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Concept

Inferring horizontal gene transfer

Publications associées (14)

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

Massimo Bourquin

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

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

Jacques Fellay

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

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

Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T Cell Decline and Per-Parasite Pathogenicity

Jacques Fellay

Pathogen strains may differ in virulence because they attain different loads in their hosts, or because they induce different disease-causing mechanisms independent of their load. In evolutionary ecology, the latter is referred to as" per-parasite pathogen ...

Oxford University Press2018

A maximum-likelihood approach for building cell-type trees by lifting

Bernard Moret, Philipp Bucher, Yu Lin, Mingfu Shao, Nishanth Ulhas Nair

Background: In cell differentiation, a less specialized cell differentiates into a more specialized one, even though all cells in one organism have (almost) the same genome. Epigenetic factors such as histone modifications are known to play a significant r ...

2016

Study of cell differentiation by phylogenetic analysis using histone modification data

Bernard Moret, Philipp Bucher, Yu Lin, Nishanth Ulhas Nair

Background: In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in ...

BioMed Central2014

Refining Regulatory Networks through Phylogenetic Transfer of Information

Bernard Moret, Xiuwei Zhang

The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while computational methods to infer these networks provide only modest accuracy. The latter can be attributed partly to the limit ...

2012

TIBA: a tool for phylogeny inference from rearrangement data with bootstrap analysis

Bernard Moret, Yu Lin, Vaibhav Rajan

TIBA is a tool to reconstruct phylogenetic trees from rearrangement data that consist of ordered lists of synteny blocks (or genes), where each synteny block is shared with all of its homologues in the input genomes. The evolution of these synteny blocks, ...

Oxford University Press2012

Reconstruction of Large-Scale Phylogenies : Advances in Algorithms and Statistical Methods

Vaibhav Rajan

The evolutionary relationships between organisms or phylogenies are fundamental to biology. They are invaluable as guiding tools to mine, organize and exploit the enormous amounts of biological data in the post-genomic era. The advent of high-throughput se ...

EPFL2012

Bootstrapping phylogenies inferred from rearrangement data

Bernard Moret, Yu Lin, Vaibhav Rajan

Background: Large-scale sequencing of genomes has enabled the inference of phylogenies based on the evolution of genomic architecture, under such events as rearrangements, duplications, and losses. Many evolutionary models and associated algorithms have be ...

BioMed Central2012

Transcriptional Regulatory Networks across Species : Evolution, Inference, and Refinement

Xiuwei Zhang

The determination of transcriptional regulatory networks is key to the understanding of biological systems. However, the experimental determination of transcriptional regulatory networks in the laboratory remains difficult and time-consuming, while current ...

EPFL2011

On Exploring Genome Rearrangement Phylogenetic Patterns

The study of genorne rearrangement is much harder than the corresponding problems on DNA and protein sequences, because of the occurrences of numerous combinatorial structures. By explicitly exploring these combinatorial structures, the recently developed ...

Springer-Verlag New York2010

Evolution of whole genomes through inversions : models and algorithms for duplicates, ancestors, and edit scenarios

Krister Swenson

Advances in sequencing technology are yielding DNA sequence data at an alarming rate – a rate reminiscent of Moore's law. Biologists' abilities to analyze this data, however, have not kept pace. On the other hand, the discrete and mechanical nature of the ...

EPFL2009

A Network Coding Approach to Network Tomography

Christina Fragouli

Network tomography aims at inferring internal network characteristics based on measurements at the edge of the network. In loss tomography, in particular, the characteristic of interest is the loss rate of individual links. There is a signiﬁcant body of wo ...

2009