Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

(2018) Jianfang Liu et al.   CELL

Opportunities and obstacles for deep learning in biology and medicine

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

Improving the value of public RNA-seq expression data by phenotype prediction

(2018) Shannon E Ellis et al.   NUCLEIC ACIDS RESEARCH

Massive mining of publicly available RNA-seq data from human and mouse

(2018) Alexander Lachmann et al.   Nature Communications

Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes

(2018) Kourosh Zarringhalam et al.   Scientific Reports

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Reproducible RNA-seq analysis using recount2

(2017) Leonardo Collado-Torres et al.   NATURE BIOTECHNOLOGY

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Integrating gene set analysis and nonlinear predictive modeling of disease phenotypes using a Bayesian multitask formulation

(2016) Mehmet Gönen   BMC BIOINFORMATICS

Association Between Response to Etrolizumab and Expression of Integrin αE and Granzyme A in Colon Biopsies of Patients With Ulcerative Colitis

(2016) Gaik W. Tew et al.   GASTROENTEROLOGY

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development

(2016) Ivan V. Ozerov et al.   Nature Communications

MicroRNAs Classify Different Disease Behavior Phenotypes of Crohnʼs Disease and May Have Prognostic Utility

(2015) Bailey C. E. Peck et al.   INFLAMMATORY BOWEL DISEASES

RNA sequencing atopic dermatitis transcriptome profiling provides insights into novel disease mechanisms with potential therapeutic implications

(2015) Mayte Suárez-Fariñas et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Proteogenomic analysis of psoriasis reveals discordant and concordant changes in mRNA and protein abundance

(2015) William R. Swindell et al.   Genome Medicine

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks

(2014) Kourosh Zarringhalam et al.   BIOINFORMATICS

Activation of the Aryl Hydrocarbon Receptor Dampens the Severity of Inflammatory Skin Conditions

(2014) Paola Di Meglio et al.   IMMUNITY

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism

(2014) J. Fadista et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

CellMix: a comprehensive toolbox for gene expression deconvolution

(2013) R. Gaujoux et al.   BIOINFORMATICS

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors

(2013) Konika Chawla et al.   BIOINFORMATICS

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets

(2011) Alyssa C Frazee et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Gene expression deconvolution in clinical samples

(2011) Yingdong Zhao et al.   Genome Medicine

Cell type–specific gene expression differences in complex tissues

(2010) Shai S Shen-Orr et al.   NATURE METHODS