Bray MA and Carpenter AE. 2012. “Advanced Assay Development Guidelines for Image-Based High Content Screening and Analysis.” In: Sittampalam GS et al., eds. Assay Guidance Manual. .
Ljosa V, Sokolnicki KL, and Carpenter AE. 2012. “Annotated high-throughput microscopy image sets for validation.” Nature Methods 9(7):637. Publisher's Version
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, Moore CB, Bliss-Moreau M, Verplank L, Tolliday NJ, Mishra R, Vemula S, Shi J, Wei L, Kapur R, Lopez CK, Gerby B, Ballerini P, Pflumio F, Gilliland DG, Goldberg L, Birger Y, Izraeli S, Gamis AS, Smith FO, Woods WG, Taub J, Scherer CA, Bradner JE, Goh BC, Mercher T, Carpenter AE, Gould RJ, Clemons PA, Carr SA, Root DE, Schreiber SL, Stern AM, and Crispino JD. 2012. “Identification of Regulators of Polyploidization Presents Therapeutic Targets for Treatment of AMKL.” Cell 150(3):575-89. Publisher's Version
Carpenter AE. 2011. “Extracting biomedically important information from large, automated imaging experiments.” In ISBI 2011 (Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro), 1723-1726. Publisher's Version
Lindquist RA, Ottina KA, Wheeler DB, Hsu PP, Thoreen CC, Guertin DA, Siraj MA, Senguptal S, Shaul YD, Lamprecht MR, Madden KL, Papallo AR, Jones T, Sabatini DM, and Carpenter AE. 2011. “Genome-scale RNAi on living-cell microarrays identifies novel regulators of Drosophila melanogaster TORC1 - S6K pathway signaling.” Genome Research 2011, 21:433-446. Publisher's Version
Elkabets M, Gifford AM, Scheel C, Nilsson B, Reinhardt F, Bray MA, Carpenter AE, Jirström K, Magnusson K, Ebert BL, Pontén F, Weinberg RA, and McAllister SS. 2011. “Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice.” Journal of Clinical Investigation 121(2): 784-99. Publisher's Version
Kamentsky L, Jones TR, Fraser A, Bray M, Logan D, Madden K, Ljosa V, Rueden C, Harris GB, Eliceiri K, and Carpenter AE. 2011. “Improved structure, function, and compatibility for CellProfiler: modular high-throughput image analysis software.” Bioinformatics 2011. Publisher's Version
Peterson TR, Sengupta SS, Harris TE, Carmack AE, Balderas E, Guertin DA, Madden KL, Carpenter AE, Finck BN, and Sabatini DM. 2011. “mTOR complex 1 regulates lipin 1 localization to control the SREBP pathway.” Cell 146(3):408-420. Publisher's Version
Pretorius AJ, Bray M-A, Carpenter AE, and Ruddle R. 2011. “Visualization of parameter space for image analysis.” In InfoVis 2011 (Proceedings of the 2011 IEEE Symposium on Information Visualization), 2402-11. Publisher's Version
High-content screening: Practical advice, tools and resources.
Carpenter AE. 10/2010. “High-content screening: Practical advice, tools and resources.” SBS News 47:2.
High-content screening: FAQs about trends, technologies, and outcomes.
Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM, and Carpenter AE. 2010. “Resolving clustered worms via probabilistic shape models.” In ISBI 2010 (Proceedings of the IEEE International Symposium on Biomedical Imaging: From Nano to Macro), 552-555. Publisher's Version
Logan DJ and Carpenter AE. 2010. “Screening Cellular Feature Measurements for Image-based Assay Development.” Journal of Biomolecular Screening 15(7):840-6. Publisher's Version
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, and Hériché J-K. 2010. “Visualization of image data from cells to organisms.” Nature Methods Supplement 7(3):S27-41. Publisher's Version
Cataldo AM, McPhie DL, Lange NT, Punzell S, Elmiligy, Ye NZ, Froimowitz MP, Hassinger LC, Menesale EB, Sargent LW, Logan DJ, Carpenter AE, and Cohen BM. 2010. “Abnormalities in Mitochondrial Structure in Cells of Patients with Bipolar Disorder.” American Journal of Pathology 177(2):575-85. Publisher's Version
Automated tracking of yeast cell lineages.
Kim K, Rowat AC., and Carpenter AE. 2010. “Automated tracking of yeast cell lineages.” Proceedings of SPIE 7798, 779823. Publisher's Version
Riklin-Raviv T, Ljosa V, Conery AL, Ausubel FM, Carpenter AE, Golland P, and Wählby C. 2010. “Morphology-guided graph search for untangling objects: C elegans analysis.” In Medical Image Computing and Computer Assisted Intervention (MICCAI) 2010; 13(3):634-641. Publisher's Version
Castoreno AB, Smurnyy Y, Torres AD, Vokes MS, and Jones TR. 2010. “Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis.” Nature Chemical Biology. Publisher's Version
Jones TR**, Carpenter AE**, Lamprecht MR, Moffat J, Silver SJ, Grenier JK, Castoreno AB, Eggert US, Root DE, Golland P, and Sabatini DM. 2009. “Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning.” PNAS 106(6):1826-31. Publisher's Version
Nilsson B, Johansson M, Al-Shahrour F, Carpenter AE, and Ebert BL. 2009. “Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution.” Bioinformatics 25(8):1078-79. Publisher's Version