A. Converting neXtProt into Linked Data and nanopublications. Semantic Web 2015;6(2):147-153 (url)
• Chila R, Basana A, Lupi M, Guffanti F, Gaudio E, Rinaldi A, Cascione L, Restelli V, Tarantelli C, Bertoni F, Damia G, Carrassa L. Combined inhibition of Chk1 and Wee1 as a new therapeutic strategy for mantle cell lymphoma. Oncotarget 2015;6(5):3394-408. (url)
• Chitikova Z, Pusztaszeri M, Makhlouf AM, Berczy M, Delucinge-Vivier C, Triponez F, Meyer P, Philippe J, Dibner C. Identification of new biomarkers for human papillary thyroid carcinoma employing NanoString analysis. Oncotarget 2015;6(13):10978-93. (url)
• Clivaz C. Pratiques de lecture, identités et prise de conscience : la question des miniatures et du Biblaridion d'Apocalypse 10, 2.9-10. Les judaïsmes dans tous leurs états aux Ier-IIIe siècles (Les Judéens des synagogues, les chrétiens et les rabbins). Actes du colloque de Lausanne 12-14 décembre 2012, 2015;JAOC 5, Turnhout: Brepols:321-344. (url)
• Clivaz C. Mais où est le corps? L'Homme augmenté comme lieu des Humanities Digitales. L'Homme Augmenté, Lausanne: VITAL-DH/Swiss Institute of Bioinformatics 2015. (url)
• Clivaz C. Trois éléments du dossier sans fin des sources et réécritures d'1 Cor 2,9. La littérature apocryphe chrétienne et les Ecritures juives (Publications de l'Institut Romand des Sciences Bibliques 7 2015;Prangins: Ed. du Zèbre(dans R. Gounelle - B. Mounier (éd.)):439-458. (url)
• Clivaz C. Jésus était-il un bel homme? dans Gilles Bourquin (éd.), Jésus - 12 questions impertinentes, OPEC et Olivétan 2015:43-44. (url)
• Clivaz C. En quête des couvertures et corpus. Quelques éclats d’humanités digitales. Carayol Valerie, Morandi Franc (éd.), Le Tournant Numérique des Sciences Humaines et Sociales, Pessac, MSHA 2015:97-109. (url)
• Clivaz C, Mimouni S, Pouderon B. Les judaïsmes dans tous leurs états aux Ier-IIIe siècles (Les Judéens des synagogues, les chrétiens et les rabbins). Actes du colloque de Lausanne 12-14 décembre 2012. 2015;JAOC 5, Turnhout: Brepols. (url)
• Clivaz C, Rivoal M, Sankar M. A New Plateform for Editing Digital Multimedia: The eTalks. New Avenues for Electronic Publishing in the Age of Infinite Collections and Citizen Science: Scale, Openness and Trust 2015:156-159. (url)
• Coffee, Caffeine Genetics & CO. Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption. Mol Psychiatry 2015;20(5):647-56. (url)
• Conconi A, Franceschetti S, Aprile von Hohenstaufen K, Margiotta-Casaluci G, Stathis A, Moccia AA, Bertoni F, Ramponi A, Mazzucchelli L, Cavalli F, Gaidano G, Zucca E. Histologic transformation in marginal zone lymphomasdagger. Ann Oncol 2015;26(11):2329-35. (url)
• Conconi A, Lobetti-Bodoni C, Montoto S, Lopez-Guillermo A, Coutinho R, Matthews J, Franceschetti S, Bertoni F, Moccia A, Rancoita PM, Gribben J, Cavalli F, Gaidano G, Lister TA, Montserrat E, Ghielmini M, Zucca E. Life expectancy of young adults with follicular lymphoma. Ann Oncol 2015;26(11):2317-22. (url)
• Consortium GT. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 2015;348(6235):648-60. (url)
• Constantinescu S, Szczurek E, Mohammadi P, Rahnenfuhrer J, Beerenwinkel N. TiMEx: a waiting time model for mutually exclusive cancer alterations. Bioinformatics 2015. (url)
• Cordey S, Bel M, Petty TJ, Docquier M, Sacco L, Turin L, Cherpillod P, Emonet S, Louis-Simonet M, Zdobnov EM, Ambrosioni J, Kaiser L. Toscana virus meningitis case in Switzerland: an example of the ezVIR bioinformatics pipeline utility for the identification of emerging viruses. Clin Microbiol Infect 2015;21(4):387 e1-4. (url)
• Cornet E, Debliquis A, Rimelen V, Civic N, Docquier M, Troussard X, Drenou B, Matthes T. Developing Molecular Signatures for Chronic Lymphocytic Leukemia. PLoS One 2015;10(6):e0128990. (url)
• Dall'Olio GM, Vahdati AR, Bertranpetit J, Wagner A, Laayouni H. VCF2Networks: applying genotype networks to single-nucleotide variants data. Bioinformatics 2015;31(3):438-9. (url)
• Daub JT, Dupanloup I, Robinson-Rechavi M, Excoffier L. Inference of Evolutionary Forces Acting on Human Biological Pathways. Genome Biol Evol 2015;7(6):1546-58. (url)
• Daub JT, Merks RM. Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit. Methods Mol Biol 2015;1214:67-127. (url)
• de Barsy M, Bertelli C, Jacquier N, Kebbi-Beghdadi C, Greub G. ESCCAR international congress on Rickettsia and other intracellular bacteria. Microbes Infect 2015;17(10):680-8. (url)
• de Vargas Roditi L, Claassen M. Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics. Curr Opin Biotechnol 2015;34:9-15. (url)
• De Vrieze M, Pandey P, Bucheli TD, Varadarajan AR, Ahrens CH, Weisskopf L, Bailly A. Volatile Organic Compounds from Native Potato-associated Pseudomonas as Potential Anti-oomycete Agents. Front Microbiol 2015;6:1295. (url)
• Decker B, Davis BW, Rimbault M, Long AH, Karlins E, Jagannathan V, Reiman R, Parker HG, Drogemuller C, Corneveaux JJ, Chapman ES, Trent JM, Leeb T, Huentelman MJ, Wayne RK, Karyadi DM, Ostrander EA. Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor. Genome Res 2015;25(11):1646-55. (url)
• Delacretaz A, Preisig M, Vandenberghe F, Saigi Morgui N, Quteineh L, Choong E, Gholam-Rezaee M, Kutalik Z, Magistretti P, Aubry JM, von Gunten A, Castelao E, Vollenweider P, Waeber G, Conus P, Eap CB. Influence of MCHR2 and MCHR2-AS1 Genetic Polymorphisms on Body Mass Index in Psychiatric Patients and In Population-Based Subjects with Present or Past Atypical Depression. PLoS One 2015;10(10):e0139155. (url)
• Demaria O, De Gassart A, Coso S, Gestermann N, Di Domizio J, Flatz L, Gaide O, Michielin O, Hwu P, Petrova TV, Martinon F, Modlin RL, Speiser DE, Gilliet M. STING activation of tumor endothelial cells initiates spontaneous and therapeutic antitumor immunity. Proc Natl Acad Sci U S A 2015;112(50):15408-13. (url)
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• Zhao C, Escalante LN, Chen H, Benatti TR, Qu J, Chellapilla S, Waterhouse RM, Wheeler D, Andersson MN, Bao R, Batterton M, Behura SK, Blankenburg KP, Caragea D, Carolan JC, Coyle M, El-Bouhssini M, Francisco L, Friedrich M, Gill N, Grace T, Grimmelikhuijzen CJ, Han Y, Hauser F, Herndon N, Holder M, Ioannidis P, Jackson L, Javaid M, Jhangiani SN, Johnson AJ, Kalra D, Korchina V, Kovar CL, Lara F, Lee SL, Liu X, Lofstedt C, Mata R, Mathew T, Muzny DM, Nagar S, Nazareth LV, Okwuonu G, Ongeri F, Perales L, Peterson BF, Pu LL, Robertson HM, Schemerhorn BJ, Scherer SE, Shreve JT, Simmons D, Subramanyam S, Thornton RL, Xue K, Weissenberger GM, Williams CE, Worley KC, Zhu D, Zhu Y, Harris MO, Shukle RH, Werren JH, Zdobnov EM, Chen MS, Brown SJ, Stuart JJ, Richards S. A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor. Curr Biol 2015;25(5):613-20. (url)
• Zhou X, Law CW, Robinson M. benchmarkR: an R package for benchmarking genome-scale methods. bioRxiv 2015. (url)
• Zhou X, Robinson MD. Do count-based differential expression methods perform poorly when genes are expressed in only one condition? Genome Biol 2015;16:222. (url)
• Zhu Z, Frey O, Haandbaek N, Franke F, Rudolf F, Hierlemann A. Time-lapse electrical impedance spectroscopy for monitoring the cell cycle of single immobilized S. pombe cells. Sci Rep 2015;5:17180. (url)
• Zisaki A, Miskovic L, Hatzimanikatis V. Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches. Curr Pharm Des 2015;21(6):806-22. (url)
• Zoller B, Nicolas D, Molina N, Naef F. Structure of silent transcription intervals and noise characteristics of mammalian genes. Mol Syst Biol 2015;11(7):823. (url)
• Zoller S, Boskova V, Anisimova M. Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions. Mol Biol Evol 2015;32(8):2208-16. (url)

