Publications by SIB Members for the year 2016

Peer-reviewed journal articles

  • Abriata LA, Bovigny C, Dal Peraro M. Detection and sequence/structure mapping of biophysical constraints to protein variation in saturated mutational libraries and protein sequence alignments with a dedicated server. BMC Bioinformatics 2016;17(1):242. (url)
  • Andreozzi S, Chakrabarti A, Soh KC, Burgard A, Yang TH, Van Dien S, Miskovic L, Hatzimanikatis V. Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models. Metab Eng 2016. (url)
  • Andreozzi S, Miskovic L, Hatzimanikatis V. iSCHRUNK - In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks. Metab Eng 2016;33:158-68. (url)
  • Agerholm JS, Menzi F, McEvoy FJ, Jagannathan V, Drogemuller C. Lethal chondrodysplasia in a family of Holstein cattle is associated with a de novo splice site variant of COL2A1. BMC Vet Res 2016;12:100. (url)
  • Alcala N, Jensen JD, Telenti A, Vuilleumier S. The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV. G3 (Bethesda) 2016;6(1):107-20. (url)
  • Alexander HK, Lambert A, Stadler T. Quantifying Age-dependent Extinction from Species Phylogenies. Syst Biol 2016;65(1):35-50. (url)
  • Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjolander K, Jensen LJ, Martin MJ, Muffato M, Quest for Orthologs c, Gabaldon T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. Standardized benchmarking in the quest for orthologs. Nat Methods 2016;13(5):425-30. (url)
  • Alves I, Arenas M, Currat M, Sramkova Hanulova A, Sousa VC, Ray N, Excoffier L. Long-Distance Dispersal Shaped Patterns of Human Genetic Diversity in Eurasia. Mol Biol Evol 2016;33(4):946-58. (url)
  • An P, Penugonda S, Thorball CW, Bartha I, Goedert JJ, Donfield S, Buchbinder S, Binns-Roemer E, Kirk GD, Zhang W, Fellay J, Yu XF, Winkler CA. Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis Pneumonia. PLoS Genet 2016;12(3):e1005921. (url)
  • Artois J, Newman SH, Dhingra MS, Chaiban C, Linard C, Cattoli G, Monne I, Fusaro A, Xenarios I, Engler R, Liechti R, Kuznetsov D, Pham TL, Nguyen T, Pham VD, Castellan D, Von Dobschuetz S, Claes F, Dauphin G, Inui K, Gilbert M. Clade-level Spatial Modelling of HPAI H5N1 Dynamics in the Mekong Region Reveals New Patterns and Associations with Agro-Ecological Factors. Sci Rep 2016;6:30316. (url)
  • Bady P, Delorenzi M, Hegi ME. Sensitivity Analysis of the MGMT-STP27 Model and Impact of Genetic and Epigenetic Context to Predict the MGMT Methylation Status in Gliomas and Other Tumors. J Mol Diagn 2016;18(3):350-61. (url)
  • Barillari C, Ottoz DS, Fuentes-Serna JM, Ramakrishnan C, Rinn B, Rudolf F. openBIS ELN-LIMS: an open-source database for academic laboratories. Bioinformatics 2016;32(4):638-40. (url)
  • Benoit JB, Adelman ZN, Reinhardt K, Dolan A, Poelchau M, Jennings EC, Szuter EM, Hagan RW, Gujar H, Shukla JN, Zhu F, Mohan M, Nelson DR, Rosendale AJ, Derst C, Resnik V, Wernig S, Menegazzi P, Wegener C, Peschel N, Hendershot JM, Blenau W, Predel R, Johnston PR, Ioannidis P, Waterhouse RM, Nauen R, Schorn C, Ott MC, Maiwald F, Johnston JS, Gondhalekar AD, Scharf ME, Peterson BF, Raje KR, Hottel BA, Armisen D, Crumiere AJ, Refki PN, Santos ME, Sghaier E, Viala S, Khila A, Ahn SJ, Childers C, Lee CY, Lin H, Hughes DS, Duncan EJ, Murali SC, Qu J, Dugan S, Lee SL, Chao H, Dinh H, Han Y, Doddapaneni H, Worley KC, Muzny DM, Wheeler D, Panfilio KA, Vargas Jentzsch IM, Vargo EL, Booth W, Friedrich M, Weirauch MT, Anderson MA, Jones JW, Mittapalli O, Zhao C, Zhou JJ, Evans JD, Attardo GM, Robertson HM, Zdobnov EM, Ribeiro JM, Gibbs RA, Werren JH, Palli SR, Schal C, Richards S. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nat Commun 2016;7:10165. (url)
