Publications associées à Classification phylogénétique

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

Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania

Jacques Fellay, Zhi Ming Xu

The Mycobacterium tuberculosis complex (MTBC) comprises nine human-adapted lineages that differ in their geographical distribution. Local adaptation of specific MTBC genotypes to the respective human host population has been invoked in this context. We aim ...

Nature Portfolio2024

A benchmark dataset for machine learning in ecotoxicology

Kristin Schirmer, Marco Baity-Jesi, Fernando Perez Cruz

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

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

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

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

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

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

Meta-omics-aided isolation of an elusive anaerobic arsenic-methylating soil bacterium

Rizlan Bernier-Latmani, Karin Lederballe Meibom, Karen Elda Viacava Romo, Nicolas Louis Maurice Jacquemin, Matthew Charles Reid, Jiangtao Qiao

Soil microbiomes harbor unparalleled functional and phylogenetic diversity and are sources of novel metabolisms. However, extracting isolates with a targeted function from complex microbiomes is not straightforward, particularly if the associated phenotype ...

2022

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

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

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

Thermal resistance of ventilated air-spaces behind external claddings; definitions and challenges (ASHRAE 1759-RP)

Dolaana Khovalyg, Mohammad Rahiminejad

The presence of an air-space within a building envelope is known to have a varying contribution to the overall thermal performance of the wall assembly due to the combined effect of convection and radiation in the air cavity. In particular, the thermal res ...

2021