Jacques Fellay

Publications | Phd and Masters theses

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240 publications

2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | ...
2024
 
Paediatric Personalized Research Network Switzerland (SwissPedHealth): a joint paediatric national data stream.
Mozun R., Belle F.N., Agostini A., Baumgartner M.R., Fellay J., Forrest C.B., Froese D.S., Giannoni E., Goetze S., Hofmann K. et al., 2024/12/26. BMJ open, 14 (12) pp. e091884. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0D97A1EE436B]
EBNA-1 and VCA-p18 immunoglobulin markers link Epstein-Barr virus immune response and brain's myelin content to fatigue in a community-dwelling cohort.
Gayer M., Xu Z.M., Hodel F., Preisig M., Strippoli M.F., Vollenweider P., Vaucher J., Lutti A., Kherif F., Penner I.K. et al., 2024/12. Brain, behavior, & immunity - health, 42 p. 100896. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B7A7533FF87E]
Weight, Anthropometric and Metabolic Changes After Discontinuing Antiretroviral Therapy Containing Tenofovir Alafenamide in People With HIV.
Damas J., Munting A., Fellay J., Haerry D., Marzolini C., Tarr P.E., Steffen A., Braun D.L., Stoeckle M., Bernasconi E. et al., 2024/10/15. Clinical infectious diseases, 79 (4) pp. 990-998. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A22E1C92231B]
Loss of tolerance precedes triggering and lifelong persistence of pathogenic type I interferon autoantibodies.
Fernbach S., Mair N.K., Abela I.A., Groen K., Kuratli R., Lork M., Thorball C.W., Bernasconi E., Filippidis P., Leuzinger K. et al., 2024/09/02. The Journal of experimental medicine, 221 (9). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_091D90E14C02]
Prevalence of actionable pharmacogenetic variants and high-risk drug prescriptions: A Swiss hospital-based cohort study.
Hodel F., De Min M.B., Thorball C.W., Redin C., Vollenweider P., Girardin F., Fellay J., 2024/09. Clinical and translational science, 17 (9) pp. e70009. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1F053E42785D]
Using viral diversity to identify HIV-1 variants under HLA-dependent selection in a systematic viral genome-wide screen.
Neuner-Jehle N., Zeeb M., Thorball C.W., Fellay J., Metzner K.J., Frischknecht P., Neumann K., Leeman C., Rauch A., Stöckle M. et al., 2024/08. PLoS pathogens, 20 (8) pp. e1012385. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A3A54E74EB11]
Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection.
Marchal A., Cirulli E.T., Neveux I., Bellos E., Thwaites R.S., Schiabor Barrett K.M., Zhang Y., Nemes-Bokun I., Kalinova M., Catchpole A. et al., 2024/07/25. HGG advances, 5 (3) p. 100300. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_45B960D632E8]
 
Paediatric Personalized Research Network Switzerland (SwissPedHealth): A Joint Paediatric National Data Stream
Mozun R, Belle F, Agostini A, Baumgartner M, Fellay J, Forrest C, Froese S, Giannoni E, Goetze S, Hofmann K et al., 2024/07/24..
[DOI][serval:BIB_65BC2307FBC9]
Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation.
Xu Z.M., Gnouamozi G.E., Rüeger S., Shea P.R., Buti M., Chan H.L., Marcellin P., Lawless D., Naret O., Zeller M. et al., 2024/06/06. American journal of human genetics, 111 (6) pp. 1018-1034. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_9CF13B4886CA]
Diagnostic accuracy of a sequence-specific Mtb-DNA hybridization assay in urine: a case-control study including subclinical TB cases.
Tschan Y., Sasamalo M., Hiza H., Fellay J., Gagneux S., Reither K., Hella J., Portevin D., 2024/06/04. Microbiology spectrum, 12 (6) pp. e0042624. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4CA88B9A5608]
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 B.M., Fontana S., Mdawar-Bailly E., Moradpour D., Fellay J. et al., 2024/06/01. Hepatology, 79 (6) pp. 1421-1431. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_212560170173]
Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania.
Hiza H., Zwyer M., Hella J., Arbués A., Sasamalo M., Borrell S., Xu Z.M., Ross A., Brites D., Fellay J. et al., 2024/04/23. Scientific reports, 14 (1) p. 9287. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_288A15B47D51]
A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy.
Chong A.Y., Brenner N., Jimenez-Kaufmann A., Cortes A., Hill M., Littlejohns T.J., Gilchrist J.J., Fairfax B.P., Knight J.C., Hodel F. et al., 2024/02/01. American journal of human genetics, 111 (2) pp. 295-308. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_17B73429046E]
Correction: 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. et al., 2024/01/06. Genome medicine, 16 (1) p. 6. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_CA23CC25F766]
Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study.
Zeeb M., Pasin C., Cavassini M., Bieler-Aeschlimann M., Frischknecht P., Kusejko K., Fellay J., Blanquart F., Metzner K.J., Neumann K. et al., 2024. Brain communications, 6 (4) pp. fcae188. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F4D8C677D8C6]
2023
 
Transcriptomics and chromatin accessibility in multiple African population samples.
DeGorter M.K., Goddard P.C., Karakoc E., Kundu S., Yan S.M., Nachun D., Abell N., Aguirre M., Carstensen T., Chen Z. et al., 2023/11/06..
[DOI][Pmid][serval:BIB_77F4C9A66043]
G2GSnake: a Snakemake workflow for host-pathogen genomic association studies.
Xu Z.M., Naret O., Oumelloul M.A., Fellay J., 2023/10. Bioinformatics advances, 3 (1) pp. vbad142. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_5457A30782C8]
Association of a Polygenic Risk Score With Osteoporosis in People Living With HIV: The Swiss HIV Cohort Study.
Schwenke J.M., Thorball C.W., Schoepf I.C., Ryom L., Hasse B., Lamy O., Calmy A., Wandeler G., Marzolini C., Kahlert C.R. et al., 2023/09/15. The Journal of infectious diseases, 228 (6) pp. 742-750. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_44F15B89FB36]
Autoantibodies neutralizing type I IFNs underlie West Nile virus encephalitis in ∼40% of patients.
Gervais A., Rovida F., Avanzini M.A., Croce S., Marchal A., Lin S.C., Ferrari A., Thorball C.W., Constant O., Le Voyer T. et al., 2023/09/04. The Journal of experimental medicine, 220 (9) pp. e20230661. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_36E7457158FD]
 
Author Correction: Africa-specific human genetic variation near CHD1L associates with HIV-1 load.
McLaren P.J., Porreca I., Iaconis G., Mok H.P., Mukhopadhyay S., Karakoc E., Cristinelli S., Pomilla C., Bartha I., Thorball C.W. et al., 2023/09. Nature, 621 (7979) pp. E42. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5534E0BE7C51]
Human Genomics of COVID-19 Pneumonia: Contributions of Rare and Common Variants.
Cobat A., Zhang Q., COVID Human Genetic Effort, Abel L., Casanova J.L., Fellay J., 2023/08/10. Annual review of biomedical data science, 6 pp. 465-486. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FAD92BD97EE4]
 
Africa-specific human genetic variation near CHD1L associates with HIV-1 load.
McLaren P.J., Porreca I., Iaconis G., Mok H.P., Mukhopadhyay S., Karakoc E., Cristinelli S., Pomilla C., Bartha I., Thorball C.W. et al., 2023/08. Nature, 620 (7976) pp. 1025-1030. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B1BEC83916D3]
Genetic features and genomic targets of human KRAB-zinc finger proteins.
de Tribolet-Hardy J., Thorball C.W., Forey R., Planet E., Duc J., Coudray A., Khubieh B., Offner S., Pulver C., Fellay J. et al., 2023/08. Genome research, 33 (8) pp. 1409-1423. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_41F4935182BD]
A metagenome-wide association study of HIV disease progression in HIV controllers.
Real L.M., Sáez M.E., Corma-Gómez A., Gonzalez-Pérez A., Thorball C., Ruiz R., Jimenez-Leon M.R., Gonzalez-Serna A., Gasca-Capote C., Bravo M.J. et al., 2023/07/21. iScience, 26 (7) p. 107214. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6F6159861097]
Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study.
Avery E.F., Kleynhans J.N., Ledergerber B., Schoepf I.C., Thorball C.W., Kootstra N.A., Reiss P., Ryom L., Braun D.L., Thurnheer M.C. et al., 2023/06/08. Clinical infectious diseases, 76 (11) pp. 1969-1979. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E1546C7A7084]
Multiancestry sex-stratified genomic associations with HIV viral load and controller status from the ICGH.
Vergara C., Tuff J.F., International Collaboration for the Genomics of HIV (ICGH), Fellay J., Duggal P., Scully E.P., McLaren P.J., 2023/06/08. JCI insight, 8 (11). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_18D55776D514]
Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort.
Lawless D., McKennan C.G., Das S.R., Junier T., Xu Z.M., Anderson L.J., Gebretsadik T., Shilts M.H., Larkin E., Rosas-Salazar C. et al., 2023/05/12. The Journal of infectious diseases, 227 (10) pp. 1194-1202. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0C12920D2B3E]
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 C.W., Redin C., Fournier S., Müller O., Strambo D., Michel P., Vollenweider P., Marques-Vidal P., Fellay J. et al., 2023/05/09. European journal of preventive cardiology, 30 (7) pp. 561-571. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_A980F8B766B6]
Secondary structure of the human mitochondrial genome affects formation of deletions.
Shamanskiy V., Mikhailova A.A., Tretiakov E.O., Ushakova K., Mikhailova A.G., Oreshkov S., Knorre D.A., Ree N., Overdevest J.B., Lukowski S.W. et al., 2023/05/08. BMC biology, 21 (1) p. 103. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7910069ADAE8]
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. et al., 2023/04/05. Genome medicine, 15 (1) p. 22. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_31798B2B6490]
Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania.
Zwyer M., Rutaihwa L.K., Windels E., Hella J., Menardo F., Sasamalo M., Sommer G., Schmülling L., Borrell S., Reinhard M. et al., 2023/04. PLoS pathogens, 19 (4) pp. e1010893. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6BF85513B900]
 
Polygenic Risk Scores for Prediction of Subclinical Coronary Artery Disease in Persons With Human Immunodeficiency Virus (HIV): The Swiss HIV Cohort Study.
Schoepf I.C., Thorball C.W., Kovari H., Ledergerber B., Buechel R.R., Calmy A., Weber R., Kaufmann P.A., Nkoulou R., Schwenke J.M. et al., 2023/01/06. Clinical infectious diseases, 76 (1) pp. 48-56. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F8C439A0D50D]
Associations of genetic and infectious risk factors with coronary heart disease.
Hodel F., Xu Z.M., Thorball C.W., de La Harpe R., Letang-Mathieu P., Brenner N., Butt J., Bender N., Waterboer T., Marques-Vidal P.M. et al., 2023. eLife, 12 pp. e79742. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_ACB0182B565D]
Predicting type 2 diabetes risk before and after solid organ transplantation using polygenic scores in a Danish cohort.
Dos Santos Q., Leung P., Thorball C.W., Ledergerber B., Fellay J., MacPherson C.R., Hornum M., Terrones-Campos C., Rasmussen A., Gustafsson F. et al., 2023. Frontiers in molecular biosciences, 10 p. 1282412. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_19C243A8DA7F]
The HLA-B*57:01 allele corresponds to a very large MHC haploblock likely explaining its massive effect for HIV-1 elite control.
Rahmouni M., De Marco L., Spadoni J.L., Tison M., Medina-Santos R., Labib T., Noirel J., Tamouza R., Limou S., Delaneau O. et al., 2023. Frontiers in immunology, 14 p. 1305856. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_91A1B1570EDA]
2022
Visual masking deficits in schizophrenia: a view into the genetics of the disease through an endophenotype.
Shaqiri A., Hodel F., da Cruz J.R., Roinishvili M., Chkonia E., Brand A., Fellay J., Herzog M.H., 2022/12/31. Translational psychiatry, 12 (1) p. 529. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_47A6F37C5EAD]
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 D.C., Bhuiyan Z., Porretta A.P., Monney P., Bedoni N., Maurer F., Sekarski N., Atallah I., Émeline D. et al., 2022/12. European journal of medical genetics, 65 (12) p. 104627. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_36267BDE9D6F]
 
Variability of Primary Sjögren's Syndrome Is Driven by Interferon-α and Interferon-α Blood Levels Are Associated With the Class II HLA-DQ Locus.
Trutschel D., Bost P., Mariette X., Bondet V., Llibre A., Posseme C., Charbit B., Thorball C.W., Jonsson R., Lessard C.J. et al., 2022/12. Arthritis & rheumatology, 74 (12) pp. 1991-2002. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E91D437CA3D3]
 
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., 2022/11/01. BMC medicine, 20 (1) p. 416. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4DE6669585E5]
A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand.
Mikhailova A.G., Mikhailova A.A., Ushakova K., Tretiakov E.O., Iliushchenko D., Shamansky V., Lobanova V., Kozenkov I., Efimenko B., Yurchenko A.A. et al., 2022/10/14. Nucleic acids research, 50 (18) pp. 10264-10277. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AC322A4B5E86]
A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits.
Nadeau S., Thorball C.W., Kouyos R., Günthard H.F., Böni J., Yerly S., Perreau M., Klimkait T., Rauch A., Hirsch H.H. et al., 2022/08/03. Molecular biology and evolution, 39 (8) pp. msac163. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C0A2EB45D9AE]
 
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 C.W., Zeymer O., Zhou X. et al., 2022/08/01. Journal of immunology, 209 (3) pp. 535-547. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_99B41F98BEAA]
Host genomics of SARS-CoV-2 infection.
Redin C., Thorball C.W., Fellay J., 2022/08. European journal of human genetics, 30 (8) pp. 908-914. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_610172074A67]
Improving polygenic prediction with genetically inferred ancestry.
Naret O., Kutalik Z., Hodel F., Xu Z.M., Marques-Vidal P., Fellay J., 2022/07/14. HGG advances, 3 (3) p. 100109. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DFFCB5547228]
Author Correction: Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV.
Bick A.G., Popadin K., Thorball C.W., Uddin M.M., Zanni M.V., Yu B., Cavassini M., Rauch A., Tarr P., Schmid P. et al., 2022/07/08. Scientific reports, 12 (1) p. 11638. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3C87FA69CB82]
 
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 H.H., Eto S., Garcia-Prat M. et al., 2022/05/24. Proceedings of the National Academy of Sciences of the United States of America, 119 (21) pp. e2200413119. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1C589D62C589]
 
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 I.C., Thorball C.W., Ledergerber B., Kootstra N.A., Reiss P., Raffenberg M., Engel T., Braun D.L., Hasse B., Thurnheer C. et al., 2022/05/04. The Journal of infectious diseases, 225 (9) pp. 1581-1591. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_39DB29D8297F]
 
Cohort Profile Update: The Swiss HIV Cohort Study (SHCS).
Scherrer A.U., Traytel A., Braun D.L., Calmy A., Battegay M., Cavassini M., Furrer H., Schmid P., Bernasconi E., Stoeckle M. et al., 2022/02/18. International journal of epidemiology, 51 (1) pp. 33-34j. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_CAE07421BB63]
 
A highly virulent variant of HIV-1 circulating in the Netherlands.
Wymant C., Bezemer D., Blanquart F., Ferretti L., Gall A., Hall M., Golubchik T., Bakker M., Ong S.H., Zhao L. et al., 2022/02/04. Science, 375 (6580) pp. 540-545. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_24048155C295]
A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection.
Andreakos E., Abel L., Vinh D.C., Kaja E., Drolet B.A., Zhang Q., O'Farrelly C., Novelli G., Rodríguez-Gallego C., Haerynck F. et al., 2022/02. Nature immunology, 23 (2) pp. 159-164. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E0EC5686999F]
Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV.
Bick A.G., Popadin K., Thorball C.W., Uddin M.M., Zanni M.V., Yu B., Cavassini M., Rauch A., Tarr P., Schmid P. et al., 2022/01/12. Scientific reports, 12 (1) p. 577. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_482297EB27F3]
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., 2022. Frontiers in medicine, 9 p. 821776. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BDB41F7DEE7D]
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load.
Zhao L., Wymant C., Blanquart F., Golubchik T., Gall A., Bakker M., Bezemer D., Hall M., Ong S.H., Albert J. et al., 2022. Virus evolution, 8 (1) pp. veac022. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DED149CC980B]
Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations.
Xu Z.M., Rüeger S., Zwyer M., Brites D., Hiza H., Reinhard M., Rutaihwa L., Borrell S., Isihaka F., Temba H. et al., 2022/01. PLoS computational biology, 18 (1) pp. e1009628. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_3994C147BF6F]
2021
 
Author Correction: A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response.
Luo Y., Kanai M., Choi W., Li X., Sakaue S., Yamamoto K., Ogawa K., Gutierrez-Arcelus M., Gregersen P.K., Stuart P.E. et al., 2021/12. Nature genetics, 53 (12) p. 1722. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_49102EA5EBAA]
Author Correction: Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption
Froelicher David, Troncoso-Pastoriza Juan R., Raisaro Jean Louis, Cuendet Michel A., Sousa Joao Sa, Cho Hyunghoon, Berger Bonnie, Fellay Jacques, Hubaux Jean-Pierre, 2021/12. Nature Communications, 12 (1). Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_BA7A4545F831]
Blood virosphere in febrile Tanzanian children.
Cordey S., Laubscher F., Hartley M.A., Junier T., Keitel K., Docquier M., Guex N., Iseli C., Vieille G., Le Mercier P. et al., 2021/12. Emerging microbes & infections, 10 (1) pp. 982-993. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B0B6B061E9F0]
From Your Nose to Your Toes: A Review of Severe Acute Respiratory Syndrome Coronavirus 2 Pandemic‒Associated Pernio.
Arkin L.M., Moon J.J., Tran J.M., Asgari S., O'Farrelly C., Casanova J.L., Cowen E.W., Mays J.W., Singh A.M., Drolet B.A. et al., 2021/12. The Journal of investigative dermatology, 141 (12) pp. 2791-2796. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_867ED9E568B7]
 
Impact of Delaying Antiretroviral Treatment During Primary Human Immunodeficiency Virus Infection on Telomere Length.
Raffenberg M., Engel T., Schoepf I.C., Kootstra N.A., Reiss P., Braun D.L., Thorball C.W., Fellay J., Kouyos R.D., Ledergerber B. et al., 2021/11/22. The Journal of infectious diseases, 224 (10) pp. 1775-1784. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AB2761A109CD]
 
Coronary Artery Disease-Associated and Longevity-Associated Polygenic Risk Scores for Prediction of Coronary Artery Disease Events in Persons Living With Human Immunodeficiency Virus: The Swiss HIV Cohort Study.
Schoepf I.C., Thorball C.W., Ledergerber B., Engel T., Raffenberg M., Kootstra N.A., Reiss P., Hasse B., Marzolini C., Thurnheer C. et al., 2021/11/02. Clinical infectious diseases, 73 (9) pp. 1597-1604. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_782F7251FD8F]
Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure.
Smith D.A., Fernandez-Antunez C., Magri A., Bowden R., Chaturvedi N., Fellay J., McLauchlan J., Foster G.R., Irving W.L., STOP-HCV Consortium et al., 2021/10/20. Nature communications, 12 (1) p. 6105. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1FACB1601518]
Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption.
Froelicher D., Troncoso-Pastoriza J.R., Raisaro J.L., Cuendet M.A., Sousa J.S., Cho H., Berger B., Fellay J., Hubaux J.P., 2021/10/11. Nature communications, 12 (1) p. 5910. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3683F2C63090]
 
Telomere Length, Traditional Risk Factors, Factors Related to Human Immunodeficiency Virus (HIV) and Coronary Artery Disease Events in Swiss Persons Living With HIV.
Engel T., Raffenberg M., Schoepf I.C., Kootstra N.A., Reiss P., Thorball C.W., Hasse B., Hirzel C., Wissel K., Roth J.A. et al., 2021/10/05. Clinical infectious diseases, 73 (7) pp. e2070-e2076. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_43BB2F3F0EDE]
A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response.
Luo Y., Kanai M., Choi W., Li X., Sakaue S., Yamamoto K., Ogawa K., Gutierrez-Arcelus M., Gregersen P.K., Stuart P.E. et al., 2021/10. Nature genetics, 53 (10) pp. 1504-1516. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B110F32BA2DA]
HIV-1 and human genetic variation.
McLaren P.J., Fellay J., 2021/10. Nature reviews. Genetics, 22 (10) pp. 645-657. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_16DF9AACD3B9]
 
Immunological lessons from genome-wide association studies of infections.
Thorball C.W., Fellay J., Borghesi A., 2021/10. Current opinion in immunology, 72 pp. 87-93. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B2F8837F7024]
Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths.
Bastard P., Gervais A., Le Voyer T., Rosain J., Philippot Q., Manry J., Michailidis E., Hoffmann H.H., Eto S., Garcia-Prat M. et al., 2021/08/19. Science immunology, 6 (62) pp. eabl4340. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_15CBA872BCCD]
Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma.
Thorball C.W., Oudot-Mellakh T., Ehsan N., Hammer C., Santoni F.A., Niay J., Costagliola D., Goujard C., Meyer L., Wang S.S. et al., 2021/08/01. Haematologica, 106 (8) pp. 2233-2241. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_B72746EA3CA7]
 
Rapid Progression of Kidney Dysfunction in People Living With HIV: Use of Polygenic and Data Collection on Adverse Events of Anti-HIV Drugs (D:A:D) Risk Scores.
Dietrich L.G., Thorball C.W., Ryom L., Burkhalter F., Hasse B., Thurnheer M.C., Weisser M., Schmid P., Bernasconi E., Darling KEA et al., 2021/06/15. The Journal of infectious diseases, 223 (12) pp. 2145-2153. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D0776243F8D5]
Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link.
Nguyen H., Thorball C.W., Fellay J., Böni J., Yerly S., Perreau M., Hirsch H.H., Kusejko K., Thurnheer M.C., Battegay M. et al., 2021/06/01. eLife, 10. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_CDF338C143A7]
 
Author Correction: The influence of human genetic variation on Epstein-Barr virus sequence diversity.
Rüeger S., Hammer C., Loetscher A., McLaren P.J., Lawless D., Naret O., Khanna N., Bernasconi E., Cavassini M., Günthard H.F. et al., 2021/04/20..
[DOI][WoS][Pmid][serval:BIB_4F1041DEFB49]
 
Citizen-centered, auditable and privacy-preserving population genomics.
Grishin D., Raisaro J.L., Troncoso-Pastoriza J.R., Obbad K., Quinn K., Misbach M., Gollhardt J., Sa J., Fellay J., Church G.M. et al., 2021/03. Nature computational science, 1 (3) pp. 192-198. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C0580E5093AA]
Revolutionizing Medical Data Sharing Using Advanced Privacy-Enhancing Technologies: Technical, Legal, and Ethical Synthesis.
Scheibner J., Raisaro J.L., Troncoso-Pastoriza J.R., Ienca M., Fellay J., Vayena E., Hubaux J.P., 2021/02/25. Journal of medical Internet research, 23 (2) pp. e25120. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E2683B6181C3]
The influence of human genetic variation on Epstein-Barr virus sequence diversity.
Rüeger S., Hammer C., Loetscher A., McLaren P.J., Lawless D., Naret O., Khanna N., Bernasconi E., Cavassini M., Günthard H.F. et al., 2021/02/25. Scientific reports, 11 (1) p. 4586. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_0350B2DA3BE2]
Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles.
Benet S., Gálvez C., Drobniewski F., Kontsevaya I., Arias L., Monguió-Tortajada M., Erkizia I., Urrea V., Ong R.Y., Luquin M. et al., 2021/01. Journal of extracellular vesicles, 10 (3) pp. e12046. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_3994DD1EFC01]
2020
Whole-exome Sequencing for the Identification of Rare Variants in Primary Immunodeficiency Genes in Children With Sepsis: A Prospective, Population-based Cohort Study.
Borghesi A., Trück J., Asgari S., Sancho-Shimizu V., Agyeman PKA, Bellos E., Giannoni E., Stocker M., Posfay-Barbe K.M., Heininger U. et al., 2020/12/17. Clinical infectious diseases, 71 (10) pp. e614-e623. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_D6F373E4D323]
 
Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment.
Thorball C.W., Borghesi A., Bachmann N., Von Siebenthal C., Vongrad V., Turk T., Neumann K., Beerenwinkel N., Bogojeska J., Roth V. et al., 2020/12/01. Journal of acquired immune deficiency syndromes, 85 (4) pp. 517-524. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FDF7A2D4587F]
Pharmacogénomique et aide à la prescription médicamenteuse [Pharmacogenomics : a toolbox to improve drug prescription]
Jaccard E., Redin C., Girardin F., Waeber G., Fellay J., Vollenweider P., 2020/11/25. Revue medicale suisse, 16 (716) pp. 2259-2263. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_227B3780CEBD]
HLA tapasin independence: broader peptide repertoire and HIV control.
Bashirova A.A., Viard M., Naranbhai V., Grifoni A., Garcia-Beltran W., Akdag M., Yuki Y., Gao X., O'hUigin C., Raghavan M. et al., 2020/11/10. Proceedings of the National Academy of Sciences of the United States of America, 117 (45) pp. 28232-28238. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_2878DD324F2A]
 
Increased CHIP Prevalence Amongst People Living with HIV.
Bick A.G., Popadin K., Thorball C.W., Uddin M.M., Zanni M., Yu B., Cavassini M., Rauch A., Tarr P., Schmid P. et al., 2020/11/07..
[DOI][Pmid][serval:BIB_A38E810FE3BD]
Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART.
Wan C., Bachmann N., Mitov V., Blanquart F., Céspedes S.P., Turk T., Neumann K., Beerenwinkel N., Bogojeska J., Fellay J. et al., 2020/11/02. Nature communications, 11 (1) p. 5542. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_EC2E5183286F]
Virosaurus A Reference to Explore and Capture Virus Genetic Diversity.
Gleizes A., Laubscher F., Guex N., Iseli C., Junier T., Cordey S., Fellay J., Xenarios I., Kaiser L., Mercier P.L., 2020/11/01. Viruses, 12 (11) pp. E1248. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5E9093826570]
Inborn errors of type I IFN immunity in patients with life-threatening COVID-19.
Zhang Q., Bastard P., Liu Z., Le Pen J., Moncada-Velez M., Chen J., Ogishi M., Sabli IKD, Hodeib S., Korol C. et al., 2020/10/23. Science, 370 (6515) pp. eabd4570. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_38514EC06F0A]
La médecine de précision : au carrefour de la biologie moléculaire, des sciences de l’information et des humanités [Precision medicine : at the crossroad of molecular biology, information sciences and humanities]
Gosselin R.D., Redin C., Ristorcelli É., Raisaro J.L., Fellay J., 2020/09/02. Revue medicale suisse, 16 (704) pp. 1574-1578. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_4B7013A0A5F6]
 
Ongoing evolution of KRAB zinc finger protein-coding genes in modern humans
Christian Thorball, Evarist Planet, Jonas de Tribolet-Hardy, Alexandre Coudray, Jacques Fellay, Priscilla Turelli, Didier Trono, 2020/09/01..
[DOI][serval:BIB_3015AF6A34EE]
 
Phenotype prediction from genome-wide genotyping data: a crowdsourcing experiment
Olivier Naret, David AA Baranger, Sharada Prasanna Mohanty, Bastian Greshake Tzovaras, Marcel Salathé, Jacques Fellay, 2020/08/25..
[DOI][serval:BIB_6A01D4BA4CFC]
GenoShare: Supporting Privacy-Informed Decisions for Sharing Individual-Level Genetic Data.
Raisaro J.L., Troncoso-Pastoriza J.R., El-Zein Y., Humbert M., Troncoso C., Fellay J., Hubaux J.P., 2020/06/16. pp. 238-241 dans Digital Personalized Health and Medicine, IOS Press.
[URN][DOI][WoS][Pmid][serval:BIB_E4D4CB80455C]
SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery.
Raisaro J.L., Troncoso-Pastoriza J.R., Pradervand S., Cuendet M., Misbach M., Sa J., Marino F., Freundler N., Rosat N., Cavin D. et al., 2020/06/16. pp. 1161-1162 dans Digital Personalized Health and Medicine, IOS Press.
[URN][DOI][Pmid][serval:BIB_3077196DA0EB]
 
Exploring the interactions between the human and viral genomes.
Fellay J., Pedergnana V., 2020/06. Human genetics, 139 (6-7) pp. 777-781. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_884272B1E6CF]
 
Susceptibility to infection in early life: a growing role for human genetics.
Borghesi A., Marzollo A., Michev A., Fellay J., 2020/06. Human genetics, 139 (6-7) pp. 733-743. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_F64BB0115109]
Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland
Lemaitre Joseph C, Perez-Saez Javier, Azman Andrew S, Rinaldo Andrea, Fellay Jacques, 2020/05/30. Swiss Medical Weekly.
[URN][DOI][Pmid][serval:BIB_63C488E8606D]
HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation.
Arora J., Pierini F., McLaren P.J., Carrington M., Fellay J., Lenz T.L., 2020/03/01. Molecular biology and evolution, 37 (3) pp. 639-650. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_4A4E20C0A676]
 
Contribution of Genetic Background and Data Collection on Adverse Events of Anti-human Immunodeficiency Virus (HIV) Drugs (D:A:D) Clinical Risk Score to Chronic Kidney Disease in Swiss HIV-infected Persons With Normal Baseline Estimated Glomerular Filtration Rate.
Dietrich L.G., Barceló C., Thorball C.W., Ryom L., Burkhalter F., Hasse B., Furrer H., Weisser M., Steffen A., Bernasconi E. et al., 2020/02/14. Clinical infectious diseases, 70 (5) pp. 890-897. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CEFAD592E5CD]
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 J.R., Raisaro J.L., Hubaux J.P., Fellay J., Vayena E., 2020. Journal of law and the biosciences, 7 (1) pp. lsaa010. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E81CB33F863F]
2019
 
Genomics of Human Respiratory Syncytial Virus Vaccine Attenuation
Thomas Junier, Laurent Kaiser, Nimisha Chaturvedi, Jacques Fellay, 2019/12/02..
[DOI][serval:BIB_0B5B93C42572]
 
Gender medicine and oncology: report and consensus of an ESMO workshop.
Wagner A.D., Oertelt-Prigione S., Adjei A., Buclin T., Cristina V., Csajka C., Coukos G., Dafni U., Dotto G.P., Ducreux M. et al., 2019/12/01. Annals of oncology, 30 (12) pp. 1914-1924. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C7C76EA90383]
Predicting the Occurrence of Variants in RAG1 and RAG2.
Lawless D., Lango Allen H., Thaventhiran J., NIHR BioResource-Rare Diseases Consortium, Hodel F., Anwar R., Fellay J., Walter J.E., Savic S., 2019/10. Journal of clinical immunology, 39 (7) pp. 688-701. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_8B2685C9BC41]
A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals.
Scepanovic P., Hodel F., Mondot S., Partula V., Byrd A., Hammer C., Alanio C., Bergstedt J., Patin E., Touvier M. et al., 2019/09/13. Microbiome, 7 (1) p. 130. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E8404D993AE8]
Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes.
Chaturvedi N., Svarovskaia E.S., Mo H., Osinusi A.O., Brainard D.M., Subramanian G.M., McHutchison J.G., Zeuzem S., Fellay J., 2019/09/03. eLife, 8. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B2FCC082A445]
Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial.
Junier T., Huber M., Schmutz S., Kufner V., Zagordi O., Neuenschwander S., Ramette A., Kubacki J., Bachofen C., Qi W. et al., 2019/08/28. Genes, 10 (9). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B438BB51FAF9]
 
HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected.
Nguyen H., Thorball C.W., Fellay J., Böni J., Yerly S., Perreau M., Klimkait T., Kusejko K., Bachmann N., Chaudron S.E. et al., 2019/08/15. Journal of acquired immune deficiency syndromes, 81 (5) pp. 508-515. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_6E0F5A3E41D4]
Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART.
Bachmann N., von Siebenthal C., Vongrad V., Turk T., Neumann K., Beerenwinkel N., Bogojeska J., Fellay J., Roth V., Kok Y.L. et al., 2019/07/19. Nature communications, 10 (1) p. 3193. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_E1256C4C82EF]
 
A global scientific strategy to cure hepatitis B.
Revill P.A., Chisari F.V., Block J.M., Dandri M., Gehring A.J., Guo H., Hu J., Kramvis A., Lampertico P., Janssen HLA et al., 2019/07. The lancet. Gastroenterology & hepatology, 4 (7) pp. 545-558. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_BCB3A34F7D9D]
HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responses.
Langer S., Hammer C., Hopfensperger K., Klein L., Hotter D., De Jesus P.D., Herbert K.M., Pache L., Smith N., van der Merwe J.A. et al., 2019/02/05. eLife, 8. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F2CB05F54083]
 
Human genomics of acute liver failure due to hepatitis B virus infection: An exome sequencing study in liver transplant recipients.
Asgari S., Chaturvedi N., Scepanovic P., Hammer C., Semmo N., Giostra E., Müllhaupt B., Angus P., Thompson A.J., Moradpour D. et al., 2019/02. Journal of viral hepatitis, 26 (2) pp. 271-277. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FF674E9FCBB2]
 
HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV control
Jatin Arora, Paul McLaren, Nimisha Chaturvedi, Mary Carrington, Jacques Fellay, Tobias Lenz, 2019/01/15. Proceedings of the National Academy of Sciences.
[DOI][serval:BIB_08FFAFD7BD2A]
Effect of Fc Receptor Genetic Diversity on HIV-1 Disease Pathogenesis.
Geraghty D.E., Thorball C.W., Fellay J., Thomas R., 2019. Frontiers in immunology, 10 p. 970. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_6AEAD24A0472]
2018
 
Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis.
Maffucci P, Bigio B, Rapaport F, Cobat A, Borghesi A, Lopez M, Patin E, Bolze A, Shang L, Bendavid M et al., 2018/12. Proceedings of the National Academy of Sciences of the United States of America.
[DOI][Pmid][serval:BIB_BAF1DFA3E78A]
 
Pervasive Adaptation of Hepatitis C Virus to Interferon Lambda Polymorphism Across Multiple Genotypes
Nimisha Chaturvedi, Evguenia Svarovskaia, Hongmei Mo, Anu Osinusi, Diana Brainard, G Mani Subramanian, John McHutchison, Stefan Zeuzem, Jacques Fellay, 2018/11/30..
[DOI][serval:BIB_1ED1A21E9418]
Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines.
Scepanovic P., Alanio C., Hammer C., Hodel F., Bergstedt J., Patin E., Thorball C.W., Chaturvedi N., Charbit B., Abel L. et al., 2018/07/27. Genome medicine, 10 (1) p. 59. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_44965C59FD25]
 
Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1.
Martin MP, Naranbhai V, Shea PR, Qi Y, Ramsuran V, Vince N, Gao X, Thomas R, Brumme ZL, Carlson JM et al., 2018/04. The Journal of clinical investigation.
[DOI][Pmid][serval:BIB_19B56F612B25]
Detection of novel astroviruses MLB1 and MLB2 in the sera of febrile Tanzanian children.
Cordey S., Hartley M.A., Keitel K., Laubscher F., Brito F., Junier T., Kagoro F., Samaka J., Masimba J., Said Z. et al., 2018/03/14. Emerging microbes & infections, 7 (1) p. 27. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C49470704598]
 
Are privacy-enhancing technologies for genomic data ready for the clinic? A survey of medical experts of the Swiss HIV Cohort Study.
Raisaro J.L., McLaren P.J., Fellay J., Cavassini M., Klersy C., Hubaux J.P., Swiss HIV Cohort Study, 2018/03. Journal of biomedical informatics, 79 pp. 1-6. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_AA11676A72A9]
 
Genetics of human susceptibility to active and latent tuberculosis: present knowledge and future perspectives.
Abel L., Fellay J., Haas D.W., Schurr E., Srikrishna G., Urbanowski M., Chaturvedi N., Srinivasan S., Johnson D.H., Bishai W.R., 2018/03. The Lancet. Infectious diseases, 18 (3) pp. e64-e75. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_D74CAA9CC4FF]
Differential Immunodominance Hierarchy of CD8+ T-Cell Responses in HLA-B*27:05- and -B*27:02-Mediated Control of HIV-1 Infection.
Adland E., Hill M., Lavandier N., Csala A., Edwards A., Chen F., Radkowski M., Kowalska J.D., Paraskevis D., Hatzakis A. et al., 2018/02/15. Journal of virology, 92 (4). Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_810E750E7E66]
 
Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors.
Patin E, Hasan M, Bergstedt J, Rouilly V, Libri V, Urrutia A, Alanio C, Scepanovic P, Hammer C, Jönsson F et al., 2018/02. Nature immunology.
[DOI][Pmid][serval:BIB_76ECA64022A3]
 
Time to Switch to Second-line Antiretroviral Therapy in Children With Human Immunodeficiency Virus in Europe and Thailand.
European Pregnancy and Paediatric HIV Cohort Collaboration (EPPICC) Study Group in EuroCoord, Goetghebuer T., 2018/02/01. Clinical infectious diseases, 66 (4) pp. 594-603. Peer-reviewed.
[DOI][Pmid][serval:BIB_498102734DE0]
Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges.
Piasecka B., Duffy D., Urrutia A., Quach H., Patin E., Posseme C., Bergstedt J., Charbit B., Rouilly V., MacPherson C.R. et al., 2018/01/16. Proceedings of the National Academy of Sciences of the United States of America, 115 (3) pp. E488-E497. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_5F55BC16BE09]
Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen Genomes.
Naret O., Chaturvedi N., Bartha I., Hammer C., Fellay J., Swiss HIV Cohort Study (SHCS), 2018. Frontiers in genetics, 9 p. 266. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_74507151A9A8]
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Wymant C, Blanquart F, Golubchik T, Gall A, Bakker M, Bezemer D, Croucher NJ, Hall M, Hillebregt M, Ong SH et al., 2018/01. Virus evolution.
[URN][DOI][Pmid][serval:BIB_0200C8AC6ED0]
Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells.
Ramsuran V, Naranbhai V, Horowitz A, Qi Y, Martin MP, Yuki Y, Gao X, Walker-Sperling V, Del Prete GQ, Schneider DK et al., 2018/01. Science (New York, N.Y.).
[URN][DOI][Pmid][serval:BIB_3BFDCD49227E]
 
Sequence Alignment Through the Looking Glass
Appuswamy R, Fellay J, Chaturvedi N, 2018/01..
[DOI][serval:BIB_B18032F10C14]
2017
HLA-B*14:02-Restricted Env-Specific CD8+ T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection.
Fellay Jacques, 2017/11. Journal of virology.
[URN][DOI][Pmid][serval:BIB_BC76F3F3C49A]
Evaluating the Impact of Functional Genetic Variation on HIV-1 Control
Paul J McLaren, Sara L Pulit, Deepti Gurdasani, Istvan Bartha, Patrick R Shea, Cristina Pomilla, Namrata Gupta, Effrossyni Gkrania-Klotsas, Elizabeth H Young, Norbert Bannert et al., 2017/09/09. The Journal of Infectious Diseases.
[URN][DOI][serval:BIB_F21F3E81D0EB]
 
A genome-wide polygenic approach to HIV uncovers link to inflammatory bowel disease and identifies potential novel genetic variants
Robert A Power, Christian W Thorball, Istvan Bartha, Perry John, Paul J McLaren, Tulio de Oliveira, Jacques Fellay, 2017/06..
[DOI][serval:BIB_4C7EC4ADFAE8]
 
Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe
François Blanquart, Chris Wymant, Marion Cornelissen, Astrid Gall, Margreet Bakker, Daniela Bezemer, Matthew Hall, Mariska Hillebregt, Swee Hoe Ong, Jan Albert et al., 2017/06. PLOS Biology.
[DOI][serval:BIB_86F41E2D614B]
Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus.
Ansari M.A., Pedergnana V., L C Ip C., Magri A., Von Delft A., Bonsall D., Chaturvedi N., Bartha I., Smith D., Nicholson G. et al., 2017/05. Nature genetics, 49 (5) pp. 666-673. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_179F1128ACCA]
Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control
István Bartha, Paul J McLaren, Chanson Brumme, Richard Harrigan, Amalio Telenti, Jacques Fellay, 2017/02/09. PLOS Computational Biology.
[DOI][serval:BIB_4A55B9269FCE]
Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune Responses.
Borghesi A., Stronati M., Fellay J., 2017. Frontiers in immunology, 8 p. 215. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_05860502AB4E]
 
No Evidence for Association of β-Defensin Genomic Copy Number with HIV Susceptibility, HIV Load during Clinical Latency, or Progression to AIDS.
Abujaber R., Shea P.R., McLaren P.J., Lakhi S., Gilmour J., Allen S., Fellay J., Hollox E.J., IAVI Africa HIV Prevention Partnership Swiss HIV Cohort Study, 2017/01. Annals of human genetics, 81 (1) pp. 27-34. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_0C137198D58A]
2016
 
