NetCoMi: network construction and comparison for microbiome data in R

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes

(2020) Bin Ma et al.   Microbiome

Cross-Domain and Viral Interactions in the Microbiome

(2019) Aislinn D. Rowan-Nash et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations

(2019) Mehdi Layeghifard et al.   npj Biofilms and Microbiomes

Difficulty in inferring microbial community structure based on co-occurrence network approaches

(2019) Hokuto Hirano et al.   BMC BIOINFORMATICS

Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data

(2019) Grace Yoon et al.   Frontiers in Genetics

Consistent and correctable bias in metagenomic sequencing experiments

(2019) Michael R McLaren et al.   eLife

Rapid Inference of Direct Interactions in Large-Scale Ecological Networks from Heterogeneous Microbial Sequencing Data

(2019) Janko Tackmann et al.   Cell Systems

Fungi stabilize connectivity in the lung and skin microbial ecosystems

(2018) Laura Tipton et al.   Microbiome

American Gut: an Open Platform for Citizen Science Microbiome Research

(2018) Daniel McDonald et al.   mSystems

Balances: a New Perspective for Microbiome Analysis

(2018) J. Rivera-Pinto et al.   mSystems

Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

SILGGM: An extensive R package for efficient statistical inference in large-scale gene networks

(2018) Rong Zhang et al.   PLoS Computational Biology

Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data

(2018) Nicole M. Davis et al.   Microbiome

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

gCoda: Conditional Dependence Network Inference for Compositional Data

(2017) Huaying Fang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Accessible, curated metagenomic data through ExperimentHub

(2017) Edoardo Pasolli et al.   NATURE METHODS

A Bayesian method for detecting pairwise associations in compositional data

(2017) Emma Schwager et al.   PLoS Computational Biology

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Inference of Environmental Factor-Microbe and Microbe-Microbe Associations from Metagenomic Data Using a Hierarchical Bayesian Statistical Model

(2017) Yuqing Yang et al.   Cell Systems

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

(2017) Thomas P. Quinn et al.   Scientific Reports

CompNet: a GUI based tool for comparison of multiple biological interaction networks

(2016) Bhusan K. Kuntal et al.   BMC BIOINFORMATICS

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Learning Microbial Interaction Networks from Metagenomic Count Data

(2016) Surojit Biswas et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Faster permutation inference in brain imaging

(2016) Anderson M. Winkler et al.   NEUROIMAGE

Microbiome Networks: A Systems Framework for Identifying Candidate Microbial Assemblages for Disease Management

(2016) R. Poudel et al.   PHYTOPATHOLOGY

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

(2016) Matthew T. Agler et al.   PLOS BIOLOGY

The discordant method: a novel approach for differential correlation

(2015) Charlotte Siska et al.   BIOINFORMATICS

CCLasso: correlation inference for compositional data through Lasso

(2015) Huaying Fang et al.   BIOINFORMATICS

zCompositions — R package for multivariate imputation of left-censored data under a compositional approach

(2015) Javier Palarea-Albaladejo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

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

network: A Package for Managing Relational Data inR

(2015) Carter T. Butts   Journal of Statistical Software

statnet: Software Tools for the Representation, Visualization, Analysis and Simulation of Network Data

(2015) Mark S. Handcock et al.   Journal of Statistical Software

Alignment-free protein interaction network comparison

(2014) Waqar Ali et al.   BIOINFORMATICS

Bayesian-multiplicative treatment of count zeros in compositional data sets

(2014) Josep-Antoni Martín-Fernández et al.   STATISTICAL MODELLING

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

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

Efficiency of a "Small-World" Brain Network Depends on Consciousness Level: A Resting-State fMRI Study

(2013) T. Uehara et al.   CEREBRAL CORTEX

Significance test of the adjusted Rand index. Application to the free sorting task

(2013) El Mostafa Qannari et al.   FOOD QUALITY AND PREFERENCE

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

A Plea for Neutral Comparison Studies in Computational Sciences

(2013) Anne-Laure Boulesteix et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Values below detection limit in compositional chemical data

(2012) J. Palarea-Albaladejo et al.   ANALYTICA CHIMICA ACTA

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

The GABRIEL Advanced Surveys: study design, participation and evaluation of bias

(2011) Jon Genuneit et al.   PAEDIATRIC AND PERINATAL EPIDEMIOLOGY

A statistical framework for differential network analysis from microarray data

(2010) Ryan Gill et al.   BMC BIOINFORMATICS

Permutation P-values Should Never Be Zero: Calculating Exact P-values When Permutations Are Randomly Drawn

(2010) Belinda Phipson et al.   Statistical Applications in Genetics and Molecular Biology

Functional Molecular Ecological Networks

(2010) J. Zhou et al.   mBio

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fewer permutations, more accurate P-values

(2009) Theo A. Knijnenburg et al.   BIOINFORMATICS

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

(2008) K. Strimmer   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

On Modularity Clustering

(2008) U. Brandes et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing

(2008) Susan M. Huse et al.   PLoS Genetics

A modified EM alr-algorithm for replacing rounded zeros in compositional data sets

(2007) J. Palarea-Albaladejo et al.   COMPUTERS & GEOSCIENCES