Publications associées à Computational phylogenetics

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

The time-domain Cartesian multipole expansion of electromagnetic fields

Farhad Rachidi-Haeri, Marcos Rubinstein, Elias Per Joachim Le Boudec, Nicolas Mora Parra, Chaouki Kasmi, Emanuela Radici

Time-domain solutions of Maxwell’s equations in homogeneous and isotropic media are paramount to studying transient or broadband phenomena. However, analytical solutions are generally unavailable for practical applications, while numerical solutions are co ...

Nature Publishing Group2024

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

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

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

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

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

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

Quantitative Methods for Omnichannel Decision-Making

Andrey Vasilyev

Omnichannel retail has emerged as the new standard in today's commerce landscape, with retailers integrating their physical and online channels to enhance the customer shopping experience. However, such integration presents significant challenges for retai ...

EPFL2023

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

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