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

Multimodal CRISPR perturbations of GWAS loci associated with coronary artery disease in vascular endothelial cells

(2023) Florian Wünnemann et al.   PLoS Genetics

Transcriptome-wide association study in UK Biobank Europeans identifies associations with blood cell traits

(2022) Bryce Rowland et al.   HUMAN MOLECULAR GENETICS

Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types

(2022) Jia Wen et al.   PLoS Genetics

An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs

(2022) Eric B. Fauman et al.   BMC BIOINFORMATICS

A genome-scale screen for synthetic drivers of T cell proliferation

(2022) Mateusz Legut et al.   NATURE

New insights into the genetic etiology of Alzheimer’s disease and related dementias

(2022) Céline Bellenguez et al.   NATURE GENETICS

Increasing the Targeting Scope of CRISPR Base Editing System Beyond NGG

(2022) Si-Yue Yu et al.   CRISPR Journal

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

(2022) Joseph M. Replogle et al.   CELL

Massively parallel assessment of human variants with base editor screens

(2021) Ruth E. Hanna et al.   CELL

Functional interrogation of DNA damage response variants with base editing screens

(2021) Raquel Cuella-Martin et al.   CELL

Integrated cross-study datasets of genetic dependencies in cancer

(2021) Clare Pacini et al.   Nature Communications

Genome-wide enhancer maps link risk variants to disease genes

(2021) Joseph Nasser et al.   NATURE

Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens

(2021) Noa Liscovitch-Brauer et al.   NATURE BIOTECHNOLOGY

CRISPR-Cas9 cytidine and adenosine base editing of splice-sites mediates highly-efficient disruption of proteins in primary and immortalized cells

(2021) Mitchell G. Kluesner et al.   Nature Communications

Landscape of allele-specific transcription factor binding in the human genome

(2021) Sergey Abramov et al.   Nature Communications

Tissue specificity-aware TWAS (TSA-TWAS) framework identifies novel associations with metabolic, immunologic, and virologic traits in HIV-positive adults

(2021) Binglan Li et al.   PLoS Genetics

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

A compendium of uniformly processed human gene expression and splicing quantitative trait loci

(2021) Nurlan Kerimov et al.   NATURE GENETICS

From variant to function in human disease genetics

(2021) Tuuli Lappalainen et al.   SCIENCE

Measurement of differential chromatin interactions with absolute quantification of architecture (AQuA-HiChIP)

(2020) Berkley E. Gryder et al.   Nature Protocols

High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation

(2020) Mateusz Legut et al.   Cell Reports

Massively parallel Cas13 screens reveal principles for guide RNA design

(2020) Hans-Hermann Wessels et al.   NATURE BIOTECHNOLOGY

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Genetic variants modulate gene expression statin response in human lymphoblastoid cell lines

(2020) Elizabeth Theusch et al.   BMC GENOMICS

Identification of required host factors for SARS-CoV-2 infection in human cells

(2020) Zharko Daniloski et al.   CELL

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations

(2020) Ming-Huei Chen et al.   CELL

The Polygenic and Monogenic Basis of Blood Traits and Diseases

(2020) Dragana Vuckovic et al.   CELL

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Multifaceted Actions of GFI1 and GFI1B in Hematopoietic Stem Cell Self-Renewal and Lineage Commitment

(2020) Hugues Beauchemin et al.   Frontiers in Genetics

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

(2019) Molly Gasperini et al.   CELL

Gfi1b regulates the level of Wnt/β-catenin signaling in hematopoietic stem cells and megakaryocytes

(2019) Peiman Shooshtarizadeh et al.   Nature Communications

Clinical use of current polygenic risk scores may exacerbate health disparities

(2019) Alicia R. Martin et al.   NATURE GENETICS

Interrogation of human hematopoiesis at single-cell and single-variant resolution

(2019) Jacob C. Ulirsch et al.   NATURE GENETICS

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

A functional variant in the miR‐142 promoter modulating its expression and conferring risk of Alzheimer disease

(2019) Mohsen Ghanbari et al.   HUMAN MUTATION

Apolipoprotein C1: Its Pleiotropic Effects in Lipid Metabolism and Beyond

(2019) Elena V. Fuior et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Identification of significant chromatin contacts from HiChIP data by FitHiChIP

(2019) Sourya Bhattacharyya et al.   Nature Communications

Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules

(2019) Shiqi Xie et al.   Cell Reports

The biochemical basis of microRNA targeting efficacy

(2019) Sean E. McGeary et al.   SCIENCE

FlashFry: a fast and flexible tool for large-scale CRISPR target design

(2018) Aaron McKenna et al.   BMC BIOLOGY

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Optimized base editors enable efficient editing in cells, organoids and mice

(2018) Maria Paz Zafra et al.   NATURE BIOTECHNOLOGY

Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response

(2018) Kaur Alasoo et al.   NATURE GENETICS

An enhanced CRISPR repressor for targeted mammalian gene regulation

(2018) Nan Cher Yeo et al.   NATURE METHODS

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

(2018) Benjamin J. Schmiedel et al.   CELL

An atlas of genetic influences on osteoporosis in humans and mice

(2018) John A. Morris et al.   NATURE GENETICS

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

Trans-ethnic meta-regression of genome-wide association studies accounting for ancestry increases power for discovery and improves fine-mapping resolution

(2017) Reedik Mägi et al.   HUMAN MOLECULAR GENETICS

Common genetic variation drives molecular heterogeneity in human iPSCs

(2017) Helena Kilpinen et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens

(2017) Walter F Lenoir et al.   NUCLEIC ACIDS RESEARCH

Massively parallel digital transcriptional profiling of single cells

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

C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis

(2017) Kaido Lepik et al.   PLoS Computational Biology

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types

(2017) Athanasia D. Panopoulos et al.   Stem Cell Reports

Transcription Factor GFI1B in Health and Disease

(2017) Eduardo Anguita et al.   Frontiers in Oncology

FINEMAP: efficient variable selection using summary data from genome-wide association studies

(2016) Christian Benner et al.   BIOINFORMATICS

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

(2016) William J. Astle et al.   CELL

Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens

(2016) Yohann Nédélec et al.   CELL

Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations

(2016) Hélène Quach 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

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

CRISPR Screens to Discover Functional Noncoding Elements

(2016) Jason B. Wright et al.   TRENDS IN GENETICS

From cytopenia to leukemia: the role of Gfi1 and Gfi1b in blood formation

(2015) T. Moroy et al.   BLOOD

Regulation and function of the NFE2 transcription factor in hematopoietic and non-hematopoietic cells

(2015) Jadwiga J. Gasiorek et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Identification of Campath-1 (CD52) as Novel Drug Target in Neoplastic Stem Cells in 5q-Patients with MDS and AML

(2014) K. Blatt et al.   CLINICAL CANCER RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins

(2014) Alfonso Buil et al.   NATURE GENETICS

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation

(2014) Jacob C. Ulirsch et al.   PLoS Genetics

miR-142 orchestrates a network of actin cytoskeleton regulators during megakaryopoiesis

(2014) Elik Chapnik et al.   eLife

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

A role for RUNX1 in hematopoiesis and myeloid leukemia

(2013) Motoshi Ichikawa et al.   INTERNATIONAL JOURNAL OF HEMATOLOGY

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Robust rank aggregation for gene list integration and meta-analysis

(2012) Raivo Kolde et al.   BIOINFORMATICS

Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and number

(2012) V. G. Sankaran et al.   GENES & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Bayesian refinement of association signals for 14 loci in 3 common diseases

(2012) Julian B Maller et al.   NATURE GENETICS

Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits

(2012) Jian Yang et al.   NATURE GENETICS

High CD33 expression levels in acute myeloid leukemia cells carrying the nucleophosmin (NPM1) mutation

(2011) M. S. De Propris et al.   HAEMATOLOGICA

GCTA: A Tool for Genome-wide Complex Trait Analysis

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

APOE and cholesterol homeostasis in Alzheimer's disease

(2010) Valérie Leduc et al.   TRENDS IN MOLECULAR MEDICINE

Genome-Wide Association Study of Lp-PLA2 Activity and Mass in the Framingham Heart Study

(2010) Sunil Suchindran et al.   PLoS Genetics

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL