Misty Mountain clustering: Application to fast unsupervised flow cytometry gating

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Sugár, István P ^a   Sealfon, Stuart C ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFFINITY PROPAGATION; AUTOMATED FLOW CYTOMETRY; COMPUTATIONAL BIOLOGY; MODEL BASED APPROACH; MODEL-BASED CLUSTERING; MULTI-DIMENSIONAL DATASETS; MULTIDIMENSIONAL CLUSTERING; OPTIMAL CLUSTER NUMBER;

AUTOMATION; BIOINFORMATICS; FLOW CYTOMETRY; GRAPHIC METHODS; HEURISTIC METHODS; LANDFORMS;

CLUSTERING ALGORITHMS;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPUTER PROGRAM; FACTUAL DATABASE; FLOW CYTOMETRY; METHODOLOGY;

ALGORITHMS; CLUSTER ANALYSIS; DATABASES, FACTUAL; FLOW CYTOMETRY; SOFTWARE;

EID: 77957550165     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-502     Document Type: Article

References (46)

1. MacQueen JB. Some methods for classification and analysis of multivariate observations. Proceedings of fifth Berkeley Symposium on Mathematical Statistics and Probability: 1967, Berkeley 1967, 281-297. University of California Press.
2. Cornuejols G, Fisher ML, Nemhauser GL. Location of bank accounts to optimize float - Analytic study of exact and approximate algorithms. Management Science 1977, 23(8):789-810.
3. Rousseeuw PJ, Kaufman L, Trauwaert E. Fuzzy clustering using scatter matrices. Computational Statistics & Data Analysis 1996, 23(1):135-151.
4. Frey BJ, Dueck D. Clustering by passing messages between data points. Science 2007, 315(5814):972-976. 10.1126/science.1136800, 17218491.
5. Donath WE, Hoffman AJ. Lower bounds for partitioning of graphs. Ibm Journal of Research and Development 1973, 17(5):420-425.
6. Fiedler M. Algebraic connectivity of graphs. Czechoslovak Mathematical Journal 1973, 23(2):298-305.
7. Heyer LJ, Kruglyak S, Yooseph S. Exploring expression data: Identification and analysis of coexpressed genes. Genome Research 1999, 9(11):1106-1115. 10.1101/gr.9.11.1106, 310826, 10568750.
8. Hartigan JA. Clustering Algorithms. 1975, New York, Wiley & Sons.
9. Fraley C, Raftery AE. How many clusters? Which clustering method? Answers via model-based cluster analysis. Computer Journal 1998, 41(8):578-588.
10. McLachlan GJ, Basford KE. Mixture Models: Inference and Applications to Clustering. 1988, New York: Marcel Dekker.
11. Dempster AP, Laird NM, Rubin DB. Maximum likelihood from incomplete data via tha EM algorithm. Journal of the Royal Statistical Society B 1977, 39:1-22.
12. Celeux G, Govaert G. Gaussian parsimonious clustering models. Pattern Recognition 1995, 28:781-793.
13. Pyne S, Hu X, Wang K, Rossin E, Lin T-I, Mailer LM, Baecher-Allan C, McLachlan GJ, Tamayo P, Hafler DA, et al. Automated high dimensional flow cytometric data analysis. Proc Natl Acad Sci USA 2009, 106:8519-8524. 10.1073/pnas.0903028106, 2682540, 19443687.
14. Schwarz G. Estimating the dimension of a model. Annals of Statistics 1978, 6:461-454.
15. Lo K, Brinkman RR, Gottardo R. Automated gating of flow cytometry data via robust model-based clustering. Cytometry 2008, 73:321-332. 10.1002/cyto.a.20531, 18307272.
16. Lizard G. Flow Cytometry analyses and bioinformatics: Interest in new softwares to optimize novel technologies and to favor the emergence of innovative concepts in cell research. Cytometry Part A 2007, 71A(9):646-647.
17. Murphy RF. Automated identification of subpopulations in flow cytometric list mode data using cluster analysis. Cytometry Part A 1985, 6:302-309.
18. Bakker Schut TC, Grooth BDG, Greve J. Cluster analysis of flow cytometric list mode data on a personal computer. Cytometry Part A 1993, 14:649-659.
19. Demers S, Kim J, Legendre P, Legendre L. Analyzing multivariate flow cytometric data in aquatic sciences. Cytometry 1992, 13(3):291-298. 10.1002/cyto.990130311, 1576894.
20. Wilkins MF, Hardy SA, Boddy L, Morris CW. Comparison of five clustering algorithms to classify phytoplankton from flow cytometry data. Cytometry 2001, 44(3):210-217. 10.1002/1097-0320(20010701)44:3<210::AID-CYTO1113>3.0.CO;2-Y, 11429771.
21. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. PNAS 1998, 95:14863-14868. 10.1073/pnas.95.25.14863, 24541, 9843981.
22. Breiman L, Friedman JH, Olshen RA, Stone CJ. Classification and Regression Trees. 1984, Monterey, CA: Wadsworth & Brooks.
23. Boddy L, Morris CW. Artificial neural networks for pattern recognition. Machine Learning Methods for Ecological Applications 1999, 37-87. Boston: Kluwer, Fielding AH.
24. Scholkopf B, Smola AJ. Learning with Kernels: Support Vector Machines, Regularization, Optimization and Beyond. 2002, Cambridge: MIT Press.
25. Burges CJC. A Tutorial on Support Vector Machines for Pattern Recognition. 1998, Boston: Kluwer.
26. Beckman RJ, Salzman GC, Stewart CC. Classification and regression trees for bone-marrow immunophenotyping. Cytometry 1995, 20(3):210-217. 10.1002/cyto.990200304, 7587706.
27. Boddy L, Morris CW, Wilkins MF, Al-Haddad L, Tarran GA, Jonker RR, Burkill PH. Identification of 72 phytoplankton species by radial basis function neural network analysis of flow cytometric data. Marine Ecology-Progress Series 2000, 195:47-59.
28. Kothari R, Cualing H, Balachander T. Neural network analysis of flow cytometry immunophenotype data. Ieee Transactions on Biomedical Engineering 1996, 43(8):803-810. 10.1109/10.508551, 9216152.
29. Morris CW, Autret A, Boddy L. Support vector machines for identifying organisms - a comparison with strongly partitioned radial basis function networks. Ecological Modelling: 2001 2001, 57-67.
30. Boyell RL, Ruston H. Hybrid techniques for real-time radar simulation. The Fall Joint Computer Conference 1963, Las Vegas, USA.
31. Jang W. Nonparametric density estimation and clustering in astronomical sky survey. Comput Stat Data Anal 2006, 50:760-774.
32. Jang W, Hendry M. Cluster analysis of massive datasets in astronomy. Statistics and Computing 2007, 17:253-262.
33. Cuevas A, Febrero M, Fraiman R. Estimating the number of clusters. Can J Stat 2000, 28:367-382.
34. Cuevas A, Febrero M, Fraiman R. Cluster analysis: a further approach based on density estimation. Comput Stat Data Anal 2001, 36:441-459.
35. Knuth KH. Optimal data-based binning for histograms. arXiv:physics/0605197v1 [physicsdata-an] 2006,
36. Hoshen J, Kopelman R. Percolation and cluster distribution. 1. Cluster multiple labeling technique and critical concentration algorithm. Physical Review B 1976, 14(8):3438-3445.
37. Stauffer D, Aharony A. Introduction to Percolation Theory. 1994, London: Taylor and Francis, 2.
38. Tseng GC, Wong WH. Tight clustering: A resampling-based approach for identifying stable and tight patterns in data. Biometrics 2005, 61(1):10-16. 10.1111/j.0006-341X.2005.031032.x, 15737073.
39. Kirkpatrick S, Gelatt CD, Vecchi MP. Optimization by simulated annealing. Science 1983, 220(4598):671-680. 10.1126/science.220.4598.671, 17813860.
40. Krutzik PO, Nolan GP. Fluorescent cell barcoding in flow cytometery allows high-throughput drug screening and signaling profiling. Nature Methods 2006, 3:361-368. 10.1038/nmeth872, 16628206.
41. Brinkman RR, Gasparetto M, Lee SJJ, Ribickas AJ, Perkins J, Janssen W, Smiley R, Smith C. High-content flow cytometry and temporal data analysis for defining a cellular signature graft-versus-host disease. Biology of Blood and Marrow Transplantation 2007, 13(6):691-700. 10.1016/j.bbmt.2007.02.002, 2000975, 17531779.
42. Lo K, Hahne F, Brinkman RR, Gottardo R. flowClust: a Bioconductor package for automated gating of flow cytometry data. Bmc Bioinformatics 2009, 10. 10.1186/1471-2105-10-145, 2701419, 19442304.
43. Hotelling H. Analysis of a complex of statistical variable into principal components. J Educ Psych 1933, 24:417-441.
44. Wand MP. Data-based choice of histogram bin width. The American Statistician 1997, 51:59-64.
45. Feller W. An Introduction to Probability Theory and Its Applications. 1968, 1. New York: John Wiley and Sons.
46. Box GEP, Muller ME. A note on the generation of random normal deviates. The Annals of Mathematical Statistics 1958, 29:610-611.