Publications by SIB Members published in 2018

Listed in Europe PMC, latest update: 2018-07-01.

Peer-reviewed articles and conference proceedings

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  1. Aguilar-Bultet L, Nicholson P, Rychener L, Dreyer M, Gözel B, Origgi FC, Oevermann A, Frey J, Falquet L. Genetic Separation of Listeria monocytogenes Causing Central Nervous System Infections in Animals. Front Cell Infect Microbiol 2018;8:20
  2. Aguilar-Rodríguez J, Peel L, Stella M, Wagner A, Payne JL. The architecture of an empirical genotype-phenotype map. Evolution 2018;72(6):1242-1260
  3. Alocci D, Ghraichy M, Barletta E, Gastaldello A, Mariethoz J, Lisacek F. Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes. Glycobiology 2018;28(6):349-362
  4. Altenhoff AM, Glover NM, Train CM, Kaleb K, Warwick Vesztrocy A, Dylus D, de Farias TM, Zile K, Stevenson C, Long J, Redestig H, Gonnet GH, Dessimoz C. The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. Nucleic Acids Res 2018;46(d1):D477-D485
  5. Bady P, Kurscheid S, Delorenzi M, Gorlia T, van den Bent MJ, Hoang-Xuan K, Vauléon É, Gijtenbeek A, Enting R, Thiessen B, Chinot O, Dhermain F, Brandes AA, Reijneveld JC, Marosi C, Taphoorn MJB, Wick W, von Deimling A, French P, Stupp R, Baumert BG, Hegi ME. The DNA methylome of DDR genes and benefit from RT or TMZ in IDH mutant low-grade glioma treated in EORTC 22033. Acta Neuropathol 2018;135(4):601-615
  6. Bairoch A. The Cellosaurus, a Cell-Line Knowledge Resource. J Biomol Tech 2018
  7. Barido-Sottani J, Bošková V, Plessis LD, 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 2018;67(1):170-174
  8. Bast J, Parker DJ, Dumas Z, Jalvingh KM, Tran Van P, Jaron KS, Figuet E, Brandt A, Galtier N, Schwander T. Consequences of Asexuality in Natural Populations: Insights from Stick Insects. Mol Biol Evol 2018;35(7):1668-1677
  9. Battistello E, Katanayeva N, Dheilly E, Tavernari D, Donaldson MC, Bonsignore L, Thome M, Christie AL, Murakami MA, Michielin O, Ciriello G, Zoete V, Oricchio E. Pan-SRC kinase inhibition blocks B-cell receptor oncogenic signaling in non-Hodgkin lymphoma. Blood 2018;131(21):2345-2356
  10. Bekkar A, Estreicher A, Niknejad A, Casals-Casas C, Bridge A, Xenarios I, Dorier J, Crespo I. Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation. Database (Oxford) 2018;2018
  11. Bellazzo A, Di Minin G, Valentino E, Sicari D, Torre D, Marchionni L, Serpi F, Stadler MB, Taverna D, Zuccolotto G, Montagner IM, Rosato A, Tonon F, Zennaro C, Agostinis C, Bulla R, Mano M, Del Sal G, Collavin L. Cell-autonomous and cell non-autonomous downregulation of tumor suppressor DAB2IP by microRNA-149-3p promotes aggressiveness of cancer cells. Cell Death Differ 2018
  12. Bellini L, Campana M, Rouch C, Chacinska M, Bugliani M, Meneyrol K, Hainault I, Lenoir V, Denom J, Véret J, Kassis N, Thorens B, Ibberson M, Marchetti P, Blachnio-Zabielska A, Cruciani-Guglielmacci C, Prip-Buus C, Magnan C, Le Stunff H. Protective role of the ELOVL2/docosahexaenoic acid axis in glucolipotoxicity-induced apoptosis in rodent beta cells and human islets. Diabetologia 2018
  13. Bobisse S, Genolet R, Roberti A, Tanyi JL, Racle J, Stevenson BJ, Iseli C, Michel A, Le Bitoux MA, Guillaume P, Schmidt J, Bianchi V, Dangaj D, Fenwick C, Derré L, Xenarios I, Michielin O, Romero P, Monos DS, Zoete V, Gfeller D, Kandalaft LE, Coukos G, Harari A. Sensitive and frequent identification of high avidity neo-epitope specific CD8 + T cells in immunotherapy-naive ovarian cancer. Nat Commun 2018;9(1):1092
  14. Bologna NG, Iselin R, Abriata LA, Sarazin A, Pumplin N, Jay F, Grentzinger T, Dal Peraro M, Voinnet O. Nucleo-cytosolic Shuttling of ARGONAUTE1 Prompts a Revised Model of the Plant MicroRNA Pathway. Mol Cell 2018;69(4):709-719.e5
  15. Boskova V, Stadler T, Magnus C. The influence of phylodynamic model specifications on parameter estimates of the Zika virus epidemic. Virus Evol 2018;4(1):vex044
  16. Burton KJ, Pimentel G, Zangger N, Vionnet N, Drai J, McTernan PG, Pralong FP, Delorenzi M, Vergères G. Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men. PLoS One 2018;13(2):e0192947
  17. Cassatella D, Howard SR, Acierno JS, Xu C, Papadakis GE, Santoni FA, Dwyer AA, Santini S, Sykiotis GP, Chambion C, Meylan J, Marino L, Favre L, Li J, Liu X, Zhang J, Bouloux PM, Geyter C, Paepe A, Dhillo WS, Ferrara JM, Hauschild M, Lang-Muritano M, Lemke JR, Flück C, Nemeth A, Phan-Hug F, Pignatelli D, Popovic V, Pekic S, Quinton R, Szinnai G, l'Allemand D, Konrad D, Sharif S, Iyidir ÖT, Stevenson BJ, Yang H, Dunkel L, Pitteloud N. Congenital hypogonadotropic hypogonadism and constitutional delay of growth and puberty have distinct genetic architectures. Eur J Endocrinol 2018;178(4):377-388
  18. Castro-Giner F, Scheidmann MC, Aceto N. Beyond Enumeration: Functional and Computational Analysis of Circulating Tumor Cells to Investigate Cancer Metastasis. Front Med (Lausanne) 2018;5:34
  19. Chevrier S, Crowell HL, Zanotelli VRT, Engler S, Robinson MD, Bodenmiller B. Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry. Cell Syst 2018;6(5):612-620.e5
  20. Chu HY, Sprouffske K, Wagner A. Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing. BMC Evol Biol 2018;18(1):54
  21. Cicenas J, Zalyte E, Bairoch A, Gaudet P. Kinases and Cancer. Cancers (Basel) 2018;10(3)
  22. Cissé OH, Ma L, Wei Huang D, Khil PP, Dekker JP, Kutty G, Bishop L, Liu Y, Deng X, Hauser PM, Pagni M, Hirsch V, Lempicki RA, Stajich JE, Cuomo CA, Kovacs JA. Comparative Population Genomics Analysis of the Mammalian Fungal Pathogen Pneumocystis. MBio 2018;9(3)
  23. Cordey S, Hartley MA, Keitel K, Laubscher F, Brito F, Junier T, Kagoro F, Samaka J, Masimba J, Said Z, Temba H, Mlaganile T, Docquier M, Fellay J, Kaiser L, D'Acremont V. Detection of novel astroviruses MLB1 and MLB2 in the sera of febrile Tanzanian children. Emerg Microbes Infect 2018;7(1):27
  24. Daina A, Blatter MC, Gerritsen VB, Zoete V. Educational Tools to Introduce Computer-Aided Drug Design to Students and to the Public at Large. Chimia (Aarau) 2018;72(1):55-61
  25. Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P. Exploring autophagy with Gene Ontology. Autophagy 2018;14(3):419-436
  26. Ding W, Baumdicker F, Neher RA. panX: pan-genome analysis and exploration. Nucleic Acids Res 2018;46(1):e5
  27. Dorier J, Goundaroulis D, Benedetti F, Stasiak A. Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids. Bioinformatics 2018
  28. 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 2018;46(d1):D175-D180
  29. Dunne PD, Coleman HG, Bankhead P, Alderdice M, Gray RT, McQuaid S, Bingham V, Loughrey MB, James JA, McCorry AMB, Gilmore A, Holohan C, Klingbiel D, Tejpar S, Johnston PG, McArt DG, Di Nicolantonio F, Longley DB, Lawler M. Bcl-xL as a poor prognostic biomarker and predictor of response to adjuvant chemotherapy specifically in BRAF-mutant stage II and III colon cancer. Oncotarget 2018;9(17):13834-13847
  30. Fassnacht C, Tocchini C, Kumari P, Gaidatzis D, Stadler MB, Ciosk R. The CSR-1 endogenous RNAi pathway ensures accurate transcriptional reprogramming during the oocyte-to-embryo transition in Caenorhabditis elegans. PLoS Genet 2018;14(3):e1007252
