Publication
Identification of potential HIV restriction factors by combining evolutionary genomic signatures with functional analyses
Publications associées (47)
Statistical learning quantifies transposable element-mediated cis-regulation
Didier Trono, Evaristo Jose Planet Letschert, Julien Léonard Duc, Alexandre Coudray, Julien Paul André Pontis, Delphine Yvette L Grun, Cyril David Son-Tuyên Pulver, Shaoline Sheppard
Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...
2023Integrative transcriptome analyses of Transposable Elements (TEs) and genes contribute to a better understanding of colorectal cancer
Cancer is the second leading cause of death worldwide. Cancer develops through multiple hallmark functions including apoptosis evasion, unlimited replicative potential, metastasis, and immune avoidance. Over the past few decades, researchers have reported ...
EPFL2022A highly virulent variant of HIV-1 circulating in the Netherlands
We discovered a highly virulent variant of subtype-B HIV-1 in the Netherlands. One hundred nine individuals with this variant had a 0.54 to 0.74 log(10) increase (i.e., a similar to 3.5-fold to 5.5-fold increase) in viral load compared with, and exhibited ...
AMER ASSOC ADVANCEMENT SCIENCE2022Toward a mechanistic understanding of variable chromatin modules
Our genome is a long sequence of DNA that contains all the information to be able to constitute a living organism like us, similarly to what the letters in a book do to create a story. This sequence, which is a stretch of molecules called nucleotides, is a ...
EPFL2021HIV-1 and human genetic variation
Over the past four decades, research on the natural history of HIV infection has described how HIV wreaks havoc on human immunity and causes AIDS. HIV host genomic research, which aims to understand how human genetic variation affects our response to HIV i ...
NATURE RESEARCH2021Prioritization of cell types responsive to biological perturbations in single-cell data with Augur
Grégoire Courtine, Jordan Squair, Matthieu Pierre Gautier, Michael Alexander Skinnider
Advances in single-cell genomics now enable large-scale comparisons of cell states across two or more experimental conditions. Numerous statistical tools are available to identify individual genes, proteins or chromatin regions that differ between conditio ...
NATURE RESEARCH2021Computational study of transcription factor binding sites
Any living organism contains a whole set of instructions encoded as genes on the DNA. This set of instructions contains all the necessary information that the organism will ever need, from its development to a mature individual to environment specific resp ...
EPFL2020Gene expression across mammalian organ development
Maria del Carmen Sandi Perez, Ioannis Xenarios
The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early or ...
2019Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes
Denis Duboule, Lucille Delisle, Edgardo Rodriguez Carballo, Nayuta Yakushiji
Background The spatial organization of the mammalian genome relies upon the formation of chromatin domains of various scales. At the level of gene regulation in cis, collections of enhancer sequences define large regulatory landscapes that usually match wi ...
2019Identifying gene function and module connections by the integration of multispecies expression compendia
Johan Auwerx, Kristina Schoonjans, Stephan Morgenthaler, Hao Li, Maroun Bou Sleiman, Elena Katsyuba, Wen Gao, Daria Rukina, Qingyao Huang, Yang Li, Changmyung Oh, Andrea Komljenovic
The functions of many eukaryotic genes are still poorly understood. Here, we developed and validated a new method, termed GeneBridge, which is based on two linked approaches to impute gene function and bridge genes with biological processes. First, Gene-Mo ...
Cold Spring Harbor Laboratory2019