Quantification and clustering of phenotypic screening data using time-series analysis for chemotherapy of schistosomiasis

Series on Advances in Bioinformatics and Computational Biology

Volumn 13, Issue , 2012, Pages

  Lee, Hyokyeong ^a   Moody Davis, Asher ^a   Saha, Utsab ^a   Suzuki, Brian M ^b   Asarnow, Daniel ^a   Chen, Steven ^b   Arkin, Michelle ^b   Caffrey, Conor R ^b,c   Singh, Rahul ^a  

^a SAN FRANCISCO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHENOTYPIC SCREENING;

ANTISCHISTOSOMAL AGENT; MEVINOLIN; PRAZIQUANTEL;

ALGORITHM; ARTICLE; BIOLOGY; DRUG SCREENING; HUMAN; METHODOLOGY; PHENOTYPE; SCHISTOSOMIASIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DRUG EVALUATION, PRECLINICAL; HUMANS; LOVASTATIN; PHENOTYPE; PRAZIQUANTEL; SCHISTOSOMIASIS; SCHISTOSOMICIDES;

EID: 84862265241     PISSN: 17516404     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1186/1471-2164-13-S1-S4     Document Type: Conference Paper

References (47)

1. Hotez PJ, Fenwick A, Savioli L, Molyneux DH: Rescuing the bottom billion through control of neglected tropical diseases. Lancet 2009, 373:1570-1575.
2. Hotez PJ, Pecoul B: Manifesto for advancing the control and elimination of neglected tropical diseases. PLoS Negl Trop Dis 2010, 4(5):e718.
3. Keiser J, Utzinger J: Advances in the discovery and development of trematocidal drugs. Expert Opin Drug Discov 2007, 2(Suppl 1):S9-S23.
4. King CH, Dangerfield-Cha M: The unacknowledged impact of chronic schistosomiasis. Chronic Illn 2008, 4:65-79.
5. Utzinger J, Keiser J: Schistosomiasis and soil-transmitted helminthiasis: common drugs for treatment and control. Expert Opin Pharmacother 2004, 5:263-285.
6. Caffrey CR: Chemotherapy of schistosomiasis: present and future. Curr Opin Chem Biol 2007, 11:433-439.
7. Doenhoff MJ, Pica-Mattoccia L: Praziquantel for the treatment of schistosomiasis: its use for control in areas with endemic disease and prospects for drug resistance. Expert Rev Anti Infect Ther 2006, 4:199-210.
8. Doenhoff MJ, Cioli D, Utzinger J: Praziquantel: mechanisms of action, resistance and new derivatives for schistosomiasis. Curr Opin Infect Dis 2008, 21:659-667.
9. Fallon PG, Doenhoff MJ: Drug-resistant schistosomiasis: resistance to praziquantel and oxamniquine induced in Schistosoma mansoni in mice is drug specific. Am J Trop Med Hyg 1994, 51:83-88.
10. Ismail M, Botros S, Metwally A, William S, Farghally A, Tao LF, Day TA, Bennett JL: Resistance to praziquantel: direct evidence from Schistosoma mansoniisolated from Egyptian villagers. Am J Trop Med Hyg 1999, 60:932-935.
11. Melman SD, Steinauer ML, Cunningham C, Kubatko LS, Mwangi IN, Wynn NB, Mutuku MW, Karanja DM, Colley DG, Black CL, Secor WE, Mkoji GM, Loker ES: Reduced susceptibility to praziquantel among naturally occurring Kenyan isolates of Schistosoma mansoni. PLoS Negl Trop Dis 2009, 3:e504.
12. Silva IM, Thiengo R, Conceicao MJ, Rey L, Lenzi HL, Pereira Filho E, Ribeiro PC: Therapeutic failure of praziquantel in the treatment of Schistosoma haematobium infection in Brazilians returning from Africa. Mem Inst Oswaldo Cruz 2005, 100:445-449.
13. William S, Botros S, Ismail M, Farghally A, Day TA, Bennett JL: Praziquantelinduced tegumental damage in vitro is diminished in schistosomes derived from praziquantel-resistant infections. Parasitology 2001, 122(Pt 1):63-66.
14. Botros S, Pica-Mattoccia L, William S, El-Lakkani N, Cioli D: Effect of praziquantel on the immature stages of Schistosoma haematobium. Int J Parasitol 2005, 35:1453-1457.
15. Sabah AA, Fletcher C, Webbe G, Doenhoff MJ: Schistosoma mansoni: chemotherapy of infections of different ages. Exp Parasitol 1986, 61:294-303.
16. Xiao SH, Yue WJ, Yang YQ, You JQ: Susceptibility of Schistosoma japonicum to different developmental stages to praziquantel. Chin Med J (Engl) 1987, 100:759-768.
17. Cioli D, Pica-Mattoccia L: Praziquantel. Parasitol Res 2003, 90(Suppl 1):S3-9.
18. Nwaka S, Hudson A: Innovative lead discovery strategies for tropical diseases. Nat Rev Drug Discov 2006, 5:941-955.
19. Simeonov A, Jadhav A, Sayed AA, Wang Y, Nelson ME, Thomas CJ, Inglese J, Williams DL, Austin CP: Quantitative high-throughput screen identifies inhibitors of the Schistosoma mansoni redox cascade. PLoS Negl Trop Dis 2008, 2:e127.
20. Abdulla MH, Ruelas DS, Wolff B, Snedecor J, Lim KC, Xu F, Renslo AR, Williams J, McKerrow JH, Caffrey CR: Drug discovery for schistosomiasis: hit and lead compounds identified in a library of known drugs by medium-throughput phenotypic screening. PLoS Negl Trop Dis 2009, 3: e478.
21. Feterer RH, Pax RA, Bennett JL: Praziquantel, potassium, and 2,4-dinitrophenol: analysis of their action on the musculature of Schistosoma mansoni. Eur J Pharmacol 1980, 64:31-38.
22. Pax R, Bennett JL, Fetterer R: A benzodiazepine derivative and praziquantel: effects on musculature of Schistosoma mansoni and Schistosoma japonicum. Naunyn Schmiedebergs Arch Pharmacol 1978, 304(3):309-315.
23. Utzinger J, Xiao S, Tanner M, Keiser J: Artemisinins for schistosomiasis and beyond. Curr Opin Investig Drugs 2007, 8(2):105-116.
24. Yousif F, Hifnawy MS, Soliman G, Boulos L, Labib T, Mahmoud S, Ramzy F, Yousif M, Hassan I, Mahmoud K, El-Hallouty SM, El-Gendy M, Gohar L, El-Manawaty M, Fayyad W, El-Menshawi BS: Large-scale in vitro screening of Egyptian native and cultivated plants for schistosomicidal activity. Pharm Biol 2007, 45:501-510.
25. Michael S, Auld D, Klumpp C, Jadhav A, Zheng W, Thorne N, Austin CP, Inglese J, Simeonov A: A robotic platform for quantitative high throughput screening. Assay Drug Dev Technol 2008, 6:637-657.
26. Baek JH, Cosman P, Feng Z, Silver J, Schafer WR: Using machine vision to analyze and classify Caenorhabditis elegans behavioral phenotypes quantitatively. J Neurosci Methods 2002, 118:9-21.
27. Cronin CJ, Mendel JE, Mukhtar S, Kim YM, Stirbl RC, Bruck J, Sternberg PW: An automated system for measuring parameters of nematode sinusoidal movement. BMC Genet 2005, 6:5.
28. Huang K, P Cosman, WR Schafer: Using articulated models for tracking multiple C. elegans in physical contact. JSP 2009, 55:113-126.
29. Roussel N, Morton CA, Finger FP, Roysam B: A computational model for C. elegans locomotory behavior: application to multiworm tracking. IEEE Trans Biomed Eng 2007, 54:1786-1797.
30. Stephens GJ, Johnson-Kerner B, Bialek W, Ryu WS: Dimensionality and dynamics in the behavior of C. elegans. PLoS Comput Biol 2008, 4: e1000028.
31. Jones TR, Carpenter AE, Lamprecht MR, et al: Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. Proc Natl Acad Sci U S A 2009, 106(6):1826-1831.
32. Perlman ZE, Slack MD, Feng Y, et al: Multidimensional drug profiling by automated microscopy. Science 2004, 306:1194-1198.
33. Tanaka M, Bateman R, Rauh D, et al: An unbiased cell morphology-based screen for new biologically active small molecules. PLoS Biol 2005, 3:e128.
34. Singh R, Pittas M, Heskia I, Xu F, McKerrow JH, Caffrey C: Automated image-based phenotypic screening for high-throughput drug discovery. IEEE Symp Computer-Based Medical Systems (CBMS) 2009, 1-8.
35. Mennillo A, Moody-Davis L, Singh R: Region-based segmentation of parasites for high-throughput screening. Int'l Symposium on Visual Computing, LNCS 2011, 6938:44-54.
36. Srinivasa G, Fickus MC, Guo Y, Linstedt AD, Kovacevic J: Active mask segmentation of fluorescence microscope images. IEEE Trans Image Process 2009, 18(8):1817-1829.
37. Canny J: A computational approach to edge detection. IEEE Trans Pattern Anal Mach Intell 1986, 8(6):679-698.
38. Comaniciu D, Meer P: Mean shift: a robust approach toward feature space analysis. IEEE Trans Pattern Anal Mach Intell 2002, 24(5):603-619.
39. Deng Y, Manjunath BS: Unsupervised segmentation of color-texture regions in images and video. IEEE Trans Pattern Anal Mach Intell 2001, 23(8):800-810.
40. Masoud O, Papanikolopoulos N: A novel method for tracking and counting pedestrians in real-time using a single camera. IEEE Trans Vehicular Technology 2001, 50(5):1267-1278.
41. Lin J, Keogh E, Lonardi S, Chiu B: A symbolic representation of time series, with implications for streaming algorithms. ACM SIGMOD Workshop on Research Issues in Data Mining and Knowledge Discovery 2003.
42. Ray BK, Ray KS: Determination of optimal polygon from digital curve using L1 norm. Patt Recog 1993, 26(4):505-509.
43. Levenshtein VI: Binary codes capable of correcting deletions, insertions, and reversals. Soviet Physics Doklady 1996, 10:707-710.
44. Ester M, Kriegel H-P, Sander J, Xu X: A density-based algorithm for discovering clusters in large spatial databases with noise. Int'l Conf Knowledge Discovery and Data Mining 1996, 44-50.
45. Indyk P, Koudas N, Muthukrishnan S: Indentifying representative trends in massive time series data sets using sketches. Int'l Conf Very Large Data Bases 2000, 363-372.
46. Breunig MM, Kriegel H-P, Ng R, Sander J: LOF: identifying density-based local outliers. ACM SIGMOD Int'l Conf Management of Data 2000, 93-104.
47. MATLAB version 7.8.0. Natick, Massachusetts: The MathWorks Inc; 2009.