Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome

Tropane Alkaloids: Chemistry, Pharmacology, Biosynthesis and Production

(2019) Kathrin Kohnen-Johannsen et al.   MOLECULES

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

(2019) Jason Lloyd-Price et al.   NATURE

Multi-Omic Analysis of the Microbiome and Metabolome in Healthy Subjects Reveals Microbiome-Dependent Relationships Between Diet and Metabolites

(2019) Zheng-Zheng Tang et al.   Frontiers in Genetics

Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer

(2019) Shinichi Yachida et al.   NATURE MEDICINE

Volatile metabolites in breath strongly correlate with gut microbiome in CD patients

(2018) Agnieszka Smolinska et al.   ANALYTICA CHIMICA ACTA

Understanding sequencing data as compositions: an outlook and review

(2018) Thomas P Quinn et al.   BIOINFORMATICS

Opportunities and obstacles for deep learning in biology and medicine

(2018) Travers Ching et al.   Journal of the Royal Society Interface

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Evaluation of metabolite-microbe correlation detection methods

(2018) Yijun You et al.   ANALYTICAL BIOCHEMISTRY

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

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

(2016) Chen Meng et al.   BRIEFINGS IN 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

A gene-based association method for mapping traits using reference transcriptome data

(2015) Eric R Gamazon et al.   NATURE GENETICS

Learning Understandable Neural Networks With Nonnegative Weight Constraints

(2015) Jan Chorowski et al.   IEEE Transactions on Neural Networks and Learning Systems

Metabolome of human gut microbiome is predictive of host dysbiosis

(2015) Peter E. Larsen et al.   GigaScience

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

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

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

The gut microbiota in IBD

(2012) Chaysavanh Manichanh et al.   Nature Reviews Gastroenterology & Hepatology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY