Chemical address tags of fluorescent bioimaging probes

Cytometry Part A

Volumn 77, Issue 5, 2010, Pages 429-438

  Shedden, Kerby ^a   Rosania, Gus R ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Bioimaging; Cheminformatics; Combinatorial chemistry; Fluorescence; High content screening; Image cytometry; Machine vision

Indexed keywords

ALDEHYDE; FLUORESCENT DYE; PYRIDINIUM DERIVATIVE; QUINOLINE DERIVATIVE;

ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; ISOMERISM; METHODOLOGY; MOLECULAR IMAGING; SPECTROFLUOROMETRY;

ALDEHYDES; CLUSTER ANALYSIS; FLUORESCENT DYES; ISOMERISM; MOLECULAR IMAGING; PYRIDINIUM COMPOUNDS; QUINOLINIUM COMPOUNDS; SPECTROMETRY, FLUORESCENCE;

EID: 77951157190     PISSN: 15524922     EISSN: 15524930     Source Type: Journal    
DOI: 10.1002/cyto.a.20847     Document Type: Article

References (32)

1. Loo LH, Wu LF, Altschuler SJ. Image-based multivariate profiling of drug responses from single cells. Nat Methods 2007;4:445-453.
2. Perlman ZE, Slack MD, Feng Y, Mitchison TJ, Wu LF, Altschuler SJ. Multidimensional drug profiling by automated microscopy. Science 2004;306:1194-1198.
3. Slack MD, Martinez ED, Wu LF, Altschuler SJ. Characterizing heterogeneous cellular responses to perturbations. Proc Natl Acad Sci USA 2008;105:19306-19311.
4. Wagner BK, Carrinski HA, Ahn YH, Kim YK, Gilbert TJ, Fomina DA, Schreiber SL, Chang YT, Clemons PA. Small-molecule fluorophores to detect cell-state switching in the context of high-throughput screening. J Am Chem Soc 2008;130:4208-4209.
5. Lee JW, Jung M, Rosania GR, Chang YT. Development of novel cell-permeable DNA sensitive dyes using combinatorial synthesis and cell-based screening. Chem Com-mun (Camb) 2003(15):1852-1853.
6. Li Q, Kim YK, Namm J, Kulkarni A, Rosania G, Ahn YH, Chang YT. RNA-selective, live cell imaging probes for studying nuclear structure and function. Chem Biol 13: 615-623.
7. Abraham VC, Taylor DL, Haskins JR. High content screening applied to large-scale cellbiology. Trends Biotechnol2004;22:15-22.
8. Cervantes S, Prudhomme J, Carter D, Gopi KG, Li Q, Chang YT, Le Roch KG. High-content live cell imaging with RNA probes: Advancements in high-throughput anti-malarial drug discovery. BMC Cell Biol 2009;10:45.
9. Giuliano KA. Optimizing the integration of immunoreagents and fluorescent probes for multiplexed high content screening assays. Methods Mol Biol 2007;356: 189-193.
10. Mitchison TJ. Small-molecule screening and profiling by using automated microscopy. Chembiochem 2005;6:33-39.
11. Giuliano KA, Post PL, Hahn KM, Taylor DL. Fluorescent protein biosensors: measurement of molecular dynamics in living cells. Annu Rev Biophys Biomol Struct 1995;24:405-434.
12. Giuliano KA, Taylor DL. Fluorescent-protein biosensors: New tools for drug discovery. Trends Biotechnol 1998;16:135-140.
13. Giuliano KA, Taylor DL, Waggoner AS. Reagents to measure and manipulate cell functions. Methods Mol Biol2007;356:141-163.
14. Taylor DL, De Biasio R, La Rocca G, Pane D, Post P, Kolega J, Giuliano K, Burton K, Gough B, Dow A, Yu J, Wagonner AS, Farkas DL. Potential of machine-vision light microscopy in toxicologic pathology. Toxicol Pathol 1994;22:145-159.
15. Ljosa V, Carpenter AE. High-throughput screens for fluorescent dye discovery. Trends Biotechnol 2008;26:527-530.
16. Chen VY, Khersonsky SM, Shedden K, Chang YT, Rosania GR. System dynamics of subcellular transport. Mol Pharm 2004;1:414-425.
17. Rosania GR, Lee JW, Ding L, Yoon HS, Chang YT. Combinatorial approach to organ-elle-targeted fluorescent library based on the styryl scaffold. J Am Chem Soc 2003;125:1130-1131.
18. Shedden K, Li Q, Liu F, Chang YT, Rosania GR. Machine vision-assisted analysis of structure-localization relationships in a combinatorial library of prospective bioima-ging probes. Cytometry A 2009;75A:482-493.
19. Shedden K, Brumer J, Chang YT, Rosania GR. Chemoinformatic analysis of a super-targeted combinatorial library of styryl molecules. J Chem Inf Comput Sci 2003;43:2068-2080.
20. Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Gollan P. Sabatini DM. Cell Profiler: Image analysis software for identifying and quantifying cell phenotypes. Genome Biol 2006;7:R100.
21. 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. Proc Natl Acad Sci USA2009;106:1826-1831.
22. Boland MV, Murphy RF. A neural network classifier capable of recognizing the pat-terns of all major subcellular structures in fluorescence microscope images of He La cells. Bioinformatics 2001;17:1213-1223.
23. Chen X, Murphy RF. Objective clustering of proteins based on subcellular location patterns. J Biomed Biotechnol 2005;2005:87-95.
24. Hu Y, Murphy RF. Automated interpretation of subcellular patterns from immuno-fluorescence microscopy. J Immunol Methods 2004;290:93-105
25. Huang K, Murphy RF. From quantitative microscopy to automated image understanding. J Biomed Opt2004;9:893-912.
26. Huang K, Murphy RF. Boosting accuracy of automated classification of fluorescence microscope images for location proteomics. BMC Bioinformatics 2004;5:78.
27. Murphy RF. Cytomics and location proteomics: Automated interpretation of subcel-lular patterns in fluorescence microscope images. Cytometry A 2005;67A:1-3.
28. Murphy RF. Location proteomics: A systems approach to subcellular location. Biochem Soc Trans 2005;33 (Part 3):535-538.
29. Hansch C. The QSAR paradigm in the design of less toxic molecules. Drug Metab Rev1984;15:1279-1294.
30. Hansch C, Leo A. Exploring QSAR: Fundamentals and Applications in Chemistry and Biology. Washington DC: American Chemical Society; 1995.
31. Lee AC, Shedden K, Rosania GR, Crippen GM. Data mining the NCI60 to predict generalized cytotoxicity. J Chem Inf Model2008;48:1379-1388.
32. Shedden K, Rosania GR. Exploratory chemoinformatic analysis of cell type-selective anticancer drug targeting. Mol Pharm 2004;1:267-280.