  • Bilbao A, Lisacek F, Hopfgartner G. Dedicated Software Enhancing Data-independent Acquisition Methods in Mass Spectrometry. Chimia (Aarau) 2016;70(4):293. (url)
  • Bischofberger M, Iacovache I, Boss D, Naef F, van der Goot FG, Molina N. Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling. Biophys J 2016;110(7):1574-81. (url)
  • Bonilla X, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy VB, Sharpe HJ, McKee T, Letourneau A, Ribaux PG, Popadin K, Basset-Seguin N, Ben Chaabene R, Santoni FA, Andrianova MA, Guipponi M, Garieri M, Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage FJ, Antonarakis SE, Nikolaev SI. Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma. Nat Genet 2016;48(4):398-406. (url)
  • Boutet E, Lieberherr D, Tognolli M, Schneider M, Bansal P, Bridge AJ, Poux S, Bougueleret L, Xenarios I. UniProtKB/Swiss-Prot, the Manually Annotated Section of the UniProt KnowledgeBase: How to Use the Entry View. Methods Mol Biol 2016;1374:23-54. (url)
  • Breda J, Rzepiela AJ, Gumienny R, van Nimwegen E, Zavolan M. Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99]. Methods 2016;104:204-205. (url)
  • Bron S, Henry L, Faes-Van't Hull E, Turrini R, Vanhecke D, Guex N, Ifticene-Treboux A, Marina Iancu E, Semilietof A, Rufer N, Lehr HA, Xenarios I, Coukos G, Delaloye JF, Doucey MA. TIE-2-expressing monocytes are lymphangiogenic and associate specifically with lymphatics of human breast cancer. Oncoimmunology 2016;5(2):e1073882. (url)
  • Buckleton J, Curran J, Goudet J, Taylor D, Thiery A, Weir BS. Population-specific FST values for forensic STR markers: A worldwide survey. Forensic Sci Int Genet 2016;23:91-100. (url)
  • Burger A, Lindsay H, Felker A, Hess C, Anders C, Chiavacci E, Zaugg J, Weber LM, Catena R, Jinek M, Robinson MD, Mosimann C. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes. Development 2016;143(11):2025-37. (url)
  • Burri R, Antoniazza S, Gaigher A, Ducrest AL, Simon C, European Barn Owl N, Fumagalli L, Goudet J, Roulin A. The genetic basis of color-related local adaptation in a ring-like colonization around the Mediterranean. Evolution 2016;70(1):140-53. (url)
  • Cattin S, Fellay B, Pradervand S, Trojan A, Ruhstaller T, Ruegg C, Furstenberger G. Bevacizumab specifically decreases elevated levels of circulating KIT+CD11b+ cells and IL-10 in metastatic breast cancer patients. Oncotarget 2016;7(10):11137-50. (url)
  • Christe C, Stolting KN, Bresadola L, Fussi B, Heinze B, Wegmann D, Lexer C. Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F fertility and recurrent gene flow. Mol Ecol 2016. (url)
  • Civenni G, Longoni N, Costales P, Dallavalle C, Garcia Inclan C, Albino D, Nunez LE, Moris F, Carbone GM, Catapano CV. EC-70124, a novel glycosylated indolocarbazole multi-kinase inhibitor, reverts tumorigenic and stem cell properties in prostate cancer by inhibiting STAT3 and NF-kappaB. Mol Cancer Ther 2016. (url)
  • Colaianna M, Ilmjarv S, Peterson H, Kern I, Julien S, Baquie M, Pallocca G, Bosgra S, Sachinidis A, Hengstler JG, Leist M, Krause KH. Fingerprinting of neurotoxic compounds using a mouse embryonic stem cell dual luminescence reporter assay. Arch Toxicol 2016. (url)
  • Crespo I, Doucey MA, Xenarios I. Social networks help to infer causality in the tumor microenvironment. BMC Res Notes 2016;9:168. (url)
  • Cordey S, Brito F, Vu DL, Turin L, Kilowoko M, Kyungu E, Genton B, Zdobnov EM, D'Acremont V, Kaiser L. Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology. Emerg Microbes Infect 2016;5(7):e67. (url)
  • Cordey S, Vu DL, Schibler M, L'Huillier AG, Brito F, Docquier M, Posfay-Barbe KM, Petty TJ, Turin L, Zdobnov EM, Kaiser L. Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection. Emerg Infect Dis 2016;22(5):846-53. (url)
  • Crippa S, Nemir M, Ounzain S, Ibberson M, Berthonneche C, Sarre A, Boisset G, Maison D, Harshman K, Xenarios I, Diviani D, Schorderet D, Pedrazzini T. Comparative transcriptome profiling of the injured zebrafish and mouse hearts identifies miRNA-dependent repair pathways. Cardiovasc Res 2016;110(1):73-84. (url)
  • Daina A, Zoete V. A BOILED-Egg To Predict Gastrointestinal Absorption and Brain Penetration of Small Molecules. ChemMedChem 2016;11(11):1117-21. (url)
  • Degueurce G, D'Errico I, Pich C, Ibberson M, Schutz F, Montagner A, Sgandurra M, Mury L, Jafari P, Boda A, Meunier J, Rezzonico R, Brembilla NC, Hohl D, Kolios A, Hofbauer G, Xenarios I, Michalik L. Identification of a novel PPARbeta/delta/miR-21-3p axis in UV-induced skin inflammation. EMBO Mol Med 2016;8(8):919-36. (url)
  • Delaleu N, Mydel P, Brun JG, Jonsson MV, Alimonti A, Jonsson R. Sjogren's syndrome patients with ectopic germinal centers present with a distinct salivary proteome. Rheumatology (Oxford) 2016;55(6):1127-37. (url)
  • Di Mitri D, Alimonti A. Non-Cell-Autonomous Regulation of Cellular Senescence in Cancer. Trends Cell Biol 2016;26(3):215-26. (url)
  • Doelle M, Linder KE, Boche J, Jagannathan V, Leeb T, Linek M. Initial characterization of stiff skin-like syndrome in West Highland white terriers. Vet Dermatol 2016;27(3):210-e53. (url)
  • Dousse A, Junier T, Zdobnov EM. CEGA-a catalog of conserved elements from genomic alignments. Nucleic Acids Res 2016;44(D1):D96-D100. (url)
  • Druce M, Hulo C, Masson P, Sommer P, Xenarios I, Le Mercier P, De Oliveira T. Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. Database (Oxford) 2016;2016. (url)
  • Drummond AJ, Stadler T. Bayesian phylogenetic estimation of fossil ages. Philos Trans R Soc Lond B Biol Sci 2016;371(1699). (url)
  • Dummer R, Siano M, Hunger RE, Lindenblatt N, Braun R, Michielin O, Mihic-Probst D, von Moos R, Najafi Y, Guckenberger M, Arnold A. The updated Swiss guidelines 2016 for the treatment and follow-up of cutaneous melanoma. Swiss Med Wkly 2016;146:w14279. (url)
  • Emery M, Nanchen N, Preitner F, Ibberson M, Roduit R. Biological Characterization of Gene Response to Insulin-Induced Hypoglycemia in Mouse Retina. PLoS One 2016;11(2):e0150266. (url)
  • Ewing GB, Jensen JD. The consequences of not accounting for background selection in demographic inference. Mol Ecol 2016;25(1):135-41. (url)
  • Fabre G, Garroum I, Mazurek S, Daraspe J, Mucciolo A, Sankar M, Humbel BM, Nawrath C. The ABCG transporter PEC1/ABCG32 is required for the formation of the developing leaf cuticle in Arabidopsis. New Phytol 2016;209(1):192-201. (url)
  • Ferrer-Admetlla A, Leuenberger C, Jensen JD, Wegmann D. An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data. Genetics 2016;203(2):831-46. (url)
  • Filippidou S, Jaussi M, Junier T, Wunderlin T, Jeanneret N, Palmieri F, Palmieri I, Roussel-Delif L, Vieth-Hillebrand A, Vetter A, Chain PS, Regenspurg S, Junier P. Anoxybacillus geothermalis sp. nov., a facultative anaerobic endospore-forming bacterium isolated from mineral deposits in a geothermal station. Int J Syst Evol Microbiol 2016. (url)
  • Flori M, Schmid CA, Sumrall ET, Tzankov A, Law CW, Robinson MD, Muller A. The hematopoietic oncoprotein FOXP1 promotes tumor cell survival in diffuse large B-cell lymphoma by repressing S1PR2 signaling. Blood 2016;127(11):1438-48. (url)
  • Foote AD, Vijay N, Avila-Arcos MC, Baird RW, Durban JW, Fumagalli M, Gibbs RA, Hanson MB, Korneliussen TS, Martin MD, Robertson KM, Sousa VC, Vieira FG, Vinar T, Wade P, Worley KC, Excoffier L, Morin PA, Gilbert MT, Wolf JB. Genome-culture coevolution promotes rapid divergence of killer whale ecotypes. Nat Commun 2016;7:11693. (url)
  • Franceschini A, Lin J, von Mering C, Jensen LJ. SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. Bioinformatics 2016;32(7):1085-7. (url)
  • Fuentes A, Carlos N, Ruiz Y, Callard D, Sanchez Y, Ochagavia ME, Seguin J, Malpica-Lopez N, Hohn T, Lecca MR, Perez R, Doreste V, Rehrauer H, Farinelli L, Pujol M, Pooggin MM. Field Trial and Molecular Characterization of RNAi-Transgenic Tomato Plants That Exhibit Resistance to Tomato Yellow Leaf Curl Geminivirus. Mol Plant Microbe Interact 2016;29(3):197-209. (url)
  • Gaidatzis D, Burger L, Florescu M, Stadler MB. Erratum: Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat Biotechnol 2016;34(2):210. (url)
  • Gaigher A, Burri R, Gharib WH, Taberlet P, Roulin A, Fumagalli L. Family-assisted inference of the genetic architecture of MHC variation. Mol Ecol Resour 2016. (url)
  • Gaudio E, Tarantelli C, Kwee I, Barassi C, Bernasconi E, Rinaldi A, Ponzoni M, Cascione L, Targa A, Stathis A, Goodstal S, Zucca E, Bertoni F. Combination of the MEK inhibitor pimasertib with BTK or PI3K-delta inhibitors is active in preclinical models of aggressive lymphomas. Ann Oncol 2016;27(6):1123-8. (url)
  • Genna V, Gaspari R, Dal Peraro M, De Vivo M. Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-eta. Nucleic Acids Res 2016;44(6):2827-36. (url)
  • Genomes Consortium. Electronic address mngoaa, Genomes C. 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana. Cell 2016;166(2):481-91. (url)
  • Glover NM, Antoniadi I, George GM, Gotzenberger L, Gutzat R, Koorem K, Liancourt P, Rutowicz K, Saharan K, You W, Mayer P. A Pragmatic Approach to Getting Published: 35 Tips for Early Career Researchers. Front Plant Sci 2016;7:610. (url)
  • Glover NM, Redestig H, Dessimoz C. Homoeologs: What Are They and How Do We Infer Them? Trends Plant Sci 2016;21(7):609-21. (url)
  • Golay J, Choblet S, Iwaszkiewicz J, Cerutti P, Ozil A, Loisel S, Pugniere M, Ubiali G, Zoete V, Michielin O, Berthou C, Kadouche J, Mach JP, Duonor-Cerutti M. Design and Validation of a Novel Generic Platform for the Production of Tetravalent IgG1-like Bispecific Antibodies. J Immunol 2016;196(7):3199-211. (url)
  • Gomez HF, Hucka M, Keating SM, Nudelman G, Iber D, Sealfon SC. MOCCASIN: converting MATLAB ODE models to SBML. Bioinformatics 2016;32(12):1905-6. (url)
  • Gori K, Suchan T, Alvarez N, Goldman N, Dessimoz C. Clustering Genes of Common Evolutionary History. Mol Biol Evol 2016;33(6):1590-605. (url)
  • Gourgues G, Barre A, Beaudoing E, Weber J, Magdelenat G, Barbe V, Schieck E, Jores J, Vashee S, Blanchard A, Lartigue C, Sirand-Pugnet P. Complete Genome Sequence of Mycoplasma mycoides subsp. mycoides T1/44, a Vaccine Strain against Contagious Bovine Pleuropneumonia. Genome Announc 2016;4(2). (url)
  • Gulia-Nuss M, Nuss AB, Meyer JM, Sonenshine DE, Roe RM, Waterhouse RM, Sattelle DB, de la Fuente J, Ribeiro JM, Megy K, Thimmapuram J, Miller JR, Walenz BP, Koren S, Hostetler JB, Thiagarajan M, Joardar VS, Hannick LI, Bidwell S, Hammond MP, Young S, Zeng Q, Abrudan JL, Almeida FC, Ayllon N, Bhide K, Bissinger BW, Bonzon-Kulichenko E, Buckingham SD, Caffrey DR, Caimano MJ, Croset V, Driscoll T, Gilbert D, Gillespie JJ, Giraldo-Calderon GI, Grabowski JM, Jiang D, Khalil SM, Kim D, Kocan KM, Koci J, Kuhn RJ, Kurtti TJ, Lees K, Lang EG, Kennedy RC, Kwon H, Perera R, Qi Y, Radolf JD, Sakamoto JM, Sanchez-Gracia A, Severo MS, Silverman N, Simo L, Tojo M, Tornador C, Van Zee JP, Vazquez J, Vieira FG, Villar M, Wespiser AR, Yang Y, Zhu J, Arensburger P, Pietrantonio PV, Barker SC, Shao R, Zdobnov EM, Hauser F, Grimmelikhuijzen CJ, Park Y, Rozas J, Benton R, Pedra JH, Nelson DR, Unger MF, Tubio JM, Tu Z, Robertson HM, Shumway M, Sutton G, Wortman JR, Lawson D, Wikel SK, Nene VM, Fraser CM, Collins FH, Birren B, Nelson KE, Caler E, Hill CA. Genomic insights into the Ixodes scapularis tick vector of Lyme disease. Nat Commun 2016;7:10507. (url)
  • Haba-Rubio J, Marti-Soler H, Marques-Vidal P, Tobback N, Andries D, Preisig M, Waeber G, Vollenweider P, Kutalik Z, Tafti M, Heinzer R. Prevalence and determinants of periodic limb movements in the general population. Ann Neurol 2016;79(3):464-74. (url)
  • Hatakeyama M, Opitz L, Russo G, Qi W, Schlapbach R, Rehrauer H. SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis. BMC Bioinformatics 2016;17(1):228. (url)
  • Henn BM, Botigue LR, Peischl S, Dupanloup I, Lipatov M, Maples BK, Martin AR, Musharoff S, Cann H, Snyder MP, Excoffier L, Kidd JM, Bustamante CD. Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proc Natl Acad Sci U S A 2016;113(4):E440-9. (url)
  • Herve V, Junier T, Bindschedler S, Verrecchia E, Junier P. Diversity and ecology of oxalotrophic bacteria. World J Microbiol Biotechnol 2016;32(2):28. (url)
  • Hofmanova Z, Kreutzer S, Hellenthal G, Sell C, Diekmann Y, Diez-Del-Molino D, van Dorp L, Lopez S, Kousathanas A, Link V, Kirsanow K, Cassidy LM, Martiniano R, Strobel M, Scheu A, Kotsakis K, Halstead P, Triantaphyllou S, Kyparissi-Apostolika N, Urem-Kotsou D, Ziota C, Adaktylou F, Gopalan S, Bobo DM, Winkelbach L, Blocher J, Unterlander M, Leuenberger C, Cilingiroglu C, Horejs B, Gerritsen F, Shennan SJ, Bradley DG, Currat M, Veeramah KR, Wegmann D, Thomas MG, Papageorgopoulou C, Burger J. Early farmers from across Europe directly descended from Neolithic Aegeans. Proc Natl Acad Sci U S A 2016;113(25):6886-91. (url)
  • Horlacher O, Lisacek F, Muller M. Mining Large Scale Tandem Mass Spectrometry Data for Protein Modifications Using Spectral Libraries. J Proteome Res 2016;15(3):721-31. (url)
  • Hoy MA, Waterhouse RM, Wu K, Estep AS, Ioannidis P, Palmer WJ, Pomerantz AF, Simao FA, Thomas J, Jiggins FM, Murphy TD, Pritham EJ, Robertson HM, Zdobnov EM, Gibbs RA, Richards S. Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution. Genome Biol Evol 2016;8(6):1762-75. (url)
  • Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res 2016;44(D1):D286-93. (url)
  • Hytonen MK, Arumilli M, Lappalainen AK, Owczarek-Lipska M, Jagannathan V, Hundi S, Salmela E, Venta P, Sarkiala E, Jokinen T, Gorgas D, Kere J, Nieminen P, Drogemuller C, Lohi H. Molecular Characterization of Three Canine Models of Human Rare Bone Diseases: Caffey, van den Ende-Gupta, and Raine Syndromes. PLoS Genet 2016;12(5):e1006037. (url)
  • Iacovache I, De Carlo S, Cirauqui N, Dal Peraro M, van der Goot FG, Zuber B. Cryo-EM structure of aerolysin variants reveals a novel protein fold and the pore-formation process. Nat Commun 2016;7:12062. (url)