Conference proceedings

• Abriata L, Dal Peraro M. Experimental and computational studies of the effects of highly concentrated solutes on proteins: Insights into the causes and consequences of quinary protein structure and cytoplasmic organization. Protein Science; 2015: Wiley-Blackwell; 2015. p. 102-102. (url)
• Shao M, Moret BME. A fast and exact algorithm for the exemplar breakpoint distance. 9029 LNiCS, editor. RECOMB'15; 2015 April 12-15; Warsaw, Poland: Springer Verlag 2015. p. 309-322. (url)

Book Chapters

• Anisimova M, Gil M. Methodologies for Phylogenetic Inference. Wiley, editor. eLS; 2015. (url)
• Cascella M, Dal Peraro M, De Vivo M. Computational Chemistry Strategies Tackling Function and Inhibition of Pharmaceutically Relevant Targets. Zaheer Ul-Haq JDM, editor. Frontiers in Computational Chemistry; 2015. p. 290-343. (url)
• Gobeill J, Gaudinat A, Ruch P. Instance-Based Learning for Tweet Monitoring and Categorization Experimental IR Meets Multilinguality, Multimodality, and Interaction: Springer; 2015. p. 235–240. (url)

Other articles

• Baillie Gerritsen V. Taming genes. Protein Spotlight 2015 (167). (url)
• Baillie Gerritsen V. A question of perspective. Protein Spotlight 2015 (168). (url)
• Baillie Gerritsen V. Another shade of red. Protein Spotlight 2015 (169). (url)
• Baillie Gerritsen V. The length of things. Protein Spotlight 2015 (170). (url)
• Baillie Gerritsen V. Becoming two. Protein Spotlight 2015 (171). (url)
• Baillie Gerritsen V. Approaching happiness. Protein Spotlight 2015 (172). (url)
• Baillie Gerritsen V. The makings of a face. Protein Spotlight 2015 (173). (url)
• Baillie Gerritsen V. The smell of the sea. Protein Spotlight 2015 (174). (url)