Searching journal content for articles similar to Kosakovsky Pond et al. 19 (11): 2144.

Displaying results 1-10 of 1804

For checked items

view abstracts
download to citation manager

Select this article
Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...Strain-level metagenomic profiling using pan graphs with PanTax Wenhai Zhang1,2,5, Yuansheng Liu3,5, Guangyi Li2,5, Jialu Xu2, Enlian Chen2, Alexander Schönhuth4 and Xiao Luo1,2 1Hunan Research Center of the Basic Discipline for Cell Signaling, Hunan University, Changsha, Hunan 410082, China; 2...
OPEN ACCESS ARTICLE
Select this article
Method: Real-time analysis and visualization of nanopore metagenomic samples with MARTi
- Ned Peel,
- Samuel Martin,
- Darren Heavens,
- Douglas W. Yu,
- Matthew D. Clark,
- and Richard M. Leggett
Genome Res. November 2025 35: 2488-2500; Published in Advance October 27, 2025, doi:10.1101/gr.280550.125
...platform is currently the most well-known example of a real-time metagenomic analysis tool. Initially, ONT developed the EPI2ME Agent software, which featured several cloud-based analysis workflows including two popular metagenomic pipelines: What's In My Pot (WIMP) and Antimicrobial Resistance Mapping...
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
...of Epidemiology and Biostatistics, University of California, San Francisco, California 94158, USA Corresponding author: katherine.pollard@gladstone.ucsf.eduAbstractMetagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across...
OPEN ACCESS ARTICLE
Select this article
Method: Graph-based self-supervised learning for repeat detection in metagenomic assembly
- Ali Azizpour,
- Advait Balaji,
- Todd J. Treangen,
- and Santiago Segarra
Genome Res. September 2024 34: 1468-1476; Published in Advance July 19, 2024, doi:10.1101/gr.279136.124
...the case in which repeat labels for some contigs are available. This setting might arise, for example, if we have knowledge about specific organisms present in the metagenomic sample and their corresponding reference s are accessible. GraSSRep can seamlessly accommodate this case. In our pipeline, we can...
Select this article
Resource: The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
- Simon Bray,
- John Chilton,
- Matthias Bernt,
- Nicola Soranzo,
- Marius van den Beek,
- Bérénice Batut,
- Helena Rasche,
- Martin Čech,
- Peter J.A. Cock,
- Björn Grüning,
- and Anton Nekrutenko
Genome Res. February 2023 33: 261-268; Published in Advance February 24, 2023, doi:10.1101/gr.276963.122
...step and initiates the process of updating a dependent artifact, generally by means of a GitHub pull request (PR).View larger version: In this window In a new window Figure 2. Automation pipeline for Bioconda packages, BioContainers, Galaxy tools, and workflows.The CI pipelines developed by Bioconda...
OPEN ACCESS ARTICLE
Select this article
Method: The Nubeam reference-free approach to analyze metagenomic sequencing reads
- Hang Dai and
- Yongtao Guan
Genome Res. September 2020 30: 1364-1375; Published in Advance September 3, 2020, doi:10.1101/gr.261750.120
...metagenomics whole shotgun (WGS) sequencing, where the amount of unmapped reads is substantial. When applied to a WGS sequencing data set to quantify distances between metagenomics samples from various human body habitats, Nubeam recapitulates findings made by mapping-based methods and sheds light...
OPEN ACCESS ARTICLE
Select this article
Method: High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic Nanopore sequencing
- Nicholas D. Sanderson,
- Jeremy Swann,
- Leanne Barker,
- James Kavanagh,
- Sarah Hoosdally,
- Derrick Crook,
- The GonFast Investigators Group,
- Teresa L. Street,
- and David W. Eyre
Genome Res. September 2020 30: 1354-1363; Published in Advance September 1, 2020, doi:10.1101/gr.262865.120
...-resistant Neisseria gonorrhoeae is a significant public health concern. Against this background, rapid culture-independent diagnostics may allow targeted treatment and prevent onward transmission. We have previously shown metagenomic sequencing of urine samples from men with urethral gonorrhea can recover near...
OPEN ACCESS ARTICLE
Select this article
Method: metaSPAdes: a new versatile metagenomic assembler
- Sergey Nurk,
- Dmitry Meleshko,
- Anton Korobeynikov,
- and Pavel A. Pevzner
Genome Res. May 2017 27: 824-834; Published in Advance March 15, 2017, doi:10.1101/gr.213959.116
..., St. Petersburg, Russia 198515; 3Department of Computer Science and Engineering, University of California, San Diego, California 92093-0404, USA While metagenomics has emerged as a technology of choice for analyzing bacterial populations, the assembly of metagenomic data remains challenging, thus...
Select this article
Method: Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid
- Steve Miller,
- Samia N. Naccache,
- Erik Samayoa,
- Kevin Messacar,
- Shaun Arevalo,
- Scot Federman,
- Doug Stryke,
- Elizabeth Pham,
- Becky Fung,
- William J. Bolosky,
- Danielle Ingebrigtsen,
- Walter Lorizio,
- Sandra M. Paff,
- John A. Leake,
- Rick Pesano,
- Roberta DeBiasi,
- Samuel Dominguez,
- and Charles Y. Chiu
Genome Res. May 2019 29: 831-842; Published in Advance April 16, 2019, doi:10.1101/gr.238170.118
...; 9Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, California 94143, USA ↵10 These authors contributed equally to this work. Corresponding author: charles.chiu@ucsf.eduAbstractMetagenomic next-generation sequencing (mNGS) for pan...
OPEN ACCESS ARTICLE
Select this article
Method: Accurate and robust inference of microbial growth dynamics from metagenomic sequencing reveals personalized growth rates
- Tyler A. Joseph,
- Philippe Chlenski,
- Aviya Litman,
- Tal Korem,
- and Itsik Pe'er
Genome Res. March 2022 32: 558-568; Published in Advance January 5, 2022, doi:10.1101/gr.275533.121
...overall. We further develop a theory formalizing a biological interpretation for PTRs. Using a reference database of 2935 species, we applied CoPTR to a case-control study of 1304 metagenomic samples from 106 individuals with inflammatory bowel disease. We show that growth rates are personalized, are only...

For checked items

view abstracts
download to citation manager

Searching journal content for articles similar to Kosakovsky Pond et al. 19 (11): 2144.

Search Results

Modify Results

This search

Preprint Server

Current Issue

In This Issue

Citation format:
Results / page:
Results order: