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 [Internet]. PLoS ONE 4(10):e7339 2009; Publisher's Version
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 [Internet]. ACS Chemical Biology 4 2009; Publisher's Version PDF
Nilsson B, Johansson M, Al-Shahrour F, Carpenter AE, Ebert BL. Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. [Internet]. Bioinformatics 25(8):1078-79 2009; Publisher's Version PDF
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 [Internet]. PNAS 106(6):1826-31 2009; Publisher's Version

[** Authors Jones, TR and Carpenter, AE contributed equally.]

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 [Internet]. BMC Bioinformatics 9(1):482 2008; Publisher's Version PDF
Pan H, Yu J, Zhang L, Carpenter AE, Zhu H, Li L, Ma D, Yuan J. A novel small molecule regulator of guanine nucleotide exchange activity of ARF and golgi membrane trafficking [Internet]. Journal of Biological Chemistry 283(45):31087-9 2008; Publisher's Version PDF
CellProfiler: Open-source software to automatically quantify images
Vokes MS, Carpenter AE. CellProfiler: Open-source software to automatically quantify images. Microscopy Today 16(5):38-39 2008; PDF
Ljosa V, Carpenter AE. High-throughput screens for fluorescent dye discovery. [Internet]. Trends in Biotechnology 10:527-30 2008; Publisher's Version PDF
Vokes MS, Carpenter AE. Using CellProfiler for automatic identification and measurement of biological objects in images. In: Ausubel, FM et al., eds. Current Protocols in Molecular Biology 82:14.17.1-14.17.12. 2008; PDF
PMID: 18425761
Jones TR, Carpenter AE, Golland P, Sabatini DM. Methods for high-content, high throughput image-based cell screening. Microscopic Image Analysis for Life Science Applications. 2008;:209-221.
Carpenter AE. Image-based chemical screening. [Internet]. Nature Chemical Biology. 3:461-465 2007; NatChemBiology link PDF
Carpenter AE. Extracting rich information from images. In: Clemons PA et al., eds. Cell-Based Assays for High-Throughput Screening. Methods in Molecular Biology 2007;486:193-211. PDF
PMID: 19347625
Flexible Image Analysis
Jones TR, Carpenter AE. Flexible Image Analysis. Biophotonics Journal. 14(7):31-32. 2007; PDF
Carpenter AE. Software opens the door to quantitative imaging. Nature Methods. 4(2):120-1. 2007; PDF
Lamprecht MR, Sabatini DM, Carpenter AE. CellProfiler: free, versatile software for automated biological image analysis. Biotechniques. 42(1):71-75. 2007; PDF
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. [Internet]. Genome Biology, 7:R100 2006; Publisher's Version
Hartwell KH, Muir B, Reinhardt F, Carpenter AE, Sgroi DC, Weinberg RA. The Spemann Organizer gene, Goosecoid, promotes tumor metastasis. [Internet]. PNAS. 103(50):18969-74 2006; Publisher's Version
Cowen LE, Carpenter AE, Matangkasombut O, Fink GR, Lindquist S. Genetic architecture of Hsp90-dependent drug resistance. [Internet]. Eukaryotic Cell. 5(12):2184-8 2006; Publisher's Version
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(12):1430_1434. 2006; PDF
Sigal A, Milo M, 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(7):525-31. 2006; PDF