Single-cell image analysis to explore cell-to-cell heterogeneity in isogenic populations

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

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

DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes

(2021) Dylan Bannon et al.   NATURE METHODS

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

(2021) Diana Mahdessian et al.   NATURE

Imaging cell lineage with a synthetic digital recording system

(2021) Ke-Huan K. Chow et al.   SCIENCE

Systematic genetics and single‐cell imaging reveal widespread morphological pleiotropy and cell‐to‐cell variability

(2020) Mojca Mattiazzi Usaj et al.   Molecular Systems Biology

HSF1 phase transition mediates stress adaptation and cell fate decisions

(2020) Giorgio Gaglia et al.   NATURE CELL BIOLOGY

A genome-wide approach for identification and characterisation of metabolite-inducible systems

(2020) Erik K. R. Hanko et al.   Nature Communications

Single cell analysis reveals multiple requirements for zinc in the mammalian cell cycle

(2020) Maria N Lo et al.   eLife

Single-Cell Tracing Dissects Regulation of Maintenance and Inheritance of Transcriptional Reinduction Memory

(2020) Poonam Bheda et al.   MOLECULAR CELL

Temporal integration of mitogen history in mother cells controls proliferation of daughter cells

(2020) Mingwei Min et al.   SCIENCE

DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning

(2020) Jean-Baptiste Lugagne et al.   PLoS Computational Biology

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

(2020) Nicholas Hasle et al.   Molecular Systems Biology

Single-cell multiomics: technologies and data analysis methods

(2020) Jeongwoo Lee et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

A physicochemical perspective of aging from single-cell analysis of pH, macromolecular and organellar crowding in yeast

(2020) Sara N Mouton et al.   eLife

Divergent Aging of Isogenic Yeast Cells Revealed through Single-Cell Phenotypic Dynamics

(2019) Meng Jin et al.   Cell Systems

Escalating Threat Levels of Bacterial Infection Can Be Discriminated by Distinct MAPK and NF-κB Signaling Dynamics in Single Host Cells

(2019) Keara Lane et al.   Cell Systems

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Self-organization and symmetry breaking in intestinal organoid development

(2019) Denise Serra et al.   NATURE

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

The next generation of CRISPR–Cas technologies and applications

(2019) Adrian Pickar-Oliver et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images

(2019) Juan C. Caicedo et al.   CYTOMETRY PART A

Age-dependent deterioration of nuclear pore assembly in mitotic cells decreases transport dynamics

(2019) Irina L Rempel et al.   eLife

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting

(2019) Alex X. Lu et al.   PLoS Computational Biology

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription

(2019) Amjad Askary et al.   NATURE BIOTECHNOLOGY

Analysis of the Human Protein Atlas Image Classification competition

(2019) Wei Ouyang et al.   NATURE METHODS

Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor

(2019) Francisca Monteiro et al.   Molecular Systems Biology

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images

(2018) Eric M. Christiansen et al.   CELL

RNA Interference (RNAi) Screening inDrosophila

(2018) Florian Heigwer et al.   GENETICS

Arrayed CRISPR screen with image-based assay reliably uncovers host genes required for coxsackievirus infection

(2018) Heon Seok Kim et al.   GENOME RESEARCH

Large‐scale image‐based profiling of single‐cell phenotypes in arrayed CRISPR‐Cas9 gene perturbation screens

(2018) Reinoud de Groot et al.   Molecular Systems Biology

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Integrating images from multiple microscopy screens reveals diverse patterns of change in the subcellular localization of proteins

(2018) Alex X Lu et al.   eLife

RNA Interference (RNAi) Screening inDrosophila

(2018) Florian Heigwer et al.   GENETICS

Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH

(2018) Eduardo Torre et al.   Cell Systems

Phenotypic Image Analysis Software Tools for Exploring and Understanding Big Image Data from Cell-Based Assays

(2018) Kevin Smith et al.   Cell Systems

Integration of Multiple Metabolic Signals Determines Cell Fate Prior to Commitment

(2018) Orlando Argüello-Miranda et al.   MOLECULAR CELL

Deep learning is combined with massive-scale citizen science to improve large-scale image classification

(2018) Devin P Sullivan et al.   NATURE BIOTECHNOLOGY

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

(2018) Chawin Ounkomol et al.   NATURE METHODS

Analysis of redox landscapes and dynamics in living cells and in vivo using genetically encoded fluorescent sensors

(2018) Yejun Zou et al.   Nature Protocols

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

Ki67 is a Graded Rather than a Binary Marker of Proliferation versus Quiescence

(2018) Iain Miller et al.   Cell Reports

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity

(2018) Joseph Rodriguez et al.   CELL

Replicative aging as a source of cell heterogeneity in budding yeast

(2018) Dmitry A. Knorre et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Real-Time Imaging of Mitochondrial ATP Dynamics Reveals the Metabolic Setting of Single Cells

(2018) Maria R. Depaoli et al.   Cell Reports

High-content analysis screening for cell cycle regulators using arrayed synthetic crRNA libraries

(2017) Žaklina Strezoska et al.   JOURNAL OF BIOTECHNOLOGY

Digging deep into Golgi phenotypic diversity with unsupervised machine learning

(2017) Shaista Hussain et al.   MOLECULAR BIOLOGY OF THE CELL

Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization

(2017) Brock Roberts et al.   MOLECULAR BIOLOGY OF THE CELL

Genetically Encoded Tools for Optical Dissection of the Mammalian Cell Cycle

(2017) Asako Sakaue-Sawano et al.   MOLECULAR CELL

Automated analysis of high‐content microscopy data with deep learning

(2017) Oren Z Kraus et al.   Molecular Systems Biology

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Data-analysis strategies for image-based cell profiling

(2017) Juan C Caicedo et al.   NATURE METHODS

Genetically encoded fluorescent sensors reveal dynamic regulation of NADPH metabolism

(2017) Rongkun Tao et al.   NATURE METHODS

Profiling the transcriptome with RNA SPOTs

(2017) Chee-Huat Linus Eng et al.   NATURE METHODS

Image Data Resource: a bioimage data integration and publication platform

(2017) Eleanor Williams et al.   NATURE METHODS

Multigenerational silencing dynamics control cell aging

(2017) Yang Li 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

Quantitative Cell Cycle Analysis Based on an Endogenous All-in-One Reporter for Cell Tracking and Classification

(2017) Thomas Zerjatke et al.   Cell Reports

Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning

(2017) Tanel Pärnamaa et al.   G3-Genes Genomes Genetics

High-Throughput, High-Resolution Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing

(2016) Takayasu Mikuni et al.   CELL

Machine learning and computer vision approaches for phenotypic profiling

(2016) Ben T. Grys et al.   JOURNAL OF CELL BIOLOGY

Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes

(2016) Mark-Anthony Bray et al.   Nature Protocols

A scalable strategy for high-throughput GFP tagging of endogenous human proteins

(2016) Manuel D. Leonetti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) M. Costanzo et al.   SCIENCE

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

High-Content Screening for Quantitative Cell Biology

(2016) Mojca Mattiazzi Usaj et al.   TRENDS IN CELL BIOLOGY

Asymmetric Inheritance of Aggregated Proteins and Age Reset in Yeast Are Regulated by Vac17-Dependent Vacuolar Functions

(2016) Sandra Malmgren Hill et al.   Cell Reports

Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci

(2016) Erin B. Styles et al.   Cell Systems

Analysis of Cell Lineage Trees by Exact Bayesian Inference Identifies Negative Autoregulation of Nanog in Mouse Embryonic Stem Cells

(2016) Justin Feigelman et al.   Cell Systems

Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements

(2016) Sahand Hormoz et al.   Cell Systems

A genome-wide imaging-based screening to identify genes involved in synphilin-1 inclusion formation in Saccharomyces cerevisiae

(2016) Lei Zhao et al.   Scientific Reports

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

(2015) Yolanda T. Chong et al.   CELL

Microscopy-Based High-Content Screening

(2015) Michael Boutros et al.   CELL

SoNar, a Highly Responsive NAD+/NADH Sensor, Allows High-Throughput Metabolic Screening of Anti-tumor Agents

(2015) Yuzheng Zhao et al.   Cell Metabolism

Single-cell phenomics in budding yeast

(2015) Yoshikazu Ohya et al.   MOLECULAR BIOLOGY OF THE CELL

Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR

(2015) Michael Boettcher et al.   MOLECULAR CELL

A functional perspective on phenotypic heterogeneity in microorganisms

(2015) Martin Ackermann   NATURE REVIEWS MICROBIOLOGY

A Hierarchical Map of Regulatory Genetic Interactions in Membrane Trafficking

(2014) Prisca Liberali et al.   CELL

High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells

(2014) Sergi Regot et al.   CELL

A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression

(2014) Veronika Graml et al.   DEVELOPMENTAL CELL

Role of SAGA in the asymmetric segregation of DNA circles during yeast ageing

(2014) Annina Denoth-Lippuner et al.   eLife

The details in the distributions: why and how to study phenotypic variability

(2013) KA Geiler-Samerotte et al.   CURRENT OPINION IN BIOTECHNOLOGY

A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes

(2013) Zheng Yin et al.   NATURE CELL BIOLOGY

Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae

(2013) Aprotim Mazumder et al.   NUCLEIC ACIDS RESEARCH

A chemostat array enables the spatio-temporal analysis of the yeast proteome

(2013) N. Denervaud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell analysis of population context advances RNAi screening at multiple levels

(2012) Berend Snijder et al.   Molecular Systems Biology

An early age increase in vacuolar pH limits mitochondrial function and lifespan in yeast

(2012) Adam L. Hughes et al.   NATURE

Tandem fluorescent protein timers for in vivo analysis of protein dynamics

(2012) Anton Khmelinskii et al.   NATURE BIOTECHNOLOGY

OMERO: flexible, model-driven data management for experimental biology

(2012) Chris Allan et al.   NATURE METHODS

Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress Protectant

(2012) Sasha F. Levy et al.   PLOS BIOLOGY

Systematic exploration of essential yeast gene function with temperature-sensitive mutants

(2011) Zhijian Li et al.   NATURE BIOTECHNOLOGY

Genomic Screening with RNAi: Results and Challenges

(2010) Stephanie Mohr et al.   Annual Review of Biochemistry

Metadata matters: access to image data in the real world

(2010) Melissa Linkert et al.   JOURNAL OF CELL BIOLOGY

Integrating high-throughput genetic interaction mapping and high-content screening to explore yeast spindle morphogenesis

(2010) Franco J. Vizeacoumar et al.   JOURNAL OF CELL BIOLOGY

Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes

(2010) Beate Neumann et al.   NATURE

Population context determines cell-to-cell variability in endocytosis and virus infection

(2009) Berend Snijder et al.   NATURE

Replicative Aging in Yeast: The Means to the End

(2008) K.A. Steinkraus et al.   Annual Review of Cell and Developmental Biology

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS