Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Batch effects and the effective design of single-cell gene expression studies

(2017) Po-Yuan Tung et al.   Scientific Reports

Parsing the Interferon Transcriptional Network and Its Disease Associations

(2016) Sara Mostafavi et al.   CELL

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans

(2016) Yang Li et al.   CELL

Fast and accurate long-range phasing in a UK Biobank cohort

(2016) Po-Ru Loh et al.   NATURE GENETICS

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits

(2016) Raul Aguirre-Gamboa et al.   Cell Reports

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Microfluidic single-cell whole-transcriptome sequencing

(2014) A. M. Streets et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intersection of population variation and autoimmunity genetics in human T cell activation

(2014) C. J. Ye et al.   SCIENCE

Common Genetic Variants Modulate Pathogen-Sensing Responses in Human Dendritic Cells

(2014) M. N. Lee et al.   SCIENCE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Integrative genomic analysis of the human immune response to influenza vaccination

(2013) Luis M Franco et al.   eLife

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update

(2011) X. Wang et al.   NUCLEIC ACIDS RESEARCH

Balancing Selection Maintains a Form of ERAP2 that Undergoes Nonsense-Mediated Decay and Affects Antigen Presentation

(2010) Aida M. Andrés et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS