Phylogenetic convolutional neural networks in metagenomics

gCoda: Conditional Dependence Network Inference for Compositional Data

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

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

(2017) Julia Fukuyama et al.   PLoS Computational Biology

Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition

(2017) Adriana Alberti et al.   Scientific Data

Fungal microbiota dysbiosis in IBD

(2016) Harry Sokol et al.   GUT

Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters

(2016) Yifeng Li et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

Multi-Layer and Recursive Neural Networks for Metagenomic Classification

(2015) Gregory Ditzler et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting

(2015) Davide Albanese et al.   PLoS Computational Biology

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Algebraic Comparison of Partial Lists in Bioinformatics

(2012) Giuseppe Jurman et al.   PLoS One

A Comparison of MCC and CEN Error Measures in Multi-Class Prediction

(2012) Giuseppe Jurman et al.   PLoS One

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Euclidean Nature of Phylogenetic Distance Matrices

(2011) Damien M. de Vienne et al.   SYSTEMATIC BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

“compositions”: A unified R package to analyze compositional data

(2007) K. Gerald van den Boogaart et al.   COMPUTERS & GEOSCIENCES

Sparse principal component analysis via regularized low rank matrix approximation

(2007) Haipeng Shen et al.   JOURNAL OF MULTIVARIATE ANALYSIS