  31. Gainza-Cirauqui P, Correia BE. Computational protein design-the next generation tool to expand synthetic biology applications. Curr Opin Biotechnol 2018;52:145-152
  32. Gao B, Huang Q, Baudis M. segment_liftover : a Python tool to convert segments between genome assemblies. F1000Res 2018;7
  33. Golumbeanu M, Cristinelli S, Rato S, Munoz M, Cavassini M, Beerenwinkel N, Ciuffi A. Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells. Cell Rep 2018;23(4):942-950
  34. Halbritter AH, Fior S, Keller I, Billeter R, Edwards PJ, Holderegger R, Karrenberg S, Pluess AR, Widmer A, Alexander JM. Trait differentiation and adaptation of plants along elevation gradients. J Evol Biol 2018;31(6):784-800
  35. Huang LC, Ross KE, Baffi TR, Drabkin H, Kochut KJ, Ruan Z, D'Eustachio P, McSkimming D, Arighi C, Chen C, Natale DA, Smith C, Gaudet P, Newton AC, Wu C, Kannan N. Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources. Sci Rep 2018;8(1):6518
  36. Huang X, Anderle P, Hostettler L, Baumann MU, Surbek DV, Ontsouka EC, Albrecht C. Identification of placental nutrient transporters associated with intrauterine growth restriction and pre-eclampsia. BMC Genomics 2018;19(1):173
  37. Ibrahim B, Arkhipova K, Andeweg AC, Posada-Céspedes S, Enault F, Gruber A, Koonin EV, Kupczok A, Lemey P, McHardy AC, McMahon DP, Pickett BE, Robertson DL, Scheuermann RH, Zhernakova A, Zwart MP, Schönhuth A, Dutilh BE, Marz M. Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting. Viruses 2018;10(5)
  38. Iyer PS, Mavoungou LO, Ronzoni F, Zemla J, Schmid-Siegert E, Antonini S, Neff LA, Dorchies OM, Jaconi M, Lekka M, Messina G, Mermod N. Autologous Cell Therapy Approach for Duchenne Muscular Dystrophy using PiggyBac Transposons and Mesoangioblasts. Mol Ther 2018;26(4):1093-1108
  39. Jackson L, Hunter J, Cele S, Ferreira IM, Young AC, Karim F, Madansein R, Dullabh KJ, Chen CY, Buckels NJ, Ganga Y, Khan K, Boulle M, Lustig G, Neher RA, Sigal A. Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death. Elife 2018;7
  40. Kaiser M, Jug F, Julou T, Deshpande S, Pfohl T, Silander OK, Myers G, van Nimwegen E. Monitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software. Nat Commun 2018;9(1):212
  41. Kanitz R, Guillot EG, Antoniazza S, Neuenschwander S, Goudet J. Complex genetic patterns in human arise from a simple range-expansion model over continental landmasses. PLoS One 2018;13(2):e0192460
  42. Knuckles P, Lence T, Haussmann IU, Jacob D, Kreim N, Carl SH, Masiello I, Hares T, Villaseñor R, Hess D, Andrade-Navarro MA, Biggiogera M, Helm M, Soller M, Bühler M, Roignant JY. Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA-binding factor Rbm15/Spenito to the m6A machinery component Wtap/Fl(2)d. Genes Dev 2018;32(5-6):415-429
  43. Kühnert D, Coscolla M, Brites D, Stucki D, Metcalfe J, Fenner L, Gagneux S, Stadler T. Tuberculosis outbreak investigation using phylodynamic analysis. Epidemics 2018
  44. Kühnert D, Kouyos R, Shirreff G, Pečerska J, Scherrer AU, Böni J, Yerly S, Klimkait T, Aubert V, Günthard HF, Stadler T, Bonhoeffer S, Swiss HIV Cohort Study. Quantifying the fitness cost of HIV-1 drug resistance mutations through phylodynamics. PLoS Pathog 2018;14(2):e1006895
  45. Kurtz A, Seltmann S, Bairoch A, Bittner MS, Bruce K, Capes-Davis A, Clarke L, Crook JM, Daheron L, Dewender J, Faulconbridge A, Fujibuchi W, Gutteridge A, Hei DJ, Kim YO, Kim JH, Kokocinski AK, Lekschas F, Lomax GP, Loring JF, Ludwig T, Mah N, Matsui T, Müller R, Parkinson H, Sheldon M, Smith K, Stachelscheid H, Stacey G, Streeter I, Veiga A, Xu RH. A Standard Nomenclature for Referencing and Authentication of Pluripotent Stem Cells. Stem Cell Reports 2018;10(1):1-6
  46. Lang BM, Beerenwinkel N, Misselwitz B. Editorial: the influence of genetic factors in mediating the effects of tobacco smoke in IBD-Authors' reply. Aliment Pharmacol Ther 2018;47(2):307-308
  47. Lannagan TRM, Lee YK, Wang T, Roper J, Bettington ML, Fennell L, Vrbanac L, Jonavicius L, Somashekar R, Gieniec K, Yang M, Ng JQ, Suzuki N, Ichinose M, Wright JA, Kobayashi H, Putoczki TL, Hayakawa Y, Leedham SJ, Abud HE, Yilmaz ÖH, Marker J, Klebe S, Wirapati P, Mukherjee S, Tejpar S, Leggett BA, Whitehall VLJ, Worthley DL, Woods SL. Genetic editing of colonic organoids provides a molecularly distinct and orthotopic preclinical model of serrated carcinogenesis. Gut 2018
  48. Lardi M, Liu Y, Giudice G, Ahrens CH, Zamboni N, Pessi G. Metabolomics and Transcriptomics Identify Multiple Downstream Targets of Paraburkholderia phymatum σ54 During Symbiosis with Phaseolus vulgaris. Int J Mol Sci 2018;19(4)
  49. Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias JE, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani-Sternberg M. Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE). Proteomics 2018;18(12):e1800110
  50. Littringer K, Moresi C, Rakebrandt N, Zhou X, Schorer M, Dolowschiak T, Kirchner F, Rost F, Keller CW, McHugh D, LeibundGut-Landmann S, Robinson MD, Joller N. Common Features of Regulatory T Cell Specialization During Th1 Responses. Front Immunol 2018;9
  51. Lopes MB, Veríssimo A, Carrasquinha E, Casimiro S, Beerenwinkel N, Vinga S. Ensemble outlier detection and gene selection in triple-negative breast cancer data. BMC Bioinformatics 2018;19(1):168
  52. Lucek K, Keller I, Nolte AW, Seehausen O. Distinct colonization waves underlie the diversification of the freshwater sculpin (Cottus gobio) in the Central European Alpine region. J Evol Biol 2018
  53. Madueño L, Paul C, Junier T, Bayrychenko Z, Filippidou S, Beck K, Greub G, Bürgmann H, Junier P. A historical legacy of antibiotic utilization on bacterial seed banks in sediments. PeerJ 2018;6:e4197
  54. Makrythanasis P, Maroofian R, Stray-Pedersen A, Musaev D, Zaki MS, Mahmoud IG, Selim L, Elbadawy A, Jhangiani SN, Coban Akdemir ZH, Gambin T, Sorte HS, Heiberg A, McEvoy-Venneri J, James KN, Stanley V, Belandres D, Guipponi M, Santoni FA, Ahangari N, Tara F, Doosti M, Iwaszkiewicz J, Zoete V, Backe PH, Hamamy H, Gleeson JG, Lupski JR, Karimiani EG, Antonarakis SE. Biallelic variants in KIF14 cause intellectual disability with microcephaly. Eur J Hum Genet 2018;26(3):330-339
  55. Martinelli F, Cannarozzi G, Balan B, Siegrist F, Weichert A, Blösch R, Tadele Z. Identification of miRNAs linked with the drought response of tef [Eragrostis tef (Zucc.) Trotter]. J Plant Physiol 2018;224-225:163-172
  56. Merkle PS, Gotfryd K, Cuendet MA, Leth-Espensen KZ, Gether U, Loland CJ, Rand KD. Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT. Sci Adv 2018;4(5):eaar6179
  57. Mhimbira F, Hiza H, Mbuba E, Hella J, Kamwela L, Sasamalo M, Ticlla M, Said K, Mhalu G, Chiryamkubi M, Schindler C, Reither K, Gagneux S, Fenner L. Prevalence and clinical significance of respiratory viruses and bacteria detected in tuberculosis patients compared to household contact controls in Tanzania: a cohort study. Clin Microbiol Infect 2018
  58. Mietchen D, Wodak S, Wasik S, Szostak N, Dessimoz C. Submit a Topic Page to PLOS Computational Biology and Wikipedia. PLoS Comput Biol 2018;14(5):e1006137
  59. Mitov V, Stadler T. A Practical Guide to Estimating the Heritability of Pathogen Traits. Mol Biol Evol 2018
  60. Möller S, du Plessis L, Stadler T. Impact of the tree prior on estimating clock rates during epidemic outbreaks. Proc Natl Acad Sci U S A 2018;115(16):4200-4205
  61. Noh H, Shoemaker JE, Gunawan R. Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection. Nucleic Acids Res 2018;46(6):e34
  62. Paul C, Bayrychenko Z, Junier T, Filippidou S, Beck K, Bueche M, Greub G, Bürgmann H, Junier P. Dissemination of antibiotic resistance genes associated with the sporobiota in sediments impacted by wastewater. PeerJ 2018;6:e4989
  63. Payne JL, Khalid F, Wagner A. RNA-mediated gene regulation is less evolvable than transcriptional regulation. Proc Natl Acad Sci U S A 2018;115(15):E3481-E3490
  64. Praz CR, Menardo F, Robinson MD, Müller MC, Wicker T, Bourras S, Keller B. Non-parent of Origin Expression of Numerous Effector Genes Indicates a Role of Gene Regulation in Host Adaption of the Hybrid Triticale Powdery Mildew Pathogen. Front Plant Sci 2018;9:49
  65. Racko D, Benedetti F, Dorier J, Stasiak A. Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes. Nucleic Acids Res 2018;46(4):1648-1660
  66. Raisaro JL, McLaren PJ, Fellay J, Cavassini M, Klersy C, Hubaux JP, Swiss HIV Cohort Study. Are privacy-enhancing technologies for genomic data ready for the clinic? A survey of medical experts of the Swiss HIV Cohort Study. J Biomed Inform 2018;79:1-6
  67. Ramsuran V, Naranbhai V, Horowitz A, Qi Y, Martin MP, Yuki Y, Gao X, Walker-Sperling V, Del Prete GQ, Schneider DK, Lifson JD, Fellay J, Deeks SG, Martin JN, Goedert JJ, Wolinsky SM, Michael NL, Kirk GD, Buchbinder S, Haas D, Ndung'u T, Goulder P, Parham P, Walker BD, Carlson JM, Carrington M. Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells. Science 2018;359(6371):86-90
  68. Reh L, Magnus C, Kadelka C, Kühnert D, Uhr T, Weber J, Morris L, Moore PL, Trkola A. Phenotypic deficits in the HIV-1 envelope are associated with the maturation of a V2-directed broadly neutralizing antibody lineage. PLoS Pathog 2018;14(1):e1006825
  69. Richard S, Almeida JMGCF, Cissé OH, Luraschi A, Nielsen O, Pagni M, Hauser PM. Functional and Expression Analyses of the Pneumocystis MAT Genes Suggest Obligate Sexuality through Primary Homothallism within Host Lungs. MBio 2018;9(1)
  70. Rolland J, Silvestro D, Litsios G, Faye L, Salamin N. Clownfishes evolution below and above the species level. Proc Biol Sci 2018;285(1873)
  71. Rüeger S, McDaid A, Kutalik Z. Evaluation and application of summary statistic imputation to discover new height-associated loci. PLoS Genet 2018;14(5):e1007371
  72. Rychener L, In-Albon S, Djordjevic SP, Chowdhury PR, Nicholson P, Ziech RE, de Vargas AC, Frey J, Falquet L. Corrigendum: Clostridium chauvoei, an Evolutionary Dead-End Pathogen. Front Microbiol 2018;9:421
  73. Ryll R, Eiden M, Heuser E, Weinhardt M, Ziege M, Höper D, Groschup MH, Heckel G, Johne R, Ulrich RG. Hepatitis E virus in feral rabbits along a rural-urban transect in Central Germany. Infect Genet Evol 2018;61:155-159
  74. Sagulenko P, Puller V, Neher RA. TreeTime: Maximum-likelihood phylodynamic analysis. Virus Evol 2018;4(1):vex042
  75. Sajic T, Liu Y, Arvaniti E, Surinova S, Williams EG, Schiess R, Hüttenhain R, Sethi A, Pan S, Brentnall TA, Chen R, Blattmann P, Friedrich B, Niméus E, Malander S, Omlin A, Gillessen S, Claassen M, Aebersold R. Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MS. Cell Rep 2018;23(9):2819-2831.e5
  76. Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Cancer Genome Atlas Research Network, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 2018;173(2):321-337.e10
