Jacques Fellay
EPFL SV GHI UPFELLAY
AAB 2 40 (Bâtiment AAB)
Station 19
1015 Lausanne
+41 21 693 18 49
+41 21 693 72 32
Local:
AAB 2 40
EPFL
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SV
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GHI
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UPFELLAY
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
Articles
2024
Paediatric Personalized Research Network Switzerland (SwissPedHealth): a joint paediatric national data stream
BMJ open. 2024. DOI : 10.1136/bmjopen-2024-091884.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
Brain, Behavior, and Immunity - Health. 2024. DOI : 10.1016/j.bbih.2024.100896.Weight, Anthropometric and Metabolic Changes After Discontinuing Antiretroviral Therapy Containing Tenofovir Alafenamide in People With HIV
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2024. DOI : 10.1093/cid/ciae189.SARS-CoV-2 brainstem encephalitis in human inherited DBR1 deficiency
Journal of Experimental Medicine. 2024. DOI : 10.1084/jem.20231725.Using viral diversity to identify HIV-1 variants under HLA-dependent selection in a systematic viral genome-wide screen
PLOS PATHOGENS. 2024. DOI : 10.1371/journal.ppat.1012385.Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection
HGG advances. 2024. DOI : 10.1016/j.xhgg.2024.100300.Loss of tolerance precedes triggering and lifelong persistence of pathogenic type I interferon autoantibodies
JOURNAL OF EXPERIMENTAL MEDICINE. 2024. DOI : 10.1084/jem.20240365.Self-reported neurocognitive complaints in the Swiss HIV Cohort Study: a viral genome-wide association study
BRAIN COMMUNICATIONS. 2024. DOI : 10.1093/braincomms/fcae188.Epistatic interaction between ERAP2 and HLA modulates HIV-1 adaptation and disease outcome in an Australian population
PLoS pathogens. 2024. DOI : 10.1371/journal.ppat.1012359.Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
American Journal Of Human Genetics. 2024. DOI : 10.1016/j.ajhg.2024.04.013.Diagnostic accuracy of a sequence-specific Mtb-DNA hybridization assay in urine: a case-control study including subclinical TB cases
Microbiology Spectrum. 2024. DOI : 10.1128/spectrum.00426-24.Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania
Scientific Reports. 2024. DOI : 10.1038/s41598-024-60001-0.Smoking changes adaptive immunity with persistent effects
Nature. 2024. DOI : 10.1038/s41586-023-06968-8.A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy
American Journal Of Human Genetics. 2024. DOI : 10.1016/j.ajhg.2023.12.013.Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19 (vol 15, 22, 2023)
Genome Medicine. 2024. DOI : 10.1186/s13073-023-01278-0.2023
Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs
Science immunology. 2023. DOI : 10.1126/sciimmunol.abp8966.The HLA-B*57:01 allele corresponds to a very large MHC haploblock likely explaining its massive effect for HIV-1 elite control
Frontiers In Immunology. 2023. DOI : 10.3389/fimmu.2023.1305856.Inborn errors of type I interferon immunity in patients with symptomatic acute hepatitis E
Hepatology. 2023. DOI : 10.1097/HEP.0000000000000701.Predicting type 2 diabetes risk before and after solid organ transplantation using polygenic scores in a Danish cohort
Frontiers In Molecular Biosciences. 2023. DOI : 10.3389/fmolb.2023.1282412.Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency
Nature. 2023. DOI : 10.1038/s41586-023-06717-x.Africa-specific human genetic variation near CHD1L associates with HIV-1 load
Nature. 2023. DOI : 10.1038/s41586-023-06370-4.Variation in African genomes linked to control of HIV
Nature. 2023. DOI : 10.1038/d41586-023-02277-2.A metagenome-wide association study of HIV disease progression in HIV controllers
Iscience. 2023. DOI : 10.1016/j.isci.2023.107214.Autoantibodies neutralizing type I IFNs underlie West Nile virus encephalitis in & SIM;40% of patients
Journal Of Experimental Medicine. 2023. DOI : 10.1084/jem.20230661.Multiancestry sex-stratified genomic associations with HIV viral load and controller status from the ICGH
Jci Insight. 2023. DOI : 10.1172/jci.insight.170068.Association of a Polygenic Risk Score With Osteoporosis in People Living With HIV: The Swiss HIV Cohort Study
