Our publications
The tidyomics ecosystem: enhancing omic data analyses.
Hutchison WJ, Keyes TJ, tidyomics Consortium, Crowell HL, Serizay J, Soneson C, Davis ES, Sato N, Moses L, Tarlinton B, Nahid AA, Kosmac M, Clayssen Q, Yuan V, Mu W, Park JE, Mamede I, Ryu MH, Axisa PP, Paiz P, Poon CL, Tang M, Gottardo R, Morgan M, Lee S, Lawrence M, Hicks SC, Nolan GP, Davis KL, Papenfuss AT, Love MI, Mangiola S
Nat Methods. 2024 Jun 14
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation.
Xu ZM, Gnouamozi GE, Rüeger S, Shea PR, Buti M, Chan HL, Marcellin P, Lawless D, Naret O, Zeller M, Schneuing A, Scheck A, Junier T, Moradpour D, Podlaha O, Suri V, Gaggar A, Subramanian M, Correia B, Gfeller D, Urban S, Fellay J
Am J Hum Genet. 2024 Jun 6;111(6):1018-1034
Long-term Remissions Following CD20-directed Chimeric Antigen Receptor Adoptive T cell Therapy.
Mo G, Lee SY, Coffey DG, Voillet V, Kirsch IR, Gottardo R, Smythe KS, Yeung CCS, Greenbaum A, Green DJ, Maloney DG, Till BG
Blood Cancer Discov. 2024 May 15
Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection.
Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, Zhang Y, Nemes-Bokun I, Kalinova M, Catchpole A, Tangye SG, Spaan AN, Lack JB, Ghosn J, Burdet C, Gorochov G, Tubach F, Hausfater P, COVID Human Genetic Effort, COVIDeF Study Group, French COVID Cohort Study Group, CoV-Contact Cohort, COVID-STORM Clinicians, COVID Clinicians, Orchestra Working Group, Amsterdam UMC Covid-19 Biobank, NIAID-USUHS COVID Study Group, Dalgard CL, Zhang SY, Zhang Q, Chiu C, Fellay J, Grzymski JJ, Sancho-Shimizu V, Abel L, Casanova JL, Cobat A, Bolze A
HGG Adv. 2024 Apr 26:100300
Overcoming limitations in current measures of drug response may enable AI-driven precision oncology.
Ovchinnikova K, Born J, Chouvardas P, Rapsomaniki M, Kruithof-de Julio M
NPJ Precis Oncol. 2024 Apr 24;8(1):95
Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania.
Hiza H, Zwyer M, Hella J, Arbués A, Sasamalo M, Borrell S, Xu ZM, Ross A, Brites D, Fellay J, Reither K, Gagneux S, Portevin D
Sci Rep. 2024 Apr 23;14(1):9287
Weight, anthropometric and metabolic changes after discontinuing antiretroviral therapy containing tenofovir alafenamide (TAF) in people with HIV.
Damas J, Munting A, Fellay J, Haerry D, Marzolini C, Tarr PE, Steffen A, Braun DL, Stoeckle M, Bernasconi E, Tshikung ON, Fux CA, Darling KEA, Béguelin C, Wandeler G, Cavassini M, Surial B, Swiss HIV Cohort Study (SHCS)
Clin Infect Dis. 2024 Apr 12
ScLinear predicts protein abundance at single-cell resolution.
Hanhart D, Gossi F, Rapsomaniki MA, Kruithof-de Julio M, Chouvardas P
Commun Biol. 2024 Mar 4;7(1):267
An approach for integrating multimodal omics data into sparse and interpretable models.
Dong Y, Gottardo R
Cell Rep Methods. 2024 Feb 26;4(2):100718
Signaling via a CD27-TRAF2-SHP-1 axis during naive T cell activation promotes memory-associated gene regulatory networks.
Jaeger-Ruckstuhl CA, Lo Y, Fulton E, Waltner OG, Shabaneh TB, Simon S, Muthuraman PV, Correnti CE, Newsom OJ, Engstrom IA, Kanaan SB, Bhise SS, Peralta JMC, Ruff R, Price JP, Stull SM, Stevens AR, Bugos G, Kluesner MG, Voillet V, Muhunthan V, Morrish F, Olson JM, Gottardo R, Sarthy JF, Henikoff S, Sullivan LB, Furlan SN, Riddell SR
Immunity. 2024 Feb 13;57(2):287-302.e12
Response to tumor-infiltrating lymphocyte adoptive therapy is associated with preexisting CD8(+) T-myeloid cell networks in melanoma.
Barras D, Ghisoni E, Chiffelle J, Orcurto A, Dagher J, Fahr N, Benedetti F, Crespo I, Grimm AJ, Morotti M, Zimmermann S, Duran R, Imbimbo M, de Olza MO, Navarro B, Homicsko K, Bobisse S, Labes D, Tsourti Z, Andriakopoulou C, Herrera F, Pétremand R, Dummer R, Berthod G, Kraemer AI, Huber F, Thevenet J, Bassani-Sternberg M, Schaefer N, Prior JO, Matter M, Aedo V, Dromain C, Corria-Osorio J, Tissot S, Kandalaft LE, Gottardo R, Pittet M, Sempoux C, Michielin O, Dafni U, Trueb L, Harari A, Laniti DD, Coukos G
Sci Immunol. 2024 Feb 2;9(92):eadg7995
Enhancing immunogenic responses through CDK4/6 and HIF2α inhibition in Merkel cell carcinoma.
Lee JH, Lee JD, Paulson K, Voillet V, Berndt A, Church C, Lachance K, Park SY, Yamamoto NK, Cromwell EA, Gottardo R, Chapuis AG, Nghiem P
Heliyon. 2024 Jan 15;10(1):e23521
Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E.
Saadat A, Gouttenoire J, Ripellino P, Semela D, Amar S, Frey BM, Fontana S, Mdawar-Bailly E, Moradpour D, Fellay J, Fraga M, HEV Human Genetics Collaborators
Hepatology. 2023 Dec 8
Transcriptomics and chromatin accessibility in multiple African population samples.
DeGorter MK, Goddard PC, Karakoc E, Kundu S, Yan SM, Nachun D, Abell N, Aguirre M, Carstensen T, Chen Z, Durrant M, Dwaracherla VR, Feng K, Gloudemans MJ, Hunter N, Moorthy MPS, Pomilla C, Rodrigues KB, Smith CJ, Smith KS, Ungar RA, Balliu B, Fellay J, Fl
bioRxiv. 2023 Nov 6
Development of a Predictive Model for Hospital-Acquired Pressure Injuries.
Pouzols S, Despraz J, Mabire C, Raisaro JL
Comput Inform Nurs. 2023 Nov 1;41(11):884-891
The BioRef Infrastructure, a Framework for Real-Time, Federated, Privacy-Preserving, and Personalized Reference Intervals: Design, Development, and Application.
Blatter TU, Witte H, Fasquelle-Lopez J, Theodoros Naka C, Raisaro JL, Leichtle AB
J Med Internet Res. 2023 Oct 18;25:e47254
G2GSnake: a Snakemake workflow for host-pathogen genomic association studies.
Xu ZM, Naret O, Oumelloul MA, Fellay J
Bioinform Adv. 2023;3(1):vbad142
Single-cell Profiling Uncovers a Muc4-Expressing Metaplastic Gastric Cell Type Sustained by Helicobacter pylori-driven Inflammation.
O'Brien VP, Kang Y, Shenoy MK, Finak G, Young WC, Dubrulle J, Koch L, Rodriguez Martinez AE, Williams J, Donato E, Batra SK, Yeung CCS, Grady WM, Koch MA, Gottardo R, Salama NR
Cancer Res Commun. 2023 Sep;3(9):1756-1769
Autoantibodies neutralizing type I IFNs underlie West Nile virus encephalitis in ∼40% of patients.
Gervais A, Rovida F, Avanzini MA, Croce S, Marchal A, Lin SC, Ferrari A, Thorball CW, Constant O, Le Voyer T, Philippot Q, Rosain J, Angelini M, Pérez Lorenzo M, Bizien L, Achille C, Trespidi F, Burdino E, Cassaniti I, Lilleri D, Fornara C, Sammartino JC,
J Exp Med. 2023 Sep 4;220(9)
Africa-specific human genetic variation near CHD1L associates with HIV-1 load.
McLaren PJ, Porreca I, Iaconis G, Mok HP, Mukhopadhyay S, Karakoc E, Cristinelli S, Pomilla C, Bartha I, Thorball CW, Tough RH, Angelino P, Kiar CS, Carstensen T, Fatumo S, Porter T, Jarvis I, Skarnes WC, Bassett A, DeGorter MK, Sathya Moorthy MP, Tuff JF
Nature. 2023 Aug;620(7976):1025-1030
Genetic features and genomic targets of human KRAB-zinc finger proteins.
de Tribolet-Hardy J, Thorball CW, Forey R, Planet E, Duc J, Coudray A, Khubieh B, Offner S, Pulver C, Fellay J, Imbeault M, Turelli P, Trono D
Genome Res. 2023 Aug;33(8):1409-1423
Differentiation of IL-26(+) T(H)17 intermediates into IL-17A producers via epithelial crosstalk in psoriasis.
Fries A, Saidoune F, Kuonen F, Dupanloup I, Fournier N, Guerra de Souza AC, Haniffa M, Ma F, Gudjonsson JE, Roesner L, Li Y, Werfel T, Conrad C, Gottardo R, Modlin RL, Di Domizio J, Gilliet M
Nat Commun. 2023 Jun 30;14(1):3878
Single-cell protein expression profiling resolves circulating and resident memory T cell diversity across tissues and infection contexts.
Evrard M, Becht E, Fonseca R, Obers A, Park SL, Ghabdan-Zanluqui N, Schroeder J, Christo SN, Schienstock D, Lai J, Burn TN, Clatch A, House IG, Beavis P, Kallies A, Ginhoux F, Mueller SN, Gottardo R, Newell EW, Mackay LK
Immunity. 2023 Jun 27
A metagenome-wide association study of HIV disease progression in HIV controllers.
Real LM, Sáez ME, Corma-Gómez A, Gonzalez-Pérez A, Thorball C, Ruiz R, Jimenez-Leon MR, Gonzalez-Serna A, Gasca-Capote C, Bravo MJ, Royo JL, Perez-Gomez A, Camacho-Sojo MI, Gallego I, Vitalle J, Bachiller S, Gutierrez-Valencia A, Vidal F, Fellay J, Lichte
iScience. 2023 Jul 21;26(7):107214
An information theoretic approach to detecting spatially varying genes.
Jones DC, Danaher P, Kim Y, Beechem JM, Gottardo R, Newell EW
Cell Rep Methods. 2023 Jun 26;3(6):100507
Intradermal skin test with mRNA vaccines as a surrogate marker of T cell immunity in immunocompromised patients.
Fallet B, Foglierini M, Porret R, Alcaraz-Serna A, Sauvage C, Jenelten R, Caplanusi T, Gilliet M, Perez L, Fenwick C, Genolet R, Harari A, Bobisse S, Gottardo R, Pantaleo G, Muller YD
J Infect. 2023 Jun 14
Multiancestry sex-stratified genomic associations with HIV viral load and controller status from the ICGH.
Vergara C, Tuff JF, International Collaboration for the Genomics of HIV (ICGH), Fellay J, Duggal P, Scully EP, McLaren PJ
JCI Insight. 2023 Jun 8;8(11)
Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study.
Avery EF, Kleynhans JN, Ledergerber B, Schoepf IC, Thorball CW, Kootstra NA, Reiss P, Ryom L, Braun DL, Thurnheer MC, Marzolini C, Seneghini M, Bernasconi E, Cavassini M, Buvelot H, Kouyos RD, Fellay J, Günthard HF, Tarr PE, Swiss HIV Cohort Study
Clin Infect Dis. 2023 Jun 8;76(11):1969-1979
Association of a Polygenic Risk Score with Osteoporosis in People Living with HIV: The Swiss HIV Cohort Study.
Schwenke JM, Thorball CW, Schoepf IC, Ryom L, Hasse B, Lamy O, Calmy A, Wandeler G, Marzolini C, Kahlert CR, Bernasconi E, Kouyos R, Günthard HF, Ledergerber B, Fellay J, Burkhalter F, Tarr PE, Swiss HIV Cohort Study
J Infect Dis. 2023 May 24
Matching single cells across modalities with contrastive learning and optimal transport.
Gossi F, Pati P, Chouvardas P, Martinelli AL, Kruithof-de Julio M, Rapsomaniki MA
Brief Bioinform. 2023 May 19;24(3)
Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants.