  77. Schmid M, Muri J, Melidis D, Varadarajan AR, Somerville V, Wicki A, Moser A, Bourqui M, Wenzel C, Eugster-Meier E, Frey JE, Irmler S, Ahrens CH. Comparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level. Front Microbiol 2018;9:63
  78. Schwalie PC, Dong H, Zachara M, Russeil J, Alpern D, Akchiche N, Caprara C, Sun W, Schlaudraff KU, Soldati G, Wolfrum C, Deplancke B. A stromal cell population that inhibits adipogenesis in mammalian fat depots. Nature 2018
  79. 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 MP, 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 2018;34(1):107-108
  80. Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S. Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions. BMC Bioinformatics 2018;19(1):134
  81. Soneson C, Robinson MD. Towards unified quality verification of synthetic count data with countsimQC. Bioinformatics 2018;34(4):691-692
  82. Sprouffske K, Aguilar-Rodríguez J, Sniegowski P, Wagner A. High mutation rates limit evolutionary adaptation in Escherichia coli. PLoS Genet 2018;14(4):e1007324
  83. Stadler T, Gavryushkina A, Warnock RCM, Drummond AJ, Heath TA. The fossilized birth-death model for the analysis of stratigraphic range data under different speciation modes. J Theor Biol 2018;447:41-55
  84. Stadler T, Meinel D, Aguilar-Bultet L, Huisman JS, Schindler R, Egli A, Seth-Smith HMB, Eichenberger L, Brodmann P, Hübner P, Bagutti C, Tschudin-Sutter S. Transmission of ESBL-producing Enterobacteriaceae and their mobile genetic elements-identification of sources by whole genome sequencing: study protocol for an observational study in Switzerland. BMJ Open 2018;8(2):e021823
  85. Stévant I, Nef S. Single cell transcriptome sequencing: A new approach for the study of mammalian sex determination. Mol Cell Endocrinol 2018;468:11-18
  86. Stévant I, Neirijnck Y, Borel C, Escoffier J, Smith LB, Antonarakis SE, Dermitzakis ET, Nef S. Deciphering Cell Lineage Specification during Male Sex Determination with Single-Cell RNA Sequencing. Cell Rep 2018;22(6):1589-1599
  87. Stévant I, Papaioannou MD, Nef S. A brief history of sex determination. Mol Cell Endocrinol 2018;468:3-10
  88. Subramaniam S, Schmid CD, Guan XL, Mäser P. Using Yeast Synthetic Lethality To Inform Drug Combination for Malaria. Antimicrob Agents Chemother 2018;62(4)
  89. Sugiyama M, Ghisu ME, Llinares-López F, Borgwardt K. graphkernels: R and Python packages for graph comparison. Bioinformatics 2018;34(3):530-532
  90. Tanyi JL, Bobisse S, Ophir E, Tuyaerts S, Roberti A, Genolet R, Baumgartner P, Stevenson BJ, Iseli C, Dangaj D, Czerniecki B, Semilietof A, Racle J, Michel A, Xenarios I, Chiang C, Monos DS, Torigian DA, Nisenbaum HL, Michielin O, June CH, Levine BL, Powell DJ, Gfeller D, Mick R, Dafni U, Zoete V, Harari A, Coukos G, Kandalaft LE. Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer. Sci Transl Med 2018;10(436)
  91. Tejpar S, Yan P, Piessevaux H, Dietrich D, Brauchli P, Klingbiel D, Fiocca R, Delorenzi M, Bosman F, Roth AD. Clinical and pharmacogenetic determinants of 5-fluorouracyl/leucovorin/irinotecan toxicity: Results of the PETACC-3 trial. Eur J Cancer 2018;99:66-77
  92. Teodoro D, Sundvall E, João Junior M, Ruch P, Miranda Freire S. ORBDA: An openEHR benchmark dataset for performance assessment of electronic health record servers. PLoS One 2018;13(1):e0190028
  93. 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 2018;46(d1):D1150-D1156
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