Concept
Phylogénie
Publications associées (119)
From trees to barcodes and back again II: Combinatorial and probabilistic aspects of a topological inverse problem
Kathryn Hess Bellwald, Lida Kanari, Adélie Eliane Garin
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general position, based ...
2024The 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 ...
EPFL2024Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania
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 Portfolio2024Analysis of a Class of Multilevel Markov Chain Monte Carlo Algorithms Based on Independent Metropolis–Hastings
Fabio Nobile, Juan Pablo Madrigal Cianci
In this work, we present, analyze, and implement a class of multilevel Markov chain Monte Carlo(ML-MCMC) algorithms based on independent Metropolis--Hastings proposals for Bayesian inverse problems. In this context, the likelihood function involves solving ...
2023Impact of phylogeny on structural contact inference from protein sequence data
Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Umberto Lupo
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 SOC2023Extracting 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 PORTFOLIO2022Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis
Didier Trono, Laurence Gouzi Abrami, Evaristo Jose Planet Letschert, Julien Léonard Duc, Laia Simo Riudalbas, Sandra Eloise Kjeldsen, 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 ...
2022Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load
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 PRESS2022From Trees to Barcodes and Back Again:A Combinatorial, Probabilistic and Geometric Study of a Topological Inverse Problem
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 involve ...
EPFL2022