  • Isakova A, Berset Y, Hatzimanikatis V, Deplancke B. Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models. J Biol Chem 2016;291(19):10293-306. (url)
  • Ison J, Rapacki K, Menager H, Kalas M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Gruning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Micetic I, Friborg RM, Moretti S, Morris C, Moller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwammle V, Smith C, Sperotto MM, Stockinger H, Varekova RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Longreen P, Brunak S. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res 2016;44(D1):D38-47. (url)
  • Janich P, Arpat AB, Castelo-Szekely V, Gatfield D. Analyzing the temporal regulation of translation efficiency in mouse liver. Genom Data 2016;8:41-4. (url)
  • Janowski R, Heinz GA, Schlundt A, Wommelsdorf N, Brenner S, Gruber AR, Blank M, Buch T, Buhmann R, Zavolan M, Niessing D, Heissmeyer V, Sattler M. Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40. Nat Commun 2016;7:11032. (url)
  • Jensen JD, Foll M, Bernatchez L. The past, present and future of genomic scans for selection. Mol Ecol 2016;25(1):1-4. (url)
  • Jiang L, Liu P, Bank C, Renzette N, Prachanronarong K, Yilmaz LS, Caffrey DR, Zeldovich KB, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Bolon DN. A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance. J Mol Biol 2016;428(3):538-53. (url)
  • Kamkina P, Snoek LB, Grossmann J, Volkers RJ, Sterken MG, Daube M, Roschitzki B, Fortes C, Schlapbach R, Roth A, von Mering C, Hengartner MO, Schrimpf SP, Kammenga JE. Natural Genetic Variation Differentially Affects the Proteome and Transcriptome in Caenorhabditis elegans. Mol Cell Proteomics 2016;15(5):1670-80. (url)
  • Kapopoulou A, Mathew L, Wong A, Trono D, Jensen JD. The evolution of gene expression and binding specificity of the largest transcription factor family in primates. Evolution 2016;70(1):167-80. (url)
  • Kapun M, Fabian DK, Goudet J, Flatt T. Genomic Evidence for Adaptive Inversion Clines in Drosophila melanogaster. Mol Biol Evol 2016. (url)
  • Kapuria V, Rohrig UF, Bhuiyan T, Borodkin VS, van Aalten DM, Zoete V, Herr W. Proteolysis of HCF-1 by Ser/Thr glycosylation-incompetent O-GlcNAc transferase:UDP-GlcNAc complexes. Genes Dev 2016;30(8):960-72. (url)
  • Karli P, Oevermann A, Bauer A, Jagannathan V, Leeb T. MFSD8 single-base pair deletion in a Chihuahua with neuronal ceroid lipofuscinosis. Anim Genet 2016. (url)
  • Kilpelainen TO & CO. Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels. Nat Commun 2016;7:10494. (url)
  • Kousathanas A, Leuenberger C, Helfer J, Quinodoz M, Foll M, Wegmann D. Likelihood-Free Inference in High-Dimensional Models. Genetics 2016;203(2):893-904. (url)
  • Kumar S, Bucher P. Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. BMC Bioinformatics 2016;17 Suppl 1:4. (url)
  • Lamparter D, Marbach D, Rueedi R, Kutalik Z, Bergmann S. Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. PLoS Comput Biol 2016;12(1):e1004714. (url)
  • Laurent S, Pfeifer SP, Settles ML, Hunter SS, Hardwick KM, Ormond L, Sousa VC, Jensen JD, Rosenblum EB. The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards. Mol Ecol 2016;25(1):306-23. (url)
  • Leake SL, Pagni M, Falquet L, Taroni F, Greub G. The salivary microbiome for differentiating individuals: proof of principle. Microbes Infect 2016;18(6):399-405. (url)
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Publications 2015