Cargando…

Accurate genome relative abundance estimation for closely related species in a metagenomic sample

BACKGROUND: Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely th...

Descripción completa

Detalles Bibliográficos
Autores principales:	Sohn, Michael B, An, Lingling, Pookhao, Naruekamol, Li, Qike
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2014
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131027/ https://www.ncbi.nlm.nih.gov/pubmed/25027647 http://dx.doi.org/10.1186/1471-2105-15-242

Ejemplares similares

Accurate Genome Relative Abundance Estimation Based on Shotgun Metagenomic Reads
por: Xia, Li C., et al.
Publicado: (2011)

The devil is in the detail: estimating species richness, density, and relative abundance of tropical island herpetofauna
por: Surendran, Harikrishnan, et al.
Publicado: (2015)

Fast estimation of genetic relatedness between members of heterogeneous populations of closely related genomic variants
por: Tsyvina, Viachaslau, et al.
Publicado: (2018)

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes
por: Nayfach, Stephen, et al.
Publicado: (2015)

Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples
por: Lewandowska, Dagmara W., et al.
Publicado: (2017)

A completeness-independent method for pre-selection of closely related genomes for species delineation in prokaryotes
por: Zhou, Yizhuang, et al.
Publicado: (2020)

Metagenomic abundance estimation and diagnostic testing on species level
por: Lindner, Martin S., et al.
Publicado: (2013)

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
por: Lind, Abigail L., et al.
Publicado: (2021)

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
por: Hammond, Maria, et al.
Publicado: (2016)

Absolute quantitation of microbiota abundance in environmental samples
por: Tkacz, Andrzej, et al.
Publicado: (2018)

Improved methods for estimating abundance and related demographic parameters from mark‐resight data
por: McClintock, Brett T., et al.
Publicado: (2019)

How Poor Is Your Sample? A Simple Approach for Estimating the Relative Economic Status of Small and Nonrepresentative Samples
por: Ostermann, Jan, et al.
Publicado: (2023)

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics
por: Goussarov, Gleb, et al.
Publicado: (2022)

Novel intron markers to study the phylogeny of closely related mammalian species
por: Igea, Javier, et al.
Publicado: (2010)

Benchmarking different approaches for Norovirus genome assembly in metagenome samples
por: Fuentes-Trillo, Azahara, et al.
Publicado: (2021)

HirBin: high-resolution identification of differentially abundant functions in metagenomes
por: Österlund, Tobias, et al.
Publicado: (2017)

READSCAN: a fast and scalable pathogen discovery program with accurate genome relative abundance estimation
por: Naeem, Raeece, et al.
Publicado: (2013)

Bisulfite-based epityping on pooled genomic DNA provides an accurate estimate of average group DNA methylation
por: Docherty, Sophia J, et al.
Publicado: (2009)

A robust approach to estimate relative phytoplankton cell abundances from metagenomes
por: Pierella Karlusich, Juan José, et al.
Publicado: (2022)

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
por: Martin, Samuel, et al.
Publicado: (2022)

A comprehensive method for amplicon-based and metagenomic characterization of viruses, bacteria, and eukaryotes in freshwater samples
por: Uyaguari-Diaz, Miguel I., et al.
Publicado: (2016)

Microarray MAPH: accurate array-based detection of relative copy number in genomic DNA
por: Gibbons, Brian, et al.
Publicado: (2006)

CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads
por: Ai, Dongmei, et al.
Publicado: (2018)

Smart density: a more accurate method of measuring rural residential density for health-related research
por: Owens, Peter M, et al.
Publicado: (2010)

Accurate Measurement of the Relative Abundance of Different DNA Species in Complex DNA Mixtures
por: Jeong, Sangkyun, et al.
Publicado: (2012)

HMM-FRAME: accurate protein domain classification for metagenomic sequences containing frameshift errors
por: Zhang, Yuan, et al.
Publicado: (2011)

Power estimation and sample size determination for replication studies of genome-wide association studies
por: Jiang, Wei, et al.
Publicado: (2016)

A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses
por: Han, Mo, et al.
Publicado: (2018)

Estimating animal abundance: closed populations
por: Borchers, D L, et al.
Publicado: (2002)

Sampling designs matching species biology produce accurate and affordable abundance indices
por: Harris, Grant, et al.
Publicado: (2013)

High throughput accurate method for estimating in vitro dry matter digestibility of maize silage
por: Lopez-Marnet, P.-L., et al.
Publicado: (2021)

Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut
por: Pipek, O., et al.
Publicado: (2017)

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles
por: Nalbantoglu, Ozkan U, et al.
Publicado: (2011)

Estimating relative biomasses of organisms in microbiota using “phylopeptidomics”
por: Pible, Olivier, et al.
Publicado: (2020)

On the Bias of Precision Estimation Under Separate Sampling
por: Xie, Shuilian, et al.
Publicado: (2019)

Spatial epi-proteomics enabled by histone post-translational modification analysis from low-abundance clinical samples
por: Noberini, Roberta, et al.
Publicado: (2021)

Accurately Measuring Recombination between Closely Related HIV-1 Genomes
por: Schlub, Timothy E., et al.
Publicado: (2010)

Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes
por: Lim, Joe J., et al.
Publicado: (2023)

Considering sampling bias in close‐kin mark–recapture abundance estimates of Atlantic salmon
por: Wacker, Sebastian, et al.
Publicado: (2021)

Quantifying the relative importance of experimental data points in parameter estimation
por: Jeong, Jenny E., et al.
Publicado: (2018)

Cannot write session to /tmp/vufind_sessions/sess_s0tkldjdrj2fodv292nr41cm0t