Understanding health and disease with multidimensional single-cell methods

Journal of Physics Condensed Matter

Volumn 26, Issue 7, 2014, Pages

  Candia, Julián ^a,b,c   Banavar, Jayanth R ^a   Losert, Wolfgang ^a  

^a Bldg 142   (United States)

^b UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^c Instituto de Fisica de Liquidos y Sistemas Biologicos   (Argentina)

Author keywords

cell imaging; complexity; flow cytometry; singlecell biophysics; supercells

Indexed keywords

BIOMEDICAL RESEARCH; CELL IMAGING; CHARACTERISTIC LENGTH; COMPLEXITY; INTERDISCIPLINARY FIELDS; MOLECULAR UNDERSTANDING; SINGLE CELLS; SUPER CELL;

CELLS; FLOW CYTOMETRY; HEALTH;

CYTOLOGY;

ANIMAL; DISEASES; FLOW CYTOMETRY; HEALTH; HUMAN; METHODOLOGY; MICROSCOPY; PHENOTYPE; REVIEW; SINGLE CELL ANALYSIS;

ANIMALS; DISEASE; FLOW CYTOMETRY; HEALTH; HUMANS; MICROSCOPY; PHENOTYPE; SINGLE-CELL ANALYSIS;

EID: 84893382471     PISSN: 09538984     EISSN: 1361648X     Source Type: Journal    
DOI: 10.1088/0953-8984/26/7/073102     Document Type: Review

References (108)

