Jacques Fellay

Professeur associé
jacques.fellay@epfl.ch +41 21 693 18 49 http://fellay-lab.epfl.ch
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
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
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.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.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.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.Determinants of HIV-1 broadly neutralizing antibody induction
Nature Medicine. 2016. DOI : 10.1038/nm.4187.Corrigendum: Exome Sequencing reveals Primary immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis (vol 7, 357, 2016)
Frontiers In Immunology. 2016. DOI : 10.3389/fimmu.2016.00447.Identification of Siglec-1 null individuals infected with HIV-1
Nature Communications. 2016. DOI : 10.1038/ncomms12412.The Drosophila gut response to infection
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-7151.Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis Pneumonia
Plos Genetics. 2016. DOI : 10.1371/journal.pgen.1005921.Privacy-preserving genomic testing in the clinic: a model using HIV treatment
Genetics in medicine : official journal of the American College of Medical Genetics. 2016. DOI : 10.1038/gim.2015.167.Host and pathogen genomics of severe pediatric infections
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6656.Amino Acid Variation in HLA Class II Proteins Is a Major Determinant of Humoral Response to Common Viruses
American Journal Of Human Genetics. 2015. DOI : 10.1016/j.ajhg.2015.09.008.Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2015. DOI : 10.1073/pnas.1514867112.The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome
Plos Computational Biology. 2015. DOI : 10.1371/journal.pcbi.1004647.The Interplay Between Host Genetic Variation, Viral Replication, and Microbial Translocation in Untreated HIV-Infected Individuals
The Journal of infectious diseases. 2015. DOI : 10.1093/infdis/jiv089.Privacy in the Genomic Era
ACM Computing Surveys. 2015. DOI : 10.1145/2767007.Adaptation on a genomic scale
eLife. 2015. DOI : 10.7554/eLife.06193.Human genetic variation in HIV disease: beyond genome-wide association studies
Current opinion in HIV and AIDS. 2015. DOI : 10.1097/COH.0000000000000133.Quantifying Genomic Privacy via Inference Attack with High-Order SNV Correlations
2015. 2nd International Workshop on Genome Privacy and Security (in conjunction with IEEE S&P 2015), San Jose, CA, USA, May 21, 2015.GenoGuard: Protecting Genomic Data against Brute-Force Attacks
2015. 36th IEEE Symposium on Security and Privacy (S&P 2015), San Jose, CA, USA, May 18-20, 2015.GenoGuard: Protecting Genomic Data Against Brute-Force Attacks
2015Valparaíso en 02h01. Promenade d'un port à l'autre
2014Médecine génomique et Maladies infectieuses [Genomic medicine and infectious diseases]
Praxis. 2014. DOI : 10.1024/1661-8157/a001658.A Novel Acute Retroviral Syndrome Severity Score Predicts the Key Surrogate Markers for HIV-1 Disease Progression
Plos One. 2014. DOI : 10.1371/journal.pone.0114111.HLA class I and KIR genes do not protect against HIV type 1 infection in highly exposed uninfected individuals with hemophilia A
The Journal of infectious diseases. 2014. DOI : 10.1093/infdis/jiu214.Disentangling human tolerance and resistance against HIV
PLoS biology. 2014. DOI : 10.1371/journal.pbio.1001951.Practical Solutions for Protecting Individual Genomic Privacy
American Society of Human Genetics (ASHG), San Diego, CA, USA, October 2014.Dynamics of HIV Latency and Reactivation in a Primary CD4+T Cell Model
Plos Pathogens. 2014. DOI : 10.1371/journal.ppat.1004156.Analysis of Stop-Gain and Frameshift Variants in Human Innate Immunity Genes
Plos Computational Biology. 2014. DOI : 10.1371/journal.pcbi.1003757.LILRB2 Interaction with HLA Class I Correlates with Control of HIV-1 Infection
Plos Genetics. 2014. DOI : 10.1371/journal.pgen.1004196.Benzothiazinones: from a new lead to new combination therapies against Mycobacterium tuberculosis
Lausanne, EPFL, 2014. DOI : 10.5075/epfl-thesis-6239.GuavaH: a compendium of host genomic data in HIV biology and disease
Retrovirology. 2014. DOI : 10.1186/1742-4690-11-6.European genetic diversity and susceptibility to pathogens
Human heredity. 2013. DOI : 10.1159/000357758.A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control
Elife. 2013. DOI : 10.7554/eLife.01123.Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease
Proceedings Of The National Academy Of Sciences Of The United States Of America. 2013. DOI : 10.1073/pnas.1312237110.Detection of Drug-Protein Interactions with an Improved Yeast Three-Hybrid System
Lausanne, EPFL, 2013. DOI : 10.5075/epfl-thesis-5944.Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data (poster version)
USENIX Security Workshop on Health Information Technologies (HealthTech '13), Washington, DC, USA, August, 2013.A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A
Human Molecular Genetics. 2013. DOI : 10.1093/hmg/ddt033.Enseignement & Phd
Enseignement
Life Sciences Engineering