Jacques Fellay
EPFL SV GHI GR-FE
SV 3824 (Bâtiment SV)
Station 19
CH-1015 Lausanne
+41 21 693 18 49
+41 21 693 72 32
Local:
SV 3824
EPFL
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SV
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GR-FE
Web site: Site web: https://fellay-lab.epfl.ch
Domaines de compétences
Human genomics of infectious diseases - Immunogenetics - Virus-host interactions - Translational genomics - Personalized health
Mission
Human genetic variation plays a key role in determining individual outcomes after exposure to infectious agents. The mission of our laboratory is to contribute to a better understanding of inter-individual differences in response to infections, using a range of contemporary genomic tools. Approaches include genome-wide genotyping and association analysis, exome/genome sequencing and transcriptomics.Biography
Jacques Fellay is a medical scientist with expertise in infectious diseases and human genomics. He obtained his MD from the University of Lausanne in 2002 and his PhD from University of Utrecht. After a clinical training in infectious diseases in Switzerland and a 4-years postdoctoral fellowship at Duke University, he joined the EPFL in April 2011 with an SNF Professorship. On top of his EPFL affiliation, Jacques is also Head of Precision Medicine at the University Hospital (CHUV) in Lausanne, Group Leader at the Swiss Institute of Bioinformatics, and Co-director of the Health2030 Genome Center at Campus Biotech in Geneva.Publications
Publications Infoscience
Infoscience
Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load
Virus Evolution. 2022-04-07. DOI : 10.1093/ve/veac022.Risk of mitochondrial deletions is affected by the global secondary structure of the mitochondrial genome
2022-04-01. p. 438-439.Increased CHIP prevalence amongst people living with HIV
2022-04-01. p. 75-75.A billion-year trend of amino acid substitutions in the mitochondrial genome
2022-04-01. p. 535-535.Mitochondrial mutational spectrum in human cancers is sensitive to cellular hypoxia
2022-04-01. p. 413-414.A highly virulent variant of HIV-1 circulating in the Netherlands
Science. 2022-02-04. DOI : 10.1126/science.abk1688.Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV
Scientific Reports. 2022-01-12. DOI : 10.1038/s41598-021-04308-2.Human genomics of the humoral immune response against polyomaviruses
Virus Evolution. 2021-12-01. DOI : 10.1093/ve/veab058.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
Clinical Infectious Diseases. 2021-11-01. DOI : 10.1093/cid/ciab521.Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure
Nature Communications. 2021-10-20. DOI : 10.1038/s41467-021-25649-6.A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection
Nature Immunology. 2021-10-18. DOI : 10.1038/s41590-021-01030-z.Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption
Nature Communications. 2021-10-11. DOI : 10.1038/s41467-021-25972-y.A high-resolution HLA reference panel capturing global population diversity enables multi-ancestry fine-mapping in HIV host response
Nature Genetics. 2021-10-01. DOI : 10.1038/s41588-021-00935-7.Immunological lessons from genome-wide association studies of infections
Current Opinion In Immunology. 2021-10-01. DOI : 10.1016/j.coi.2021.03.017.Autoantibodies neutralizing type I IFNs are present in similar to 4% of uninfected individuals over 70 years old and account for similar to 20% of COVID-19 deaths
Science Immunology. 2021-08-01. DOI : 10.1126/sciimmunol.abl4340.Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma
Haematologica. 2021-08-01. DOI : 10.3324/haematol.2020.247023.Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group
Clinical Infectious Diseases. 2021-07-20. DOI : 10.1093/cid/ciab628.HIV-1 and human genetic variation
Nature Reviews Genetics. 2021-06-24. DOI : 10.1038/s41576-021-00378-0.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
Journal Of Infectious Diseases. 2021-06-15. DOI : 10.1093/infdis/jiaa695.Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link
Elife. 2021-06-01. DOI : 10.7554/eLife.67388.Revolutionizing Medical Data Sharing Using Advanced Privacy-Enhancing Technologies: Technical, Legal, and Ethical Synthesis
Journal Of Medical Internet Research. 2021-02-25. DOI : 10.2196/25120.The influence of human genetic variation on Epstein–Barr virus sequence diversity
Scientific Reports. 2021-02-25. DOI : 10.1038/s41598-021-84070-7.Blood virosphere in febrile Tanzanian children
Emerging Microbes & Infections. 2021-01-01. DOI : 10.1080/22221751.2021.1925161.The genetic architecture of complex human traits at the dawn of genomic medicine
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8464.Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles
Journal Of Extracellular Vesicles. 2021-01-01. DOI : 10.1002/jev2.12046.Genome-to-genome analysis identifies an Asian-specific variant in the gene encoding NTCP that leads to specific HBV escape mutations during chronic infection
2020-12-01. p. 316-317.Human genomics of the humoral response against polyomaviruses
2020-12-01. p. 312-313.An indel in the promoter region of NFKB1 confers protection against infection but increases risk of allergy
2020-12-01. p. 311-312.Using reference-fixed principal components to improve polygenic risk score prediction
2020-12-01. p. 134-135.Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment
Jaids-Journal Of Acquired Immune Deficiency Syndromes. 2020-12-01. DOI : 10.1097/QAI.0000000000002473.Whole-exome Sequencing for the Identification of Rare Variants in Primary Immunodeficiency Genes in Children With Sepsis: A Prospective, Population-based Cohort Study
Clinical Infectious Diseases. 2020-11-15. DOI : 10.1093/cid/ciaa290.HLA tapasin independence: broader peptide repertoire and HIV control
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2020-11-10. DOI : 10.1073/pnas.2013554117.Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART
Nature Communications. 2020-11-02. DOI : 10.1038/s41467-020-19198-7.Virosaurus A Reference to Explore and Capture Virus Genetic Diversity
Viruses-Basel. 2020-11-01. DOI : 10.3390/v12111248.Inborn errors of type I IFN immunity in patients with life-threatening COVID-19
Science. 2020-10-23. DOI : 10.1126/science.abd4570.Designing a Tanzanian Specific SNP Array Add-On to Capture Population-Specific Genetic Variations and to Improve Genotype Imputation
2020-07-01. 48th European Mathematical Genetics Meeting (EMGM), Lausanne, SWITZERLAND, Apr 16-17, 2020. p. 227-227. DOI : 10.1159/000507248.Susceptibility to infection in early life: a growing role for human genetics
Human Genetics. 2020-06-01. DOI : 10.1007/s00439-019-02109-2.Exploring the interactions between the human and viral genomes
Human Genetics. 2020-06-01. DOI : 10.1007/s00439-019-02089-3.Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland
Swiss Medical Weekly. 2020-05-30. DOI : 10.4414/smw.20295.COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation
Swiss Medical Weekly. 2020-03-19. DOI : 10.4414/smw.2020.20225.HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation
Molecular Biology And Evolution. 2020-03-01. DOI : 10.1093/molbev/msz249.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
Clinical Infectious Diseases. 2020-03-01. DOI : 10.1093/cid/ciz280.SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery
2020-01-01. 30th Medical Informatics Europe (MIE) Conference, Geneva, SWITZERLAND, Apr, 2020. p. 1161-1162. DOI : 10.3233/SHTI200345.GenoShare: Supporting Privacy-Informed Decisions for Sharing Individual-Level Genetic Data
2020-01-01. 30th Medical Informatics Europe (MIE) Conference, Geneva, SWITZERLAND, Apr, 2020. p. 238-241. DOI : 10.3233/SHTI200158.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
Journal Of Law And The Biosciences. 2020-01-01. DOI : 10.1093/jlb/lsaa010.Contact networks across ages: computational analysis of epidemiological dynamics
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-7482.Impact of Genetic and Nongenetic Factors on Body Mass Index and Waist-Hip Ratio Change in HIV-Infected Individuals Initiating Antiretroviral Therapy
Open Forum Infectious Diseases. 2020-01-01. DOI : 10.1093/ofid/ofz464.HIV host genomics in the era of effective antiretroviral therapy
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10132.Gender medicine and oncology: report and consensus of an ESMO workshop
Annals Of Oncology. 2019-12-01. DOI : 10.1093/annonc/mdz414.Systems Biology in 874 Patients with Primary Sjogren's Syndrome Indicates the Predominant Role of Interferon Alpha Compared to Interferon Gamma, Its Association with Systemic Complications, and a New Aspect of the Genetic Contribution of HLA
2019-10-01.Genome-to-genome analysis of Epstein-Barr virus infection
2019-10-01. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1365-1365.Rare variants in antiviral response genes drive severe viral respiratory infections in children
2019-10-01. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1374-1375.Human genetic determinants of chronic low-grade inflammation in the general population
2019-10-01. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1747-1748.Predicting the Occurrence of Variants in RAG1 and RAG2
Journal Of Clinical Immunology. 2019-10-01. DOI : 10.1007/s10875-019-00670-z.A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals
Microbiome. 2019-09-13. DOI : 10.1186/s40168-019-0747-x.Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes
Elife. 2019-09-03. DOI : 10.7554/eLife.42542.HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected
Jaids-Journal Of Acquired Immune Deficiency Syndromes. 2019-08-15. DOI : 10.1097/QAI.0000000000002077.Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART
Nature Communications. 2019-07-19. DOI : 10.1038/s41467-019-10884-9.Effect of Fc Receptor Genetic Diversity on HIV-1 Disease Pathogenesis
Frontiers In Immunology. 2019-05-09. DOI : 10.3389/fimmu.2019.00970.Associations between usual diet and gut microbiota composition: results from the Milieu Interieur cross-sectional study
American Journal Of Clinical Nutrition. 2019-05-01. DOI : 10.1093/ajcn/nqz029.Human genomics of acute liver failure due to hepatitis B virus infection: An exome sequencing study in liver transplant recipients
Journal Of Viral Hepatitis. 2019-02-01. DOI : 10.1111/jvh.13019.Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2019-01-15. DOI : 10.1073/pnas.1808403116.HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV control
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2019-01-15. DOI : 10.1073/pnas.1812548116.A viral vector based in vivo model of tauopathy to explore therapeutic strategies against tau pathology
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9532.Exploring on Protein-DNA interactions
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9426.HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responses
eLife. 2019. DOI : 10.7554/eLife.41930.Virucidal nanomaterials against influenza
Lausanne, EPFL, 2019. DOI : 10.5075/epfl-thesis-9114.Interferon lambda 3/4 polymorphisms are associated with AIDS-related Kaposi's sarcoma
Aids. 2018-11-28. DOI : 10.1097/QAD.0000000000002004.Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines
Genome Medicine. 2018-07-27. DOI : 10.1186/s13073-018-0568-8.Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver
Virus Evolution. 2018-05-18. DOI : 10.1093/ve/vey007.Killer cell immunoglobulin–like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1
Journal of Clinical Investigation. 2018-05-01. DOI : 10.1172/JCI98463.Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors
Nature Immunology. 2018-03-19. DOI : 10.1038/s41590-018-0049-7.Detection of novel astroviruses MLB1 and MLB2 in the sera of febrile Tanzanian children
Emerging Microbes & Infections. 2018-03-14. DOI : 10.1038/s41426-018-0025-1.Are privacy-enhancing technologies for genomic data ready for the clinic? A survey of medical experts of the Swiss HIV Cohort Study
Journal of Biomedical Informatics. 2018-03-01. DOI : 10.1016/j.jbi.2017.12.013.Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells
Science. 2018-01-05. DOI : 10.1126/science.aam8825.Visual masking deficits in schizophrenia: A view into the genetics of the disease through an endophenotype
2018. Annual meeting of the American Society of Human Genetics (ASHG), San Diego, USA, October 16-20, 2018.Genetic determinants of healthy human immune variance: from humoral response to microbiome diversity
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8955.Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen Genomes
Frontiers in Genetics. 2018. DOI : 10.3389/fgene.2018.00266.Computational and Statistical analyses of Molecular Evolution and Demography using Large-scale Sequencing Data
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8748.Genomics: a Swiss army knife to fight leprosy
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8482.On Secure Cloud Computing for Genomic Data: From Storage to Analysis
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8367.Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T Cell Decline and Per-Parasite Pathogenicity
Molecular biology and evolution. 2018. DOI : 10.1093/molbev/msx246.Differential immunodominance hierarchy of CD8+ T cell responses in HLA-B*27:05 and B*27:02-mediated control of HIV-1 infection
Journal of virology. 2018. DOI : 10.1128/JVI.01685-17.Genetics of human susceptibility to active and latent tuberculosis: present knowledge and future perspectives
The Lancet. Infectious Diseases. 2018. DOI : 10.1016/S1473-3099(17)30623-0.HLA-B*14:02-Restricted Env-Specific CD8+ T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection
Journal of virology. 2017. DOI : 10.1128/JVI.00544-17.Evaluating the Impact of Functional Genetic Variation on HIV-1 Control
The Journal of infectious diseases. 2017. DOI : 10.1093/infdis/jix470.Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges
Proceedings of the National Academy of Sciences of the United States of America. 2017. DOI : 10.1073/pnas.1714765115.Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe
Plos Biology. 2017. DOI : 10.1371/journal.pbio.2001855.Severe viral respiratory infections in children with IFIH1 loss-of-function mutations
Proceedings of the National Academy of Sciences of the United States of America. 2017. DOI : 10.1073/pnas.1704259114.SQC: Secure Quality Control for Meta-Analysis of Genome-Wide Association Studies
Bioinformatics. 2017. DOI : 10.1093/bioinformatics/btx193.Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus
Nature Genetics. 2017. DOI : 10.1038/ng.3835.Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control
PLoS Computational Biology. 2017. DOI : 10.1371/journal.pcbi.1005339.Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune Responses
Frontiers In Immunology. 2017. DOI : 10.3389/fimmu.2017.00215.No Evidence for Association of beta-Defensin Genomic Copy Number with HIV Susceptibility, HIV Load during Clinical Latency, or Progression to AIDS
Annals Of Human Genetics. 2017. DOI : 10.1111/ahg.12182.A privacy-preserving solution for compressed storage and selective retrieval of genomic data
Genome Research. 2016-10-27. DOI : 10.1101/gr.206870.116.Contribution of Genetic Background and Clinical Risk Factors to Low-Trauma Fractures in Human Immunodeficiency Virus (HIV)-Positive Persons: The Swiss HIV Cohort Study
Open Forum Infectious Diseases. 2016-04-01. DOI : 10.1093/ofid/ofw101.Privacy-enhancing technologies for medical tests using genomic data
EP2895980 ; US9536047 ; US2016224735 ; US9306443 ; US9270446 ; US2015236849 ; EP2895980 ; CN103677065 ; WO2014040964 ; US2014077757 ; EP2709028 ; TW201411310 . 2016.Exome Sequencing Reveals Primary Immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis
Frontiers In Immunology. 2016. DOI : 10.3389/fimmu.2016.00357.Multiple HCV Amino Acid Variants Associate with Interferon Lambda Polymorphism in Genotype 1a, 1b and 3a Infections
2016. 67th Annual Meeting of the American-Association-for-the-Study-of-Liver-Diseases (AASLD), Boston, MA, NOV 11-15, 2016. p. 33A-33A.Familial segregation of group B streptococcal infection in a consanguineous kindred
International Journal Of Infectious Diseases. 2016. DOI : 10.1016/j.ijid.2016.08.010.Enseignement & Phd
Enseignement
Life Sciences Engineering
Programmes doctoraux
Doctoral Program in Biotechnology and Bioengineering
Doctoral Program in Computational and Quantitative Biology
Doctorants
Hodel Flavia Aurelia Shoko, Saadat Varnosfaderanii Ali, Timonina Valeriia, Xu Zhi Ming,A dirigé les thèses EPFL de
Asgari Samira , Huang Zhicong , Naret Olivier Noël Marie , Scepanovic Petar , Thorball Christian Axel Wandall ,Cours
Genetics and genomics
La partie théorique du cours couvre la génétique classique et la génomique contemporaine. Le cours comprend également une introduction au langage de programmation R, important pour la recherche en génomique, suivie d'applications pratiques aux analyses génomiques, y compris un projet de groupe.