Sparse dictionary learning recovers pleiotropy from human cell fitness screens

A genome-wide CRISPR/Cas9 screen in acute myeloid leukemia cells identifies regulators of TAK-243 sensitivity

(2021) Samir H. Barghout et al.   JCI Insight

Structure of the catalytic core of the Integrator complex

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

Disruption of pathways regulated by Integrator complex in Galloway–Mowat syndrome due to WDR73 mutations

(2021) F. C. Tilley et al.   Scientific Reports

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

(2021) Michael Wainberg et al.   NATURE GENETICS

A proximity-dependent biotinylation map of a human cell

(2021) Christopher D. Go et al.   NATURE

Haploid genetic screens identify SPRING/C12ORF49 as a determinant of SREBP signaling and cholesterol metabolism

(2020) Anke Loregger et al.   Nature Communications

A Genetic Map of the Response to DNA Damage in Human Cells

(2020) Michele Olivieri et al.   CELL

Drug mechanism‐of‐action discovery through the integration of pharmacological and CRISPR screens

(2020) Emanuel Gonçalves et al.   Molecular Systems Biology

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

(2020) Kevin Sabath et al.   Nature Communications

POST1/C12ORF49 regulates the SREBP pathway by promoting site-1 protease maturation

(2020) Jian Xiao et al.   Protein & Cell

BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms

(2020) Scott Barish et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2020) Hai Zheng et al.   SCIENCE

Fitness variation across subtle environmental perturbations reveals local modularity and global pleiotropy of adaptation

(2020) Grant Kinsler et al.   eLife

FIREWORKS: a bottom-up approach to integrative coessentiality network analysis

(2020) David R Amici et al.   Life Science Alliance

Global Genetic Networks and the Genotype-to-Phenotype Relationship

(2019) Michael Costanzo et al.   CELL

Theoretical guarantees for graph sparse coding

(2019) Yael Yankelevsky et al.   APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS

Context-dependent genetic interactions in cancer

(2019) Luisa Henkel et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

(2019) Fiona M. Behan et al.   NATURE

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

(2019) Uku Raudvere et al.   NUCLEIC ACIDS RESEARCH

Paf1C regulates RNA polymerase II progression by modulating elongation rate

(2019) Liming Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Integrator complex cleaves nascent mRNAs to attenuate transcription

(2019) Deirdre C. Tatomer et al.   GENES & DEVELOPMENT

A global overview of pleiotropy and genetic architecture in complex traits

(2019) Kyoko Watanabe et al.   NATURE GENETICS

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

Identifying chemogenetic interactions from CRISPR screens with drugZ

(2019) Medina Colic et al.   Genome Medicine

A consensus set of genetic vulnerabilities to ATR inhibition

(2019) Nicole Hustedt et al.   Open Biology

The meanings of 'function' in biology and the problematic case of de novo gene emergence

(2019) Diane Marie Keeling et al.   eLife

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

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

Targeted Enhancer Activation by a Subunit of the Integrator Complex

(2018) Elisa Barbieri et al.   MOLECULAR CELL

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens

(2018) Joshua Pan et al.   Cell Systems

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Enter the Matrix: Factorization Uncovers Knowledge from Omics

(2018) Genevieve L. Stein-O’Brien et al.   TRENDS IN GENETICS

Control of the polyamine biosynthesis pathway by G2-quadruplexes

(2018) Helen Louise Lightfoot et al.   eLife

Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes

(2018) Nazar Mashtalir et al.   CELL

High‐resolution mapping of cancer cell networks using co‐functional interactions

(2018) Evan A Boyle et al.   Molecular Systems Biology

A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation

(2018) Brittany C. Michel et al.   NATURE CELL BIOLOGY

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

(2018) Kendall R. Sanson et al.   Nature Communications

VAPs and ACBD5 tether peroxisomes to the ER for peroxisome maintenance and lipid homeostasis

(2017) Rong Hua et al.   JOURNAL OF CELL BIOLOGY

ACBD5 and VAPB mediate membrane associations between peroxisomes and the ER

(2017) Joseph L. Costello et al.   JOURNAL OF CELL BIOLOGY

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

(2017) Robin M Meyers et al.   NATURE GENETICS

Emerging and evolving concepts in gene essentiality

(2017) Giulia Rancati et al.   NATURE REVIEWS GENETICS

CRISPR-Cas9 mediated genetic engineering for the purification of the endogenous integrator complex from mammalian cells

(2016) David Baillat et al.   PROTEIN EXPRESSION AND PURIFICATION

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

Multiomic Analysis of the UV-Induced DNA Damage Response

(2016) Stefan Boeing et al.   Cell Reports

Genetic pleiotropy in complex traits and diseases: implications for genomic medicine

(2016) Jacob Gratten et al.   Genome Medicine

The detection and characterization of pleiotropy: discovery, progress, and promise

(2015) Anna L. Tyler et al.   BRIEFINGS IN BIOINFORMATICS

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

Integrator: surprisingly diverse functions in gene expression

(2015) David Baillat et al.   TRENDS IN BIOCHEMICAL SCIENCES

A novel Fanconi anaemia subtype associated with a dominant-negative mutation in RAD51

(2015) Najim Ameziane et al.   Nature Communications

A map of directional genetic interactions in a metazoan cell

(2015) Bernd Fischer et al.   eLife

Inferring gene ontologies from pairwise similarity data

(2014) M. Kramer et al.   BIOINFORMATICS

Subunit Architecture and Functional Modular Rearrangements of the Transcriptional Mediator Complex

(2014) Kuang-Lei Tsai et al.   CELL

Integrator Regulates Transcriptional Initiation and Pause Release following Activation

(2014) Alessandro Gardini et al.   MOLECULAR CELL

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Integrator complex regulates NELF-mediated RNA polymerase II pause/release and processivity at coding genes

(2014) Bernd Stadelmayer et al.   Nature Communications

Pleiotropy in complex traits: challenges and strategies

(2013) Nadia Solovieff et al.   NATURE REVIEWS GENETICS

ATAC-king the complexity of SAGA during evolution

(2012) G. Spedale et al.   GENES & DEVELOPMENT

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Dictionaries for Sparse Representation Modeling

(2010) Ron Rubinstein et al.   PROCEEDINGS OF THE IEEE

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

Genomic patterns of pleiotropy and the evolution of complexity

(2010) Z. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE