Anne's Home Page
CellProfiler Project
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Email Anne: anne "AT" broad.mit.edu

7 Cambridge Center

Cambridge, MA 02142

phone 617 258 9538

this page last updated September 4, 2008

photo credit

Publications
*=not peer-reviewed.

List of publications directly from PubMed

32. Ljosa V, Carpenter AE (2008) High-throughput screens for fluorescent dye
discovery. Trends in Biotechnology, doi: 10.1016/j.tibtech 2008.06.008. In press. (Review
article) [pdf]

31. Vokes MS, Carpenter AE (2008) Using CellProfiler for automatic identification and measurement of biological objects in images. Current Protocols in Molecular Biology 82:14.17.1-14.17.12. PMID: 18425761 (Book chapter) [pdf]

30. Carpenter AE (2007) Image-based chemical screening. Nature Chemical Biology. 3:461-465 PMID: 17637778 (Review article) [NatChemBiology link] [pdf]

29. Carpenter AE (2007) Data analysis: Extracting rich information from images. Methods in Molecular Biology. In press. (Book chapter) PMID-none

28*. Jones TR, Carpenter AE (2007) Flexible Image Analysis. Biophotonics Journal. 14(7):31-32. (Short review article) [pdf] PMID-none

27*. Carpenter AE (2007) Software opens the door to quantitative imaging. Nature Methods. 4(2):120-1. PMID: 17264858 (Short review article) [pdf]

26. Lamprecht MR, Sabatini DM, Carpenter AE (2007) CellProfiler: free, versatile software for automated biological image analysis. Biotechniques. 42(1):71-75. PMID: 17269487 (Research article) [pdf]

25. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology, 7:R100. PMID: 17076895 (Research article) [link to paper at Genome Biology]

24. Hartwell KH, Muir B, Reinhardt F, Carpenter AE, Sgroi DC, Weinberg RA (2006) The Spemann Organizer gene, Goosecoid, promotes tumor metastasis. PNAS. 103(50):18969-74 PMID: 17142318 (Research article) [pdf]

23. Cowen LE, Carpenter AE, Matangkasombut O, Fink GR, Lindquist S (2006) Genetic architecture of Hsp90-dependent drug resistance. Eukaryotic Cell. 5(12):2184-8. PMID 17056742 (Research article) [pdf]

22. Baltus AE, Menke DB, Hu YC, Goodheart ML, Carpenter AE, de Rooij DG, Page DC (2006) In germ cells of mouse embryonic ovaries, the decision to enter meiosis precedes premeiotic DNA replication. Nature Genetics. 38(12):1430_1434. PMID: 17115059 (Research article) [pdf]

21. Jones TR, Carpenter AE, Golland P, Sabatini DM (2006) Methods for high-content, high-throughput image-based cell screening. Proceedings of the Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB). Metaxas DN, Whitaker RT, Rittcher J, Sebastian T (Eds). Copenhagen, Denmark, October 5, pp 65-72. (Research article) [pdf] PMID-none

     Updated as a book chapter:

     Jones TR, Carpenter AE, Golland P, Sabatini DM (2008) Methods for high-content, high throughput image-based cell screening. In: Rittscher J, Machiraju R, Wong STC , editors. Microscopic Image Analysis for Life Science Applications. Norwood, MA: Artech House Publishers, pp. 209-221 (Book chapter)

20. 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 (2006) Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nature Methods, 3(7):525-31. PMID 16791210 (Research article) [pdf]

19. Chuang CH, Carpenter AE, Fuchsova B, Johnson T, de Lanerolle P, Belmont AS (2006) Inducible, long-range directional movement of an interphase chromosome locus. Current Biology, 16:1-7. PMID 16631592 (Research article) [pdf]

18. 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 ES, Sabatini DM, Root DE (2006) A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell, 124(6):1283-98. PMID 16564017 (Research article) [pdf]

17. Bailey SN, Ali SM, Carpenter AE, Higgins CO, Sabatini DM (2006) Microarrays of lentiviruses for gene function screens in immortalized and primary cells. Nature Methods, 3(2):117-22. PMID 16432521 (Research article) [pdf]

16. Jones TR, Carpenter AE, Golland P (2005) Voronoi-based segmentation of cells on image manifolds. Proceedings of the Workshop on Computer Vision for Biomedical Image Applications (CVBIA). Yanxi Liu, Tianzi Jiang, Changshui Zhang (Eds.). Beijing, China, October 21. Lecture Notes in Computer Science 3765. Published by Springer-Verlag, Berlin, p. 535-543, ISBN 3-540-29411-2 (Research article) [pdf] PMID-none

15. Wheeler DB, Carpenter AE, Sabatini DM (2005) Cell microarrays and RNA interference chip away at gene function. Nature Genetics, 37 Supplement: S25-30. PMID 15920526 (Review) [pdf]

14. Verschure PJ, van der Kraan I, de Leeuw W, van der Vlag J, Carpenter AE, Belmont AS, van Driel R (2005) In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation. Molecular and Cellular Biology, 25(11):4552-64. PMID 15899859 (Research article) [pdf]

13. Rai D, Frolova A, Frasor J, Carpenter AE, Katzenellenbogen BS (2005) Distinctive actions of membrane-targeted versus nuclear localized estrogen receptors in breast cancer cells. Molecular Endocrinology, 19(6):1606-17. PMID 15831524 (Research article) [pdf]

12. Wheeler DB, Bailey SN, Guertin DA, Carpenter AE, Higgins CO, Sabatini DM (2004) RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells. Nature Methods, 1(2):127-32. PMID 15782175 (Research article) [pdf][download News&Views article referring to this work][download blurb referring to this work]

11. Carpenter AE, Memedula S, Plutz MJ, Belmont AS. Common effects of acidic activators on large-scale chromatin structure and transcription (2005) Molecular and Cellular Biology, 25(3):958-968. PMID 15657424 (Research article) [pdf]

10. Carpenter AE, Ashouri A, Belmont AS (2004) Automated microscopy identifies estrogen receptor subdomains with large-scale chromatin structure unfolding activity. Cytometry A, 58A(2):157-166. PMID 15057969 (Research article) [pdf]

9. Carpenter AE, Sabatini DM (2004) Systematic genome-wide screens of gene function. Nature Reviews Genetics, 5(1):11-22. PMID 14708012 (Review) [pdf]

8*. Carpenter AE, Belmont AS (2004) Direct visualization of transcription factor-induced chromatin remodeling and cofactor recruitment in vivo. Methods in Enzymology, 375:366-81. PMID 14870678 (A methods paper which includes substantial unpublished research) [pdf]

(please note name change in 2003 from AC Nye to AE Carpenter)

___7.5 ---- Ph.D. thesis ---> [download Word document]

7. Nye AC, Rajendran RR, Belmont AS (2003) Chromosomes and Chromatin. In: Cooper DN (ed.) Nature Encyclopedia of the Human Genome, vol. 1:766-773. London: Nature Publishing Group. PMID-none (Review) [pdf]

6. Rajendran RR, Nye AC, Frasor J, Balsara RD, Martini PGV, Katzenellenbogen BS (2003) Regulation of nuclear receptor transcriptional activity by a novel DEAD box RNA helicase (DP97). Journal of Biological Chemistry, 278(7):4628-38. PMID 12466272 (Research article) [pdf]

5. Nye AC, Rajendran RR, Stenoien DL, Mancini MA, Katzenellenbogen BS, Belmont AS (2002) Alteration of large-scale chromatin structure by estrogen receptor. Molecular and Cellular Biology, 22(10):3437-49. PMID 11971975 (Research article) [pdf]

4. Ye Q, Hu YF, Zhong H, Nye AC, Belmont AS, Li R (2001) BRCA1-induced large-scale chromatin unfolding and allele-specific effects of cancer-predisposing mutations. Journal of Cell Biology, 155(6):911-21. PMID 11739404 (Research article) [pdf][download intro(bottom of 2nd page)]

3. Stenoien DL, Nye AC, Mancini MG, Patel K, Dutertre M, O’Malley BW, Smith CL, Belmont AS, Mancini MA (2001) Ligand-mediated assembly and real-time cellular dynamics of estrogen receptor alpha-coactivator complexes in living cells. Molecular and Cellular Biology, 21(13):4404-12. PMID 11390668 (Research article) [pdf]

2*. Nye AC, Rajendran RR, Katzenellenbogen BS, Belmont AS (2000) The estrogen receptor alters large-scale chromatin structure. Trends in Cell Biology GFP in Motion CD-ROM, volume 2, ed. B Ludin and A Matus. PMID-none (Movie & caption) [movie (sorry, it doesn't always work)][abstract][background]

1*. Belmont AS, Dietzel SD, Nye AC, Tumbar T, Strukov Y (1999) Large scale chromatin structure and function. Current Opinion in Cell Biology, 11(3):307-311. PMID 10395564 (Review) [pdf]