High-speed fluorescence image–enabled cell sorting

High-content imaging-based pooled CRISPR screens in mammalian cells

(2021) Xiaowei Yan et al.   JOURNAL OF CELL BIOLOGY

Image-based pooled whole-genome CRISPRi screening for subcellular phenotypes

(2021) Gil Kanfer et al.   JOURNAL OF CELL BIOLOGY

High-throughput multiparametric imaging flow cytometry: toward diffraction-limited sub-cellular detection and monitoring of sub-cellular processes

(2021) Gregor Holzner et al.   Cell Reports

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

(2020) John P. Ray et al.   Nature Communications

Virtual-freezing fluorescence imaging flow cytometry

(2020) Hideharu Mikami et al.   Nature Communications

Pooled CRISPR screens with imaging on microraft arrays reveals stress granule-regulatory factors

(2020) Emily C. Wheeler et al.   NATURE METHODS

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

(2020) Daniel Schraivogel et al.   NATURE METHODS

Latexin deficiency in mice up-regulates inflammation and aggravates colitis through HECTD1/Rps3/NF-κB pathway

(2020) Yaping Li et al.   Scientific Reports

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library

(2020) Luisa Henkel et al.   BMC BIOLOGY

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization

(2019) Chong Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

(2019) Andrea Cossarizza et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

RNF31 Regulates Skin Homeostasis by Protecting Epidermal Keratinocytes from Cell Death

(2018) Yong Tang et al.   JOURNAL OF IMMUNOLOGY

Ghost cytometry

(2018) Sadao Ota et al.   SCIENCE

On-chip light-sheet fluorescence imaging flow cytometry at a high flow speed of 1 m/s

(2018) Taichi Miura et al.   Biomedical Optics Express

The INO80 chromatin remodeler sustains metabolic stability by promoting TOR signaling and regulating histone acetylation

(2018) Sean L. Beckwith et al.   PLoS Genetics

Single-Cell Analysis of Morphological and Metabolic Heterogeneity in Euglena gracilis by Fluorescence-Imaging Flow Cytometry

(2018) Hector E. Muñoz et al.   ANALYTICAL CHEMISTRY

Intelligent Image-Activated Cell Sorting

(2018) Nao Nitta et al.   CELL

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

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov 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

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

(2017) Shashikant Pujar et al.   NUCLEIC ACIDS RESEARCH

The BioStudies database—one stop shop for all data supporting a life sciences study

(2017) Ugis Sarkans et al.   NUCLEIC ACIDS RESEARCH

CREB coactivators CRTC2 and CRTC3 modulate bone marrow hematopoiesis

(2017) Jeong-Ho Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

Sharing the SAGA

(2017) Dominique Helmlinger et al.   TRENDS IN BIOCHEMICAL SCIENCES

Massively parallel digital transcriptional profiling of single cells

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

The p38 pathway, a major pleiotropic cascade that transduces stress and metastatic signals in endothelial cells

(2017) Isabelle Corre et al.   Oncotarget

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

(2017) Traver Hart et al.   G3-Genes Genomes Genetics

High-Throughput Multi-parametric Imaging Flow Cytometry

(2017) Anandkumar S. Rane et al.   Chem

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding

(2017) Payam Shahi et al.   Scientific Reports

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

Ki-67 acts as a biological surfactant to disperse mitotic chromosomes

(2016) Sara Cuylen et al.   NATURE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

HOXA1 binds RBCK1/HOIL-1 and TRAF2 and modulates the TNF/NF-κB pathway in a transcription-independent manner

(2016) Arnaud Taminiau et al.   NUCLEIC ACIDS RESEARCH

NF-κB oscillations translate into functionally related patterns of gene expression

(2016) Samuel Zambrano et al.   eLife

Microscopy-Based High-Content Screening

(2015) Michael Boutros et al.   CELL

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

(2015) Traver Hart et al.   CELL

INO80 Chromatin Remodeler Facilitates Release of RNA Polymerase II from Chromatin for Ubiquitin-Mediated Proteasomal Degradation

(2015) Anne Lafon et al.   MOLECULAR CELL

Variable importance analysis: A comprehensive review

(2015) Pengfei Wei et al.   RELIABILITY ENGINEERING & SYSTEM SAFETY

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

The intersection of flow cytometry with microfluidics and microfabrication

(2014) Menake E. Piyasena et al.   LAB ON A CHIP

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

Dual specificity phosphatase 1 expression inversely correlates with NF-κB activity and expression in prostate cancer and promotes apoptosis through a p38 MAPK dependent mechanism

(2013) Beatriz Gil-Araujo et al.   Molecular Oncology

Digitally synthesized beat frequency multiplexing for sub-millisecond fluorescence microscopy

(2013) Eric D. Diebold et al.   Nature Photonics

Regulation of NF-κB signaling by the A20 deubiquitinase

(2012) Noula Shembade et al.   Cellular & Molecular Immunology

FlowRepository: A resource of annotated flow cytometry datasets associated with peer-reviewed publications

(2012) Josef Spidlen et al.   CYTOMETRY PART A

The Kelch Repeat Protein KLHDC10 Regulates Oxidative Stress-Induced ASK1 Activation by Suppressing PP5

(2012) Yusuke Sekine et al.   MOLECULAR CELL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

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

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

High-throughput single-microparticle imaging flow analyzer

(2012) K. Goda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TRAF7 Protein Promotes Lys-29-linked Polyubiquitination of IκB Kinase (IKKγ)/NF-κB Essential Modulator (NEMO) and p65/RelA Protein and Represses NF-κB Activation

(2011) Tiziana Zotti et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Subunit Organization of the Human INO80 Chromatin Remodeling Complex

(2011) Lu Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Role of the Transcription Factor CREB in Immune Function

(2010) A. Y. Wen et al.   JOURNAL OF IMMUNOLOGY

Live-cell imaging RNAi screen identifies PP2A–B55α and importin-β1 as key mitotic exit regulators in human cells

(2010) Michael H. A. Schmitz et al.   NATURE CELL BIOLOGY

GCN5 is a required cofactor for a ubiquitin ligase that targets NF- B/RelA

(2009) X. Mao et al.   GENES & DEVELOPMENT

Accumulation of Pax2 Transactivation Domain Interaction Protein (PTIP) at Sites of DNA Breaks via RNF8-dependent Pathway Is Required for Cell Survival after DNA Damage

(2009) Zihua Gong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Multi-parameter phenotypic profiling: using cellular effects to characterize small-molecule compounds

(2009) Yan Feng et al.   NATURE REVIEWS DRUG DISCOVERY