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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
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  0.44
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  0.44
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.44
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  0.6
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  0.44
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  0.6
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  0.44
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  0.6
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
2016 Berger AH, Brooks AN, Wu X, Shrestha Y, Chouinard C, Piccioni F, Bagul M, Kamburov A, Imielinski M, Hogstrom L, Zhu C, Yang X, Pantel S, Sakai R, Watson J, ... ... Singh S, et al. High-throughput Phenotyping of Lung Cancer Somatic Mutations. Cancer Cell. PMID 27478040 DOI: 10.1016/j.ccell.2016.06.022  0.44
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  0.44
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  0.44
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  0.44
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  0.44
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  0.44
2013 Verma S, Farkouh ME, Yanagawa B, Fitchett DH, Ahsan MR, Ruel M, Sud S, Gupta M, Singh S, Gupta N, Cheema AN, Leiter LA, Fedak PW, Teoh H, Latter DA, et al. Comparison of coronary artery bypass surgery and percutaneous coronary intervention in patients with diabetes: a meta-analysis of randomised controlled trials. The Lancet. Diabetes & Endocrinology. 1: 317-28. PMID 24622417 DOI: 10.1016/S2213-8587(13)70089-5  0.44
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  0.44
2013 Singh S, Wang Y, Ding L. Who is repinning? Predicting a brand's user interactions using social media retrieval Proceedings of the 13th International Workshop On Multimedia Data Mining, Mdmkdd 2013 - Held in Conjunction With the Acm Sigkdd 2013 Conference. DOI: 10.1145/2501217.2501218  0.44
2012 Chen HZ, Ouseph MM, Li J, Pécot T, Chokshi V, Kent L, Bae S, Byrne M, Duran C, Comstock G, Trikha P, Mair M, Senapati S, Martin CK, Gandhi S, ... ... Singh S, et al. Canonical and atypical E2Fs regulate the mammalian endocycle. Nature Cell Biology. 14: 1192-202. PMID 23064266 DOI: 10.1038/ncb2595  0.44
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  0.44
2011 Singh S, Janoos F, Pécot T, Caserta E, Huang K, Rittscher J, Leone G, Machiraju R. Non-parametric population analysis of cellular phenotypes. Medical Image Computing and Computer-Assisted Intervention : Miccai ... International Conference On Medical Image Computing and Computer-Assisted Intervention. 14: 343-51. PMID 21995047 DOI: 10.1007/978-3-642-23629-7_42  0.44
2011 Janoos F, Singh S, Machiraju R, Wells WM, Mórocz IA. State-space models of mental processes from fMRI. Information Processing in Medical Imaging : Proceedings of the ... Conference. 22: 588-99. PMID 21761688 DOI: 10.1007/978-3-642-22092-0_48  0.44
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  0.44
2011 Janoos F, Machiraju R, Singh S, Morocz IÁ. Spatio-temporal models of mental processes from fMRI. Neuroimage. 57: 362-77. PMID 21440069 DOI: 10.1016/j.neuroimage.2011.03.047  0.44
2010 Singh S, Raman S, Caserta E, Leone G, Ostrowski M, Rittscher J, Machiraju R. Analysis of spatial variation of nuclear morphology in tissue microenvironments 2010 7th Ieee International Symposium On Biomedical Imaging: From Nano to Macro, Isbi 2010 - Proceedings. 1293-1296. DOI: 10.1109/ISBI.2010.5490233  0.44
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  0.44
2007 Janoos F, Singh S, Irfanoglu O, Machiraju R, Parent R. Activity analysis using spatio-temporal trajectory volumes in surveillance applications Vast Ieee Symposium On Visual Analytics Science and Technology 2007, Proceedings. 3-10. DOI: 10.1109/VAST.2007.4388990  0.44
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