Publications related to Codon usage bias

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Amer Soc Microbiology2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero, Mohan Vamsi Nallapareddy

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Felix Naef, Cédric Gobet

Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that have remained dif ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2022

A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand

Jacques Fellay, Konstantin Popadin, Dmitrii Iliushchenko, Stepan Denisov

The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria are ...

OXFORD UNIV PRESS2022

Circadian dynamics of RNA localisation in the mammalian liver

Clémence Yumie Syloun Hurni

Gene expression in eukaryotes is a complex multi-step process. It starts in the nucleus with transcription, the synthesis of a mRNA copy from a DNA template. While in the nucleus, the RNA transcript is subject to multiple co- and post-transcriptional modif ...

EPFL2021

Robust landscapes of ribosome dwell times and aminoacyl-tRNAs in response to nutrient stress in liver

Felix Naef, Cédric Gobet, Frédéric Bruno Martin Gachon, Benjamin Dieter Weger, Nagammal Neelagandan

Translation depends on messenger RNA (mRNA)-specific initiation, elongation, and termination rates. While translation elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here we combined ribosome and transfer RNA (tRNA) pr ...

National Academy of Sciences2020

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...

Nature Research2020

Single-cell studies of Mycobacterium smegmatis cell cycle using time-lapse fluorescence microscopy

Joëlle Xiao Yuan Ven

Cell division is one of the most primordial cellular processes and is essential for life propagation. It is composed of crucial events, namely genome duplication, chromosomes segregation and membrane separation. Failure of these processes will have dramati ...

EPFL2019

The fitness landscape of the codon space across environments

Jeffrey David Jensen, Claudia Bank, Sebastian Matuszewski

Fitness landscapes map the relationship between genotypes and fitness. However, most fitness landscape studies ignore the genetic architecture imposed by the codon table and thereby neglect the potential role of synonymous mutations. To quantify the fitnes ...

NATURE PUBLISHING GROUP2018

Circadian clock- and feeding-dependent regulation of translation initiation and elongation in the liver

Cédric Gobet

Circadian rhythms allow organisms to anticipate and adapt to periodic environmental changes related to the day-night cycle. These rhythms originate from a genetic network ticking in almost every cell of our body and the coordination between different organ ...

EPFL2018

Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis

Jérémie Piton

The PIN domain plays a central role in cellular RNA biology and is involved in processes as diverse as rRNA maturation, mRNA decay and telomerase function. Here, we solve the crystal structure of the Rae1 (YacP) protein of Bacillus subtilis, a founding mem ...

Wiley2017

Computational methods and modeling of cellular function for the optimization of protein production and the study of cellular disease states

Joana Raquel Pinto Vieira

Systems biology is a multidisciplinary field that weaves together all the basic sciences through the use of computational and bioinformatics tools, to provide a more integrative view of the complex molecular interactions taking place within and among cells ...

EPFL2017

Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell

Vassily Hatzimanikatis, Julien Racle, Joana Raquel Pinto Vieira

Understanding the mechanisms behind translation and its rate-limiting steps is crucial for both the development of drug targets and improvement of heterologous protein production with many biotechnological applications, such as in pharmaceutical and biofue ...

Elsevier2016

Olfactory receptor pseudo-pseudogenes

Matteo Dal Peraro, Benoîte Bargeton

Pseudogenes are generally considered to be non-functional DNA sequences that arise through nonsense or frame-shift mutations of protein-coding genes(1). Although certain pseudogene-derived RNAs have regulatory roles(2), and some pseudogene fragments are tr ...

Nature Publishing Group2016

Transcriptional and post-transcriptional limitations of high-yielding, PEI-mediated transient transfection with CHO and HEK-293E cells

Florian Maria Wurm, David Hacker, Lucia Baldi Unser, Yashas Rajendra, Divor Kiseljak

Transient gene expression (TGE) in human embryonic kidney (HEK-293) and Chinese hamster ovary (CHO) cells is a well-established technology for the rapid generation of recombinant proteins. Although the maximum TGE yields have reached 1 g/L or more, the amo ...

American Chemical Society2015

Unraveling Patterns of Site-to-Site Synonymous Rates Variation and Associated Gene Properties of Protein Domains and Families

Slavica Dimitrieva Janeva

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To ev ...

Public Library of Science2014

Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters

Felix Naef, Cédric Gobet, Kyle Gustafson, Mathieu Quinodoz

Background: In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles th ...

BioMed Central2014

Characterizing the localization and role of lin-5 and era-1 mRNAs in early C. elegans embryos

Zoltán Péter Spiró

Asymmetric cell division is essential for the generation of diversity during development and the function of stem cell lineages. The Caenorhabditis elegans zygote is an attractive model to investigate the mechanisms of spindle positioning during asymmetric ...

EPFL2014

Searching the coding region for microRNA targets

Jiri Vanicek, Ray Marcel Marin Florez, Miroslav Sulc

Finding microRNA targets in the coding region is difficult due to the overwhelming signal encoding the amino acid sequence. Here, we introduce an algorithm (called PACCMIT-CDS) that finds potential microRNA targets within coding sequences by searching for ...

2013

The influence of genomic context on mutation patterns in the human genome inferred from rare variants

Jian Li

Understanding patterns of spontaneous mutations is of fundamental interest in studies of human genome evolution and genetic disease. Here, we used extremely rare variants in humans to model the molecular spectrum of single-nucleotide mutations. Compared to ...

Cold Spring Harbor Lab Press, Publications Dept2013