Anne E. Carpenter - Publications

Affiliations: 
The Broad Institute 
Area:
Imaging
Website:
http://www.broadinstitute.org/~anne/

135 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 Filby A, Carpenter AE. A New Image for Cell Sorting. The New England Journal of Medicine. 386: 1755-1758. PMID 35507488 DOI: 10.1056/NEJMcibr2200971  0.358
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  0.634
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  0.624
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  0.698
2021 Jamali N, Dobson ET, Eliceiri KW, Carpenter AE, Cimini BA. 2020 BioImage Analysis Survey: Community experiences and needs for the future. Biological Imaging. 1. PMID 35387317 DOI: 10.1017/S2633903X21000039  0.763
2021 Boivin B, Roet KCD, Huang X, Karhohs KW, Rohban MH, Sandoe J, Wiskow O, Maeda R, Grantham A, Dornon MK, Shao J, Frost D, Baker D, Eggan K, Carpenter AE, et al. A Multiparametric Activity Profiling Platform for Neuron Disease Phenotyping and Drug Screening. Molecular Biology of the Cell. mbcE21100481. PMID 34910584 DOI: 10.1091/mbc.E21-10-0481  0.787
2021 Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A. CellProfiler 4: improvements in speed, utility and usability. Bmc Bioinformatics. 22: 433. PMID 34507520 DOI: 10.1186/s12859-021-04344-9  0.823
2021 Stirling DR, Carpenter AE, Cimini BA. CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis. Bioinformatics (Oxford, England). PMID 34478488 DOI: 10.1093/bioinformatics/btab634  0.767
2021 Wills JW, Verma JR, Rees BJ, Harte DSG, Haxhiraj Q, Barnes CM, Barnes R, Rodrigues MA, Doan M, Filby A, Hewitt RE, Thornton CA, Cronin JG, Kenny JD, Buckley R, ... ... Carpenter AE, et al. Inter-laboratory automation of the in vitro micronucleus assay using imaging flow cytometry and deep learning. Archives of Toxicology. PMID 34245348 DOI: 10.1007/s00204-021-03113-0  0.778
2021 Tomov ML, O'Neil A, Abbasi HS, Cimini BA, Carpenter AE, Rubin LL, Bathe M. Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Communications Biology. 4: 786. PMID 34168275 DOI: 10.1038/s42003-021-02276-x  0.786
2021 Doan M, Barnes C, McQuin C, Caicedo JC, Goodman A, Carpenter AE, Rees P. Deepometry, a framework for applying supervised and weakly supervised deep learning to imaging cytometry. Nature Protocols. PMID 34145434 DOI: 10.1038/s41596-021-00549-7  0.813
2021 Dobson ETA, Cimini B, Klemm AH, Wählby C, Carpenter AE, Eliceiri KW. ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. Current Protocols. 1: e89. PMID 34038030 DOI: 10.1002/cpz1.89  0.819
2021 Lucas AM, Ryder PV, Li B, Cimini BA, Eliceiri KW, Carpenter AE. Open-source deep-learning software for bioimage segmentation. Molecular Biology of the Cell. 32: 823-829. PMID 33872058 DOI: 10.1091/mbc.E20-10-0660  0.775
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  0.742
2020 Hollandi R, Szkalisity A, Toth T, Tasnadi E, Molnar C, Mathe B, Grexa I, Molnar J, Balind A, Gorbe M, Kovacs M, Migh E, Goodman A, Balassa T, Koos K, ... ... Carpenter AE, et al. nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer. Cell Systems. 10: 453-458.e6. PMID 34222682 DOI: 10.1016/j.cels.2020.04.003  0.751
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  0.764
2020 Chandrasekaran SN, Ceulemans H, Boyd JD, Carpenter AE. Image-based profiling for drug discovery: due for a machine-learning upgrade? Nature Reviews. Drug Discovery. PMID 33353986 DOI: 10.1038/s41573-020-00117-w  0.35
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  0.636
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, ... ... Carpenter AE, 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  0.789
2020 Taga M, Petyuk VA, White C, Marsh G, Ma Y, Klein HU, Connor SM, Kroshilina A, Yung CJ, Khairallah A, Olah M, Schneider J, Karhohs K, Carpenter AE, Ransohoff R, et al. BIN1 protein isoforms are differentially expressed in astrocytes, neurons, and microglia: neuronal and astrocyte BIN1 are implicated in tau pathology. Molecular Neurodegeneration. 15: 44. PMID 32727516 DOI: 10.1186/S13024-020-00387-3  0.757
2020 French SL, Vijey P, Karhohs KW, Wilkie AR, Horin LJ, Ray A, Posorske B, Carpenter AE, Machlus KR, Italiano JE. High Content, Label-Free Analysis of Proplatelet Production from Megakaryocytes. Journal of Thrombosis and Haemostasis : Jth. PMID 32662223 DOI: 10.1111/Jth.15012  0.756
2020 Hung J, Goodman A, Ravel D, Lopes SCP, Rangel GW, Nery OA, Malleret B, Nosten F, Lacerda MVG, Ferreira MU, Rénia L, Duraisingh MT, Costa FTM, Marti M, Carpenter AE. Keras R-CNN: library for cell detection in biological images using deep neural networks. Bmc Bioinformatics. 21: 300. PMID 32652926 DOI: 10.1186/S12859-020-03635-X  0.767
2020 Boyd J, Fennell M, Carpenter A. Harnessing the power of microscopy images to accelerate drug discovery: what are the possibilities? Expert Opinion On Drug Discovery. 15: 639-642. PMID 32200648 DOI: 10.1080/17460441.2020.1743675  0.353
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  0.8
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  0.771
2020 Hollandi R, Szkalisity A, Toth T, Tasnadi E, Molnar C, Mathe B, Grexa I, Molnar J, Balind A, Gorbe M, Kovacs M, Migh E, Goodman A, Balassa T, Koos K, ... ... Carpenter AE, et al. nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer Cell Systems. 10: 453-458.e6. DOI: 10.1016/J.Cels.2020.04.003  0.767
2019 Lee CX, Cheah JH, Soule CK, Ding H, Whittaker CA, Karhohs K, Burds AA, Subramanyam KS, Carpenter AE, Eisner BH, Cima MJ. Identification and local delivery of vasodilators for the reduction of ureteral contractions. Nature Biomedical Engineering. PMID 31792422 DOI: 10.1038/S41551-019-0482-4  0.749
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  0.805
2019 Shlevkov E, Basu H, Bray MA, Sun Z, Wei W, Apaydin K, Karhohs K, Chen PF, Smith JLM, Wiskow O, Roet K, Huang X, Eggan K, Carpenter AE, Kleiman RJ, et al. A High-Content Screen Identifies TPP1 and Aurora B as Regulators of Axonal Mitochondrial Transport. Cell Reports. 28: 3224-3237.e5. PMID 31533043 DOI: 10.1016/J.Celrep.2019.08.035  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  0.805
2019 Rueden CT, Ackerman J, Arena ET, Eglinger J, Cimini BA, Goodman A, Carpenter AE, Eliceiri KW. Scientific Community Image Forum: A discussion forum for scientific image software. Plos Biology. 17: e3000340. PMID 31216269 DOI: 10.1371/Journal.Pbio.3000340  0.806
2019 Kulikov V, Guo SM, Stone M, Goodman A, Carpenter A, Bathe M, Lempitsky V. DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. Plos Computational Biology. 15: e1007012. PMID 31083649 DOI: 10.1371/Journal.Pcbi.1007012  0.718
2019 Nassar M, Doan M, Filby A, Wolkenhauer O, Fogg DK, Piasecka J, Thornton CA, Carpenter AE, Summers HD, Rees P, Hennig H. Label-Free Identification of White Blood Cells Using Machine Learning. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. PMID 31081599 DOI: 10.1002/Cyto.A.23794  0.799
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  0.795
2019 Doan M, Carpenter AE. Leveraging machine vision in cell-based diagnostics to do more with less. Nature Materials. 18: 414-418. PMID 31000804 DOI: 10.1038/S41563-019-0339-Y  0.742
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  0.773
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  0.664
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  0.798
2018 Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, ... ... Carpenter AE, et al. Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface. 15. PMID 29618526 DOI: 10.1098/Rsif.2017.0387  0.33
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  0.658
2018 Doan M, Vorobjev I, Rees P, Filby A, Wolkenhauer O, Goldfeld AE, Lieberman J, Barteneva N, Carpenter AE, Hennig H. Diagnostic Potential of Imaging Flow Cytometry. Trends in Biotechnology. PMID 29395345 DOI: 10.1016/J.Tibtech.2017.12.008  0.816
2018 Bray MA, Carpenter AE. Quality Control for High-Throughput Imaging Experiments Using Machine Learning in Cellprofiler. Methods in Molecular Biology (Clifton, N.J.). 1683: 89-112. PMID 29082489 DOI: 10.1007/978-1-4939-7357-6_7  0.492
2017 Hung J, Lopes SCP, Nery OA, Nosten F, Ferreira MU, Duraisingh MT, Marti M, Ravel D, Rangel G, Malleret B, Lacerda MVG, Rénia L, Costa FTM, Carpenter AE. Applying Faster R-CNN for Object Detection on Malaria Images. Conference On Computer Vision and Pattern Recognition Workshops. Ieee Computer Society Conference On Computer Vision and Pattern Recognition. Workshops. 2017: 808-813. PMID 34938593 DOI: 10.1109/cvprw.2017.112  0.317
2017 Eulenberg P, Köhler N, Blasi T, Filby A, Carpenter AE, Rees P, Theis FJ, Wolf FA. Reconstructing cell cycle and disease progression using deep learning. Nature Communications. 8: 463. PMID 28878212 DOI: 10.1038/S41467-017-00623-3  0.456
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, ... ... Carpenter AE, et al. Data-analysis strategies for image-based cell profiling. Nature Methods. 14: 849-863. PMID 28858338 DOI: 10.1038/Nmeth.4397  0.792
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  0.754
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, ... Carpenter AE, 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  0.62
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, ... ... Carpenter AE, 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  0.713
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  0.637
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  0.617
2017 Doan M, Case M, Mašić D, Hennig H, McQuin C, Goodman A, Caicedo J, Wolkenhauer O, Summers H, Carpenter AE, Filby A, Rees P, Irving J. Label-Free Analyses of Minimal Residual Disease in ALL Using Deep Learning and Imaging Flow Cytometry Blood. 130: 1437-1437. DOI: 10.1182/Blood.V130.Suppl_1.1437.1437  0.823
2016 Goodman A, Carpenter AE. High-Throughput, Automated Image Processing for Large-Scale Fluorescence Microscopy Experiments. Microscopy and Microanalysis : the Official Journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. 22: 538-539. PMID 28386206 DOI: 10.1017/S1431927616003548  0.733
2016 Meijering E, Carpenter AE, Peng H, Hamprecht FA, Olivo-Marin JC. Imagining the future of bioimage analysis. Nature Biotechnology. 34: 1250-1255. PMID 27926723 DOI: 10.1038/Nbt.3722  0.361
2016 Shan J, Logan DJ, Root DE, Carpenter AE, Bhatia SN. High-Throughput Platform for Identifying Molecular Factors Involved in Phenotypic Stabilization of Primary Human Hepatocytes In Vitro. Journal of Biomolecular Screening. 21: 897-911. PMID 27650791 DOI: 10.1177/1087057116660277  0.673
2016 Hennig H, Rees P, Blasi T, Kamentsky L, Hung J, Dao D, Carpenter AE, Filby A. An open-source solution for advanced imaging flow cytometry data analysis using machine learning. Methods (San Diego, Calif.). PMID 27594698 DOI: 10.1016/J.Ymeth.2016.08.018  0.688
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  0.734
2016 Neves BJ, Dantas RF, Senger MR, Melo-Filho CC, Valente WC, de Almeida AC, Lima EF, Rezende-Neto JM, Paveley RA, Furnham N, Muratov EN, Kamentsky L, Carpenter AE, Braga RC, Junior FP, et al. Discovery of New Anti-Schistosomal Hits by Integration of QSAR-Based Virtual Screening and High Content Screening. Journal of Medicinal Chemistry. PMID 27396732 DOI: 10.1021/Acs.Jmedchem.5B02038  0.318
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  0.697
2016 Melo-Filho CC, Dantas RF, Braga RC, Neves BJ, Senger MR, Valente WC, Rezende-Neto JM, Chaves WT, Muratov EN, Paveley RA, Furnham N, Kamentsky L, Carpenter AE, Junior FP, Andrade CH. QSAR-Driven Discovery of Novel Chemical Scaffolds Active Against Schistosoma mansoni. Journal of Chemical Information and Modeling. PMID 27253773 DOI: 10.1021/Acs.Jcim.6B00055  0.308
2016 Dordea AC, Bray MA, Allen K, Logan D, Fei F, Malhotra R, Gregory M, Carpenter AE, Buys ES. An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells. Experimental Eye Research. PMID 27119563 DOI: 10.1016/J.Exer.2016.04.012  0.713
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  0.723
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  0.669
2016 Jolly AL, Luan CH, Dusel BE, Dunne SF, Winding M, Dixit VJ, Robins C, Saluk JL, Logan DJ, Carpenter AE, Sharma M, Dean D, Cohen AR, Gelfand VI. A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells. Cell Reports. PMID 26774481 DOI: 10.1016/J.Celrep.2015.12.051  0.653
2016 Blasi T, Hennig H, Summers HD, Theis FJ, Cerveira J, Patterson JO, Davies D, Filby A, Carpenter AE, Rees P. Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nature Communications. 7: 10256. PMID 26739115 DOI: 10.1038/Ncomms10256  0.655
2015 Logan DJ, Shan J, Bhatia SN, Carpenter AE. Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification. Methods (San Diego, Calif.). PMID 26687239 DOI: 10.1016/J.Ymeth.2015.12.002  0.727
2015 Bray MA, Carpenter AE. CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data. Bmc Bioinformatics. 16: 368. PMID 26537300 DOI: 10.1186/S12859-015-0759-X  0.38
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  0.653
2015 Jeong YM, Duanting Z, Hennig H, Samanta A, Agrawalla BK, Bray MA, Carpenter AE, Chang YT. CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells. Chemistry & Biology. 22: 299-307. PMID 25601075 DOI: 10.1016/J.Chembiol.2014.11.018  0.577
2015 Bray MA, Vokes MS, Carpenter AE. Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. 109: 14.17.1-14.17.13. PMID 25559103 DOI: 10.1002/0471142727.Mb1417S109  0.474
2015 Jolly AL, Luan CH, Dusel BE, Dunne SF, Winding M, Dixit VJ, Robins C, Saluk JL, Logan DJ, Carpenter AE, Sharma M, Dean D, Cohen AR, Gelfand VI. A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells Cell Reports. DOI: 10.1016/j.celrep.2015.12.051  0.629
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  0.712
2014 Rees P, Wills JW, Brown MR, Tonkin J, Holton MD, Hondow N, Brown AP, Brydson R, Millar V, Carpenter AE, Summers HD. Nanoparticle vesicle encoding for imaging and tracking cell populations. Nature Methods. 11: 1177-81. PMID 25218182 DOI: 10.1038/Nmeth.3105  0.376
2014 Khan IA, Fraser A, Bray MA, Smith PJ, White NS, Carpenter AE, Errington RJ. ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. Bioinformatics (Oxford, England). 30: 3440-2. PMID 25150250 DOI: 10.1093/Bioinformatics/Btu554  0.491
2014 Wawer MJ, Li K, Gustafsdottir SM, Ljosa V, Bodycombe NE, Marton MA, Sokolnicki KL, Bray MA, Kemp MM, Winchester E, Taylor B, Grant GB, Hon CS, Duvall JR, Wilson JA, ... ... Carpenter AE, et al. Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling. Proceedings of the National Academy of Sciences of the United States of America. 111: 10911-6. PMID 25024206 DOI: 10.1073/Pnas.1410933111  0.371
2014 Wählby C, Conery AL, Bray MA, Kamentsky L, Larkins-Ford J, Sokolnicki KL, Veneskey M, Michaels K, Carpenter AE, O'Rourke EJ. High- and low-throughput scoring of fat mass and body fat distribution in C. elegans. Methods (San Diego, Calif.). 68: 492-9. PMID 24784529 DOI: 10.1016/J.Ymeth.2014.04.017  0.338
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  0.67
2014 Nieland TJ, Logan DJ, Saulnier J, Lam D, Johnson C, Root DE, Carpenter AE, Sabatini BL. High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons. Plos One. 9: e91744. PMID 24633176 DOI: 10.1371/Journal.Pone.0091744  0.671
2014 Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, ... ... Carpenter AE, et al. ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Reports. 6: 313-24. PMID 24440720 DOI: 10.1016/J.Celrep.2013.12.032  0.66
2013 Gustafsdottir SM, Ljosa V, Sokolnicki KL, Anthony Wilson J, Walpita D, Kemp MM, Petri Seiler K, Carrel HA, Golub TR, Schreiber SL, Clemons PA, Carpenter AE, Shamji AF. Multiplex cytological profiling assay to measure diverse cellular states. Plos One. 8: e80999. PMID 24312513 DOI: 10.1371/Journal.Pone.0080999  0.382
2013 Hartwell KA, Miller PG, Mukherjee S, Kahn AR, Stewart AL, Logan DJ, Negri JM, Duvet M, Järås M, Puram R, Dancik V, Al-Shahrour F, Kindler T, Tothova Z, Chattopadhyay S, ... ... Carpenter AE, et al. Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nature Chemical Biology. 9: 840-8. PMID 24161946 DOI: 10.1038/Nchembio.1367  0.678
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  0.698
2013 March S, Ng S, Velmurugan S, Galstian A, Shan J, Logan DJ, Carpenter AE, Thomas D, Sim BK, Mota MM, Hoffman SL, Bhatia SN. A microscale human liver platform that supports the hepatic stages of Plasmodium falciparum and vivax. Cell Host & Microbe. 14: 104-15. PMID 23870318 DOI: 10.1016/J.Chom.2013.06.005  0.626
2013 Shan J, Schwartz RE, Ross NT, Logan DJ, Thomas D, Duncan SA, North TE, Goessling W, Carpenter AE, Bhatia SN. Identification of small molecules for human hepatocyte expansion and iPS differentiation. Nature Chemical Biology. 9: 514-20. PMID 23728495 DOI: 10.1038/Nchembio.1270  0.658
2013 Floyd SR, Pacold ME, Huang Q, Clarke SM, Lam FC, Cannell IG, Bryson BD, Rameseder J, Lee MJ, Blake EJ, Fydrych A, Ho R, Greenberger BA, Chen GC, Maffa A, ... ... Carpenter AE, et al. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Nature. 498: 246-50. PMID 23728299 DOI: 10.1038/Nature12147  0.71
2013 Ljosa V, Sokolnicki KL, Carpenter AE. Erratum: Corrigendum: Annotated high-throughput microscopy image sets for validation Nature Methods. 10: 445-445. DOI: 10.1038/Nmeth0513-445D  0.329
2012 Wen Q, Goldenson B, Silver SJ, Schenone M, Dancik V, Huang Z, Wang LZ, Lewis TA, An WF, Li X, Bray MA, Thiollier C, Diebold L, Gilles L, Vokes MS, ... ... Carpenter AE, et al. Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL. Cell. 150: 575-89. PMID 22863010 DOI: 10.1016/J.Cell.2012.06.032  0.362
2012 Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurman N, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Biological imaging software tools. Nature Methods. 9: 697-710. PMID 22743775 DOI: 10.1038/Nmeth.2084  0.427
2012 Ljosa V, Sokolnicki KL, Carpenter AE. Annotated high-throughput microscopy image sets for validation. Nature Methods. 9: 637. PMID 22743765 DOI: 10.1038/Nmeth.2083  0.435
2012 Wählby C, Kamentsky L, Liu ZH, Riklin-Raviv T, Conery AL, O'Rourke EJ, Sokolnicki KL, Visvikis O, Ljosa V, Irazoqui JE, Golland P, Ruvkun G, Ausubel FM, Carpenter AE. An image analysis toolbox for high-throughput C. elegans assays. Nature Methods. 9: 714-6. PMID 22522656 DOI: 10.1038/Nmeth.1984  0.813
2012 Kitami T, Logan DJ, Negri J, Hasaka T, Tolliday NJ, Carpenter AE, Spiegelman BM, Mootha VK. A chemical screen probing the relationship between mitochondrial content and cell size. Plos One. 7: e33755. PMID 22479437 DOI: 10.1371/Journal.Pone.0033755  0.677
2012 Bray MA, Fraser AN, Hasaka TP, Carpenter AE. Workflow and metrics for image quality control in large-scale high-content screens. Journal of Biomolecular Screening. 17: 266-74. PMID 21956170 DOI: 10.1177/1087057111420292  0.466
2012 Yusuf RZ, Acharya SS, Yu VW, Saez B, Cobert JM, Doench J, Bullinger L, S'aulis D, Lee D, Palchaudhuri R, Uzosike AC, Duvet M, Logan DJ, Das S, Cook CM, ... ... Carpenter AE, et al. Aldehyde Dehydrogenase 3a2 (Aldh3a2) Represents a Distinct Metabolic Vulnerability in MLL-AF9 AML Leukemia Initiating Cells Blood. 120: 208-208. DOI: 10.1182/Blood.V120.21.208.208  0.678
2012 Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Erratum: Corrigendum: Biological imaging software tools Nature Methods. 9: 1031-1031. DOI: 10.1038/Nmeth1012-1031B  0.422
2012 Eliceiri KW, Berthold MR, Goldberg IG, Ibáñez L, Manjunath BS, Martone ME, Murphy RF, Peng H, Plant AL, Roysam B, Stuurmann N, Swedlow JR, Tomancak P, Carpenter AE. Erratum: Corrigendum: Biological imaging software tools Nature Methods. 9: 1031-1031. DOI: 10.1038/Nmeth1012-1031A  0.34
2011 Carpenter AE. EXTRACTING BIOMEDICALLY IMPORTANT INFORMATION FROM LARGE, AUTOMATED IMAGING EXPERIMENTS. Proceedings / Ieee International Symposium On Biomedical Imaging: From Nano to Macro. Ieee International Symposium On Biomedical Imaging. 1723-1726. PMID 24525841 DOI: 10.1109/ISBI.2011.5872737  0.33
2011 Pretorius AJ, Bray MA, Carpenter AE, Ruddle RA. Visualization of parameter space for image analysis. Ieee Transactions On Visualization and Computer Graphics. 17: 2402-11. PMID 22034361 DOI: 10.1109/Tvcg.2011.253  0.34
2011 Unadkat HV, Hulsman M, Cornelissen K, Papenburg BJ, Truckenmüller RK, Carpenter AE, Wessling M, Post GF, Uetz M, Reinders MJ, Stamatialis D, van Blitterswijk CA, de Boer J. An algorithm-based topographical biomaterials library to instruct cell fate. Proceedings of the National Academy of Sciences of the United States of America. 108: 16565-70. PMID 21949368 DOI: 10.1073/Pnas.1109861108  0.305
2011 Peterson TR, Sengupta SS, Harris TE, Carmack AE, Kang SA, Balderas E, Guertin DA, Madden KL, Carpenter AE, Finck BN, Sabatini DM. mTOR complex 1 regulates lipin 1 localization to control the SREBP pathway. Cell. 146: 408-20. PMID 21816276 DOI: 10.1016/J.Cell.2011.06.034  0.48
2011 Kamentsky L, Jones TR, Fraser A, Bray MA, Logan DJ, Madden KL, Ljosa V, Rueden C, Eliceiri KW, Carpenter AE. Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics (Oxford, England). 27: 1179-80. PMID 21349861 DOI: 10.1093/Bioinformatics/Btr095  0.688
2011 Lindquist RA, Ottina KA, Wheeler DB, Hsu PP, Thoreen CC, Guertin DA, Ali SM, Sengupta S, Shaul YD, Lamprecht MR, Madden KL, Papallo AR, Jones TR, Sabatini DM, Carpenter AE. Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1-S6K pathway signaling. Genome Research. 21: 433-46. PMID 21239477 DOI: 10.1101/Gr.111492.110  0.531
2011 Hartwell KA, Miller PG, Stewart AL, Kahn AR, Logan DJ, Negri J, Duvet M, Chattopadhyay S, Shterental S, Chu LP, Shieh JH, Jaeraas M, Dancik V, Narayan R, Huang C, ... ... Carpenter AE, et al. Niche-Based Screening Reveals Leukemia Stem Cell Specific Therapeutics Blood. 118: 760-760. DOI: 10.1182/Blood.V118.21.760.760  0.703
2011 Yusuf RZ, Acharya SS, Yu V, Saez B, Duvet M, Scadden E, Warraich G, Clish C, Churchill M, Doench J, Logan DJ, Cook C, Das S, Brown A, Sykes SM, ... ... Carpenter AE, et al. Distinct Metabolic Dependency of Normal and Leukemic Cells in a Mouse Model Blood. 118: 759-759. DOI: 10.1182/Blood.V118.21.759.759  0.678
2010 Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM, Carpenter AE. RESOLVING CLUSTERED WORMS VIA PROBABILISTIC SHAPE MODELS. Proceedings / Ieee International Symposium On Biomedical Imaging: From Nano to Macro. Ieee International Symposium On Biomedical Imaging. 2010: 552-555. PMID 21383863 DOI: 10.1109/ISBI.2010.5490286  0.776
2010 Cataldo AM, McPhie DL, Lange NT, Punzell S, Elmiligy S, Ye NZ, Froimowitz MP, Hassinger LC, Menesale EB, Sargent LW, Logan DJ, Carpenter AE, Cohen BM. Abnormalities in mitochondrial structure in cells from patients with bipolar disorder. The American Journal of Pathology. 177: 575-85. PMID 20566748 DOI: 10.2353/Ajpath.2010.081068  0.653
2010 Logan DJ, Carpenter AE. Screening cellular feature measurements for image-based assay development. Journal of Biomolecular Screening. 15: 840-6. PMID 20516293 DOI: 10.1177/1087057110370895  0.739
2010 Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Hériché JK. Visualization of image data from cells to organisms. Nature Methods. 7: S26-41. PMID 20195255 DOI: 10.1038/Nmeth.1431  0.429
2010 Wen QJ, Silver S, Lewis T, Ponduru S, Dancik V, Goldenson B, Bray M, Carpenter A, Clemons P, Root D, Stern A, Gould R, Crispino J. A Kinome shRNA Screen to Identify Pathways That Regulate Megakaryocyte Polyploidization and New Targets for Differentiation Therapy Blood. 116: 89-89. DOI: 10.1182/Blood.V116.21.89.89  0.347
2010 Kim K, Rowat AC, Carpenter AE. Automated tracking of yeast cell lineages Proceedings of Spie - the International Society For Optical Engineering. 7798. DOI: 10.1117/12.859770  0.454
2010 Walter T, Shattuck DW, Baldock R, Bastin ME, Carpenter AE, Duce S, Ellenberg J, Fraser A, Hamilton N, Pieper S, Ragan MA, Schneider JE, Tomancak P, Hériché JK. Erratum: Visualization of image data from cells to organisms Nature Methods. 7: 479-479. DOI: 10.1038/Nmeth0610-479A  0.397
2009 Ljosa V, Carpenter AE. Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening. Plos Computational Biology. 5: e1000603. PMID 20041172 DOI: 10.1371/Journal.Pcbi.1000603  0.501
2009 Tsui M, Xie T, Orth JD, Carpenter AE, Rudnicki S, Kim S, Shamu CE, Mitchison TJ. An intermittent live cell imaging screen for siRNA enhancers and suppressors of a kinesin-5 inhibitor. Plos One. 4: e7339. PMID 19802393 DOI: 10.1371/Journal.Pone.0007339  0.425
2009 Carpenter AE. Extracting rich information from images. Methods in Molecular Biology (Clifton, N.J.). 486: 193-211. PMID 19347625 DOI: 10.1007/978-1-60327-545-3_14  0.49
2009 Jones TR, Carpenter AE, Lamprecht MR, Moffat J, Silver SJ, Grenier JK, Castoreno AB, Eggert US, Root DE, Golland P, Sabatini DM. Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proceedings of the National Academy of Sciences of the United States of America. 106: 1826-31. PMID 19188593 DOI: 10.1073/Pnas.0808843106  0.651
2008 Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE. CellProfiler Analyst: data exploration and analysis software for complex image-based screens. Bmc Bioinformatics. 9: 482. PMID 19014601 DOI: 10.1186/1471-2105-9-482  0.644
2008 Ljosa V, Carpenter AE. High-throughput screens for fluorescent dye discovery. Trends in Biotechnology. 26: 527-30. PMID 18706725 DOI: 10.1016/J.Tibtech.2008.06.008  0.335
2008 Vokes MS, Carpenter AE. Using CellProfiler for automatic identification and measurement of biological objects in images. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 14.17. PMID 18425761 DOI: 10.1002/0471142727.mb1417s82  0.372
2008 Vokes MS, Carpenter AE. CellProfiler: Open-Source Software to Automatically Quantify Images Microscopy Today. 16: 38-39. DOI: 10.1017/S1551929500061757  0.474
