Zobrazeno 1 - 10
of 23
pro vyhledávání: '"Jim Shaw"'
Autor:
Jim Shaw, Yun William Yu
Publikováno v:
Microbiome, Vol 12, Iss 1, Pp 1-10 (2024)
Abstract Background Metagenomic binning, the clustering of assembled contigs that belong to the same genome, is a crucial step for recovering metagenome-assembled genomes (MAGs). Contigs are linked by exploiting consistent signatures along a genome,
Externí odkaz:
https://doaj.org/article/f77300fb0b224c038718c4e822d9351d
Publikováno v:
BMC Bioinformatics, Vol 25, Iss 1, Pp 1-18 (2024)
Abstract Background Taxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community, but correctly assigning sequencing reads to the strain or sub-species level has remained a challen
Externí odkaz:
https://doaj.org/article/49cab98897c847afb0115ea04022830f
Autor:
Yun William Yu, Jim Shaw
Publikováno v:
Journal of Computational Biology. 29:195-211
Resolving haplotypes in polyploid genomes using phase information from sequencing reads is an important and challenging problem. We introduce two new mathematical formulations of polyploid haplotype phasing: (1) the min-sum max tree partition problem
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9d051c7f1b68f745cd7383efe0895839
https://doi.org/10.1089/cmb.2021.0436
https://doi.org/10.1089/cmb.2021.0436
Publikováno v:
Bioinformatics. 39
Motivation We face an increasing flood of genetic sequence data, from diverse sources, requiring rapid computational analysis. Rapid analysis can be achieved by sampling a subset of positions in each sequence. Previous sequence-sampling methods, such
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e32c23a7a727e2925e145cd87d2e8b95
https://doi.org/10.1093/bioinformatics/btad057
https://doi.org/10.1093/bioinformatics/btad057
Autor:
Yun William Yu, Jim Shaw
Publikováno v:
Bioinformatics. 38:4659-4669
Motivation Selecting a subset of k-mers in a string in a local manner is a common task in bioinformatics tools for speeding up computation. Arguably the most well-known and common method is the minimizer technique, which selects the ‘lowest-ordered
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::232e48eb9fbc45e29409144cbf9e2ed1
https://doi.org/10.1093/bioinformatics/btab790
https://doi.org/10.1093/bioinformatics/btab790
Taxonomic classification of reads obtained by metagenomic sequencing is often a first step for understanding a microbial community. While species level classification has become routine, correctly assigning sequencing reads to the strain or sub-speci
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2319716cb10690eba6f622d2afa8765b
https://doi.org/10.1101/2022.10.18.512733
https://doi.org/10.1101/2022.10.18.512733
Autor:
Yun William Yu, Jim Shaw
Seed-chain-extend with k-mer seeds is a powerful heuristic technique for sequence alignment employed by modern sequence aligners. While effective in practice for both runtime and accuracy, theoretical guarantees on the resulting alignment do not exis
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c7b0e91059a5aed5e483d6716930c25b
https://doi.org/10.1101/2022.10.14.512303
https://doi.org/10.1101/2022.10.14.512303
We face an increasing flood of genetic sequence data, from diverse sources, requiring rapid computational analysis. Rapid analysis can be achieved by sampling a subset of positions in each sequence. Previous sequence-sampling methods, such as minimiz
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::5c16a8e870f75ea1024dbafdd73cb8ed
https://doi.org/10.1101/2022.08.18.504476
https://doi.org/10.1101/2022.08.18.504476
Autor:
Jim Shaw, Yun William Yu
Publikováno v:
Genome Research. :gr.277637.122
Seed-chain-extend withk-mer seeds is a powerful heuristic technique for sequence alignment employed by modern sequence aligners. While effective in practice for both runtime and accuracy, theoretical guarantees on the resulting alignment do not exist
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b773e8772548cee887e162faa7529ebb
https://doi.org/10.1101/gr.277637.122
https://doi.org/10.1101/gr.277637.122
Publikováno v:
Ergonomics. 61(10)
Physical employment standards evaluate whether a worker possesses the physical abilities to safely and efficiently perform all critical on-the-job tasks. Initial Attack (IA) wildland fire fighters (WFF) must perform such critical tasks in all terrain
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::147c25f9df7360b8569e7230f5a152e5
https://pubmed.ncbi.nlm.nih.gov/29637835
https://pubmed.ncbi.nlm.nih.gov/29637835