Cobat A, Zhang Q, Covid Human Genetic Effort, Abel L, Casanova JL, Fellay J
Annu Rev Biomed Data Sci. 2023 May 17
Combining European and U.S. risk prediction models with polygenic risk scores to refine cardiovascular prevention: the CoLaus|PsyCoLaus Study.
de La Harpe R, Thorball CW, Redin C, Fournier S, Müller O, Strambo D, Michel P, Vollenweider P, Marques-Vidal P, Fellay J, Vaucher J
Eur J Prev Cardiol. 2023 May 9;30(7):561-571
Secondary structure of the human mitochondrial genome affects formation of deletions.
Shamanskiy V, Mikhailova AA, Tretiakov EO, Ushakova K, Mikhailova AG, Oreshkov S, Knorre DA, Ree N, Overdevest JB, Lukowski SW, Gostimskaya I, Yurov V, Liou CW, Lin TK, Kunz WS, Reymond A, Mazunin I, Bazykin GA, Fellay J, Tanaka M, Khrapko K, Gunbin K, Po
BMC Biol. 2023 May 8;21(1):103
Epigenetic ageing accelerates before antiretroviral therapy and decelerates after viral suppression in people with HIV in Switzerland: a longitudinal study over 17 years.
Schoepf IC, Esteban-Cantos A, Thorball CW, Rodés B, Reiss P, Rodríguez-Centeno J, Riebensahm C, Braun DL, Marzolini C, Seneghini M, Bernasconi E, Cavassini M, Buvelot H, Thurnheer MC, Kouyos RD, Fellay J, Günthard HF, Arribas JR, Ledergerber B, Tarr PE, S
Lancet Healthy Longev. 2023 May;4(5):e211-e218
Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19.
Matuozzo D, Talouarn E, Marchal A, Zhang P, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Abou Tayoun A, Aiuti A, Alavi Darazam I, Allende LM, Alonso-Arias R, Ar
Genome Med. 2023 Apr 5;15(1):22
Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania.
Zwyer M, Rutaihwa LK, Windels E, Hella J, Menardo F, Sasamalo M, Sommer G, Schmülling L, Borrell S, Reinhard M, Dötsch A, Hiza H, Stritt C, Sikalengo G, Fenner L, De Jong BC, Kato-Maeda M, Jugheli L, Ernst JD, Niemann S, Jeljeli L, Ballif M, Egger M, Rako
PLoS Pathog. 2023 Apr;19(4):e1010893
FAIRification of health-related data using semantic web technologies in the Swiss Personalized Health Network.
Touré V, Krauss P, Gnodtke K, Buchhorn J, Unni D, Horki P, Raisaro JL, Kalt K, Teixeira D, Crameri K, Österle S
Sci Data. 2023 Mar 10;10(1):127
An End-to-End Natural Language Processing Application for Prediction of Medical Case Coding Complexity: Algorithm Development and Validation.
Xu HA, Maccari B, Guillain H, Herzen J, Agri F, Raisaro JL
JMIR Med Inform. 2023 Jan 19;11:e38150
Antibody Correlates of Protection From Severe Respiratory Syncytial Virus Disease in a Vaccine Efficacy Trial.
Fong Y, Huang Y, Borate B, van der Laan LWP, Zhang W, Carpp LN, Cho I, Glenn G, Fries L, Gottardo R, Gilbert PB
Open Forum Infect Dis. 2023 Jan;10(1):ofac693
Visual masking deficits in schizophrenia: a view into the genetics of the disease through an endophenotype.
Shaqiri A, Hodel F, da Cruz JR, Roinishvili M, Chkonia E, Brand A, Fellay J, Herzog MH
Transl Psychiatry. 2022 Dec 31;12(1):529
Defining cellular population dynamics at single-cell resolution during prostate cancer progression.
Germanos AA, Arora S, Zheng Y, Goddard ET, Coleman IM, Ku AT, Wilkinson S, Song H, Brady NJ, Amezquita RA, Zager M, Long A, Yang YC, Bielas JH, Gottardo R, Rickman DS, Huang FW, Ghajar CM, Nelson PS, Sowalsky AG, Setty M, Hsieh AC
Elife. 2022 Dec 13;11
The «Amish» NM_000256.3:c.3330+2T>G splice variant in MYBPC3 associated with hypertrophic cardiomyopathy is an ancient Swiss mutation.
Redin C, Pavlidou DC, Bhuiyan Z, Porretta AP, Monney P, Bedoni N, Maurer F, Sekarski N, Atallah I, Émeline D, Jeanrenaud X, Pruvot E, Fellay J, Superti-Furga A
Eur J Med Genet. 2022 Dec;65(12):104627
Viral genetic determinants of prolonged respiratory syncytial virus infection among infants in a healthy term birth cohort.
Lawless D, McKennan CG, Das SR, Junier T, Xu ZM, Anderson LJ, Gebretsadik T, Shilts MH, Larkin E, Rosas-Salazar C, Chappell JD, Fellay J, Hartert TV
J Infect Dis. 2022 Nov 15
The combined impact of persistent infections and human genetic variation on C-reactive protein levels.
Hodel F, Naret O, Bonnet C, Brenner N, Bender N, Waterboer T, Marques-Vidal P, Vollenweider P, Fellay J
BMC Med. 2022 Nov 1;20(1):416
Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses.
Hagan T, Gerritsen B, Tomalin LE, Fourati S, Mulè MP, Chawla DG, Rychkov D, Henrich E, Miller HER, Diray-Arce J, Dunn P, Lee A, Human Immunology Project Consortium (HIPC), Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Sékaly RP, Kleinstein SH
Nat Immunol. 2022 Oct 31
Pan-vaccine analysis reveals innate immune endotypes predictive of antibody responses to vaccination.
Fourati S, Tomalin LE, Mulè MP, Chawla DG, Gerritsen B, Rychkov D, Henrich E, Miller HER, Hagan T, Diray-Arce J, Dunn P, Human Immunology Project Consortium (HIPC), Levy O, Gottardo R, Sarwal MM, Tsang JS, Suárez-Fariñas M, Pulendran B, Kleinstein SH, Sék
Nat Immunol. 2022 Oct 31
Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19.
Matuozzo D, Talouarn E, Marchal A, Manry J, Seeleuthner Y, Zhang Y, Bolze A, Chaldebas M, Milisavljevic B, Zhang P, Gervais A, Bastard P, Asano T, Bizien L, Barzaghi F, Abolhassani H, Tayoun AA, Aiuti A, Darazam IA, Allende LM, Alonso-Arias R, Arias AA, A
medRxiv. 2022 Oct 25
The Immune Signatures data resource, a compendium of systems vaccinology datasets.
Diray-Arce J, Miller HER, Henrich E, Gerritsen B, Mulè MP, Fourati S, Gygi J, Hagan T, Tomalin L, Rychkov D, Kazmin D, Chawla DG, Meng H, Dunn P, Campbell J, Human Immunology Project Consortium (HIPC), Sarwal M, Tsang JS, Levy O, Pulendran B, Sekaly R, Fl
Sci Data. 2022 Oct 20;9(1):635
A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand.
Mikhailova AG, Mikhailova AA, Ushakova K, Tretiakov EO, Iliushchenko D, Shamansky V, Lobanova V, Kozenkov I, Efimenko B, Yurchenko AA, Kozenkova E, Zdobnov EM, Makeev V, Yurov V, Tanaka M, Gostimskaya I, Fleischmann Z, Annis S, Franco M, Wasko K, Denisov
Nucleic Acids Res. 2022 Sep 21
Polygenic Risk Scores for Prediction of Subclinical Coronary Artery Disease in Persons Living with HIV: The Swiss HIV Cohort Study.
Schoepf IC, Thorball CW, Kovari H, Ledergerber B, Buechel RR, Calmy A, Weber R, Kaufmann PA, Nkoulou R, Schwenke JM, Braun DL, Fellay J, Tarr PE, Swiss HIV Cohort Study.
Clin Infect Dis. 2022 Sep 13
Transcriptional and functional analyses of neoantigen-specific CD4 T cells during a profound response to anti-PD-L1 in metastatic Merkel cell carcinoma.
Church C, Pulliam T, Longino N, Park SY, Smythe KS, Makarov V, Riaz N, Jing L, Amezquita R, Campbell JS, Gottardo R, Pierce RH, Choi J, Chan TA, Koelle DM, Nghiem P
J Immunother Cancer. 2022 Sep;10(9)
The deficiency in Th2-like Tfh cells affects the maturation and quality of HIV-specific B cell response in viremic infection.
Noto A, Suffiotti M, Joo V, Mancarella A, Procopio FA, Cavet G, Leung Y, Corpataux JM, Cavassini M, Riva A, Stamatatos L, Gottardo R, McDermott AB, Koup RA, Fenwick C, Perreau M, Pantaleo G
Front Immunol. 2022;13:960120
A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits.
Nadeau S, Thorball CW, Kouyos R, Günthard HF, Böni J, Yerly S, Perreau M, Klimkait T, Rauch A, Hirsch HH, Cavassini M, Vernazza P, Bernasconi E, Fellay J, Mitov V, Stadler T, Swiss HIV Cohort Study (SHCS) .
Mol Biol Evol. 2022 Aug 3;39(8)
Host genomics of SARS-CoV-2 infection.
Redin C, Thorball CW, Fellay J
Eur J Hum Genet. 2022 Aug;30(8):908-914
Th2-Biased Transcriptional Profile Predicts HIV Envelope-Specific Polyfunctional CD4<sup>+</sup> T Cells That Correlated with Reduced Risk of Infection in RV144 Trial.
Cohen KW, Tian Y, Thayer C, Seese A, Amezquita R, McElrath MJ, De Rosa SC, Gottardo R
J Immunol. 2022 Aug 1;209(3):526-534
An In Vivo Model of Human Macrophages in Metastatic Melanoma.
Voillet V, Berger TR, McKenna KM, Paulson KG, Tan WH, Smythe KS, Hunter DS, Valente WJ, Weaver S, Campbell JS, Kim TS, Byrd DR, Bielas JH, Pierce RH, Chapuis AG, Gottardo R, Rongvaux A
J Immunol. 2022 Aug 1;209(3):606-620
Early and Long-Term HIV-1 Immunogenicity Induced in Macaques by the Combined Administration of DNA, NYVAC and Env Protein-Based Vaccine Candidates: The AUP512 Study.
Perdiguero B, Asbach B, Gómez CE, Köstler J, Barnett SW, Koutsoukos M, Weiss DE, Cristillo AD, Foulds KE, Roederer M, Montefiori DC, Yates NL, Ferrari G, Shen X, Sawant S, Tomaras GD, Sato A, Fulp WJ, Gottardo R, Ding S, Heeney JL, Pantaleo G, Esteban M,
Front Immunol. 2022;13:939627
scQUEST: Quantifying tumor ecosystem heterogeneity from mass or flow cytometry data.
Martinelli AL, Wagner J, Bodenmiller B, Rapsomaniki MA
STAR Protoc. 2022 Sep 16;3(3):101578
A Baseline Cellular Antiviral State Is Maintained by cGAS and Its Most Frequent Naturally Occurring Variant rs610913.
Kazmierski J, Elsner C, Döhner K, Xu S, Ducroux A, Pott F, Jansen J, Thorball CW, Zeymer O, Zhou X, Fedorov R, Fellay J, Löffler MW, Weber ANR, Sodeik B, Goffinet C
J Immunol. 2022 Jul 18
Variability in primary Sjögren's syndrome is driven by interferon alpha, and genetically associated with the class II HLA DQ locus.
Trutschel D Dr rer nat, Bost P, Mariette X, Bondet V, Llibre A, Posseme C, Charbit B, Thorball CW, Jonsson R Prof, Lessard CJ, Felten R, Ng WF Prof, Chatenoud L Prof, Dumortier H, Sibilia J, Fellay J, Brokstad KA Prof, Appel S Prof Dr rer nat, Tarn Dr JR,
Arthritis Rheumatol. 2022 Jun 20
Monocyte Transcriptional Responses to Mycobacterium tuberculosis Associate with Resistance to Tuberculin Skin Test and Interferon Gamma Release Assay Conversion.
Simmons JD, Dill-McFarland KA, Stein CM, Van PT, Chihota V, Ntshiqa T, Maenetje P, Peterson GJ, Benchek P, Nsereko M, Velen K, Fielding KL, Grant AD, Gottardo R, Mayanja-Kizza H, Wallis RS, Churchyard G, Boom WH, Hawn TR
mSphere. 2022 Jun 13:e0015922
Quantification of tumor heterogeneity: from data acquisition to metric generation.
Kashyap A, Rapsomaniki MA, Barros V, Fomitcheva-Khartchenko A, Martinelli AL, Rodriguez AF, Gabrani M, Rosen-Zvi M, Kaigala G
Trends Biotechnol. 2022 Jun;40(6):647-676
ATHENA: analysis of tumor heterogeneity from spatial omics measurements.
Martinelli AL, Rapsomaniki MA
Bioinformatics. 2022 May 26;38(11):3151-3153
Generation and Evaluation of Synthetic Data in a University Hospital Setting.
Kaabachi B, Despraz J, Meurers T, Prasser F, Raisaro JL
Stud Health Technol Inform. 2022 May 25;294:141-142
An Ontology and Data Converter from RDF to the i2b2 Data Model.
Fasquelle-Lopez J, Louis Raisaro J
Stud Health Technol Inform. 2022 May 25;294:372-376
The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies.
Manry J, Bastard P, Gervais A, Le Voyer T, Rosain J, Philippot Q, Michailidis E, Hoffmann HH, Eto S, Garcia-Prat M, Bizien L, Parra-Martínez A, Yang R, Haljasmägi L, Migaud M, Särekannu K, Maslovskaja J, de Prost N, Tandjaoui-Lambiotte Y, Luyt CE, Amador-
Proc Natl Acad Sci U S A. 2022 May 24;119(21):e2200413119
Telomere Length Declines in Persons With Human Immunodeficiency Virus Before Antiretroviral Therapy Start but Not After Viral Suppression: A Longitudinal Study Over >17 Years.
Schoepf IC, Thorball CW, Ledergerber B, Kootstra NA, Reiss P, Raffenberg M, Engel T, Braun DL, Hasse B, Thurnheer C, Marzolini C, Seneghini M, Bernasconi E, Cavassini M, Buvelot H, Arribas JR, Kouyos RD, Fellay J, Günthard HF, Tarr PE
J Infect Dis. 2022 May 4;225(9):1581-1591
Extricating human tumour immune alterations from tissue inflammation.
Mair F, Erickson JR, Frutoso M, Konecny AJ, Greene E, Voillet V, Maurice NJ, Rongvaux A, Dixon D, Barber B, Gottardo R, Prlic M
Nature. 2022 May;605(7911):728-735
Improving polygenic prediction with genetically inferred ancestry.
Naret O, Kutalik Z, Hodel F, Xu ZM, Marques-Vidal P, Fellay J
HGG Adv. 2022 Jul 14;3(3):100109
CD38 Expression by Antigen-Specific CD4 T Cells Is Significantly Restored 5 Months After Treatment Initiation Independently of Sputum Bacterial Load at the Time of Tuberculosis Diagnosis.
Hiza H, Hella J, Arbués A, Sasamalo M, Misana V, Fellay J, Gagneux S, Reither K, Portevin D
Front Med (Lausanne). 2022;9:821776
Neoantigen-specific CD4<sup>+</sup> T cells in human melanoma have diverse differentiation states and correlate with CD8<sup>+</sup> T cell, macrophage, and B cell function.
Veatch JR, Lee SM, Shasha C, Singhi N, Szeto JL, Moshiri AS, Kim TS, Smythe K, Kong P, Fitzgibbon M, Jesernig B, Bhatia S, Tykodi SS, Hall ET, Byrd DR, Thompson JA, Pillarisetty VG, Duhen T, McGarry Houghton A, Newell E, Gottardo R, Riddell SR
Cancer Cell. 2022 Apr 11;40(4):393-409.e9
Optimizing clinical dosing of combination broadly neutralizing antibodies for HIV prevention.
Mayer BT, deCamp AC, Huang Y, Schiffer JT, Gottardo R, Gilbert PB, Reeves DB
PLoS Comput Biol. 2022 Apr;18(4):e1010003
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.
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Tian Y, Carpp LN, Miller HER, Zager M, Newell EW, Gottardo R
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PLoS One. 2021;16(11):e0259332
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Vick SC, Frutoso M, Mair F, Konecny AJ, Greene E, Wolf CR, Logue JK, Franko NM, Boonyaratanakornkit J, Gottardo R, Schiffer JT, Chu HY, Prlic M, Lund JM
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Spatial transcriptomics at subspot resolution with BayesSpace.
Zhao E, Stone MR, Ren X, Guenthoer J, Smythe KS, Pulliam T, Williams SR, Uytingco CR, Taylor SEB, Nghiem P, Bielas JH, Gottardo R
Nat Biotechnol. 2021 Nov;39(11):1375-1384
Spatial UMAP and Image Cytometry for Topographic Immuno-oncology Biomarker Discovery.
Giraldo NA, Berry S, Becht E, Ates D, Schenk KM, Engle EL, Green B, Nguyen P, Soni A, Stein JE, Succaria F, Ogurtsova A, Xu H, Gottardo R, Anders RA, Lipson EJ, Danilova L, Baras AS, Taube JM
Cancer Immunol Res. 2021 Nov;9(11):1262-1269
New interpretable machine-learning method for single-cell data reveals correlates of clinical response to cancer immunotherapy.
Greene E, Finak G, D'Amico LA, Bhardwaj N, Church CD, Morishima C, Ramchurren N, Taube JM, Nghiem PT, Cheever MA, Fling SP, Gottardo R
Patterns (N Y). 2021 Dec 10;2(12):100372
Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption.
Froelicher D, Troncoso-Pastoriza JR, Raisaro JL, Cuendet MA, Sousa JS, Cho H, Berger B, Fellay J, Hubaux JP
Nat Commun. 2021 Oct 11;12(1):5910
High-throughput single-cell quantification of hundreds of proteins using conventional flow cytometry and machine learning.
Becht E, Tolstrup D, Dutertre CA, Morawski PA, Campbell DJ, Ginhoux F, Newell EW, Gottardo R, Headley MB
Sci Adv. 2021 Sep 24;7(39):eabg0505
Comparative analysis of TCR and CAR signaling informs CAR designs with superior antigen sensitivity and in vivo function.
Salter AI, Rajan A, Kennedy JJ, Ivey RG, Shelby SA, Leung I, Templeton ML, Muhunthan V, Voillet V, Sommermeyer D, Whiteaker JR, Gottardo R, Veatch SL, Paulovich AG, Riddell SR
Sci Signal. 2021 Aug 24;14(697)
Monocyte metabolic transcriptional programs associate with resistance to tuberculin skin test/interferon-γ release assay conversion.
Simmons JD, Van PT, Stein CM, Chihota V, Ntshiqa T, Maenetje P, Peterson GJ, Reynolds A, Benchek P, Velen K, Fielding KL, Grant AD, Graustein AD, Nguyen FK, Seshadri C, Gottardo R, Mayanja-Kizza H, Wallis RS, Churchyard G, Boom WH, Hawn TR
J Clin Invest. 2021 Jul 15;131(14)
The human memory T cell compartment changes across tissues of the female reproductive tract.
Woodward Davis AS, Vick SC, Pattacini L, Voillet V, Hughes SM, Lentz GM, Kirby AC, Fialkow MF, Gottardo R, Hladik F, Lund JM, Prlic M
Mucosal Immunol. 2021 Jul;14(4):862-872
Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression.
Wu SJ, Furlan SN, Mihalas AB, Kaya-Okur HS, Feroze AH, Emerson SN, Zheng Y, Carson K, Cimino PJ, Keene CD, Sarthy JF, Gottardo R, Ahmad K, Henikoff S, Patel AP
Nat Biotechnol. 2021 Jul;39(7):819-824
Safety and immunogenicity of an HIV-1 gp120-CD4 chimeric subunit vaccine in a phase 1a randomized controlled trial.
Chua JV, Davis C, Husson JS, Nelson A, Prado I, Flinko R, Lam KWJ, Mutumbi L, Mayer BT, Dong D, Fulp W, Mahoney C, Gerber M, Gottardo R, Gilliam BL, Greene K, Gao H, Yates N, Ferrari G, Tomaras G, Montefiori D, Schwartz JA, Fouts T, DeVico AL, Lewis GK, G
Vaccine. 2021 Jun 29;39(29):3879-3891
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Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jain J, Srivastava A, Stuart T, Fleming LM, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert
Cell. 2021 Jun 24;184(13):3573-3587.e29
A National, Semantic-Driven, Three-Pillar Strategy to Enable Health Data Secondary Usage Interoperability for Research Within the Swiss Personalized Health Network: Methodological Study.
Gaudet-Blavignac C, Raisaro JL, Touré V, Österle S, Crameri K, Lovis C
JMIR Med Inform. 2021 Jun 24;9(6):e27591
Comprehensive Data Integration Approach to Assess Immune Responses and Correlates of RTS,S/AS01-Mediated Protection From Malaria Infection in Controlled Human Malaria Infection Trials.
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Front Big Data. 2021;4:672460
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Richert-Spuhler LE, Mar CM, Shinde P, Wu F, Hong T, Greene E, Hou S, Thomas K, Gottardo R, Mugo N, de Bruyn G, Celum C, Baeten JM, Lingappa JR, Lund JM, Partners in Prevention HSV/HIV Transmission Study., and the Partners PrEP Study Teams.
Cell Rep Med. 2021 Jun 15;2(6):100322
A differential regulatory T cell signature distinguishes the immune landscape of COVID-19 hospitalized patients from those hospitalized with other respiratory viral infections.
Vick SC, Frutoso M, Mair F, Konecny AJ, Greene E, Wolf CR, Logue JK, Boonyaratanakornkit J, Gottardo R, Schiffer JT, Chu HY, Prlic M, Lund JM
medRxiv. 2021 Mar 26
Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models.
Vitanza NA, Biery MC, Myers C, Ferguson E, Zheng Y, Girard EJ, Przystal JM, Park G, Noll A, Pakiam F, Winter CA, Morris SM, Sarthy J, Cole BL, Leary SES, Crane C, Lieberman NAP, Mueller S, Nazarian J, Gottardo R, Brusniak MY, Mhyre AJ, Olson JM
Neuro Oncol. 2021 Mar 25;23(3):376-386
Revolutionizing Medical Data Sharing Using Advanced Privacy-Enhancing Technologies: Technical, Legal, and Ethical Synthesis.
Scheibner J, Raisaro JL, Troncoso-Pastoriza JR, Ienca M, Fellay J, Vayena E, Hubaux JP
J Med Internet Res. 2021 Feb 25;23(2):e25120
Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade.
Srivastava S, Furlan SN, Jaeger-Ruckstuhl CA, Sarvothama M, Berger C, Smythe KS, Garrison SM, Specht JM, Lee SM, Amezquita RA, Voillet V, Muhunthan V, Yechan-Gunja S, Pillai SPS, Rader C, Houghton AM, Pierce RH, Gottardo R, Maloney DG, Riddell SR
Cancer Cell. 2021 Feb 8;39(2):193-208.e10
Development of a clinically relevant ovarian cancer model incorporating surgical cytoreduction to evaluate treatment of micro-metastatic disease.
Morse CB, Voillet V, Bates BM, Chiu EY, Garcia NM, Gottardo R, Greenberg PD, Anderson KG
Gynecol Oncol. 2021 Feb;160(2):427-437
In silico analysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity.
Rapsomaniki MA, Maxouri S, Nathanailidou P, Garrastacho MR, Giakoumakis NN, Taraviras S, Lygeros J, Lygerou Z
NAR Genom Bioinform. 2021 Mar;3(1):lqaa112
Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19.
Su Y, Chen D, Yuan D, Lausted C, Choi J, Dai CL, Voillet V, Duvvuri VR, Scherler K, Troisch P, Baloni P, Qin G, Smith B, Kornilov SA, Rostomily C, Xu A, Li J, Dong S, Rothchild A, Zhou J, Murray K, Edmark R, Hong S, Heath JE, Earls J, Zhang R, Xie J, Li S
Cell. 2020 Dec 10;183(6):1479-1495.e20
SCOR: A secure international informatics infrastructure to investigate COVID-19.
Raisaro JL, Marino F, Troncoso-Pastoriza J, Beau-Lejdstrom R, Bellazzi R, Murphy R, Bernstam EV, Wang H, Bucalo M, Chen Y, Gottlieb A, Harmanci A, Kim M, Kim Y, Klann J, Klersy C, Malin BA, Méan M, Prasser F, Scudeller L, Torkamani A, Vaucher J, Puppala M
J Am Med Inform Assoc. 2020 Nov 1;27(11):1721-1726
PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.
