Publications associées à On Exploring Genome Rearrangement Phylogenetic Patterns

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

Statistical Inference for Inverse Problems: From Sparsity-Based Methods to Neural Networks

Pakshal Narendra Bohra

In inverse problems, the task is to reconstruct an unknown signal from its possibly noise-corrupted measurements. Penalized-likelihood-based estimation and Bayesian estimation are two powerful statistical paradigms for the resolution of such problems. They ...

EPFL2024

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

Spatiotemporal wildfire modeling through point processes with moderate and extreme marks

Jonathan Koh Boon Han

Accurate spatiotemporal modeling of conditions leading to moderate and large wildfires provides better understanding of mechanisms driving fire-prone ecosystems and improves risk management. Here, we develop a joint model for the occurrence intensity and t ...

2023

Machine Learning Security in Industry: A Quantitative Survey

Kathrin Grosse

Despite the large body of academic work on machine learning security, little is known about the occurrence of attacks on machine learning systems in the wild. In this paper, we report on a quantitative study with 139 industrial practitioners. We analyze at ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2023

Analysis 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 ...

2023

Higher Order Asymptotics: Applications to Satellite Conjunction and Boundary Problems

Soumaya Elkantassi

Higher-order asymptotics provide accurate approximations for use in parametric statistical modelling. In this thesis, we investigate using higher-order approximations in two-specific settings, with a particular emphasis on the tangent exponential model. ...

EPFL2023

An Unbiased Method of Measuring the Ratio of Two Data Sets

Jean-Paul Richard Kneib, Huanyuan Shan

In certain cases of astronomical data analysis, the meaningful physical quantity to extract is the ratio R between two data sets. Examples include the lensing ratio, the interloper rate in spectroscopic redshift samples, and the decay rate of gravitational ...

IOP Publishing Ltd2023

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

Pascal Fua, Sean Lewis Hill, Amos Sironi, Jiancheng Yang, Jian Zhou, Siqi Liu, Xiang Li, Jie Zhou

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in m ...

2023

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

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

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

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

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

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

HIERARCHICAL MARKOV CHAIN MONTE CARLO METHODS FOR BAYESIAN INVERSE PROBLEMS

Juan Pablo Madrigal Cianci

This thesis is devoted to the construction, analysis, and implementation of two types of hierarchical Markov Chain Monte Carlo (MCMC) methods for the solution of large-scale Bayesian Inverse Problems (BIP). The first hierarchical method we present is base ...

EPFL2022

Convex Quantization Preserves Logconcavity

Pol del Aguila Pla

A logconcave likelihood is as important to proper statistical inference as a convex cost function is important to variational optimization. Quantization is often disregarded when writing likelihood models, ignoring the limitations of the physical detectors ...

IEEE Institute of Electrical and Electronics Engineers2022

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

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