Publications associées à Common descent

Cellularization across eukaryotes: Conserved mechanisms and novel strategies

Many eukaryotes form multinucleated cells during their devel-opment. Some cells persist as such during their lifetime, others choose to cleave each nucleus individually using a specialized cytokinetic process known as cellularization. What is cellula-rizat ...

CURRENT BIOLOGY LTD2023

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

Energy-harnessing problem solving of primordial life: Modeling the emergence of catalytic host-nested parasite life cycles

Christian Iseli

All life forms on earth ultimately descended from a primordial population dubbed the last universal common ancestor or LUCA via Darwinian evolution. Extant living systems share two salient functional features, a metabolism extracting and transforming energ ...

2023

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

Jacques Fellay, Zhi Ming Xu, Sina Rüeger

Genome-wide association studies rely on the statistical inference of untyped variants, called imputation, to increase the coverage of genotyping arrays. However, the results are often suboptimal in populations underrepresented in existing reference panels ...

Public Library Science2022

Evolutionary history expands the range of signaling interactions in hybrid multikinase networks

Anne-Florence Raphaëlle Bitbol, Mohamed Barakat

Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonic ...

NATURE RESEARCH2021

KRAB zinc finger protein-mediated control of transposon-embedded regulatory sequences from human germline to early embryos

Alexandra Iouranova

Transposable elements (TEs), also called jumping genes, are genetic elements capable of changing their position within the genome of their host. They make up large fractions of genomes, including 45% of human DNA content, according to current estimates. S ...

EPFL2021

Distributed Learning in Non-Convex Environments-Part I: Agreement at a Linear Rate

Ali H. Sayed, Stefan Vlaski

Driven by the need to solve increasingly complex optimization problems in signal processing and machine learning, there has been increasing interest in understanding the behavior of gradient-descent algorithms in non-convex environments. Most available wor ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2021

Barcoding analysis and taxonomic revision of Goliathus Lamarck, 1802 (Scarabaeidae, Cetoniinae)

Michele De Palma

We conducted barcoding analysis of valid taxa in the genus Goliathus Lamarck, 1802 and clarified their relationships. Specimens of Goliathus goliatus (Drury, 1770) sampled in tropical rainforests from Cameroon to Kenya display degrees of genetic and phenot ...

2020

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

Jacques Fellay, Alessandro Borghesi

The unique vulnerability to infection of newborns and young infants is generally explained by a constellation of differences between early-life immune responses and immune responses at later ages, often referred to as neonatal immune immaturity. This devel ...

SPRINGER2020

Beyond silence : a functional and evolutionary study of KRAB zinc finger proteins

Pierre-Yves Joseph Laurent Helleboid

Transposable elements (TEs) are genetic units capable of spreading within the genomes of their host. TEs contribute a readily recognizable 45% of the human DNA, reflecting in part their co-option for some as source of protein-coding sequences, for others a ...

EPFL2019

Cellular advective-diffusion drives the emergence of bacterial surface colonization patterns and heterogeneity

Alexandre Louis André Persat, Tamara Rossy

Microorganisms navigate and divide on surfaces to form multicellular structures called biofilms, the most widespread survival strategy found in the bacterial world. One common assumption is that cellular components guide the spatial architecture and arrang ...

Nature Research2019

Enhanced 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 ...

2019

Neuronal morphologies: the shapes of thoughts

Lida Kanari

The mammalian brain, one of the most fascinating systems in nature, is a complex biological structure that has kept scientists busy for over a century. Many of the brain's mysteries have been unraveled due to the enormous efforts of the scientific communit ...

EPFL2018

Trypanosoma brucei UMSBP2 is a single-stranded telomeric DNA binding protein essential for chromosome end protection

Galina Glousker

Universal minicircle sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind a single-stranded G-rich sequence, UMS, conserved at the replication origins of the mitochondrial (kinetoplast) DNA of trypanosomatids. Here, we report tha ...

OXFORD UNIV PRESS2018

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

Didier Trono, Michaël Imbeault, Pierre-Yves Joseph Laurent Helleboid

The human genome encodes some 350 Kruppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), the products of a rapidly evolving gene family that has been traced back to early tetrapods(1,2). The function of most KZFPs is unknown, but a f ...

Nature Publishing Group2017

Form - function relationships in dragonfly mandibles under an evolutionary perspective

Alessandra Patera

Functional requirements may constrain phenotypic diversification or foster it. For insect mouthparts, the quantification of the relationship between shape and function in an evolutionary framework remained largely unexplored. Here, the question of a functi ...

Royal Soc2017

Avalanches in dry and saturated disordered media at fracture in shear and mixed mode scenarios

Jean-François Molinari, Enrico Milanese, Okan Yilmaz

We investigate shear and mixed mode fracture scenarios in inhomogeneous dry and fully saturated porous media with a 2D central force lattice model. For the fully saturated case we adopt the extended Biot's theory. The bars of the lattice break only under t ...

Elsevier2017

Red squirrels in the British Isles are infected with leprosy bacilli

Stewart Cole, Andrej Benjak, Charlotte Avanzi, Philippe Busso, Jérémie Piton, Chloé Marie Loiseau

Leprosy, caused by infection with Mycobacterium leprae or the recently discovered Mycobacterium lepromatosis, was once endemic in humans in the British Isles. Red squirrels in Great Britain (Sciurus vulgaris) have increasingly been observed with leprosy-li ...

American Association for the Advancement of Science2016

Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis

Stewart Cole, Andrej Benjak, Charlotte Avanzi, Philippe Busso, Pushpendra Singh

Mycobacterium lepromatosis is an uncultured human pathogen associated with diffuse lepromatous leprosy and a reactional state known as Lucio's phenomenon. By using deep sequencing with and without DNA enrichment, we obtained the near-complete genome sequen ...

National Academy of Sciences2015

Selection methods regulate evolution of cooperation in digital evolution

Dario Floreano, Laurent Keller, Pawel Lichocki

A key, yet often neglected, component of digital evolution and evolutionary models is the 'selection method' which assigns fitness (number of offspring) to individuals based on their performance scores (efficiency in performing tasks). Here, we study with ...

Royal Soc2014