Anne E. Carpenter - Publications

The Broad Institute 

119 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
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  1
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  1
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  1
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  1
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  0.96
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  1
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  1
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  1
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  1
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  1
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  0.96
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  0.96
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  1
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  1
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  0.92
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  1
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  1
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  1
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  1
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  1
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  1
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  0.32
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  1
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  1
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  1
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  1
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  1
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  0.96
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2015 Metelo AM, Noonan HR, Li X, Jin Y, Baker R, Kamentsky L, Zhang Y, van Rooijen E, Shin J, Carpenter AE, Yeh JR, Peterson RT, Iliopoulos O. Pharmacological HIF2α inhibition improves VHL disease-associated phenotypes in zebrafish model. The Journal of Clinical Investigation. 125: 1987-97. PMID 25866969 DOI: 10.1172/JCI73665  1
2015 Du Z, Abedalthagafi M, Aizer AA, McHenry AR, Sun HH, Bray MA, Viramontes O, Machaidze R, Brastianos PK, Reardon DA, Dunn IF, Freeman GJ, Ligon KL, Carpenter AE, Alexander BM, et al. Increased expression of the immune modulatory molecule PD-L1 (CD274) in anaplastic meningioma. Oncotarget. 6: 4704-16. PMID 25609200  1
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  1
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  1
2015 Gilad T, Bray MA, Carpenter AE, Raviv TR. Symmetry-based mitosis detection in time-lapse microscopy Proceedings - International Symposium On Biomedical Imaging. 2015: 164-167. DOI: 10.1109/ISBI.2015.7163841  1
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  1
2015 Arbelle A, Drayman N, Bray M, Alon U, Carpenter A, Raviv TR. Analysis of high-throughput microscopy videos: Catching up with cell dynamics Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 9351: 218-225. DOI: 10.1007/978-3-319-24574-4_26  1
2015 Du Z, Abedalthagafi M, Aizer AA, McHenry AR, Sun HH, Bray MA, Viramontes O, Machaidze R, Brastianos PK, Reardon DA, Dunn IF, Freeman GJ, Ligon KL, Carpenter AE, Alexander BM, et al. Increased expression of the immune modulatory molecule PDL1 (CD274) in anaplastic meningioma Oncotarget. 6: 4704-4716.  1
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  1
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  0.32
2014 Sheik-Khalil E, Bray MA, Özkaya ?ahin G, Scarlatti G, Jansson M, Carpenter AE, Fenyö EM. Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition. Bmc Infectious Diseases. 14: 472. PMID 25176034 DOI: 10.1186/1471-2334-14-472  1
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  1
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  1
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  1
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  1
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  1
2014 Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, Bray MA, Carpenter AE, Moore CB, Siddiqi N, Rubin EJ, Hung DT. Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. Plos Pathogens. 10: e1003946. PMID 24586159 DOI: 10.1371/journal.ppat.1003946  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2012 Carpenter AE, Kamentsky L, Eliceiri KW. A call for bioimaging software usability. Nature Methods. 9: 666-70. PMID 22743771 DOI: 10.1038/nmeth.2073  1
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  1
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  1
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  1
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  1
2012 Unadkat HV, Hulsman M, Cornelissen K, Papenburg BJ, Truckenmüller RK, Carpenter AE, Wessling M, Post GF, Uetz M, Reinders MJT, 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 (2011) 108, 40 (16565-16570) DOI: 10.1073/pnas.1109861108) Proceedings of the National Academy of Sciences of the United States of America. 109: 5905. DOI: 10.1073/pnas.1204360109  1
