Publications related to Phylogenetics

The microbiome of cryospheric ecosystems

Tom Ian Battin, Hannes Markus Peter, Susheel Bhanu Busi, Grégoire Marie Octave Edouard Michoud, Leïla Ezzat, Massimo Bourquin, Tyler Joe Kohler, Stylianos Fodelianakis

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. The melting of th ...

NATURE PORTFOLIO2022

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits

Jacques Fellay, Christian Axel Wandall Thorball

Infectious diseases are particularly challenging for genome-wide association studies (GWAS) because genetic effects from two organisms (pathogen and host) can influence a trait. Traditional GWAS assume individual samples are independent observations. Howev ...

OXFORD UNIV PRESS2022

MATHICSE Technical Report : Analysis of a class of Multi-Level 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 Multi-Level Markov chain Monte Carlo (ML-MCMC) algorithms based on independent Metropolis-Hastings proposals for Bayesian inverse problems. In this context, the likelihood function involves solvin ...

MATHICSE2021

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

Bart Deplancke, Bastien Mangeat, Vincent Roland Julien Gardeux, Julie Marie Russeil, Jörn Pezoldt, Elisa Cora, Daniel Alpern

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- ...

PUBLIC LIBRARY SCIENCE2021

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

MPGM: Scalable and Accurate Multiple Network Alignment

Matthias Grossglauser, Ehsan Kazemi

Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of conserved network mot ...

IEEE COMPUTER SOC2020

A modern scleractinian coral with a two-component calcite–aragonite skeleton

Anders Meibom, Jaroslaw Hubert Stolarski

One of the most conserved traits in the evolution of biomineralizing organisms is the taxon-specific selection of skeletal minerals. All modern scleractinian corals are thought to produce skeletons exclusively of the calcium-carbonate polymorph aragonite. ...

2020

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

Mary-Anne Hartley, Thomas Junier

Fever is the leading cause of paediatric outpatient consultations in Sub-Saharan Africa. Although most are suspected to be of viral origin, a putative causative pathogen is not identified in over a quarter of these febrile episodes. Using a de novo assembl ...

TAYLOR & FRANCIS LTD2019

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Phylogenetics

The microbiome of cryospheric ecosystems

HIERARCHICAL MARKOV CHAIN MONTE CARLO METHODS FOR BAYESIAN INVERSE PROBLEMS

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits

Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group

MATHICSE Technical Report : Analysis of a class of Multi-Level Markov Chain Monte Carlo algorithms based on Independent Metropolis-Hastings

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

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

MPGM: Scalable and Accurate Multiple Network Alignment

A modern scleractinian coral with a two-component calcite–aragonite skeleton

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

Graph Chatbot

Chat with Graph Search

HIERARCHICAL MARKOV CHAIN MONTE CARLO METHODS FOR BAYESIAN INVERSE PROBLEMS

MATHICSE Technical Report : Analysis of a class of Multi-Level Markov Chain Monte Carlo algorithms based on Independent Metropolis-Hastings

The microbiome of cryospheric ecosystems

Identifying and Characterizing Trans Women in the Swiss HIV Cohort Study as an Epidemiologically Distinct Risk Group

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

MPGM: Scalable and Accurate Multiple Network Alignment

A modern scleractinian coral with a two-component calcite–aragonite skeleton

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium