Analysis and correction of compositional bias in sparse sequencing count data

Towards standards for human fecal sample processing in metagenomic studies

(2017) Paul I Costea et al.   NATURE BIOTECHNOLOGY

Modeling bias and variation in the stochastic processes of small RNA sequencing

(2017) Christos Argyropoulos et al.   NUCLEIC ACIDS RESEARCH

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

Universal Poisson Statistics of mRNAs with Complex Decay Pathways

(2016) Mukund Thattai   BIOPHYSICAL JOURNAL

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

CCLasso: correlation inference for compositional data through Lasso

(2015) Huaying Fang et al.   BIOINFORMATICS

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

(2015) J Paul Brooks et al.   BMC MICROBIOLOGY

The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses

(2015) Kaifu Chen et al.   MOLECULAR AND CELLULAR BIOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Comparative metagenomics reveals impact of contaminants on groundwater microbiomes

(2015) Christopher L. Hemme et al.   Frontiers in Microbiology

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

Assessing the Accuracy of Quantitative Molecular Microbial Profiling

(2014) Denise O'Sullivan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

(2014) Ying Yu et al.   Nature Communications

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

(2014) Mihai Pop et al.   GENOME BIOLOGY

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Considerations for the development and application of control materials to improve metagenomic microbial community profiling

(2012) Jim F. Huggett et al.   ACCREDITATION AND QUALITY ASSURANCE

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

(2012) Patricio S. La Rosa et al.   PLoS One

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Microbial Ecology of the Dark Ocean above, at, and below the Seafloor

(2011) B. N. Orcutt et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Statistical inferences for isoform expression in RNA-Seq

(2009) Hui Jiang et al.   BIOINFORMATICS

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Sulfur cycling and methanogenesis primarily drive microbial colonization of the highly sulfidic Urania deep hypersaline basin

(2009) S. Borin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Aerobic production of methane in the sea

(2008) David M. Karl et al.   Nature Geoscience

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS