Scientific Publications

Identification of regulators of polyploidization presents therapeutic targets for treatment of AMKL.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., et al. Cell, 2012/08/03, Volume 150, Issue 3, p.575-89, (2012) Read More / View Supplemental Materials

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Abstract

Annotated high-throughput microscopy image sets for validation.Ljosa, V., Sokolnicki KL, and Carpenter AE Nature methods, 2012/06/28, Volume 9, Issue 7, p.637, (2012) Read More / View Supplemental Materials

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A call for bioimaging software usability.Carpenter, AE, Kamentsky L., and Eliceiri KW Nature methods, 2012/06/28, Volume 9, Issue 7, p.666-70, (2012) Read More / View Supplemental Materials

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An image analysis toolbox for high-throughput C. elegans assays.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, and Carpenter AE Nature methods, 2012/04/22, (2012) Read More / View Supplemental Materials

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Abstract

Extracting rich information from images.Carpenter, AE Methods in molecular biology (Clifton, N.J.), 2012/01/09, Volume 486, p.193-211, (2012) Read More / View Supplemental Materials

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Abstract

A Chemical Screen Probing the Relationship between Mitochondrial Content and Cell Size.Kitami, T., Logan DJ, Negri J., Hasaka T., Tolliday NJ, Carpenter AE, Spiegelman BM, and Mootha VK PloS one, 2012/01/01, Volume 7, Issue 3, p.e33755, (2012) Read More / View Supplemental Materials

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Abstract

Visualization of parameter space for image analysis.Pretorius, AJ, Bray MA, Carpenter AE, and Ruddle RA IEEE transactions on visualization and computer graphics, 2011/12/01, Volume 17, Issue 12, p.2402-11, (2011) Read More / View Supplemental Materials

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Abstract

Workflow and Metrics for Image Quality Control in Large-Scale High-Content Screens.Bray, MA, Fraser AN, Hasaka TP, and Carpenter AE Journal of biomolecular screening, 2011/09/28, (2011) Read More / View Supplemental Materials

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Abstract

Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.Kamentsky, L., Jones TR, Fraser A., Bray MA, Logan DJ, Madden KL, Ljosa V., Rueden C., Eliceiri KW, and Carpenter AE Bioinformatics (Oxford, England), 2011/04/15, Volume 27, Issue 8, p.1179-80, (2011) Read More / View Supplemental Materials

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Abstract

Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice.Elkabets, M., Gifford AM, Scheel C., Nilsson B., Reinhardt F., Bray MA, Carpenter AE, Jirström K., Magnusson K., Ebert BL, Pontén F., Weinberg R. A., and McAllister SS The Journal of clinical investigation, 2011/02/01, Volume 121, Issue 2, p.784-99, (2011) Read More / View Supplemental Materials

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Abstract

Screening cellular feature measurements for image-based assay development.Logan, DJ, and Carpenter AE Journal of biomolecular screening, 2010/08/01, Volume 15, Issue 7, p.840-6, (2010) Read More / View Supplemental Materials

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Abstract

RESOLVING CLUSTERED WORMS VIA PROBABILISTIC SHAPE MODELS.Wählby, C., Riklin-Raviv T., Ljosa V., Conery AL, Golland P., Ausubel FM, and Carpenter AE Proceedings / IEEE International Symposium on Biomedical Imaging: from nano to macro. IEEE International Symposium on Biomedical Imaging, 2010/06/21, Volume 2010, Issue 14-17 April 2010, p.552-555, (2010) Read More / View Supplemental Materials

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Abstract

Introduction to the quantitative analysis of two-dimensional fluorescence microscopy images for cell-based screening.Ljosa, V., and Carpenter AE PLoS computational biology, 2009/12/01, Volume 5, Issue 12, p.e1000603, (2009) Read More / View Supplemental Materials

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Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution.Nilsson, B., Johansson M., Al-Shahrour F., Carpenter AE, and Ebert BL Bioinformatics (Oxford, England), 2009/04/15, Volume 25, Issue 8, p.1078-9, (2009) Read More / View Supplemental Materials

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Abstract

Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning.Jones, TR, Carpenter AE, Lamprecht MR, Moffat J., Silver SJ, Grenier JK, Castoreno AB, Eggert US, Root DE, Golland P., and Sabatini DM Proceedings of the National Academy of Sciences of the United States of America, 2009/02/10, Volume 106, Issue 6, p.1826-31, (2009) Read More / View Supplemental Materials

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Abstract

CellProfiler Analyst: data exploration and analysis software for complex image-based screens.Jones, TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A., Sabatini DM, Golland P., and Carpenter AE BMC bioinformatics, 2008/11/15, Volume 9, p.482, (2008) Read More / View Supplemental Materials

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Abstract

High-throughput screens for fluorescent dye discovery.Ljosa, V., and Carpenter AE Trends in biotechnology, 2008/10/01, Volume 26, Issue 10, p.527-30, (2008) Read More / View Supplemental Materials

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Abstract

Using CellProfiler for automatic identification and measurement of biological objects in images.Vokes, MS, and Carpenter AE Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.], 2008/04/01, Volume Chapter 14, p.Unit 14.17, (2008) Read More / View Supplemental Materials

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Abstract

Image-based chemical screening.Carpenter, AE Nature chemical biology, 2007/08/01, Volume 3, Issue 8, p.461-5, (2007) Read More / View Supplemental Materials

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Abstract

A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen.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., Hahn WC, Lander E. S., Sabatini DM, and Root DE Cell, 2006/03/24, Volume 124, Issue 6, p.1283-98, (2006) Read More / View Supplemental Materials

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Abstract