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Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes

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What this work says

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

inferredcites →https://doi.org/10.1002/0470857897.ch8openalex-snapshot

The KEGG Database

inferredcites →https://doi.org/10.1007/978-1-4939-3369-3_13openalex-snapshot

MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function

inferredcites →https://doi.org/10.1007/978-1-4939-3369-3_16openalex-snapshot

Metatranscriptomics of Soil Eukaryotic Communities

inferredcites →https://doi.org/10.1016/j.chom.2014.08.014openalex-snapshot

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

inferredcites →https://doi.org/10.1016/j.ijmm.2005.06.009openalex-snapshot

Enterohaemorrhagic Escherichia coli in human medicine

inferredcites →https://doi.org/10.1016/j.mib.2004.08.002openalex-snapshot

Metagenomics – the key to the uncultured microbes

inferredcites →https://doi.org/10.1016/j.physa.2014.03.021openalex-snapshot

SICR rumor spreading model in complex networks: Counterattack and self-resistance

inferredcites →https://doi.org/10.1016/s1074-5521(98)90108-9openalex-snapshot

Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products

inferredcites →https://doi.org/10.1021/acsnano.5b07826openalex-snapshot

Tools for the Microbiome: Nano and Beyond

inferredcites →https://doi.org/10.1038/ismej.2011.212openalex-snapshot

The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates

inferredcites →https://doi.org/10.1038/ismej.2014.195openalex-snapshot

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

inferredcites →https://doi.org/10.1038/nature07540openalex-snapshot

A core gut microbiome in obese and lean twins

inferredcites →https://doi.org/10.1038/nature08821openalex-snapshot

A human gut microbial gene catalogue established by metagenomic sequencing

inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot

Structure, function and diversity of the healthy human microbiome

inferredcites →https://doi.org/10.1038/nature11632openalex-snapshot

An integrated map of genetic variation from 1,092 human genomes

inferredcites →https://doi.org/10.1038/nbt.3319openalex-snapshot

ConStrains identifies microbial strains in metagenomic datasets

inferredcites →https://doi.org/10.1038/nbt.3329openalex-snapshot

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

inferredcites →https://doi.org/10.1038/ncomms3304openalex-snapshot

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.1975openalex-snapshot

Predicting bacterial community assemblages using an artificial neural network approach

inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot

UPARSE: highly accurate OTU sequences from microbial amplicon reads

inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot

Fast and sensitive protein alignment using DIAMOND

inferredcites →https://doi.org/10.1038/nmeth.3589openalex-snapshot

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

inferredcites →https://doi.org/10.1038/nmeth.3802openalex-snapshot

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot

DADA2: High-resolution sample inference from Illumina amplicon data

inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot

QIIME allows analysis of high-throughput community sequencing data

inferredcites →https://doi.org/10.1038/srep26447openalex-snapshot

MetaTrans: an open-source pipeline for metatranscriptomics

inferredcites →https://doi.org/10.1038/srep40200openalex-snapshot

MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes

inferredcites →https://doi.org/10.1073/pnas.1319284111openalex-snapshot

Relating the metatranscriptome and metagenome of the human gut

inferredcites →https://doi.org/10.1093/bib/bbs033openalex-snapshot

Functional assignment of metagenomic data: challenges and applications

inferredcites →https://doi.org/10.1093/bib/bbs039openalex-snapshot

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

inferredcites →https://doi.org/10.1093/bib/bbw005openalex-snapshot

An analysis of human microbe–disease associations

inferredcites →https://doi.org/10.1093/bioinformatics/btn322openalex-snapshot

Database indexing for production MegaBLAST searches

inferredcites →https://doi.org/10.1093/bioinformatics/btp336openalex-snapshot

SOAP2: an improved ultrafast tool for short read alignment

inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot

The Sequence Alignment/Map format and SAMtools

inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot

Search and clustering orders of magnitude faster than BLAST

inferredcites →https://doi.org/10.1093/bioinformatics/btr507openalex-snapshot

FLASH: fast length adjustment of short reads to improve genome assemblies

inferredcites →https://doi.org/10.1093/bioinformatics/bts611openalex-snapshot

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

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btu641openalex-snapshot

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

inferredcites →https://doi.org/10.1093/bioinformatics/btv584openalex-snapshot

SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data

inferredcites →https://doi.org/10.1093/bioinformatics/btw635openalex-snapshot

QUBIC: a bioconductor package for qualitative biclustering analysis of gene co-expression data

inferredcites →https://doi.org/10.1093/database/bar009openalex-snapshot

UniProt Knowledgebase: a hub of integrated protein data

inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/28.1.33openalex-snapshot

The COG database: a tool for genome-scale analysis of protein functions and evolution

inferredcites →https://doi.org/10.1093/nar/30.1.412openalex-snapshot

TTD: Therapeutic Target Database

inferredcites →https://doi.org/10.1093/nar/gkg039openalex-snapshot

The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy

inferredcites →https://doi.org/10.1093/nar/gki008openalex-snapshot

VFDB: a reference database for bacterial virulence factors

inferredcites →https://doi.org/10.1093/nar/gki866openalex-snapshot

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

inferredcites →https://doi.org/10.1093/nar/gkj067openalex-snapshot

DrugBank: a comprehensive resource for in silico drug discovery and exploration

inferredcites →https://doi.org/10.1093/nar/gkl842openalex-snapshot

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

inferredcites →https://doi.org/10.1093/nar/gkl858openalex-snapshot

PATRIC: The VBI PathoSystems Resource Integration Center

inferredcites →https://doi.org/10.1093/nar/gkm321openalex-snapshot

KAAS: an automatic genome annotation and pathway reconstruction server

inferredcites →https://doi.org/10.1093/nar/gkm796openalex-snapshot

eggNOG: automated construction and annotation of orthologous groups of genes

inferredcites →https://doi.org/10.1093/nar/gkm864openalex-snapshot

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

inferredcites →https://doi.org/10.1093/nar/gkm869openalex-snapshot

IMG/M: a data management and analysis system for metagenomes

inferredcites →https://doi.org/10.1093/nar/gkn201openalex-snapshot

NCBI BLAST: a better web interface

inferredcites →https://doi.org/10.1093/nar/gkn656openalex-snapshot

ARDB--Antibiotic Resistance Genes Database

inferredcites →https://doi.org/10.1093/nar/gkn787openalex-snapshot

GtRNAdb: a database of transfer RNA genes detected in genomic sequence

inferredcites →https://doi.org/10.1093/nar/gkn879openalex-snapshot

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

inferredcites →https://doi.org/10.1093/nar/gkp491openalex-snapshot

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data

inferredcites →https://doi.org/10.1093/nar/gkq747openalex-snapshot

FragGeneScan: predicting genes in short and error-prone reads

inferredcites →https://doi.org/10.1093/nar/gks1005openalex-snapshot

Rfam 11.0: 10 years of RNA families

inferredcites →https://doi.org/10.1093/nar/gks1195openalex-snapshot

GenBank

inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

inferredcites →https://doi.org/10.1093/nar/gkt1099openalex-snapshot

PATRIC, the bacterial bioinformatics database and analysis resource

inferredcites →https://doi.org/10.1093/nar/gkt1103openalex-snapshot

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

inferredcites →https://doi.org/10.1093/nar/gkt1226openalex-snapshot

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

inferredcites →https://doi.org/10.1093/nar/gkt1274openalex-snapshot

RefSeq microbial genomes database: new representation and annotation strategy

inferredcites →https://doi.org/10.1093/nar/gku138openalex-snapshot

Strain/species identification in metagenomes using genome-specific markers

inferredcites →https://doi.org/10.1093/nar/gkv1230openalex-snapshot

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

inferredcites →https://doi.org/10.1093/nar/gkw1092openalex-snapshot

KEGG: new perspectives on genomes, pathways, diseases and drugs

inferredcites →https://doi.org/10.1096/fj.12-220806openalex-snapshot

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters

inferredcites →https://doi.org/10.1101/gr.216242.116openalex-snapshot

Microbial strain-level population structure and genetic diversity from metagenomes

inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot

BLAT —The BLAST -Like Alignment Tool

inferredcites →https://doi.org/10.1126/science.1183605openalex-snapshot

A Catalog of Reference Genomes from the Human Microbiome

inferredcites →https://doi.org/10.1126/science.aac5992openalex-snapshot

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

inferredcites →https://doi.org/10.1128/aac.00419-13openalex-snapshot

The Comprehensive Antibiotic Resistance Database

inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

inferredcites →https://doi.org/10.1128/aem.02345-10openalex-snapshot

Metagenomic Analyses: Past and Future Trends

inferredcites →https://doi.org/10.1128/aem.03006-05openalex-snapshot

Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

inferredcites →https://doi.org/10.1128/jcm.01228-07openalex-snapshot

16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls

inferredcites →https://doi.org/10.1128/mmbr.68.4.669-685.2004openalex-snapshot

Metagenomics: Application of Genomics to Uncultured Microorganisms

inferredcites →https://doi.org/10.1142/s0219720012300018openalex-snapshot

PROGRESS IN COMPUTATIONAL STUDIES OF HOST–PATHOGEN INTERACTIONS

inferredcites →https://doi.org/10.1142/s0219720015500237openalex-snapshot

Computational methodology for predicting the landscape of the human–microbial interactome region level influence

inferredcites →https://doi.org/10.1146/annurev.genet.38.072902.091216openalex-snapshot

Metagenomics: Genomic Analysis of Microbial Communities

inferredcites →https://doi.org/10.1186/1471-2105-11-485openalex-snapshot

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

inferredcites →https://doi.org/10.1186/1471-2105-13-141openalex-snapshot

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

inferredcites →https://doi.org/10.1186/1471-2105-9-386openalex-snapshot

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

inferredcites →https://doi.org/10.1186/1471-2164-14-530openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1752-0509-8-24openalex-snapshot

Computational prediction of the human-microbial oral interactome

inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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/s12859-016-1270-8openalex-snapshot

SAMSA: a comprehensive metatranscriptome analysis pipeline

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/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1371/journal.pbio.1002050openalex-snapshot

Where Next for Microbiome Research?

inferredcites →https://doi.org/10.1371/journal.pcbi.1000465openalex-snapshot

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

inferredcites →https://doi.org/10.1371/journal.pcbi.1002358openalex-snapshot

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

inferredcites →https://doi.org/10.1371/journal.pone.0142102openalex-snapshot

COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets

inferredcites →https://doi.org/10.2165/00066982-200106040-00012openalex-snapshot

16S rRNA Gene Sequencing for Bacterial Pathogen Identification in the Clinical Laboratory

inferredcites →https://doi.org/10.3389/fgene.2013.00041openalex-snapshot

Multivariate analysis of functional metagenomes

inferredcites →https://doi.org/10.3389/fmicb.2012.00417openalex-snapshot

Fundamentals of Microbial Community Resistance and Resilience

inferredcites →https://doi.org/10.3389/fmicb.2015.00896openalex-snapshot

Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota

inferredcites →https://doi.org/10.3389/fmicb.2016.00712openalex-snapshot

Tracking Strains in the Microbiome: Insights from Metagenomics and Models

inferredcites →https://doi.org/10.4137/bbi.s34610openalex-snapshot

Use of Metatranscriptomics in Microbiome Research

inferredcites →https://doi.org/10.7717/peerj.425openalex-snapshot

FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares

What points at this work

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

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Response Mechanisms of Phaeodactylum Tricornutum to 2,6-Di-Tert-Butyl-P-Cresol (Bht) Stress: Implications of Indole-3-Acetic Acid (Iaa) in Microalgae-Bacteria Interactions

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Microbial Omics: Role in Ecological Studies and Environmental Control Measures

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High-Throughput Analysis to Decipher Bacterial Diversity and their Functional Properties in Freshwater Bodies

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Omic Technologies and Cold Adaptations

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The influence of 2,6-Di-tert-butyl-p-cresol stress on the microalga Phaeodactylum tricornutum and phycosphere bacteria community

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Biotechnological approaches in agriculture and environmental management - bacterium Kocuria rhizophila 14ASP as heavy metal and salt- tolerant plant growth- promoting strain

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Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists

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Unravelling the sandalwood microbiome and their interactions using NGS-based approaches to improve agroforestry management practices

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Discovering a thermophilic xylanase and a β-xylosidase for synergistic degradation of corncob

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Genomic insights of plant endophyte interaction: prospective and impact on plant fitness

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Spinal cord injury and the gut microbiota

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Deciphering soil microbiota using metagenomic approach for sustainable agriculture: an overview

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Role of bioinformatics tools in microbial prospectives and its future

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Gene prediction through metagenomics

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Significance of Upcoming Technologies and Their Potential Applications in Understanding Microbial Diversity

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Exploring the Microbial Diversity in Extreme Acidic Environment Using Molecular Techniques

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Evolution of microbial genomics: conceptual shifts over a century

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Bioprospecting lignin for biorefinery: Emerging innovations and strategies in microbial technology

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Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data

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The occurrence of banana Fusarium wilt aggravates antibiotic resistance genes dissemination in soil

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Advancements in drug delivery systems for women’s reproductive health: Vaginal microbiome as a target for innovative drug delivery systems

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Hierarchically Labeled Database Indexing Allows Scalable Characterization of Microbiomes

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Roadmap to functional characterization of the human intestinal microbiota in its interaction with the host

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Identifying potential bacterial pathogens in wastewater by expert reliability analysis of full-length 16S rRNA and untargeted RNA sequencing data processed with four bioinformatic workflows

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Updates on metaQuantome Software for Quantitative Metaproteomics

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Discovering and Designing a Chimeric Hyperthermophilic Chitinase for Crystalline Chitin Degradation

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Identification of Antibiotic Resistance Proteins via MiCId’s Augmented Workflow. A Mass Spectrometry-Based Proteomics Approach

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Metagenomics-enabled microbial surveillance

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Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods

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Sneathia: an emerging pathogen in female reproductive disease and adverse perinatal outcomes

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Network analyses in microbiome based on high-throughput multi-omics data

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A review on the application of bioinformatics tools in food microbiome studies

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Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data

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Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes

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A review of methods and databases for metagenomic classification and assembly

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Interpretation of differential gene expression results of RNA-seq data: review and integration

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MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome

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An approach for deriving water quality guideline values for antimicrobials that integrates ecotoxicity and antimicrobial resistance endpoints

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Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research

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Probing the functional significance of wild animal microbiomes using omics data

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Environmental DNA methylation of Lymnaea stagnalis varies with age and is hypermethylated compared to tissue DNA

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High-throughput DNA sequencing technologies for water and wastewater analysis

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Metagenomic applications in exploration and development of novel enzymes from nature: a review

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Metagenomics and Its Tools and Softwares

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Analysis of the Metatranscriptome of Microbial Communities by Comparison of Different Assembly Tools Reveals Improved Functional Annotation

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Synergistic Response of Phycosphere Bacteria with Microalga Phaeodactylum tricornutum under the 2,6-Di-tert-butyl-p-cresol Stress

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Biosynthetic activity of Marine Sponge Microbiota

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Approaches to metagenomic classification and assembly

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rSeqTU—A Machine-Learning Based R Package for Prediction of Bacterial Transcription Units

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Current Trends in Experimental and Computational Approaches to Combat Antimicrobial Resistance

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Decoding the microbial universe with metagenomics: a brief insight

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CNN_FunBar: Advanced Learning Technique for Fungi ITS Region Classification

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Nitrogen Acquisition Strategies Mediated by Insect Symbionts: A Review of Their Mechanisms, Methodologies, and Case Studies

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Periodontal treatment and microbiome-targeted therapy in management of periodontitis-related nonalcoholic fatty liver disease with oral and gut dysbiosis

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Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods

inferred← citeshttps://doi.org/10.5772/intechopen.89944openalex-snapshot

High-Throughput Sequencing and Metagenomic Data Analysis

inferred← citeshttps://doi.org/10.70675/1b47c678zf649z43a9z8435z643e9168fe33openalex-snapshot

Étude de la diversité du domaine Bacteria et du règne Fungi au cours du rouissage du lin sur champ par une approche de metabarcoding

inferred← citeshttps://doi.org/10.7717/peerj.15145openalex-snapshot

Inference of differentially expressed genes using generalized linear mixed models in a pairwise fashion

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