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

Sparse dictionary learning recovers pleiotropy from human cell fitness screens

(2022) Joshua Pan et al.   Cell Systems

Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation

(2021) Eric Wang et al.   Cell Stem Cell

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

(2021) Kirsten A. Reimer et al.   MOLECULAR CELL

Structure of the catalytic core of the Integrator complex

(2021) Moritz M. Pfleiderer et al.   MOLECULAR CELL

Mechanisms and regulation of protein synthesis in mitochondria

(2021) Eva Kummer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identifying transposable element expression dynamics and heterogeneity during development at the single-cell level with a processing pipeline scTE

(2021) Jiangping He et al.   Nature Communications

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

(2021) James K. Nuñez et al.   CELL

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes

(2021) Michael Wainberg et al.   NATURE GENETICS

TMEM70 and TMEM242 help to assemble the rotor ring of human ATP synthase and interact with assembly factors for complex I

(2021) Joe Carroll et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An erythroid to myeloid cell fate conversion is elicited by LSD1 inactivation

(2021) Lei Yu et al.   BLOOD

Nucleolar maturation of the human small subunit processome

(2021) Sameer Singh et al.   SCIENCE

Structural basis of Integrator-mediated transcription regulation

(2021) Isaac Fianu et al.   SCIENCE

Mitochondrial stress is relayed to the cytosol by an OMA1–DELE1–HRI pathway

(2020) Xiaoyan Guo et al.   NATURE

A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol

(2020) Evelyn Fessler et al.   NATURE

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

(2020) Joseph M. Replogle et al.   NATURE BIOTECHNOLOGY

Distinct mitochondrial defects trigger the integrated stress response depending on the metabolic state of the cell

(2020) Eran Mick et al.   eLife

INTS10–INTS13–INTS14 form a functional module of Integrator that binds nucleic acids and the cleavage module

(2020) Kevin Sabath et al.   Nature Communications

Integrator Recruits Protein Phosphatase 2A to Prevent Pause Release and Facilitate Transcription Termination

(2020) Kai-Lieh Huang et al.   MOLECULAR CELL

An efficient KRAB domain for CRISPRi applications in human cells

(2020) Nader Alerasool et al.   NATURE METHODS

Identification of Integrator-PP2A complex (INTAC), an RNA polymerase II phosphatase

(2020) Hai Zheng et al.   SCIENCE

The Integrator complex at the crossroad of coding and noncoding RNA

(2020) Nina Kirstein et al.   CURRENT OPINION IN CELL BIOLOGY

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

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

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

Context is everything: aneuploidy in cancer

(2019) Uri Ben-David et al.   NATURE REVIEWS GENETICS

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

Mapping human cell phenotypes to genotypes with single-cell genomics

(2019) J. Gray Camp et al.   SCIENCE

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

Biological plasticity rescues target activity in CRISPR knock outs

(2019) Arne H. Smits et al.   NATURE METHODS

The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes

(2019) Nathan D. Elrod et al.   MOLECULAR CELL

Molecular Wiring of a Mitochondrial Translational Feedback Loop

(2019) Roger Salvatori et al.   MOLECULAR CELL

Mechanisms and regulation of cholesterol homeostasis

(2019) Jie Luo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Oxidative damage diminishes mitochondrial DNA polymerase replication fidelity

(2019) Andrew P Anderson et al.   NUCLEIC ACIDS RESEARCH

ORY-1001, a Potent and Selective Covalent KDM1A Inhibitor, for the Treatment of Acute Leukemia

(2018) Tamara Maes et al.   CANCER CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

CRISPR–Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity

(2018) Nicholas J. Kramer et al.   NATURE GENETICS

CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response

(2018) Emma Haapaniemi et al.   NATURE MEDICINE

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

CORUM: the comprehensive resource of mammalian protein complexes—2019

(2018) Madalina Giurgiu et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals

(2017) Pedro M. Quirós et al.   JOURNAL OF CELL BIOLOGY

The CoRR hypothesis for genes in organelles

(2017) John F. Allen   JOURNAL OF THEORETICAL BIOLOGY

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

(2017) Marco Jost et al.   MOLECULAR CELL

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Am I ready for CRISPR? A user's guide to genetic screens

(2017) John G. Doench   NATURE REVIEWS GENETICS

Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression

(2017) Joseph Rosenbluh 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

Mitochondrial Protein Synthesis Adapts to Influx of Nuclear-Encoded Protein

(2016) Ricarda Richter-Dennerlein et al.   CELL

Mitochondrial unfolded protein response controls matrix pre-RNA processing and translation

(2016) Christian Münch et al.   NATURE

Mitonuclear communication in homeostasis and stress

(2016) Pedro M. Quirós et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ESCRT proteins restrict constitutive NF-κB signaling by trafficking cytokine receptors

(2016) Agnieszka Mamińska et al.   Science Signaling

Multiomic Analysis of the UV-Induced DNA Damage Response

(2016) Stefan Boeing et al.   Cell Reports

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Global, quantitative and dynamic mapping of protein subcellular localization

(2016) Daniel N Itzhak et al.   eLife

ESCRT proteins restrict constitutive NF-κB signaling by trafficking cytokine receptors

(2016) Agnieszka Mamińska et al.   Science Signaling

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Short- and long-term effects of chromosome mis-segregation and aneuploidy

(2015) Stefano Santaguida et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

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

(2014) Luke A. Gilbert et al.   CELL

Mitochondrial form and function

(2014) Jonathan R. Friedman et al.   NATURE

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

The Human Mitochondrial Transcriptome

(2011) Tim R. Mercer et al.   CELL

Transcription Factor Nrf1 Mediates the Proteasome Recovery Pathway after Proteasome Inhibition in Mammalian Cells

(2010) Senthil K. Radhakrishnan et al.   MOLECULAR CELL

Streamlined analysis schema for high-throughput identification of endogenous protein complexes

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

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL

Mps1 Phosphorylates Borealin to Control Aurora B Activity and Chromosome Alignment

(2008) Nannette Jelluma et al.   CELL