Shantanu Singh
Shantanu Singh
Senior Group Leader, Broad Institute of MIT and Harvard
Verified email at - Homepage
Cited by
Cited by
CellProfiler 3.0: Next-generation image processing for biology
C McQuin, A Goodman, V Chernyshev, L Kamentsky, BA Cimini, ...
PLoS biology 16 (7), 2018
Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes
MA Bray, S Singh, H Han, CT Davis, B Borgeson, C Hartland, ...
Nature Protocols 11 (9), 1757-1774, 2016
Data-analysis strategies for image-based cell profiling
JC Caicedo, S Cooper, F Heigwer, S Warchal, P Qiu, C Molnar, ...
Nature methods 14 (9), 849-863, 2017
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl
JC Caicedo, A Goodman, KW Karhohs, BA Cimini, J Ackerman, ...
Nature methods 16 (12), 1247-1253, 2019
Evaluation of deep learning strategies for nucleus segmentation in fluorescence images
JC Caicedo, J Roth, A Goodman, T Becker, KW Karhohs, M Broisin, ...
Cytometry Part A 95 (9), 952-965, 2019
Increasing the Content of High-Content Screening An Overview
S Singh, AE Carpenter, A Genovesio
Journal of biomolecular screening 19 (5), 640-650, 2014
Repurposing high-throughput image assays enables biological activity prediction for drug discovery
J Simm, G Klambauer, A Arany, M Steijaert, JK Wegner, E Gustin, ...
Cell chemical biology 25 (5), 611-618. e3, 2018
High-throughput phenotyping of lung cancer somatic mutations
AH Berger, AN Brooks, X Wu, Y Shrestha, C Chouinard, F Piccioni, ...
Cancer Cell 30 (2), 214-228, 2016
Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment
V Ljosa, PD Caie, R ter Horst, KL Sokolnicki, EL Jenkins, S Daya, ...
Journal of biomolecular screening 18 (10), 1321-1329, 2013
Canonical and atypical E2Fs regulate the mammalian endocycle
HZ Chen, MM Ouseph, J Li, T Pécot, V Chokshi, L Kent, S Bae, M Byrne, ...
Nature Cell Biology, 2012
Applications in image-based profiling of perturbations
JC Caicedo, S Singh, AE Carpenter
Current Opinion in Biotechnology 39, 134-142, 2016
A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay
MA Bray, SM Gustafsdottir, MH Rohban, S Singh, V Ljosa, KL Sokolnicki, ...
GigaScience 6 (12), giw014, 2017
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets
D Dao, AN Fraser, J Hung, V Ljosa, S Singh, AE Carpenter
Bioinformatics 32 (20), 3210-3212, 2016
Systematic morphological profiling of human gene and allele function via Cell Painting
MH Rohban, S Singh, X Wu, JB Berthet, MA Bray, Y Shrestha, X Varelas, ...
eLife 6, e24060, 2017
Pipeline for illumination correction of images for high‐throughput microscopy
S Singh, MA Bray, TR Jones, AE Carpenter
Journal of microscopy, 2014
Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence
AK Barczak, R Avraham, S Singh, SS Luo, WR Zhang, MA Bray, ...
PLoS Pathogens 13 (5), e1006363, 2017
Predicting cell health phenotypes using image-based morphology profiling
GP Way, M Kost-Alimova, T Shibue, WF Harrington, S Gill, F Piccioni, ...
Molecular Biology of the Cell 32 (9), 995-1005, 2021
Automating Morphological Profiling with Generic Deep Convolutional Networks
N Pawlowski, JC Caicedo, S Singh, AE Carpenter, A Storkey
bioRxiv, 085118, 2016
Anomaly detection using negative selection based on the r-contiguous matching rule
S Singh
1st International Conference on Artificial Immune Systems (ICARIS …, 2002
Weakly supervised learning of single-cell feature embeddings
JC Caicedo, C McQuin, A Goodman, S Singh, AE Carpenter
Proceedings of the IEEE Conference on Computer Vision and Pattern …, 2018
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