Publications by SIB Members published in 2019

Listed in Europe PMC, latest update: 2019-05-01.

Peer-reviewed articles and conference proceedings

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  1. Akarsu H, Bordes P, Mansour M, Bigot DJ, Genevaux P, Falquet L. TASmania: A bacterial Toxin-Antitoxin Systems database. PLoS Comput Biol 2019;15(4):e1006946
  2. Alocci D, Mariethoz J, Gastaldello A, Gasteiger E, Karlsson NG, Kolarich D, Packer NH, Lisacek F. GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical. J Proteome Res 2019;18(2):664-677
  3. Antinori P, Michelot T, Lescuyer P, Müller M, Acosta-Martin AE. Detection of Unknown Chemical Adduct Modifications on Proteins: From Wet to Dry Laboratory. Methods Mol Biol 2019;1977:99-113
  4. Arribas AJ, Rinaldi A, Chiodin G, Kwee I, Mensah AA, Cascione L, Rossi D, Kanduri M, Rosenquist R, Zucca E, Johnson PW, Gaidano G, Oakes CC, Bertoni F, Forconi F. Genome-wide promoter methylation of hairy cell leukemia. Blood Adv 2019;3(3):384-396
  5. Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S, Gene Ontology Consortium. Annotation of gene product function from high-throughput studies using the Gene Ontology. Database (Oxford) 2019;2019
  6. Babic Z, Capes-Davis A, Martone ME, Bairoch A, Ozyurt IB, Gillespie TH, Bandrowski AE. Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines. Elife 2019;8
  7. Bagger FO, Kinalis S, Rapin N. BloodSpot: a database of healthy and malignant haematopoiesis updated with purified and single cell mRNA sequencing profiles. Nucleic Acids Res 2019;47(d1):D881-D885
  8. Baillie Gerritsen V, Palagi PM, Durinx C. Bioinformatics on a national scale: an example from Switzerland. Brief Bioinform 2019;20(2):361-369
  9. Bargeton B, Iwaszkiewicz J, Bonifacio G, Roy S, Zoete V, Kellenberger S. Mutations in the palm domain disrupt modulation of acid-sensing ion channel 1a currents by neuropeptides. Sci Rep 2019;9(1):2599
  10. Bezler A, Braukmann F, West SM, Duplan A, Conconi R, Schütz F, Gönczy P, Piano F, Gunsalus K, Miska EA, Keller L. Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment. PLoS Genet 2019;15(2):e1007905
  11. Bonnardel F, Kumar A, Wimmerova M, Lahmann M, Perez S, Varrot A, Lisacek F, Imberty A. Architecture and Evolution of Blade Assembly in β-propeller Lectins. Structure 2019
  12. Bonnardel F, Mariethoz J, Salentin S, Robin X, Schroeder M, Perez S, Lisacek F, Imberty A. UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands. Nucleic Acids Res 2019;47(d1):D1236-D1244
  13. Braun RO, Brunner L, Wyler K, Auray G, García-Nicolás O, Python S, Zumkehr B, Gaschen V, Stoffel MH, Collin N, Barnier-Quer C, Bruggmann R, Summerfield A. Erratum: Author Correction: System immunology-based identification of blood transcriptional modules correlating to antibody responses in sheep. NPJ Vaccines 2019;4:10
  14. Buetti-Dinh A, Galli V, Bellenberg S, Ilie O, Herold M, Christel S, Boretska M, Pivkin IV, Wilmes P, Sand W, Vera M, Dopson M. Deep neural networks outperform human expert's capacity in characterizing bioleaching bacterial biofilm composition. Biotechnol Rep (Amst) 2019;22:e00321
  15. Castro Dias M, Coisne C, Lazarevic I, Baden P, Hata M, Iwamoto N, Francisco DMF, Vanlandewijck M, He L, Baier FA, Stroka D, Bruggmann R, Lyck R, Enzmann G, Deutsch U, Betsholtz C, Furuse M, Tsukita S, Engelhardt B. Claudin-3-deficient C57BL/6J mice display intact brain barriers. Sci Rep 2019;9(1):203
  16. Cheng HW, Onder L, Novkovic M, Soneson C, Lütge M, Pikor N, Scandella E, Robinson MD, Miyazaki JI, Tersteegen A, Sorg U, Pfeffer K, Rülicke T, Hehlgans T, Ludewig B. Origin and differentiation trajectories of fibroblastic reticular cells in the splenic white pulp. Nat Commun 2019;10(1):1739
  17. Clerc O, Mariethoz J, Rivet A, Lisacek F, Pérez S, Ricard-Blum S. A pipeline to translate glycosaminoglycan sequences into 3D models. Application to the exploration of glycosaminoglycan conformational space. Glycobiology 2019;29(1):36-44
  18. Cordey S, Laubscher F, Hartley MA, Junier T, Pérez-Rodriguez FJ, Keitel K, Vieille G, Samaka J, Mlaganile T, Kagoro F, Boillat-Blanco N, Mbarack Z, Docquier M, Brito F, Eibach D, May J, Sothmann P, Aldrich C, Lusingu J, Tapparel C, D'Acremont V, Kaiser L. Detection of dicistroviruses RNA in blood of febrile Tanzanian children. Emerg Microbes Infect 2019;8(1):613-623
  19. D'Amico L, Menzel U, Prummer M, Müller P, Buchi M, Kashyap A, Haessler U, Yermanos A, Gébleux R, Briendl M, Hell T, Wolter FI, Beerli RR, Truxova I, Radek Š, Vlajnic T, Grawunder U, Reddy S, Zippelius A. A novel anti-HER2 anthracycline-based antibody-drug conjugate induces adaptive anti-tumor immunity and potentiates PD-1 blockade in breast cancer. J Immunother Cancer 2019;7(1):16
  20. Dabrowski-Tumanski P, Rubach P, Goundaroulis D, Dorier J, Sulkowski P, Millett KC, Rawdon EJ, Stasiak A, Sulkowska JI. KnotProt 2.0: a database of proteins with knots and other entangled structures. Nucleic Acids Res 2019;47(d1):D367-D375
  21. de Jonge K, Ebering A, Nassiri S, Maby-El Hajjami H, Ouertatani-Sakouhi H, Baumgaertner P, Speiser DE. Circulating CD56bright NK cells inversely correlate with survival of melanoma patients. Sci Rep 2019;9(1):4487
  22. Deforges J, Reis RS, Jacquet P, Sheppard S, Gadekar VP, Hart-Smith G, Tanzer A, Hofacker IL, Iseli C, Xenarios I, Poirier Y. Control of cognate sense mRNA translation by cis-natural antisense RNAs. Plant Physiol 2019
  23. Dharmarajan L, Kaltenbach HM, Rudolf F, Stelling J. A Simple and Flexible Computational Framework for Inferring Sources of Heterogeneity from Single-Cell Dynamics. Cell Syst 2019;8(1):15-26.e11
  24. Dietrich LG, Barceló C, Thorball CW, Ryom L, Burkhalter F, Hasse B, Furrer H, Weisser M, Steffen A, Bernasconi E, Cavassini M, de Seigneux S, Csajka C, Fellay J, Ledergerber B, Tarr PE, Swiss HIV CohortS Study. Contribution of genetic background and clinical D:A:D risk score to chronic kidney disease in Swiss HIV-positive persons with normal baseline estimated glomerular filtration rate. Clin Infect Dis 2019
  25. Dobay A, Haas C, Fucile G, Downey N, Morrison HG, Kratzer A, Arora N. Microbiome-based body fluid identification of samples exposed to indoor conditions. Forensic Sci Int Genet 2019;40:105-113
  26. Duchene S, Bouckaert R, Duchene DA, Stadler T, Drummond AJ. Phylodynamic Model Adequacy Using Posterior Predictive Simulations. Syst Biol 2019;68(2):358-364
  27. Famiglietti ML, Estreicher A, Breuza L, Poux S, Redaschi N, Xenarios I, Bridge A, UniProt Consortium. An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar. Database (Oxford) 2019;2019
  28. Fennell L, Dumenil T, Wockner L, Hartel G, Nones K, Bond C, Borowsky J, Liu C, McKeone D, Bowdler L, Montgomery G, Klein K, Hoffmann I, Patch AM, Kazakoff S, Pearson J, Waddell N, Wirapati P, Lochhead P, Imamura Y, Ogino S, Shao R, Tejpar S, Leggett B, Whitehall V. Integrative Genome-Scale DNA Methylation Analysis of a Large and Unselected Cohort Reveals Five Distinct Subtypes of Colorectal Adenocarcinomas. Cell Mol Gastroenterol Hepatol 2019
  29. Filippidou S, Junier T, Wunderlin T, Kooli WM, Palmieri I, Al-Dourobi A, Molina V, Lienhard R, Spangenberg JE, Johnson SL, Chain PSG, Dorador C, Junier P. Adaptive Strategies in a Poly-Extreme Environment: Differentiation of Vegetative Cells in Serratia ureilytica and Resistance to Extreme Conditions. Front Microbiol 2019;10:102
  30. Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S. Federated discovery and sharing of genomic data using Beacons. Nat Biotechnol 2019;37(3):220-224
  31. Fiume M, Cupak M, Keenan S, Rambla J, de la Torre S, Dyke SOM, Brookes AJ, Carey K, Lloyd D, Goodhand P, Haeussler M, Baudis M, Stockinger H, Dolman L, Lappalainen I, Törnroos J, Linden M, Spalding JD, Ur-Rehman S, Page A, Flicek P, Sherry S, Haussler D, Varma S, Saunders G, Scollen S. Publisher Correction: Federated discovery and sharing of genomic data using Beacons. Nat Biotechnol 2019;37(4):480
  32. Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S, Mitraka E, Schriml LM, Gaudet P, Hobbs ET, Erill I, Siegele DA, Hu JC, Mungall C, Chibucos MC. ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic Acids Res 2019;47(d1):D1186-D1194
  33. Gkountela S, Castro-Giner F, Szczerba BM, Vetter M, Landin J, Scherrer R, Krol I, Scheidmann MC, Beisel C, Stirnimann CU, Kurzeder C, Heinzelmann-Schwarz V, Rochlitz C, Weber WP, Aceto N. Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding. Cell 2019;176(1-2):98-112.e14
  34. Glover NM, Altenhoff A, Dessimoz C. Assigning confidence scores to homoeologs using fuzzy logic. PeerJ 2019;6:e6231
  35. Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection. Sci Rep 2019;9(1):213
  36. González-Rincón J, Méndez M, Gómez S, García JF, Martín P, Bellas C, Pedrosa L, Rodríguez-Pinilla SM, Camacho FI, Quero C, Pérez-Callejo D, Rueda A, Llanos M, Gómez-Codina J, Piris MA, Montes-Moreno S, Bárcena C, Rodríguez-Abreu D, Menárguez J, de la Cruz-Merino L, Monsalvo S, Parejo C, Royuela A, Kwee I, Cascione L, Arribas A, Bertoni F, Mollejo M, Provencio M, Sánchez-Beato M. Unraveling transformation of follicular lymphoma to diffuse large B-cell lymphoma. PLoS One 2019;14(2):e0212813
  37. Gregory AC, Zayed AA, Conceição-Neto N, Temperton B, Bolduc B, Alberti A, Ardyna M, Arkhipova K, Carmichael M, Cruaud C, Dimier C, Domínguez-Huerta G, Ferland J, Kandels S, Liu Y, Marec C, Pesant S, Picheral M, Pisarev S, Poulain J, Tremblay JÉ, Vik D, Tara Oceans Coordinators, Babin M, Bowler C, Culley AI, de Vargas C, Dutilh BE, Iudicone D, Karp-Boss L, Roux S, Sunagawa S, Wincker P, Sullivan MB. Marine DNA Viral Macro- and Microdiversity from Pole to Pole. Cell 2019
  38. Hartl D, Krebs AR, Grand RS, Baubec T, Isbel L, Wirbelauer C, Burger L, Schübeler D. CG dinucleotides enhance promoter activity independent of DNA methylation. Genome Res 2019;29(4):554-563
  39. Hendrikx S, Coso S, Prat-Luri B, Wetterwald L, Sabine A, Franco CA, Nassiri S, Zangger N, Gerhardt H, Delorenzi M, Petrova TV. Endothelial Calcineurin Signaling Restrains Metastatic Outgrowth by Regulating Bmp2. Cell Rep 2019;26(5):1227-1241.e6
  40. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, von Mering C, Bork P. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019;47(d1):D309-D314
  41. Ilmjärv S, Augsburger F, Bolleman JT, Liechti R, Bridge AJ, Sandström J, Jaquet V, Xenarios I, Krause KH. Navigating in vitro bioactivity data by investigating available resources using model compounds. Sci Data 2019;6(1):45
  42. Jayachandran R, Gumienny A, Bolinger B, Ruehl S, Lang MJ, Fucile G, Mazumder S, Tchang V, Woischnig AK, Stiess M, Kunz G, Claudi B, Schmaler M, Siegmund K, Li J, Dertschnig S, Holländer G, Medina E, Karrer U, Moshous D, Bumann D, Khanna N, Rossi SW, Pieters J. Disruption of Coronin 1 Signaling in T Cells Promotes Allograft Tolerance while Maintaining Anti-Pathogen Immunity. Immunity 2019;50(1):152-165.e8
  43. Jores J, Ma L, Ssajjakambwe P, Schieck E, Liljander A, Chandran S, Stoffel MH, Cippa V, Arfi Y, Assad-Garcia N, Falquet L, Sirand-Pugnet P, Blanchard A, Lartigue C, Posthaus H, Labroussaa F, Vashee S. Removal of a Subset of Non-essential Genes Fully Attenuates a Highly Virulent Mycoplasma Strain. Front Microbiol 2019;10:664
  44. Justice AE, Karaderi T, Highland HM, Young KL, Graff M, Lu Y, Turcot V, Auer PL, Fine RS, Guo X, Schurmann C, Lempradl A, Marouli E, Mahajan A, Winkler TW, Locke AE, Medina-Gomez C, Esko T, Vedantam S, Giri A, Lo KS, Alfred T, Mudgal P, Ng MCY, Heard-Costa NL, Feitosa MF, Manning AK, Willems SM, Sivapalaratnam S, Abecasis G, Alam DS, Allison M, Amouyel P, Arzumanyan Z, Balkau B, Bastarache L, Bergmann S, Bielak LF, Blüher M, Boehnke M, Boeing H, Boerwinkle E, Böger CA, Bork-Jensen J, Bottinger EP, Bowden DW, Brandslund I, Broer L, Burt AA, Butterworth AS, Caulfield MJ, Cesana G, Chambers JC, Chasman DI, Chen YI, Chowdhury R, Christensen C, Chu AY, Collins FS, Cook JP, Cox AJ, Crosslin DS, Danesh J, de Bakker PIW, Denus S, Mutsert R, Dedoussis G, Demerath EW, Dennis JG, Denny JC, Angelantonio ED, Dörr M, Drenos F, Dubé MP, Dunning AM, Easton DF, Elliott P, Evangelou E, Farmaki AE, Feng S, Ferrannini E, Ferrieres J, Florez JC, Fornage M, Fox CS, Franks PW, Friedrich N, Gan W, Gandin I, Gasparini P, Giedraitis V, Girotto G, Gorski M, Grallert H, Grarup N, Grove ML, Gustafsson S, Haessler J, Hansen T, Hattersley AT, Hayward C, Heid IM, Holmen OL, Hovingh GK, Howson JMM, Hu Y, Hung YJ, Hveem K, Ikram MA, Ingelsson E, Jackson AU, Jarvik GP, Jia Y, Jørgensen T, Jousilahti P, Justesen JM, Kahali B, Karaleftheri M, Kardia SLR, Karpe F, Kee F, Kitajima H, Komulainen P, Kooner JS, Kovacs P, Krämer BK, Kuulasmaa K, Kuusisto J, Laakso M, Lakka TA, Lamparter D, Lange LA, Langenberg C, Larson EB, Lee NR, Lee WJ, Lehtimäki T, Lewis CE, Li H, Li J, Li-Gao R, Lin LA, Lin X, Lind L, Lindström J, Linneberg A, Liu CT, Liu DJ, Luan J, Lyytikäinen LP, MacGregor S, Mägi R, Männistö S, Marenne G, Marten J, Masca NGD, McCarthy MI, Meidtner K, Mihailov E, Moilanen L, Moitry M, Mook-Kanamori DO, Morgan A, Morris AP, Müller-Nurasyid M, Munroe PB, Narisu N, Nelson CP, Neville M, Ntalla I, O'Connell JR, Owen KR, Pedersen O, Peloso GM, Pennell CE, Perola M, Perry JA, Perry JRB, Pers TH, Ewing A, Polasek O, Raitakari OT, Rasheed A, Raulerson CK, Rauramaa R, Reilly DF, Reiner AP, Ridker PM, Rivas MA, Robertson NR, Robino A, Rudan I, Ruth KS, Saleheen D, Salomaa V, Samani NJ, Schreiner PJ, Schulze MB, Scott RA, Segura-Lepe M, Sim X, Slater AJ, Small KS, Smith BH, Smith JA, Southam L, Spector TD, Speliotes EK, Stefansson K, Steinthorsdottir V, Stirrups KE, Strauch K, Stringham HM, Stumvoll M, Sun L, Surendran P, Swart KMA, Tardif JC, Taylor KD, Teumer A, Thompson DJ, Thorleifsson G, Thorsteinsdottir U, Thuesen BH, Tönjes A, Torres M, Tsafantakis E, Tuomilehto J, Uitterlinden AG, Uusitupa M, van Duijn CM, Vanhala M, Varma R, Vermeulen SH, Vestergaard H, Vitart V, Vogt TF, Vuckovic D, Wagenknecht LE, Walker M, Wallentin L, Wang F, Wang CA, Wang S, Wareham NJ, Warren HR, Waterworth DM, Wessel J, White HD, Willer CJ, Wilson JG, Wood AR, Wu Y, Yaghootkar H, Yao J, Yerges-Armstrong LM, Young R, Zeggini E, Zhan X, Zhang W, Zhao JH, Zhao W, Zheng H, Zhou W, Zillikens MC, CHD Exome+ Consortium, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium, EPIC-CVD Consortium, ExomeBP Consortium, Global Lipids Genetic Consortium, GoT2D Genes Consortium, InterAct, ReproGen Consortium, T2D-Genes Consortium, MAGIC Investigators, Rivadeneira F, Borecki IB, Pospisilik JA, Deloukas P, Frayling TM, Lettre G, Mohlke KL, Rotter JI, Kutalik Z, Hirschhorn JN, Cupples LA, Loos RJF, North KE, Lindgren CM. Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution. Nat Genet 2019;51(3):452-469
  45. Kaiser J, Maibach M, Salpeter I, Hagenbuch N, Souza VBC, Robinson MD, Schwab ME. The spinal transcriptome after cortical stroke - In search of molecular factors regulating spontaneous recovery in the spinal cord. J Neurosci 2019
  46. Kaleb K, Vesztrocy AW, Altenhoff A, Dessimoz C. Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python. F1000Res 2019;8:42
  47. Kapheim KM, Pan H, Li C, Blatti C, Harpur BA, Ioannidis P, Jones BM, Kent CF, Ruzzante L, Sloofman L, Stolle E, Waterhouse RM, Zayed A, Zhang G, Wcislo WT. Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi). G3 (Bethesda) 2019;9(3):625-634
  48. Khamis A, Canouil M, Siddiq A, Crouch H, Falchi M, Bulow MV, Ehehalt F, Marselli L, Distler M, Richter D, Weitz J, Bokvist K, Xenarios I, Thorens B, Schulte AM, Ibberson M, Bonnefond A, Marchetti P, Solimena M, Froguel P. Laser capture microdissection of human pancreatic islets reveals novel eQTLs associated with type 2 diabetes. Mol Metab 2019
  49. Kilpeläinen TO, Bentley AR, Noordam R, Sung YJ, Schwander K, Winkler TW, Jakupović H, Chasman DI, Manning A, Ntalla I, Aschard H, Brown MR, de Las Fuentes L, Franceschini N, Guo X, Vojinovic D, Aslibekyan S, Feitosa MF, Kho M, Musani SK, Richard M, Wang H, Wang Z, Bartz TM, Bielak LF, Campbell A, Dorajoo R, Fisher V, Hartwig FP, Horimoto ARVR, Li C, Lohman KK, Marten J, Sim X, Smith AV, Tajuddin SM, Alver M, Amini M, Boissel M, Chai JF, Chen X, Divers J, Evangelou E, Gao C, Graff M, Harris SE, He M, Hsu FC, Jackson AU, Zhao JH, Kraja AT, Kühnel B, Laguzzi F, Lyytikäinen LP, Nolte IM, Rauramaa R, Riaz M, Robino A, Rueedi R, Stringham HM, Takeuchi F, van der Most PJ, Varga TV, Verweij N, Ware EB, Wen W, Li X, Yanek LR, Amin N, Arnett DK, Boerwinkle E, Brumat M, Cade B, Canouil M, Chen YI, Concas MP, Connell J, de Mutsert R, de Silva HJ, de Vries PS, Demirkan A, Ding J, Eaton CB, Faul JD, Friedlander Y, Gabriel KP, Ghanbari M, Giulianini F, Gu CC, Gu D, Harris TB, He J, Heikkinen S, Heng CK, Hunt SC, Ikram MA, Jonas JB, Koh WP, Komulainen P, Krieger JE, Kritchevsky SB, Kutalik Z, Kuusisto J, Langefeld CD, Langenberg C, Launer LJ, Leander K, Lemaitre RN, Lewis CE, Liang J, Lifelines Cohort Study, Liu J, Mägi R, Manichaikul A, Meitinger T, Metspalu A, Milaneschi Y, Mohlke KL, Mosley TH, Murray AD, Nalls MA, Nang EK, Nelson CP, Nona S, Norris JM, Nwuba CV, O'Connell J, Palmer ND, Papanicolau GJ, Pazoki R, Pedersen NL, Peters A, Peyser PA, Polasek O, Porteous DJ, Poveda A, Raitakari OT, Rich SS, Risch N, Robinson JG, Rose LM, Rudan I, Schreiner PJ, Scott RA, Sidney SS, Sims M, Smith JA, Snieder H, Sofer T, Starr JM, Sternfeld B, Strauch K, Tang H, Taylor KD, Tsai MY, Tuomilehto J, Uitterlinden AG, van der Ende MY, van Heemst D, Voortman T, Waldenberger M, Wennberg P, Wilson G, Xiang YB, Yao J, Yu C, Yuan JM, Zhao W, Zonderman AB, Becker DM, Boehnke M, Bowden DW, de Faire U, Deary IJ, Elliott P, Esko T, Freedman BI, Froguel P, Gasparini P, Gieger C, Kato N, Laakso M, Lakka TA, Lehtimäki T, Magnusson PKE, Oldehinkel AJ, Penninx BWJH, Samani NJ, Shu XO, van der Harst P, Van Vliet-Ostaptchouk JV, Vollenweider P, Wagenknecht LE, Wang YX, Wareham NJ, Weir DR, Wu T, Zheng W, Zhu X, Evans MK, Franks PW, Gudnason V, Hayward C, Horta BL, Kelly TN, Liu Y, North KE, Pereira AC, Ridker PM, Tai ES, van Dam RM, Fox ER, Kardia SLR, Liu CT, Mook-Kanamori DO, Province MA, Redline S, van Duijn CM, Rotter JI, Kooperberg CB, Gauderman WJ, Psaty BM, Rice K, Munroe PB, Fornage M, Cupples LA, Rotimi CN, Morrison AC, Rao DC, Loos RJF. Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity. Nat Commun 2019;10(1):376
  50. Kirchner FR, Littringer K, Altmeier S, Tran VDT, Schönherr F, Lemberg C, Pagni M, Sanglard D, Joller N, LeibundGut-Landmann S. Persistence of Candida albicans in the Oral Mucosa Induces a Curbed Inflammatory Host Response That Is Independent of Immunosuppression. Front Immunol 2019;10:330
  51. Kriventseva EV, Kuznetsov D, Tegenfeldt F, Manni M, Dias R, Simão FA, Zdobnov EM. OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic Acids Res 2019;47(d1):D807-D811
  52. Langer S, Hammer C, Hopfensperger K, Klein L, Hotter D, De Jesus PD, Herbert KM, Pache L, Smith N, van der Merwe JA, Chanda SK, Fellay J, Kirchhoff F, Sauter D. HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responses. Elife 2019;8
  53. Le Mercier P, Mariethoz J, Lascano-Maillard J, Bonnardel F, Imberty A, Ricard-Blum S, Lisacek F. A Bioinformatics View of Glycan⁻Virus Interactions. Viruses 2019;11(4)
  54. Liljander A, Sacchini F, Stoffel MH, Schieck E, Stokar-Regenscheit N, Labroussaa F, Heller M, Salt J, Frey J, Falquet L, Goovaerts D, Jores J. Reproduction of contagious caprine pleuropneumonia reveals the ability of convalescent sera to reduce hydrogen peroxide production in vitro. Vet Res 2019;50(1):10
  55. Lombardot T, Morgat A, Axelsen KB, Aimo L, Hyka-Nouspikel N, Niknejad A, Ignatchenko A, Xenarios I, Coudert E, Redaschi N, Bridge A. Updates in Rhea: SPARQLing biochemical reaction data. Nucleic Acids Res 2019;47(d1):D596-D600
  56. Marcelino I, Colomé-Calls N, Holzmuller P, Lisacek F, Reynaud Y, Canals F, Vachiéry N. Sweet and Sour Ehrlichia: Glycoproteomics and Phosphoproteomics Reveal New Players in Ehrlichia ruminantium Physiology and Pathogenesis. Front Microbiol 2019;10:450
  57. Mayorov A, Dal Peraro M, Abriata LA. Active site-induced evolutionary constraints follow fold polarity principles in soluble globular enzymes. Mol Biol Evol 2019
  58. Meyer X, Dib L, Salamin N. CoevDB: a database of intramolecular coevolution among protein-coding genes of the bony vertebrates. Nucleic Acids Res 2019;47(d1):D50-D54
  59. Meyer-Schaller N, Cardner M, Diepenbruck M, Saxena M, Tiede S, Lüönd F, Ivanek R, Beerenwinkel N, Christofori G. A Hierarchical Regulatory Landscape during the Multiple Stages of EMT. Dev Cell 2019;48(4):539-553.e6
  60. Micossé C, von Meyenn L, Steck O, Kipfer E, Adam C, Simillion C, Seyed Jafari SM, Olah P, Yawlkar N, Simon D, Borradori L, Kuchen S, Yerly D, Homey B, Conrad C, Snijder B, Schmidt M, Schlapbach C. Human "TH9" cells are a subpopulation of PPAR-γ+ TH2 cells. Sci Immunol 2019;4(31)
  61. Milanese A, Mende DR, Paoli L, Salazar G, Ruscheweyh HJ, Cuenca M, Hingamp P, Alves R, Costea PI, Coelho LP, Schmidt TSB, Almeida A, Mitchell AL, Finn RD, Huerta-Cepas J, Bork P, Zeller G, Sunagawa S. Microbial abundance, activity and population genomic profiling with mOTUs2. Nat Commun 2019;10(1):1014
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