Concept
Reference genome
Related publications (288)
Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012
Melanie Blokesch, Sandrine Stutzmann, Alexandre Lemopoulos, Natalia Carolina Drebes Dorr
Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...
2024Ancestral 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 ...
2024Transposable elements mediate genetic effects altering the expression of nearby genes in colorectal cancer
Didier Trono, Evaristo Jose Planet Letschert, Nikolaos Lykoskoufis
Transposable elements (TEs) are prevalent repeats in the human genome, play a significant role in the regulome, and their disruption can contribute to tumorigenesis. However, TE influence on gene expression in cancer remains unclear. Here, we analyze 275 n ...
2024Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities
Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...
EPFL2024Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter
Christof Holliger, Julien Maillard, Aline Sondra Adler, Marco Pagni, Simon Marius Jean Poirier
Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...
WILEY2022