Publications

Preprints
Hollandi R, Szkalisity A, Toth T, Tasnadi E, Molnar C, Mathe B, Grexa I, Molnar J, Balind A, Gorbe M, Kovacs M, E M, Goodman A, Balassa T, Koos K, Wang W, Bara N, Kovacs F, Paavolainen L, Danka T, Kirston A, Carpenter AE, Horvath P. A deep learning framework for nucleus segmentation using image style transfer. BioRxiv 580605 Preprints;
2019
Shlevkov E, Basu H, Bray MA, Sun Z, Wei W, Apaydin K, Karhohs KW, Chen PF, Smith JLM, Wiskow O, Roet K, Huang X, Eggan K, Carpenter AE, Kleiman RJ, Schwarz TL. A High-Content Screen Identifies TPP1 and Aurora B as Regulators of Axonal Mitochondrial Transport [Internet]. Cell Reports 2019;28(12):3224-3237.e5. Publisher's Version
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 [Internet]. Nature Methods 2019;16:1247–1253. Publisher's Version PDF
Lafarge MW, Caicedo JC, Carpenter AE, Pluim JPW, Singh S, Veta M. Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning. [Internet]. Proceedings of Machine Learning Research 2019;102:315–325. Publisher's Version
Caicedo JC, Roth J, Goodman A, Becker T, Karhohs KW, Broisin M, Molnar C, McQuin C, Singh S, Theis F, Carpenter AE. Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images. Cytometry 2019;(95):952-965.
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 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 [Internet]. Cytometry A 2019;95(8):836-842. Publisher's Version
Kulikov V, Guo SM, Stone M, Goodman A, Carpenter AE, Bathe M, Lempitsky V. DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images [Internet]. PLoS Computational Biology 2019;15(5):e1007012. Publisher's Version
Rohban MH, Shafqat-Abbasi H, Singh S, Carpenter AE. Capturing single-cell heterogeneity via data fusion improves image-based profiling [Internet]. Nature Communications 2019;10(2082) Publisher's Version
Doan M, Carpenter AE. Leveraging machine vision in cell-based diagnostics to do more with less [Internet]. Nature Materials 2019;(18):414-418. Publisher's Version
2018
Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini BA, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner A, Bittker J, Meyerson M, Getz G, Beroukhim R, Golub TR. Genetic and transcriptional evolution alters cancer cell line drug response [Internet]. Nature 2018;560(7718):325-330. Publisher's Version

[Carpenter lab paper: Carpenter not co-author]

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 [Internet]. PLoS Biol. 16(7):e2005970 2018; Publisher's Version
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. [Internet]. Front Bioeng Biotechnol. 6:87 2018; Publisher's Version
Caicedo JC, McQuin C, Goodman A, Singh S, Carpenter AE. Weakly supervised learning of single-cell feature embeddings. [Internet]. 2018 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) bioRxiv 2018;:293431. Publisher's Version
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS. Opportunities and obstacles for deep learning in biology and medicine [Internet]. J R Soc Interface 2018;15(141) Publisher's Version
Becker T, Caicedo JC, Singh S, Weckmann M, Carpenter AE. Combining morphological and migration profiles of in vitro time-lapse data. 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018) 2018;:965–968. PDF
Goldsborough P, Pawlowski N, Caicedo JC, Singh S, Carpenter AE. CytoGAN: Generative Modeling of Cell Images [Internet]. 2018; Publisher's Version
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, Hochreiter S, Moreau CH. Repurposed High-Throughput Images Enable Biological Activity Prediction For Drug Discovery. [Internet]. Cell Chem Biol 2018; Publisher's Version
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. [Internet]. Trends Biotechnol 112:39-45 2018; Publisher's Version
Bray MA, Carpenter AE. Quality Control for High-Throughput Imaging Experiments Using Machine Learning in CellProfiler. [Internet]. Methods Mol Biol 1683:89-112 2018; Publisher's Version

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