Publications

List of publications directly from PubMed

Publications and citation metrics from ResearcherID

* - not peer-reviewed.

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56. Bray, M-A, Fraser AN, Hasaka TP, Carpenter AE (2012) Workflow and metrics for image quality control in large-scale high-content screens. Journal of Biomolecular Screening 17(2):135-143/doi. PMID: 21956170 PMCID: In process (Research article) [pdf]

55. Pretorius AJ, Bray M-A, Carpenter AE, Ruddle R (2011) Visualization of parameter space for image analysis. In InfoVis 2011 (Proceedings of the 2011 IEEE Symposium on Information Visualization), 2402-11/doi. PMID: 22034361 PMCID: In process (Research article) [pdf]

54. Peterson TR, Sengupta SS, Harris TE, Carmack AE, Balderas E, Guertin DA, Madden KL, Carpenter AE, Finck BN, Sabatini DM (2011) mTOR complex 1 regulates lipin 1 localization to control the SREBP pathway. Cell 146(3):408-420/doi. PMID: 2186276 PMCID: In process (Research article)

53. 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/doi. PMID: In process (Research article) [pdf]

52. Kamentsky L, Jones TR, Fraser A, Bray M, Logan D, Madden K, Ljosa V, Rueden C, Harris GB, Eliceiri K, Carpenter AE (2011) Improved structure, function, and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics 2011/doi. PMID: 21349861 PMCID: PMC3072555 (Research article)

51. Elkabets M, Gifford AM, Scheel C, Nilsson B, Reinhardt F, Bray MA, Carpenter AE, Jirström K, Magnusson K, Ebert BL, Pontén F, Weinberg RA, 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/doi. PMID: 21266779 PMCID: PMC3026724 (Research article) [CellProfiler published pipeline]

50. 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, 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/doi. PMID: 21239477 PMCID: PMC3044857 (Research article) [pdf]

49.* Kim K, Rowat AC. Carpenter AE (2010) Automated tracking of yeast cell lineages. Proceedings of SPIE 7798, 779823, DOI:10.1117/12.859770. (Research article) [SPIE link]

48.* Carpenter AE (2010). High-content screening: Practical advice, tools and resources. SBS News 47:2, October 2010. [SBS news link ]

47.* Carpenter AE (2010). High-content screening: FAQs about trends, technologies, and outcomes. SBS News 47:2, August 2010. [SBS news link ]

46. Riklin-Raviv T, Ljosa V, Conery AL, Ausubel FM, Carpenter AE, Golland P, 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/doi. PMID: 20879454 PMCID: PMC3050593 (Research article) [pdf]

45. Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM, 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/doi. PMID: 21383863 PMCID: PMC3048333 (Research article) [pdf]

44. Cataldo AM, McPhie DL, Lange NT, Punzell S, Elmiligy, Ye NZ, Froimowitz MP, Hassinger LC, Menesale EB, Sargent LW, Logan DJ, Carpenter AE, Cohen BM (2010). Abnormalities in Mitochondrial Structure in Cells of Patients with Bipolar Disorder. American Journal of Pathology 177(2):575-85/doi. PMID: 20566748 PMCID: PMC2913344 (Research article) [American Journal of Pathology Link]

43. Logan DJ and Carpenter AE (2010). Screening Cellular Feature Measurements for Image-based Assay Development. Journal of Biomolecular Screening 15(7):840-6/doi. PMID: 20516293 PMCID: PMC3145348 (Research article) [pdf]

42. Castoreno AB, Smurnyy Y, Torres AD, Vokes MS, Jones TR, Carpenter AE, Eggert US (2010). Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis. Nature Chemical Biology doi. PMID: 20436488 PMCID: PMC2873065 (Research article) [pdf]

41. 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, Hériché J-K (2010) Visualization of image data from cells to organisms. Nature Methods Supplement 7(3):S27-41/doi. PMID: 20195255 PMCID: In process (Review article) [Nature Methods Supplement Link] [pdf]

40. Ljosa V, Carpenter AE (2009) Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening. PLoS Computational Biology 5(12):e1000603/doi. PMID: 20041172 PMCID: PMC2791844 (Tutorial) [PLoS Computational Biology Link] [pdf]

39. Tsui M, Xie T, Orth JD, Carpenter AE, Rudnicki S, Kim S, Shamu CE, Mitchison TJ (2009). An intermittent live cell imaging screen for siRNA enhancers and suppressors of a kinesin-5 inhibitor. PLoS One 4(10):e7339/doi. PMID: 19802393 PMCID: PMC2752188 (Research article) [PLoS ONE Link] [pdf]

38. Moy TI, Conery AL, Larkins-Ford J, Wu G, Mazitschek R, Casadei G, Lewis K, Carpenter AE, Ausubel FM (2009) High throughput screen for novel antimicrobials using a whole animal infection model. ACS Chemical Biology 4/doi. PMID: 19572548 PMCID: PMC2745594 (Research article) [ACS Chemical Biology link] [pdf]

37. Nilsson B, Johansson M, Al-Shahrour F, Carpenter AE, Ebert BL (2009) Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. Bioinformatics 25(8):1078-79/doi. PMID: 19228802 (Research article) [pdf]

36. Jones TR**, Carpenter AE**, Lamprecht MR, Moffat J, Silver SJ, Grenier JK, Castoreno AB, Eggert US, Root DE, Golland P, Sabatini DM (2009). Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. PNAS 106(6):1826-31/doi. PMID: 19188593 PMCID: PMC2634799 (Research article) [PNAS link]

     **These authors contributed equally.

35. Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE (2008). CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics 9(1):482/doi. PMID: 19014601 PMCID: PMC2614436 (Research article) [BioMed Central link] [pdf]

34. Pan H, Yu J, Zhang L, Carpenter AE, Zhu, H, Li L, Ma D, Yuan J (2008) A novel small molecule regulator of guanine nucleotide exchange activity of ARF and golgi membrane trafficking. Journal of Biological Chemistry 283(45):31087-9/doi. PMID: 18799457 PMCID: PMC2576541 (Research article) [pdf]

33*. Vokes MS, Carpenter AE (2008) CellProfiler: Open-source software to automatically quantify images. Microscopy Today 16(5):38-39 PMID-none (Short review article) [pdf]

32. Ljosa V, Carpenter AE (2008) High-throughput screens for fluorescent dye discovery. Trends in Biotechnology 10:527-30/doi. PMID: 18706725 (Review article) [pdf]

31. Vokes MS, Carpenter AE (2008) 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. 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) Extracting rich information from images. In: Clemons PA et al., eds. Cell-Based Assays for High-Throughput Screening, Methods in Molecular Biology 486:14. New York, NY: Humana Press; 193-211. PMID: 19347625 (Book chapter) [pdf]

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, Sabatini DM, Golland P (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 article) [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 article) [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 article) [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 article) [pdf]