Simon S, Voillet V, Vignard V, Wu Z, Dabrowski C, Jouand N, Beauvais T, Khammari A, Braudeau C, Josien R, Adotevi O, Laheurte C, Aubin F, Nardin C, Rulli S, Gottardo R, Ramchurren N, Cheever M, Fling SP, Church CD, Nghiem P, Dreno B, Riddell SR, Labarrier
J Immunother Cancer. 2020 Nov;8(2)
A Potent Anti-Malarial Human Monoclonal Antibody Targets Circumsporozoite Protein Minor Repeats and Neutralizes Sporozoites in the Liver.
Wang LT, Pereira LS, Flores-Garcia Y, O'Connor J, Flynn BJ, Schön A, Hurlburt NK, Dillon M, Yang ASP, Fabra-García A, Idris AH, Mayer BT, Gerber MW, Gottardo R, Mason RD, Cavett N, Ballard RB, Kisalu NK, Molina-Cruz A, Nelson J, Vistein R, Barillas-Mury C
Immunity. 2020 Oct 13;53(4):733-744.e8
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Gosselin RD, Redin C, Ristorcelli É, Raisaro JL, Fellay J
Rev Med Suisse. 2020 Sep 2;16(704):1574-1578
Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories.
Su Y, Chen D, Lausted C, Yuan D, Choi J, Dai C, Voillet V, Scherler K, Troisch P, Duvvuri VR, Baloni P, Qin G, Smith B, Kornilov S, Rostomily C, Xu A, Li J, Dong S, Rothchild A, Zhou J, Murray K, Edmark R, Hong S, Jones L, Zhou Y, Roper R, Mackay S, O'Mah
bioRxiv. 2020 Jul 31
Optimal priming of poxvirus vector (NYVAC)-based HIV vaccine regimens for T cell responses requires three DNA injections. Results of the randomized multicentre EV03/ANRS VAC20 Phase I/II Trial.
Lévy Y, Lacabaratz C, Ellefsen-Lavoie K, Stöhr W, Lelièvre JD, Bart PA, Launay O, Weber J, Salzberger B, Wiedemann A, Surenaud M, Koelle DM, Wolf H, Wagner R, Rieux V, Montefiori DC, Yates NL, Tomaras GD, Gottardo R, Mayer B, Ding S, Thiébaut R, McCormack
PLoS Pathog. 2020 Jun;16(6):e1008522
3M-052, a synthetic TLR-7/8 agonist, induces durable HIV-1 envelope-specific plasma cells and humoral immunity in nonhuman primates.
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Sci Immunol. 2020 Jun 19;5(48)
MedCo2: Privacy-Preserving Cohort Exploration and Analysis.
Froelicher D, Misbach M, Troncoso-Pastoriza JR, Raisaro JL, Hubaux JP
Stud Health Technol Inform. 2020 Jun 16;270:317-321
SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery.
Raisaro JL, Troncoso-Pastoriza JR, Pradervand S, Cuendet M, Misbach M, Sa J, Marino F, Freundler N, Rosat N, Cavin D, Leichtle A, Fellay J, Michielin O, Hubaux JP
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GenoShare: Supporting Privacy-Informed Decisions for Sharing Individual-Level Genetic Data.
Raisaro JL, Troncoso-Pastoriza JR, El-Zein Y, Humbert M, Troncoso C, Fellay J, Hubaux JP
Stud Health Technol Inform. 2020 Jun 16;270:238-241
Aggregating transcript-level analyses for single-cell differential gene expression.
Becht E, Zhao E, Amezquita R, Gottardo R
Nat Methods. 2020 Jun;17(6):583-585
Data protection and ethics requirements for multisite research with health data: a comparative examination of legislative governance frameworks and the role of data protection technologies.
Scheibner J, Ienca M, Kechagia S, Troncoso-Pastoriza JR, Raisaro JL, Hubaux JP, Fellay J, Vayena E
J Law Biosci. 2020 Jan-Jun;7(1):lsaa010
A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level.
Mair F, Erickson JR, Voillet V, Simoni Y, Bi T, Tyznik AJ, Martin J, Gottardo R, Newell EW, Prlic M
Cell Rep. 2020 Apr 7;31(1):107499
Characterization of two in vivo challenge models to measure functional activity of monoclonal antibodies to Plasmodium falciparum circumsporozoite protein.
Raghunandan R, Mayer BT, Flores-Garcia Y, Gerber MW, Gottardo R, Jhun H, Herrera SM, Perez-Ramos DW, Locke E, King CR, Zavala F
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Publisher Correction: Orchestrating single-cell analysis with Bioconductor.
Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC
Nat Methods. 2020 Feb;17(2):242
Orchestrating single-cell analysis with Bioconductor.
Amezquita RA, Lun ATL, Becht E, Carey VJ, Carpp LN, Geistlinger L, Marini F, Rue-Albrecht K, Risso D, Soneson C, Waldron L, Pagès H, Smith ML, Huber W, Morgan M, Gottardo R, Hicks SC
Nat Methods. 2020 Feb;17(2):137-145
Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy.
Sheih A, Voillet V, Hanafi LA, DeBerg HA, Yajima M, Hawkins R, Gersuk V, Riddell SR, Maloney DG, Wohlfahrt ME, Pande D, Enstrom MR, Kiem HP, Adair JE, Gottardo R, Linsley PS, Turtle CJ
Nat Commun. 2020 Jan 10;11(1):219
BCG revaccination boosts adaptive polyfunctional Th1/Th17 and innate effectors in IGRA+ and IGRA- Indian adults.
Rakshit S, Ahmed A, Adiga V, Sundararaj BK, Sahoo PN, Kenneth J, D'Souza G, Bonam W, Johnson C, Franken KL, Ottenhoff TH, Finak G, Gottardo R, Stuart KD, De Rosa SC, McElrath MJ, Vyakarnam A
JCI Insight. 2019 Dec 19;4(24)
A composite immune signature parallels disease progression across T1D subjects.
Speake C, Skinner SO, Berel D, Whalen E, Dufort MJ, Young WC, Odegard JM, Pesenacker AM, Gorus FK, James EA, Levings MK, Linsley PS, Akirav EM, Pugliese A, Hessner MJ, Nepom GT, Gottardo R, Long SA
JCI Insight. 2019 Dec 5;4(23)
Antibody Fc effector functions and IgG3 associate with decreased HIV-1 risk.
Neidich SD, Fong Y, Li SS, Geraghty DE, Williamson BD, Young WC, Goodman D, Seaton KE, Shen X, Sawant S, Zhang L, deCamp AC, Blette BS, Shao M, Yates NL, Feely F, Pyo CW, Ferrari G, HVTN 505 Team., Frank I, Karuna ST, Swann EM, Mascola JR, Graham BS, Hamm
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J Virol. 2019 Nov 1;93(21)
Engineered Adoptive T-cell Therapy Prolongs Survival in a Preclinical Model of Advanced-Stage Ovarian Cancer.
Anderson KG, Voillet V, Bates BM, Chiu EY, Burnett MG, Garcia NM, Oda SK, Morse CB, Stromnes IM, Drescher CW, Gottardo R, Greenberg PD
Cancer Immunol Res. 2019 Sep;7(9):1412-1425
MedCo: Enabling Secure and Privacy-Preserving Exploration of Distributed Clinical and Genomic Data.
Raisaro JL, Troncoso-Pastoriza JR, Misbach M, Sousa JS, Pradervand S, Missiaglia E, Michielin O, Ford B, Hubaux JP
IEEE/ACM Trans Comput Biol Bioinform. 2019 Jul-Aug;16(4):1328-1341
T cell receptor gene therapy targeting WT1 prevents acute myeloid leukemia relapse post-transplant.
Chapuis AG, Egan DN, Bar M, Schmitt TM, McAfee MS, Paulson KG, Voillet V, Gottardo R, Ragnarsson GB, Bleakley M, Yeung CC, Muhlhauser P, Nguyen HN, Kropp LA, Castelli L, Wagener F, Hunter D, Lindberg M, Cohen K, Seese A, McElrath MJ, Duerkopp N, Gooley TA
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Tumor suppression of novel anti-PD-1 antibodies mediated through CD28 costimulatory pathway.
Fenwick C, Loredo-Varela JL, Joo V, Pellaton C, Farina A, Rajah N, Esteves-Leuenberger L, Decaillon T, Suffiotti M, Noto A, Ohmiti K, Gottardo R, Weissenhorn W, Pantaleo G
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GRAPHICAL MODELS FOR ZERO-INFLATED SINGLE CELL GENE EXPRESSION.
McDavid A, Gottardo R, Simon N, Drton M
Ann Appl Stat. 2019 Jun;13(2):848-873
A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer.
Wagner J, Rapsomaniki MA, Chevrier S, Anzeneder T, Langwieder C, Dykgers A, Rees M, Ramaswamy A, Muenst S, Soysal SD, Jacobs A, Windhager J, Silina K, van den Broek M, Dedes KJ, Rodríguez Martínez M, Weber WP, Bodenmiller B
Cell. 2019 May 16;177(5):1330-1345.e18
Integrated systems approach defines the antiviral pathways conferring protection by the RV144 HIV vaccine.
Fourati S, Ribeiro SP, Blasco Tavares Pereira Lopes F, Talla A, Lefebvre F, Cameron M, Kaewkungwal J, Pitisuttithum P, Nitayaphan S, Rerks-Ngarm S, Kim JH, Thomas R, Gilbert PB, Tomaras GD, Koup RA, Michael NL, McElrath MJ, Gottardo R, Sékaly RP
Nat Commun. 2019 Feb 20;10(1):863
Priming with a Potent HIV-1 DNA Vaccine Frames the Quality of Immune Responses prior to a Poxvirus and Protein Boost.
Asbach B, Kibler KV, Köstler J, Perdiguero B, Yates NL, Stanfield-Oakley S, Tomaras GD, Kao SF, Foulds KE, Roederer M, Seaman MS, Montefiori DC, Parks R, Ferrari G, Forthal DN, Phogat S, Tartaglia J, Barnett SW, Self SG, Gottardo R, Cristillo AD, Weiss DE
J Virol. 2019 Feb 1;93(3)
Replication-Competent NYVAC-KC Yields Improved Immunogenicity to HIV-1 Antigens in Rhesus Macaques Compared to Nonreplicating NYVAC.
Kibler KV, Asbach B, Perdiguero B, García-Arriaza J, Yates NL, Parks R, Stanfield-Oakley S, Ferrari G, Montefiori DC, Tomaras GD, Roederer M, Foulds KE, Forthal DN, Seaman MS, Self S, Gottardo R, Phogat S, Tartaglia J, Barnett S, Cristillo AD, Weiss D, Ga
J Virol. 2019 Feb 1;93(3)
CytoML for cross-platform cytometry data sharing.
Finak G, Jiang W, Gottardo R
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Van P, Jiang W, Gottardo R, Finak G
Bioinformatics. 2018 Nov 15;34(22):3951-3953
Effect of Adding Motolimod to Standard Combination Chemotherapy and Cetuximab Treatment of Patients With Squamous Cell Carcinoma of the Head and Neck: The Active8 Randomized Clinical Trial.
Ferris RL, Saba NF, Gitlitz BJ, Haddad R, Sukari A, Neupane P, Morris JC, Misiukiewicz K, Bauman JE, Fenton M, Jimeno A, Adkins DR, Schneider CJ, Sacco AG, Shirai K, Bowles DW, Gibson M, Nwizu T, Gottardo R, Manjarrez KL, Dietsch GN, Bryan JK, Hershberg R
JAMA Oncol. 2018 Nov 1;4(11):1583-1588
T Cell-Dependent Affinity Maturation and Innate Immune Pathways Differentially Drive Autoreactive B Cell Responses in Rheumatoid Arthritis.
Lu DR, McDavid AN, Kongpachith S, Lingampalli N, Glanville J, Ju CH, Gottardo R, Robinson WH
Arthritis Rheumatol. 2018 Nov;70(11):1732-1744
cytometree: A binary tree algorithm for automatic gating in cytometry analysis.
Commenges D, Alkhassim C, Gottardo R, Hejblum B, Thiébaut R
Cytometry A. 2018 Nov;93(11):1132-1140
CD32<sup>+</sup> and PD-1<sup>+</sup> Lymph Node CD4 T Cells Support Persistent HIV-1 Transcription in Treated Aviremic Individuals.
Noto A, Procopio FA, Banga R, Suffiotti M, Corpataux JM, Cavassini M, Riva A, Fenwick C, Gottardo R, Perreau M, Pantaleo G
J Virol. 2018 Oct 15;92(20)
Protecting Privacy and Security of Genomic Data in i2b2 with Homomorphic Encryption and Differential Privacy.
Raisaro JL, Gwangbae Choi, Pradervand S, Colsenet R, Jacquemont N, Rosat N, Mooser V, Hubaux JP
IEEE/ACM Trans Comput Biol Bioinform. 2018 Sep-Oct;15(5):1413-1426
Phosphoproteomic analysis of chimeric antigen receptor signaling reveals kinetic and quantitative differences that affect cell function.
Salter AI, Ivey RG, Kennedy JJ, Voillet V, Rajan A, Alderman EJ, Voytovich UJ, Lin C, Sommermeyer D, Liu L, Whiteaker JR, Gottardo R, Paulovich AG, Riddell SR
Sci Signal. 2018 Aug 21;11(544)
DataPackageR: Reproducible data preprocessing, standardization and sharing using R/Bioconductor for collaborative data analysis.
Finak G, Mayer B, Fulp W, Obrecht P, Sato A, Chung E, Holman D, Gottardo R
Gates Open Res. 2018;2:31
EasyFRAP-web: a web-based tool for the analysis of fluorescence recovery after photobleaching data.
Koulouras G, Panagopoulos A, Rapsomaniki MA, Giakoumakis NN, Taraviras S, Lygerou Z
Nucleic Acids Res. 2018 Jul 2;46(W1):W467-W472
Clinical, Radiologic, Pathologic, and Molecular Characteristics of Long-Term Survivors of Diffuse Intrinsic Pontine Glioma (DIPG): A Collaborative Report From the International and European Society for Pediatric Oncology DIPG Registries.
Hoffman LM, Veldhuijzen van Zanten SEM, Colditz N, Baugh J, Chaney B, Hoffmann M, Lane A, Fuller C, Miles L, Hawkins C, Bartels U, Bouffet E, Goldman S, Leary S, Foreman NK, Packer R, Warren KE, Broniscer A, Kieran MW, Minturn J, Comito M, Broxson E, Shih
J Clin Oncol. 2018 Jul 1;36(19):1963-1972
Whole blood transcriptome changes following controlled human malaria infection in malaria pre-exposed volunteers correlate with parasite prepatent period.
Rothen J, Murie C, Carnes J, Anupama A, Abdulla S, Chemba M, Mpina M, Tanner M, Lee Sim BK, Hoffman SL, Gottardo R, Daubenberger C, Stuart K
PLoS One. 2018;13(6):e0199392
Feasibility of Homomorphic Encryption for Sharing I2B2 Aggregate-Level Data in the Cloud.
Raisaro JL, Klann JG, Wagholikar KB, Estiri H, Hubaux JP, Murphy SN
AMIA Jt Summits Transl Sci Proc. 2018;2017:176-185
Generation and characterization of a bivalent protein boost for future clinical trials: HIV-1 subtypes CR01_AE and B gp120 antigens with a potent adjuvant.
Wen Y, Trinh HV, Linton CE, Tani C, Norais N, Martinez-Guzman D, Ramesh P, Sun Y, Situ F, Karaca-Griffin S, Hamlin C, Onkar S, Tian S, Hilt S, Malyala P, Lodaya R, Li N, Otten G, Palladino G, Friedrich K, Aggarwal Y, LaBranche C, Duffy R, Shen X, Tomaras
PLoS One. 2018;13(4):e0194266
Human MAIT cells exit peripheral tissues and recirculate via lymph in steady state conditions.
Voillet V, Buggert M, Slichter CK, Berkson JD, Mair F, Addison MM, Dori Y, Nadolski G, Itkin MG, Gottardo R, Betts MR, Prlic M
JCI Insight. 2018 Apr 5;3(7)
Are privacy-enhancing technologies for genomic data ready for the clinic? A survey of medical experts of the Swiss HIV Cohort Study.
Raisaro JL, McLaren PJ, Fellay J, Cavassini M, Klersy C, Hubaux JP, Swiss HIV Cohort Study.
J Biomed Inform. 2018 Mar;79:1-6
CellCycleTRACER accounts for cell cycle and volume in mass cytometry data.
Rapsomaniki MA, Lun XK, Woerner S, Laumanns M, Bodenmiller B, Martínez MR
Nat Commun. 2018 Feb 12;9(1):632
Correction for Hraber et al., "Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments".
Hraber P, Rademeyer C, Williamson C, Seaman MS, Gottardo R, Tang H, Greene K, Gao H, LaBranche C, Mascola JR, Morris L, Montefiori DC, Korber B
J Virol. 2018 Jan 1;92(1)
Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120.
deCamp AC, Rolland M, Edlefsen PT, Sanders-Buell E, Hall B, Magaret CA, Fiore-Gartland AJ, Juraska M, Carpp LN, Karuna ST, Bose M, LePore S, Miller S, O'Sullivan A, Poltavee K, Bai H, Dommaraju K, Zhao H, Wong K, Chen L, Ahmed H, Goodman D, Tay MZ, Gottar
PLoS One. 2017;12(11):e0185959
DNA Priming Increases Frequency of T-Cell Responses to a Vesicular Stomatitis Virus HIV Vaccine with Specific Enhancement of CD8<sup>+</sup> T-Cell Responses by Interleukin-12 Plasmid DNA.
Li SS, Kochar NK, Elizaga M, Hay CM, Wilson GJ, Cohen KW, De Rosa SC, Xu R, Ota-Setlik A, Morris D, Finak G, Allen M, Tieu HV, Frank I, Sobieszczyk ME, Hannaman D, Gottardo R, Gilbert PB, Tomaras GD, Corey L, Clarke DK, Egan MA, Eldridge JH, McElrath MJ,
Clin Vaccine Immunol. 2017 Nov;24(11)
Safety and immunogenicity of a mRNA rabies vaccine in healthy adults: an open-label, non-randomised, prospective, first-in-human phase 1 clinical trial.
Alberer M, Gnad-Vogt U, Hong HS, Mehr KT, Backert L, Finak G, Gottardo R, Bica MA, Garofano A, Koch SD, Fotin-Mleczek M, Hoerr I, Clemens R, von Sonnenburg F
Lancet. 2017 Sep 23;390(10101):1511-1520
Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments.
Hraber P, Rademeyer C, Williamson C, Seaman MS, Gottardo R, Tang H, Greene K, Gao H, LaBranche C, Mascola JR, Morris L, Montefiori DC, Korber B
J Virol. 2017 Oct 1;91(19)
A Functional Toll-Interacting Protein Variant Is Associated with Bacillus Calmette-Guérin-Specific Immune Responses and Tuberculosis.
Shah JA, Musvosvi M, Shey M, Horne DJ, Wells RD, Peterson GJ, Cox JS, Daya M, Hoal EG, Lin L, Gottardo R, Hanekom WA, Scriba TJ, Hatherill M, Hawn TR
Am J Respir Crit Care Med. 2017 Aug 15;196(4):502-511
Efficient and secure outsourcing of genomic data storage.
Sousa JS, Lefebvre C, Huang Z, Raisaro JL, Aguilar-Melchor C, Killijian MO, Hubaux JP
BMC Med Genomics. 2017 Jul 26;10(Suppl 2):46
Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks.
Raisaro JL, Tramèr F, Ji Z, Bu D, Zhao Y, Carey K, Lloyd D, Sofia H, Baker D, Flicek P, Shringarpure S, Bustamante C, Wang S, Jiang X, Ohno-Machado L, Tang H, Wang X, Hubaux JP
J Am Med Inform Assoc. 2017 Jul 1;24(4):799-805
Controlled Human Malaria Infection Leads to Long-Lasting Changes in Innate and Innate-like Lymphocyte Populations.
Mpina M, Maurice NJ, Yajima M, Slichter CK, Miller HW, Dutta M, McElrath MJ, Stuart KD, De Rosa SC, McNevin JP, Linsley PS, Abdulla S, Tanner M, Hoffman SL, Gottardo R, Daubenberger CA, Prlic M
J Immunol. 2017 Jul 1;199(1):107-118
Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4<sup>+</sup> T Cells in Peripheral Blood of Subjects with Type 1 Diabetes.
Cerosaletti K, Barahmand-Pour-Whitman F, Yang J, DeBerg HA, Dufort MJ, Murray SA, Israelsson E, Speake C, Gersuk VH, Eddy JA, Reijonen H, Greenbaum CJ, Kwok WW, Wambre E, Prlic M, Gottardo R, Nepom GT, Linsley PS
J Immunol. 2017 Jul 1;199(1):323-335
Combined single-cell quantitation of host and SIV genes and proteins ex vivo reveals host-pathogen interactions in individual cells.
Bolton DL, McGinnis K, Finak G, Chattopadhyay P, Gottardo R, Roederer M
PLoS Pathog. 2017 Jun;13(6):e1006445
Higher T-Cell Responses Induced by DNA/rAd5 HIV-1 Preventive Vaccine Are Associated With Lower HIV-1 Infection Risk in an Efficacy Trial.
Janes HE, Cohen KW, Frahm N, De Rosa SC, Sanchez B, Hural J, Magaret CA, Karuna S, Bentley C, Gottardo R, Finak G, Grove D, Shen M, Graham BS, Koup RA, Mulligan MJ, Koblin B, Buchbinder SP, Keefer MC, Adams E, Anude C, Corey L, Sobieszczyk M, Hammer SM, G
J Infect Dis. 2017 May 1;215(9):1376-1385
Superiority in Rhesus Macaques of Targeting HIV-1 Env gp140 to CD40 versus LOX-1 in Combination with Replication-Competent NYVAC-KC for Induction of Env-Specific Antibody and T Cell Responses.
Zurawski G, Shen X, Zurawski S, Tomaras GD, Montefiori DC, Roederer M, Ferrari G, Lacabaratz C, Klucar P, Wang Z, Foulds KE, Kao SF, Yu X, Sato A, Yates NL, LaBranche C, Stanfield-Oakley S, Kibler K, Jacobs B, Salazar A, Self S, Fulp W, Gottardo R, Galmin
J Virol. 2017 May 1;91(9)
HIV/AIDS Vaccine Candidates Based on Replication-Competent Recombinant Poxvirus NYVAC-C-KC Expressing Trimeric gp140 and Gag-Derived Virus-Like Particles or Lacking the Viral Molecule B19 That Inhibits Type I Interferon Activate Relevant HIV-1-Specific B
García-Arriaza J, Perdiguero B, Heeney JL, Seaman MS, Montefiori DC, Yates NL, Tomaras GD, Ferrari G, Foulds KE, Roederer M, Self SG, Borate B, Gottardo R, Phogat S, Tartaglia J, Barnett SW, Burke B, Cristillo AD, Weiss DE, Lee C, Kibler KV, Jacobs BL, Wa
J Virol. 2017 May 1;91(9)
Analysis of Protein Kinetics Using Fluorescence Recovery After Photobleaching (FRAP).
Giakoumakis NN, Rapsomaniki MA, Lygerou Z
Methods Mol Biol. 2017;1563:243-267
Bayesian hierarchical modeling for subject-level response classification in peptide microarray immunoassays.
Imholte G, Gottardo R
Biometrics. 2016 Dec;72(4):1206-1215
Privacy-preserving genomic testing in the clinic: a model using HIV treatment.
McLaren PJ, Raisaro JL, Aouri M, Rotger M, Ayday E, Bartha I, Delgado MB, Vallet Y, Günthard HF, Cavassini M, Furrer H, Doco-Lecompte T, Marzolini C, Schmid P, Di Benedetto C, Decosterd LA, Fellay J, Hubaux JP, Telenti A
Genet Med. 2016 Aug;18(8):814-22
IPP Complex Reinforces Adhesion by Relaying Tension-Dependent Signals to Inhibit Integrin Turnover.
Vakaloglou KM, Chrysanthis G, Rapsomaniki MA, Lygerou Z, Zervas CG
Cell Rep. 2016 Jul 12;16(2):596
The contribution of cell cycle to heterogeneity in single-cell RNA-seq data.
McDavid A, Finak G, Gottardo R
Nat Biotechnol. 2016 Jun 9;34(6):591-3
Distinct activation thresholds of human conventional and innate-like memory T cells.
Slichter CK, McDavid A, Miller HW, Finak G, Seymour BJ, McNevin JP, Diaz G, Czartoski JL, McElrath MJ, Gottardo R, Prlic M
JCI Insight. 2016 Jun 2;1(8)
Targeting HIV-1 Env gp140 to LOX-1 Elicits Immune Responses in Rhesus Macaques.
Zurawski G, Zurawski S, Flamar AL, Richert L, Wagner R, Tomaras GD, Montefiori DC, Roederer M, Ferrari G, Lacabaratz C, Bonnabau H, Klucar P, Wang Z, Foulds KE, Kao SF, Yates NL, LaBranche C, Jacobs BL, Kibler K, Asbach B, Kliche A, Salazar A, Reed S, Sel
PLoS One. 2016;11(4):e0153484
Potential To Streamline Heterologous DNA Prime and NYVAC/Protein Boost HIV Vaccine Regimens in Rhesus Macaques by Employing Improved Antigens.
Asbach B, Kliche A, Köstler J, Perdiguero B, Esteban M, Jacobs BL, Montefiori DC, LaBranche CC, Yates NL, Tomaras GD, Ferrari G, Foulds KE, Roederer M, Landucci G, Forthal DN, Seaman MS, Hawkins N, Self SG, Sato A, Gottardo R, Phogat S, Tartaglia J, Barne
J Virol. 2016 Apr;90(8):4133-4149
IPP Complex Reinforces Adhesion by Relaying Tension-Dependent Signals to Inhibit Integrin Turnover.
Vakaloglou KM, Chrysanthis G, Rapsomaniki MA, Lygerou Z, Zervas CG
Cell Rep. 2016 Mar 22;14(11):2668-82
Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium.
Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, Pontikos N, Diaz A, Heck S, Villanova F, Terrazzini N, Kern F, Qian Y, Stanton R, Wang K, Brandes A, Ramey J, Aghaeepour N, Mosmann T, Scheuerma
Sci Rep. 2016 Feb 10;6:20686
Promises and Pitfalls of High-Throughput Biological Assays.
Finak G, Gottardo R
Methods Mol Biol. 2016;1415:225-43
Automated analysis of flow cytometry data comes of age.
Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH
Cytometry A. 2016 Jan;89(1):13-5
Analyzing Peptide Microarray Data with the R pepStat Package.
Imholte G, Sauteraud R, Gottardo R
Methods Mol Biol. 2016;1352:127-42
A benchmark for evaluation of algorithms for identification of cellular correlates of clinical outcomes.
Aghaeepour N, Chattopadhyay P, Chikina M, Dhaene T, Van Gassen S, Kursa M, Lambrecht BN, Malek M, McLachlan GJ, Qian Y, Qiu P, Saeys Y, Stanton R, Tong D, Vens C, Walkowiak S, Wang K, Finak G, Gottardo R, Mosmann T, Nolan GP, Scheuermann RH, Brinkman RR
Cytometry A. 2016 Jan;89(1):16-21
Late-Stage Cancer Patients Remain Highly Responsive to Immune Activation by the Selective TLR8 Agonist Motolimod (VTX-2337).
Dietsch GN, Randall TD, Gottardo R, Northfelt DW, Ramanathan RK, Cohen PA, Manjarrez KL, Newkirk M, Bryan JK, Hershberg RM
Clin Cancer Res. 2015 Dec 15;21(24):5445-52
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK, Slichter CK, Miller HW, McElrath MJ, Prlic M, Linsley PS, Gottardo R
Genome Biol. 2015 Dec 10;16:278
T Cell Responses against Mycobacterial Lipids and Proteins Are Poorly Correlated in South African Adolescents.
Seshadri C, Lin L, Scriba TJ, Peterson G, Freidrich D, Frahm N, DeRosa SC, Moody DB, Prandi J, Gilleron M, Mahomed H, Jiang W, Finak G, Hanekom WA, Gottardo R, McElrath MJ, Hawn TR
J Immunol. 2015 Nov 15;195(10):4595-603
State-of-the-Art in the Computational Analysis of Cytometry Data.
Brinkman RR, Aghaeepour N, Finak G, Gottardo R, Mosmann T, Scheuermann RH
Cytometry A. 2015 Jul;87(7):591-3
Identification and visualization of multidimensional antigen-specific T-cell populations in polychromatic cytometry data.
Lin L, Frelinger J, Jiang W, Finak G, Seshadri C, Bart PA, Pantaleo G, McElrath J, DeRosa S, Gottardo R
Cytometry A. 2015 Jul;87(7):675-82
CK1δ restrains lipin-1 induction, lipid droplet formation and cell proliferation under hypoxia by reducing HIF-1α/ARNT complex formation.
Kourti M, Ikonomou G, Giakoumakis NN, Rapsomaniki MA, Landegren U, Siniossoglou S, Lygerou Z, Simos G, Mylonis I
Cell Signal. 2015 Jun;27(6):1129-40
COMPASS identifies T-cell subsets correlated with clinical outcomes.
Lin L, Finak G, Ushey K, Seshadri C, Hawn TR, Frahm N, Scriba TJ, Mahomed H, Hanekom W, Bart PA, Pantaleo G, Tomaras GD, Rerks-Ngarm S, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Michael NL, Kim JH, Robb ML, O'Connell RJ, Karasavvas N, Gilbert P, C De
Nat Biotechnol. 2015 Jun;33(6):610-6
flowCL: ontology-based cell population labelling in flow cytometry.
Courtot M, Meskas J, Diehl AD, Droumeva R, Gottardo R, Jalali A, Taghiyar MJ, Maecker HT, McCoy JP, Ruttenberg A, Scheuermann RH, Brinkman RR
Bioinformatics. 2015 Apr 15;31(8):1337-9
Correction: Musosal effects for tenofovir 1% gel.
Hladik F, Burgener A, Ballweber L, Gottardo R, Vojtech L, Fourati S, Dai JY, Cameron MJ, Strobl J, Hughes SM, Hoesley C, Andrew P, Johnson S, Piper J, Friend DR, Ball TB, Cranston RD, Mayer KH, McElrath MJ, McGowan I
Elife. 2015 Mar 24;4
flowDensity: reproducing manual gating of flow cytometry data by automated density-based cell population identification.
Malek M, Taghiyar MJ, Chong L, Finak G, Gottardo R, Brinkman RR
Bioinformatics. 2015 Feb 15;31(4):606-7
Mucosal effects of tenofovir 1% gel.
Hladik F, Burgener A, Ballweber L, Gottardo R, Vojtech L, Fourati S, Dai JY, Cameron MJ, Strobl J, Hughes SM, Hoesley C, Andrew P, Johnson S, Piper J, Friend DR, Ball TB, Cranston RD, Mayer KH, McElrath MJ, McGowan I
Elife. 2015 Feb 3;4
Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.
Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Kijak GH, Bose M, RV144 Sequencing Team., Arroyo MA, O'Connell RJ, Nitayaphan S, P
PLoS Comput Biol. 2015 Feb;11(2):e1003973
Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments.
Rapsomaniki MA, Cinquemani E, Giakoumakis NN, Kotsantis P, Lygeros J, Lygerou Z
Bioinformatics. 2015 Feb 1;31(3):355-62
Orchestrating high-throughput genomic analysis with Bioconductor.
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D,
Nat Methods. 2015 Feb;12(2):115-21
Vaccine-induced Human Antibodies Specific for the Third Variable Region of HIV-1 gp120 Impose Immune Pressure on Infecting Viruses.
Zolla-Pazner S, Edlefsen PT, Rolland M, Kong XP, deCamp A, Gottardo R, Williams C, Tovanabutra S, Sharpe-Cohen S, Mullins JI, deSouza MS, Karasavvas N, Nitayaphan S, Rerks-Ngarm S, Pitisuttihum P, Kaewkungwal J, O'Connell RJ, Robb ML, Michael NL, Kim JH,
EBioMedicine. 2014 Nov 1;1(1):37-45
The inner foreskin of healthy males at risk of HIV infection harbors epithelial CD4+ CCR5+ cells and has features of an inflamed epidermal barrier.
Lemos MP, Lama JR, Karuna ST, Fong Y, Montano SM, Ganoza C, Gottardo R, Sanchez J, McElrath MJ
PLoS One. 2014;9(9):e108954
FCGR2C polymorphisms associate with HIV-1 vaccine protection in RV144 trial.
Li SS, Gilbert PB, Tomaras GD, Kijak G, Ferrari G, Thomas R, Pyo CW, Zolla-Pazner S, Montefiori D, Liao HX, Nabel G, Pinter A, Evans DT, Gottardo R, Dai JY, Janes H, Morris D, Fong Y, Edlefsen PT, Li F, Frahm N, Alpert MD, Prentice H, Rerks-Ngarm S, Pitis
J Clin Invest. 2014 Sep;124(9):3879-90
OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis.
Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, Kalams SA, De Rosa SC, Gottardo R
PLoS Comput Biol. 2014 Aug;10(8):e1003806
Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial.
Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, Kijak GH, Edlefsen PT, Frahm N, Larsen BB, Tovanabutra S, Sanders-Buell E, deCamp AC, Magaret CA, Ahmed H, Goodridge JP, Chen L, Konopa P, Nariya S, Stoddard JN,
J Virol. 2014 Aug;88(15):8242-55
Modeling bi-modality improves characterization of cell cycle on gene expression in single cells.
McDavid A, Dennis L, Danaher P, Finak G, Krouse M, Wang A, Webster P, Beechem J, Gottardo R
PLoS Comput Biol. 2014 Jul;10(7):e1003696
Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions.
Vojtech L, Woo S, Hughes S, Levy C, Ballweber L, Sauteraud RP, Strobl J, Westerberg K, Gottardo R, Tewari M, Hladik F
Nucleic Acids Res. 2014 Jun;42(11):7290-304
Patient privacy in the genomic era.
Raisaro JL, Ayday E, Hubaux JP
Praxis (Bern 1994). 2014 May 7;103(10):579-86
High-throughput flow cytometry data normalization for clinical trials.
Finak G, Jiang W, Krouse K, Wei C, Sanz I, Phippard D, Asare A, De Rosa SC, Self S, Gottardo R
Cytometry A. 2014 Mar;85(3):277-86
Global panel of HIV-1 Env reference strains for standardized assessments of vaccine-elicited neutralizing antibodies.
deCamp A, Hraber P, Bailer RT, Seaman MS, Ochsenbauer C, Kappes J, Gottardo R, Edlefsen P, Self S, Tang H, Greene K, Gao H, Daniell X, Sarzotti-Kelsoe M, Gorny MK, Zolla-Pazner S, LaBranche CC, Mascola JR, Korber BT, Montefiori DC
J Virol. 2014 Mar;88(5):2489-507
Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium.
Brusic V, Gottardo R, Kleinstein SH, Davis MM, HIPC steering committee.
Nat Biotechnol. 2014 Feb;32(2):146-8
Immunological and virological mechanisms of vaccine-mediated protection against SIV and HIV.
Roederer M, Keele BF, Schmidt SD, Mason RD, Welles HC, Fischer W, Labranche C, Foulds KE, Louder MK, Yang ZY, Todd JP, Buzby AP, Mach LV, Shen L, Seaton KE, Ward BM, Bailer RT, Gottardo R, Gu W, Ferrari G, Alam SM, Denny TN, Montefiori DC, Tomaras GD, Kor
Nature. 2014 Jan 23;505(7484):502-8
Mixture models for single-cell assays with applications to vaccine studies.
Finak G, McDavid A, Chattopadhyay P, Dominguez M, De Rosa S, Roederer M, Gottardo R
Biostatistics. 2014 Jan;15(1):87-101
Multi-step loading of human minichromosome maintenance proteins in live human cells.
Symeonidou IE, Kotsantis P, Roukos V, Rapsomaniki MA, Grecco HE, Bastiaens P, Taraviras S, Lygerou Z
J Biol Chem. 2013 Dec 13;288(50):35852-67
iBMQ: a R/Bioconductor package for integrated Bayesian modeling of eQTL data.
Imholte GC, Scott-Boyer MP, Labbe A, Deschepper CF, Gottardo R
Bioinformatics. 2013 Nov 1;29(21):2797-8
A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling.
Imholte GC, Sauteraud R, Korber B, Bailer RT, Turk ET, Shen X, Tomaras GD, Mascola JR, Koup RA, Montefiori DC, Gottardo R
J Immunol Methods. 2013 Sep 30;395(1-2):1-13
Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial.
Gottardo R, Bailer RT, Korber BT, Gnanakaran S, Phillips J, Shen X, Tomaras GD, Turk E, Imholte G, Eckler L, Wenschuh H, Zerweck J, Greene K, Gao H, Berman PW, Francis D, Sinangil F, Lee C, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Tart
PLoS One. 2013;8(9):e75665
PING 2.0: an R/Bioconductor package for nucleosome positioning using next-generation sequencing data.
Woo S, Zhang X, Sauteraud R, Robert F, Gottardo R
Bioinformatics. 2013 Aug 15;29(16):2049-50
Comparability and reproducibility of biomedical data.
Huang Y, Gottardo R
Brief Bioinform. 2013 Jul;14(4):391-401
Therapeutic vaccination expands and improves the function of the HIV-specific memory T-cell repertoire.
Casazza JP, Bowman KA, Adzaku S, Smith EC, Enama ME, Bailer RT, Price DA, Gostick E, Gordon IJ, Ambrozak DR, Nason MC, Roederer M, Andrews CA, Maldarelli FM, Wiegand A, Kearney MF, Persaud D, Ziemniak C, Gottardo R, Ledgerwood JE, Graham BS, Koup RA, VRC
J Infect Dis. 2013 Jun 15;207(12):1829-40
Highly multiplexed quantitation of gene expression on single cells.
Dominguez MH, Chattopadhyay PK, Ma S, Lamoreaux L, McDavid A, Finak G, Gottardo R, Koup RA, Roederer M
J Immunol Methods. 2013 May 31;391(1-2):133-45
Critical assessment of automated flow cytometry data analysis techniques.
Aghaeepour N, Finak G, FlowCAP Consortium., DREAM Consortium., Hoos H, Mosmann TR, Brinkman R, Gottardo R, Scheuermann RH
Nat Methods. 2013 Mar;10(3):228-38
Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments.
McDavid A, Finak G, Chattopadyay PK, Dominguez M, Lamoreaux L, Ma SS, Roederer M, Gottardo R
Bioinformatics. 2013 Feb 15;29(4):461-7
Analysis of V2 antibody responses induced in vaccinees in the ALVAC/AIDSVAX HIV-1 vaccine efficacy trial.
Zolla-Pazner S, deCamp AC, Cardozo T, Karasavvas N, Gottardo R, Williams C, Morris DE, Tomaras G, Rao M, Billings E, Berman P, Shen X, Andrews C, O'Connell RJ, Ngauy V, Nitayaphan S, de Souza M, Korber B, Koup R, Bailer RT, Mascola JR, Pinter A, Montefior
PLoS One. 2013;8(1):e53629
The Thai Phase III HIV Type 1 Vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120.
Karasavvas N, Billings E, Rao M, Williams C, Zolla-Pazner S, Bailer RT, Koup RA, Madnote S, Arworn D, Shen X, Tomaras GD, Currier JR, Jiang M, Magaret C, Andrews C, Gottardo R, Gilbert P, Cardozo TJ, Rerks-Ngarm S, Nitayaphan S, Pitisuttithum P, Kaewkungw
AIDS Res Hum Retroviruses. 2012 Nov;28(11):1444-57
QUAliFiER: an automated pipeline for quality assessment of gated flow cytometry data.
Finak G, Jiang W, Pardo J, Asare A, Gottardo R
BMC Bioinformatics. 2012 Sep 28;13:252
The association of genetic variants with hepatic steatosis in patients with genotype 1 chronic hepatitis C infection.
Clark PJ, Thompson AJ, Zhu Q, Vock DM, Zhu M, Patel K, Harrison SA, Naggie S, Ge D, Tillmann HL, Urban TJ, Shianna K, Fellay J, Goodman Z, Noviello S, Pedicone LD, Afdhal N, Sulkowski M, Albrecht JK, Goldstein DB, McHutchison JG, Muir AJ
Dig Dis Sci. 2012 Aug;57(8):2213-21
An integrated hierarchical Bayesian model for multivariate eQTL mapping.
Scott-Boyer MP, Imholte GC, Tayeb A, Labbe A, Deschepper CF, Gottardo R
Stat Appl Genet Mol Biol. 2012 Jul 12;11(4)
easyFRAP: an interactive, easy-to-use tool for qualitative and quantitative analysis of FRAP data.
Rapsomaniki MA, Kotsantis P, Symeonidou IE, Giakoumakis NN, Taraviras S, Lygerou Z
Bioinformatics. 2012 Jul 1;28(13):1800-1
B cells with high side scatter parameter by flow cytometry correlate with inferior survival in diffuse large B-cell lymphoma.
Bashashati A, Johnson NA, Khodabakhshi AH, Whiteside MD, Zare H, Scott DW, Lo K, Gottardo R, Brinkman FS, Connors JM, Slack GW, Gascoyne RD, Weng AP, Brinkman RR
Am J Clin Pathol. 2012 May;137(5):805-14
Role of retroviral restriction factors in the interferon-α-mediated suppression of HIV-1 in vivo.
Pillai SK, Abdel-Mohsen M, Guatelli J, Skasko M, Monto A, Fujimoto K, Yukl S, Greene WC, Kovari H, Rauch A, Fellay J, Battegay M, Hirschel B, Witteck A, Bernasconi E, Ledergerber B, Günthard HF, Wong JK, Swiss HIV Cohort Study.
Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3035-40
Genome-wide association study of interferon-related cytopenia in chronic hepatitis C patients.
Thompson AJ, Clark PJ, Singh A, Ge D, Fellay J, Zhu M, Zhu Q, Urban TJ, Patel K, Tillmann HL, Naggie S, Afdhal NH, Jacobson IM, Esteban R, Poordad F, Lawitz EJ, McCone J, Shiffman ML, Galler GW, King JW, Kwo PY, Shianna KV, Noviello S, Pedicone LD, Brass
J Hepatol. 2012 Feb;56(2):313-9
Probabilistic inference for nucleosome positioning with MNase-based or sonicated short-read data.
Zhang X, Robertson G, Woo S, Hoffman BG, Gottardo R
PLoS One. 2012;7(2):e32095
Flexible mixture modeling via the multivariate t distribution with the Box-Cox transformation: an alternative to the skew-t distribution.
Lo K, Gottardo R
Stat Comput. 2012 Jan 1;22(1):33-52
A polymorphism in the leptin gene promoter is associated with anemia in patients with HIV disease.
Vanasse GJ, Jeong JY, Tate J, Bathulapalli H, Anderson D, Steen H, Fleming M, Mattocks K, Telenti A, Fellay J, Justice AC, Berliner N
Blood. 2011 Nov 17;118(20):5401-8
Copy number variation of KIR genes influences HIV-1 control.
Pelak K, Need AC, Fellay J, Shianna KV, Feng S, Urban TJ, Ge D, De Luca A, Martinez-Picado J, Wolinsky SM, Martinson JJ, Jamieson BD, Bream JH, Martin MP, Borrow P, Letvin NL, McMichael AJ, Haynes BF, Telenti A, Carrington M, Goldstein DB, Alter G, NIAID
PLoS Biol. 2011 Nov;9(11):e1001208
Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints.
Snoeck J, Fellay J, Bartha I, Douek DC, Telenti A
Retrovirology. 2011 Nov 1;8:87
Pharmacogenomics of HIV therapy: summary of a workshop sponsored by the National Institute of Allergy and Infectious Diseases.
Haas DW, Kuritzkes DR, Ritchie MD, Amur S, Gage BF, Maartens G, Masys D, Fellay J, Phillips E, Ribaudo HJ, Freedberg KA, Petropoulos C, Manolio TA, Gulick RM, Haubrich R, Kim P, Dehlinger M, Abebe R, Telenti A, Workshop Pharmacogenomics-A Path Towards Per
HIV Clin Trials. 2011 Sep-Oct;12(5):277-85
Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque.
Rotger M, Dalmau J, Rauch A, McLaren P, Bosinger SE, Martinez R, Sandler NG, Roque A, Liebner J, Battegay M, Bernasconi E, Descombes P, Erkizia I, Fellay J, Hirschel B, Miró JM, Palou E, Hoffmann M, Massanella M, Blanco J, Woods M, Günthard HF, de Bakker
J Clin Invest. 2011 Jun;121(6):2391-400
Impact of phenotype definition on genome-wide association signals: empirical evaluation in human immunodeficiency virus type 1 infection.
Evangelou E, Fellay J, Colombo S, Martinez-Picado J, Obel N, Goldstein DB, Telenti A, Ioannidis JP
Am J Epidemiol. 2011 Jun 1;173(11):1336-42
Estimating the net contribution of interleukin-28B variation to spontaneous hepatitis C virus clearance.
di Iulio J, Ciuffi A, Fitzmaurice K, Kelleher D, Rotger M, Fellay J, Martinez R, Pulit S, Furrer H, Günthard HF, Battegay M, Bernasconi E, Schmid P, Hirschel B, Barnes E, Klenerman P, Telenti A, Rauch A, Swiss HIV Cohort Study.
Hepatology. 2011 May;53(5):1446-54
Inosine triphosphate protects against ribavirin-induced adenosine triphosphate loss by adenylosuccinate synthase function.
Hitomi Y, Cirulli ET, Fellay J, McHutchison JG, Thompson AJ, Gumbs CE, Shianna KV, Urban TJ, Goldstein DB
Gastroenterology. 2011 Apr;140(4):1314-21
Host genetic determinants of T cell responses to the MRKAd5 HIV-1 gag/pol/nef vaccine in the step trial.
Fellay J, Frahm N, Shianna KV, Cirulli ET, Casimiro DR, Robertson MN, Haynes BF, Geraghty DE, McElrath MJ, Goldstein DB, National Institute of Allergy and Infectious Diseases Center for HIV/AIDS Vaccine Immunology., NIAID HIV Vaccine Trials Network.
J Infect Dis. 2011 Mar 15;203(6):773-9
Personalized hepatitis C therapy: opportunities and pitfalls.
Rauch A, Fellay J
Expert Rev Mol Diagn. 2011 Mar;11(2):127-9
PICS: probabilistic inference for ChIP-seq.
Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, Jones S, Gottardo R
Biometrics. 2011 Mar;67(1):151-63
Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages.
Bol SM, Moerland PD, Limou S, van Remmerden Y, Coulonges C, van Manen D, Herbeck JT, Fellay J, Sieberer M, Sietzema JG, van 't Slot R, Martinson J, Zagury JF, Schuitemaker H, van 't Wout AB
PLoS One. 2011 Feb 25;6(2):e17190
Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population.
Petrovski S, Fellay J, Shianna KV, Carpenetti N, Kumwenda J, Kamanga G, Kamwendo DD, Letvin NL, McMichael AJ, Haynes BF, Cohen MS, Goldstein DB, Center for HIV/AIDS Vaccine Immunology.
AIDS. 2011 Feb 20;25(4):513-8
An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq.
Mercier E, Droit A, Li L, Robertson G, Zhang X, Gottardo R
PLoS One. 2011 Feb 16;6(2):e16432
Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure.
Lingappa JR, Petrovski S, Kahle E, Fellay J, Shianna K, McElrath MJ, Thomas KK, Baeten JM, Celum C, Wald A, de Bruyn G, Mullins JI, Nakku-Joloba E, Farquhar C, Essex M, Donnell D, Kiarie J, Haynes B, Goldstein D, Partners in Prevention HSV/HIV Transmissio
PLoS One. 2011;6(12):e28632
IL28B genotype is associated with differential expression of intrahepatic interferon-stimulated genes in patients with chronic hepatitis C.
Urban TJ, Thompson AJ, Bradrick SS, Fellay J, Schuppan D, Cronin KD, Hong L, McKenzie A, Patel K, Shianna KV, McHutchison JG, Goldstein DB, Afdhal N
Hepatology. 2010 Dec;52(6):1888-96
Hepatitis C trials that combine investigational agents with pegylated interferon should be stratified by interleukin-28B genotype.
Thompson AJ, Muir AJ, Sulkowski MS, Patel K, Tillmann HL, Clark PJ, Naggie S, Fellay J, Ge D, McCarthy JJ, Goldstein DB, McHutchison JG
Hepatology. 2010 Dec;52(6):2243-4
Evidence of dysregulation of dendritic cells in primary HIV infection.
Sabado RL, O'Brien M, Subedi A, Qin L, Hu N, Taylor E, Dibben O, Stacey A, Fellay J, Shianna KV, Siegal F, Shodell M, Shah K, Larsson M, Lifson J, Nadas A, Marmor M, Hutt R, Margolis D, Garmon D, Markowitz M, Valentine F, Borrow P, Bhardwaj N
Blood. 2010 Nov 11;116(19):3839-52
Optimizing transformations for automated, high throughput analysis of flow cytometry data.
Finak G, Perez JM, Weng A, Gottardo R
BMC Bioinformatics. 2010 Nov 4;11:546
Host genetics and HIV-1: the final phase?
Fellay J, Shianna KV, Telenti A, Goldstein DB
PLoS Pathog. 2010 Oct 14;6(10):e1001033
Variants in the ITPA gene protect against ribavirin-induced hemolytic anemia and decrease the need for ribavirin dose reduction.
Thompson AJ, Fellay J, Patel K, Tillmann HL, Naggie S, Ge D, Urban TJ, Shianna KV, Muir AJ, Fried MW, Afdhal NH, Goldstein DB, McHutchison JG
Gastroenterology. 2010 Oct;139(4):1181-9
The characterization of twenty sequenced human genomes.
Pelak K, Shianna KV, Ge D, Maia JM, Zhu M, Smith JP, Cirulli ET, Fellay J, Dickson SP, Gumbs CE, Heinzen EL, Need AC, Ruzzo EK, Singh A, Campbell CR, Hong LK, Lornsen KA, McKenzie AM, Sobreira NL, Hoover-Fong JE, Milner JD, Ottman R, Haynes BF, Goedert JJ
PLoS Genet. 2010 Sep 9;6(9):e1001111
Counteraction of HLA-C-mediated immune control of HIV-1 by Nef.
Specht A, Telenti A, Martinez R, Fellay J, Bailes E, Evans DT, Carrington M, Hahn BH, Goldstein DB, Kirchhoff F
J Virol. 2010 Jul;84(14):7300-11
Interleukin-28B polymorphism improves viral kinetics and is the strongest pretreatment predictor of sustained virologic response in genotype 1 hepatitis C virus.
Thompson AJ, Muir AJ, Sulkowski MS, Ge D, Fellay J, Shianna KV, Urban T, Afdhal NH, Jacobson IM, Esteban R, Poordad F, Lawitz EJ, McCone J, Shiffman ML, Galler GW, Lee WM, Reindollar R, King JW, Kwo PY, Ghalib RH, Freilich B, Nyberg LM, Zeuzem S, Poynard
Gastroenterology. 2010 Jul;139(1):120-9.e18
Combining Mixture Components for Clustering.
Baudry JP, Raftery AE, Celeux G, Lo K, Gottardo R
J Comput Graph Stat. 2010 Jun 1;9(2):332-353
Host determinants of HIV-1 control in African Americans.
Pelak K, Goldstein DB, Walley NM, Fellay J, Ge D, Shianna KV, Gumbs C, Gao X, Maia JM, Cronin KD, Hussain SK, Carrington M, Michael NL, Weintrob AC, Infectious Disease Clinical Research Program HIV Working Group., National Institute of Allergy and Infecti
J Infect Dis. 2010 Apr 15;201(8):1141-9
ITPA gene variants protect against anaemia in patients treated for chronic hepatitis C.
Fellay J, Thompson AJ, Ge D, Gumbs CE, Urban TJ, Shianna KV, Little LD, Qiu P, Bertelsen AH, Watson M, Warner A, Muir AJ, Brass C, Albrecht J, Sulkowski M, McHutchison JG, Goldstein DB
Nature. 2010 Mar 18;464(7287):405-8
rMAT--an R/Bioconductor package for analyzing ChIP-chip experiments.
Droit A, Cheung C, Gottardo R
Bioinformatics. 2010 Mar 1;26(5):678-9
Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals.
Rotger M, Dang KK, Fellay J, Heinzen EL, Feng S, Descombes P, Shianna KV, Ge D, Günthard HF, Goldstein DB, Telenti A, Swiss HIV Cohort Study., Center for HIV/AIDS Vaccine Immunology.
PLoS Pathog. 2010 Feb 26;6(2):e1000781
Role of human leukocyte antigen class I alleles in progressive multifocal leukoencephalopathy.
Gheuens S, Fellay J, Goldstein DB, Koralnik IJ
J Neurovirol. 2010 Feb;16(1):41-7
A polymorphism in the HCP5 gene associated with HLA-B*5701 does not restrict HIV-1 in vitro.
Yoon W, Ma BJ, Fellay J, Huang W, Xia SM, Zhang R, Shianna KV, Liao HX, Haynes BF, Goldstein DB, NIAID Center for HIV/AIDS Vaccine Immunology.
AIDS. 2010 Jan 2;24(1):155-7
HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C.
Thomas R, Apps R, Qi Y, Gao X, Male V, O'hUigin C, O'Connor G, Ge D, Fellay J, Martin JN, Margolick J, Goedert JJ, Buchbinder S, Kirk GD, Martin MP, Telenti A, Deeks SG, Walker BD, Goldstein D, McVicar DW, Moffett A, Carrington M
Nat Genet. 2009 Dec;41(12):1290-4
Common genetic variation and the control of HIV-1 in humans.
Fellay J, Ge D, Shianna KV, Colombo S, Ledergerber B, Cirulli ET, Urban TJ, Zhang K, Gumbs CE, Smith JP, Castagna A, Cozzi-Lepri A, De Luca A, Easterbrook P, Günthard HF, Mallal S, Mussini C, Dalmau J, Martinez-Picado J, Miro JM, Obel N, Wolinsky SM, Mart
PLoS Genet. 2009 Dec;5(12):e1000791
CCL3L1 and HIV/AIDS susceptibility.
Urban TJ, Weintrob AC, Fellay J, Colombo S, Shianna KV, Gumbs C, Rotger M, Pelak K, Dang KK, Detels R, Martinson JJ, O'Brien SJ, Letvin NL, McMichael AJ, Haynes BF, Carrington M, Telenti A, Michael NL, Goldstein DB
Nat Med. 2009 Oct;15(10):1110-2
Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance.
Ge D, Fellay J, Thompson AJ, Simon JS, Shianna KV, Urban TJ, Heinzen EL, Qiu P, Bertelsen AH, Muir AJ, Sulkowski M, McHutchison JG, Goldstein DB
Nature. 2009 Sep 17;461(7262):399-401
X chromosomal variation is associated with slow progression to AIDS in HIV-1-infected women.
Siddiqui RA, Sauermann U, Altmüller J, Fritzer E, Nothnagel M, Dalibor N, Fellay J, Kaup FJ, Stahl-Hennig C, Nürnberg P, Krawczak M, Platzer M
Am J Hum Genet. 2009 Aug;85(2):228-39
flowClust: a Bioconductor package for automated gating of flow cytometry data.
Lo K, Hahne F, Brinkman RR, Gottardo R
BMC Bioinformatics. 2009 May 14;10:145
The Duffy antigen receptor for chemokines null promoter variant does not influence HIV-1 acquisition or disease progression.
Walley NM, Julg B, Dickson SP, Fellay J, Ge D, Walker BD, Carrington M, Cohen MS, de Bakker PI, Goldstein DB, Shianna KV, Haynes BF, Letvin NL, McMichael AJ, Michael NL, Weintrob AC
Cell Host Microbe. 2009 May 8;5(5):408-10; author reply 418-9
Recent bioinformatics advances in the analysis of high throughput flow cytometry data.
Gottardo R, Brinkman RR, Luta G, Wand MP
Adv Bioinformatics. 2009:461763
Merging mixture components for cell population identification in flow cytometry.
Finak G, Bashashati A, Brinkman R, Gottardo R
Adv Bioinformatics. 2009:247646
A pipeline for automated analysis of flow cytometry data: preliminary results on lymphoma sub-type diagnosis.
Bashashati A, Lo K, Gottardo R, Gascoyne RD, Weng A, Brinkman R
Annu Int Conf IEEE Eng Med Biol Soc. 2009;2009:4945-8
Modeling and analysis of ChIP-chip experiments.
Gottardo R
Methods Mol Biol. 2009;567:133-43
Host genetics influences on HIV type-1 disease.
Fellay J
Antivir Ther. 2009;14(6):731-8
Challenges facing young investigators.
Alter G, Brenchley J, Fellay J
IAVI Rep. 2009 Jan-Feb;13(1):14-7
The HCP5 single-nucleotide polymorphism: a simple screening tool for prediction of hypersensitivity reaction to abacavir.
Colombo S, Rauch A, Rotger M, Fellay J, Martinez R, Fux C, Thurnheer C, Günthard HF, Goldstein DB, Furrer H, Telenti A, Swiss HIV Cohort Study.
J Infect Dis. 2008 Sep 15;198(6):864-7
A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments.
Gottardo R, Li W, Johnson WE, Liu XS
Biometrics. 2008 Jun;64(2):468-78
Automated gating of flow cytometry data via robust model-based clustering.
Lo K, Brinkman RR, Gottardo R
Cytometry A. 2008 Apr;73(4):321-32
WGAViewer: software for genomic annotation of whole genome association studies.
Ge D, Zhang K, Need AC, Martin O, Fellay J, Urban TJ, Telenti A, Goldstein DB
Genome Res. 2008 Apr;18(4):640-3
MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis.
Chu VT, Gottardo R, Raftery AE, Bumgarner RE, Yeung KY
Genome Biol. 2008;9(7):R118
Efficacy and safety of universal valganciclovir prophylaxis combined with a tacrolimus/mycophenolate-based regimen in kidney transplantation.
Manuel O, Venetz JP, Fellay J, Wasserfallen JB, Sturzenegger N, Fontana M, Matter M, Meylan PR, Pascual M
Swiss Med Wkly. 2007 Dec 1;137(47-48):669-76
A whole-genome association study of major determinants for host control of HIV-1.
Fellay J, Shianna KV, Ge D, Colombo S, Ledergerber B, Weale M, Zhang K, Gumbs C, Castagna A, Cossarizza A, Cozzi-Lepri A, De Luca A, Easterbrook P, Francioli P, Mallal S, Martinez-Picado J, Miro JM, Obel N, Smith JP, Wyniger J, Descombes P, Antonarakis SE
Science. 2007 Aug 17;317(5840):944-7
Flexible empirical Bayes models for differential gene expression.
Lo K, Gottardo R
Bioinformatics. 2007 Feb 1;23(3):328-35
Model-based analysis of tiling-arrays for ChIP-chip.
Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12457-62
HIV and solid organ transplantation: the Swiss experience.
Müller NJ, Furrer H, Kaiser L, Hirschel B, Cavassini M, Fellay J, Chave JP, Wüthrich RP, Weber M, Müllhaupt B, Candinas D, Reichen J, Giostra E, Mentha G, Halkic N, Hirsch HH, Weber R, Swiss HIV Cohort Study.
Swiss Med Wkly. 2006 Mar 18;136(11-12):194-6
Bayesian robust inference for differential gene expression in microarrays with multiple samples.
Gottardo R, Raftery AE, Yeung KY, Bumgarner RE
Biometrics. 2006 Mar;62(1):10-8
Probabilistic segmentation and intensity estimation for microarray images.
Gottardo R, Besag J, Stephens M, Murua A
Biostatistics. 2006 Jan;7(1):85-99
Treatment of cytomegalovirus infection or disease in solid organ transplant recipients with valganciclovir.
Fellay J, Venetz JP, Pascual M, Aubert JD, Seudoux C, Meylan PR
Am J Transplant. 2005 Jul;5(7):1781-2; author reply 1783
Variations of CYP3A activity induced by antiretroviral treatment in HIV-1 infected patients.
Fellay J, Marzolini C, Decosterd L, Golay KP, Baumann P, Buclin T, Telenti A, Eap CB
Eur J Clin Pharmacol. 2005 Feb;60(12):865-73
Evaluation of the host transcriptional response to human cytomegalovirus infection.
Challacombe JF, Rechtsteiner A, Gottardo R, Rocha LM, Browne EP, Shenk T, Altherr MR, Brettin TS
Physiol Genomics. 2004 Jun 17;18(1):51-62
CYP3A activity measured by the midazolam test is not related to 3435 C >T polymorphism in the multiple drug resistance transporter gene.
Eap CB, Fellay J, Buclin T, Bleiber G, Golay KP, Brocard M, Baumann P, Telenti A
Pharmacogenetics. 2004 Apr;14(4):255-60
Statistical analysis of microarray data: a Bayesian approach.
Gottardo R, Pannucci JA, Kuske CR, Brettin T
Biostatistics. 2003 Oct;4(4):597-620
Population pharmacokinetics and effects of efavirenz in patients with human immunodeficiency virus infection.
Csajka C, Marzolini C, Fattinger K, Décosterd LA, Fellay J, Telenti A, Biollaz J, Buclin T
Clin Pharmacol Ther. 2003 Jan;73(1):20-30
Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria.
Xie G, Bonner CA, Brettin T, Gottardo R, Keyhani NO, Jensen RA
Genome Biol. 2003;4(2):R14
HIV lipoatrophy and mosquito bites.
Greub G, Fellay J, Telenti A
Clin Infect Dis. 2002 Jan 15;34(2):288-9
Response to antiretroviral treatment in HIV-1-infected individuals with allelic variants of the multidrug resistance transporter 1: a pharmacogenetics study.
Fellay J, Marzolini C, Meaden ER, Back DJ, Buclin T, Chave JP, Decosterd LA, Furrer H, Opravil M, Pantaleo G, Retelska D, Ruiz L, Schinkel AH, Vernazza P, Eap CB, Telenti A, Swiss HIV Cohort Study.
Lancet. 2002 Jan 5;359(9300):30-6
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