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Gist – an ensemble approach to the taxonomic classification of metatranscriptomic sequence data

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/3-540-48194-x_6openalex-snapshot

Better Filtering with Gapped q-Grams

inferredcites →https://doi.org/10.1016/s0166-218x(03)00382-2openalex-snapshot

On spaced seeds for similarity search

inferredcites →https://doi.org/10.1016/s0723-2020(11)80197-9openalex-snapshot

Methanococcus igneus sp. nov., a Novel Hyperthermophilic Methanogen from a Shallow Submarine Hydrothermal System

inferredcites →https://doi.org/10.1038/ismej.2012.63openalex-snapshot

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

inferredcites →https://doi.org/10.1038/ncomms2432openalex-snapshot

Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen

inferredcites →https://doi.org/10.1038/nmeth.1358openalex-snapshot

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

inferredcites →https://doi.org/10.1093/bfgp/elr035openalex-snapshot

Comparison of the two major classes of assembly algorithms: overlap-layout-consensus and de-bruijn-graph

inferredcites →https://doi.org/10.1093/bioinformatics/18.3.440openalex-snapshot

PatternHunter: faster and more sensitive homology search

inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot

Fast and accurate short read alignment with Burrows–Wheeler transform

inferredcites →https://doi.org/10.1093/bioinformatics/btv419openalex-snapshot

Spaced seeds improve k -mer-based metagenomic classification

inferredcites →https://doi.org/10.1093/bioinformatics/btw542openalex-snapshot

Higher classification sensitivity of short metagenomic reads with CLARK- S

inferredcites →https://doi.org/10.1093/dnares/dss020openalex-snapshot

Deciphering the Genome of Polyphosphate Accumulating Actinobacterium Microlunatus phosphovorus

inferredcites →https://doi.org/10.1093/nar/25.17.3389openalex-snapshot

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

inferredcites →https://doi.org/10.1093/nar/gks335openalex-snapshot

Rapid identification of high-confidence taxonomic assignments for metagenomic data

inferredcites →https://doi.org/10.1093/nar/gks666openalex-snapshot

Modelling and simulating generic RNA-Seq experiments with the flux simulator

inferredcites →https://doi.org/10.1093/nar/gks828openalex-snapshot

Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms

inferredcites →https://doi.org/10.1101/gr.150151.112openalex-snapshot

Pathoscope : Species identification and strain attribution with unassembled sequencing data

inferredcites →https://doi.org/10.1126/science.1134196openalex-snapshot

The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella

inferredcites →https://doi.org/10.1126/science.1179721openalex-snapshot

Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5

inferredcites →https://doi.org/10.1128/aem.00062-07openalex-snapshot

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

inferredcites →https://doi.org/10.1155/2008/205969openalex-snapshot

Metagenome Fragment Classification Using N‐Mer Frequency Profiles

inferredcites →https://doi.org/10.1155/2014/309650openalex-snapshot

Evaluation and Comparison of Multiple Aligners for Next-Generation Sequencing Data Analysis

inferredcites →https://doi.org/10.1186/1471-2105-10-56openalex-snapshot

TACOA – Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach

inferredcites →https://doi.org/10.1186/1471-2105-11-544openalex-snapshot

Clustering metagenomic sequences with interpolated Markov models

inferredcites →https://doi.org/10.1186/1471-2105-12-41openalex-snapshot

RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles

inferredcites →https://doi.org/10.1186/1471-2105-13-92openalex-snapshot

A comparative evaluation of sequence classification programs

inferredcites →https://doi.org/10.1186/1471-2164-11-571openalex-snapshot

Comparing de novo assemblers for 454 transcriptome data

inferredcites →https://doi.org/10.1186/1745-6150-6-45openalex-snapshot

A Rooted Net of Life

inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot

Kraken: ultrafast metagenomic sequence classification using exact alignments

inferredcites →https://doi.org/10.1186/s12864-015-1419-2openalex-snapshot

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

inferredcites →https://doi.org/10.1371/journal.pone.0003373openalex-snapshot

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

inferredcites →https://doi.org/10.1371/journal.pone.0017447openalex-snapshot

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

inferredcites →https://doi.org/10.1371/journal.pone.0028967openalex-snapshot

Metatranscriptomics Reveals the Diversity of Genes Expressed by Eukaryotes in Forest Soils

inferredcites →https://doi.org/10.1371/journal.pone.0036009openalex-snapshot

Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing

inferredcites →https://doi.org/10.3389/fgene.2013.00237openalex-snapshot

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

inferredcites →https://doi.org/10.3402/mehd.v23i0.19260openalex-snapshot

Short-chain fatty acid fermentation products of the gut microbiome: implications in autism spectrum disorders

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/bioadv/vbae016openalex-snapshot

HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads

inferred← citeshttps://doi.org/10.1128/msystems.00884-20openalex-snapshot

Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

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