Publications related to Maximum parsimony (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

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

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

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

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, 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

Towards an Evolutionary Theory of Stress Responses

Maria del Carmen Sandi Perez

All organisms have a stress response system to cope with environmental threats, yet its precise form varies hugely within and across individuals, populations, and species. While the physiological mechanisms are increasingly understood, how stress responses ...

2021

The foreign oligochaete species Quistadrilus multisetosus (Smith, 1900) in Lake Geneva: morphological and molecular characterization and environmental influences on its distribution

Benoît Jean Dominique Ferrari, Régis Lionel Vivien

The presence of the oligochaete species Quistadrilus multisetosus (Smith, 1900) originating from North America has been mentioned for several decades in Europe, the Middle East and Russia. Its distribution and abundance in Europe is still unknown but it ca ...

2020

A Maximum-Likelihood-based Multi-User LoRa Receiver Implemented in GNU Radio

Andreas Peter Burg, Alexios Konstantinos Balatsoukas Stimming, Orion Afisiadis, Joachim Tobias Tapparel, Mathieu Pierre Xhonneux

LoRa is a popular low-power wide-area network (LPWAN) technology that uses spread-spectrum to achieve long-range connectivity and resilience to noise and interference. For energy efficiency reasons, LoRa adopts a pure ALOHA access scheme, which leads to re ...

IEEE2020

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

Jacques Fellay, Gabriel Leventhal

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

Neuronal morphologies: the shapes of thoughts

Lida Kanari

The mammalian brain, one of the most fascinating systems in nature, is a complex biological structure that has kept scientists busy for over a century. Many of the brain's mysteries have been unraveled due to the enormous efforts of the scientific communit ...

EPFL2018

Form - function relationships in dragonfly mandibles under an evolutionary perspective

Alessandra Patera

Functional requirements may constrain phenotypic diversification or foster it. For insect mouthparts, the quantification of the relationship between shape and function in an evolutionary framework remained largely unexplored. Here, the question of a functi ...

Royal Soc2017

Genotyping Of Bacillus Spp. Isolate Collection From Natural Samples

The aim of this study was genotyping and identification of collection of 164 Bacillus spp. isolates, from samples of soil, manure, and straw gathered from across Serbia, using Pulse field gel electrophoresis (PFGE) combined with sequencing of tuf gene, one ...

2017

Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

Jacques Fellay

HIV-1 set-point viral load-the approximately stable value of viraemia in the first years of chronic infection-is a strong predictor of clinical outcome and is highly variable across infected individuals. To better understand HIV-1 pathogenesis and the evol ...

Public Library Science2017

Discrimination of numerical proportions: A comparison of binomial and Gaussian models

Aire Raidvee

Observers discriminated the numerical proportion of two sets of elements (N = 9, 13, 33, and 65) that differed either by color or orientation. According to the standard Thurstonian approach, the accuracy of proportion discrimination is determined by irredu ...

Springer2017

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

Bernard Moret, Philipp Bucher, Yu Lin, Mingfu Shao, Nishanth Ulhas Nair, Paulina Grnarova, Laura Madeleine Hunter

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

Attached biofilms and suspended aggregates are distinct microbial lifestyles emanating from differing hydraulics

Tom Ian Battin, Hannes Markus Peter

Small-scale hydraulics affects microbial behaviour at the cell level1, trophic interactions in marine aggregates2 and the physical structure and function of stream biofilms3,4. However, it remains unclear how hydraulics, predictably changing from small str ...

Nature Publishing Group2016

Red squirrels in the British Isles are infected with leprosy bacilli

Stewart Cole, Andrej Benjak, Charlotte Avanzi, Philippe Busso, Jérémie Piton, Chloé Marie Loiseau

Leprosy, caused by infection with Mycobacterium leprae or the recently discovered Mycobacterium lepromatosis, was once endemic in humans in the British Isles. Red squirrels in Great Britain (Sciurus vulgaris) have increasingly been observed with leprosy-li ...

American Association for the Advancement of Science2016