Computer vision for high content screening

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

(2015) Yolanda T. Chong et al.   CELL

ImageNet Large Scale Visual Recognition Challenge

(2015) Olga Russakovsky et al.   INTERNATIONAL JOURNAL OF COMPUTER VISION

Deep Neural Nets as a Method for Quantitative Structure–Activity Relationships

(2015) Junshui Ma et al.   Journal of Chemical Information and Modeling

Deep learning

(2015) Yann LeCun et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries

(2015) Kenji L. Kurita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

Accurate cell segmentation in microscopy images using membrane patterns

(2014) Sotiris Dimopoulos et al.   BIOINFORMATICS

Phenotypic screening in cancer drug discovery — past, present and future

(2014) John G. Moffat et al.   NATURE REVIEWS DRUG DISCOVERY

Single-cell and multivariate approaches in genetic perturbation screens

(2014) Prisca Liberali et al.   NATURE REVIEWS GENETICS

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Multiple instance classification: Review, taxonomy and comparative study

(2013) Jaume Amores   ARTIFICIAL INTELLIGENCE

A novel single-cell screening platform reveals proteome plasticity during yeast stress responses

(2013) Michal Breker et al.   JOURNAL OF CELL BIOLOGY

Machine learning in cell biology – teaching computers to recognize phenotypes

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

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

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

(2013) Zheng Yin et al.   NATURE CELL BIOLOGY

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

(2013) Nico Battich et al.   NATURE METHODS

Cell Segmentation: 50 Years Down the Road [Life Sciences]

(2012) Erik Meijering   IEEE SIGNAL PROCESSING MAGAZINE

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

(2012) Geoffrey Hinton et al.   IEEE SIGNAL PROCESSING MAGAZINE

Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress

(2012) Johnny M. Tkach et al.   NATURE CELL BIOLOGY

Unsupervised modeling of cell morphology dynamics for time-lapse microscopy

(2012) Qing Zhong et al.   NATURE METHODS

PhenoRipper: software for rapidly profiling microscopy images

(2012) Satwik Rajaram et al.   NATURE METHODS

Annotated high-throughput microscopy image sets for validation

(2012) Vebjorn Ljosa et al.   NATURE METHODS

An image analysis toolbox for high-throughput C. elegans assays

(2012) Carolina Wählby et al.   NATURE METHODS

Biological imaging software tools

(2012) Kevin W Eliceiri et al.   NATURE METHODS

Origins of regulated cell-to-cell variability

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

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

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

High-Content Phenotypic Profiling of Drug Response Signatures across Distinct Cancer Cells

(2010) P. D. Caie et al.   MOLECULAR CANCER THERAPEUTICS

Patterns of basal signaling heterogeneity can distinguish cellular populations with different drug sensitivities

(2010) Dinesh Kumar Singh et al.   Molecular Systems Biology

Clustering phenotype populations by genome-wide RNAi and multiparametric imaging

(2010) Florian Fuchs et al.   Molecular Systems Biology

CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging

(2010) Michael Held et al.   NATURE METHODS

Phenomics: the next challenge

(2010) David Houle et al.   NATURE REVIEWS GENETICS

Pattern Recognition Software and Techniques for Biological Image Analysis

(2010) Lior Shamir et al.   PLoS Computational Biology

Temporal clustering by affinity propagation reveals transcriptional modules in Arabidopsis thaliana

(2009) S. J. Kiddle et al.   BIOINFORMATICS

CellClassifier: supervised learning of cellular phenotypes

(2009) Pauli Rämö et al.   BIOINFORMATICS

Multidimensional quantification of subcellular morphology of Saccharomyces cerevisiae using CalMorph, the high-throughput image-processing program

(2009) Takahiro Negishi et al.   JOURNAL OF BIOTECHNOLOGY

Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning

(2009) Thouis R. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CellProfiler Analyst: data exploration and analysis software for complex image-based screens

(2008) Thouis R Jones et al.   BMC BIOINFORMATICS

Constraint factor graph cut-based active contour method for automated cellular image segmentation in RNAi screening

(2008) C. CHEN et al.   JOURNAL OF MICROSCOPY