Publications by SIB Members published in 2017

Listed in Europe PMC, latest update: 2017-11-01.

Peer-reviewed articles and conference proceedings

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  1. Aalders KC, Kuijer A, Straver ME, Slaets L, Litiere S, Viale G, Van't Veer LJ, Glas AM, Delorenzi M, van Dalen T, Tryfonidis K, Piccart MJ, Cardoso F, Rutgers EJ, TRANSBIG Consortium and the MINDACT Investigators. Characterisation of multifocal breast cancer using the 70-gene signature in clinical low-risk patients enrolled in the EORTC 10041/BIG 03-04 MINDACT trial. Eur J Cancer 2017;79:98-105
  2. Abriata LA, Albanesi D, Dal Peraro M, de Mendoza D. Signal Sensing and Transduction by Histidine Kinases as Unveiled through Studies on a Temperature Sensor. Acc Chem Res 2017;50(6):1359-1366
  3. Aeschbacher S, Selby JP, Willis JH, Coop G. Population-genomic inference of the strength and timing of selection against gene flow. Proc Natl Acad Sci U S A 2017;114(27):7061-7066
  4. Aeschimann F, Kumari P, Bartake H, Gaidatzis D, Xu L, Ciosk R, Großhans H. LIN41 Post-transcriptionally Silences mRNAs by Two Distinct and Position-Dependent Mechanisms. Mol Cell 2017;65(3):476-489.e4
  5. Aguilar-Rodríguez J, Payne JL, Wagner A. A thousand empirical adaptive landscapes and their navigability. Nat Ecol Evol 2017;1(2):45
  6. Akhmedov M, Kedaigle A, Chong RE, Montemanni R, Bertoni F, Fraenkel E, Kwee I. PCSF: An R-package for network-based interpretation of high-throughput data. PLoS Comput Biol 2017;13(7):e1005694
  7. Alberti-Servera L, von Muenchow L, Tsapogas P, Capoferri G, Eschbach K, Beisel C, Ceredig R, Ivanek R, Rolink A. Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors. EMBO J 2017
  8. Alghanem B, Nikitin F, Stricker T, Duchoslav E, Luban J, Strambio-De-Castillia C, Muller M, Lisacek F, Varesio E, Hopfgartner G. Optimization by infusion of multiple reaction monitoring transitions for sensitive quantification of peptides by liquid chromatography/mass spectrometry. Rapid Commun Mass Spectrom 2017;31(9):753-761
  9. An J, Ponthier CM, Sack R, Seebacher J, Stadler MB, Donovan KA, Fischer ES. pSILAC mass spectrometry reveals ZFP91 as IMiD-dependent substrate of the CRL4CRBN ubiquitin ligase. Nat Commun 2017;8:15398
  10. Anderson WP, Global Life Science Data Resources Working Group. Data management: A global coalition to sustain core data. Nature 2017;543(7644):179
  11. Anikster Y, Haack TB, Vilboux T, Pode-Shakked B, Thöny B, Shen N, Guarani V, Meissner T, Mayatepek E, Trefz FK, Marek-Yagel D, Martinez A, Huttlin EL, Paulo JA, Berutti R, Benoist JF, Imbard A, Dorboz I, Heimer G, Landau Y, Ziv-Strasser L, Malicdan MCV, Gemperle-Britschgi C, Cremer K, Engels H, Meili D, Keller I, Bruggmann R, Strom TM, Meitinger T, Mullikin JC, Schwartz G, Ben-Zeev B, Gahl WA, Harper JW, Blau N, Hoffmann GF, Prokisch H, Opladen T, Schiff M. Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability. Am J Hum Genet 2017;100(2):257-266
  12. Ansar M, Riazuddin S, Sarwar MT, Makrythanasis P, Paracha SA, Iqbal Z, Khan J, Assir MZ, Hussain M, Razzaq A, Polla DL, Taj AS, Holmgren A, Batool N, Misceo D, Iwaszkiewicz J, de Brouwer APM, Guipponi M, Hanquinet S, Zoete V, Santoni FA, Frengen E, Ahmed J, Riazuddin S, van Bokhoven H, Antonarakis SE. Biallelic variants in LINGO1 are associated with autosomal recessive intellectual disability, microcephaly, speech and motor delay. Genet Med 2017
  13. Antiochos P, Marques-Vidal P, Virzi J, Pagano S, Satta N, Hartley O, Montecucco F, Mach F, Kutalik Z, Waeber G, Vollenweider P, Vuilleumier N. Impact of CD14 Polymorphisms on Anti-Apo A-1 (Apolipoprotein A-1) IgG-Related Coronary Artery Disease Prediction in the General Population. Arterioscler Thromb Vasc Biol 2017
  14. Antiochos P, Marques-Vidal P, Virzi J, Pagano S, Satta N, Hartley O, Montecucco F, Mach F, Kutalik Z, Waeber G, Vollenweider P, Vuilleumier N. Anti-Apolipoprotein A-1 IgG Predict All-Cause Mortality and Are Associated with Fc Receptor-Like 3 Polymorphisms. Front Immunol 2017;8:437
  15. Arvaniti E, Claassen M. Sensitive detection of rare disease-associated cell subsets via representation learning. Nat Commun 2017;8:14825
  16. Asgari S, Schlapbach LJ, Anchisi S, Hammer C, Bartha I, Junier T, Mottet-Osman G, Posfay-Barbe KM, Longchamp D, Stocker M, Cordey S, Kaiser L, Riedel T, Kenna T, Long D, Schibler A, Telenti A, Tapparel C, McLaren PJ, Garcin D, Fellay J. Severe viral respiratory infections in children with IFIH1 loss-of-function mutations. Proc Natl Acad Sci U S A 2017;114(31):8342-8347
  17. Avalle L, Incarnato D, Savino A, Gai M, Marino F, Pensa S, Barbieri I, Stadler MB, Provero P, Oliviero S, Poli V. MicroRNAs-143 and -145 induce epithelial to mesenchymal transition and modulate the expression of junction proteins. Cell Death Differ 2017;24(10):1750-1760
  18. Awasthi Mishra N, Drögemüller C, Jagannathan V, Keller I, Wüthrich D, Bruggmann R, Beck J, Schütz E, Brenig B, Demmel S, Moser S, Signer-Hasler H, Pieńkowska-Schelling A, Schelling C, Sande M, Rongen R, Rieder S, Kelsh RN, Mercader N, Leeb T. A structural variant in the 5'-flanking region of the TWIST2 gene affects melanocyte development in belted cattle. PLoS One 2017;12(6):e0180170
  19. Barido-Sottani J, Bošková V, du Plessis L, Kühnert D, Magnus C, Mitov V, Müller NF, Pecerska J, Rasmussen DA, Zhang C, Drummond AJ, Heath TA, Pybus OG, Vaughan TG, Stadler T. Taming the BEAST - A community teaching material resource for BEAST 2. Syst Biol 2017
  20. Bartha I, McLaren PJ, Brumme C, Harrigan R, Telenti A, Fellay J. Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control. PLoS Comput Biol 2017;13(2):e1005339
  21. Bassani-Sternberg M, Chong C, Guillaume P, Solleder M, Pak H, Gannon PO, Kandalaft LE, Coukos G, Gfeller D. Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity. PLoS Comput Biol 2017;13(8):e1005725
  22. Becker E, Schmidt TSB, Bengs S, Poveda L, Opitz L, Atrott K, Stanzel C, Biedermann L, Rehman A, Jonas D, von Mering C, Rogler G, Frey-Wagner I. Effects of oral antibiotics and isotretinoin on the murine gut microbiota. Int J Antimicrob Agents 2017;50(3):342-351
  23. Benedetti F, Racko D, Dorier J, Burnier Y, Stasiak A. Transcription-induced supercoiling explains formation of self-interacting chromatin domains in S. pombe. Nucleic Acids Res 2017;45(17):9850-9859
  24. Bernasconi E, Gaudio E, Lejeune P, Tarantelli C, Cascione L, Kwee I, Spriano F, Rinaldi A, Mensah AA, Chung E, Stathis A, Siegel S, Schmees N, Ocker M, Zucca E, Haendler B, Bertoni F. Preclinical evaluation of the BET bromodomain inhibitor BAY 1238097 for the treatment of lymphoma. Br J Haematol 2017;178(6):936-948
  25. Bertelli C, Mueller L, Thomas V, Pillonel T, Jacquier N, Greub G. Cedratvirus lausannensis - digging into Pithoviridae diversity. Environ Microbiol 2017;19(10):4022-4034
  26. Bhosale PG, Cristea S, Ambatipudi S, Desai RS, Kumar R, Patil A, Kane S, Borges AM, Schäffer AA, Beerenwinkel N, Mahimkar MB. Chromosomal Alterations and Gene Expression Changes Associated with the Progression of Leukoplakia to Advanced Gingivobuccal Cancer. Transl Oncol 2017;10(3):396-409
  27. Binder V, Bergum B, Jaisson S, Gillery P, Scavenius C, Spriet E, Nyhaug AK, Roberts HM, Chapple ILC, Hellvard A, Delaleu N, Mydel P. Impact of fibrinogen carbamylation on fibrin clot formation and stability. Thromb Haemost 2017;117(5):899-910
  28. Blanquart F, Wymant C, Cornelissen M, Gall A, Bakker M, Bezemer D, Hall M, Hillebregt M, Ong SH, Albert J, Bannert N, Fellay J, Fransen K, Gourlay AJ, Grabowski MK, Gunsenheimer-Bartmeyer B, Günthard HF, Kivelä P, Kouyos R, Laeyendecker O, Liitsola K, Meyer L, Porter K, Ristola M, van Sighem A, Vanham G, Berkhout B, Kellam P, Reiss P, Fraser C, BEEHIVE collaboration. Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe. PLoS Biol 2017;15(6):e2001855
  29. Boareto M, Iber D, Taylor V. Differential interactions between Notch and ID factors control neurogenesis by modulating Hes factor autoregulation. Development 2017;144(19):3465-3474
  30. Borghesi A, Stronati M, Fellay J. Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune Responses. Front Immunol 2017;8:215
  31. Bosshard L, Dupanloup I, Tenaillon O, Bruggmann R, Ackermann M, Peischl S, Excoffier L. Accumulation of Deleterious Mutations During Bacterial Range Expansions. Genetics 2017;207(2):669-684
  32. Bovay A, Zoete V, Dolton G, Bulek AM, Cole DK, Rizkallah PJ, Fuller A, Beck K, Michielin O, Speiser DE, Sewell AK, Fuertes Marraco SA. T cell Receptor Alpha Variable 12-2 bias in the immunodominant response to Yellow fever virus. Eur J Immunol 2017
  33. Bramsen JB, Rasmussen MH, Ongen H, Mattesen TB, Ørntoft MW, Árnadóttir SS, Sandoval J, Laguna T, Vang S, Øster B, Lamy P, Madsen MR, Laurberg S, Esteller M, Dermitzakis ET, Ørntoft TF, Andersen CL. Molecular-Subtype-Specific Biomarkers Improve Prediction of Prognosis in Colorectal Cancer. Cell Rep 2017;19(6):1268-1280
  34. Bratulic S, Toll-Riera M, Wagner A. Mistranslation can enhance fitness through purging of deleterious mutations. Nat Commun 2017;8:15410
  35. Britschgi A, Duss S, Kim S, Couto JP, Brinkhaus H, Koren S, De Silva D, Mertz KD, Kaup D, Varga Z, Voshol H, Vissieres A, Leroy C, Roloff T, Stadler MB, Scheel CH, Miraglia LJ, Orth AP, Bonamy GM, Reddy VA, Bentires-Alj M. The Hippo kinases LATS1 and 2 control human breast cell fate via crosstalk with ERα. Nature 2017;541(7638):541-545
  36. Brown AA, Viñuela A, Delaneau O, Spector TD, Small KS, Dermitzakis ET. Predicting causal variants affecting expression by using whole-genome sequencing and RNA-seq from multiple human tissues. Nat Genet 2017
  37. Brown AA. veqtl-mapper: variance association mapping for molecular phenotypes. Bioinformatics 2017;33(17):2772-2773
  38. Bryois J, Buil A, Ferreira PG, Panousis NI, Brown AA, Viñuela A, Planchon A, Bielser D, Small K, Spector T, Dermitzakis ET. Time-dependent genetic effects on gene expression implicate aging processes. Genome Res 2017;27(4):545-552
  39. Burley SK, Kurisu G, Markley JL, Nakamura H, Velankar S, Berman HM, Sali A, Schwede T, Trewhella J. PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models. Structure 2017;25(9):1317-1318
  40. Campbell MP, Peterson RA, Gasteiger E, Mariethoz J, Lisacek F, Packer NH. Navigating the Glycome Space and Connecting the Glycoproteome. Methods Mol Biol 2017;1558:139-158
  41. Carapito C, Duek P, Macron C, Seffals M, Rondel K, Delalande F, Lindskog C, Fréour T, Vandenbrouck Y, Lane L, Pineau C. Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods. J Proteome Res 2017
  42. Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A, Gfeller D. Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Res 2017;27(3):451-461
  43. Carrat GR, Hu M, Nguyen-Tu MS, Chabosseau P, Gaulton KJ, van de Bunt M, Siddiq A, Falchi M, Thurner M, Canouil M, Pattou F, Leclerc I, Pullen TJ, Cane MC, Prabhala P, Greenwald W, Schulte A, Marchetti P, Ibberson M, MacDonald PE, Manning Fox JE, Gloyn AL, Froguel P, Solimena M, McCarthy MI, Rutter GA. Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice. Am J Hum Genet 2017;100(2):238-256
  44. Cascione L, Rinaldi A, Chiappella A, Kwee I, Ciccone G, Altenbuchinger M, Kohler C, Vitolo U, Inghirami G, Bertoni F. Diffuse large B cell lymphoma cell of origin by digital expression profiling in the REAL07 Phase 1-2 study. Br J Haematol 2017
  45. Castelli M, Clementi N, Pfaff J, Sautto GA, Diotti RA, Burioni R, Doranz BJ, Dal Peraro M, Clementi M, Mancini N. A Biologically-validated HCV E1E2 Heterodimer Structural Model. Sci Rep 2017;7(1):214
  46. Castelo-Szekely V, Arpat AB, Janich P, Gatfield D. Translational contributions to tissue specificity in rhythmic and constitutive gene expression. Genome Biol 2017;18(1):116
  47. Chang H, Hoshina N, Zhang C, Ma Y, Cao H, Wang Y, Wu DD, Bergen SE, Landén M, Hultman CM, Preisig M, Kutalik Z, Castelao E, Grigoroiu-Serbanescu M, Forstner AJ, Strohmaier J, Hecker J, Schulze TG, Müller-Myhsok B, Reif A, Mitchell PB, Martin NG, Schofield PR, Cichon S, Nöthen MM, Swedish Bipolar Study Group, MooDS Bipolar Consortium, Walter H, Erk S, Heinz A, Amin N, van Duijn CM, Meyer-Lindenberg A, Tost H, Xiao X, Yamamoto T, Rietschel M, Li M. The protocadherin 17 gene affects cognition, personality, amygdala structure and function, synapse development and risk of major mood disorders. Mol Psychiatry 2017
  48. Chen H, Cade BE, Gleason KJ, Bjonnes AC, Stilp AM, Sofer T, Conomos MP, Ancoli-Israel S, Arens R, Azarbarzin A, Bell GI, Below JE, Chun S, Evans DS, Ewert R, Frazier-Wood AC, Gharib SA, Haba-Rubio J, Hagen EW, Heinzer R, Hillman DR, Johnson WC, Kutalik Z, Lane JM, Larkin EK, Lee SK, Liang J, Loredo JS, Mukherjee S, Palmer LJ, Papanicolaou GJ, Penzel T, Peppard PE, Post WS, Ramos AR, Rice K, Rotter JI, Sands SA, Shah NA, Shin C, Stone KL, Stubbe B, Sul JH, Tafti M, Taylor KD, Teumer A, Thornton TA, Tranah GJ, Wang C, Wang H, Warby SC, Wellman DA, Zee PC, Hanis CL, Laurie CC, Gottlieb DJ, Patel SR, Zhu X, Sunyaev SR, Saxena R, Lin X, Redline S. Multi-ethnic Meta-analysis Identifies RAI1 as a Possible Obstructive Sleep Apnea Related Quantitative Trait Locus in Men. Am J Respir Cell Mol Biol 2017
  49. Chen W, Gardeux V, Meireles-Filho A, Deplancke B. Profiling of Single-Cell Transcriptomes. Curr Protoc Mouse Biol 2017;7(3):145-175
  50. Chevalier MF, Trabanelli S, Racle J, Salomé B, Cesson V, Gharbi D, Bohner P, Domingos-Pereira S, Dartiguenave F, Fritschi AS, Speiser DE, Rentsch CA, Gfeller D, Jichlinski P, Nardelli-Haefliger D, Jandus C, Derré L. ILC2-modulated T cell-to-MDSC balance is associated with bladder cancer recurrence. J Clin Invest 2017;127(8):2916-2929
  51. Chevrier S, Levine JH, Zanotelli VRT, Silina K, Schulz D, Bacac M, Ries CH, Ailles L, Jewett MAS, Moch H, van den Broek M, Beisel C, Stadler MB, Gedye C, Reis B, Pe'er D, Bodenmiller B. An Immune Atlas of Clear Cell Renal Cell Carcinoma. Cell 2017;169(4):736-749.e18
  52. Crippa S, Ancey PB, Vazquez J, Angelino P, Rougemont AL, Guettier C, Zoete V, Delorenzi M, Michielin O, Meylan E. Mutant CTNNB1 and histological heterogeneity define metabolic subtypes of hepatoblastoma. EMBO Mol Med 2017
  53. Cruciani-Guglielmacci C, Bellini L, Denom J, Oshima M, Fernandez N, Normandie-Levi P, Berney XP, Kassis N, Rouch C, Dairou J, Gorman T, Smith DM, Marley A, Liechti R, Kuznetsov D, Wigger L, Burdet F, Lefèvre AL, Wehrle I, Uphues I, Hildebrandt T, Rust W, Bernard C, Ktorza A, Rutter GA, Scharfmann R, Xenarios I, Le Stunff H, Thorens B, Magnan C, Ibberson M. Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion. Mol Metab 2017;6(4):340-351
  54. Daina A, Michielin O, Zoete V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 2017;7:42717
  55. Darwiche R, Mène-Saffrané L, Gfeller D, Asojo OA, Schneiter R. The pathogen-related yeast protein Pry1, a member of the CAP protein superfamily, is a fatty acid-binding protein. J Biol Chem 2017;292(20):8304-8314
  56. Daub JT, Moretti S, Davydov II, Excoffier L, Robinson-Rechavi M. Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. Mol Biol Evol 2017;34(6):1391-1402
  57. Davydov II, Robinson-Rechavi M, Salamin N. State aggregation for fast likelihood computations in molecular evolution. Bioinformatics 2017;33(3):354-362
  58. de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017;26(10):2608-2622
  59. Dhillon DS, Milinkovitch MC, Zwicker M. Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces. Bull Math Biol 2017;79(4):788-827
  60. Ding W, Baumdicker F, Neher RA. panX: pan-genome analysis and exploration. Nucleic Acids Res 2017
  61. Dobay MP, Lemonnier F, Missiaglia E, Bastard C, Vallois D, Jais JP, Scourzic L, Dupuy A, Fataccioli V, Pujals A, Parrens M, Le Bras F, Rousset T, Picquenot JM, Martin N, Haioun C, Delarue R, Bernard OA, Delorenzi M, de Leval L, Gaulard P. Integrative clinicopathological and molecular analyses of angioimmunoblastic T-cell lymphoma and other nodal lymphomas of follicular helper T-cell origin. Haematologica 2017;102(4):e148-e151
  62. Dréos R, Ambrosini G, Groux R, Périer RC, Bucher P. MGA repository: a curated data resource for ChIP-seq and other genome annotated data. Nucleic Acids Res 2017
  63. Egli T, Vukojevic V, Sengstag T, Jacquot M, Cabezón R, Coynel D, Freytag V, Heck A, Vogler C, de Quervain DJ, Papassotiropoulos A, Milnik A. Exhaustive search for epistatic effects on the human methylome. Sci Rep 2017;7(1):13669
  64. Essaidi-Laziosi M, Brito F, Benaoudia S, Royston L, Cagno V, Fernandes-Rocha M, Piuz I, Zdobnov E, Huang S, Constant S, Boldi MO, Kaiser L, Tapparel C. Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures. J Allergy Clin Immunol 2017
  65. Feigelman R, Kahlert CR, Baty F, Rassouli F, Kleiner RL, Kohler P, Brutsche MH, von Mering C. Sputum DNA sequencing in cystic fibrosis: non-invasive access to the lung microbiome and to pathogen details. Microbiome 2017;5(1):20
  66. Fonseca Costa SS, Wegmann D, Ripperger JA. Normalisation against Circadian and Age-Related Disturbances Enables Robust Detection of Gene Expression Changes in Liver of Aged Mice. PLoS One 2017;12(1):e0169615
  67. Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT, Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics 2017
  68. Frismantas V, Dobay MP, Rinaldi A, Tchinda J, Dunn SH, Kunz J, Richter-Pechanska P, Marovca B, Pail O, Jenni S, Diaz-Flores E, Chang BH, Brown TJ, Collins RH, Uhrig S, Balasubramanian GP, Bandapalli OR, Higi S, Eugster S, Voegeli P, Delorenzi M, Cario G, Loh ML, Schrappe M, Stanulla M, Kulozik AE, Muckenthaler MU, Saha V, Irving JA, Meisel R, Radimerski T, Von Stackelberg A, Eckert C, Tyner JW, Horvath P, Bornhauser BC, Bourquin JP. Ex vivo drug response profiling detects recurrent sensitivity patterns in drug-resistant acute lymphoblastic leukemia. Blood 2017;129(11):e26-e37
  69. Gardeux V, David FPA, Shajkofci A, Schwalie PC, Deplancke B. ASAP: a web-based platform for the analysis and interactive visualization of single-cell RNA-seq data. Bioinformatics 2017;33(19):3123-3125
  70. Gegenschatz-Schmid K, Verkauskas G, Demougin P, Bilius V, Dasevicius D, Stadler MB, Hadziselimovic F. DMRTC2, PAX7, BRACHYURY/T and TERT Are Implicated in Male Germ Cell Development Following Curative Hormone Treatment for Cryptorchidism-Induced Infertility. Genes (Basel) 2017;8(10)
  71. Gille D, Zangger N, Soneson C, Bütikofer U, Delorenzi M, Schwander F, Kopf-Bolanz KA, Chollet M, Walther B, Laederach K, Vergères G. Caloric dose-responsive genes in blood cells differentiate the metabolic status of obese men. J Nutr Biochem 2017;43:156-165
  72. Gnügge R, Rudolf F. Saccharomyces cerevisiae Shuttle vectors. Yeast 2017;34(5):205-221
  73. Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F, Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Syst 2017
  74. Goundaroulis D, Dorier J, Benedetti F, Stasiak A. Studies of global and local entanglements of individual protein chains using the concept of knotoids. Sci Rep 2017;7(1):6309
  75. Gouy A, Daub JT, Excoffier L. Detecting gene subnetworks under selection in biological pathways. Nucleic Acids Res 2017;45(16):e149
  76. Gouy A, Zieger M. STRAF-A convenient online tool for STR data evaluation in forensic genetics. Forensic Sci Int Genet 2017;30:148-151
  77. Graff M, Scott RA, Justice AE, Young KL, Feitosa MF, Barata L, Winkler TW, Chu AY, Mahajan A, Hadley D, Xue L, Workalemahu T, Heard-Costa NL, den Hoed M, Ahluwalia TS, Qi Q, Ngwa JS, Renström F, Quaye L, Eicher JD, Hayes JE, Cornelis M, Kutalik Z, Lim E, Luan J, Huffman JE, Zhang W, Zhao W, Griffin PJ, Haller T, Ahmad S, Marques-Vidal PM, Bien S, Yengo L, Teumer A, Smith AV, Kumari M, Harder MN, Justesen JM, Kleber ME, Hollensted M, Lohman K, Rivera NV, Whitfield JB, Zhao JH, Stringham HM, Lyytikäinen LP, Huppertz C, Willemsen G, Peyrot WJ, Wu Y, Kristiansson K, Demirkan A, Fornage M, Hassinen M, Bielak LF, Cadby G, Tanaka T, Mägi R, van der Most PJ, Jackson AU, Bragg-Gresham JL, Vitart V, Marten J, Navarro P, Bellis C, Pasko D, Johansson Å, Snitker S, Cheng YC, Eriksson J, Lim U, Aadahl M, Adair LS, Amin N, Balkau B, Auvinen J, Beilby J, Bergman RN, Bergmann S, Bertoni AG, Blangero J, Bonnefond A, Bonnycastle LL, Borja JB, Brage S, Busonero F, Buyske S, Campbell H, Chines PS, Collins FS, Corre T, Smith GD, Delgado GE, Dueker N, Dörr M, Ebeling T, Eiriksdottir G, Esko T, Faul JD, Fu M, Færch K, Gieger C, Gläser S, Gong J, Gordon-Larsen P, Grallert H, Grammer TB, Grarup N, van Grootheest G, Harald K, Hastie ND, Havulinna AS, Hernandez D, Hindorff L, Hocking LJ, Holmens OL, Holzapfel C, Hottenga JJ, Huang J, Huang T, Hui J, Huth C, Hutri-Kähönen N, James AL, Jansson JO, Jhun MA, Juonala M, Kinnunen L, Koistinen HA, Kolcic I, Komulainen P, Kuusisto J, Kvaløy K, Kähönen M, Lakka TA, Launer LJ, Lehne B, Lindgren CM, Lorentzon M, Luben R, Marre M, Milaneschi Y, Monda KL, Montgomery GW, De Moor MHM, Mulas A, Müller-Nurasyid M, Musk AW, Männikkö R, Männistö S, Narisu N, Nauck M, Nettleton JA, Nolte IM, Oldehinkel AJ, Olden M, Ong KK, Padmanabhan S, Paternoster L, Perez J, Perola M, Peters A, Peters U, Peyser PA, Prokopenko I, Puolijoki H, Raitakari OT, Rankinen T, Rasmussen-Torvik LJ, Rawal R, Ridker PM, Rose LM, Rudan I, Sarti C, Sarzynski MA, Savonen K, Scott WR, Sanna S, Shuldiner AR, Sidney S, Silbernagel G, Smith BH, Smith JA, Snieder H, Stančáková A, Sternfeld B, Swift AJ, Tammelin T, Tan ST, Thorand B, Thuillier D, Vandenput L, Vestergaard H, van Vliet-Ostaptchouk JV, Vohl MC, Völker U, Waeber G, Walker M, Wild S, Wong A, Wright AF, Zillikens MC, Zubair N, Haiman CA, Lemarchand L, Gyllensten U, Ohlsson C, Hofman A, Rivadeneira F, Uitterlinden AG, Pérusse L, Wilson JF, Hayward C, Polasek O, Cucca F, Hveem K, Hartman CA, Tönjes A, Bandinelli S, Palmer LJ, Kardia SLR, Rauramaa R, Sørensen TIA, Tuomilehto J, Salomaa V, Penninx BWJH, de Geus EJC, Boomsma DI, Lehtimäki T, Mangino M, Laakso M, Bouchard C, Martin NG, Kuh D, Liu Y, Linneberg A, März W, Strauch K, Kivimäki M, Harris TB, Gudnason V, Völzke H, Qi L, Järvelin MR, Chambers JC, Kooner JS, Froguel P, Kooperberg C, Vollenweider P, Hallmans G, Hansen T, Pedersen O, Metspalu A, Wareham NJ, Langenberg C, Weir DR, Porteous DJ, Boerwinkle E, Chasman DI, CHARGE Consortium, EPIC-InterAct Consortium, PAGE Consortium, Abecasis GR, Barroso I, McCarthy MI, Frayling TM, O'Connell JR, van Duijn CM, Boehnke M, Heid IM, Mohlke KL, Strachan DP, Fox CS, Liu CT, Hirschhorn JN, Klein RJ, Johnson AD, Borecki IB, Franks PW, North KE, Cupples LA, Loos RJF, Kilpeläinen TO. Genome-wide physical activity interactions in adiposity - A meta-analysis of 200,452 adults. PLoS Genet 2017;13(4):e1006528
  78. Gros-Balthazard M, Galimberti M, Kousathanas A, Newton C, Ivorra S, Paradis L, Vigouroux Y, Carter R, Tengberg M, Battesti V, Santoni S, Falquet L, Pintaud JC, Terral JF, Wegmann D. The Discovery of Wild Date Palms in Oman Reveals a Complex Domestication History Involving Centers in the Middle East and Africa. Curr Biol 2017;27(14):2211-2218.e8
  79. Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES. Systematic dissection of genomic features determining transcription factor binding and enhancer function. Proc Natl Acad Sci U S A 2017;114(7):E1291-E1300
  80. Gschwind AR, Singh A, Certa U, Reymond A, Heckel T. Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis. BMC Genomics 2017;18(1):144
  81. Gunawan R, Hutter S. Assessing and Resolving Model Misspecifications in Metabolic Flux Analysis. Bioengineering (Basel) 2017;4(2)
  82. Hadziselimovic F, Gegenschatz-Schmid K, Verkauskas G, Demougin P, Bilius V, Dasevicius D, Stadler MB. Genes Involved in Long-Term Memory Are Expressed in Testis of Cryptorchid Boys and Respond to GnRHa Treatment. Cytogenet Genome Res 2017;152(1):9-15
  83. Harlander S, Schönenberger D, Toussaint NC, Prummer M, Catalano A, Brandt L, Moch H, Wild PJ, Frew IJ. Combined mutation in Vhl, Trp53 and Rb1 causes clear cell renal cell carcinoma in mice. Nat Med 2017;23(7):869-877
  84. Hass H, Masson K, Wohlgemuth S, Paragas V, Allen JE, Sevecka M, Pace E, Timmer J, Stelling J, MacBeath G, Schoeberl B, Raue A. Predicting ligand-dependent tumors from multi-dimensional signaling features. NPJ Syst Biol Appl 2017;3:27
  85. Hatakeyama M, Aluri S, Balachadran MT, Sivarajan SR, Patrignani A, Grüter S, Poveda L, Shimizu-Inatsugi R, Baeten J, Francoijs KJ, Nataraja KN, Reddy YAN, Phadnis S, Ravikumar RL, Schlapbach R, Sreeman SM, Shimizu KK. Multiple hybrid de novo genome assembly of finger millet, an orphan allotetraploid crop. DNA Res 2017
  86. Heer FT, Posson DJ, Wojtas-Niziurski W, Nimigean CM, Bernèche S. Mechanism of activation at the selectivity filter of the KcsA K(+) channel. Elife 2017;6
  87. Heilmann-Heimbach S, Herold C, Hochfeld LM, Hillmer AM, Nyholt DR, Hecker J, Javed A, Chew EG, Pechlivanis S, Drichel D, Heng XT, Del Rosario RC, Fier HL, Paus R, Rueedi R, Galesloot TE, Moebus S, Anhalt T, Prabhakar S, Li R, Kanoni S, Papanikolaou G, Kutalik Z, Deloukas P, Philpott MP, Waeber G, Spector TD, Vollenweider P, Kiemeney LA, Dedoussis G, Richards JB, Nothnagel M, Martin NG, Becker T, Hinds DA, Nöthen MM. Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness. Nat Commun 2017;8:14694
  88. Herdman C, Mars JC, Stefanovsky VY, Tremblay MG, Sabourin-Felix M, Lindsay H, Robinson MD, Moss T. A unique enhancer boundary complex on the mouse ribosomal RNA genes persists after loss of Rrn3 or UBF and the inactivation of RNA polymerase I transcription. PLoS Genet 2017;13(7):e1006899
  89. Heulot M, Jacquier N, Aeby S, Le Roy D, Roger T, Trofimenko E, Barras D, Greub G, Widmann C. The Anticancer Peptide TAT-RasGAP317-326 Exerts Broad Antimicrobial Activity. Front Microbiol 2017;8:994
  90. Hilber-Bodmer M, Schmid M, Ahrens CH, Freimoser FM. Competition assays and physiological experiments of soil and phyllosphere yeasts identify Candida subhashii as a novel antagonist of filamentous fungi. BMC Microbiol 2017;17(1):4
  91. Hinard V, Britan A, Schaeffer M, Zahn-Zabal M, Thomet U, Rougier JS, Bairoch A, Abriel H, Gaudet P. Annotation of functional impact of voltage-gated sodium channel mutations. Hum Mutat 2017;38(5):485-493
  92. Hofmann AL, Behr J, Singer J, Kuipers J, Beisel C, Schraml P, Moch H, Beerenwinkel N. Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers. BMC Bioinformatics 2017;18(1):8
  93. Horro C, Cook M, Attwood TK, Brazas MD, Hancock JM, Palagi P, Corpas M, Jimenez R. BioCIDER: a Contextualisation InDEx for biological Resources discovery. Bioinformatics 2017;33(16):2607-2608
  94. Horvathova I, Voigt F, Kotrys AV, Zhan Y, Artus-Revel CG, Eglinger J, Stadler MB, Giorgetti L, Chao JA. The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells. Mol Cell 2017
  95. Hosseini SR, Wagner A. Constraint and Contingency Pervade the Emergence of Novel Phenotypes in Complex Metabolic Systems. Biophys J 2017;113(3):690-701
  96. Huang Z, Lin H, Fellay J, Kutalik Z, Hubaux JP. SQC: secure quality control for meta-analysis of genome-wide association studies. Bioinformatics 2017;33(15):2273-2280
  97. Huerta-Cepas J, Forslund K, Coelho LP, Szklarczyk D, Jensen LJ, von Mering C, Bork P. Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. Mol Biol Evol 2017;34(8):2115-2122
