Searching journal content for articles similar to Ames et al. 25 (7): 1056.

Displaying results 1-10 of 88

For checked items

view abstracts
download to citation manager

Select this article
Review: Accurate and complete genomes from metagenomes
- Lin-Xing Chen,
- Karthik Anantharaman,
- Alon Shaiber,
- A. Murat Eren,
- and Jillian F. Banfield
Genome Res. March 2020 30: 315-333; Published in Advance March 18, 2020, doi:10.1101/gr.258640.119
..., the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as -resolved metagenomics, can circumvent this limitation by obtaining meta...
OPEN ACCESS ARTICLE
Select this article
Method: Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC
- Byron J. Smith,
- Chunyu Zhao,
- Veronika Dubinkina,
- Xiaofan Jin,
- Liron Zahavi,
- Saar Shoer,
- Jacqueline Moltzau-Anderson,
- Eran Segal,
- and Katherine S. Pollard
Genome Res. May 2025 35: 1247-1260; Published in Advance April 10, 2025, doi:10.1101/gr.279543.124
...PGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.In both diseased and healthy individuals, distinct strains of the same microbial species can differ in medically relevant traits...
OPEN ACCESS ARTICLE
Select this article
Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...Sachdeva1, Brett J. Baker3,4, David F. Savage1,7,8 and Jillian F. Banfield1,4,9,10 1Innovative Genomics Institute, University of California, Berkeley, California 94720, USA; 2Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA; 3Department of Marine Science...
OPEN ACCESS ARTICLE
Select this article
Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
- Marcus W. Fedarko,
- Mikhail Kolmogorov,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
...mutations (Toprak et al. 2012; Leyn et al. 2021; Zlamal et al. 2021): The tasks of identifying rare mutations in a microbial population and monitoring how some of them evolve into frequent mutations are important for understanding the dynamics of the acquisition of antibiotic resistance in a pathogen...
Select this article
Method: Microbial strain-level population structure and genetic diversity from metagenomes
- Duy Tin Truong,
- Adrian Tett,
- Edoardo Pasolli,
- Curtis Huttenhower,
- and Nicola Segata
Genome Res. April 2017 27: 626-638; Published in Advance February 6, 2017, doi:10.1101/gr.216242.116
..., and herewe targeted the seven samples in which the markers of the B. animalis species recruited at Microbial population genetics from metas Genome Research 627 www..org least 2× coverage. Comparison of our inferred strain consensus profiles to the reference achieved <0.01% single nucleotide errors, which...
OPEN ACCESS ARTICLE
Select this article
Method: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
- Donovan H. Parks,
- Michael Imelfort,
- Connor T. Skennerton,
- Philip Hugenholtz,
- and Gene W. Tyson
Genome Res. July 2015 25: 1043-1055; Published in Advance May 14, 2015, doi:10.1101/gr.186072.114
...from metagenomic data represent a consensus across amicrobial population. CheckMwas applied to 146 population s recovered from four metagenomic studies (Table 2). Table 2. Completeness and contamination of s from large-scale sequencing projects Genomes Completeness (% of s) Contamination (% of s) 100...
OPEN ACCESS ARTICLE
Select this article
Method: Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities
- John Beaulaurier,
- Elaine Luo,
- John M. Eppley,
- Paul Den Uyl,
- Xiaoguang Dai,
- Andrew Burger,
- Daniel J. Turner,
- Matthew Pendelton,
- Sissel Juul,
- Eoghan Harrington,
- and Edward F. DeLong
Genome Res. March 2020 30: 437-446; Published in Advance February 19, 2020, doi:10.1101/gr.251686.119
...; Roux et al. 2016b, 2019; Aylward et al. 2017; Luo et al. 2017).However, the ecological richness, evenness, and genomic complexity of viral assemblages complicate the determination of full-length virus sequences from naturally occurring viral populations. Most previous viral metagenomic studies have...
OPEN ACCESS ARTICLE
Select this article
Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
- Zhemin Zhou,
- Jane Charlesworth,
- and Mark Achtman
Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
...reflecting the vertical accumulation of mutations and can be used for assignments of bacterial strains to populations.An early genomic comparison of eight strains of Streptococcus agalactiae indicated that for some bacterial species, the total size of the pan may increase indefinitely with the number of s...
OPEN ACCESS ARTICLE
Select this article
Research: Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling
- Yichen Hu,
- Amnon Amir,
- Xiaochang Huang,
- Yan Li,
- Shi Huang,
- Elaine Wolfe,
- Sophie Weiss,
- Rob Knight,
- and Zhenjiang Zech Xu
Genome Res. June 2022 32: 1112-1123; Published in Advance June 10, 2022, doi:10.1101/gr.276482.121
...we collected saliva samples from 19 subjects before and while they ate lunch (lunch data set). We observed similar changes in these eating-increased and eating-decreased bacteria in most subjects, suggesting consistent microbial dynamics associated with eating in populations (Fig. 2C).The rise...
Select this article
Method: Genome-reconstruction for eukaryotes from complex natural microbial communities
- Patrick T. West,
- Alexander J. Probst,
- Igor V. Grigoriev,
- Brian C. Thomas,
- and Jillian F. Banfield
Genome Res. April 2018 28: 569-580; Published in Advance March 1, 2018, doi:10.1101/gr.228429.117
...of single-cell s (Woyke et al. 2010). Alternatively, metagenomic sequencing reads from environmental samples are mapped against reference s to detect organisms and constrain metabolisms, but this approach is restricted to study of organisms with sequenced relatives.Many current studies of natural ecosystems...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Ames et al. 25 (7): 1056.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: