An integrative transcriptomic atlas of organogenesis in human embryos

Human pancreas development

(2015) R. E. Jennings et al.   DEVELOPMENT

Linking RNA biology to lncRNAs

(2015) Loyal A. Goff et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors

(2015) Inês Cebola et al.   NATURE CELL BIOLOGY

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Discovery and annotation of long noncoding RNAs

(2015) John S Mattick et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas

(2015) Matthias S. Roost et al.   Stem Cell Reports

Human Hepatocytes with Drug Metabolic Function Induced from Fibroblasts by Lineage Reprogramming

(2014) Yuanyuan Du et al.   Cell Stem Cell

Direct Reprogramming of Human Fibroblasts to Functional and Expandable Hepatocytes

(2014) Pengyu Huang et al.   Cell Stem Cell

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

(2014) Andrew E Jaffe et al.   NATURE NEUROSCIENCE

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb

(2013) Justin Cotney et al.   CELL

Development of the Human Pancreas From Foregut to Endocrine Commitment

(2013) R. E. Jennings et al.   DIABETES

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

adephylo: new tools for investigating the phylogenetic signal in biological traits

(2010) Thibaut Jombart et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

Transcriptome Analysis of Early Organogenesis in Human Embryos

(2010) Hai Fang et al.   DEVELOPMENTAL CELL

Putting phylogeny into the analysis of biological traits: A methodological approach

(2010) Thibaut Jombart et al.   JOURNAL OF THEORETICAL BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

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