2008 Carpenter AE, Jones TR. Extracting rich, quantitative information from images using open-source software Microscopy and Microanalysis. 14: 604-605. DOI: 10.1017/S1431927608081166  0.377
2007 Carpenter AE. Image-based chemical screening. Nature Chemical Biology. 3: 461-5. PMID 17637778 DOI: 10.1038/Nchembio.2007.15  0.395
2007 Lamprecht MR, Sabatini DM, Carpenter AE. CellProfiler: free, versatile software for automated biological image analysis. Biotechniques. 42: 71-5. PMID 17269487 DOI: 10.2144/000112257  0.623
2007 Carpenter AE. Software opens the door to quantitative imaging. Nature Methods. 4: 120-1. PMID 17264858 DOI: 10.1038/Nmeth0207-120  0.457
2007 Jones TR, Carpenter AE. Flexible image analysis Biophotonics International. 14: 31-32.  0.342
2006 Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology. 7: R100. PMID 17076895 DOI: 10.1186/Gb-2006-7-10-R100  0.644
2006 Sigal A, Milo R, Cohen A, Geva-Zatorsky N, Klein Y, Alaluf I, Swerdlin N, Perzov N, Danon T, Liron Y, Raveh T, Carpenter AE, Lahav G, Alon U. Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nature Methods. 3: 525-31. PMID 16791210 DOI: 10.1038/Nmeth892  0.317
2006 Chuang CH, Carpenter AE, Fuchsova B, Johnson T, de Lanerolle P, Belmont AS. Long-range directional movement of an interphase chromosome site. Current Biology : Cb. 16: 825-31. PMID 16631592 DOI: 10.1016/J.Cub.2006.03.059  0.658
2006 Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N, et al. A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell. 124: 1283-98. PMID 16564017 DOI: 10.1016/J.Cell.2006.01.040  0.559
2006 Bailey SN, Ali SM, Carpenter AE, Higgins CO, Sabatini DM. Microarrays of lentiviruses for gene function screens in immortalized and primary cells. Nature Methods. 3: 117-22. PMID 16432521 DOI: 10.1038/Nmeth848  0.557
2005 Wheeler DB, Carpenter AE, Sabatini DM. Cell microarrays and RNA interference chip away at gene function. Nature Genetics. 37: S25-30. PMID 15920526 DOI: 10.1038/Ng1560  0.541
2005 Verschure PJ, van der Kraan I, de Leeuw W, van der Vlag J, Carpenter AE, Belmont AS, van Driel R. In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation. Molecular and Cellular Biology. 25: 4552-64. PMID 15899859 DOI: 10.1128/Mcb.25.11.4552-4564.2005  0.546
2005 Carpenter AE, Memedula S, Plutz MJ, Belmont AS. Common effects of acidic activators on large-scale chromatin structure and transcription. Molecular and Cellular Biology. 25: 958-68. PMID 15657424 DOI: 10.1128/Mcb.25.3.958-968.2005  0.519
2005 Jones TR, Carpenter A, Golland P. Voronoi-based segmentation of cells on image manifolds Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3765: 535-543.  0.358
2004 Wheeler DB, Bailey SN, Guertin DA, Carpenter AE, Higgins CO, Sabatini DM. RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells. Nature Methods. 1: 127-32. PMID 15782175 DOI: 10.1038/Nmeth711  0.565
2004 Carpenter AE, Ashouri A, Belmont AS. Automated microscopy identifies estrogen receptor subdomains with large-scale chromatin structure unfolding activity. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. 58: 157-66. PMID 15057969 DOI: 10.1002/Cyto.A.10113  0.591
2004 Carpenter AE, Belmont AS. Direct visualization of transcription factor-induced chromatin remodeling and cofactor recruitment in vivo. Methods in Enzymology. 375: 366-81. PMID 14870678 DOI: 10.1016/S0076-6879(03)75023-X  0.549
2004 Carpenter AE, Sabatini DM. Systematic genome-wide screens of gene function. Nature Reviews. Genetics. 5: 11-22. PMID 14708012 DOI: 10.1038/Nrg1248  0.518
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