| Year |
Citation |
Score |
| 2024 |
Kalinin AA, Arevalo J, Vulliard L, Serrano E, Tsang H, Bornholdt M, Rajwa B, Carpenter AE, Way GP, Singh S. A versatile information retrieval framework for evaluating profile strength and similarity. Biorxiv : the Preprint Server For Biology. PMID 38617315 DOI: 10.1101/2024.04.01.587631 |
0.591 |
|
| 2024 |
Chandrasekaran SN, Cimini BA, Goodale A, Miller L, Kost-Alimova M, Jamali N, Doench JG, Fritchman B, Skepner A, Melanson M, Kalinin AA, Arevalo J, Haghighi M, Caicedo JC, Kuhn D, ... ... Singh S, et al. Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nature Methods. PMID 38594452 DOI: 10.1038/s41592-024-02241-6 |
0.779 |
|
| 2024 |
Moshkov N, Bornholdt M, Benoit S, Smith M, McQuin C, Goodman A, Senft RA, Han Y, Babadi M, Horvath P, Cimini BA, Carpenter AE, Singh S, Caicedo JC. Learning representations for image-based profiling of perturbations. Nature Communications. 15: 1594. PMID 38383513 DOI: 10.1038/s41467-024-45999-1 |
0.787 |
|
| 2024 |
Weisbart E, Kumar A, Arevalo J, Carpenter AE, Cimini BA, Singh S. Cell Painting Gallery: an open resource for image-based profiling. Arxiv. PMID 38351939 |
0.782 |
|
| 2024 |
Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. Journal of Chemical Information and Modeling. PMID 38300851 DOI: 10.1021/acs.jcim.3c01834 |
0.52 |
|
| 2024 |
Carpenter AE, Singh S. Bringing computation to biology by bridging the last mile. Nature Cell Biology. 26: 5-7. PMID 38228822 DOI: 10.1038/s41556-023-01286-7 |
0.43 |
|
| 2024 |
Tegtmeyer M, Arora J, Asgari S, Cimini BA, Nadig A, Peirent E, Liyanage D, Way GP, Weisbart E, Nathan A, Amariuta T, Eggan K, Haghighi M, McCarroll SA, O'Connor L, ... ... Singh S, et al. High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature Communications. 15: 347. PMID 38184653 DOI: 10.1038/s41467-023-44045-w |
0.792 |
|
| 2024 |
Seal S, Carreras-Puigvert J, Singh S, Carpenter AE, Spjuth O, Bender A. From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability. Molecular Biology of the Cell. mbcE23080298. PMID 38170589 DOI: 10.1091/mbc.E23-08-0298 |
0.591 |
|
| 2023 |
Serrano E, Chandrasekaran SN, Bunten D, Brewer KI, Tomkinson J, Kern R, Bornholdt M, Fleming S, Pei R, Arevalo J, Tsang H, Rubinetti V, Tromans-Coia C, Becker T, Weisbart E, ... ... Singh S, et al. Reproducible image-based profiling with Pycytominer. Arxiv. PMID 38045474 |
0.797 |
|
| 2023 |
Seal S, Spjuth O, Hosseini-Gerami L, García-Ortegón M, Singh S, Bender A, Carpenter AE. Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank. Biorxiv : the Preprint Server For Biology. PMID 37905146 DOI: 10.1101/2023.10.15.562398 |
0.539 |
|
| 2023 |
Kelley ME, Berman AY, Stirling DR, Cimini BA, Han Y, Singh S, Carpenter AE, Kapoor TM, Way GP. High-content microscopy reveals a morphological signature of bortezomib resistance. Elife. 12. PMID 37753907 DOI: 10.7554/eLife.91362 |
0.769 |
|
| 2023 |
Arevalo J, van Dijk R, Carpenter AE, Singh S. Evaluating batch correction methods for image-based cell profiling. Biorxiv : the Preprint Server For Biology. PMID 37745478 DOI: 10.1101/2023.09.15.558001 |
0.657 |
|
| 2023 |
Lacoste J, Haghighi M, Haider S, Lin ZY, Segal D, Reno C, Qian WW, Xiong X, Shafqat-Abbasi H, Ryder PV, Senft R, Cimini BA, Roth FP, Calderwood M, Hill D, ... ... Singh S, et al. Pervasive mislocalization of pathogenic coding variants underlying human disorders. Biorxiv : the Preprint Server For Biology. PMID 37732209 DOI: 10.1101/2023.09.05.556368 |
0.714 |
|
| 2023 |
Ramezani M, Bauman J, Singh A, Weisbart E, Yong J, Lozada M, Way GP, Kavari SL, Diaz C, Haghighi M, Batista TM, Pérez-Schindler J, Claussnitzer M, Singh S, Cimini BA, et al. A genome-wide atlas of human cell morphology. Biorxiv : the Preprint Server For Biology. PMID 37609130 DOI: 10.1101/2023.08.06.552164 |
0.797 |
|
| 2023 |
Yu S, Kalinin AA, Paraskevopoulou MD, Maruggi M, Cheng J, Tang J, Icke I, Luo Y, Wei Q, Scheibe D, Hunter J, Singh S, Nguyen D, Carpenter AE, Horman SR. Integrating inflammatory biomarker analysis and artificial intelligence-enabled image-based profiling to identify drug targets for intestinal fibrosis. Cell Chemical Biology. PMID 37437569 DOI: 10.1016/j.chembiol.2023.06.014 |
0.571 |
|
| 2023 |
Cimini BA, Chandrasekaran SN, Kost-Alimova M, Miller L, Goodale A, Fritchman B, Byrne P, Garg S, Jamali N, Logan DJ, Concannon JB, Lardeau CH, Mouchet E, Singh S, Shafqat Abbasi H, et al. Optimizing the Cell Painting assay for image-based profiling. Nature Protocols. PMID 37344608 DOI: 10.1038/s41596-023-00840-9 |
0.79 |
|
| 2023 |
Dagher M, Ongo G, Robichaud N, Kong J, Rho W, Teahulos I, Tavakoli A, Bovaird S, Merjaneh S, Tan A, Edwardson K, Scheepers C, Ng A, Hajjar A, Lee A, ... ... Singh S, et al. nELISA: A high-throughput, high-plex platform enables quantitative profiling of the secretome. Biorxiv : the Preprint Server For Biology. PMID 37131604 DOI: 10.1101/2023.04.17.535914 |
0.501 |
|
| 2023 |
Wieder N, Fried JC, Kim C, Sidhom EH, Brown MR, Marshall JL, Arevalo C, Dvela-Levitt M, Kost-Alimova M, Sieber J, Gabriel KR, Pacheco J, Clish C, Abbasi HS, Singh S, et al. FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity. Cell Metabolism. PMID 37075753 DOI: 10.1016/j.cmet.2023.03.018 |
0.763 |
|
| 2023 |
Moshkov N, Becker T, Yang K, Horvath P, Dancik V, Wagner BK, Clemons PA, Singh S, Carpenter AE, Caicedo JC. Predicting compound activity from phenotypic profiles and chemical structures. Nature Communications. 14: 1967. PMID 37031208 DOI: 10.1038/s41467-023-37570-1 |
0.675 |
|
| 2023 |
Wakui T, Negishi M, Murakami Y, Tominaga S, Shiraishi Y, Carpenter AE, Singh S, Segawa H. Predicting reprogramming-related gene expression from cell morphology in human induced pluripotent stem cells. Molecular Biology of the Cell. mbcE22060215. PMID 36947171 DOI: 10.1091/mbc.E22-06-0215 |
0.579 |
|
| 2023 |
Garcia-Fossa F, Cruz MC, Haghighi M, de Jesus MB, Singh S, Carpenter AE, Cimini BA. Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization. Current Protocols. 3: e713. PMID 36921124 DOI: 10.1002/cpz1.713 |
0.779 |
|
| 2023 |
Dahlin JL, Hua BK, Zucconi BE, Nelson SD, Singh S, Carpenter AE, Shrimp JH, Lima-Fernandes E, Wawer MJ, Chung LPW, Agrawal A, O'Reilly M, Barsyte-Lovejoy D, Szewczyk M, Li F, et al. Reference compounds for characterizing cellular injury in high-content cellular morphology assays. Nature Communications. 14: 1364. PMID 36914634 DOI: 10.1038/s41467-023-36829-x |
0.529 |
|
| 2023 |
Wieder N, Fried JC, Kim C, Sidhom EH, Brown MR, Marshall JL, Arevalo C, Dvela-Levitt M, Kost-Alimova M, Sieber J, Gabriel KR, Pacheco J, Clish C, Abbasi HS, Singh S, et al. FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity. Biorxiv : the Preprint Server For Biology. PMID 36865221 DOI: 10.1101/2023.02.19.529127 |
0.769 |
|
| 2022 |
Way GP, Natoli T, Adeboye A, Litichevskiy L, Yang A, Lu X, Caicedo JC, Cimini BA, Karhohs K, Logan DJ, Rohban MH, Kost-Alimova M, Hartland K, Bornholdt M, Chandrasekaran SN, ... ... Singh S, et al. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Systems. 13: 911-923.e9. PMID 36395727 DOI: 10.1016/j.cels.2022.10.001 |
0.783 |
|
| 2022 |
Haghighi M, Caicedo JC, Cimini BA, Carpenter AE, Singh S. High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations. Nature Methods. PMID 36344834 DOI: 10.1038/s41592-022-01667-0 |
0.76 |
|
| 2022 |
Lemmel S, Weckmann M, Wohlers A, Jirmo AC, Grychtol R, Ricklefs I, Nissen G, Bachmann A, Singh S, Caicedo J, Bahmer T, Hansen G, Von Mutius E, Rabe KF, Fuchs O, et al. neutrophil migration is associated with inhaled corticosteroid treatment and serum cytokines in pediatric asthma. Frontiers in Pharmacology. 13: 1021317. PMID 36304163 DOI: 10.3389/fphar.2022.1021317 |
0.628 |
|
| 2022 |
Rohban MH, Fuller AM, Tan C, Goldstein JT, Syangtan D, Gutnick A, DeVine A, Nijsure MP, Rigby M, Sacher JR, Corsello SM, Peppler GB, Bogaczynska M, Boghossian A, Ciotti GE, ... ... Singh S, et al. Virtual screening for small-molecule pathway regulators by image-profile matching. Cell Systems. PMID 36057257 DOI: 10.1016/j.cels.2022.08.003 |
0.784 |
|
| 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 |
0.627 |
|
| 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 |
0.59 |
|
| 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 |
0.767 |
|
| 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 |
0.806 |
|
| 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 |
0.809 |
|
| 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 |
0.7 |
|
| 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 |
0.568 |
|
| 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 |
0.783 |
|
| 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 |
0.796 |
|
| 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 |
0.761 |
|
| 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 |
0.794 |
|
| 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 |
0.797 |
|
| 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 |
0.807 |
|
| 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 |
0.404 |
|
| 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 |
0.513 |
|
| 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 |
0.597 |
|
| 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 |
0.788 |
|
| 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 |
0.608 |
|
| 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 |
0.772 |
|
| 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 |
0.541 |
|
| 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 |
0.553 |
|
| 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 |
0.663 |
|
| 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 |
0.591 |
|
| 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 |
0.565 |
|
| 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 |
0.704 |
|
| 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 |
0.641 |
|
| 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 |
0.691 |
|
| 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 |
0.599 |
|
| 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 |
0.614 |
|
| 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 |
0.655 |
|
| 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 |
0.61 |
|
| 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 |
0.659 |
|
| 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 |
0.34 |
|
| Show low-probability matches. |