Publications related to Genome-to-genome analysis of Epstein-Barr virus infection

Related publications (28)

Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

2025

Antagonism as a Foraging Strategy in Microbial Communities

Martin Ackermann, Lucas Pierre Antoine Paoli

In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependent antagonism. Using single-cell live imaging and isotopi ...

AMER ASSOC ADVANCEMENT SCIENCE2025

DNA methylation enables recurrent endogenization of giant viruses in an animal relative

Omaya Pierre Dudin, Marine Olivetta

5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. The causes for 5mC retention an ...

2024

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

Clement Helsens

Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address thes ...

LIFE SCIENCE ALLIANCE LLC2023

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Christof Holliger, Julien Maillard, Aline Sondra Adler, Simon Marius Jean Poirier

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...

WILEY2022

Host genomics of SARS-CoV-2 infection

Jacques Fellay, Christian Axel Wandall Thorball

SARS-CoV-2 infected a large fraction of humans in the past 2 years. The clinical presentation of acute infection varies greatly between individuals, ranging from asymptomatic or mild to life-threatening COVID-19 pneumonia with multi-organ complications. De ...

SPRINGERNATURE2022

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits

Jacques Fellay, Christian Axel Wandall Thorball

Infectious diseases are particularly challenging for genome-wide association studies (GWAS) because genetic effects from two organisms (pathogen and host) can influence a trait. Traditional GWAS assume individual samples are independent observations. Howev ...

OXFORD UNIV PRESS2022

Tcf1 is essential for initiation of oncogenic Notch1-driven chromatin topology in T-ALL

Christelle Dubey, Freddy Radtke, Ute Koch, Nadine Fournier, Mateusz Waldemar Antoszewski, Marianne Nkosi, Tara Kimberly Sugrue

NOTCH1 is a well-established lineage specifier for T cells and among the most frequently mutated genes throughout all subclasses of T cell acute lymphoblastic leukemia (T-ALL). How oncogenic NOTCH1 signaling launches a leukemia-prone chromatin landscape du ...

AMER SOC HEMATOLOGY2022

Towards a physical understanding of developmental patterning

Andrew Charles Oates, Jose Negrete Jr

The temporal coordination of events at cellular and tissue scales is essential for the proper development of organisms, and involves cell-intrinsic processes that can be coupled by local cellular signalling and instructed by global signalling, thereby crea ...

NATURE RESEARCH2021

Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation

Jean-Pierre Hubaux, Juan Ramón Troncoso-Pastoriza, David Jules Froelicher, Jean-Philippe Léonard Bossuat

Genotype imputation is a fundamental step in genomic data analysis, where missing variant genotypes are predicted using the existing genotypes of nearby "tag"variants. Although researchers can outsource genotype imputation, privacy concerns may prohibit ge ...

CELL PRESS2021

Mouse Systems Genetics as a Prelude to Precision Medicine

Johan Auwerx, Hao Li

Mouse models have been instrumental in understanding human disease biology and proposing possible new treatments. The precise control of the environment and genetic composition of mice allows more rigorous observations, but limits the generalizability and ...

2020

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

Bart Deplancke, Maroun Bou Sleiman, Vincent Roland Julien Gardeux, Riccardo Dainese, Maria Litovchenko, Michael Vincent Frochaux, Dani Osman, Brian Dennis Hollis, Virginie Sandra Braman

Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understan ...

2020

On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF

Jaume Bonet Martinez

Cis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. To date, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict ...

OXFORD UNIV PRESS2020

Rare variants in antiviral response genes drive severe viral respiratory infections in children

Jacques Fellay, Dylan Lawless, Samira Asgari

NATURE PUBLISHING GROUP2019

Allele-specific gene disruption through discrimination of a single base change by S. aureus Cas9-KKH prevents progressive hearing loss after AAV-mediated gene delivery

Bernard Schneider, Paola Andrea Solanes Vega, Sofia Carmen Suzanne Spataro

MARY ANN LIEBERT, INC2019

Mutation update: TGFBI pathogenic and likely pathogenic variants in corneal dystrophies

Daniel Francis Schorderet

Human transforming growth factor beta-induced (TGFBI), is a gene responsible for various corneal dystrophies. TGFBI produces a protein called TGFBI, which is involved in cell adhesion and serves as a recognition sequence for integrins. An alteration in cel ...

2019

Scaling Out Bioinformatics in the Data Center

Sam David Whitlock

Whole Genome Sequencing is a process in the field of bioinformatics that transforms biological samples of DNA into an electronic dataset of genetic bases. The process consists of two sequential components. First, the laboratory process of sequencing transf ...

EPFL2019

Structure and transformation of bacteriophage A511 baseplate and tail upon infection of Listeria cells

Petr Leiman, Sergey Nazarov, Mikhail Shneyder, Ricardo Cesar Guerrero Ferreira, Nicholas Michael Ian Taylor

Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteri ...

WILEY2019

A Tale of Two Tumors: Unraveling the Complexities of Epigenetic Dysregulation in Cancer

Maria Christine Donaldson

Epigenetics plays an important role in cancer development and progression. Cancer cells hijack the epigenome by modifying the histone protein units responsible for packaging DNA, or by modifying the DNA itself, resulting in changes to chromatin topology an ...

EPFL2019

Delivery of CRISPR/Cas9 using AAV-PHP.B in the inner ear leads to allele-specific inactivation of the mutated Tmc1 allele and protects auditory function in Beethoven mice

Bernard Schneider, Paola Andrea Solanes Vega, Sofia Carmen Suzanne Spataro

Hearing Loss (HL) is the most prevalent sensorineural disorder, affecting 360 million people worldwide. As genetic causes lead to 50% of pre-lingual deafness, gene therapy is considered as a potential therapeutic strategy. Mutations in the TMC1 gene are li ...

MARY ANN LIEBERT, INC2019