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  1
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  1
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  1
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  1
2011 Elkabets M, Gifford AM, Scheel C, Nilsson B, Reinhardt F, Bray MA, Carpenter AE, Jirström K, Magnusson K, Ebert BL, Pontén F, Weinberg RA, McAllister SS. Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice. The Journal of Clinical Investigation. 121: 784-99. PMID 21266779 DOI: 10.1172/JCI43757  1
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  1
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  1
2010 Raviv TR, Ljosa V, Conery AL, Ausubel FM, Carpenter AE, Golland P, Wählby C. Morphology-guided graph search for untangling objects: C. elegans analysis. Medical Image Computing and Computer-Assisted Intervention : Miccai ... International Conference On Medical Image Computing and Computer-Assisted Intervention. 13: 634-41. PMID 20879454 DOI: 10.1007/978-3-642-15711-0_79  1
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  1
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  1
2010 Castoreno AB, Smurnyy Y, Torres AD, Vokes MS, Jones TR, Carpenter AE, Eggert US. Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis. Nature Chemical Biology. 6: 457-63. PMID 20436488 DOI: 10.1038/nchembio.363  1
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  1
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  1
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  1
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  1
2009 Moy TI, Conery AL, Larkins-Ford J, Wu G, Mazitschek R, Casadei G, Lewis K, Carpenter AE, Ausubel FM. High-throughput screen for novel antimicrobials using a whole animal infection model. Acs Chemical Biology. 4: 527-33. PMID 19572548 DOI: 10.1021/cb900084v  1
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  1
2009 Nilsson B, Johansson M, Al-Shahrour F, Carpenter AE, Ebert BL. Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. Bioinformatics (Oxford, England). 25: 1078-9. PMID 19228802 DOI: 10.1093/bioinformatics/btp091  1
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  1
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  1
2008 Pan H, Yu J, Zhang L, Carpenter A, Zhu H, Li L, Ma D, Yuan J. A novel small molecule regulator of guanine nucleotide exchange activity of the ADP-ribosylation factor and golgi membrane trafficking. The Journal of Biological Chemistry. 283: 31087-96. PMID 18799457 DOI: 10.1074/jbc.M806592200  1
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  1
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  1
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  1
2007 Carpenter AE. Image-based chemical screening. Nature Chemical Biology. 3: 461-5. PMID 17637778 DOI: 10.1038/nchembio.2007.15  1
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  1
2007 Carpenter AE. Software opens the door to quantitative imaging. Nature Methods. 4: 120-1. PMID 17264858 DOI: 10.1038/nmeth0207-120  1
2007 Jones TR, Carpenter AE. Flexible image analysis Biophotonics International. 14: 31-32.  1
2006 Hartwell KA, Muir B, Reinhardt F, Carpenter AE, Sgroi DC, Weinberg RA. The Spemann organizer gene, Goosecoid, promotes tumor metastasis. Proceedings of the National Academy of Sciences of the United States of America. 103: 18969-74. PMID 17142318 DOI: 10.1073/pnas.0608636103  1
2006 Baltus AE, Menke DB, Hu YC, Goodheart ML, Carpenter AE, de Rooij DG, Page DC. In germ cells of mouse embryonic ovaries, the decision to enter meiosis precedes premeiotic DNA replication. Nature Genetics. 38: 1430-4. PMID 17115059 DOI: 10.1038/ng1919  1
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  1
2006 Cowen LE, Carpenter AE, Matangkasombut O, Fink GR, Lindquist S. Genetic architecture of Hsp90-dependent drug resistance. Eukaryotic Cell. 5: 2184-8. PMID 17056742 DOI: 10.1128/EC.00274-06  1
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  1
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  1
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  1
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  1
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  1
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  1
2005 Rai D, Frolova A, Frasor J, Carpenter AE, Katzenellenbogen BS. Distinctive actions of membrane-targeted versus nuclear localized estrogen receptors in breast cancer cells. Molecular Endocrinology (Baltimore, Md.). 19: 1606-17. PMID 15831524 DOI: 10.1210/me.2004-0468  1
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  1
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.  1
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  1
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  1
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  1
2004 Carpenter AE, Sabatini DM. Systematic genome-wide screens of gene function. Nature Reviews. Genetics. 5: 11-22. PMID 14708012 DOI: 10.1038/nrg1248  1
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