Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements

The role of the microbiome in ovarian cancer: mechanistic insights into oncobiosis and to bacterial metabolite signaling

(2021) Adrienn Sipos et al.   MOLECULAR MEDICINE

Taxonomic signatures of cause-specific mortality risk in human gut microbiome

(2021) Aaro Salosensaari et al.   Nature Communications

An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities

(2021) Denise M. O’Sullivan et al.   Scientific Reports

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Evaluation of the Microba Community Profiler for Taxonomic Profiling of Metagenomic Datasets From the Human Gut Microbiome

(2021) Donovan H. Parks et al.   Frontiers in Microbiology

Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements

(2021) Dieter M. Tourlousse et al.   Microbiome

Dissecting and tuning primer editing by proofreading polymerases

(2021) Daryl M Gohl et al.   NUCLEIC ACIDS RESEARCH

Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

(2020) Andrei Prodan et al.   PLoS One

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms

(2020) Patrick Denis Browne et al.   GigaScience

Impact of DNA Extraction Method on Variation in Human and Built Environment Microbial Community and Functional Profiles Assessed by Shotgun Metagenomics Sequencing

(2020) Hui-yu Sui et al.   Frontiers in Microbiology

Developing standards for the microbiome field

(2020) Gregory C. A. Amos et al.   Microbiome

Multicenter assessment of microbial community profiling using 16S rRNA gene sequencing and shotgun metagenomic sequencing

(2020) Dongsheng Han et al.   Journal of Advanced Research

Health and disease markers correlate with gut microbiome composition across thousands of people

(2020) Ohad Manor et al.   Nature Communications

Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment

(2019) Muneer Ahmad Malla et al.   Frontiers in Immunology

Microbial abundance, activity and population genomic profiling with mOTUs2

(2019) Alessio Milanese et al.   Nature Communications

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Perspectives for Consideration in the Development of Microbial Cell Reference Materials

(2019) Emma Allen-Vercoe et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Benchmarking Metagenomics Tools for Taxonomic Classification

(2019) Simon H. Ye et al.   CELL

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

Microbiome Diagnostics

(2019) Robert Schlaberg   CLINICAL CHEMISTRY

OUP accepted manuscript

(2018)   BIOINFORMATICS

Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run

(2018) Yi-Chun Yeh et al.   mSystems

Microbiome: Focus on Causation and Mechanism

(2018) Michael A. Fischbach   CELL

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

RefSeq: an update on prokaryotic genome annotation and curation

(2017) Daniel H Haft et al.   NUCLEIC ACIDS RESEARCH

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

Microbiome therapeutics — Advances and challenges

(2016) Mark Mimee et al.   ADVANCED DRUG DELIVERY REVIEWS

Trimming of sequence reads alters RNA-Seq gene expression estimates

(2016) Claire R. Williams et al.   BMC BIOINFORMATICS

A method for assessing efficiency of bacterial cell disruption and DNA release

(2016) Olle M. de Bruin et al.   BMC MICROBIOLOGY

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing

(2016) Dieter M. Tourlousse et al.   NUCLEIC ACIDS RESEARCH

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS