Massively multiplex chemical transcriptomics at single-cell resolution

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Multiplexed single-cell RNA-seq via transient barcoding for simultaneous expression profiling of various drug perturbations

(2019) Dongju Shin et al.   Science Advances

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

DRUG-seq for miniaturized high-throughput transcriptome profiling in drug discovery

(2018) Chaoyang Ye et al.   Nature Communications

Combined CRISPRi/a-Based Chemical Genetic Screens Reveal that Rigosertib Is a Microtubule-Destabilizing Agent

(2017) Marco Jost et al.   MOLECULAR CELL

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens

(2017) Erin C. Bush et al.   Nature Communications

High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines

(2016) Channing Yu et al.   NATURE BIOTECHNOLOGY

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia

(2015) Jae-Seok Roe et al.   MOLECULAR CELL

Improving drug discovery with high-content phenotypic screens by systematic selection of reporter cell lines

(2015) Jungseog Kang et al.   NATURE BIOTECHNOLOGY

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

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Dose-Response Analysis Using R

(2015) Christian Ritz et al.   PLoS One

Acetate Dependence of Tumors

(2014) Sarah A. Comerford et al.   CELL

Chromatin: a capacitor of acetate for integrated regulation of gene expression and cell physiology

(2014) Siavash K Kurdistani   CURRENT OPINION IN GENETICS & DEVELOPMENT

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

(2013) Leif Väremo et al.   NUCLEIC ACIDS RESEARCH

Morphobase, an Encyclopedic Cell Morphology Database, and Its Use for Drug Target Identification

(2012) Yushi Futamura et al.   CHEMISTRY & BIOLOGY

Loss of tumor suppressor NF1 activates HSF1 to promote carcinogenesis

(2012) Chengkai Dai et al.   JOURNAL OF CLINICAL INVESTIGATION

Histone Acetylation Regulates Intracellular pH

(2012) Matthew A. McBrian et al.   MOLECULAR CELL

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Histone Deacetylase Inhibitors Downregulate Checkpoint Kinase 1 Expression to Induce Cell Death in Non-Small Cell Lung Cancer Cells

(2010) William Brazelle et al.   PLoS One

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation

(2009) K. E. Wellen et al.   SCIENCE

A high density assay format for the detection of novel cytotoxic agents in large chemical libraries

(2008) David Shum et al.   JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY