Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex

Cerebellar granule cells encode the expectation of reward

(2017) Mark J. Wagner et al.   NATURE

Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq

(2017) Pingzhu Zhou et al.   eLife

A Microfluidic Device with Integrated Sonication and Immunoprecipitation for Sensitive Epigenetic Assays

(2016) Zhenning Cao et al.   ANALYTICAL CHEMISTRY

Single-molecule decoding of combinatorially modified nucleosomes

(2016) E. Shema et al.   SCIENCE

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

One-post patterning of multiple protein gradients using a low-cost flash foam stamp

(2015) Ling Yu et al.   CHEMICAL COMMUNICATIONS

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

A microfluidic device for epigenomic profiling using 100 cells

(2015) Zhenning Cao et al.   NATURE METHODS

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Deciphering H3K4me3 broad domains associated with gene-regulatory networks and conserved epigenomic landscapes in the human brain

(2015) A Dincer et al.   Translational Psychiatry

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

(2013) Li Shen et al.   PLoS One

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Human-Specific Histone Methylation Signatures at Transcription Start Sites in Prefrontal Neurons

(2012) Hennady P. Shulha et al.   PLOS BIOLOGY

Histone modification analysis by chromatin immunoprecipitation from a low number of cells on a microfluidic platform

(2011) Tao Geng et al.   LAB ON A CHIP

Induction of human neuronal cells by defined transcription factors

(2011) Zhiping P. Pang et al.   NATURE

A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells

(2011) Chao Ma et al.   NATURE MEDICINE

Single-tube linear DNA amplification (LinDA) for robust ChIP-seq

(2011) Pattabhiraman Shankaranarayanan et al.   NATURE METHODS

Discover regulatory DNA elements using chromatin signatures and artificial neural network

(2010) Hiram A. Firpi et al.   BIOINFORMATICS

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

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors

(2010) Mazhar Adli et al.   NATURE METHODS

Developmental regulation and individual differences of neuronal H3K4me3 epigenomes in the prefrontal cortex

(2010) I. Cheung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Integrated barcode chips for rapid, multiplexed analysis of proteins in microliter quantities of blood

(2008) Rong Fan et al.   NATURE BIOTECHNOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY