Machine learning and computer vision approaches for phenotypic profiling

Classifying and segmenting microscopy images with deep multiple instance learning

(2016) Oren Z. Kraus et al.   BIOINFORMATICS

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

Learning a hierarchical representation of the yeast transcriptomic machinery using an autoencoder model

(2016) Lujia Chen et al.   BMC BIOINFORMATICS

Computer vision for high content screening

(2016) Oren Z. Kraus et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Applications in image-based profiling of perturbations

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

High-Content Screening for Quantitative Cell Biology

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

A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells

(2016) Amber L. Jolly et al.   Cell Reports

Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks

(2016) Yiheng Wang et al.   Scientific Reports

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

(2015) Yolanda T. Chong et al.   CELL

Image Outlier Detection and Feature Extraction via L1-Norm-Based 2D Probabilistic PCA

(2015) Fujiao Ju et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

Outlier detection and removal improves accuracy of machine learning approach to multispectral burn diagnostic imaging

(2015) Weizhi Li et al.   JOURNAL OF BIOMEDICAL OPTICS

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

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Automatic Detection of White Matter Hyperintensities in Healthy Aging and Pathology Using Magnetic Resonance Imaging: A Review

(2015) Maria Eugenia Caligiuri et al.   NEUROINFORMATICS

Functional genome-wide siRNA screen identifies KIAA0586 as mutated in Joubert syndrome

(2015) Susanne Roosing et al.   eLife

Performance evaluation of image segmentation algorithms on microscopic image data

(2014) MIROSLAV BENEŠ et al.   JOURNAL OF MICROSCOPY

Single-cell and multivariate approaches in genetic perturbation screens

(2014) Prisca Liberali et al.   NATURE REVIEWS GENETICS

TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization

(2013) Jean Ollion et al.   BIOINFORMATICS

Label-Free Detection of Neuronal Differentiation in Cell Populations Using High-Throughput Live-Cell Imaging of PC12 Cells

(2013) Sebastian Weber et al.   PLoS One

Multiplex Cytological Profiling Assay to Measure Diverse Cellular States

(2013) Sigrun M. Gustafsdottir et al.   PLoS One

High-throughput hyperdimensional vertebrate phenotyping

(2013) Carlos Pardo-Martin et al.   Nature Communications

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

(2013) Louis-François Handfield et al.   PLoS Computational Biology

Cell Size Control in Yeast

(2012) Jonathan J. Turner et al.   CURRENT BIOLOGY

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

(2012) Erik Meijering   IEEE SIGNAL PROCESSING MAGAZINE

PhenoRipper: software for rapidly profiling microscopy images

(2012) Satwik Rajaram et al.   NATURE METHODS

Biological imaging software tools

(2012) Kevin W Eliceiri et al.   NATURE METHODS

A Chemical Screen Probing the Relationship between Mitochondrial Content and Cell Size

(2012) Toshimori Kitami et al.   PLoS One

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Mapping of signaling networks through synthetic genetic interaction analysis by RNAi

(2011) Thomas Horn et al.   NATURE METHODS

Clustering phenotype populations by genome-wide RNAi and multiparametric imaging

(2010) Florian Fuchs et al.   Molecular Systems Biology

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

(2010) Beate Neumann et al.   NATURE

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

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

(2010) Michael Held et al.   NATURE METHODS

Quantifying Phenotypic Variation in Isogenic Caenorhabditis elegans Expressing Phsp-16.2::gfp by Clustering 2D Expression Patterns

(2010) Alexander K. Seewald et al.   PLoS One

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

(2009) Takahiro Negishi et al.   JOURNAL OF BIOTECHNOLOGY

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

(2009) Berend Snijder et al.   NATURE