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Publications associées (62)
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 Portfolio2024Spatiotemporal wildfire modeling through point processes with moderate and extreme marks
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 ...
2023BigNeuron: 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 PORTFOLIO2023Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load
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 PRESS2022Extracting 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 PORTFOLIO2022Protein 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 PORTFOLIO2022Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data
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 SCIENCE2022Towards an Evolutionary Theory of Stress Responses
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 ...
2021The 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 ...
2020A 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