Scalable genetic screening for regulatory circuits using compressed Perturb-seq

Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens

(2023) John A. Morris et al.   SCIENCE

Inferring sparse structure in genotype–phenotype maps

(2023) Samantha Petti et al.   GENETICS

Autism genes converge on asynchronous development of shared neuron classes

(2022) Bruna Paulsen et al.   NATURE

Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease

(2022) Seyhan Yazar et al.   SCIENCE

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

(2022) Joseph M. Replogle et al.   CELL

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

(2022) Jacob W. Freimer et al.   NATURE GENETICS

Inferring and perturbing cell fate regulomes in human brain organoids

(2022) Jonas Simon Fleck et al.   NATURE

Mostly natural sequencing-by-synthesis for scRNA-seq using Ultima sequencing

(2022) Sean K. Simmons et al.   NATURE BIOTECHNOLOGY

Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics

(2022) Karthik A. Jagadeesh et al.   NATURE GENETICS

Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion

(2021) Chris J. Frangieh et al.   NATURE GENETICS

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome

(2021) Edward L. Huttlin et al.   CELL

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

Compressed sensing for highly efficient imaging transcriptomics

(2021) Brian Cleary et al.   NATURE BIOTECHNOLOGY

The distribution of common-variant effect sizes

(2021) Luke J. O’Connor   NATURE GENETICS

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

(2021) Urmo Võsa et al.   NATURE GENETICS

Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

(2021) Paul Datlinger et al.   NATURE METHODS

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Targeted Perturb-seq enables genome-scale genetic screens in single cells

(2020) Daniel Schraivogel et al.   NATURE METHODS

Where Are the Disease-Associated eQTLs?

(2020) Benjamin D. Umans et al.   TRENDS IN GENETICS

glmGamPoi: Fitting Gamma-Poisson Generalized Linear Models on Single Cell Count Data

(2020) Constantin Ahlmann-Eltze et al.   BIOINFORMATICS

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

(2020) Xin Jin et al.   SCIENCE

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

Trans Effects on Gene Expression Can Drive Omnigenic Inheritance

(2019) Xuanyao Liu et al.   CELL

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

NF-κB Signaling in Macrophages: Dynamics, Crosstalk, and Signal Integration

(2019) Michael G. Dorrington et al.   Frontiers in Immunology

Extreme Polygenicity of Complex Traits Is Explained by Negative Selection

(2019) Luke J. O'Connor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

OMIM.org: leveraging knowledge across phenotype–gene relationships

(2018) Joanna S Amberger et al.   NUCLEIC ACIDS RESEARCH

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

Linkage disequilibrium–dependent architecture of human complex traits shows action of negative selection

(2017) Steven Gazal et al.   NATURE GENETICS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression

(2017) Joseph Rosenbluh et al.   Nature Communications

Genetic correlations reveal the shared genetic architecture of transcription in human peripheral blood

(2017) Samuel W. Lukowski et al.   Nature Communications

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

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

MYC regulates the antitumor immune response through CD47 and PD-L1

(2016) S. C. Casey et al.   SCIENCE

Stepping Out of the Shade: Control of Neuronal Activity by the Scaffold Protein Kidins220/ARMS

(2016) Joachim Scholz-Starke et al.   Frontiers in Cellular Neuroscience

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

(2016) A. J. Aguirre et al.   Cancer Discovery

Innate Immune Pattern Recognition: A Cell Biological Perspective

(2015) Sky W. Brubaker et al.   Annual Review of Immunology

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

(2015) Oren Parnas et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Partitioning heritability by functional annotation using genome-wide association summary statistics

(2015) Hilary K Finucane et al.   NATURE GENETICS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

No Major Host Genetic Risk Factor Contributed to A(H1N1)2009 Influenza Severity

(2015) Koldo Garcia-Etxebarria et al.   PLoS One

THP-1 cell line: An in vitro cell model for immune modulation approach

(2014) Wasaporn Chanput et al.   INTERNATIONAL IMMUNOPHARMACOLOGY

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics

(2014) Claudia Giambartolomei et al.   PLoS Genetics

Molecular Mechanisms That Influence the Macrophage M1–M2 Polarization Balance

(2014) Nan Wang et al.   Frontiers in Immunology

ER stress induced impaired TLR signaling and macrophage differentiation of human monocytes

(2013) Takuya Komura et al.   CELLULAR IMMUNOLOGY

Systematic identification of trans eQTLs as putative drivers of known disease associations

(2013) Harm-Jan Westra et al.   NATURE GENETICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Concerted action of wild-type and mutant TNF receptors enhances inflammation in TNF receptor 1-associated periodic fever syndrome

(2010) A. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inhibition of NF- B Signaling by A20 Through Disruption of Ubiquitin Enzyme Complexes

(2010) N. Shembade et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

An Introduction To Compressive Sampling

(2008) E.J. Candes et al.   IEEE SIGNAL PROCESSING MAGAZINE