Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love, Wolfgang Huber, Simon Anders

Genome biology

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg

Nature Methods

Long-read SequencingSequence AssemblyNatural SciencesComputational BiologyMolecular Biology +5

limma powers differential expression analyses for RNA-sequencing and microarray studies

Matthew E. Ritchie, Belinda Phipson, Di Wu, +4

Nucleic Acids Research

GeneticsMolecular BiologyTranscriptomics TechnologyLimma PackageGenomics +17

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan, Ira M. Hall

Bioinformatics

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

Sven Heinz, Christopher Benner, Nathanael J. Spann, +7

Molecular Cell

Transcriptional RegulationB Cell IdentitiesCell LineageGeneticsGene Regulation +7

Super-Enhancers in the Control of Cell Identity and Disease

Denes Hnisz, Brian J. Abraham, Tong Ihn Lee, +5

Cell

Cell RegulationAutoimmunityCell IdentityMedicineCell Biology +2

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

Xi Chen, Xu Han, Ping Yuan, +20

Cell

Transcriptional RegulationSystems BiologyDevelopmental BiologyCell LineageCore Transcriptional Network +12

Identifying ChIP-seq enrichment using MACS

Jianxing Feng, Tao Liu, Bo Qin, +2

Nature Protocols

Hardware SecuritySystem On ChipEngineeringHardware EmulationProgram Analysis +5

Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture

Qi‐Long Ying, Marios P. Stavridis, Dean Griffiths, +2

Nature Biotechnology

Regenerative MedicineRegenerationEmbryo CultureNeuroectodermal PrecursorsDevelopmental Biology +13

Early Lineage Segregation between Epiblast and Primitive Endoderm in Mouse Blastocysts through the Grb2-MAPK Pathway

Claire Chazaud, Yojiro Yamanaka, Tony Pawson, +1

Developmental Cell

Cell LineageDevelopmental BiologyCell DivisionPrimitive EndodermMedicine +8