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

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

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

nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer

(2020) Reka Hollandi et al.   Cell Systems

High‐throughput, microscope‐based sorting to dissect cellular heterogeneity

(2020) Nicholas Hasle et al.   Molecular Systems Biology

Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap

(2019) Jüri Reimand et al.   Nature Protocols

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

Opto-magnetic capture of individual cells based on visual phenotypes

(2019) Loïc Binan et al.   eLife

CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons

(2019) Ruilin Tian et al.   NEURON

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl

(2019) Juan C. Caicedo et al.   NATURE METHODS

Mapping the Genetic Landscape of Human Cells

(2018) Max A. Horlbeck et al.   CELL

The complex relationship between TFEB transcription factor phosphorylation and subcellular localization

(2018) Rosa Puertollano et al.   EMBO JOURNAL

Points of significance: Machine learning: supervised methods

(2018) Danilo Bzdok et al.   NATURE METHODS

Ghost cytometry

(2018) Sadao Ota et al.   SCIENCE

Signaling Lymphocyte Activation Molecule Family 5 Enhances Autophagy and Fine-Tunes Cytokine Response in Monocyte-Derived Dendritic Cells via Stabilization of Interferon Regulatory Factor 8

(2018) Zsofia Agod et al.   Frontiers in Immunology

Intelligent Image-Activated Cell Sorting

(2018) Nao Nitta et al.   CELL

Tuning model parameters in class‐imbalanced learning with precision‐recall curve

(2018) Guang‐Hui Fu et al.   BIOMETRICAL JOURNAL

A deep learning-based algorithm for 2-D cell segmentation in microscopy images

(2018) Yousef Al-Kofahi et al.   BMC BIOINFORMATICS

Requirement of Pitx2 for skeletal muscle homeostasis

(2018) Chih-Ning Chang et al.   DEVELOPMENTAL BIOLOGY

High-throughput, image-based screening of pooled genetic-variant libraries

(2017) George Emanuel et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

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

TMEM184b Promotes Axon Degeneration and Neuromuscular Junction Maintenance

(2016) M. R. C. Bhattacharya et al.   JOURNAL OF NEUROSCIENCE

Hypoxia induces TFE3 expression in head and neck squamous cell carcinoma

(2016) Zhi-Jun Sun et al.   Oncotarget

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

(2016) Max A Horlbeck et al.   eLife

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R

(2015) Jan Grau et al.   BIOINFORMATICS

MiT/TFE transcription factors are activated during mitophagy downstream of Parkin and Atg5

(2015) Catherine L. Nezich et al.   JOURNAL OF CELL BIOLOGY

PROPER: comprehensive power evaluation for differential expression using RNA-seq

(2014) Hao Wu et al.   BIOINFORMATICS

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

(2014) Luke A. Gilbert et al.   CELL

Transcriptional regulation of autophagy by an FXR–CREB axis

(2014) Sunmi Seok et al.   NATURE

Rag GTPases mediate amino acid–dependent recruitment of TFEB and MITF to lysosomes

(2013) Jose A. Martina et al.   JOURNAL OF CELL BIOLOGY

Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping

(2013) Christina Laufer et al.   NATURE METHODS

A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB

(2012) Carmine Settembre et al.   EMBO JOURNAL

TFEB Links Autophagy to Lysosomal Biogenesis

(2011) C. Settembre et al.   SCIENCE

EBImage--an R package for image processing with applications to cellular phenotypes

(2010) G. Pau et al.   BIOINFORMATICS

Germinal Center Dynamics Revealed by Multiphoton Microscopy with a Photoactivatable Fluorescent Reporter

(2010) Gabriel D. Victora et al.   CELL

Cell Nuclei and Cytoplasm Joint Segmentation Using the Sliding Band Filter

(2010) Pedro Quelhas et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Termination of autophagy and reformation of lysosomes regulated by mTOR

(2010) Li Yu et al.   NATURE

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A Gene Network Regulating Lysosomal Biogenesis and Function

(2009) Marco Sardiello et al.   SCIENCE

Parkin is recruited selectively to impaired mitochondria and promotes their autophagy

(2008) Derek Narendra et al.   JOURNAL OF CELL BIOLOGY