Choulet, Frédéric Wang, Xi Spannagl, Manuel Swarbreck, David Rimbert, Hélène Leroy, Philippe Lasserre-Zuber, Pauline Papon, Nathan
Wheat genome sequencing has passed through major steps in a decade, starting from the sequencing of large contiguous sequences obtained from chromosome-specific BAC libraries, to reach high-quality genome assemblies of a dozen of bread wheat varieties and wild relatives. While access to an assembled genome sequence is crucial for research, the reso...
Abécassis, Judith Dumas, Elise Alberge, Julie Varoquaux, Gaël
The increasing accumulation of medical data brings the hope of data-driven medical decision-making, but its increasing complexity -as text or images in electronic health records-calls for complex models, such as machine learning. Here, we review how machine learning can be used to inform decisions for individualized interventions, a causal question...
Amaral, Andreia Baudement, Marie-Odile Bonath, Franziska Charles, Mathieu Di Tommaso, Paolo Djebali, Sarah Eynard, Sonia Fischer, Daniel Foissac, Sylvain Gabernet, Gisela
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Standardised analysis pipelines are an important part of FAIR bioinformatics research. Over the last decade, there has been a notable shift from point-and-click pipeline solutions such as Galaxy towards command-line solutions such as Nextflow and Snakemake. We report on recent developments in the nf-core and Nextflow frameworks that have led to wid...
Vermeiren, Peter Charles, Sandrine Muñoz, Cynthia C.
We aimed to address two common challenges for scientists working with observational data: "how to quantify the relation between two observed variables", and, "how to account for censored observations" (i.e., observations whose value is only known to fall within a range). Quantifying the relationship between observed variables, and predicting one me...
By reproducing differential expression analysis simulation results presented by Li et al , we identified a caveat in the data generation process. Data not truly generated under the null hypothesis led to incorrect comparisons of benchmark methods. We provide corrected simulation results that demonstrate the good performance of dearseq and argue aga...
Jay, Paul Tezenas Du Montcel, Emilie Véber, Amandine Giraud, Tatiana
In the manuscript entitled “Do deleterious mutations promote the evolution of recombination suppression between X and Y chromosomes?” [1], the authors question the methodology and findings presented in our study on the role of deleterious mutations in the formation of sex chromosomes [2]. The present document is intended to answer the expressed con...
Bénitìere, Florian Lefébure, Tristan Duret, Laurent
Abstract Early studies in invertebrate model organisms (fruit flies, nematodes) showed that their synonymous codon usage is under selective pressure to optimize translation efficiency in highly expressed genes (a process called translational selection). In contrast, mammals show little evidence of selection for translationally optimal codons. To un...
Rahbé, Yvan Jacquet, Angelo
La plateforme Symbiotron (Lyon 1 Campus de la Doua) a été conçue pour mutualiser des espaces de travail dans des environnements contrôlés et sécurisés, adaptés à l’expérimentation sur les interactions entre insectes, microorganismes, plantes, dans le cadre d'études symbiotiques (sensu lato).Le symbiotron dispose 600 m² de laboratoires équipés hors ...
Wang, Belinda Vartak, Rasika Zaltsman, Yefim Naing, Zun Zar Chi Hennick, Kelsey Polacco, Benjamin Bashir, Ali Eckhardt, Manon Bouhaddou, Mehdi Xu, Jiewei
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Summary Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD bu...
Verneret, Marie Le, van Anthony Faraut, Thomas Turpin, Jocelyn Lerat, Emmanuelle
Transposable elements (TEs) have an important role in genome evolution but are challenging for bioinformatics detection due to their repetitive nature and ability to move and replicate within genomes. New sequencing technologies now enable the characterization of nucleotide and structural variations within species. Among them, TE polymorphism is cr...
