Zobrazeno 1 - 10
of 76
pro vyhledávání: '"Gavin A. Huttley"'
Autor:
Benjamin D. Kaehler, Nicholas A. Bokulich, Daniel McDonald, Rob Knight, J. Gregory Caporaso, Gavin A. Huttley
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-10 (2019)
Taxonomy classification of amplicon sequences is an important step in investigating microbial communities in microbiome analysis. Here, the authors show incorporating environment-specific taxonomic abundance information can lead to improved species-l
Externí odkaz:
https://doaj.org/article/02ad09f101884255b75a2601aa36326e
Autor:
Nicholas A. Bokulich, Benjamin D. Kaehler, Jai Ram Rideout, Matthew Dillon, Evan Bolyen, Rob Knight, Gavin A. Huttley, J. Gregory Caporaso
Publikováno v:
Microbiome, Vol 6, Iss 1, Pp 1-17 (2018)
Abstract Background Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. Results We present q2-feature-classifier (https://github.com/qiime2/q2-feature-classifier), a QIIME 2 plugin containing several novel m
Externí odkaz:
https://doaj.org/article/551b94192d324bc7b48c97a0fc6d7a3f
Publikováno v:
Genetics
Mutations contribute significantly to developing diversity in biological capabilities. Mutagenesis is an adaptive feature of normal development, e.g. generating diversity in immune cells...
There is increasing interest in developing diagnostics
There is increasing interest in developing diagnostics
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cd1b2430b574f0e5a39b54398291f060
http://europepmc.org/articles/PMC7198283
http://europepmc.org/articles/PMC7198283
Autor:
Gavin A. Huttley, Helmut Simon
The site frequency spectrum (SFS) is a commonly used statistic to summarize genetic variation in a sample of genomic sequences from a population. Such a genomic sample is associated with an imputed genealogical history with attributes such as branch
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f199b047b105942b27db1b8a6da43ef5
https://doi.org/10.1101/2021.07.23.453461
https://doi.org/10.1101/2021.07.23.453461
Autor:
Helmut Simon, Gavin A. Huttley
We present a new statistic for testing for neutral evolution from allele frequency data summarised as a site frequency spectrum, which we call the relative likelihood neutrality test or ρ. Classical methods of testing for natural selection, such as
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6356941b50ece5c877747e8aca0fa0c1
https://doi.org/10.1101/2021.07.04.451068
https://doi.org/10.1101/2021.07.04.451068
Autor:
Rob Knight, Gavin A. Huttley, Daniel McDonald, Benjamin D. Kaehler, J. Gregory Caporaso, Nicholas A. Bokulich
Publikováno v:
Nature Communications, Vol 10, Iss 1, Pp 1-10 (2019)
Nature communications, vol 10, iss 1
Nature Communications
Nature Communications, 10 (1)
Nature communications, vol 10, iss 1
Nature Communications
Nature Communications, 10 (1)
Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumpti
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1c711bb9b243a5397a10287d863220ab
https://doaj.org/article/02ad09f101884255b75a2601aa36326e
https://doaj.org/article/02ad09f101884255b75a2601aa36326e
Autor:
Gavin A. Huttley, Helmut Simon
Publikováno v:
G3: Genes|Genomes|Genetics
G3: Genes, Genomes, Genetics, Vol 10, Iss 8, Pp 2641-2652 (2020)
G3: Genes, Genomes, Genetics, Vol 10, Iss 8, Pp 2641-2652 (2020)
We report work to quantify the impact on the probability of human genome polymorphism both of recombination and of sequence context at different scales. We use population-based analyses of data on human genetic variants obtained from the public Ensem
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4aa7f4d7771e317cf99dc229ed8a9706
https://pubmed.ncbi.nlm.nih.gov/32527747
https://pubmed.ncbi.nlm.nih.gov/32527747
Autor:
Helmut Simon, Gavin A. Huttley
Supplementary figures and tables for the paper "Quantifying influences on intragenomic mutation rate"
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::37623a81f21a73de09b3f7f6e01da59b
Autor:
Zheng Sun, Daniel McDonald, Hong-Lei Wang, Zhenjiang Xu, Xiaoquan Su, Shi Huang, Lu Liu, Gongchao Jing, Zengbin Wang, Gavin A. Huttley, Antonio Gonzalez, Jian Xu, Rob Knight, Yufeng Zhang
Publikováno v:
mSystems, vol 5, iss 2
mSystems, Vol 5, Iss 2, p e00150-20 (2020)
mSystems, Vol 5, Iss 2 (2020)
mSystems
mSystems, Vol 5, Iss 2, p e00150-20 (2020)
mSystems, Vol 5, Iss 2 (2020)
mSystems
Here, we present a search-based strategy for disease detection and classification, which detects diseased samples via their outlier novelty versus a database of samples from healthy subjects and then compares them to databases of samples from patient
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5fa81a6216223a87313b2dd478566472
https://escholarship.org/uc/item/8n202169
https://escholarship.org/uc/item/8n202169
Autor:
Antonio Gonzalez, Jeff DeReus, Gavin A. Huttley, Gail Ackermann, Daniel McDonald, Benjamin D. Kaehler, Rob Knight, Clarisse Marotz
Publikováno v:
mSystems, vol 4, iss 4
mSystems, Vol 4, Iss 4 (2019)
mSystems
mSystems, Vol 4, Iss 4 (2019)
mSystems
Although analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatically acceler
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b977745861bb91299d80b305466659ab
https://doi.org/10.1128/msystems.00215-19
https://doi.org/10.1128/msystems.00215-19