From observing to predicting single-cell structure and function with high-throughput/high-content microscopy

Hidden in plain sight: what remains to be discovered in the eukaryotic proteome?

(2019) Valerie Wood et al.   Open Biology

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

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

In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images

(2018) Eric M. Christiansen et al.   CELL

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018

(2018) Lorenzo Galluzzi et al.   CELL DEATH AND DIFFERENTIATION

Placing RNA in context and space - methods for spatially resolved transcriptomics

(2018) Carina Strell et al.   FEBS Journal

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Deep learning massively accelerates super-resolution localization microscopy

(2018) Wei Ouyang et al.   NATURE BIOTECHNOLOGY

Direct transfection of clonal organoids in Matrigel microbeads: a promising approach toward organoid-based genetic screens

(2018) Bastien Laperrousaz et al.   NUCLEIC ACIDS RESEARCH

Discovery of functional interactions among actin regulators by analysis of image fluctuations in an unperturbed motile cell system

(2018) Tadamoto Isogai et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

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

(2018) Kevin Smith et al.   Cell Systems

Experimental and computational framework for a dynamic protein atlas of human cell division

(2018) Yin Cai et al.   NATURE

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

(2018) Chawin Ounkomol et al.   NATURE METHODS

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level

(2018) Katie McDole et al.   CELL

Deep learning to predict microscope images

(2018) Roger Brent et al.   NATURE METHODS

Deep learning enables cross-modality super-resolution in fluorescence microscopy

(2018) Hongda Wang et al.   NATURE METHODS

Time-resolved mapping of genetic interactions to model rewiring of signaling pathways

(2018) Florian Heigwer et al.   eLife

An Overview of data science uses in bioimage informatics

(2017) Anatole Chessel   METHODS

A deep learning and novelty detection framework for rapid phenotyping in high-content screening

(2017) Christoph Sommer et al.   MOLECULAR BIOLOGY OF THE CELL

Automated analysis of high‐content microscopy data with deep learning

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

Applying systems-level spectral imaging and analysis to reveal the organelle interactome

(2017) Alex M. Valm et al.   NATURE

Localization-based super-resolution imaging meets high-content screening

(2017) Anne Beghin et al.   NATURE METHODS

Data-analysis strategies for image-based cell profiling

(2017) Juan C Caicedo et al.   NATURE METHODS

Image Data Resource: a bioimage data integration and publication platform

(2017) Eleanor Williams et al.   NATURE METHODS

Prospective identification of hematopoietic lineage choice by deep learning

(2017) Felix Buggenthin et al.   NATURE METHODS

Systematic epistatic mapping of cellular processes

(2017) Maximilian Billmann et al.   Cell Division

TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network

(2017) Matej Usaj et al.   G3-Genes Genomes Genetics

Microscopy, Meet Big Data

(2017) Antony Orth et al.   Cell Systems

Systematic high-content genome-wide RNAi screens of endothelial cell migration and morphology

(2017) Steven P. Williams et al.   Scientific Data

LEVER: software tools for segmentation, tracking and lineaging of proliferating cells

(2016) Mark Winter et al.   BIOINFORMATICS

Collaborative analysis of multi-gigapixel imaging data using Cytomine

(2016) Raphaël Marée et al.   BIOINFORMATICS

Automated Microscopy and High Content Screens (Phenotypic Screens) in Academia Labs

(2016) Dimitri Moreau et al.   CHIMIA

Applications in image-based profiling of perturbations

(2016) Juan C Caicedo et al.   CURRENT OPINION IN BIOTECHNOLOGY

Integrated, multi-scale, spatial–temporal cell biology – A next step in the post genomic era

