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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GHI
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GR-FE
Web site: Site web: https://fellay-lab.epfl.ch
Domaines de compétences
Génomique humaine des maladies infectieuses - Immunogénétique - Interactions virus-hôte - Génomique translationnelle - Santé personnalisée
Publications
Publications Infoscience
Infoscience
Associations of genetic and infectious risk factors with coronary heart disease
Elife. 2023-02-14. DOI : 10.7554/eLife.79742.Leukocyte Count and Coronary Artery Disease Events in People With Human Immunodeficiency Virus: A Longitudinal Study
Clinical Infectious Diseases. 2023-01-23. DOI : 10.1093/cid/ciad033.Combining European and US risk prediction models with polygenic risk scores to refine cardiovascular prevention: the CoLaus|PsyCoLaus Study
European Journal Of Preventive Cardiology. 2023-01-18. DOI : 10.1093/eurjpc/zwad012.Visual masking deficits in schizophrenia: a view into the genetics of the disease through an endophenotype
Translational Psychiatry. 2022-12-31. DOI : 10.1038/s41398-022-02275-4.Variability of Primary Sjogren's Syndrome Is Driven by Interferon alpha and Interferon alpha Blood Levels Are Associated With the Class II HLA-DQ Locus
Arthritis & Rheumatology. 2022-11-02. DOI : 10.1002/art.42265.The combined impact of persistent infections and human genetic variation on C-reactive protein levels
Bmc Medicine. 2022-11-01. DOI : 10.1186/s12916-022-02607-7.A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand
Nucleic Acids Research. 2022-09-21. DOI : 10.1093/nar/gkac779.Polygenic Risk Scores for Prediction of Subclinical Coronary Artery Disease in Persons Living With HIV: The Swiss HIV Cohort Study
Clinical Infectious Diseases. 2022-09-13. DOI : 10.1093/cid/ciac758.A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits
Molecular Biology And Evolution. 2022-08-03. DOI : 10.1093/molbev/msac163.A Baseline Cellular Antiviral State Is Maintained by cGAS and Its Most Frequent Naturally Occurring Variant rs610913
Journal Of Immunology. 2022-08-01. DOI : 10.4049/jimmunol.2100685.Improving polygenic prediction with genetically inferred ancestry
Human Genetics And Genomics Advances. 2022-07-14. DOI : 10.1016/j.xhgg.2022.100109.Host genomics of SARS-CoV-2 infection
European Journal Of Human Genetics. 2022-06-30. DOI : 10.1038/s41431-022-01136-4.The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2022-05-24. DOI : 10.1073/pnas.2200413119.Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group (vol 74, pg 1468, 2022)
Clinical Infectious Diseases. 2022-04-27. DOI : 10.1093/cid/ciac242.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
Frontiers In Medicine. 2022-04-15. DOI : 10.3389/fmed.2022.821776.Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load
Virus Evolution. 2022-04-07. DOI : 10.1093/ve/veac022.A polygenic risk score to predict sudden cardiac arrest in patients with cardiovascular disease
2022-04-01. p. 28-28.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.The interplay between human genetic variation, chronic inflammation and persistent infection: relevance for cardiovascular morbidity
Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9518.Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group
Clinical Infectious Diseases. 2022. DOI : 10.1093/cid/ciab628.A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection
Nature Immunology. 2022. DOI : 10.1038/s41590-021-01030-z.Telomere Length Declines in Persons With Human Immunodeficiency Virus Before Antiretroviral Therapy Start but Not After Viral Suppression: A Longitudinal Study Over >17 Years
Journal Of Infectious Diseases. 2021-12-16. DOI : 10.1093/infdis/jiab603.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.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.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.On the use of applied machine learning and digital infrastructure to leverage social media data in health and epidemiology
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8283.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.Enseignement & Phd
Enseignement
Life Sciences Engineering
Doctorants
Ait Oumelloul Mariam, Bandaru Tagore Sanketh, Saadat Varnosfaderanii Ali, Timonina Valeriia, Xu Zhi Ming,A dirigé les thèses EPFL de
Asgari Samira , Hodel Flavia Aurelia Shoko , 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. Comme la bioinformatique est devenue importante pour la recherche en génomique, le cours inclus également des applications pratiques aux analyses génomiques en Python, y compris des projets de groupe.