Publications related to A Rapid Bootstrap Algorithm for the RAxML Web Servers

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Umberto Lupo

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

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

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

Decentralized in-order execution of a sequential task-based code for shared-memory architectures

Charly Nicolas Lucien Castes

The hardware complexity of modern machines makes the design of adequate programming models crucial for jointly ensuring performance, portability, and productivity in high-performance computing (HPC). Sequential task-based programming models paired with adv ...

IEEE COMPUTER SOC2022

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

Predictive Reliability and Fault Management in Exascale Systems

David Atienza Alonso, Marina Zapater Sancho

Performance and power constraints come together with Complementary Metal Oxide Semiconductor technology scaling in future Exascale systems. Technology scaling makes each individual transistor more prone to faults and, due to the exponential increase in the ...

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

Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches

François Gillet, Bertrand Fournier

Understanding the factors underlying the co-occurrence of multiple species remains a challenge in ecology. Biotic interactions, environmental filtering and neutral processes are among the main mechanisms evoked to explain species co-occurrence. However, th ...

Frontiers Media Sa2016

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A Rapid Bootstrap Algorithm for the RAxML Web Servers

Impact of phylogeny on structural contact inference from protein sequence data

Analysis of a Class of Multilevel Markov Chain Monte Carlo Algorithms Based on Independent Metropolis–Hastings

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Decentralized in-order execution of a sequential task-based code for shared-memory architectures

A dual-layer MPI continuous large-scale hydrological model including Human Systems

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

Predictive Reliability and Fault Management in Exascale Systems

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

Enabling HPC for QoS-sensitive applications: the MANGO approach

Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches

Graph Chatbot

Chat with Graph Search

Analysis of a Class of Multilevel Markov Chain Monte Carlo Algorithms Based on Independent Metropolis–Hastings

Decentralized in-order execution of a sequential task-based code for shared-memory architectures

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

Predictive Reliability and Fault Management in Exascale Systems

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

Multiple Assembly Rules Drive the Co-occurrence of Orthopteran and Plant Species in Grasslands: Combining Network, Functional and Phylogenetic Approaches

Enabling HPC for QoS-sensitive applications: the MANGO approach

Impact of phylogeny on structural contact inference from protein sequence data

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

A dual-layer MPI continuous large-scale hydrological model including Human Systems