Publication
A first version of the Caenorhabditis elegans Promoterome
Related publications (42)
Integrative 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 ...
EPFL2022Unexpected post‐glacial colonisation route explains the white colour of barn owls ( Tyto alba ) from the British Isles
Nicolas Jean Philippe Guex, Christian Iseli
The climate fluctuations of the Quaternary shaped the movement of species in and out of glacial refugia. In Europe, the majority of species followed one of the described traditional postglacial recolonization routes from the southern peninsulas towards the ...
2022Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models
Vassily Hatzimanikatis, Georgios Fengos, Maria Masid Barcon, Daniel Robert Weilandt, Zhaleh Hosseini, Pierre Guy Rémy Salvy
Motivation: Large-scale kinetic models are an invaluable tool to understand the dynamic and adaptive responses of biological systems. The development and application of these models have been limited by the availability of computational tools to build and ...
OXFORD UNIV PRESS2022New and improved methods for integrated models of metabolism and gene expression
The beginning of the 21st century was marked by the advent of disruptive technologies, which ushered an era of groundbreaking advances in fundamental sciences, carried by the great pace at which computational capabilities spread and evolved. But the new ce ...
EPFL2021Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
Didier Trono, Evaristo Jose Planet Letschert, Julien Léonard Duc, Alexandre Coudray, Shaoline Sheppard, Christopher James Playfoot, Sagane Dind
Transposable elements (TEs) account for more than 50% of the human genome and many have been co-opted throughout evolution to provide regulatory functions for gene expression networks. Several lines of evidence suggest that these networks are fine-tuned by ...
COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT2021Computational 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 ...
EPFL2020Chromatin three-dimensional interactions mediate genetic effects on gene expression
David Hacker, Giovanna Ambrosini, Philipp Bucher, Sanjeev Kumar
Studying the genetic basis of gene expression and chromatin organization is key to characterizing the effect of genetic variability on the function and structure of the human genome. Here we unravel how genetic variation perturbs gene regulation using a da ...
2019Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models
Vassily Hatzimanikatis, Noushin Hadadi, Vikash Kumar Pandey
The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Current ...
2019Tissue- and sex-specific small RNAomes reveal sex differences in response to the environment
Pierre Gönczy, Alexandra Bezler, Frédéric Schütz, Laurent Keller, Raffaella Conconi
RNA interference (RNAi) related pathways are essential for germline development and fertility in metazoa and can contribute to inter- and trans-generational inheritance. In the nematode Caenorhabditis elegans, environmental double-stranded RNA provided by ...
PUBLIC LIBRARY SCIENCE2019Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis
Didier Trono, Priscilla Turelli, Evaristo Jose Planet Letschert
BackgroundAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving loss of motor neurons and having no known cure and uncertain etiology. Several studies have drawn connections between altered retrotransposon expression and ALS. C ...
2018