Publications by SIB Members published in 2019

Listed in Europe PMC, latest update: 2020-01-01.

Peer-reviewed articles and conference proceedings


  1. Akarsu H, Aguilar-Bultet L, Falquet L. deltaRpkm: an R package for a rapid detection of differential gene presence between related bacterial genomes. BMC Bioinformatics 2019;20(1):621
  2. 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
  3. Alfei F, Kanev K, Hofmann M, Wu M, Ghoneim HE, Roelli P, Utzschneider DT, von Hoesslin M, Cullen JG, Fan Y, Eisenberg V, Wohlleber D, Steiger K, Merkler D, Delorenzi M, Knolle PA, Cohen CJ, Thimme R, Youngblood B, Zehn D. TOX reinforces the phenotype and longevity of exhausted T cells in chronic viral infection. Nature 2019;571(7764):265-269
  4. 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
  5. Altenhoff AM, Glover NM, Dessimoz C. Inferring Orthology and Paralogy. Methods Mol Biol 2019;1910:149-175
  6. Altenhoff AM, Levy J, Zarowiecki M, Tomiczek B, Warwick Vesztrocy A, Dalquen DA, Müller S, Telford MJ, Glover NM, Dylus D, Dessimoz C. OMA standalone: orthology inference among public and custom genomes and transcriptomes. Genome Res 2019;29(7):1152-1163
  7. Amini P, Nassiri S, Ettlin J, Malbon A, Markkanen E. Next-generation RNA sequencing of FFPE subsections reveals highly conserved stromal reprogramming between canine and human mammary carcinoma. Dis Model Mech 2019;12(8)
  8. Ansar M, Paracha SA, Serretti A, Sarwar MT, Khan J, Ranza E, Falconnet E, Iwaszkiewicz J, Shah SF, Qaisar AA, Santoni FA, Zoete V, Megarbane A, Ahmed J, Colombo R, Makrythanasis P, Antonarakis SE. Biallelic variants in FBXL3 cause intellectual disability, delayed motor development and short stature. Hum Mol Genet 2019;28(6):972-979
  9. Ansar M, Ullah F, Paracha SA, Adams DJ, Lai A, Pais L, Iwaszkiewicz J, Millan F, Sarwar MT, Agha Z, Shah SF, Qaisar AA, Falconnet E, Zoete V, Ranza E, Makrythanasis P, Santoni FA, Ahmed J, Katsanis N, Walsh C, Davis EE, Antonarakis SE. Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features. Am J Hum Genet 2019;104(6):1073-1087
  10. 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
  11. Aoki-Kinoshita KF, Lisacek F, Mazumder R, York WS, Packer NH. The GlySpace Alliance: towards a collaborative global glycoinformatics community. Glycobiology 2019
  12. Arora J, McLaren PJ, Chaturvedi N, Carrington M, Fellay J, Lenz TL. HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV control. Proc Natl Acad Sci U S A 2019;116(3):944-949
  13. 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
  14. Attardo GM, Abd-Alla AMM, Acosta-Serrano A, Allen JE, Bateta R, Benoit JB, Bourtzis K, Caers J, Caljon G, Christensen MB, Farrow DW, Friedrich M, Hua-Van A, Jennings EC, Larkin DM, Lawson D, Lehane MJ, Lenis VP, Lowy-Gallego E, Macharia RW, Malacrida AR, Marco HG, Masiga D, Maslen GL, Matetovici I, Meisel RP, Meki I, Michalkova V, Miller WJ, Minx P, Mireji PO, Ometto L, Parker AG, Rio R, Rose C, Rosendale AJ, Rota-Stabelli O, Savini G, Schoofs L, Scolari F, Swain MT, Takáč P, Tomlinson C, Tsiamis G, Van Den Abbeele J, Vigneron A, Wang J, Warren WC, Waterhouse RM, Weirauch MT, Weiss BL, Wilson RK, Zhao X, Aksoy S. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biol 2019;20(1):187
  15. 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
  16. Azizoglu A, Stelling J. Controlling cell-to-cell variability with synthetic gene circuits. Biochem Soc Trans 2019