1. Beckman R A, Schemmann G S and Yeang C-H 2012 Proc. Natl Acad. Sci. USA 109 14586
2. De Souza N 2012 Nature Methods 9 645
3. Tang D G 2012 Cell Res. 22 457
4. Drukker M et al 2012 Nature Biotechnol. 30 531
5. Schmid J et al 2012 J. Biol. Chem. 287 41546
6. Chakrabarti L et al 2012 Front. Oncol. 2 82
7. Fujita M and Onami S 2012 PLoS ONE 7 e30224
8. Meacham C E and Morrison S J 2013 Nature 501 328
9. Burrell R A, McGranahan N, Bartek J and Swanton C 2013 Nature 501 338
10. Junttila M R and de Sauvage F J 2013 Nature 501 346
11. Bedard P L, Hansen A R, Ratain M J and Siu L L 2013 Nature 501 355
12. Perfetto S P, Chattopadhyay P K and Roederer M 2004 Nat. Rev. Immunol. 4 648
13. Sachs K et al 2005 Science 308 523 (Pubitemid 40570578)
14. Gonzalez V D et al 2008 J. Immunol. Methods 330 64
15. Cerignoli F et al 2012 J. Pharmacol. Toxicol. Methods S1056-8719 00262
16. Ornatsky O et al 2010 J. Immunol. Methods 361 1
17. Bendall S C et al 2011 Science 332 687
18. Benoist C and Hacohen N 2011 Science 332 677
19. Candia J 2013 APS March Meeting http://meetings.aps.org/link/BAPS.2013. MAR.U44.8
20. Anderson P W 1972 Science 177 393
21. Laughlin R B et al 2000 Proc. Nat Acad. Sci. USA 97 32 (Pubitemid 30055779)
22. Corté L et al 2008 Nature Phys. 4 420
23. Slotterback S et al 2012 Phys. Rev. E 85 021309
24. Klein M L and Shinoda W 2008 Science 321 798
25. Shinoda W, Devane R and Klein M L 2012 Curr. Opin. Struct. Biol. 22 175
26. Wilhelm J and Frey E 2003 Phys. Rev. Lett. 91 108103
27. Bausch A R and Kroy K 2006 Nat. Phys. 2 231 (Pubitemid 43553642)
28. Levchenko A 2013 APS March Meetinghttp://meetings.aps.org/link/BAPS.2013. MAR.UF44.8
29. Altschuler S J and Wu L F 2010 Cell 141 559
30. Candia J et al 2013 PLoS Comput. Biol. 9 e1003215
31. Driscoll M K et al 2012 Aging 4 119
32. Höfling F and Franosch T 2013 Rep. Prog. Phys. 76 046602
33. Bressloff P C and Newby J M 2013 Rev. Mod. Phys. 85 135
34. Jeon J-H, Tejedor V, Burov S, Barkai E, Selhuber-Unkel C, Berg-Sørensen K, Oddershede L and Metzler R 2011 Phys. Rev. Lett. 106 048103
35. Cherstvy A G, Chechkin A V and Metzler R 2013 New J. Phys. 15 083039
36. Cherstvy A G and Metzler R 2013 Phys. Chem. Chem. Phys. 15 20220
37. Cherstvy A G, Chechkin A. V and Metzler R 2013 (arXiv:1311.2810)
38. Baumgarth N and Roederer M 2000 J. Immunol. Methods 243 77
39. Lugli E, Roederer M and Cossarizza A 2010 Cytometry A 77 705
40. Proprietary software available at www.flowjo.com
41. Proprietary software available at www.denovosoftware.com
42. Hahne F et al 2009 BMC Bioinformatics 10 106
43. Naim I et al 2010 IEEE Acoustics Speech and Signal Processing 509
44. Qian Y et al 2010 Cytometry B 78 S69
45. Aghaeepour N et al 2012 Cytometry A 81A 1022
46. Qiu P 2012 PLoS ONE 7 e37038
47. Ge Y and Sealfon S C 2012 Bioinformatics 28 2052
48. Aghaeepour N et al 2012 Bioinformatics 28 1009
49. Zare H et al 2012 Am. J. Clin. Path. 137 75
50. Aghaeepour N et al 2013 Nature Methods 10 228
51. Qiu P et al 2011 Nature Biotechnol. 29 886
52. Rubner Y, Tomasi C and Guibas L 2000 Int. J. Comput. Vis. 40 99 (Pubitemid 32136368)
53. Kira K and Rendell L 1992 ML92: Proc. 9th Int. Workshop on Machine Learning (San Mateo, CA: Morgan Kaufmann) 249
54. Peng H 2008 Bioinformatics 24 1827
55. Shamir L, Eckley D M, Delaney J, Orlov N and Goldberg I G 2009 IEEE NIH Life Sci. Syst. Appl. Workshop 96-100
56. Rajaram S, Pavie B, Wu L F and Altschuler S J 2012 Nature Methods 9 635
57. Ljosa V and Carpenter A E 2010 PLoS Comp. Biol. 5 e1000603
58. Peng H, Ruan Z, Long F, Simpson J H and Myers E W 2010 Nature Biotechnol. 28 348
59. Otsu N 1979 IEEE Trans. Syst. Man Cybern. 9 62
60. Sahoo P K, Soltani S, Wong A K and Chen Y C 1988 Comput. Vis. Graph. Image Process. 41 233
61. Lindblad J and Bengtsson E 2001 Proc. 12th Scand. Conf. on Image Analysis 264-71
62. de Solórzano C O et al 1999 J. Microsc. 193 212 (Pubitemid 29145156)
63. Baatz M, Arini N, Schäpe A and Linssen B 2006 Cytometry A 69A 652 (Pubitemid 44060599)
64. Meyer F and Beucher S 1990 J. Vis. Commun. Image Represent. 1 21
65. Vincent L and Soille P 1991 IEEE Trans. Pattern Anal. Mach. Intell. 13 583 (Pubitemid 21675616)
66. Lindeberg T 1993 Int. J. Comput. Vis. 11 283
67. Roerdink B T M and Meijster A 2001 Fundam. Inform. 41 187
68. Cong G and Parvin B 2000 Pattern Recognit. 33 1383
69. Duan C, Bao S, Lu H and Lu J 2008 Med. Imaging Inform. 80-8
70. Vromen J and McCane B 2006 18th Proc. Ann. Colloq. Spatial Inform. Res. Ctr. 25-9
71. Driscoll M K et al 2012 PLoS Comput. Biol. 8 e1002392
72. Li G et al 2008 J. Microsc. 231 47 (Pubitemid 351951881)
73. Shamir L, Delaney J D, Orlov N, Eckley D M and Goldberg I G 2010 PLoS Comput. Biol. 6 e1000974
74. Boland M V, Markey M K and Murphy R F 1998 Cytometry 3 366
75. Hu M K 1962 IRE Trans. Inform. Theory IT-8 179-87
76. Orlov N et al 2008 Pattern Recognit. Lett. 29 1684
77. Guyon I, Gunn S, Nikravesh M and Zadeh L (ed) 2006 Feature Extraction, Foundations and Applications (New York: Springer)
78. Ding C and Peng H 2005 J. Bioinform. Comput. Biol. 3 185 (Pubitemid 40561382)
79. Holter N S et al 2000 Proc. Natl Acad. Sci. USA 97 8409 (Pubitemid 30639686)
80. Alter O, Brown P O and Botstein D 2000 Proc. Natl Acad. Sci. USA 97 10101
81. Holter N S, Maritan A, Cieplak M, Fedoroff N V and Banavar J R 2001 Proc. Natl Acad. Sci. USA 98 1693 (Pubitemid 32165560)
82. Raychaudhuri S, Stuart J M and Altman R B 2000 Pac. Symp. Biocomput. 455-66
83. Wall M E, Rechtsteiner A and Rocha L M 2003 Singular value decomposition and principal component analysis A Practical Approach to Microarray Data Analysis ed D P Berrar, W Dubitzky and M Granzow (Norwell, MA: Kluwer) 91-109
84. Tamayo P et al 1999 Proc. Natl Acad. Sci. USA 96 2907 (Pubitemid 29148817)
85. Kohonen T 2001 Self-Organizing Maps (Berlin: Springer)
86. Tenenbaum J B, de Silva V and Langford J C 2000 Science 290 2319 (Pubitemid 32041577)
87. Roweis S T and Lawrence K S 2000 Science 290 2323 (Pubitemid 32041578)
88. Borg I and Groenen P 1997 Modern Multidimensional Scaling: Theory and Applications (New York: Springer)
89. Treiser M D et al 2010 Proc. Natl Acad. Sci. USA 107 610
90. Markowetz F and Spang R 2005 Methods Inf. Med. 44 438
91. Becker N, Werft W, Toedt G, Lichter P and Benner A 2009 Bioinformatics 25 1711
92. Carpenter A E 2006 Genome Biol. 7 R100 (Pubitemid 46453508)
93. Abramoff M D R S and Magalhaes P J 2004 Biophotonics Int. 11 36
94. Boland M V and Murphy R F 2001 Bioinformatics 17 1213
95. Kreshuk A et al 2011 PLoS ONE 6 e24899
96. Zhou J, Lamichhane S, Sterne G, Ye B and Peng H 2013 BMC Bioinform. 14 291
97. Balaban N Q et al 2004 Science 305 1622 (Pubitemid 39296357)
98. Kussell E et al 2005 Genetics 169 1807 (Pubitemid 40695598)
99. McConnell M J et al 2013 Science 342 632
100. Gonzales J A and Chan C-C 2007 Int. Ophthalm. 27 241 (Pubitemid 47029020)
101. Christensen J L and Weissman I L 2001 Proc. Natl Acad. Sci. USA 98 14541 (Pubitemid 33121428)
102. Kiel M J, Yilmaz Ö H, Iwashita T, Yilmaz O H, Terhorst C and Morrison S J 2001 Cell 121 1109
103. Saitou M, Barton S C and Surani M A 2002 Nature 418 293 (Pubitemid 34790674)
104. Tang F et al 2009 Nature Methods 6 377
105. Cristianini N and Shawe-Taylor J 2000 An Introduction to Support Vector Machines and Other Kernel-based Learning Methods (Cambridge: Cambridge University Press)
106. Witten I H, Frank E and Hall M A 2011 Data Mining: Practical Machine Learning Tools and Techniques 3rd edn (Amsterdam: Morgan Kaufman)
107. Tarca A L, Carey V J, Chen X-W, Romero R and Draghici S 2007 PLoS Comp. Biol. 3 e116
108. Shao J and Tu D 1995 The Jackknife and Bootstrap (New York: Springer)