Publications related to Maximum parsimony (phylogenetics)

Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania

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

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 ...

NATURE PORTFOLIO2023

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

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, Damiano Sgarbossa, Umberto Lupo

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

Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Felix Naef, Cédric Gobet

Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that have remained dif ...

ACADEMIC PRESS INC ELSEVIER SCIENCE2022

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

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Maximum parsimony (phylogenetics)

Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania

Spatiotemporal wildfire modeling through point processes with moderate and extreme marks

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

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

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

Towards an Evolutionary Theory of Stress Responses

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

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

Graph Chatbot

Chat with Graph Search

Spatiotemporal wildfire modeling through point processes with moderate and extreme marks

Extracting phylogenetic dimensions of coevolution reveals hidden functional signals

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

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Towards an Evolutionary Theory of Stress Responses

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

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

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