Publications associées à COI Barcoding of Nebelid Testate Amoebae (Amoebozoa: Arcellinida): Extensive Cryptic Diversity and Redefinition of the Hyalospheniidae Schultze

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

EPFL2024

Mechanism balancing taxonomy

Simon Nessim Henein, Florent Cosandier, Hubert Pierre-Marie Benoît Schneegans

The balancing of mechanisms consists in distributing their moving masses, inertias, and elastic components in order to achieve key mechanical properties, such as the elimination of the shaking forces and moments exported onto their supporting structure or ...

2023

Impact of phylogeny on structural contact inference from protein sequence data

Nicola Dietler, Umberto Lupo, Anne-Florence Raphaëlle Bitbol

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

A benchmark dataset for machine learning in ecotoxicology

Kristin Schirmer, Fernando Perez Cruz, Marco Baity-Jesi

The use of machine learning for predicting ecotoxicological outcomes is promising, but underutilized. The curation of data with informative features requires both expertise in machine learning as well as a strong biological and ecotoxicological background, ...

Nature Portfolio2023

Shape Models of Lucy Targets (3548) Eurybates and (21900) Orus from Disk-integrated Photometry

Stephan Hellmich

We use our new light curves, along with historical data, to determine the rotation state, photometric properties, and convex shape models of the targets of the Lucy mission (3548) Eurybates and (21900) Orus. We determine a retrograde spin for both targets, ...

IOP Publishing Ltd2023

From Trees to Barcodes and Back Again: A Combinatorial, Probabilistic and Geometric Study of a Topological Inverse Problem

Adélie Eliane Garin

In this thesis, we investigate the inverse problem of trees and barcodes from a combinatorial, geometric, probabilistic and statistical point of view. Computing the persistent homology of a merge tree yields a barcode B. Reconstructing a tree from B invol ...

EPFL2022

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

Didier Trono, Laurence Gouzi Abrami, Julien Léonard Duc, Sandra Eloise Kjeldsen, Alexandre Coudray, Sagane Dind, Evaristo Jose Planet Letschert, Laia Simo Riudalbas

The treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we ...

Nature Research2022

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Anne-Florence Raphaëlle Bitbol

Despite the structural and functional information contained in the statistical coupling between pairs of residues in a protein, coevolution associated with function is often obscured by artifactual signals such as genetic drift, which shapes a protein's ph ...

Nature Portfolio2022

The microbiome of cryospheric ecosystems

Leïla Ezzat, Tom Ian Battin, Hannes Markus Peter, Tyler Joe Kohler, Stylianos Fodelianakis, Massimo Bourquin, Susheel Bhanu Busi, Grégoire Marie Octave Edouard Michoud

The cryosphere includes those parts of Earth where water or soil is frozen, such as snow, ice, glaciers and permafrost soils. Here, the authors present a global inventory of cryospheric microbial communities and their genetic repertoires. ...

Nature Portfolio2022

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load

Jacques Fellay, Luca Ferretti

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical opti ...

OXFORD UNIV PRESS2022

Taxonomic notes on Caelorrhina Hope, 1841, Coelorrhina Burmeister, 1842 and related genera

Michele De Palma

We here review the taxonomic standing of several generic names in the African Cetoniinae and re-establish Coelorrhina Burmeister, 1842 (= Cyprolais Thomson 1880 syn. nov.) as the first available name for Cetonia quadrimaculata Fabricius, 1781. ...

2021

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

Bastien Mangeat, Bart Deplancke, Julie Marie Russeil, Daniel Alpern, Vincent Roland Julien Gardeux, Elisa Cora, Jörn Pezoldt

Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to- ...

2021

Taxonomic revision of the Eudicella White, 1839 complex, with description of three new subgenera

Michele De Palma

Morphological and DNA barcoding analysis of representative taxa in the Eudicella White complex identified five distinct subgenera, three of which are established herein: Eudicella (Coelorrhinella) n. subg., Eudicella (Aneurhina) n. subg., and Eudicella (Ce ...

2021

Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group

Jacques Fellay

Background As trans women are disproportionately affected by the HIV epidemic, and are still understudied, we aimed to identify and characterize the trans women in the Swiss HIV Cohort Study (SHCS). Methods A combination of criteria from pre-existing cohor ...

OXFORD UNIV PRESS INC2022

High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes

Benoît Jean Dominique Ferrari, Régis Lionel Vivien

Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible o ...

Nature Research2020

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

Assessment of abundance and community composition of benthic macroinvertebrates: recommendations for improved sampling, fixation and extraction of oligochaetes

Benoît Jean Dominique Ferrari, Régis Lionel Vivien

For several decades, the abundance and community structure of benthic macroinvertebrates have been studied to assess the biological quality of aquatic ecosystems. Procedures aiming at studying the whole of macroinvertebrate communities were mainly designed ...

2020

MPGM: Scalable and Accurate Multiple Network Alignment

Matthias Grossglauser, Ehsan Kazemi

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

IEEE COMPUTER SOC2020

A modern scleractinian coral with a two-component calcite–aragonite skeleton

Anders Meibom, Jaroslaw Hubert Stolarski

One of the most conserved traits in the evolution of biomineralizing organisms is the taxon-specific selection of skeletal minerals. All modern scleractinian corals are thought to produce skeletons exclusively of the calcium-carbonate polymorph aragonite. ...

2021

The foreign oligochaete species Quistadrilus multisetosus (Smith, 1900) in Lake Geneva: morphological and molecular characterization and environmental influences on its distribution

Benoît Jean Dominique Ferrari, Régis Lionel Vivien

The presence of the oligochaete species Quistadrilus multisetosus (Smith, 1900) originating from North America has been mentioned for several decades in Europe, the Middle East and Russia. Its distribution and abundance in Europe is still unknown but it ca ...

2020