  98. Hulo C, Masson P, de Castro E, Auchincloss AH, Foulger R, Poux S, Lomax J, Bougueleret L, Xenarios I, Le Mercier P. The ins and outs of eukaryotic viruses: Knowledge base and ontology of a viral infection. PLoS One 2017;12(2):e0171746
  99. Hulo C, Masson P, Toussaint A, Osumi-Sutherland D, de Castro E, Auchincloss AH, Poux S, Bougueleret L, Xenarios I, Le Mercier P. Bacterial Virus Ontology; Coordinating across Databases. Viruses 2017;9(6)
  100. Hutter S, Villiger TK, Brühlmann D, Stettler M, Broly H, Soos M, Gunawan R. Glycosylation flux analysis reveals dynamic changes of intracellular glycosylation flux distribution in Chinese hamster ovary fed-batch cultures. Metab Eng 2017;43(pt a):9-20
  101. Ioannidis P, Simao FA, Waterhouse RM, Manni M, Seppey M, Robertson HM, Misof B, Niehuis O, Zdobnov EM. Genomic Features of the Damselfly Calopteryx splendens Representing a Sister Clade to Most Insect Orders. Genome Biol Evol 2017;9(2):415-430
  102. Irving M, Vuillefroy de Silly R, Scholten K, Dilek N, Coukos G. Engineering Chimeric Antigen Receptor T-Cells for Racing in Solid Tumors: Don't Forget the Fuel. Front Immunol 2017;8:267
  103. Isakova A, Groux R, Imbeault M, Rainer P, Alpern D, Dainese R, Ambrosini G, Trono D, Bucher P, Deplancke B. SMiLE-seq identifies binding motifs of single and dimeric transcription factors. Nat Methods 2017;14(3):316-322
  104. Japaridze A, Muskhelishvili G, Benedetti F, Gavriilidou AF, Zenobi R, De Los Rios P, Longo G, Dietler G. Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization. Nano Lett 2017;17(3):1938-1948
  105. Jeevan-Raj B, Gehrig J, Charmoy M, Chennupati V, Grandclément C, Angelino P, Delorenzi M, Held W. The Transcription Factor Tcf1 Contributes to Normal NK Cell Development and Function by Limiting the Expression of Granzymes. Cell Rep 2017;20(3):613-626
  106. Jeffares DC, Jolly C, Hoti M, Speed D, Shaw L, Rallis C, Balloux F, Dessimoz C, Bähler J, Sedlazeck FJ. Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast. Nat Commun 2017;8:14061
  107. Joshi PK, Pirastu N, Kentistou KA, Fischer K, Hofer E, Schraut KE, Clark DW, Nutile T, Barnes CLK, Timmers PRHJ, Shen X, Gandin I, McDaid AF, Hansen TF, Gordon SD, Giulianini F, Boutin TS, Abdellaoui A, Zhao W, Medina-Gomez C, Bartz TM, Trompet S, Lange LA, Raffield L, van der Spek A, Galesloot TE, Proitsi P, Yanek LR, Bielak LF, Payton A, Murgia F, Concas MP, Biino G, Tajuddin SM, Seppälä I, Amin N, Boerwinkle E, Børglum AD, Campbell A, Demerath EW, Demuth I, Faul JD, Ford I, Gialluisi A, Gögele M, Graff M, Hingorani A, Hottenga JJ, Hougaard DM, Hurme MA, Ikram MA, Jylhä M, Kuh D, Ligthart L, Lill CM, Lindenberger U, Lumley T, Mägi R, Marques-Vidal P, Medland SE, Milani L, Nagy R, Ollier WER, Peyser PA, Pramstaller PP, Ridker PM, Rivadeneira F, Ruggiero D, Saba Y, Schmidt R, Schmidt H, Slagboom PE, Smith BH, Smith JA, Sotoodehnia N, Steinhagen-Thiessen E, van Rooij FJA, Verbeek AL, Vermeulen SH, Vollenweider P, Wang Y, Werge T, Whitfield JB, Zonderman AB, Lehtimäki T, Evans MK, Pirastu M, Fuchsberger C, Bertram L, Pendleton N, Kardia SLR, Ciullo M, Becker DM, Wong A, Psaty BM, van Duijn CM, Wilson JG, Jukema JW, Kiemeney L, Uitterlinden AG, Franceschini N, North KE, Weir DR, Metspalu A, Boomsma DI, Hayward C, Chasman D, Martin NG, Sattar N, Campbell H, Esko T, Kutalik Z, Wilson JF. Genome-wide meta-analysis associates HLA-DQA1/DRB1 and LPA and lifestyle factors with human longevity. Nat Commun 2017;8(1):910
  108. Junge A, Refsgaard JC, Garde C, Pan X, Santos A, Alkan F, Anthon C, von Mering C, Workman CT, Jensen LJ, Gorodkin J. RAIN: RNA-protein Association and Interaction Networks. Database (Oxford) 2017;2017
  109. Kim DE, Procopio MG, Ghosh S, Jo SH, Goruppi S, Magliozzi F, Bordignon P, Neel V, Angelino P, Dotto GP. Convergent roles of ATF3 and CSL in chromatin control of cancer-associated fibroblast activation. J Exp Med 2017;214(8):2349-2368
  110. Knuckles P, Carl SH, Musheev M, Niehrs C, Wenger A, Bühler M. RNA fate determination through cotranscriptional adenosine methylation and microprocessor binding. Nat Struct Mol Biol 2017;24(7):561-569
  111. Koegel S, Mieulet D, Baday S, Chatagnier O, Lehmann MF, Wiemken A, Boller T, Wipf D, Bernèche S, Guiderdoni E, Courty PE. Phylogenetic, structural, and functional characterization of AMT3;1, an ammonium transporter induced by mycorrhization among model grasses. Mycorrhiza 2017
  112. Kopparam J, Chiffelle J, Angelino P, Piersigilli A, Zangger N, Delorenzi M, Meylan E. RIP4 inhibits STAT3 signaling to sustain lung adenocarcinoma differentiation. Cell Death Differ 2017;24(10):1761-1771
  113. Krebs AR, Imanci D, Hoerner L, Gaidatzis D, Burger L, Schübeler D. Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters. Mol Cell 2017;67(3):411-422.e4
  114. Križanovic K, Echchiki A, Roux J, Šikic M. Evaluation of tools for long read RNA-seq splice-aware alignment. Bioinformatics 2017
  115. Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 2017
  116. Kryshtafovych A, Monastyrskyy B, Fidelis K, Schwede T, Tramontano A. Assessment of model accuracy estimations in CASP12. Proteins 2017
  117. Kuipers J, Jahn K, Beerenwinkel N. Advances in understanding tumour evolution through single-cell sequencing. Biochim Biophys Acta 2017;1867(2):127-138
  118. Kuipers J, Jahn K, Raphael BJ, Beerenwinkel N. Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors. Genome Res 2017
  119. Lafita A, Bliven S, Kryshtafovych A, Bertoni M, Monastyrskyy B, Duarte JM, Schwede T, Capitani G. Assessment of protein assembly prediction in CASP12 CASP12 assembly. Proteins 2017
  120. Lamparter D, Marbach D, Rueedi R, Bergmann S, Kutalik Z. Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility. PLoS Comput Biol 2017;13(1):e1005311
  121. Lang BM, Biedermann L, van Haaften WT, de Vallière C, Schuurmans M, Begré S, Zeitz J, Scharl M, Turina M, Greuter T, Schreiner P, Heinrich H, Kuntzen T, Vavricka SR, Rogler G, Beerenwinkel N, Misselwitz B, Swiss IBD Cohort Study Group. Genetic polymorphisms associated with smoking behaviour predict the risk of surgery in patients with Crohn's disease. Aliment Pharmacol Ther 2017
  122. Laurent S, Salamin N, Robinson-Rechavi M. No evidence for the radiation time lag model after whole genome duplications in Teleostei. PLoS One 2017;12(4):e0176384
  123. Lavoué S, Bertrand JAM, Chen WJ, Ho HC, Motomura H, Sado T, Miya M. Phylogenetic position of the rainbow sardine Dussumieria (Dussumieriidae) and its bearing on the early evolution of the Clupeoidei. Gene 2017;623:41-47
  124. Lavoué S, Bertrand JAM, Wang HY, Chen WJ, Ho HC, Motomura H, Hata H, Sado T, Miya M. Molecular systematics of the anchovy genus Encrasicholina in the Northwest Pacific. PLoS One 2017;12(7):e0181329
  125. Lehtonen S, Silvestro D, Karger DN, Scotese C, Tuomisto H, Kessler M, Peña C, Wahlberg N, Antonelli A. Environmentally driven extinction and opportunistic origination explain fern diversification patterns. Sci Rep 2017;7(1):4831
  126. Leiba J, Sabra A, Bodinier R, Marchetti A, Lima WC, Melotti A, Perrin J, Burdet F, Pagni M, Soldati T, Lelong E, Cosson P. Vps13F links bacterial recognition and intracellular killing in Dictyostelium. Cell Microbiol 2017;19(7)
  127. Leitman EM, Willberg CB, Tsai MH, Chen H, Buus S, Chen F, Riddell L, Haas D, Fellay J, Goedert JJ, Piechocka-Trocha A, Walker BD, Martin J, Deeks S, Wolinsky SM, Martinson J, Martin M, Qi Y, Sáez-Cirión A, Yang OO, Matthews PC, Carrington M, Goulder PJR. HLA-B*14:02-Restricted Env-Specific CD8+ T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection. J Virol 2017;91(22)
  128. Lepik K, Annilo T, Kukuškina V, eQTLGen Consortium, Kisand K, Kutalik Z, Peterson P, Peterson H. C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis. PLoS Comput Biol 2017;13(9):e1005766
  129. Leuenberger P, Ganscha S, Kahraman A, Cappelletti V, Boersema PJ, von Mering C, Claassen M, Picotti P. Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability. Science 2017;355(6327)
  130. Leys M, Keller I, Robinson CT, Räsänen K. Cryptic lineages of a common alpine mayfly show strong life-history divergence. Mol Ecol 2017;26(6):1670-1686
  131. Li L, He J, Wang L, Chen W, Chang Z. Gene expression profiles of fin regeneration in loach (Paramisgurnus dabryanu). Gene Expr Patterns 2017;25-26:124-130
  132. Li L, Yang H, Li T, Feng J, Chen W, Ao L, Shi X, Lin Y, Liu H, Zheng E, Lin Q, Bu J, Zeng Y, Zheng M, Xu Y, Liao Z, Lin J, He Y, Lin D. The ubiquitin-specific protease USP6 regulates the stability of the c-Jun protein. Mol Cell Biol 2017
  133. Linke C, Chasapi A, González-Novo A, Al Sawad I, Tognetti S, Klipp E, Loog M, Krobitsch S, Posas F, Xenarios I, Barberis M. A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle. NPJ Syst Biol Appl 2017;3:7
  134. Lisacek F, Mariethoz J, Alocci D, Rudd PM, Abrahams JL, Campbell MP, Packer NH, Ståhle J, Widmalm G, Mullen E, Adamczyk B, Rojas-Macias MA, Jin C, Karlsson NG. Databases and Associated Tools for Glycomics and Glycoproteomics. Methods Mol Biol 2017;1503:235-264
