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Shantanu Singh - Publications

Affiliations: 
2011-2014 The Broad Institute 
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36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Lafarge MW, Caicedo JC, Carpenter AE, Pluim JPW, Singh S, Veta M. Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning. Proceedings of Machine Learning Research. 103: 315-325. PMID 35874600  0.665
2022 Caicedo JC, Arevalo J, Piccioni F, Bray MA, Hartland CL, Wu X, Brooks AN, Berger AH, Boehm JS, Carpenter AE, Singh S. Cell Painting predicts impact of lung cancer variants. Molecular Biology of the Cell. mbcE21110538. PMID 35353015 DOI: 10.1091/mbc.E21-11-0538  0.57
2022 Chow YL, Singh S, Carpenter AE, Way GP. Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. Plos Computational Biology. 18: e1009888. PMID 35213530 DOI: 10.1371/journal.pcbi.1009888  0.562
2022 Way GP, Spitzer H, Burnham P, Raj A, Theis F, Singh S, Carpenter AE. Image-based profiling: a powerful and challenging new data type. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 27: 407-411. PMID 34890168  0.682
2021 Way GP, Kost-Alimova M, Shibue T, Harrington WF, Gill S, Piccioni F, Becker T, Shafqat-Abbasi H, Hahn WC, Carpenter AE, Vazquez F, Singh S. Predicting cell health phenotypes using image-based morphology profiling. Molecular Biology of the Cell. mbcE20120784. PMID 33534641 DOI: 10.1091/mbc.E20-12-0784  0.708
2020 Danielson E, Perez de Arce K, Cimini B, Wamhoff EC, Singh S, Cottrell JR, Carpenter AE, Bathe M. Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging. Eneuro. PMID 33355295 DOI: 10.1523/ENEURO.0286-20.2020  0.751
2020 Vasilevich AS, Vermeulen S, Kamphuis M, Roumans N, Eroumé S, Hebels DGAJ, van de Peppel J, Reihs R, Beijer NRM, Carlier A, Carpenter AE, Singh S, de Boer J. On the correlation between material-induced cell shape and phenotypical response of human mesenchymal stem cells. Scientific Reports. 10: 18988. PMID 33149200 DOI: 10.1038/s41598-020-76019-z  0.56
2020 Doan M, Sebastian JA, Caicedo JC, Siegert S, Roch A, Turner TR, Mykhailova O, Pinto RN, McQuin C, Goodman A, Parsons MJ, Wolkenhauer O, Hennig H, Singh S, Wilson A, et al. Objective assessment of stored blood quality by deep learning. Proceedings of the National Academy of Sciences of the United States of America. PMID 32839303 DOI: 10.1073/Pnas.2001227117  0.77
2020 Doan M, Case M, Masic D, Hennig H, McQuin C, Caicedo J, Singh S, Goodman A, Wolkenhauer O, Summers HD, Jamieson D, Delft FV, Filby A, Carpenter AE, Rees P, et al. Label-Free Leukemia Monitoring by Computer Vision. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. PMID 32091180 DOI: 10.1002/Cyto.A.23987  0.781
2020 Caicedo JC, Goodman A, Karhohs KW, Cimini BA, Ackerman J, Haghighi M, Heng C, Becker T, Doan M, McQuin C, Rohban M, Singh S, Carpenter AE. Publisher Correction: Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nature Methods. PMID 31969730 DOI: 10.1038/S41592-020-0733-Z  0.73
2019 Caicedo JC, Goodman A, Karhohs KW, Cimini BA, Ackerman J, Haghighi M, Heng C, Becker T, Doan M, McQuin C, Rohban M, Singh S, Carpenter AE. Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nature Methods. PMID 31636459 DOI: 10.1038/S41592-019-0612-7  0.76
2019 Caicedo JC, Roth J, Goodman A, Becker T, Karhohs KW, Broisin M, Molnar C, McQuin C, Singh S, Theis FJ, Carpenter AE. Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. PMID 31313519 DOI: 10.1002/Cyto.A.23863  0.792
2019 Rohban MH, Abbasi HS, Singh S, Carpenter AE. Capturing single-cell heterogeneity via data fusion improves image-based profiling. Nature Communications. 10: 2082. PMID 31064985 DOI: 10.1038/S41467-019-10154-8  0.742
2019 Raman S, Singh S, Pécot T, Caserta E, Huang K, Rittscher J, Leone G, Machiraju R. Capturing variations in nuclear phenotypes Journal of Computational Science. 36: 101014. DOI: 10.1016/J.Jocs.2019.07.001  0.4
2018 Caicedo JC, McQuin C, Goodman A, Singh S, Carpenter AE. Weakly Supervised Learning of Single-Cell Feature Embeddings. Proceedings. Ieee Computer Society Conference On Computer Vision and Pattern Recognition. 2018: 9309-9318. PMID 30918435 DOI: 10.1109/CVPR.2018.00970  0.54
2018 Vasilevich AS, Mourcin F, Mentink A, Hulshof F, Beijer N, Zhao Y, Levers M, Papenburg B, Singh S, Carpenter AE, Stamatialis D, van Blitterswijk C, Tarte K, de Boer J. Designed Surface Topographies Control ICAM-1 Expression in Tonsil-Derived Human Stromal Cells. Frontiers in Bioengineering and Biotechnology. 6: 87. PMID 30003080 DOI: 10.3389/Fbioe.2018.00087  0.596
2018 McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE. CellProfiler 3.0: Next-generation image processing for biology. Plos Biology. 16: e2005970. PMID 29969450 DOI: 10.1371/Journal.Pbio.2005970  0.748
2018 Simm J, Klambauer G, Arany A, Steijaert M, Wegner JK, Gustin E, Chupakhin V, Chong YT, Vialard J, Buijnsters P, Velter I, Vapirev A, Singh S, Carpenter AE, Wuyts R, et al. Repurposing High-Throughput Image Assays Enables Biological Activity Prediction for Drug Discovery. Cell Chemical Biology. PMID 29503208 DOI: 10.1016/J.Chembiol.2018.01.015  0.598
2017 Caicedo JC, Cooper S, Heigwer F, Warchal S, Qiu P, Molnar C, Vasilevich AS, Barry JD, Bansal HS, Kraus O, Wawer M, Paavolainen L, Herrmann MD, Rohban M, Hung J, ... ... Singh S, et al. Data-analysis strategies for image-based cell profiling. Nature Methods. 14: 849-863. PMID 28858338 DOI: 10.1038/Nmeth.4397  0.786
2017 Vasilevich AS, Carlier A, de Boer J, Singh S. How Not To Drown in Data: A Guide for Biomaterial Engineers. Trends in Biotechnology. PMID 28693857 DOI: 10.1016/J.Tibtech.2017.05.007  0.35
2017 Hulshof FFB, Papenburg B, Vasilevich A, Hulsman M, Zhao Y, Levers M, Fekete N, de Boer M, Yuan H, Singh S, Beijer N, Bray MA, Logan DJ, Reinders M, Carpenter AE, et al. Mining for osteogenic surface topographies: In silico design to in vivo osseo-integration. Biomaterials. 137: 49-60. PMID 28535442 DOI: 10.1016/J.Biomaterials.2017.05.020  0.545
2017 Barczak AK, Avraham R, Singh S, Luo SS, Zhang WR, Bray MA, Hinman AE, Thompson M, Nietupski RM, Golas A, Montgomery P, Fitzgerald M, Smith RS, White DW, Tischler AD, et al. Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence. Plos Pathogens. 13: e1006363. PMID 28505176 DOI: 10.1371/Journal.Ppat.1006363  0.551
2017 Bray MA, Gustafsdottir SM, Ljosa V, Singh S, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancík V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, et al. A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay. Gigascience. PMID 28327978 DOI: 10.1093/Gigascience/Giw014  0.683
2017 Rohban MH, Singh S, Wu X, Berthet JB, Bray MA, Shrestha Y, Varelas X, Boehm JS, Carpenter AE. Systematic morphological profiling of human gene and allele function via Cell Painting. Elife. 6. PMID 28315521 DOI: 10.7554/Elife.24060  0.575
2017 Rohban MH, Singh S, Wu X, Berthet JB, Bray M, Shrestha Y, Varelas X, Boehm JS, Carpenter AE. Author response: Systematic morphological profiling of human gene and allele function via Cell Painting Elife. DOI: 10.7554/Elife.24060.022  0.55
2016 Bray MA, Singh S, Han H, Davis CT, Borgeson B, Hartland C, Kost-Alimova M, Gustafsdottir SM, Gibson CC, Carpenter AE. Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nature Protocols. 11: 1757-1774. PMID 27560178 DOI: 10.1038/Nprot.2016.105  0.711
2016 Dao D, Fraser AN, Hung J, Ljosa V, Singh S, Carpenter AE. CellProfiler Analyst: interactive data exploration, analysis, and classification of large biological image sets. Bioinformatics (Oxford, England). PMID 27354701 DOI: 10.1093/Bioinformatics/Btw390  0.68
2016 Caicedo JC, Singh S, Carpenter AE. Applications in image-based profiling of perturbations. Current Opinion in Biotechnology. 39: 134-142. PMID 27089218 DOI: 10.1016/J.Copbio.2016.04.003  0.695
2016 Uhlmann V, Singh S, Carpenter AE. CP-CHARM: segmentation-free image classification made accessible. Bmc Bioinformatics. 17: 51. PMID 26817459 DOI: 10.1186/S12859-016-0895-Y  0.645
2015 Singh S, Wu X, Ljosa V, Bray MA, Piccioni F, Root DE, Doench JG, Boehm JS, Carpenter AE. Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects. Plos One. 10: e0131370. PMID 26197079 DOI: 10.1371/Journal.Pone.0131370  0.601
2014 Singh S, Bray MA, Jones TR, Carpenter AE. Pipeline for illumination correction of images for high-throughput microscopy. Journal of Microscopy. 256: 231-6. PMID 25228240 DOI: 10.1111/Jmi.12178  0.698
2014 Singh S, Carpenter AE, Genovesio A. Increasing the Content of High-Content Screening: An Overview. Journal of Biomolecular Screening. 19: 640-650. PMID 24710339 DOI: 10.1177/1087057114528537  0.616
2013 Ljosa V, Caie PD, Ter Horst R, Sokolnicki KL, Jenkins EL, Daya S, Roberts ME, Jones TR, Singh S, Genovesio A, Clemons PA, Carragher NO, Carpenter AE. Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment. Journal of Biomolecular Screening. 18: 1321-9. PMID 24045582 DOI: 10.1177/1087057113503553  0.666
2012 Pecot T, Singh S, Caserta E, Huang K, MacHiraju R, Leone G. Non parametric cell nuclei segmentation based on a tracking over depth from 3D fluorescence confocal images Proceedings - International Symposium On Biomedical Imaging. 170-173. DOI: 10.1109/ISBI.2012.6235511  0.347
2011 Singh S, Janoos F, Pécot T, Caserta E, Leone G, Rittscher J, Machiraju R. Identifying nuclear phenotypes using semi-supervised metric learning. Information Processing in Medical Imaging : Proceedings of the ... Conference. 22: 398-410. PMID 21761673 DOI: 10.1007/978-3-642-22092-0_33  0.366
2008 Singh S, Mosaliganti K, Machiraju R. Microstructure preserving synthesis of biomedical images 2008 5th Ieee International Symposium On Biomedical Imaging: From Nano to Macro, Proceedings, Isbi. 404-407. DOI: 10.1109/ISBI.2008.4541018  0.375
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