Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities

Machine Learning and Integrative Analysis of Biomedical Big Data

(2019) Bilal Mirza et al.   Genes

Mapping the microbial interactome: Statistical and experimental approaches for microbiome network inference

(2019) Anders B Dohlman et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

A Novel Human Microbe-Disease Association Prediction Method Based on the Bidirectional Weighted Network

(2019) Hao Li et al.   Frontiers in Microbiology

Detection of multi-dimensional co-exclusion patterns in microbial communities

(2018) Levent Albayrak et al.   BIOINFORMATICS

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

(2018) Benjamin Kleaveland et al.   CELL

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression

(2018) Wei Zhang et al.   NATURE GENETICS

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses

(2018) Olivier B. Bakker et al.   NATURE IMMUNOLOGY

Multi-omics analysis reveals neoantigen-independent immune cell infiltration in copy-number driven cancers

(2018) Daniel J. McGrail et al.   Nature Communications

Impact of sequencing depth on the characterization of the microbiome and resistome

(2018) Rahat Zaheer et al.   Scientific Reports

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

(2018) Dinka Mandakovic et al.   Scientific Reports

Node property of weighted networks considering connectability to nodes within two degrees of separation

(2018) Sun-ichi Amano et al.   Scientific Reports

Nonparametric Bayesian learning of heterogeneous dynamic transcription factor networks

(2018) Xiangyu Luo et al.   Annals of Applied Statistics

Penalized co-inertia analysis with applications to -omics data

(2018) Eun Jeong Min et al.   BIOINFORMATICS

Integration of Multi-omics Data for Gene Regulatory Network Inference and Application to Breast Cancer

(2018)   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

(2018) Yan He et al.   NATURE MEDICINE

Using Multi-Scale Genetic, Neuroimaging and Clinical Data for Predicting Alzheimer’s Disease and Reconstruction of Relevant Biological Mechanisms

(2018) Shashank Khanna et al.   Scientific Reports

A multi-omics approach for identifying important pathways and genes in human cancer

(2018) H. Robert Frost et al.   BMC BIOINFORMATICS

Computational approaches for the analysis of RNA–protein interactions: A primer for biologists

(2018) Kat S. Moore et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Microbiome interactions shape host fitness

(2018) Alison L. Gould et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Methods for normalizing microbiome data: an ecological perspective

(2018) Donald T. McKnight et al.   Methods in Ecology and Evolution

A statistical approach to participant selection in location-based social networks for offline event marketing

(2018) Yuxin Liu et al.   INFORMATION SCIENCES

Bayesian sparse reduced rank multivariate regression

(2017) Gyuhyeong Goh et al.   JOURNAL OF MULTIVARIATE ANALYSIS

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows

(2017) Ilma Tapio et al.   PLoS One

Disentangling Interactions in the Microbiome: A Network Perspective

(2017) Mehdi Layeghifard et al.   TRENDS IN MICROBIOLOGY

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

(2017) Yunan Luo et al.   Nature Communications

Structure Learning in Graphical Modeling

(2017) Mathias Drton et al.   Annual Review of Statistics and Its Application

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

More Is Better: Recent Progress in Multi-Omics Data Integration Methods

(2017) Sijia Huang et al.   Frontiers in Genetics

Statistical analysis of co-occurrence patterns in microbial presence-absence datasets

(2017) Kumar P. Mainali et al.   PLoS One

Regression analysis for microbiome compositional data

(2016) Pixu Shi et al.   Annals of Applied Statistics

Methods for the integration of multi-omics data: mathematical aspects

(2016) Matteo Bersanelli et al.   BMC BIOINFORMATICS

Dimension reduction techniques for the integrative analysis of multi-omics data

(2016) Chen Meng et al.   BRIEFINGS IN BIOINFORMATICS

A review on machine learning principles for multi-view biological data integration

(2016) Yifeng Li et al.   BRIEFINGS IN BIOINFORMATICS

Interactions between the colonic transcriptome, metabolome, and microbiome in mouse models of obesity-induced intestinal cancer

(2016) Anna C. Pfalzer et al.   PHYSIOLOGICAL GENOMICS

The identification of age-associated cancer markers by an integrative analysis of dynamic DNA methylation changes

(2016) Yihan Wang et al.   Scientific Reports

Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics

(2016) Juan Jovel et al.   Frontiers in Microbiology

Compact Integration of Multi-Network Topology for Functional Analysis of Genes

(2016) Hyunghoon Cho et al.   Cell Systems

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

(2016) Anna Heintz-Buschart et al.   Nature Microbiology

Triclosan Exposure Is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish

(2016) Christopher A. Gaulke et al.   PLoS One

Differential network analysis from cross-platform gene expression data

(2016) Xiao-Fei Zhang et al.   Scientific Reports

Learning directed acyclic graphical structures with genetical genomics data

(2015) Bin Gao et al.   BIOINFORMATICS

Exploiting ontology graph for predicting sparsely annotated gene function

(2015) Sheng Wang et al.   BIOINFORMATICS

CCLasso: correlation inference for compositional data through Lasso

(2015) Huaying Fang et al.   BIOINFORMATICS

Investigating microbial co-occurrence patterns based on metagenomic compositional data

(2015) Yuguang Ban 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

Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults

(2015) Julien Tap et al.   ENVIRONMENTAL MICROBIOLOGY

Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks

(2015) Andrey Morgun et al.   GUT

Gene Regulation Network Inference With Joint Sparse Gaussian Graphical Models

(2015) Hyonho Chun et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Bayesian Inference of Multiple Gaussian Graphical Models

(2015) Christine Peterson et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

(2015) Eric A. Franzosa et al.   NATURE REVIEWS MICROBIOLOGY

Microbial community transcriptional networks are conserved in three domains at ocean basin scales

(2015) Frank O. Aylward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular cartography of the human skin surface in 3D

(2015) Amina Bouslimani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

A unified initiative to harness Earth's microbiomes

(2015) A. P. Alivisatos et al.   SCIENCE

Spectra of weighted scale-free networks

(2015) Zhongzhi Zhang et al.   Scientific Reports

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

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

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

(2015) Stephen Nayfach et al.   PLoS Computational Biology

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease

(2015) Xochitl C Morgan et al.   GENOME BIOLOGY

Detecting modules in biological networks by edge weight clustering and entropy significance

(2015) Paola Lecca et al.   Frontiers in Genetics

Assessment and Selection of Competing Models for Zero-Inflated Microbiome Data

(2015) Lizhen Xu et al.   PLoS One

Variable selection in regression with compositional covariates

(2014) W. Lin et al.   BIOMETRIKA

Variable selection for generalized canonical correlation analysis

(2014) A. Tenenhaus et al.   BIOSTATISTICS

A multivariate approach to the integration of multi-omics datasets

(2014) Chen Meng et al.   BMC BIOINFORMATICS

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

(2014)   Cell Host & Microbe

The co-inertia approach in identification of specific microRNA in early and advanced atherosclerosis plaque

(2014) Ivan Jovanović et al.   MEDICAL HYPOTHESES

Inferring gene regulatory networks by integrating ChIP-seq/chip and transcriptome data via LASSO-type regularization methods

(2014) Jing Qin et al.   METHODS

An atlas of genetic influences on human blood metabolites

(2014) So-Youn Shin et al.   NATURE GENETICS

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Bayesian-multiplicative treatment of count zeros in compositional data sets

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

Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection

(2014) Casey M. Theriot et al.   Nature Communications

Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation

(2014) Wenyuan Li et al.   PLoS Computational Biology

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

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

Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis

(2013) Jun Chen et al.   Annals of Applied Statistics

Bayesian network prior: network analysis of biological data using external knowledge