  17. 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
  18. Bachmann N, von Siebenthal C, Vongrad V, Turk T, Neumann K, Beerenwinkel N, Bogojeska J, Fellay J, Roth V, Kok YL, Thorball CW, Borghesi A, Parbhoo S, Wieser M, Böni J, Perreau M, Klimkait T, Yerly S, Battegay M, Rauch A, Hoffmann M, Bernasconi E, Cavassini M, Kouyos RD, Günthard HF, Metzner KJ, Swiss HIV Cohort Study. Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART. Nat Commun 2019;10(1):3193
  19. 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
  20. Baillie Gerritsen V, Palagi PM, Durinx C. Bioinformatics on a national scale: an example from Switzerland. Brief Bioinform 2019;20(2):361-369
  21. 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
  22. Barido-Sottani J, Aguirre-Fernández G, Hopkins MJ, Stadler T, Warnock R. Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth-death process. Proc Biol Sci 2019;286(1902):20190685
  23. Barisic D, Stadler MB, Iurlaro M, Schübeler D. Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors. Nature 2019;569(7754):136-140
  24. Barovic M, Distler M, Schöniger E, Radisch N, Aust D, Weitz J, Ibberson M, Schulte AM, Solimena M. Metabolically phenotyped pancreatectomized patients as living donors for the study of islets in health and diabetes. Mol Metab 2019;27S:S1-S6
  25. Bassani-Sternberg M, Digklia A, Huber F, Wagner D, Sempoux C, Stevenson BJ, Thierry AC, Michaux J, Pak H, Racle J, Boudousquie C, Balint K, Coukos G, Gfeller D, Martin Lluesma S, Harari A, Demartines N, Kandalaft LE. A Phase Ib Study of the Combination of Personalized Autologous Dendritic Cell Vaccine, Aspirin, and Standard of Care Adjuvant Chemotherapy Followed by Nivolumab for Resected Pancreatic Adenocarcinoma-A Proof of Antigen Discovery Feasibility in Three Patients. Front Immunol 2019;10:1832
  26. Bast J, Jaron KS, Schuseil D, Roze D, Schwander T. Asexual reproduction reduces transposable element load in experimental yeast populations. Elife 2019;8
  27. Belluzo BS, Abriata LA, Giannini E, Mihovilcevic D, Dal Peraro M, Llarrull LI. An experiment-informed signal transduction model for the role of the Staphylococcus aureus MecR1 protein in β-lactam resistance. Sci Rep 2019;9(1):19558
  28. Berger S, Pachkov M, Arnold P, Omidi S, Kelley N, Salatino S, van Nimwegen E. Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs. Genome Res 2019;29(7):1164-1177
  29. Berman HM, Adams PD, Bonvin AA, Burley SK, Carragher B, Chiu W, DiMaio F, Ferrin TE, Gabanyi MJ, Goddard TD, Griffin PR, Haas J, Hanke CA, Hoch JC, Hummer G, Kurisu G, Lawson CL, Leitner A, Markley JL, Meiler J, Montelione GT, Phillips GN, Prisner T, Rappsilber J, Schriemer DC, Schwede T, Seidel CAM, Strutzenberg TS, Svergun DI, Tajkhorshid E, Trewhella J, Vallat B, Velankar S, Vuister GW, Webb B, Westbrook JD, White KL, Sali A. Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure 2019;27(12):1745-1759
  30. 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
  31. Bick JT, Zeng S, Robinson MD, Ulbrich SE, Bauersachs S. Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. Database (Oxford) 2019;2019
  32. Binz PA, Shofstahl J, Vizcaíno JA, Barsnes H, Chalkley RJ, Menschaert G, Alpi E, Clauser K, Eng JK, Lane L, Seymour SL, Sánchez LFH, Mayer G, Eisenacher M, Perez-Riverol Y, Kapp EA, Mendoza L, Baker PR, Collins A, Van Den Bossche T, Deutsch EW. Proteomics Standards Initiative Extended FASTA Format. J Proteome Res 2019;18(6):2686-2692
  33. Biočanin M, Bues J, Dainese R, Amstad E, Deplancke B. Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip. Lab Chip 2019;19(9):1610-1620
  34. Boareto M. Patterning via local cell-cell interactions in developing systems. Dev Biol 2019
  35. Bolck HA, Corrò C, Kahraman A, von Teichman A, Toussaint NC, Kuipers J, Chiovaro F, Koelzer VH, Pauli C, Moritz W, Bode PK, Rechsteiner M, Beerenwinkel N, Schraml P, Moch H. Tracing Clonal Dynamics Reveals that Two- and Three-dimensional Patient-derived Cell Models Capture Tumor Heterogeneity of Clear Cell Renal Cell Carcinoma. Eur Urol Focus 2019
  36. 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;27(5):764-775.e3
  37. 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
  38. Bosshard L, Peischl S, Ackermann M, Excoffier L. Mutational and Selective Processes Involved in Evolution during Bacterial Range Expansions. Mol Biol Evol 2019;36(10):2313-2327
  39. Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ. BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol 2019;15(4):e1006650
  40. 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
  41. Bresadola L, Caseys C, Castiglione S, Buerkle CA, Wegmann D, Lexer C. Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits. New Phytol 2019;223(4):2076-2089
  42. 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
  43. Capes-Davis A, Bairoch A, Barrett T, Burnett EC, Dirks WG, Hall EM, Healy L, Kniss DA, Korch C, Liu Y, Neve RM, Nims RW, Parodi B, Schweppe RE, Storts DR, Tian F. Cell Lines as Biological Models: Practical Steps for More Reliable Research. Chem Res Toxicol 2019;32(9):1733-1736
  44. Cardner M, Meyer-Schaller N, Christofori G, Beerenwinkel N. Inferring signalling dynamics by integrating interventional with observational data. Bioinformatics 2019;35(14):i577-i585
  45. Cascione L, Giudice L, Ferraresso S, Marconato L, Giannuzzi D, Napoli S, Bertoni F, Giugno R, Aresu L. Long Non-Coding RNAs as Molecular Signatures for Canine B-Cell Lymphoma Characterization. Noncoding RNA 2019;5(3)
  46. 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
  47. Chatterjee B, Deng Y, Holler A, Nunez N, Azzi T, Vanoaica LD, Müller A, Zdimerova H, Antsiferova O, Zbinden A, Capaul R, Dreyer JH, Nadal D, Becher B, Robinson MD, Stauss H, Münz C. CD8+ T cells retain protective functions despite sustained inhibitory receptor expression during Epstein-Barr virus infection in vivo. PLoS Pathog 2019;15(5):e1007748
  48. Chaturvedi N, Svarovskaia ES, Mo H, Osinusi AO, Brainard DM, Subramanian GM, McHutchison JG, Zeuzem S, Fellay J. Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes. Elife 2019;8
  49. Chen X, Widmer LA, Stangier MM, Steinmetz MO, Stelling J, Barral Y. Remote control of microtubule plus-end dynamics and function from the minus-end. Elife 2019;8
  50. 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
  51. Chevalier M, Ricart E, Hanozin E, Pupin M, Jacques P, Smargiasso N, De Pauw E, Lisacek F, Leclère V, Flahaut C. Kendrick Mass Defect Approach Combined to NORINE Database for Molecular Formula Assignment of Nonribosomal Peptides. J Am Soc Mass Spectrom 2019
  52. Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R, DREAM Module Identification Challenge Consortium, Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D. Assessment of network module identification across complex diseases. Nat Methods 2019;16(9):843-852
  53. Civenni G, Bosotti R, Timpanaro A, Vàzquez R, Merulla J, Pandit S, Rossi S, Albino D, Allegrini S, Mitra A, Mapelli SN, Vierling L, Giurdanella M, Marchetti M, Paganoni A, Rinaldi A, Losa M, Mira-Catò E, D'Antuono R, Morone D, Rezai K, D'Ambrosio G, Ouafik L, Mackenzie S, Riveiro ME, Cvitkovic E, Carbone GM, Catapano CV. Epigenetic Control of Mitochondrial Fission Enables Self-Renewal of Stem-like Tumor Cells in Human Prostate Cancer. Cell Metab 2019;30(2):303-318.e6
  54. 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
  55. Codesido S, Randazzo GM, Lehmann F, González-Ruiz V, García A, Xenarios I, Liechti R, Bridge A, Boccard J, Rudaz S. DynaStI: A Dynamic Retention Time Database for Steroidomics. Metabolites 2019;9(5)
  56. Colic N, Rinaldi F. Improving spaCy dependency annotation and PoS tagging web service using independent NER services. Genomics Inform 2019;17(2):e21
  57. 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
  58. Currat M, Arenas M, Quilodràn CS, Excoffier L, Ray N. SPLATCHE3: simulation of serial genetic data under spatially explicit evolutionary scenarios including long-distance dispersal. Bioinformatics 2019;35(21):4480-4483
  59. D'Agati G, Cabello EM, Frontzek K, Rushing EJ, Klemm R, Robinson MD, White RM, Mosimann C, Burger A. Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish. Dis Model Mech 2019;12(7)
  60. 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
  61. 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
  62. Daina A, Michielin O, Zoete V. SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. Nucleic Acids Res 2019;47(w1):W357-W364
  63. Daina A, Zoete V. Application of the SwissDrugDesign Online Resources in Virtual Screening. Int J Mol Sci 2019;20(18)
  64. Dangaj D, Bruand M, Grimm AJ, Ronet C, Barras D, Duttagupta PA, Lanitis E, Duraiswamy J, Tanyi JL, Benencia F, Conejo-Garcia J, Ramay HR, Montone KT, Powell DJ, Gimotty PA, Facciabene A, Jackson DG, Weber JS, Rodig SJ, Hodi SF, Kandalaft LE, Irving M, Zhang L, Foukas P, Rusakiewicz S, Delorenzi M, Coukos G. Cooperation between Constitutive and Inducible Chemokines Enables T Cell Engraftment and Immune Attack in Solid Tumors. Cancer Cell 2019;35(6):885-900.e10
  65. Davey NE, Babu MM, Blackledge M, Bridge A, Capella-Gutierrez S, Dosztanyi Z, Drysdale R, Edwards RJ, Elofsson A, Felli IC, Gibson TJ, Gutmanas A, Hancock JM, Harrow J, Higgins D, Jeffries CM, Le Mercier P, Mészáros B, Necci M, Notredame C, Orchard S, Ouzounis CA, Pancsa R, Papaleo E, Pierattelli R, Piovesan D, Promponas VJ, Ruch P, Rustici G, Romero P, Sarntivijai S, Saunders G, Schuler B, Sharan M, Shields DC, Sussman JL, Tedds JA, Tompa P, Turewicz M, Vondrasek J, Vranken WF, Wallace BA, Wichapong K, Tosatto SCE. An intrinsically disordered proteins community for ELIXIR. F1000Res 2019;8
  66. Davydov II, Salamin N, Robinson-Rechavi M. Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection. Mol Biol Evol 2019;36(6):1316-1332
  67. 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
  68. de La Harpe R, Rüeger S, Kutalik Z, Ballabeni P, Suter M, Vionnet N, Laferrère B, Pralong F. Weight Loss Directly Influences Intermediate-Term Remission of Diabetes Mellitus After Bariatric Surgery: A Retrospective Case-Control Study. Obes Surg 2019
  69. 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;180(1):305-322
  70. Delaneau O, Zazhytska M, Borel C, Giannuzzi G, Rey G, Howald C, Kumar S, Ongen H, Popadin K, Marbach D, Ambrosini G, Bielser D, Hacker D, Romano L, Ribaux P, Wiederkehr M, Falconnet E, Bucher P, Bergmann S, Antonarakis SE, Reymond A, Dermitzakis ET. Chromatin three-dimensional interactions mediate genetic effects on gene expression. Science 2019;364(6439)
  71. Dellicour S, Lemey P, Artois J, Lam TT, Fusaro A, Monne I, Cattoli G, Kuznetsov D, Xenarios I, Dauphin G, Kalpravidh W, Von Dobschuetz S, Claes F, Newman SH, Suchard MA, Baele G, Gilbert M. Incorporating heterogeneous sampling probabilities in continuous phylogeographic inference - application to H5N1 spread in the Mekong region. Bioinformatics 2019
  72. Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J. A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters. Cell 2019;178(6):1465-1477.e17
  73. Deutsch EW, Lane L, Overall CM, Bandeira N, Baker MS, Pineau C, Moritz RL, Corrales F, Orchard S, Van Eyk JE, Paik YK, Weintraub ST, Vandenbrouck Y, Omenn GS. Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0. J Proteome Res 2019;18(12):4108-4116
  74. 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
  75. Di Mitri D, Mirenda M, Vasilevska J, Calcinotto A, Delaleu N, Revandkar A, Gil V, Boysen G, Losa M, Mosole S, Pasquini E, D'Antuono R, Masetti M, Zagato E, Chiorino G, Ostano P, Rinaldi A, Gnetti L, Graupera M, Martins Figueiredo Fonseca AR, Pereira Mestre R, Waugh D, Barry S, De Bono J, Alimonti A. Re-education of Tumor-Associated Macrophages by CXCR2 Blockade Drives Senescence and Tumor Inhibition in Advanced Prostate Cancer. Cell Rep 2019;28(8):2156-2168.e5
  76. Dias MC, 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. Publisher Correction: Claudin-3-deficient C57BL/6J mice display intact brain barriers. Sci Rep 2019;9(1):10702
  77. 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
  78. Dirmeier S, Emmenlauer M, Dehio C, Beerenwinkel N. PyBDA: a command line tool for automated analysis of big biological data sets. BMC Bioinformatics 2019;20(1):564
  79. 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
  80. Donato C, Szczerba BM, Scheidmann MC, Castro-Giner F, Aceto N. Micromanipulation of Circulating Tumor Cells for Downstream Molecular Analysis and Metastatic Potential Assessment. J Vis Exp 2019(147)
  81. Duchene S, Bouckaert R, Duchene DA, Stadler T, Drummond AJ. Phylodynamic Model Adequacy Using Posterior Predictive Simulations. Syst Biol 2019;68(2):358-364
  82. Duek P, Lane L. Worming into the Uncharacterized Human Proteome. J Proteome Res 2019;18(12):4143-4153
  83. Duroy PO, Bosshard S, Schmid-Siegert E, Neuenschwander S, Arib G, Lemercier P, Masternak J, Roesch L, Buron F, Girod PA, Xenarios I, Mermod N. Characterization and mutagenesis of Chinese hamster ovary cells endogenous retroviruses to inactivate viral particle release. Biotechnol Bioeng 2019
  84. Dyrdak R, Mastafa M, Hodcroft EB, Neher RA, Albert J. Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing. Virus Evol 2019;5(1):vez007
  85. Egli A, Koch D, Danuser J, Hendriksen RS, Driesen S, Schmid DC, Neher R, Mäusezahl M, Seth-Smith HMB, Bloemberg G, Tschudin-Sutter S, Endimiani A, Perreten V, Greub G, Schrenzel J, Stephan R. Symposium report: One Health meets sequencing. Microbes Infect 2019
  86. Eguíluz VM, Salazar G, Fernández-Gracia J, Pearman JK, Gasol JM, Acinas SG, Sunagawa S, Irigoien X, Duarte CM. Scaling of species distribution explains the vast potential marine prokaryote diversity. Sci Rep 2019;9(1):18710
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