  135. Liu Y, Gunawan R. Bioprocess optimization under uncertainty using ensemble modeling. J Biotechnol 2017;244:34-44
  136. Llinares-López F, Papaxanthos L, Bodenham D, Roqueiro D, COPDGene Investigators, Borgwardt K. Genome-wide genetic heterogeneity discovery with categorical covariates. Bioinformatics 2017;33(12):1820-1828
  137. Lykov K, Nematbakhsh Y, Shang M, Lim CT, Pivkin IV. Probing eukaryotic cell mechanics via mesoscopic simulations. PLoS Comput Biol 2017;13(9):e1005726
  138. Ma L, Boucher JI, Paulsen J, Matuszewski S, Eide CA, Ou J, Eickelberg G, Press RD, Zhu LJ, Druker BJ, Branford S, Wolfe SA, Jensen JD, Schiffer CA, Green MR, Bolon DN. CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy. Proc Natl Acad Sci U S A 2017
  139. Macé A, Tuke MA, Deelen P, Kristiansson K, Mattsson H, Nõukas M, Sapkota Y, Schick U, Porcu E, Rüeger S, McDaid AF, Porteous D, Winkler TW, Salvi E, Shrine N, Liu X, Ang WQ, Zhang W, Feitosa MF, Venturini C, van der Most PJ, Rosengren A, Wood AR, Beaumont RN, Jones SE, Ruth KS, Yaghootkar H, Tyrrell J, Havulinna AS, Boers H, Mägi R, Kriebel J, Müller-Nurasyid M, Perola M, Nieminen M, Lokki ML, Kähönen M, Viikari JS, Geller F, Lahti J, Palotie A, Koponen P, Lundqvist A, Rissanen H, Bottinger EP, Afaq S, Wojczynski MK, Lenzini P, Nolte IM, Sparsø T, Schupf N, Christensen K, Perls TT, Newman AB, Werge T, Snieder H, Spector TD, Chambers JC, Koskinen S, Melbye M, Raitakari OT, Lehtimäki T, Tobin MD, Wain LV, Sinisalo J, Peters A, Meitinger T, Martin NG, Wray NR, Montgomery GW, Medland SE, Swertz MA, Vartiainen E, Borodulin K, Männistö S, Murray A, Bochud M, Jacquemont S, Rivadeneira F, Hansen TF, Oldehinkel AJ, Mangino M, Province MA, Deloukas P, Kooner JS, Freathy RM, Pennell C, Feenstra B, Strachan DP, Lettre G, Hirschhorn J, Cusi D, Heid IM, Hayward C, Männik K, Beckmann JS, Loos RJF, Nyholt DR, Metspalu A, Eriksson JG, Weedon MN, Salomaa V, Franke L, Reymond A, Frayling TM, Kutalik Z. CNV-association meta-analysis in 191,161 European adults reveals new loci associated with anthropometric traits. Nat Commun 2017;8(1):744
  140. Mack S, Coassin S, Rueedi R, Yousri NA, Seppälä I, Gieger C, Schönherr S, Forer L, Erhart G, Marques-Vidal P, Ried JS, Waeber G, Bergmann S, Dähnhardt D, Stöckl A, Raitakari OT, Kähönen M, Peters A, Meitinger T, Strauch K, KORA-Study Group, Kedenko L, Paulweber B, Lehtimäki T, Hunt SC, Vollenweider P, Lamina C, Kronenberg F. A genome-wide association meta-analysis on lipoprotein (a) concentrations adjusted for apolipoprotein (a) isoforms. J Lipid Res 2017;58(9):1834-1844
  141. Mackay A, Burford A, Carvalho D, Izquierdo E, Fazal-Salom J, Taylor KR, Bjerke L, Clarke M, Vinci M, Nandhabalan M, Temelso S, Popov S, Molinari V, Raman P, Waanders AJ, Han HJ, Gupta S, Marshall L, Zacharoulis S, Vaidya S, Mandeville HC, Bridges LR, Martin AJ, Al-Sarraj S, Chandler C, Ng HK, Li X, Mu K, Trabelsi S, Brahim DH, Kisljakov AN, Konovalov DM, Moore AS, Carcaboso AM, Sunol M, de Torres C, Cruz O, Mora J, Shats LI, Stavale JN, Bidinotto LT, Reis RM, Entz-Werle N, Farrell M, Cryan J, Crimmins D, Caird J, Pears J, Monje M, Debily MA, Castel D, Grill J, Hawkins C, Nikbakht H, Jabado N, Baker SJ, Pfister SM, Jones DTW, Fouladi M, von Bueren AO, Baudis M, Resnick A, Jones C. Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma. Cancer Cell 2017;32(4):520-537.e5
  142. Mange F, Praz V, Migliavacca E, Willis IM, Schütz F, Hernandez N, CycliX Consortium. Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding-fasting response and the circadian clock. Genome Res 2017;27(6):973-984
  143. Manser M, Sater MR, Schmid CD, Noreen F, Murbach M, Kuster N, Schuermann D, Schär P. ELF-MF exposure affects the robustness of epigenetic programming during granulopoiesis. Sci Rep 2017;7:43345
  144. Manukyan L, Montandon SA, Fofonjka A, Smirnov S, Milinkovitch MC. A living mesoscopic cellular automaton made of skin scales. Nature 2017;544(7649):173-179
  145. Marinova Z, Maercker A, Küffer A, Robinson MD, Wojdacz TK, Walitza S, Grünblatt E, Burri A. DNA methylation profiles of elderly individuals subjected to indentured childhood labor and trauma. BMC Med Genet 2017;18(1):21
  146. Marouli E, Graff M, Medina-Gomez C, Lo KS, Wood AR, Kjaer TR, Fine RS, Lu Y, Schurmann C, Highland HM, Rüeger S, Thorleifsson G, Justice AE, Lamparter D, Stirrups KE, Turcot V, Young KL, Winkler TW, Esko T, Karaderi T, Locke AE, Masca NG, Ng MC, Mudgal P, Rivas MA, Vedantam S, Mahajan A, Guo X, Abecasis G, Aben KK, Adair LS, Alam DS, Albrecht E, Allin KH, Allison M, Amouyel P, Appel EV, Arveiler D, Asselbergs FW, Auer PL, Balkau B, Banas B, Bang LE, Benn M, Bergmann S, Bielak LF, Blüher M, Boeing H, Boerwinkle E, Böger CA, Bonnycastle LL, Bork-Jensen J, Bots ML, Bottinger EP, Bowden DW, Brandslund I, Breen G, Brilliant MH, Broer L, Burt AA, Butterworth AS, Carey DJ, Caulfield MJ, Chambers JC, Chasman DI, Chen YI, Chowdhury R, Christensen C, Chu AY, Cocca M, Collins FS, Cook JP, Corley J, Galbany JC, Cox AJ, Cuellar-Partida G, Danesh J, Davies G, de Bakker PI, de Borst GJ, de Denus S, de Groot MC, de Mutsert R, Deary IJ, Dedoussis G, Demerath EW, den Hollander AI, Dennis JG, Di Angelantonio E, Drenos F, Du M, Dunning AM, Easton DF, Ebeling T, Edwards TL, Ellinor PT, Elliott P, Evangelou E, Farmaki AE, Faul JD, Feitosa MF, Feng S, Ferrannini E, Ferrario MM, Ferrieres J, Florez JC, Ford I, Fornage M, Franks PW, Frikke-Schmidt R, Galesloot TE, Gan W, Gandin I, Gasparini P, Giedraitis V, Giri A, Girotto G, Gordon SD, Gordon-Larsen P, Gorski M, Grarup N, Grove ML, Gudnason V, Gustafsson S, Hansen T, Harris KM, Harris TB, Hattersley AT, Hayward C, He L, Heid IM, Heikkilä K, Helgeland Ø, Hernesniemi J, Hewitt AW, Hocking LJ, Hollensted M, Holmen OL, Hovingh GK, Howson JM, Hoyng CB, Huang PL, Hveem K, Ikram MA, Ingelsson E, Jackson AU, Jansson JH, Jarvik GP, Jensen GB, Jhun MA, Jia Y, Jiang X, Johansson S, Jørgensen ME, Jørgensen T, Jousilahti P, Jukema JW, Kahali B, Kahn RS, Kähönen M, Kamstrup PR, Kanoni S, Kaprio J, Karaleftheri M, Kardia SL, Karpe F, Kee F, Keeman R, Kiemeney LA, Kitajima H, Kluivers KB, Kocher T, Komulainen P, Kontto J, Kooner JS, Kooperberg C, Kovacs P, Kriebel J, Kuivaniemi H, Küry S, Kuusisto J, La Bianca M, Laakso M, Lakka TA, Lange EM, Lange LA, Langefeld CD, Langenberg C, Larson EB, Lee IT, Lehtimäki T, Lewis CE, Li H, Li J, Li-Gao R, Lin H, Lin LA, Lin X, Lind L, Lindström J, Linneberg A, Liu Y, Liu Y, Lophatananon A, Luan J, Lubitz SA, Lyytikäinen LP, Mackey DA, Madden PA, Manning AK, Männistö S, Marenne G, Marten J, Martin NG, Mazul AL, Meidtner K, Metspalu A, Mitchell P, Mohlke KL, Mook-Kanamori DO, Morgan A, Morris AD, Morris AP, Müller-Nurasyid M, Munroe PB, Nalls MA, Nauck M, Nelson CP, Neville M, Nielsen SF, Nikus K, Njølstad PR, Nordestgaard BG, Ntalla I, O'Connel JR, Oksa H, Loohuis LM, Ophoff RA, Owen KR, Packard CJ, Padmanabhan S, Palmer CN, Pasterkamp G, Patel AP, Pattie A, Pedersen O, Peissig PL, Peloso GM, Pennell CE, Perola M, Perry JA, Perry JR, Person TN, Pirie A, Polasek O, Posthuma D, Raitakari OT, Rasheed A, Rauramaa R, Reilly DF, Reiner AP, Renström F, Ridker PM, Rioux JD, Robertson N, Robino A, Rolandsson O, Rudan I, Ruth KS, Saleheen D, Salomaa V, Samani NJ, Sandow K, Sapkota Y, Sattar N, Schmidt MK, Schreiner PJ, Schulze MB, Scott RA, Segura-Lepe MP, Shah S, Sim X, Sivapalaratnam S, Small KS, Smith AV, Smith JA, Southam L, Spector TD, Speliotes EK, Starr JM, Steinthorsdottir V, Stringham HM, Stumvoll M, Surendran P, 't Hart LM, Tansey KE, Tardif JC, Taylor KD, Teumer A, Thompson DJ, Thorsteinsdottir U, Thuesen BH, Tönjes A, Tromp G, Trompet S, Tsafantakis E, Tuomilehto J, Tybjaerg-Hansen A, Tyrer JP, Uher R, Uitterlinden AG, Ulivi S, van der Laan SW, Van Der Leij AR, van Duijn CM, van Schoor NM, van Setten J, Varbo A, Varga TV, Varma R, Edwards DR, Vermeulen SH, Vestergaard H, Vitart V, Vogt TF, Vozzi D, Walker M, Wang F, Wang CA, Wang S, Wang Y, Wareham NJ, Warren HR, Wessel J, Willems SM, Wilson JG, Witte DR, Woods MO, Wu Y, Yaghootkar H, Yao J, Yao P, Yerges-Armstrong LM, Young R, Zeggini E, Zhan X, Zhang W, Zhao JH, Zhao W, Zhao W, Zheng H, Zhou W, EPIC-InterAct Consortium, CHD Exome+ Consortium, ExomeBP Consortium, T2D-Genes Consortium, GoT2D Genes Consortium, Global Lipids Genetics Consortium, ReproGen Consortium, MAGIC Investigators, Rotter JI, Boehnke M, Kathiresan S, McCarthy MI, Willer CJ, Stefansson K, Borecki IB, Liu DJ, North KE, Heard-Costa NL, Pers TH, Lindgren CM, Oxvig C, Kutalik Z, Rivadeneira F, Loos RJ, Frayling TM, Hirschhorn JN, Deloukas P, Lettre G. Rare and low-frequency coding variants alter human adult height. Nature 2017;542(7640):186-190
  147. Marti R, Schmid M, Kulli S, Schneeberger K, Naskova J, Knøchel S, Ahrens CH, Hummerjohann J. Biofilm Formation Potential of Heat-Resistant Escherichia coli Dairy Isolates and the Complete Genome of Multidrug-Resistant, Heat-Resistant Strain FAM21845. Appl Environ Microbiol 2017;83(15)
  148. Martin G, Schmidt R, Gruber AJ, Ghosh S, Keller W, Zavolan M. 3' End Sequencing Library Preparation with A-seq2. J Vis Exp 2017(128)
  149. Martín-Campos T, Mylonas R, Masselot A, Waridel P, Petricevic T, Xenarios I, Quadroni M. MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications. J Proteome Res 2017;16(8):3092-3101
  150. Masotti C, Brito LA, Nica AC, Ludwig KU, Nunes K, Savastano CP, Malcher C, Ferreira SG, Kobayashi GS, Bueno DF, Alonso N, Franco D, Rojas-Martinez A, Dos Santos SE, Galante PA, Meyer D, Hünemeier T, Mangold E, Dermitzakis ET, Passos-Bueno MR. MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach. J Dent Res 2017:22034517735805
  151. McDaid A, Logette E, Buchillier V, Muriset M, Suchon P, Pache TD, Tanackovic G, Kutalik Z, Michaud J. Risk prediction of developing venous thrombosis in combined oral contraceptive users. PLoS One 2017;12(7):e0182041
  152. McDaid AF, Joshi PK, Porcu E, Komljenovic A, Li H, Sorrentino V, Litovchenko M, Bevers RPJ, Rüeger S, Reymond A, Bochud M, Deplancke B, Williams RW, Robinson-Rechavi M, Paccaud F, Rousson V, Auwerx J, Wilson JF, Kutalik Z. Bayesian association scan reveals loci associated with human lifespan and linked biomarkers. Nat Commun 2017;8:15842
  153. McLaren PJ, Pulit SL, Gurdasani D, Bartha I, Shea PR, Pomilla C, Gupta N, Gkrania-Klotsas E, Young EH, Bannert N, Amo JD, Gill J, Gilmour J, Kellam P, Kelleher AD, Sönnerborg A, Zangerle R, Post FA, Fisher M, Haas DW, Walker BD, Porter K, Goldstein DB, Sandhu MS, de Bakker PIW, Fellay J. Evaluating the impact of functional genetic variation on HIV-1 control. J Infect Dis 2017
  154. Meccariello A, Monti SM, Romanelli A, Colonna R, Primo P, Inghilterra MG, Del Corsano G, Ramaglia A, Iazzetti G, Chiarore A, Patti F, Heinze SD, Salvemini M, Lindsay H, Chiavacci E, Burger A, Robinson MD, Mosimann C, Bopp D, Saccone G. Highly efficient DNA-free gene disruption in the agricultural pest Ceratitis capitata by CRISPR-Cas9 ribonucleoprotein complexes. Sci Rep 2017;7(1):10061
  155. Meier JI, Marques DA, Mwaiko S, Wagner CE, Excoffier L, Seehausen O. Ancient hybridization fuels rapid cichlid fish adaptive radiations. Nat Commun 2017;8:14363
  156. Mele V, Sokol L, Kölzer VH, Pfaff D, Muraro MG, Keller I, Stefan Z, Centeno I, Terracciano LM, Dawson H, Zlobec I, Iezzi G, Lugli A. The hyaluronan-mediated motility receptor RHAMM promotes growth, invasiveness and dissemination of colorectal cancer. Oncotarget 2017;8(41):70617-70629
  157. Merkle PS, Irving M, Hongjian S, Ferber M, Jørgensen TJD, Scholten K, Luescher I, Coukos G, Zoete V, Cuendet MA, Michielin O, Rand KD. The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites. Biochemistry 2017;56(30):3945-3961
  158. Michaud O, Fiorucci AS, Xenarios I, Fankhauser C. Local auxin production underlies a spatially restricted neighbor-detection response in Arabidopsis. Proc Natl Acad Sci U S A 2017;114(28):7444-7449
  159. Miki TS, Carl SH, Großhans H. Two distinct transcription termination modes dictated by promoters. Genes Dev 2017;31(18):1870-1879
  160. Mina M, Raynaud F, Tavernari D, Battistello E, Sungalee S, Saghafinia S, Laessle T, Sanchez-Vega F, Schultz N, Oricchio E, Ciriello G. Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies. Cancer Cell 2017;32(2):155-168.e6
  161. Minoux M, Holwerda S, Vitobello A, Kitazawa T, Kohler H, Stadler MB, Rijli FM. Gene bivalency at Polycomb domains regulates cranial neural crest positional identity. Science 2017;355(6332)
  162. Mohammadi P, Beerenwinkel N, Benenson Y. Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy. Cell Syst 2017;4(2):207-218.e14
  163. Mohammadi P, Castel SE, Brown AA, Lappalainen T. Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. Genome Res 2017
  164. Montes Vidal D, von Rymon-Lipinski AL, Ravella S, Groenhagen U, Herrmann J, Zaburannyi N, Zarbin PH, Varadarajan AR, Ahrens CH, Weisskopf L, Müller R, Schulz S. Long-Chain Alkyl Cyanides: Unprecedented Volatile Compounds Released by Pseudomonas and Micromonospora Bacteria. Angew Chem Int Ed Engl 2017;56(15):4342-4346
  165. Morgan SL, Palagi PM, Fernandes PL, Koperlainen E, Dimec J, Marek D, Larcombe L, Rustici G, Attwood TK, Via A, Via A. The ELIXIR-EXCELERATE Train-the-Trainer pilot programme: empower researchers to deliver high-quality training. F1000Res 2017;6
  166. Moser A, Wüthrich D, Bruggmann R, Eugster-Meier E, Meile L, Irmler S. Amplicon Sequencing of the slpH Locus Permits Culture-Independent Strain Typing of Lactobacillus helveticus in Dairy Products. Front Microbiol 2017;8:1380
  167. Mottin L, Pasche E, Gobeill J, Rech de Laval V, Gleizes A, Michel P, Bairoch A, Gaudet P, Ruch P. Triage by ranking to support the curation of protein interactions. Database: The Journal of Biological Databases and Curation 2017;2017
  168. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical Assessment of Methods of Protein Structure Prediction (CASP) - Round XII. Proteins 2017
  169. Moult J, Fidelis K, Kryshtafovych A, Schwede T. A tribute to Anna Tramontano (1957 - 2017). Proteins 2017
  170. Mueller L, Bertelli C, Pillonel T, Salamin N, Greub G. One Year Genome Evolution of Lausannevirus in Allopatric versus Sympatric Conditions. Genome Biol Evol 2017;9(6):1432-1449
  171. Müller NF, Rasmussen DA, Stadler T. The Structured Coalescent and its Approximations. Mol Biol Evol 2017
  172. Neubert NJ, Tillé L, Barras D, Soneson C, Baumgaertner P, Rimoldi D, Gfeller D, Delorenzi M, Fuertes Marraco SA, Speiser DE. Broad and Conserved Immune Regulation by Genetically Heterogeneous Melanoma Cells. Cancer Res 2017;77(7):1623-1636
  173. Neumann PE, Baud R, Sprumont P. Ordering by the numbers in anatomy and by letters Too. Clin Anat 2017;30(6):700-702
  174. Nowicka M, Krieg C, Weber LM, Hartmann FJ, Guglietta S, Becher B, Levesque MP, Robinson MD. CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets. F1000Res 2017;6:748
  175. Odhams CA, Cortini A, Chen L, Roberts AL, Viñuela A, Buil A, Small KS, Dermitzakis ET, Morris DL, Vyse TJ, Cunninghame Graham DS. Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus. Hum Mol Genet 2017;26(5):1003-1017
  176. Oldrati V, Koua D, Allard PM, Hulo N, Arrell M, Nentwig W, Lisacek F, Wolfender JL, Kuhn-Nentwig L, Stöcklin R. Peptidomic and transcriptomic profiling of four distinct spider venoms. PLoS One 2017;12(3):e0172966
  177. Omenn GS, Lane L, Lundberg EK, Overall CM, Deutsch EW. Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project. J Proteome Res 2017
  178. Omidi S, Zavolan M, Pachkov M, Breda J, Berger S, van Nimwegen E. Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Comput Biol 2017;13(7):e1005176
  179. Ongen H, Brown AA, Delaneau O, Panousis NI, Nica AC, GTEx Consortium, Dermitzakis ET. Estimating the causal tissues for complex traits and diseases. Nat Genet 2017
  180. Ormond L, Liu P, Matuszewski S, Renzette N, Bank C, Zeldovich K, Bolon DN, Kowalik TF, Finberg RW, Jensen JD, Wang JP. The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution. Genome Biol Evol 2017;9(7):1913-1924
  181. Otero-Muras I, Yordanov P, Stelling J. Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling. PLoS Comput Biol 2017;13(4):e1005454
  182. Paik YK, Omenn GS, Lane L, Overall CM. Advances in the Chromosome-Centric Human Proteome Project: Looking to the Future. Expert Rev Proteomics 2017
  183. Papili Gao N, Ud-Dean SMM, Gandrillon O, Gunawan R. SINCERITIES: Inferring gene regulatory networks from time-stamped single cell transcriptional expression profiles. Bioinformatics 2017
  184. Pawlik A, van Gelder CWG, van Gelder CWG, Nenadic A, Nenadic A, Palagi PM, Korpelainen E, Lijnzaad P, Marek D, Sansone SA, Hancock J, Hancock J, Goble C. Developing a strategy for computational lab skills training through Software and Data Carpentry: Experiences from the ELIXIR Pilot action. F1000Res 2017;6
  185. Peirs S, Frismantas V, Matthijssens F, Van Loocke W, Pieters T, Vandamme N, Lintermans B, Dobay MP, Berx G, Poppe B, Goossens S, Bornhauser BC, Bourquin JP, Van Vlierberghe P. Targeting BET proteins improves the therapeutic efficacy of BCL-2 inhibition in T-cell acute lymphoblastic leukemia. Leukemia 2017;31(10):2037-2047
  186. Pieper K, Tan J, Piccoli L, Foglierini M, Barbieri S, Chen Y, Silacci-Fregni C, Wolf T, Jarrossay D, Anderle M, Abdi A, Ndungu FM, Doumbo OK, Traore B, Tran TM, Jongo S, Zenklusen I, Crompton PD, Daubenberger C, Bull PC, Sallusto F, Lanzavecchia A. Public antibodies to malaria antigens generated by two LAIR1 insertion modalities. Nature 2017;548(7669):597-601
  187. Pirkl M, Diekmann M, van der Wees M, Beerenwinkel N, Fröhlich H, Markowetz F. Inferring modulators of genetic interactions with epistatic nested effects models. PLoS Comput Biol 2017;13(4):e1005496
  188. Plüss M, Kopps AM, Keller I, Meienberg J, Caspar SM, Dubacher N, Bruggmann R, Vogel M, Matyas G. Need for speed in accurate whole-genome data analysis: GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac. Proc Natl Acad Sci U S A 2017;114(40):E8320-E8322
  189. Poux S, Arighi CN, Magrane M, Bateman A, Wei CH, Lu Z, Boutet E, Bye-A-Jee H, Famiglietti ML, Roechert B, UniProt Consortium T. On expert curation and scalability: UniProtKB/Swiss-Prot as a case study. Bioinformatics 2017;33(21):3454-3460
  190. Poux S, Gaudet P. Best Practices in Manual Annotation with the Gene Ontology. Methods Mol Biol 2017;1446:41-54
  191. Pradhan RN, Bues JJ, Gardeux V, Schwalie PC, Alpern D, Chen W, Russeil J, Raghav SK, Deplancke B. Dissecting the brown adipogenic regulatory network using integrative genomics. Sci Rep 2017;7:42130
  192. Pradhan RN, Zachara M, Deplancke B. A systems perspective on brown adipogenesis and metabolic activation. Obes Rev 2017;18 Suppl 1:65-81
  193. Prakash MK, Lang B, Heinrich H, Valli PV, Bauerfeind P, Sonnenberg A, Beerenwinkel N, Misselwitz B. CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies. BMC Med Inform Decis Mak 2017;17(1):80
  194. Prieto-Godino LL, Rytz R, Cruchet S, Bargeton B, Abuin L, Silbering AF, Ruta V, Dal Peraro M, Benton R. Evolution of Acid-Sensing Olfactory Circuits in Drosophilids. Neuron 2017;93(3):661-676.e6
  195. Puller V, Neher R, Albert J. Estimating time of HIV-1 infection from next-generation sequence diversity. PLoS Comput Biol 2017;13(10):e1005775
  196. Racko D, Benedetti F, Dorier J, Burnier Y, Stasiak A. Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase. Methods Mol Biol 2017;1624:339-372
  197. Randazzo GM, Tonoli D, Strajhar P, Xenarios I, Odermatt A, Boccard J, Rudaz S. Enhanced metabolite annotation via dynamic retention time prediction: Steroidogenesis alterations as a case study. J Chromatogr B Analyt Technol Biomed Life Sci 2017
  198. Rashpa R, Vazquez-Pianzola P, Colombo M, Hernandez G, Beuchle D, Berger F, Peischl S, Bruggmann R, Suter B. Cbp80 is needed for the expression of piRNA components and piRNAs. PLoS One 2017;12(7):e0181743
  199. Rasmussen DA, Kouyos R, Günthard HF, Stadler T. Phylodynamics on local sexual contact networks. PLoS Comput Biol 2017;13(3):e1005448
  200. Rinaldi F, Lithgow O, Gama-Castro S, Solano H, Lopez A, Muñiz Rascado LJ, Ishida-Gutiérrez C, Méndez-Cruz CF, Collado-Vides J. Strategies towards digital and semi-automated curation in RegulonDB. Database (Oxford) 2017;2017(1)
  201. Rinaldi F, Lithgow O, Gama-Castro S, Solano H, López-Fuentes A, Muñiz Rascado LJ, Ishida-Gutiérrez C, Méndez-Cruz CF, Collado-Vides J. Strategies towards digital and semi-automated curation in RegulonDB. Database (Oxford) 2017;2017
  202. Rivera M, Locke AE, Corre T, Czamara D, Wolf C, Ching-Lopez A, Milaneschi Y, Kloiber S, Cohen-Woods S, Rucker J, Aitchison KJ, Bergmann S, Boomsma DI, Craddock N, Gill M, Holsboer F, Hottenga JJ, Korszun A, Kutalik Z, Lucae S, Maier W, Mors O, Müller-Myhsok B, Owen MJ, Penninx BWJH, Preisig M, Rice J, Rietschel M, Tozzi F, Uher R, Vollenweider P, Waeber G, Willemsen G, Craig IW, Farmer AE, Lewis CM, Breen G, McGuffin P. Interaction between the FTO gene, body mass index and depression: meta-analysis of 13701 individuals. Br J Psychiatry 2017;211(2):70-76
  203. Rodic A, Blagojevic B, Zdobnov E, Djordjevic M, Djordjevic M. Understanding key features of bacterial restriction-modification systems through quantitative modeling. BMC Syst Biol 2017;11(suppl 1):377
  204. Rodrigues JFM, Schmidt ST, Tackmann J, von Mering C. MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis. Bioinformatics 2017
  205. Röhrig UF, Zoete V, Michielin O. The Binding Mode of N-Hydroxyamidines to Indoleamine 2,3-Dioxygenase 1 (IDO1). Biochemistry 2017;56(33):4323-4325
  206. Romano V, de Beer TA, Schwede T. A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues. BMC Res Notes 2017;10(1):104
  207. Rosenfeld UM, Drewes S, Ali HS, Sadowska ET, Mikowska M, Heckel G, Koteja P, Ulrich RG. A highly divergent Puumala virus lineage in southern Poland. Arch Virol 2017;162(5):1177-1185
  208. Rot G, Wang Z, Huppertz I, Modic M, Lenče T, Hallegger M, Haberman N, Curk T, von Mering C, Ule J. High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43. Cell Rep 2017;19(5):1056-1067
  209. Roux J, Liu J, Robinson-Rechavi M. Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates. Mol Biol Evol 2017
  210. Rychener L, InAlbon S, Djordjevic SP, Chowdhury PR, Ziech RE, de Vargas AC, Frey J, Falquet L. Clostridium chauvoei, an Evolutionary Dead-End Pathogen. Front Microbiol 2017;8:1054
  211. Ryll R, Bernstein S, Heuser E, Schlegel M, Dremsek P, Zumpe M, Wolf S, Pépin M, Bajomi D, Müller G, Heiberg AC, Spahr C, Lang J, Groschup MH, Ansorge H, Freise J, Guenther S, Baert K, Ruiz-Fons F, Pikula J, Knap N, Tsakmakidis Ι, Dovas C, Zanet S, Imholt C, Heckel G, Johne R, Ulrich RG. Detection of rat hepatitis E virus in wild Norway rats (Rattus norvegicus) and Black rats (Rattus rattus) from 11 European countries. Vet Microbiol 2017;208:58-68
  212. Saladin B, Leslie AB, Wüest RO, Litsios G, Conti E, Salamin N, Zimmermann NE. Fossils matter: improved estimates of divergence times in Pinus reveal older diversification. BMC Evol Biol 2017;17(1):95
  213. Sangrithi MN, Royo H, Mahadevaiah SK, Ojarikre O, Bhaw L, Sesay A, Peters AH, Stadler M, Turner JM. Non-Canonical and Sexually Dimorphic X Dosage Compensation States in the Mouse and Human Germline. Dev Cell 2017;40(3):289-301.e3
  214. Sauerwald J, Soneson C, Robinson MD, Luschnig S. Faithful mRNA splicing depends on the Prp19 complex subunit faint sausage and is required for tracheal branching morphogenesis in Drosophila. Development 2017;144(4):657-663
  215. Savary R, Masclaux FG, Wyss T, Droh G, Cruz Corella J, Machado AP, Morton JB, Sanders IR. A population genomics approach shows widespread geographical distribution of cryptic genomic forms of the symbiotic fungus Rhizophagus irregularis. ISME J 2017
  216. Saxenhofer M, Weber de Melo V, Ulrich RG, Heckel G. Revised time scales of RNA virus evolution based on spatial information. Proc Biol Sci 2017;284(1860)
  217. Schaeffer M, Gateau A, Teixeira D, Michel PA, Zahn-Zabal M, Lane L. The neXtProt peptide uniqueness checker: a tool for the proteomics community. Bioinformatics 2017;33(21):3471-3472
  218. Schwab C, Ruscheweyh HJ, Bunesova V, Pham VT, Beerenwinkel N, Lacroix C. Trophic Interactions of Infant Bifidobacteria and Eubacterium hallii during L-Fucose and Fucosyllactose Degradation. Front Microbiol 2017;8:95
  219. Schwalie PC, Ordonez Moran P, Huelsken J, Deplancke B. Cross-Tissue Identification Of Somatic Stem And Progenitor Cells Using A Single-Cell RNA-Seq Derived Gene Signature. Stem Cells 2017
  220. Serrano-Serrano ML, Marcionetti A, Perret M, Salamin N. Transcriptomic resources for an endemic Neotropical plant lineage (Gesneriaceae). Appl Plant Sci 2017;5(4)
  221. Serrano-Serrano ML, Rolland J, Clark JL, Salamin N, Perret M. Hummingbird pollination and the diversification of angiosperms: an old and successful association in Gesneriaceae. Proc Biol Sci 2017;284(1852)
  222. Sharma A, Heinze SD, Wu Y, Kohlbrenner T, Morilla I, Brunner C, Wimmer EA, van de Zande L, Robinson MD, Beukeboom LW, Bopp D. Male sex in houseflies is determined by Mdmd, a paralog of the generic splice factor gene CWC22. Science 2017;356(6338):642-645
  223. Shaya O, Binshtok U, Hersch M, Rivkin D, Weinreb S, Amir-Zilberstein L, Khamaisi B, Oppenheim O, Desai RA, Goodyear RJ, Richardson GP, Chen CS, Sprinzak D. Cell-Cell Contact Area Affects Notch Signaling and Notch-Dependent Patterning. Dev Cell 2017;40(5):505-511.e6
  224. Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A, Rasmussen S, Dupanloup I, Nigst PR, Bosch MD, Renaud G, Allentoft ME, Margaryan A, Vasilyev SV, Veselovskaya EV, Borutskaya SB, Deviese T, Comeskey D, Higham T, Manica A, Foley R, Meltzer DJ, Nielsen R, Excoffier L, Lahr MM, Orlando L, Willerslev E. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 2017
  225. Simillion C, Liechti R, Lischer HE, Ioannidis V, Bruggmann R. Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC Bioinformatics 2017;18(1):151
  226. Singer J, Ruscheweyh HJ, Hofmann AL, Thurnherr T, Singer F, Toussaint NC, Ng CKY, Piscuoglio S, Beisel C, Christofori G, Dummer R, Hall MN, Krek W, Levesque M, Manz MG, Moch H, Papassotiropoulos A, Stekhoven DJ, Wild P, Wüst T, Rinn B, Beerenwinkel N. NGS-pipe: a flexible, easily extendable, and highly configurable framework for NGS analysis. Bioinformatics 2017
  227. Soneson C, Robinson MD. Towards unified quality verification of synthetic count data with countsimQC. Bioinformatics 2017
  228. Spodzieja M, Lach S, Iwaszkiewicz J, Cesson V, Kalejta K, Olive D, Michielin O, Speiser DE, Zoete V, Derré L, Rodziewicz-Motowidło S. Design of short peptides to block BTLA/HVEM interactions for promoting anticancer T-cell responses. PLoS One 2017;12(6):e0179201
  229. Starek G, Freites JA, Bernèche S, Tobias DJ. Gating energetics of a voltage-dependent K+ channel pore domain. J Comput Chem 2017;38(16):1472-1478
  230. Suchan T, Espíndola A, Rutschmann S, Emerson BC, Gori K, Dessimoz C, Arrigo N, Ronikier M, Alvarez N. Assessing the potential of RAD-sequencing to resolve phylogenetic relationships within species radiations: The fly genus Chiastocheta (Diptera: Anthomyiidae) as a case study. Mol Phylogenet Evol 2017;114:189-198
  231. Suffiotti M, Carmona SJ, Jandus C, Gfeller D. Identification of innate lymphoid cells in single-cell RNA-Seq data. Immunogenetics 2017;69(7):439-450
  232. Sugiyama M, Ghisu ME, Llinares-López F, Borgwardt K. graphkernels: R and Python packages for graph comparison. Bioinformatics 2017
  233. Tahi F, Du T Tran V, Boucheham A. In Silico Prediction of RNA Secondary Structure. Methods Mol Biol 2017;1543:145-168
  234. Tamò G, Maesani A, Träger S, Degiacomi MT, Floreano D, Dal Peraro M. Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies. Sci Rep 2017;7(1):235
  235. Tan JY, Smith AAT, Ferreira da Silva M, Matthey-Doret C, Rueedi R, Sönmez R, Ding D, Kutalik Z, Bergmann S, Marques AC. cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture. Cell Rep 2017;18(9):2280-2288
  236. Thornton JM, Valencia A, Schwede T. Anna Tramontano 1957-2017. Nat Struct Mol Biol 2017;24(5):431-432
  237. Tiberi S, Scarpa B, Sartori N. A composite likelihood approach to predict the sex of the baby. Stat Methods Med Res 2017:962280217702415
  238. Tiemeyer M, Aoki K, Paulson J, Cummings RD, York WS, Karlsson NG, Lisacek F, Packer NH, Campbell MP, Aoki NP, Fujita A, Matsubara M, Shinmachi D, Tsuchiya S, Yamada I, Pierce M, Ranzinger R, Narimatsu H, Aoki-Kinoshita KF. GlyTouCan: an accessible glycan structure repository. Glycobiology 2017;27(10):915-919
  239. Timón-Gómez A, Nývltová E, Abriata LA, Vila AJ, Hosler J, Barrientos A. Mitochondrial cytochrome c oxidase biogenesis: Recent developments. Semin Cell Dev Biol 2017
  240. Togninalli M, Seren Ü, Meng D, Fitz J, Nordborg M, Weigel D, Borgwardt K, Korte A, Grimm DG. The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog. Nucleic Acids Res 2017
  241. Trabanelli S, Chevalier MF, Martinez-Usatorre A, Gomez-Cadena A, Salomé B, Lecciso M, Salvestrini V, Verdeil G, Racle J, Papayannidis C, Morita H, Pizzitola I, Grandclément C, Bohner P, Bruni E, Girotra M, Pallavi R, Falvo P, Leibundgut EO, Baerlocher GM, Carlo-Stella C, Taurino D, Santoro A, Spinelli O, Rambaldi A, Giarin E, Basso G, Tresoldi C, Ciceri F, Gfeller D, Akdis CA, Mazzarella L, Minucci S, Pelicci PG, Marcenaro E, McKenzie ANJ, Vanhecke D, Coukos G, Mavilio D, Curti A, Derré L, Jandus C. Tumour-derived PGD2 and NKp30-B7H6 engagement drives an immunosuppressive ILC2-MDSC axis. Nat Commun 2017;8(1):593
  242. Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol 2017;73(pt 9):710-728
  243. Tsagkogeorga G, Müller S, Dessimoz C, Rossiter SJ. Comparative genomics reveals contraction in olfactory receptor genes in bats. Sci Rep 2017;7(1):259
  244. Turrini R, Pabois A, Xenarios I, Coukos G, Delaloye JF, Doucey MA. TIE-2 expressing monocytes in human cancers. Oncoimmunology 2017;6(4):e1303585
  245. Tyrrell J, Wood AR, Ames RM, Yaghootkar H, Beaumont RN, Jones SE, Tuke MA, Ruth KS, Freathy RM, Davey Smith G, Joost S, Guessous I, Murray A, Strachan DP, Kutalik Z, Weedon MN, Frayling TM. Gene-obesogenic environment interactions in the UK Biobank study. Int J Epidemiol 2017;46(2):559-575
  246. Vale-Silva L, Beaudoing E, Tran VDT, Sanglard D. Comparative Genomics of Two Sequential Candida glabrata Clinical Isolates. G3 (Bethesda) 2017;7(8):2413-2426
  247. Van den Berge K, Soneson C, Robinson MD, Clement L. stageR: a general stage-wise method for controlling the gene-level false discovery rate in differential expression and differential transcript usage. Genome Biol 2017;18(1):151
  248. Vesztrocy AW, Dessimoz C. A Gene Ontology Tutorial in Python. Methods Mol Biol 2017;1446:221-229
  249. Völker JM, Dergai M, Abriata LA, Mingard Y, Ysselstein D, Krainc D, Dal Peraro M, von Mollard GF, Fasshauer D, Koliwer J, Schwake M. Functional assays for the assessment of the pathogenicity of variants in GOSR2, an ER-to-Golgi SNARE involved in progressive myoclonus epilepsies. Dis Model Mech 2017
  250. Vollmer J, Fried P, Aguilar-Hidalgo D, Sánchez-Aragón M, Iannini A, Casares F, Iber D. Growth control in the Drosophila eye disc by the cytokine Unpaired. Development 2017;144(5):837-843
  251. Waese J, Fan J, Pasha A, Yu H, Fucile G, Shi R, Cumming M, Kelley LA, Sternberg MJ, Krishnakumar V, Ferlanti E, Miller J, Town C, Stuerzlinger W, Provart NJ. ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. Plant Cell 2017;29(8):1806-1821
  252. Wain LV, Vaez A, Jansen R, Joehanes R, van der Most PJ, Erzurumluoglu AM, O'Reilly PF, Cabrera CP, Warren HR, Rose LM, Verwoert GC, Hottenga JJ, Strawbridge RJ, Esko T, Arking DE, Hwang SJ, Guo X, Kutalik Z, Trompet S, Shrine N, Teumer A, Ried JS, Bis JC, Smith AV, Amin N, Nolte IM, Lyytikäinen LP, Mahajan A, Wareham NJ, Hofer E, Joshi PK, Kristiansson K, Traglia M, Havulinna AS, Goel A, Nalls MA, Sõber S, Vuckovic D, Luan J, Del Greco M F, Ayers KL, Marrugat J, Ruggiero D, Lopez LM, Niiranen T, Enroth S, Jackson AU, Nelson CP, Huffman JE, Zhang W, Marten J, Gandin I, Harris SE, Zemunik T, Lu Y, Evangelou E, Shah N, de Borst MH, Mangino M, Prins BP, Campbell A, Li-Gao R, Chauhan G, Oldmeadow C, Abecasis G, Abedi M, Barbieri CM, Barnes MR, Batini C, Beilby J, Blake T, Boehnke M, Bottinger EP, Braund PS, Brown M, Brumat M, Campbell H, Chambers JC, Cocca M, Collins F, Connell J, Cordell HJ, Damman JJ, Davies G, de Geus EJ, de Mutsert R, Deelen J, Demirkale Y, Doney ASF, Dörr M, Farrall M, Ferreira T, Frånberg M, Gao H, Giedraitis V, Gieger C, Giulianini F, Gow AJ, Hamsten A, Harris TB, Hofman A, Holliday EG, Hui J, Jarvelin MR, Johansson Å, Johnson AD, Jousilahti P, Jula A, Kähönen M, Kathiresan S, Khaw KT, Kolcic I, Koskinen S, Langenberg C, Larson M, Launer LJ, Lehne B, Liewald DCM, Lin L, Lind L, Mach F, Mamasoula C, Menni C, Mifsud B, Milaneschi Y, Morgan A, Morris AD, Morrison AC, Munson PJ, Nandakumar P, Nguyen QT, Nutile T, Oldehinkel AJ, Oostra BA, Org E, Padmanabhan S, Palotie A, Paré G, Pattie A, Penninx BWJH, Poulter N, Pramstaller PP, Raitakari OT, Ren M, Rice K, Ridker PM, Riese H, Ripatti S, Robino A, Rotter JI, Rudan I, Saba Y, Saint Pierre A, Sala CF, Sarin AP, Schmidt R, Scott R, Seelen MA, Shields DC, Siscovick D, Sorice R, Stanton A, Stott DJ, Sundström J, Swertz M, Taylor KD, Thom S, Tzoulaki I, Tzourio C, Uitterlinden AG, Völker U, Vollenweider P, Wild S, Willemsen G, Wright AF, Yao J, Thériault S, Conen D, Attia J, Sever P, Debette S, Mook-Kanamori DO, Zeggini E, Spector TD, van der Harst P, Palmer CNA, Vergnaud AC, Loos RJF, Polasek O, Starr JM, Girotto G, Hayward C, Kooner JS, Lindgren CM, Vitart V, Samani NJ, Tuomilehto J, Gyllensten U, Knekt P, Deary IJ, Ciullo M, Elosua R, Keavney BD, Hicks AA, Scott RA, Gasparini P, Laan M, Liu Y, Watkins H, Hartman CA, Salomaa V, Toniolo D, Perola M, Wilson JF, Schmidt H, Zhao JH, Lehtimäki T, van Duijn CM, Gudnason V, Psaty BM, Peters A, Rettig R, James A, Jukema JW, Strachan DP, Palmas W, Metspalu A, Ingelsson E, Boomsma DI, Franco OH, Bochud M, Newton-Cheh C, Munroe PB, Elliott P, Chasman DI, Chakravarti A, Knight J, Morris AP, Levy D, Tobin MD, Snieder H, Caulfield MJ, Ehret GB. Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the Kidney. Hypertension 2017
  253. Weir BS, Goudet J. A Unified Characterization of Population Structure and Relatedness. Genetics 2017;206(4):2085-2103
  254. Wigger L, Cruciani-Guglielmacci C, Nicolas A, Denom J, Fernandez N, Fumeron F, Marques-Vidal P, Ktorza A, Kramer W, Schulte A, Le Stunff H, Liechti R, Xenarios I, Vollenweider P, Waeber G, Uphues I, Roussel R, Magnan C, Ibberson M, Thorens B. Plasma Dihydroceramides Are Diabetes Susceptibility Biomarker Candidates in Mice and Humans. Cell Rep 2017;18(9):2269-2279
  255. Winkler TW, Justice AE, Cupples LA, Kronenberg F, Kutalik Z, Heid IM, GIANT consortium. Approaches to detect genetic effects that differ between two strata in genome-wide meta-analyses: Recommendations based on a systematic evaluation. PLoS One 2017;12(7):e0181038
  256. Wüthrich D, Berthoud H, Wechsler D, Eugster E, Irmler S, Bruggmann R. The Histidine Decarboxylase Gene Cluster of Lactobacillus parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile within the Species. Front Microbiol 2017;8:218
  257. Xu Y, Seelig A, Bernèche S. Unidirectional Transport Mechanism in an ATP Dependent Exporter. ACS Cent Sci 2017;3(3):250-258
  258. Yeganeh M, Praz V, Cousin P, Hernandez N. Transcriptional interference by RNA polymerase III affects expression of the Polr3e gene. Genes Dev 2017;31(4):413-421
  259. Zanini IM, Soneson C, Lorenzi LE, Azzalin CM. Human cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion. J Cell Sci 2017;130(4):767-778
  260. Zhan Y, Mariani L, Barozzi I, Schulz EG, Blüthgen N, Stadler M, Tiana G, Giorgetti L. Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes. Genome Res 2017;27(3):479-490
  261. Zinkernagel MS, Zysset-Burri DC, Keller I, Berger LE, Leichtle AB, Largiadèr CR, Fiedler GM, Wolf S. Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration. Sci Rep 2017;7:40826