(2016) Rick Horwitz   METHODS

Challenges in long-term imaging and quantification of single-cell dynamics

(2016) Stavroula Skylaki et al.   NATURE BIOTECHNOLOGY

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

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

(2016) M. Costanzo et al.   SCIENCE

High-Content Screening for Quantitative Cell Biology

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

More than Pictures: When MS Imaging Meets Histology

(2016) Yonghui Dong et al.   TRENDS IN PLANT SCIENCE

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

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

Single-cell phenomics in budding yeast

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

Deep learning

(2015) Yann LeCun et al.   NATURE

Single-cell biology: The power of one

(2015) J. M. Perkel   SCIENCE

Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules

(2015) Gregory R. Johnson et al.   PLoS Computational Biology

A map of directional genetic interactions in a metazoan cell

(2015) Bernd Fischer et al.   eLife

Quantitative Single-Cell Approaches to Stem Cell Research

(2014) Martin Etzrodt et al.   Cell Stem 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

Deep Imaging: the next frontier in microscopy

(2014) Vassilis Roukos et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

High throughput 3D super-resolution microscopy reveals Caulobacter crescentus in vivo Z-ring organization

(2014) S. J. Holden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

High-throughput, multiparameter analysis of single cells

(2013) Thomas Haselgrübler et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Shaping organisms with apoptosis

(2013) M Suzanne et al.   CELL DEATH AND DIFFERENTIATION

Machine learning in cell biology – teaching computers to recognize phenotypes

(2013) Christoph Sommer et al.   JOURNAL OF CELL SCIENCE

RNAi screening reveals a large signaling network controlling the Golgi apparatus in human cells

(2013) J. Chia et al.   Molecular Systems Biology

High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagy

(2013) Samuel A. Hasson et al.   NATURE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

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

(2013) Christina Laufer et al.   NATURE METHODS

Quantitative genetic-interaction mapping in mammalian cells

(2013) Assen Roguev et al.   NATURE METHODS

Imaging Morphogenesis: Technological Advances and Biological Insights

(2013) P. J. Keller   SCIENCE

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data

(2012) Richard N. Smith et al.   BIOINFORMATICS

Screens, maps & networks: from genome sequences to personalized medicine

(2012) Thomas Sandmann et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

In situ metabolomic mass spectrometry imaging: Recent advances and difficulties

(2012) Daisuke Miura et al.   Journal of Proteomics

A direct look at RNAi screens

(2012) Alexis R Barr et al.   Molecular Systems Biology

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

(2012) Berend Snijder et al.   Molecular Systems Biology

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

(2012) Chris Allan et al.   NATURE METHODS

A Probabilistic Model for Cell Population Phenotyping Using HCS Data

(2012) Edouard Pauwels et al.   PLoS One

RNAi Screening Reveals Proteasome- and Cullin3-Dependent Stages in Vaccinia Virus Infection

(2012) Jason Mercer et al.   Cell Reports

Adaptive informatics for multifactorial and high-content biological data

(2011) Bjorn L Millard et al.   NATURE METHODS

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi

(2011) Thomas Horn et al.   NATURE METHODS

Long-term single-cell imaging of mammalian stem cells

(2011) Timm Schroeder   NATURE METHODS

Origins of regulated cell-to-cell variability

(2011) Berend Snijder et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Open Knowledge Foundation: Open Data Means Better Science

(2011) Jennifer C. Molloy   PLOS BIOLOGY

Automated microscopy for high-content RNAi screening

(2010) Christian Conrad 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

Systems survey of endocytosis by multiparametric image analysis

(2010) Claudio Collinet et al.   NATURE

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

(2010) Beate Neumann et al.   NATURE

How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens

(2010) Florian Markowetz   PLoS Computational Biology

Quantitative Time-Lapse Fluorescence Microscopy in Single Cells

(2009) Dale Muzzey et al.   Annual Review of Cell and Developmental Biology

Coordination of Rho GTPase activities during cell protrusion

(2009) Matthias Machacek et al.   NATURE

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

(2009) Berend Snijder et al.   NATURE

A high-throughput method to globally study the organelle morphology in S. cerevisiae

(2009) Shabnam Tavassoli et al.   Jove-Journal of Visualized Experiments

WND-CHARM: Multi-purpose image classification using compound image transforms

(2008) Nikita Orlov et al.   PATTERN RECOGNITION LETTERS

Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy

(2008) P. J. Keller et al.   SCIENCE