Journal Of Infectious Diseases. 2023. DOI : 10.1093/infdis/jiad179.Secondary structure of the human mitochondrial genome affects formation of deletions
Bmc Biology. 2023. DOI : 10.1186/s12915-023-01606-1.Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort
Journal Of Infectious Diseases. 2023. DOI : 10.1093/infdis/jiac442.Epigenetic ageing accelerates before antiretroviral therapy and decelerates after viral suppression in people with HIV in Switzerland: a longitudinal study over 17 years
Lancet Healthy Longevity. 2023. DOI : 10.1016/S2666-7568(23)00037-5.Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19
Genome Medicine. 2023. DOI : 10.1186/s13073-023-01173-8.Back-to-Africa introductions of Mycobacterium tuberculosis as the main cause of tuberculosis in Dar es Salaam, Tanzania
Plos Pathogens. 2023. DOI : 10.1371/journal.ppat.1010893.Associations of genetic and infectious risk factors with coronary heart disease
Elife. 2023. 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. 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. DOI : 10.1093/eurjpc/zwad012.Genetic features and genomic targets of human KRAB-zinc finger proteins
Genome Research. 2023. DOI : 10.1101/gr.277722.123.2022
Visual masking deficits in schizophrenia: a view into the genetics of the disease through an endophenotype
Translational Psychiatry. 2022. 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. DOI : 10.1002/art.42265.The combined impact of persistent infections and human genetic variation on C-reactive protein levels
Bmc Medicine. 2022. 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. 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. 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. 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. DOI : 10.4049/jimmunol.2100685.Improving polygenic prediction with genetically inferred ancestry
Human Genetics And Genomics Advances. 2022. DOI : 10.1016/j.xhgg.2022.100109.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. 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. 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. DOI : 10.3389/fmed.2022.821776.Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load
Virus Evolution. 2022. DOI : 10.1093/ve/veac022.A highly virulent variant of HIV-1 circulating in the Netherlands
Science. 2022. DOI : 10.1126/science.abk1688.Increased prevalence of clonal hematopoiesis of indeterminate potential amongst people living with HIV
Scientific Reports. 2022. DOI : 10.1038/s41598-021-04308-2.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.Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations
Plos Computational Biology. 2022. DOI : 10.1371/journal.pcbi.1009628.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/ciab628.2021
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. DOI : 10.1093/infdis/jiab603.Human genomics of the humoral immune response against polyomaviruses
Virus Evolution. 2021. 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. DOI : 10.1093/cid/ciab521.Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure
Nature Communications. 2021. DOI : 10.1038/s41467-021-25649-6.Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption
Nature Communications. 2021. 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. DOI : 10.1038/s41588-021-00935-7.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. DOI : 10.1126/sciimmunol.abl4340.Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma
Haematologica. 2021. DOI : 10.3324/haematol.2020.247023.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. DOI : 10.1093/infdis/jiaa695.Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link
Elife. 2021. 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. DOI : 10.2196/25120.The influence of human genetic variation on Epstein–Barr virus sequence diversity
Scientific Reports. 2021. DOI : 10.1038/s41598-021-84070-7.Dissemination of Mycobacterium tuberculosis is associated to a SIGLEC1 null variant that limits antigen exchange via trafficking extracellular vesicles
Journal Of Extracellular Vesicles. 2021. DOI : 10.1002/jev2.12046.Blood virosphere in febrile Tanzanian children
Emerging Microbes & Infections. 2021. DOI : 10.1080/22221751.2021.1925161.2020
Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment
Jaids-Journal Of Acquired Immune Deficiency Syndromes. 2020. 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. 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. DOI : 10.1073/pnas.2013554117.Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART
Nature Communications. 2020. DOI : 10.1038/s41467-020-19198-7.Virosaurus A Reference to Explore and Capture Virus Genetic Diversity
Viruses-Basel. 2020. DOI : 10.3390/v12111248.Inborn errors of type I IFN immunity in patients with life-threatening COVID-19
Science. 2020. DOI : 10.1126/science.abd4570.Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland
Swiss Medical Weekly. 2020. DOI : 10.4414/smw.20295.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. DOI : 10.1093/cid/ciz280.HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation
Molecular Biology And Evolution. 2020. DOI : 10.1093/molbev/msz249.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. DOI : 10.1093/ofid/ofz464.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. DOI : 10.1093/jlb/lsaa010.2019
Predicting the Occurrence of Variants in RAG1 and RAG2
Journal Of Clinical Immunology. 2019. 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. DOI : 10.1186/s40168-019-0747-x.Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes
Elife. 2019. DOI : 10.7554/eLife.42542.HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected
Jaids-Journal Of Acquired Immune Deficiency Syndromes. 2019. DOI : 10.1097/QAI.0000000000002077.Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART
Nature Communications. 2019. DOI : 10.1038/s41467-019-10884-9.Associations between usual diet and gut microbiota composition: results from the Milieu Interieur cross-sectional study
American Journal Of Clinical Nutrition. 2019. 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. DOI : 10.1111/jvh.13019.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. DOI : 10.1073/pnas.1812548116.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. DOI : 10.1073/pnas.1808403116.HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responses
eLife. 2019. DOI : 10.7554/eLife.41930.2018
Interferon lambda 3/4 polymorphisms are associated with AIDS-related Kaposi's sarcoma
Aids. 2018. 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. 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. 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. DOI : 10.1172/JCI98463.Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors
Nature Immunology. 2018. 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. 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. DOI : 10.1016/j.jbi.2017.12.013.Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells
Science. 2018. DOI : 10.1126/science.aam8825.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.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)30623-0.2017
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.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.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.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.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.Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control
PLoS Computational Biology. 2017. DOI : 10.1371/journal.pcbi.1005339.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.SQC: Secure Quality Control for Meta-Analysis of Genome-Wide Association Studies
Bioinformatics. 2017. DOI : 10.1093/bioinformatics/btx193.Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune Responses
Frontiers In Immunology. 2017. DOI : 10.3389/fimmu.2017.00215.2016
A privacy-preserving solution for compressed storage and selective retrieval of genomic data
Genome Research. 2016. 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. DOI : 10.1093/ofid/ofw101.Determinants of HIV-1 broadly neutralizing antibody induction
Nature Medicine. 2016. DOI : 10.1038/nm.4187.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.Identification of Siglec-1 null individuals infected with HIV-1
Nature Communications. 2016. DOI : 10.1038/ncomms12412.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.Exome Sequencing Reveals Primary Immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis
Frontiers In Immunology. 2016. DOI : 10.3389/fimmu.2016.00357.Familial segregation of group B streptococcal infection in a consanguineous kindred
