Visualization and analysis of single-cell rna-seq data by kernel-based similarity learning

Nature Methods

Volumn 14, Issue 4, 2017, Pages 414-416

  Wang, Bo ^a   Zhu, Junjie ^a   Pierson, Emma ^a   Ramazzotti, Daniele ^a,b   Batzoglou, Serafim ^a  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; B LYMPHOCYTE; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CELL POPULATION; GENE EXPRESSION; GENE STRUCTURE; GENETIC SELECTION; HUMAN; HUMAN CELL; MACROPHAGE; MEGAKARYOCYTE; NATURAL KILLER CELL; PERIPHERAL BLOOD MONONUCLEAR CELL; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; RNA SEQUENCE; SINGLE CELL ANALYSIS; SINGLE CELL INTERPRETATION VIA MULTIKERNEL LEARNING; SOFTWARE; ALGORITHM; BIOLOGY; CYTOLOGY; NEUTROPHIL; PHYSIOLOGY; PROCEDURES; SEQUENCE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; HUMANS; NEUTROPHILS; SEQUENCE ANALYSIS, RNA; SINGLE-CELL ANALYSIS; SOFTWARE;

EID: 85014528252     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nMeth.4207     Document Type: Article

References (25)

1. Shapiro, E., Biezuner, T. & Linnarsson, S. Nat. Rev. Genet. 14, 618-630 (2013).
2. Pollen, A. A. et al. Nat. Biotechnol. 32, 1053-1058 (2014).
3. Usoskin, D. et al. Nat. Neurosci. 18, 145-153 (2015).
4. Kolodziejczyk, A. A. et al. Cell Stem Cell 17, 471-485 (2015).
5. Pierson, E. & Yau, C. Genome Biol. 16, 241 (2015).
6. Macosko, E. Z. et al. Cell 161, 1202-1214 (2015).
7. Zheng, G. X. Y. et al. Nat. Commun. 8, 14049 (2017).
8. Bach, F. R., Lanckriet, G. R. G. & Jordan, M. I. In Proc. 21st Int. Conf. Mach. Learn (eds. Greiner, R. & Schuurmans, D.) 6 (ICML, 2004).
9. Gönen, M. & Alpaydin, E. J. Mach. Learn. Res. 12, 2211-2268 (2011).
10. Wang, B. et al. Nat. Methods 11, 333-337 (2014).
11. Buettner, F. et al. Nat. Biotechnol. 33, 155-160 (2015).
12. Jolliffe, I. Principal Component Analysis (Wiley Online Library, 2002).
13. Van der Maaten, L. & Hinton, G. J. Mach. Learn. Res. 9, 2579-2605 (2008).
14. Frey, B. J. & Dueck, D. Science 315, 972-976 (2007).
15. Ding, C. & He, X. In Proc. 21st Int. Conf. Mach. Learn (eds. Greiner, R. & Schuurmans, D.) 225-232 (ICML, 2004).
16. Paul, F. et al. Cell 163, 1663-1677 (2015).
17. Zeisel, A. et al. Title. Science 347, 1138-1142 (2015).
18. von Luxburg, U. Stat. Comput. 17, 395-416 (2007).
19. Wang, B. et al. Adv. Neural Inf. Process. Syst. 3297-3305 (2016).
20. Nesterov, Y., Nemirovskii, A. & Ye, Y. Interior-Point Polynomial Algorithms in Convex Programming (SIAM, 1994).
21. Parlett, B. N. The Symmetric Eigenvalue Problem (SIAM, 1980).
22. Yang, J. & Leskovec, J. In Proc. 10th IEEE Conf. Data Min. (eds. Webb, G. I. et al.) 599-608 (IEEE, 2010).
23. He, X., Cai, D. & Niyogi, P. Adv. Neural Inf. Process. Syst. 18, 507-514 (2005).
24. Kolde, R., Laur, S., Adler, P. & Vilo, J. Bioinformatics 28, 573-580 (2012).
25. Van Der Maaten, L. J. Mach. Learn. Res. 15, 3221-3245 (2014).