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Publications associées (784)
Meeting our Makers:Uncovering the cis-regulatory activity of transposable elements using statistical learning
The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...
EPFL2024Validation of short-pulse reflectometry turbulence measurements with a synthetic diagnostic
Stefano Coda, Stephan Brunner, Oleg Krutkin, Umesh Kumar, Mackenzie Peter-Fulford Van Rossem, Samuele Mazzi
Experimental measurements of the turbulence amplitude utilizing a short pulse reflectometry method are presented. Two discharges with shaped plasma possessing opposite signs of triangularity are considered and a higher turbulence amplitude is found in the ...
Bristol2024Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants
Didier Trono, Evaristo Jose Planet Letschert, Wayo Matsushima
Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...
2024A CTCF-dependent mechanism underlies the Hox timer relation to a segmented body plan
During gastrulation, Hox genes are activated in a timesequence that follows the order of the genes along their clusters. This property, which is observed in all animals that develop following a progressive rostral-to-caudal morphogenesis, is associated wit ...
Current Biology Ltd2024The dynamic genetic determinants of increased transcriptional divergence in spermatids
Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...
Berlin2024Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network
Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...
EPFL2024Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...
Berlin2024Joint host-pathogen genomic analysis identifies hepatitis B virus mutations associated with human NTCP and HLA class I variation
Jacques Fellay, Bruno Emanuel Ferreira De Sousa Correia, Zhi Ming Xu, Andreas Scheck, Dylan Lawless, Olivier Noël Marie Naret, Arne Schneuing, David Gfeller, Thomas Junier, Sina Rüeger
Evolutionary changes in the hepatitis B virus (HBV) genome could reflect its adaptation to host -induced selective pressure. Leveraging paired human exome and ultra -deep HBV genome-sequencing data from 567 affected individuals with chronic hepatitis B, we ...
Cell Press2024Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations
BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...
2023Statistical learning quantifies transposable element-mediated cis-regulation
Didier Trono, Evaristo Jose Planet Letschert, Julien Léonard Duc, Alexandre Coudray, Julien Paul André Pontis, Delphine Yvette L Grun, Cyril David Son-Tuyên Pulver, Shaoline Sheppard
Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...
2023