International Journal Of Infectious Diseases. 2016. DOI : 10.1016/j.ijid.2016.08.010.2015
Human genetic variation in HIV disease: beyond genome-wide association studies
Current opinion in HIV and AIDS. 2015. DOI : 10.1097/COH.0000000000000133.Adaptation on a genomic scale
eLife. 2015. DOI : 10.7554/eLife.06193.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.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.The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome
Plos Computational Biology. 2015. DOI : 10.1371/journal.pcbi.1004647.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.Privacy in the Genomic Era
ACM Computing Surveys. 2015. DOI : 10.1145/2767007.2014
Dynamics of HIV Latency and Reactivation in a Primary CD4+T Cell Model
Plos Pathogens. 2014. DOI : 10.1371/journal.ppat.1004156.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.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.Médecine génomique et Maladies infectieuses [Genomic medicine and infectious diseases]
Praxis. 2014. DOI : 10.1024/1661-8157/a001658.Disentangling human tolerance and resistance against HIV
PLoS biology. 2014. DOI : 10.1371/journal.pbio.1001951.GuavaH: a compendium of host genomic data in HIV biology and disease
Retrovirology. 2014. DOI : 10.1186/1742-4690-11-6.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.1004196.2013
Association Study of Common Genetic Variants and HIV-1 Acquisition in 6,300 Infected Cases and 7,200 Controls
PLoS Pathogens. 2013. DOI : 10.1371/journal.ppat.1003515.Contribution of Genetic Background, Traditional Risk Factors, and HIV-Related Factors to Coronary Artery Disease Events in HIV-Positive Persons
Clinical Infectious Diseases. 2013. DOI : 10.1093/cid/cit196.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.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.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.Influence of HLA-C Expression Level on HIV Control
Science. 2013. DOI : 10.1126/science.1232685.2012
The association of genetic variants with hepatic steatosis in patients with genotype 1 chronic hepatitis C infection
Digestive diseases and sciences. 2012. DOI : 10.1007/s10620-012-2171-y.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
Journal of viral hepatitis. 2012. DOI : 10.1111/j.1365-2893.2011.01553.x.HLA-Bw4 identifies a population of HIV-infected patients with an increased capacity to control viral replication after structured treatment interruption
HIV Medicine. 2012. DOI : 10.1111/j.1468-1293.2012.01019.x.Role of retroviral restriction factors in the interferon- -mediated suppression of HIV-1 in vivo
Proceedings of the National Academy of Sciences. 2012. DOI : 10.1073/pnas.1111573109.2011
Copy Number Variation of KIR Genes Influences HIV-1 Control
Plos Biology. 2011. DOI : 10.1371/journal.pbio.1001208.A polymorphism in the leptin gene promoter is associated with anemia in patients with HIV disease
Blood. 2011. DOI : 10.1182/blood-2011-06-362194.Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population
AIDS. 2011. DOI : 10.1097/QAD.0b013e328343817b.Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints
Retrovirology. 2011. DOI : 10.1186/1742-4690-8-87.Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages
PloS One. 2011. DOI : 10.1371/journal.pone.0017190.Inosine triphosphate protects against ribavirin-induced adenosine triphosphate loss by adenylosuccinate synthase function
Gastroenterology. 2011. DOI : 10.1053/j.gastro.2010.12.038.Impact of Phenotype Definition on Genome-Wide Association Signals: Empirical Evaluation in Human Immunodeficiency Virus Type 1 Infection
American Journal of Epidemiology. 2011. DOI : 10.1093/aje/kwr024.Estimating the net contribution of IL28B variation to spontaneous hepatitis C virus clearance
Hepatology. 2011. DOI : 10.1002/hep.24263.Personalized hepatitis C therapy: opportunities and pitfalls
Expert review of molecular diagnostics. 2011. DOI : 10.1586/erm.10.116.Host genetic determinants of T cell responses to the MRKAd5 HIV-1 gag/pol/nef vaccine in the step trial
The Journal of infectious diseases. 2011. DOI : 10.1093/infdis/jiq125.Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque
The Journal of clinical investigation. 2011. DOI : 10.1172/JCI45235.2010
Host determinants of HIV-1 control in African Americans
The Journal of infectious diseases. 2010. DOI : 10.1086/651382.Young and Early Career Investigators: Report from a Global HIV Vaccine Enterprise Working Group
Nature Precedings. 2010. DOI : 10.1038/npre.2010.4800.2.ITPA gene variants protect against anaemia in patients treated for chronic hepatitis C
Nature. 2010. DOI : 10.1038/nature08825.Variants in the ITPA gene protect against ribavirin-induced hemolytic anemia and decrease the need for ribavirin dose reduction
Gastroenterology. 2010. DOI : 10.1053/j.gastro.2010.06.016.Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals
PLoS pathogens. 2010. DOI : 10.1371/journal.ppat.1000781.Interleukin-28B polymorphism improves viral kinetics and is the strongest pretreatment predictor of sustained virologic response in genotype 1 hepatitis C virus
Gastroenterology. 2010. DOI : 10.1053/j.gastro.2010.04.013.How the human genome can predict response to Hepatitis C therapy
Current Hepatitis Reports. 2010. DOI : 10.1007/s11901-010-0029-3.A polymorphism in the HCP5 gene associated with HLA-B*5701 does not restrict HIV-1 in vitro
AIDS. 2010. DOI : 10.1097/QAD.0b013e32833202f5.IL28B genotype is associated with differential expression of intrahepatic interferon-stimulated genes in patients with chronic hepatitis C
Hepatology. 2010. DOI : 10.1002/hep.23912.Counteraction of HLA-C-mediated immune control of HIV-1 by Nef
Journal of virology. 2010. DOI : 10.1128/JVI.00619-10.Role of human leukocyte antigen class I alleles in progressive multifocal leukoencephalopathy
Journal of neurovirology. 2010. DOI : 10.3109/13550280903552438.The characterization of twenty sequenced human genomes
PLoS genetics. 2010. DOI : 10.1371/journal.pgen.1001111.Hepatitis C trials that combine investigational agents with pegylated interferon should be stratified by interleukin-28B genotype
Hepatology. 2010. DOI : 10.1002/hep.23826.Evidence of dysregulation of dendritic cells in primary HIV infection
Blood. 2010. DOI : 10.1182/blood-2010-03-273763.2009
The Duffy antigen receptor for chemokines null promoter variant does not influence HIV-1 acquisition or disease progression
Cell host & microbe. 2009. DOI : 10.1016/j.chom.2009.04.011.CCL3L1 and HIV/AIDS susceptibility
Nature medicine. 2009. DOI : 10.1038/nm1009-1110.Common genetic variation and the control of HIV-1 in humans
PLoS genetics. 2009. DOI : 10.1371/journal.pgen.1000791.Challenges facing young investigators
IAVI report. 2009.HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C
Nature genetics. 2009. DOI : 10.1038/ng.486.X chromosomal variation is associated with slow progression to AIDS in HIV-1-infected women
American journal of human genetics. 2009. DOI : 10.1016/j.ajhg.2009.07.013.Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance
Nature. 2009. DOI : 10.1038/nature08309.2008
The HCP5 single-nucleotide polymorphism: a simple screening tool for prediction of hypersensitivity reaction to abacavir
The Journal of infectious diseases. 2008. DOI : 10.1086/591184.WGAViewer: software for genomic annotation of whole genome association studies
Genome research. 2008. DOI : 10.1101/gr.071571.107.2007
A whole-genome association study of major determinants for host control of HIV-1
Science. 2007. DOI : 10.1126/science.1143767.Host genetics: fine-tuning innate signaling
Current biology. 2007. DOI : 10.1016/j.cub.2007.04.052.Adverse events to antiretrovirals in the Swiss HIV Cohort Study: effect on mortality and treatment modification
Antiviral therapy. 2007.Efficacy and safety of universal valganciclovir prophylaxis combined with a tacrolimus/mycophenolate-based regimen in kidney transplantation
Swiss medical weekly. 2007. DOI : 10.4414/smw.2007.11961.2006
HIV and solid organ transplantation: the Swiss experience
Swiss medical weekly. 2006. DOI : 10.4414/smw.2006.11356.2005
Variations of CYP3A activity induced by antiretroviral treatment in HIV-1 infected patients
European journal of clinical pharmacology. 2005. DOI : 10.1007/s00228-004-0855-8.Treatment of cytomegalovirus infection or disease in solid organ transplant recipients with valganciclovir
American journal of transplantation. 2005. DOI : 10.1111/j.1600-6143.2005.00936.x.2004
CYP3A activity measured by the midazolam test is not related to 3435 C >T polymorphism in the multiple drug resistance transporter gene
Pharmacogenetics. 2004. DOI : 10.1097/00008571-200404000-00005.2003
Population pharmacokinetics and effects of efavirenz in patients with human immunodeficiency virus infection
Clinical pharmacology and therapeutics. 2003. DOI : 10.1067/mcp.2003.22.2002
Multidrug resistance and response to antiretroviral treatment
Lancet. 2002. DOI : 10.1016/S0140-6736(02)08922-5.Response to antiretroviral treatment in HIV-1-infected individuals with allelic variants of the multidrug resistance transporter 1: a pharmacogenetics study
Lancet. 2002. DOI : 10.1016/S0140-6736(02)07276-8.HIV lipoatrophy and mosquito bites
Clinical infectious diseases. 2002. DOI : 10.1086/323014.2001
Prevalence of adverse events associated with potent antiretroviral treatment: Swiss HIV Cohort Study
Lancet. 2001. DOI : 10.1016/S0140-6736(01)06413-3.Reviews
2022
Host genomics of SARS-CoV-2 infection
European Journal Of Human Genetics. 2022. DOI : 10.1038/s41431-022-01136-4.2021
Immunological lessons from genome-wide association studies of infections
Current Opinion In Immunology. 2021. DOI : 10.1016/j.coi.2021.03.017.HIV-1 and human genetic variation
Nature Reviews Genetics. 2021. DOI : 10.1038/s41576-021-00378-0.2020
Exploring the interactions between the human and viral genomes
Human Genetics. 2020. DOI : 10.1007/s00439-019-02089-3.Susceptibility to infection in early life: a growing role for human genetics
Human Genetics. 2020. DOI : 10.1007/s00439-019-02109-2.2019
Gender medicine and oncology: report and consensus of an ESMO workshop
Annals Of Oncology. 2019. DOI : 10.1093/annonc/mdz414.Effect of Fc Receptor Genetic Diversity on HIV-1 Disease Pathogenesis
Frontiers In Immunology. 2019. DOI : 10.3389/fimmu.2019.00970.2013
European genetic diversity and susceptibility to pathogens
Human heredity. 2013. DOI : 10.1159/000357758.2010
Host genetics and HIV-1: the final phase?
PLoS pathogens. 2010. DOI : 10.1371/journal.ppat.1001033.2009
Host genetics influences on HIV type-1 disease
Antiviral therapy. 2009. DOI : 10.3851/IMP1253.2006
[HIV-AIDS: answers to new questions]
Revue médicale suisse. 2006.Conference papers
2024
The impact of human genetics on Mycobacterium tuberculosis intra-host evolution
2024. 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, SCOTLAND, JUN 10-13, 2023. p. 346 - 346.Prevalence of actionable pharmacogenetic variants in a Swiss hospital cohort
2024. 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, SCOTLAND, JUN 10-13, 2023. p. 700 - 700.Inborn errors of type I interferon immunity in patients with severe acute hepatitis E
2024. 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, SCOTLAND, JUN 10-13, 2023. p. 451 - 451.Prevalence of clonal hematopoiesis in people living with HIV
2024. 56th Annual Conference of the European-Society-of-Human-Genetics (ESHG), Glasgow, SCOTLAND, JUN 10-13, 2023. p. 443 - 444.2023
Inborn Errors of Type I Interferon Immunity in Patients with Severe Acute Hepatitis E
2023. p. 14S - 14S.A polygenic risk score improves the prediction of cardiovascular risk associated with obstructive sleep-apnoea
2023. 55th European-Society-of-Human-Genetics (ESHG) Conference, Vienna, AUSTRIA, JUN 11-14, 2022. p. 145 - 146.A polygenic risk score to predict sudden cardiac arrest in patients with cardiovascular disease
2023. 55th European-Society-of-Human-Genetics (ESHG) Conference, Vienna, AUSTRIA, JUN 11-14, 2022. p. 691 - 691.Host genomic susceptibility to severe respiratory syncytial virus infection
2023. 55th European-Society-of-Human-Genetics (ESHG) Conference, Vienna, AUSTRIA, JUN 11-14, 2022. p. 163 - 164.2022
A billion-year trend of amino acid substitutions in the mitochondrial genome
2022. p. 535 - 535.Risk of mitochondrial deletions is affected by the global secondary structure of the mitochondrial genome
2022. p. 438 - 439.Mitochondrial mutational spectrum in human cancers is sensitive to cellular hypoxia
2022. p. 413 - 414.A polygenic risk score to predict sudden cardiac arrest in patients with cardiovascular disease
2022. 50th European Mathematical Genetics Meeting (EMGM), Univ Cambridge, MRC Biostatist Unit, Cambridge, ENGLAND, April 21-22, 2022. p. 28 - 28.Increased CHIP prevalence amongst people living with HIV
