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List of works by Jacques Fellay

A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals

scientific article published on 13 September 2019

A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

scientific article published on 29 October 2013

A genome-wide association study of resistance to HIV infection in highly exposed uninfected individuals with hemophilia A.

scientific article published on 30 January 2013

A genome-wide polygenic approach to HIV uncovers link to inflammatory bowel disease and identifies potential novel genetic variants

article

A novel Acute Retroviral Syndrome Severity Score predicts the key surrogate markers for HIV-1 disease progression

scientific article

A polymorphism in the HCP5 gene associated with HLA-B*5701 does not restrict HIV-1 in vitro

scientific article published on January 2010

A polymorphism in the leptin gene promoter is associated with anemia in patients with HIV disease

scientific article published on 16 September 2011

A privacy-preserving solution for compressed storage and selective retrieval of genomic data

scientific article

A39 Human exome sequencing to evaluate the impact of rare coding variation on HIV-1 control

scientific article

Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes

scientific article published on 03 September 2019

Adaptation on a genomic scale.

scientific article published on 3 February 2015

Adverse events to antiretrovirals in the Swiss HIV Cohort Study: effect on mortality and treatment modification

article

Amino Acid Variation in HLA Class II Proteins Is a Major Determinant of Humoral Response to Common Viruses

scientific article

Analysis of stop-gain and frameshift variants in human innate immunity genes

scientific article

Analysis of stop-gain and frameshift variants in human innate immunity genes

article

Are Privacy-Enhancing Technologies for Genomic Data Ready for the Clinic? A Survey of Medical Experts of the Swiss HIV Cohort Study.

scientific article published on 10 January 2018

Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls

scientific article

Author Correction: Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption

scientific article published in 2021

Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

scientific article published on 27 December 2018

CCL3L1 and HIV/AIDS susceptibility

scientific article published on October 2009

COVID-19 epidemic in Switzerland: on the importance of testing, contact tracing and isolation ⬇️

scientific article published on 19 March 2020

CYP3A activity measured by the midazolam test is not related to 3435 C >T polymorphism in the multiple drug resistance transporter gene

scientific article published in April 2004

Co-trimoxazole prophylaxis is associated with reduced risk of incident tuberculosis in participants in the Swiss HIV Cohort Study

scientific article

Common genetic variation and the control of HIV-1 in humans

scientific article published in December 2009

Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population

scientific article

Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque

scientific article

Contribution of Genetic Background and Clinical Risk Factors to Low-Trauma Fractures in Human Immunodeficiency Virus (HIV)-Positive Persons: The Swiss HIV Cohort Study.

scientific article published on April 2016

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 F

scientific article published on 01 February 2020

Contribution of genetic background, traditional risk factors, and HIV-related factors to coronary artery disease events in HIV-positive persons

scientific article published on 26 March 2013

Copy number variation of KIR genes influences HIV-1 control

scientific article

Correcting for Population Stratification Reduces False Positive and False Negative Results in Joint Analyses of Host and Pathogen Genomes

scholarly article by Olivier Naret et al published 2018 in Frontiers in Genetics

Correcting for population stratification reduces false positive and false negative results in joint analyses of host and pathogen genomes

Counteraction of HLA-C-mediated immune control of HIV-1 by Nef.

scientific article

Detection of novel astroviruses MLB1 and MLB2 in the sera of febrile Tanzanian children.

scientific article published on 14 March 2018

Determinants of HIV-1 broadly neutralizing antibody induction.

scientific article

Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART

scientific article published on 19 July 2019

Differential Immunodominance Hierarchy of CD8+ T-Cell Responses in HLA-B*27:05- and -B*27:02-Mediated Control of HIV-1 Infection

scientific article published on 22 November 2017

Disentangling human tolerance and resistance against HIV.

scientific article

Distinctive roles of age, sex, and genetics in shaping transcriptional variation of human immune responses to microbial challenges

scientific article published on 27 December 2017

Dynamics of HIV latency and reactivation in a primary CD4+ T cell model

scientific article

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

scientific article published in January 2018

Effect of Fc Receptor Genetic Diversity on HIV-1 Disease Pathogenesis

article

Elevated HLA-A expression impairs HIV control through inhibition of NKG2A-expressing cells

scientific article published on 4 January 2018

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

scientific article

Estimating the net contribution of interleukin-28B variation to spontaneous hepatitis C virus clearance

scientific article

Estimating the respective contributions of human and viral genetic variation to HIV control

article

European genetic diversity and susceptibility to pathogens

scientific article published on January 2013

Evaluating the impact of functional genetic variation on HIV-1 control

scientific article published on 9 September 2017

Evidence of dysregulation of dendritic cells in primary HIV infection

scientific article published on 6 August 2010

Exome Sequencing Reveals Primary Immunodeficiencies in Children with Community-Acquired Pseudomonas aeruginosa Sepsis

scientific article published on 20 September 2016

Exploring the interactions between the human and viral genomes

scientific article published on 15 November 2019

Familial segregation of group B streptococcal infection in a consanguineous kindred

scientific article

Gender medicine and oncology: report and consensus of an ESMO workshop

scientific article published on 01 December 2019

Genetic Associations with Resistance to HIV-1 Infection, Viral Control and Protection Against Disease

article

Genetic interplay between HLA-C and MIR148A in HIV control and Crohn disease

scientific article

Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance

scientific article

Genetics of human susceptibility to active and latent tuberculosis: present knowledge and future perspectives

scientific article published on 27 October 2017

GenoGuard: Protecting Genomic Data against Brute-Force Attacks

Genome-to-genome analysis highlights the effect of the human innate and adaptive immune systems on the hepatitis C virus.

scientific article published on 10 April 2017

Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages

scientific article

Genome-wide association study of interferon-related cytopenia in chronic hepatitis C patients

scientific article

Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals

scientific article

Genomewide association study for determinants of HIV-1 acquisition and viral set point in HIV-1 serodiscordant couples with quantified virus exposure

scientific article

GuavaH: a compendium of host genomic data in HIV biology and disease

scientific article

HIV Peptidome-Wide Association Study Reveals Patient-Specific Epitope Repertoires Associated with HIV Control

article

HIV Transmission Chains Exhibit Greater HLA-B Homogeneity Than Randomly Expected

scientific article published on 01 August 2019

HIV and solid organ transplantation: the Swiss experience

article

HIV lipoatrophy and mosquito bites

scientific article published in January 2002

HIV peptidome-wide association study reveals patient-specific epitope repertoires associated with HIV control

scientific article published on 02 January 2019

HIV-1 Vpu is a potent transcriptional suppressor of NF-κB-elicited antiviral immune responses

article

HLA class I and KIR genes do not protect against HIV type 1 infection in highly exposed uninfected individuals with hemophilia A.

scientific article

HLA tapasin independence: broader peptide repertoire and HIV control

scientific article published on 23 October 2020

HLA-B*14:02-Restricted Env-Specific CD8+ T-Cell Activity Has Highly Potent Antiviral Efficacy Associated with Immune Control of HIV Infection

scientific article published on 6 September 2017

HLA-Bw4 identifies a population of HIV-infected patients with an increased capacity to control viral replication after structured treatment interruption

scientific article published on 15 April 2012

HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C.

scientific article

Hepatitis C trials that combine investigational agents with pegylated interferon should be stratified by interleukin-28B genotype

scientific article published on 30 June 2010

Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART

scientific article published on 02 November 2020

Heterozygous gene truncation delineates the human haploinsufficient genome

article

Host Genetics and Genomics

article

Host determinants of HIV-1 control in African Americans

scientific article

Host genetic determinants of T cell responses to the MRKAd5 HIV-1 gag/pol/nef vaccine in the step trial

scientific article

Host genetics and HIV-1: the final phase?

scientific article

Host genetics influences on HIV type-1 disease

scientific article

Host genetics of HCV disease — IL28B

article

Host genetics: fine-tuning innate signaling

scientific article published in July 2007

How the Human Genome Can Predict Response to Hepatitis C Therapy

article

Human genetic variants and age are the strongest predictors of humoral immune responses to common pathogens and vaccines

article

Human genetic variation in HIV disease: beyond genome-wide association studies

scientific article

Human genomics of acute liver failure due to hepatitis B virus infection: an exome sequencing study in liver transplant recipients

scientific article published on 06 November 2018

IFNL3/4 polymorphisms are associated with AIDS-related Kaposiʼs sarcoma

scholarly article by Stéphanie Bibert et al published September 2018 in AIDS

IL28B genotype is associated with differential expression of intrahepatic interferon-stimulated genes in patients with chronic hepatitis C.

scientific article

ITPA gene variants protect against anaemia in patients treated for chronic hepatitis C.

scientific article

Identification of Siglec-1 null individuals infected with HIV-1.

scientific article published on 11 August 2016

Impact of phenotype definition on genome-wide association signals: empirical evaluation in human immunodeficiency virus type 1 infection

scientific article published on 13 April 2011

Increased CHIP Prevalence Amongst People Living with HIV

scientific article published on 07 November 2020

Influence of HLA-C expression level on HIV control

scientific article published on April 2013

Inosine triphosphate protects against ribavirin-induced adenosine triphosphate loss by adenylosuccinate synthase function

scientific article

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.

scientific article

Interleukin-28B polymorphism improves viral kinetics and is the strongest pretreatment predictor of sustained virologic response in genotype 1 hepatitis C virus

scientific article

Joint analysis of host and pathogen genomes

Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1.

scientific article published on 20 February 2018

LILRB2 interaction with HLA class I correlates with control of HIV-1 infection

scientific article

Mapping of positive selection sites in the HIV-1 genome in the context of RNA and protein structural constraints.

scientific article published on November 2011

Médecine génomique et Maladies infectieuses

Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

scientific article published on 23 February 2018

Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune Responses

scientific article published on 07 March 2017

No Evidence for Association of β-Defensin Genomic Copy Number with HIV Susceptibility, HIV Load during Clinical Latency, or Progression to AIDS.

scientific article published on January 2017

P08-06 LB. A genome-wide association study of host genetic determinants of T cell responses to the MRKAd5 HIV-1 gag/pol/nef vaccine in the STEP trial.

scientific article published on 22 October 2009

Personalized hepatitis C therapy: opportunities and pitfalls ⬇️

scientific article published on March 1, 2011

Pharmacogenomics of HIV Therapy: Summary of a Workshop Sponsored by the National Institute of Allergy and Infectious Diseases ⬇️

scientific article published on September 1, 2011

Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load

scientific article

Population pharmacokinetics and effects of efavirenz in patients with human immunodeficiency virus infection

scientific article published in January 2003

Predicting the Occurrence of Variants in RAG1 and RAG2

scientific article published on 06 August 2019

Prevalence of adverse events associated with potent antiretroviral treatment: Swiss HIV Cohort Study

scientific article published in October 2001

Privacy in the Genomic Era

scientific article

Privacy-preserving genomic testing in the clinic: a model using HIV treatment.

scientific article published on 14 January 2016

Publisher Correction: Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors

scientific article published on 01 June 2018

Quantifying Genomic Privacy via Inference Attack with High-Order SNV Correlations

Response to antiretroviral treatment in HIV-1-infected individuals with allelic variants of the multidrug resistance transporter 1: a pharmacogenetics study

scientific article published in January 2002

Revolutionizing Medical Data Sharing Using Advanced Privacy-Enhancing Technologies: Technical, Legal, and Ethical Synthesis

scientific article published in 2021

Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis Pneumonia

scientific article

Role of human leukocyte antigen class I alleles in progressive multifocal leukoencephalopathy

scientific article

Role of retroviral restriction factors in the interferon-α-mediated suppression of HIV-1 in vivo

scientific article published on 6 February 2012

SQC: secure quality control for meta-analysis of genome-wide association studies

scientific article

Severe viral respiratory infections in children with IFIH1 loss-of-function mutations.

scientific article

Susceptibility to infection in early life: a growing role for human genetics

scientific article published on 13 January 2020

The Characteristics of Heterozygous Protein Truncating Variants in the Human Genome

scientific article published on 7 December 2015

The Duffy antigen receptor for chemokines null promoter variant does not influence HIV-1 acquisition or disease progression

scientific article

The HCP5 single-nucleotide polymorphism: a simple screening tool for prediction of hypersensitivity reaction to abacavir

scientific article

The Interplay Between Host Genetic Variation, Viral Replication, and Microbial Translocation in Untreated HIV-Infected Individuals

scientific article

The association of genetic variants with hepatic steatosis in patients with genotype 1 chronic hepatitis C infection

scientific article

The characterization of twenty sequenced human genomes

scientific article

The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies

scientific article published on 16 May 2022

Treatment of Cytomegalovirus Infection or Disease in Solid Organ Transplant Recipients with Valganciclovir

Truly privacy-preserving federated analytics for precision medicine with multiparty homomorphic encryption

scientific article published in 2021

Variants in the ITPA gene protect against ribavirin-induced hemolytic anemia and decrease the need for ribavirin dose reduction

scientific article

Variations of CYP3A activity induced by antiretroviral treatment in HIV-1 infected patients

scientific article published on 19 January 2005

Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial

scientific article published on 28 August 2019

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

scientific article

Viral genome wide association study identifies novel hepatitis C virus polymorphisms associated with sofosbuvir treatment failure

scientific article published on 20 October 2021

Virosaurus A Reference to Explore and Capture Virus Genetic Diversity

scientific article published on 01 November 2020

Visual masking deficits in schizophrenia: a view into the genetics of the disease through an endophenotype

scientific article published in 2022

WGAViewer: software for genomic annotation of whole genome association studies

scientific article

Whole-exome sequencing for the identification of rare variants in primary immunodeficiency genes in children with sepsis - a prospective population-based cohort study

scientific article published on 18 March 2020

X chromosomal variation is associated with slow progression to AIDS in HIV-1-infected women

scientific article published on August 2009

Young and Early Career Investigators: Report from a Global HIV Vaccine Enterprise Working Group

article

[HIV-AIDS: answers to new questions]

scientific article published on 01 April 2006

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