| Year |
Citation |
Score |
| 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 |
0.674 |
|
| 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 |
0.66 |
|
| 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 |
0.556 |
|
| 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 |
0.495 |
|
| 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, ... Carpenter AE, 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 |
0.798 |
|
| 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 |
0.618 |
|
| 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, ... ... Carpenter AE, et al. Reproducible image-based profiling with Pycytominer. Arxiv. PMID 38045474 |
0.816 |
|
| 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 |
0.57 |
|
| 2023 |
Tromans-Coia C, Jamali N, Abbasi HS, Giuliano KA, Hagimoto M, Jan K, Kaneko E, Letzsch S, Schreiner A, Sexton JZ, Suzuki M, Trask OJ, Yamaguchi M, Yanagawa F, Yang M, ... Carpenter AE, et al. Assessing the performance of the Cell Painting assay across different imaging systems. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. PMID 37789738 DOI: 10.1002/cyto.a.24786 |
0.828 |
|
| 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 |
0.777 |
|
| 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 |
0.672 |
|
| 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, ... ... Carpenter AE, 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 |
0.742 |
|
| 2023 |
Barnes CM, Power AL, Barber DG, Tennant RK, Jones RT, Lee GR, Hatton J, Elliott A, Zaragoza-Castells J, Haley SM, Summers HD, Doan M, Carpenter AE, Rees P, Love J. Deductive automated pollen classification in environmental samples via exploratory deep learning and imaging flow cytometry. The New Phytologist. PMID 37678361 DOI: 10.1111/nph.19186 |
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, ... ... Carpenter AE, 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 |
0.806 |
|
| 2023 |
Laber S, Strobel S, Mercader JM, Dashti H, Dos Santos FRC, Kubitz P, Jackson M, Ainbinder A, Honecker J, Agrawal S, Garborcauskas G, Stirling DR, Leong A, Figueroa K, Sinnott-Armstrong N, ... ... Carpenter AE, et al. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. Cell Genomics. 3: 100346. PMID 37492099 DOI: 10.1016/j.xgen.2023.100346 |
0.793 |
|
| 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 |
0.615 |
|
| 2023 |
Carpenter AE, Cimini BA, Eliceiri KW. Smart microscopes of the future. Nature Methods. 20: 962-964. PMID 37434001 DOI: 10.1038/s41592-023-01912-0 |
0.612 |
|
| 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, ... ... Carpenter AE, et al. Optimizing the Cell Painting assay for image-based profiling. Nature Protocols. PMID 37344608 DOI: 10.1038/s41596-023-00840-9 |
0.838 |
|
| 2023 |
Glunk V, Laber S, Sinnott-Armstrong N, Sobreira DR, Strobel SM, Batista TM, Kubitz P, Moud BN, Ebert H, Huang Y, Brandl B, Garbo G, Honecker J, Stirling DR, Abdennur N, ... ... Carpenter AE, et al. A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. Nature Metabolism. 5: 861-879. PMID 37253881 DOI: 10.1038/s42255-023-00807-w |
0.632 |
|
| 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, ... ... Carpenter AE, 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 |
0.565 |
|
| 2023 |
Berryer MH, Rizki G, Nathanson A, Klein JA, Trendafilova D, Susco SG, Lam D, Messana A, Holton KM, Karhohs KW, Cimini BA, Pfaff K, Carpenter AE, Rubin LL, Barrett LE. High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. Elife. 12. PMID 37083703 DOI: 10.7554/eLife.80168 |
0.785 |
|
| 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, ... ... Carpenter AE, 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 |
0.774 |
|
| 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 |
0.693 |
|
| 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 |
0.612 |
|
| 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 |
0.795 |
|
| 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 |
0.577 |
|
| 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, ... ... Carpenter AE, 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 |
0.779 |
|
| 2023 |
Jamali N, Tromans-Coia C, Abbasi HS, Giuliano KA, Hagimoto M, Jan K, Kaneko E, Letzsch S, Schreiner A, Sexton JZ, Suzuki M, Trask OJ, Yamaguchi M, Yanagawa F, Yang M, ... Carpenter AE, et al. Assessing the performance of the Cell Painting assay across different imaging systems. Biorxiv : the Preprint Server For Biology. PMID 36824835 DOI: 10.1101/2023.02.15.528711 |
0.828 |
|
| 2022 |
Rees P, Summers HD, Filby A, Carpenter AE, Doan M. Imaging flow cytometry: a primer. Nature Reviews. Methods Primers. 2. PMID 37655209 DOI: 10.1038/s43586-022-00167-x |
0.749 |
|
| 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, ... ... Carpenter AE, 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 |
0.794 |
|
| 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 |
0.773 |
|
| 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, ... ... Carpenter AE, 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 |
0.661 |
|
| 2022 |
Rueden CT, Hiner MC, Evans EL, Pinkert MA, Lucas AM, Carpenter AE, Cimini BA, Eliceiri KW. PyImageJ: A library for integrating ImageJ and Python. Nature Methods. PMID 36253645 DOI: 10.1038/s41592-022-01655-4 |
0.601 |
|
| 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, ... ... Carpenter AE, 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 |
0.799 |
|
| 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 |
0.655 |
|
| 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 |
0.337 |
|
| 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 |
0.621 |
|
| 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 |
0.779 |
|
| 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 |
0.814 |
|
| 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 |
0.681 |
|
| 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 |
0.785 |
|
| 2021 |
Way GP, Greene CS, Carninci P, Carvalho BS, de Hoon M, Finley S, Gosline SJC, Lȇ Cao KA, Lee JSH, Marchionni L, Robine N, Sindi SS, Theis FJ, Yang JYH, Carpenter AE, et al. A field guide to cultivating computational biology. Plos Biology. 19: e3001419. PMID 34618807 DOI: 10.1371/journal.pbio.3001419 |
0.723 |
|
| 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 |
0.822 |
|
| 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 |
0.689 |
|
| 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 |
0.754 |
|
| 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 |
0.807 |
|
| 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 |
0.811 |
|
| 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 |
0.825 |
|
| 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 |
0.695 |
|
| 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 |
0.814 |
|
| 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 |
0.734 |
|
| 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 |
0.775 |
|
| 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 |
0.348 |
|
| 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 |
0.613 |
|
| 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 |
0.793 |
|
| 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 |
0.75 |
|
| 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 |
0.748 |
|
| 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 |
0.761 |
|
| 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 |
0.354 |
|
| 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 |
0.804 |
|
| 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 |
0.777 |
|
| 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 |
0.752 |
|
| 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 |
0.743 |
|
| 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 |
0.81 |
|
| 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 |
0.752 |
|
| 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 |
0.804 |
|
| 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 |
0.805 |
|
| 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 |
0.709 |
|
| 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 |
0.786 |
|
| 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 |
0.816 |
|
| 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 |
0.725 |
|
| 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 |
0.76 |
|
| 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 |
0.64 |
|
| 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 |
0.806 |
|
| 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 |
0.757 |
|
| 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 |
0.644 |
|
| 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 |
0.801 |
|
| 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 |
0.466 |
|
| 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 |
0.305 |
|
| 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 |
0.453 |
|
| 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 |
0.779 |
|
| 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 |
0.744 |
|
| 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 |
0.597 |
|
| 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 |
0.689 |
|
| 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 |
0.623 |
|
| 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 |
0.601 |
|
| 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 |
0.826 |
|
| 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 |
0.722 |
|
| 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 |
0.677 |
|
| 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 |
0.678 |
|
| 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 |
0.718 |
|
| 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 |
0.332 |
|
| 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 |
0.665 |
|
| 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 |
0.318 |
|
| 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 |
0.707 |
|
| 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 |
0.706 |
|
| 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 |
0.633 |
|
| 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 |
0.65 |
|
| 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 |
0.721 |
|
| 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 |
0.369 |
|
| 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 |
0.639 |
|
| 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 |
0.316 |
|
| 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 |
0.58 |
|
| 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 |
0.455 |
|
| 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 |
0.631 |
|
| 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 |
0.68 |
|
| 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 |
0.377 |
|
| 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 |
0.486 |
|
| 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 |
0.395 |
|
| 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 |
0.351 |
|
| 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 |
0.65 |
|
| 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 |
0.672 |
|
| 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 |
0.661 |
|
| 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 |
0.403 |
|
| 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 |
0.681 |
|
| 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 |
0.681 |
|
| 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 |
0.627 |
|
| 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 |
0.66 |
|
| 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 |
0.317 |
|
| 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 |
0.371 |
|
| 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 |
0.408 |
|
| 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 |
0.418 |
|
| 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 |
0.812 |
|
| 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 |
0.68 |
|
| 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 |
0.451 |
|
| 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 |
0.682 |
|
| 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 |
0.4 |
|
| 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 |
0.321 |
|
| 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 |
0.319 |
|
| 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 |
0.328 |
|
| 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 |
0.306 |
|
| 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 |
0.485 |
|
| 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 |
0.679 |
|
| 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 |
0.543 |
|
| 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 |
0.709 |
|
| 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 |
0.683 |
|
| 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 |
0.655 |
|
| 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 |
0.734 |
|
| 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 |
0.313 |
|
| 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 |
0.418 |
|
| 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 |
0.363 |
|
| 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 |
0.447 |
|
| 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 |
0.377 |
|
| 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 |
0.485 |
|
| 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 |
0.434 |
|
| 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 |
0.477 |
|
| 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 |
0.642 |
|
| 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 |
0.635 |
|
| 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 |
0.342 |
|
| 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 |
0.347 |
|
| 2008 |
Vokes MS, Carpenter AE. CellProfiler: Open-Source Software to Automatically Quantify Images Microscopy Today. 16: 38-39. DOI: 10.1017/S1551929500061757 |
0.452 |
|
| 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 |
0.362 |
|
| 2007 |
Carpenter AE. Image-based chemical screening. Nature Chemical Biology. 3: 461-5. PMID 17637778 DOI: 10.1038/Nchembio.2007.15 |
0.394 |
|
| 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 |
0.613 |
|
| 2007 |
Carpenter AE. Software opens the door to quantitative imaging. Nature Methods. 4: 120-1. PMID 17264858 DOI: 10.1038/Nmeth0207-120 |
0.432 |
|
| 2007 |
Jones TR, Carpenter AE. Flexible image analysis Biophotonics International. 14: 31-32. |
0.308 |
|
| 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 |
0.643 |
|
| 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 |
0.323 |
|
| 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 |
0.657 |
|
| 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 |
0.568 |
|
| 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 |
0.566 |
|
| 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 |
0.555 |
|
| 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 |
0.545 |
|
| 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 |
0.52 |
|
| 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. |
0.329 |
|
| 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 |
0.579 |
|
| 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 |
0.587 |
|
| 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 |
0.548 |
|
| 2004 |
Carpenter AE, Sabatini DM. Systematic genome-wide screens of gene function. Nature Reviews. Genetics. 5: 11-22. PMID 14708012 DOI: 10.1038/Nrg1248 |
0.53 |
|
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