(Q36226914)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

title

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1 reference

1 reference

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Anna Heintz-Buschart

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Cedric C Laczny

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Nicolás Pinel

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Patrick May

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

Paul Wilmes

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1

Shaman Narayanasamy

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

2

Yohan Jarosz

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

5

Malte Herold

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

6

Anne Kaysen

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

publication date

16 December 2016

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

volume

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

page(s)

260

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

https://scigraph.springernature.com/pub.10.1186/s13059-016-1116-8

30 March 2020

exact match

0 references

cites work

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Altered carbon turnover processes and microbiomes in soils under long-term extremely high CO2 exposure

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

MetaTrans: an open-source pipeline for metatranscriptomics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Whole-genome optical mapping reveals a mis-assembly between two rRNA operons of Corynebacterium pseudotuberculosis strain 1002.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

A review of bioinformatic pipeline frameworks

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

MetaQUAST: evaluation of metagenome assemblies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Anvi'o: an advanced analysis and visualization platform for 'omics data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Bioboxes: standardised containers for interchangeable bioinformatics software

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

The impact of Docker containers on the performance of genomic pipelines

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Better reporting for better research: a checklist for reproducibility

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

An ensemble strategy that significantly improves de novo assembly of microbial genomes from metagenomic next-generation sequencing data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Comparison of assembly algorithms for improving rate of metatranscriptomic functional annotation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

GroopM: an automated tool for the recovery of population genomes from related metagenomes.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Binning metagenomic contigs by coverage and composition

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Metagenomic survey for viruses in Western Arctic caribou, Alaska, through iterative assembly of taxonomic units

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

An integrated catalog of reference genes in the human gut microbiome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Relating the metatranscriptome and metagenome of the human gut.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Trimmomatic: a flexible trimmer for Illumina sequence data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Alignment-free visualization of metagenomic data by nonlinear dimension reduction.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Prokka: rapid prokaryotic genome annotation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Metagenomic species profiling using universal phylogenetic marker genes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

IDBA-MT: de novo assembler for metatranscriptomic data generated from next-generation sequencing technology.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Condensing the omics fog of microbial communities.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Computational meta'omics for microbial community studies

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

MOCAT: a metagenomics assembly and gene prediction toolkit

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

CD-HIT: accelerated for clustering the next-generation sequencing data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Snakemake--a scalable bioinformatics workflow engine

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

A biomolecular isolation framework for eco-systems biology.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Growing unculturable bacteria

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Assessment of metagenomic assembly using simulated next generation sequencing data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

NGS QC Toolkit: a toolkit for quality control of next generation sequencing data

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Interactive metagenomic visualization in a Web browser

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Full-length transcriptome assembly from RNA-Seq data without a reference genome

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Ab initio gene identification in metagenomic sequences

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

A human gut microbial gene catalogue established by metagenomic sequencing

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

BEDTools: a flexible suite of utilities for comparing genomic features

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

The Sequence Alignment/Map format and SAMtools

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Microbial ecology to manage processes in environmental biotechnology

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

KEGG: kyoto encyclopedia of genes and genomes

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

CAP3: A DNA sequence assembly program

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

NeSSM: a Next-generation Sequencing Simulator for Metagenomics

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Microbial community structure and functioning in marine sediments associated with diffuse hydrothermal venting assessed by integrated meta-omics.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Sequential isolation of metabolites, RNA, DNA, and proteins from the same unique sample.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

Beware of mis-assembled genomes.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5159968

The human microbiome project

22 September 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1116-8

SAMSA: a comprehensive metatranscriptome analysis pipeline.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1116-8

Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1116-8

Prodigal: prokaryotic gene recognition and translation initiation site identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS13059-016-1116-8

Spherical: an iterative workflow for assembling metagenomic datasets.

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27986083

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S13059-016-1116-8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

30 March 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:27986083%20AND%20SRC:MED&resulttype=core&format=json

30 March 2020

1 reference