FluReF, an automated flu virus reassortment finder based on phylogenetic trees

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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

Transposon-activated POU5F1B promotes colorectal cancer growth and metastasis

Didier Trono, Laurence Gouzi Abrami, Sandra Eloise Kjeldsen, Evaristo Jose Planet Letschert, Julien Léonard Duc, Laia Simo Riudalbas, Alexandre Coudray, Sagane Dind

The treatment of colorectal cancer (CRC) is an unmet medical need in absence of early diagnosis. Here, upon characterizing cancer-specific transposable element-driven transpochimeric gene transcripts (TcGTs) produced by this tumor in the SYSCOL cohort, we ...

Nature Research2022

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

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

Single nucleotide polymorphism determines constitutive versus inducible type VI secretion in Vibrio cholerae

Melanie Blokesch, Sandrine Stutzmann, Alexis Joseph Proutière, Loriane Bader, Natalia Carolina Drebes Dorr, Milena Jadwiga Jaskolska

Vibrio cholerae is a well-studied human pathogen that is also a common inhabitant of marine habitats. In both environments, the bacterium is subject to interbacterial competition. A molecular nanomachine that is often involved in such competitive behavior ...

2022

Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae

Melanie Blokesch, David William Adams, Milena Jadwiga Jaskolska

Horizontal gene transfer can trigger rapid shifts in bacterial evolution. Driven by a variety of mobile genetic elements—in particular bacteriophages and plasmids—the ability to share genes within and across species underpins the exceptional adaptability o ...

2022

Expiratory Aerosol pH: The Overlooked Driver of Airborne Virus Inactivation

Tamar Kohn, Athanasios Nenes, Kalliopi Violaki, Ghislain Gilles Jean-Michel Motos, Walter Hugentobler, Aline Laetitia Schaub, Shannon Christa David

Respiratory viruses, including influenza virus and SARS-CoV-2, are transmitted by the airborne route. Air filtration and ventilation mechanically reduce the concentration of airborne viruses and are necessary tools for disease mitigation. However, they ign ...

2023

Electrochemical sensors for the detection of SARS-CoV-2 virus

Somanath Jagannath, Neeraj Kumar

Coronavirus (COVID-19), a deadly pandemic has spread worldwide and created many global health issues. Though methods of its detection are being continuously developed for the early detection and monitoring of COVID-19, still there is need for more novel me ...

ELSEVIER SCIENCE SA2022

Genotype-Dependent Kinetics of Enterovirus Inactivation by Free Chlorine and Ultraviolet (UV) Irradiation

Tamar Kohn, Shotaro Torii

Inactivation kinetics of enterovirus by disinfection is often studied using a single laboratory strain of a given genotype. Environmental variants of enterovirus are genetically distinct from the corresponding laboratory strain, yet it is poorly understood ...

2022

Interferon Lambda Delays the Emergence of Influenza Virus Resistance to Oseltamivir

Francesco Stellacci, Paulo Henrique Jacob Silva, Chiara Medaglia

Influenza viruses are a leading cause of morbidity and mortality worldwide. These air-borne pathogens are able to cross the species barrier, leading to regular seasonal epidemics and sporadic pandemics. Influenza viruses also possess a high genetic variabi ...

2021

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From Trees to Barcodes and Back Again: A Combinatorial, Probabilistic and Geometric Study of a Topological Inverse Problem

Adélie Eliane Garin

EPFL2022