Médecine génomique : les enjeux de l’information en pratique clinique [Genomic medicine : the challenges of information in clinical practice]
Guessous I., Mooser V., Fellay J., Bochud M., Simeoni U., Unger S., Waeber G., Cornuz J., 2016/11/02. Revue medicale suisse, 12 (537) pp. 1838-1844. Peer-reviewed.
[Pmid][serval:BIB_68ED499361E8]
 
Determinants of HIV-1 broadly neutralizing antibody induction.
Rusert P., Kouyos R.D., Kadelka C., Ebner H., Schanz M., Huber M., Braun D.L., Hozé N., Scherrer A., Magnus C. et al., 2016/11. Nature medicine, 22 (11) pp. 1260-1267. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E6B22356AA9D]
A privacy-preserving solution for compressed storage and selective retrieval of genomic data
Zhicong Huang, Erman Ayday, Huang Lin, Aiyar Raeka, Adam Molyneaux, Zhenyu Xu, Jacques Fellay, Steinmetz Lars, Jean-Pierre Hubaux, 2016/10. Genome Research pp. gr.
[DOI][serval:BIB_68E0AD6E8219]
 
Familial segregation of group B streptococcal infection in a consanguineous kindred.
Licciardi F., Montin D., Versace A., Migliore G., Tzialla C., Fellay J., Borghesi A., 2016/10. International journal of infectious diseases, 51 pp. 22-24. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_FB8F0BC758F9]
Exome Sequencing Reveals Primary Immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis
Asgari Samira, McLaren Paul J., Peake Jane, Wong Melanie, Wong Richard, Bartha Istvan, Francis Joshua R., Abarca Katia, Gelderman Kyra A., Agyeman Philipp et al., 2016/09/20. Frontiers in Immunology, 7.
[DOI][WoS][Pmid][serval:BIB_64A265954910]
 
Standardized Whole-Blood Transcriptional Profiling Enables the Deconvolution of Complex Induced Immune Responses.
Urrutia A., Duffy D., Rouilly V., Posseme C., Djebali R., Illanes G., Libri V., Albaud B., Gentien D., Piasecka B. et al., 2016/09/06. Cell reports, 16 (10) pp. 2777-2791. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_5EC5E6043FB7]
Identification of Siglec-1 null individuals infected with HIV-1
Martinez-Picado Javier, McLaren Paul J., Erkizia Itziar, Martin Maureen P., Benet Susana, Rotger Margalida, Dalmau Judith, Ouchi Dan, Wolinsky Steven M., Penugonda Sudhir et al., 2016/08/11. Nature Communications, 7 p. 12412.
[URN][DOI][WoS][Pmid][serval:BIB_4B8F8F9C5D9A]
Privacy-preserving genomic testing in the clinic: a model using HIV treatment.
McLaren P.J., Raisaro J.L., Aouri M., Rotger M., Ayday E., Bartha I., Delgado M.B., Vallet Y., Günthard H.F., Cavassini M. et al., 2016/08. Genetics in medicine, 18 (8) pp. 814-822. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_C52D051D158A]
Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis Pneumonia.
An P., Penugonda S., Thorball C.W., Bartha I., Goedert J.J., Donfield S., Buchbinder S., Binns-Roemer E., Kirk G.D., Zhang W. et al., 2016/03. PLoS genetics, 12 (3) pp. e1005921. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_ABF6E817F8F2]
Contribution of Genetic Background and Clinical Risk Factors to Low-Trauma Fractures in Human Immunodeficiency Virus (HIV)-Positive Persons: The Swiss HIV Cohort Study.
Junier T., Rotger M., Biver E., Ledergerber B., Barceló C., Bartha I., Kovari H., Schmid P., Fux C., Bernasconi E. et al., 2016. Open Forum Infectious Diseases, 3 (2) pp. ofw101. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_F88B7CFA1164]
2015
 
The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome.
Bartha I., Rausell A., McLaren P.J., Mohammadi P., Tardaguila M., Chaturvedi N., Fellay J., Telenti A., 2015/12. PLoS computational biology, 11 (12) pp. e1004647. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_CB7E07FC1F05]
 
Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load.
McLaren P.J., Coulonges C., Bartha I., Lenz T.L., Deutsch A.J., Bashirova A., Buchbinder S., Carrington M.N., Cossarizza A., Dalmau J. et al., 2015/11/24. Proceedings of the National Academy of Sciences of the United States of America, 112 (47) pp. 14658-14663. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_2A6736196FCC]
 
Amino Acid Variation in HLA Class II Proteins Is a Major Determinant of Humoral Response to Common Viruses.
Hammer C., Begemann M., McLaren P.J., Bartha I., Michel A., Klose B., Schmitt C., Waterboer T., Pawlita M., Schulz T.F. et al., 2015/11/05. American journal of human genetics, 97 (5) pp. 738-743. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_E2708B2CF397]
 
Privacy in the Genomic Era.
Naveed M., Ayday E., Clayton E.W., Fellay J., Gunter C.A., Hubaux J.P., Malin B.A., Wang X., 2015/09. ACM computing surveys, 48 (1) pp. 1-44. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_1EF96AAD507C]
 
GenoGuard: Protecting Genomic Data against Brute-Force Attacks
Huang Zhicong, Ayday Erman, Fellay Jacques, Hubaux Jean-Pierre, Juels Ari, 2015/05., IEEE Symposium on Security and Privacy SP dans 2015 IEEE Symposium on Security and Privacy, IEEE.
[DOI][WoS][serval:BIB_CBC425917B1F]
 
Quantifying Genomic Privacy via Inference Attack with High-Order SNV Correlations
Samani Sahel Shariati, Huang Zhicong, Ayday Erman, Elliot Mark, Fellay Jacques, Hubaux Jean-Pierre, Kutalik Zoltan, 2015/05., IEEE Security and Privacy Workshops (SPW) dans 2015 IEEE Security and Privacy Workshops, IEEE.
[DOI][WoS][serval:BIB_DB40226265C6]
 
Human genetic variation in HIV disease: beyond genome-wide association studies.
McLaren P.J., Fellay J., 2015/03. Current opinion in HIV and AIDS, 10 (2) pp. 110-115. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_B2A1E118C719]
 
Adaptation on a genomic scale
István Bartha, Jacques Fellay, 2015/02. eLife, 4.
[DOI][serval:BIB_E569995A7FFD]
Opportunistic testing for urogenital infection with Chlamydia trachomatis in south-western Switzerland, 2012 : a feasibility study
Bally F., Quach A., Greub G., Jaton K., Petignat C., Ambord C., Fellay J., Masserey E., Spencer B., 2015. Euro Surveillance : Bulletin Européen Sur Les Maladies Transmissibles = European Communicable Disease Bulletin, 20 (9) pp. pii21051. Peer-reviewed.
[URN][WoS][Pmid][serval:BIB_6344F00DD1DC]
The Interplay Between Host Genetic Variation, Viral Replication, and Microbial Translocation in Untreated HIV-Infected Individuals.
Perkins M.R., Bartha I., Timmer J.K., Liebner J.C., Wollinsky D., Günthard H.F., Hauser C., Bernasconi E., Hoffmann M., Calmy A. et al., 2015. Journal of Infectious Diseases, 212 (4) pp. 578-584. Peer-reviewed.
[URN][DOI][Pmid][serval:BIB_99177D05FBA8]
2014
 
Heterozygous gene truncation delineates the human haploinsufficient genome
Bartha István, Rausell Antonio, McLaren Paul, Tardaguila Manuel, Mohammadi Pejman, Chaturvedi Nimisha, Fellay Jacques, Telenti Amalio, 2014/10..
[DOI][serval:BIB_AC2E4AFEAB20]
 
Analysis of stop-gain and frameshift variants in human innate immunity genes
Antonio Rausell, Pejman Mohammadi, Paul J McLaren, Ioannis Xenarios, Jacques Fellay, Amalio Telenti, 2014/03..
[DOI][serval:BIB_5D3EEFE8ABA0]
A Novel Acute Retroviral Syndrome Severity Score Predicts the Key Surrogate Markers for HIV-1 Disease Progression.
Braun D.L., Kouyos R., Oberle C., Grube C., Joos B., Fellay J., McLaren P.J., Kuster H., Günthard H.F., 2014. PLoS One, 9 (12) pp. e114111.
[URN][DOI][WoS][Pmid][serval:BIB_8FDD701E0789]
Analysis of stop-gain and frameshift variants in human innate immunity genes.
Rausell A., Mohammadi P., McLaren P.J., Bartha I., Xenarios I., Fellay J., Telenti A., 2014. Plos Computational Biology, 10 (7) pp. e1003757. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_238AF5BFDF14]
 
Co-trimoxazole prophylaxis is associated with reduced risk of incident tuberculosis in participants in the Swiss HIV Cohort Study.
Hasse B., Walker A.S., Fehr J., Furrer H., Hoffmann M., Battegay M., Calmy A., Fellay J., Di Benedetto C., Weber R. et al., 2014. Antimicrobial Agents and Chemotherapy, 58 (4) pp. 2363-2368. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_589B67538683]
Disentangling human tolerance and resistance against HIV.
Regoes R.R., McLaren P.J., Battegay M., Bernasconi E., Calmy A., Günthard H.F., Hoffmann M., Rauch A., Telenti A., Fellay J. et al., 2014. Plos Biology, 12 (9) pp. e1001951. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_7B977B8D6294]
Dynamics of HIV latency and reactivation in a primary CD4+ T cell model.
Mohammadi P., di Iulio J., Muñoz M., Martinez R., Bartha I., Cavassini M., Thorball C., Fellay J., Beerenwinkel N., Ciuffi A. et al., 2014. Plos Pathogens, 10 (5) pp. e1004156.
[URN][DOI][WoS][Pmid][serval:BIB_041201EF7CC4]
GuavaH: a compendium of host genomic data in HIV biology and disease.
Bartha I., McLaren P.J., Ciuffi A., Fellay J., Telenti A., 2014. Retrovirology, 11 p. 6. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_DBA77608FC4F]
 
HLA class I and KIR genes do not protect against HIV type 1 infection in highly exposed uninfected individuals with hemophilia A.
Vince N., Bashirova A.A., Lied A., Gao X., Dorrell L., McLaren P.J., Fellay J., Carrington M., 2014. Journal of Infectious Diseases, 210 (7) pp. 1047-1051. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_C899E0375C87]
LILRB2 interaction with HLA class I correlates with control of HIV-1 infection.
Bashirova A.A., Martin-Gayo E., Jones D.C., Qi Y., Apps R., Gao X., Burke P.S., Taylor C.J., Rogich J., Wolinsky S. et al., 2014. Plos Genetics, 10 (3) pp. e1004196. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_1F2D96A5F62C]
 
Médecine génomique et Maladies infectieuses [Genomic medicine and infectious diseases].
Fellay J., 2014. Praxis, 103 (10) pp. 587-590. Peer-reviewed.
[DOI][Pmid][serval:BIB_6D264BE046B9]
2013
A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control.
Bartha I., Carlson J.M., Brumme C.J., McLaren P.J., Brumme Z.L., John M., Haas D.W., Martinez-Picado J., Dalmau J., López-Galíndez C. et al., 2013. eLIFE, 2 pp. e01123. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_AD72A6E486EC]
A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A.
Lane J., McLaren P.J., Dorrell L., Shianna K.V., Stemke A., Pelak K., Moore S., Oldenburg J., Alvarez-Roman M.T., Angelillo-Scherrer A. et al., 2013. Human Molecular Genetics, 22 (9) pp. 1903-1910.
[URN][DOI][WoS][Pmid][serval:BIB_274A16CCE410]
Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls.
McLaren P.J., Coulonges C., Ripke S., van den Berg L., Buchbinder S., Carrington M., Cossarizza A., Dalmau J., Deeks S.G., Delaneau O. et al., 2013. Plos Pathogens, 9 (7) pp. e1003515.
[URN][DOI][WoS][Pmid][serval:BIB_54E83C2C9FA1]
Contribution of genetic background, traditional risk factors, and HIV-related factors to coronary artery disease events in HIV-positive persons.
Rotger M., Glass T.R., Junier T., Lundgren J., Neaton J.D., Poloni E.S., van 't Wout A.B., Lubomirov R., Colombo S., Martinez R. et al., 2013. Clinical Infectious Diseases, 57 (1) pp. 112-121. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_FF946CC0ABE7]
 
European genetic diversity and susceptibility to pathogens.
McLaren P.J., Fellay J., Telenti A., 2013. Human Heredity, 76 (3-4) pp. 187-193.
[DOI][WoS][Pmid][serval:BIB_E673562BD973]
 
Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease.
Kulkarni S., Qi Y., O'huigin C., Pereyra F., Ramsuran V., McLaren P., Fellay J., Nelson G., Chen H., Liao W. et al., 2013. Proceedings of the National Academy of Sciences of the United States of America, 110 (51) pp. 20705-20710. Peer-reviewed.
[DOI][WoS][Pmid][serval:BIB_4AC663721D54]
 
Host Genetics and Genomics
Jacques Fellay, Paul McLaren, 2013. 9.
[DOI][serval:BIB_4F24E531FE2E]
Influence of HLA-C expression level on HIV control.
Apps R., Qi Y., Carlson J.M., Chen H., Gao X., Thomas R., Yuki Y., Del Prete G.Q., Goulder P., Brumme Z.L. et al., 2013. Science, 340 (6128) pp. 87-91. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_F83E60D4E8F2]
 
Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data
Ayday Erman, Raisaro Jean Louis, McLaren Paul J, Fellay Jacques, Hubaux Jean-Pierre, 2013. dans Proceedings of the 2013 USENIX Conference on Safety, Security, Privacy and Interoperability of Health Information Technologies. Peer-reviewed.
[serval:BIB_048635477FF8]
2012
 
Genetic Associations with Resistance to HIV-1 Infection, Viral Control and Protection Against Disease
Jacques Fellay, Amalio Telenti, 2012..
[DOI][serval:BIB_3570C39F1F06]
 
Genome-wide association study of interferon-related cytopenia in chronic hepatitis C patients.
Thompson A.J., Clark P.J., Singh A., Ge D., Fellay J., Zhu M., Zhu Q., Urban T.J., Patel K., Tillmann H.L. et al., 2012. Journal of Hepatology, 56 (2) pp. 313-319.
[DOI][WoS][Pmid][serval:BIB_A440EE63322F]
 
HLA-Bw4 identifies a population of HIV-infected patients with an increased capacity to control viral replication after structured treatment interruption.
Stern M., Czaja K., Rauch A., Rickenbach M., Günthard H.F., Battegay M., Fellay J., Hirschel B., Hess C., the Swiss HIV Cohort Study Group, 2012. HIV Medicine, 13 (10) pp. 589-595.
[DOI][WoS][Pmid][serval:BIB_3EF29371DDD7]
 
Interleukin 28B polymorphisms are the only common genetic variants associated with low-density lipoprotein cholesterol (LDL-C) in genotype-1 chronic hepatitis C and determine the association between LDL-C and treatment response.
Clark P.J., Thompson A.J., Zhu M., Vock D.M., Zhu Q., Ge D., Patel K., Harrison S.A., Urban T.J., Naggie S. et al., 2012. Journal of Viral Hepatitis, 19 (5) pp. 332-340.
[DOI][WoS][Pmid][serval:BIB_3FA49FF12D3B]
 
Role of retroviral restriction factors in the interferon-α-mediated suppression of HIV-1 in vivo.
Pillai S.K., Abdel-Mohsen M., Guatelli J., Skasko M., Monto A., Fujimoto K., Yukl S., Greene W.C., Kovari H., Rauch A. et al., 2012. Proceedings of the National Academy of Sciences of the United States of America, 109 (8) pp. 3035-3040.
[DOI][WoS][Pmid][serval:BIB_056EAA58BE10]
 
The association of genetic variants with hepatic steatosis in patients with genotype 1 chronic hepatitis C infection.
Clark P.J., Thompson A.J., Zhu Q., Vock D.M., Zhu M., Patel K., Harrison S.A., Naggie S., Ge D., Tillmann H.L. et al., 2012. Digestive Diseases and Sciences, 57 (8) pp. 2213-2221.
[DOI][WoS][Pmid][serval:BIB_F787CB97909F]
2011
 
Joint analysis of host and pathogen genomes
Bartha Istvan, Telenti Amalio, Muller Viktor, Fellay Jacques, 2011/11. dans 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW), IEEE.
[DOI][serval:BIB_7D7B148DB0CF]
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 H.F. et al., 2011/05. Hepatology, 53 (5) pp. 1446-1454. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_881A0FAEAE9A]
 
A polymorphism in the leptin gene promoter is associated with anemia in patients with HIV disease.
Vanasse G.J., Jeong J.Y., Tate J., Bathulapalli H., Anderson D., Steen H., Fleming M., Mattocks K., Telenti A., Fellay J. et al., 2011. Blood, 118 (20) pp. 5401-5408.
[DOI][WoS][Pmid][serval:BIB_6382C64D159D]
 
Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population.
Petrovski S., Fellay J., Shianna K.V., Carpenetti N., Kumwenda J., Kamanga G., Kamwendo D.D., Letvin N.L., McMichael A.J., Haynes B.F. et al., 2011. Aids, 25 (4) pp. 513-518.
[DOI][WoS][Pmid][serval:BIB_D9A7084A714B]
 
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 S.E., Martinez R., Sandler N.G., Roque A., Liebner J., Battegay M. et al., 2011. Journal of Clinical Investigation, 121 (6) pp. 2391-2400.
[DOI][WoS][Pmid][serval:BIB_E778CB95165B]
Copy number variation of KIR genes influences HIV-1 control.
Pelak K., Need A.C., Fellay J., Shianna K.V., Feng S., Urban T.J., Ge D., De Luca A., Martinez-Picado J., Wolinsky S.M. et al., 2011. Plos Biology, 9 (11) pp. e1001208.
[URN][DOI][WoS][Pmid][serval:BIB_BB5F86511479]
 
Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages.
Bol S.M., Moerland P.D., Limou S., van Remmerden Y., Coulonges C., van Manen D., Herbeck J.T., Fellay J., Sieberer M., Sietzema J.G. et al., 2011. Plos One, 6 (2) pp. e17190.
[DOI][WoS][Pmid][serval:BIB_D2509C0439AB]
 
Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure.
Lingappa J.R., Petrovski S., Kahle E., Fellay J., Shianna K., McElrath M.J., Thomas K.K., Baeten J.M., Celum C., Wald A. et al., 2011. Plos One, 6 (12) pp. e28632.
[DOI][WoS][Pmid][serval:BIB_C69D0561EF9D]
 
Hepatitis C pharmacogenetics: state of the art in 2010.
Afdhal NH, McHutchison JG, Zeuzem S, Mangia A, Pawlotsky JM, Murray JS, Shianna KV, Tanaka Y, Thomas DL, Booth DR et al., 2011/01. Hepatology.
[DOI][Pmid][serval:BIB_07098F742974]
 
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 K.V., Cirulli E.T., Casimiro D.R., Robertson M.N., Haynes B.F., Geraghty D.E., McElrath M.J., Goldstein D.B. et al., 2011. Journal of Infectious Diseases, 203 (6) pp. 773-779.
[DOI][WoS][Pmid][serval:BIB_C3E94547AE93]
 
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 D.B., Telenti A., Ioannidis J.P., 2011. American Journal of Epidemiology, 173 (11) pp. 1336-1342.
[DOI][WoS][Pmid][serval:BIB_F15047AC6337]
 
Inosine triphosphate protects against ribavirin-induced adenosine triphosphate loss by adenylosuccinate synthase function.
Hitomi Y., Cirulli E.T., Fellay J., McHutchison J.G., Thompson A.J., Gumbs C.E., Shianna K.V., Urban T.J., Goldstein D.B., 2011. Gastroenterology, 140 (4) pp. 1314-1321.
[DOI][WoS][Pmid][serval:BIB_65CEDF0CED30]
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 D.C., Telenti A., 2011. Retrovirology, 8 p. 87.
[URN][DOI][WoS][Pmid][serval:BIB_294300BCD4B7]
 
Personalized hepatitis C therapy: opportunities and pitfalls.
Rauch A., Fellay J., 2011. Expert Review of Molecular Diagnostics, 11 (2) pp. 127-129.
[DOI][WoS][Pmid][serval:BIB_09AA766652FA]
Pharmacogenomics of HIV Therapy: Summary of a Workshop Sponsored by the National Institute of Allergy and Infectious Diseases
Haas D.W., Kuritzkes D.R., Ritchie M.D., Amur S., Gage B.F., Maartens G., Masys D., Fellay J., Phillips E., Ribaudo H.J. et al., 2011. HIV Clinical Trials, 12 (5) pp. 277-285. Peer-reviewed.
[URN][DOI][WoS][Pmid][serval:BIB_910B1FE61F4E]
2010
 
Young and Early Career Investigators: Report from a Global HIV Vaccine Enterprise Working Group
Nicole Frahm, Raul Rabadan, Jonathan Fuchs, Alasdair Leslie, Yong Liu, Dan Barouch, Thumbi Ndungu, Galit Alter, Timothy Cardozo, Bhavna Chohan et al., 2010/09. Nature Precedings.
[DOI][serval:BIB_20E0F817391C]
 
How the Human Genome Can Predict Response to Hepatitis C Therapy
Thompson Alexander J., Fellay Jacques, McHutchison John G., 2010/02. Current Hepatitis Reports, 9 (1) pp. 1-8.
[DOI][serval:BIB_B3757A73D176]
 
A polymorphism in the HCP5 gene associated with HLA-B*5701 does not restrict HIV-1 in vitro.
Yoon W., Ma B.J., Fellay J., Huang W., Xia S.M., Zhang R., Shianna K.V., Liao H.X., Haynes B.F., Goldstein D.B. et al., 2010. Aids, 24 (1) pp. 155-157.
[DOI][WoS][Pmid][serval:BIB_EEF89794343D]
 
Common genetic variants do not associate with IFN-induced neutropenia in a genome-wide association study of chronic hepatitis C patients in the ideal study
Thompson A.J., Clark P.J., Singh A., Ge D., Fellay J., Sulkowski M.S., Muir A.J., Tillman H.L., Patel K., Naggie S. et al., 2010. pp. 764A-765A dans 61st Annual Meeting of the American Association for the Study of Liver Diseases, Hepatology.
[WoS][serval:BIB_683CF1215470]
 
Counteraction of HLA-C-mediated immune control of HIV-1 by Nef.
Specht Anke, Telenti Amalio, Martinez Raquel, Fellay Jacques, Bailes Elizabeth, Evans David T., Carrington Mary, Hahn Beatrice H., Goldstein David B., Kirchhoff Frank, 2010. Journal of Virology, 84 (14) pp. 7300-7311.
[DOI][WoS][Pmid][serval:BIB_826062551F47]
 
Evidence of dysregulation of dendritic cells in primary HIV infection.
Sabado R.L., O'Brien M., Subedi A., Qin L., Hu N., Taylor E., Dibben O., Stacey A., Fellay J., Shianna K.V. et al., 2010. Blood, 116 (19) pp. 3839-3852.
[DOI][WoS][Pmid][serval:BIB_CC8F6E03726E]
 
Genetic markers associated with interferon-alpha response
ARTHUR BERTELSEN, JACQUES FELLAY, DONGLIANG GE, GOLDSTEIN DAVID B, MCHUTCHISON JOHN G, MURGOLO NICHOLAS J, PING QIU, ORVILLE RALSTON II ROBERT, KEVIN SHIANNA, SIMON JASON S et al., 2010/01/01..
[serval:BIB_2C942CBF0BB1]
 
Genome wide analysis of patients from the ideal study identifies a causal role for ITPA genetic variation in ribavirin-induced hemolytic anemia
Thompson A.J., Fellay J., Ge D., Urban T., Shianna K., Sulkowski M., Muir A., Afdhal N., Jacobson I., Esteban R. et al., 2010. pp. S470 dans 5th Annual Meeting of the European Association for the Study of the Liver, Journal of Hepatology. Peer-reviewed.
[DOI][WoS][serval:BIB_1E6FE0601CAC]
 
Genome-wide association study identifies an association between ITPA gene variants and IFN-induced thrombocytopenia in chronic hepatitis C patients from the ideal study
Thompson A.J., Singh A., Fellay J., Ge D., Sulkowski M.S., Muir A.J., Tillmann H.L., Patel K., Naggie S., Shianna K. et al., 2010. pp. 362A-363A dans 61st Annual Meeting of the American Association for the Study of Liver Diseases, Hepatology.
[WoS][serval:BIB_57971896E683]
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