(2013) Senol Isci et al.   BIOINFORMATICS

A Logistic Normal Multinomial Regression Model for Microbiome Compositional Data Analysis

(2013) Fan Xia et al.   BIOMETRICS

The joint graphical lasso for inverse covariance estimation across multiple classes

(2013) Patrick Danaher et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

Canonical correlation analysis for RNA-seq co-expression networks

(2013) Shengjun Hong et al.   NUCLEIC ACIDS RESEARCH

Inferring Polymorphism-Induced Regulatory Gene Networks Active in Human Lymphocyte Cell Lines by Weighted Linear Mixed Model Analysis of Multiple RNA-Seq Datasets

(2013) Wensheng Zhang et al.   PLoS One

A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel Disease

(2013) Maomeng Tong et al.   PLoS One

Exact Solutions of a Generalized Weighted Scale Free Network

(2013) Li Tan et al.   Journal of Applied Mathematics

Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships

(2013) Ian H McHardy et al.   Microbiome

Joint conditional Gaussian graphical models with multiple sources of genomic data

(2013) Hyonho Chun et al.   Frontiers in Genetics

Covariate-adjusted precision matrix estimation with an application in genetical genomics

(2012) T. T. Cai et al.   BIOMETRIKA

Sparse Estimation of Conditional Graphical Models With Application to Gene Networks

(2012) Bing Li et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

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

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

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

Aging effects on DNA methylation modules in human brain and blood tissue

(2012) Steve Horvath et al.   GENOME BIOLOGY

Mixed-model coexpression: calculating gene coexpression while accounting for expression heterogeneity

(2011) N. A. Furlotte et al.   BIOINFORMATICS

Joint estimation of multiple graphical models

(2011) J. Guo et al.   BIOMETRIKA

Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer

(2011) Stephan Gade et al.   BMC BIOINFORMATICS

Sparse partial least-squares regression and its applications to high-throughput data analysis

(2011) Donghwan Lee et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Introduction to Network Analysis in Systems Biology

(2011) A. Ma'ayan   Science Signaling

Zero-Inflated and Hurdle Models of Count Data with Extra Zeros: Examples from an HIV-Risk Reduction Intervention Trial

(2011) Mei-Chen Hu et al.   AMERICAN JOURNAL OF DRUG AND ALCOHOL ABUSE

Regularized multivariate regression for identifying master predictors with application to integrative genomics study of breast cancer

(2010) Jie Peng et al.   Annals of Applied Statistics

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

(2010) James H Bullard et al.   BMC BIOINFORMATICS

An Integrated Approach to Uncover Drivers of Cancer

(2010) Uri David Akavia et al.   CELL

Integration of ‘omics’ data: does it lead to new insights into host–microbe interactions?

(2010) Gwendoline Kint et al.   Future Microbiology

Sparse partial least squares regression for simultaneous dimension reduction and variable selection

(2010) Hyonho Chun et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Sparse canonical correlation analysis

(2010) David R. Hardoon et al.   MACHINE LEARNING

Systems biology of ovine intestinal parasite resistance: disease gene modules and biomarkers

(2010) Haja N. Kadarmideen et al.   Molecular BioSystems

A multivariate regression approach to association analysis of a quantitative trait network

(2009) S. Kim et al.   BIOINFORMATICS

Reconstruct modular phenotype-specific gene networks by knowledge-driven matrix factorization

(2009) Xuerui Yang et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Sparse Canonical Correlation Analysis with Application to Genomic Data Integration

(2009) Elena Parkhomenko et al.   Statistical Applications in Genetics and Molecular Biology

Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data

(2009) Daniela M Witten et al.   Statistical Applications in Genetics and Molecular Biology

A kernel-based integration of genome-wide data for clinical decision support

(2009) Anneleen Daemen et al.   Genome Medicine

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis

(2008) Sandra Waaijenborg et al.   Statistical Applications in Genetics and Molecular Biology

GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function

(2008) Sara Mostafavi et al.   GENOME BIOLOGY