2022. p. 75 - 75.2020
Using reference-fixed principal components to improve polygenic risk score prediction
2020. p. 134 - 135.Human genomics of the humoral response against polyomaviruses
2020. p. 312 - 313.An indel in the promoter region of NFKB1 confers protection against infection but increases risk of allergy
2020. p. 311 - 312.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. p. 316 - 317.Designing a Tanzanian Specific SNP Array Add-On to Capture Population-Specific Genetic Variations and to Improve Genotype Imputation
2020. 48th European Mathematical Genetics Meeting (EMGM), Lausanne, SWITZERLAND, Apr 16-17, 2020. p. 227 - 227. DOI : 10.1159/000507248.GenoShare: Supporting Privacy-Informed Decisions for Sharing Individual-Level Genetic Data
2020. 30th Medical Informatics Europe (MIE) Conference, Geneva, SWITZERLAND, Apr, 2020. p. 238 - 241. DOI : 10.3233/SHTI200158.SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery
2020. 30th Medical Informatics Europe (MIE) Conference, Geneva, SWITZERLAND, Apr, 2020. p. 1161 - 1162. DOI : 10.3233/SHTI200345.2019
Genome-to-genome analysis of Epstein-Barr virus infection
2019. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1365 - 1365.Human genetic determinants of chronic low-grade inflammation in the general population
2019. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1747 - 1748.Rare variants in antiviral response genes drive severe viral respiratory infections in children
2019. 52nd Conference of the European-Society-of-Human-Genetics (ESHG), Gothenburg, SWEDEN, Jun 15-18, 2019. p. 1374 - 1375.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
2019.2018
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, 2018.2016
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.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. p. 447 - 462. DOI : 10.1109/SP.2015.34.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. p. 32 - 40. DOI : 10.1109/SPW.2015.21.GenoGuard: Protecting Genomic Data Against Brute-Force Attacks
20152014
Practical Solutions for Protecting Individual Genomic Privacy
American Society of Human Genetics (ASHG), San Diego, CA, USA, October 2014.2013
Privacy-Preserving Computation of Disease Risk by Using Genomic, Clinical, and Environmental Data
2013. USENIX Security Workshop on Health Information Technologies (HealthTech '13), Washington, DC, USA, August.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.Theses
2023
Host-Pathogen Interactions Through the Genomic Lens
Lausanne, EPFL, 2023. DOI : 10.5075/epfl-thesis-10351.2022
The interplay between human genetic variation, chronic inflammation and persistent infection: relevance for cardiovascular morbidity
Lausanne, EPFL, 2022. DOI : 10.5075/epfl-thesis-9518.2021
The genetic architecture of complex human traits at the dawn of genomic medicine
Lausanne, EPFL, 2021. DOI : 10.5075/epfl-thesis-8464.2020
HIV host genomics in the era of effective antiretroviral therapy
Lausanne, EPFL, 2020. DOI : 10.5075/epfl-thesis-10132.2018
On Secure Cloud Computing for Genomic Data: From Storage to Analysis
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8367.Genetic determinants of healthy human immune variance: from humoral response to microbiome diversity
Lausanne, EPFL, 2018. DOI : 10.5075/epfl-thesis-8955.2016
Host and pathogen genomics of severe pediatric infections
Lausanne, EPFL, 2016. DOI : 10.5075/epfl-thesis-6656.Enseignement & Phd
Enseignement
Life Sciences Engineering
Doctorants
Ait Oumelloul Mariam, Fournier Lisa Mathilde Julia, Saadat Varnosfaderanii Ali, Tang Simon Sie-Mon, Timonina Valeriia,A dirigé les thèses EPFL de
Asgari Samira , Hodel Flavia Aurelia Shoko , Huang Zhicong , Naret Olivier Noël Marie , Scepanovic Petar , Thorball Christian Axel Wandall , Xu Zhi Ming ,Cours
Genomic solutions to sustainable development
Ce cours explore comment les technologies génomiques peuvent contribuer aux Objectifs de Développement Durable de l'ONU. Les étudiants découvriront l'impact de la génomique sur la santé, l'agriculture, l'énergie et la conservation via des cours, études de cas et projets pratiques.
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.