Zobrazeno 1 - 10
of 88
pro vyhledávání: '"Rayan Chikhi"'
Autor:
Camila Duitama González, Riccardo Vicedomini, Téo Lemane, Nicolas Rascovan, Hugues Richard, Rayan Chikhi
Publikováno v:
Microbiome, Vol 11, Iss 1, Pp 1-12 (2023)
Abstract Background The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) e
Externí odkaz:
https://doaj.org/article/b13556a48c1742cc9b4c234274d70530
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-19 (2023)
Abstract Background As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses. Several
Externí odkaz:
https://doaj.org/article/75120c1ff0e047c09e3f59223dc3ef0f
Autor:
Marco Forgia, Beatriz Navarro, Stefania Daghino, Amelia Cervera, Andreas Gisel, Silvia Perotto, Dilzara N. Aghayeva, Mary F. Akinyuwa, Emanuela Gobbi, Ivan N. Zheludev, Robert C. Edgar, Rayan Chikhi, Massimo Turina, Artem Babaian, Francesco Di Serio, Marcos de la Peña
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-11 (2023)
Abstract Earth’s life may have originated as self-replicating RNA, and it has been argued that RNA viruses and viroid-like elements are remnants of such pre-cellular RNA world. RNA viruses are defined by linear RNA genomes encoding an RNA-dependent
Externí odkaz:
https://doaj.org/article/3b43ed930332460d9fcf44b62c117571
Autor:
Camila Duitama González, Samarth Rangavittal, Riccardo Vicedomini, Rayan Chikhi, Hugues Richard
Publikováno v:
iScience, Vol 26, Iss 11, Pp 108057- (2023)
Summary: Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative con
Externí odkaz:
https://doaj.org/article/ad997cf3eb4a41c0a06ab9df187361e7
Publikováno v:
iScience, Vol 25, Iss 11, Pp 105305- (2022)
Summary: Sequencing errors continue to pose algorithmic challenges to methods working with sequencing data. One of the simplest and most prevalent techniques for ameliorating the detrimental effects of homopolymer expansion/contraction errors present
Externí odkaz:
https://doaj.org/article/9f30d939a3c6423daf865a86dfb9d9d4
Autor:
Christopher Quince, Sergey Nurk, Sebastien Raguideau, Robert James, Orkun S. Soyer, J. Kimberly Summers, Antoine Limasset, A. Murat Eren, Rayan Chikhi, Aaron E. Darling
Publikováno v:
Genome Biology, Vol 22, Iss 1, Pp 1-34 (2021)
Abstract We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph
Externí odkaz:
https://doaj.org/article/c74ea889eddf4483a41b363af8e7877a
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-14 (2021)
Existing long-read de novo assembly methods can partially, but not completely, separate strains. Here, the authors develop Strainberry, a metagenome assembly bioinformatic pipeline that exclusively uses longread data to accurately separate and recons
Externí odkaz:
https://doaj.org/article/6319ba8e68474bc9b3176b9f70701619
Publikováno v:
Algorithms for Molecular Biology, Vol 16, Iss 1, Pp 1-14 (2021)
Abstract K-mer based methods have become prevalent in many areas of bioinformatics. In applications such as database search, they often work with large multi-terabyte-sized datasets. Storing such large datasets is a detriment to tool developers, tool
Externí odkaz:
https://doaj.org/article/7126c47cc903415d9ed68f00ae1e8d99
Autor:
Gintare Lasaviciute, Anna Höbinger, Dorina Ujvari, Daniel Salamon, Aisha Yusuf, Mikael Sundin, Eva Sverremark-Ekström, Rayan Chikhi, Anna Nilsson, Shanie Saghafian-Hedengren
Publikováno v:
Hemato, Vol 2, Iss 1, Pp 154-166 (2021)
Various subsets of bone marrow mesenchymal stromal cells (BM MSCs), including fibroblasts, endothelial, fat and reticular cells, are implicated in the regulation of the hematopoietic microenvironment and the survival of long-lived antibody-secreting
Externí odkaz:
https://doaj.org/article/7277533e2db84d02a38d647075e58728
Publikováno v:
G3: Genes, Genomes, Genetics, Vol 10, Iss 2, Pp 437-442 (2020)
The North American mountain goat (Oreamnos americanus) is an iconic alpine species that faces stressors from climate change, industrial development, and recreational activities. This species’ phylogenetic position within the Caprinae lineage has no
Externí odkaz:
https://doaj.org/article/e523c8a70141403bb88fef437fe81729