-
1
-
-
1542290446
-
Expression profiling-best practices for data generation and interpretation in clinical trials
-
Hoffman, E. P. et al. Expression profiling-best practices for data generation and interpretation in clinical trials. Nat. Rev. Genet. 5, 229-237 (2004).
-
(2004)
Nat. Rev. Genet
, vol.5
, pp. 229-237
-
-
Hoffman, E.P.1
-
2
-
-
9144264883
-
In silico dissection of cell-type-associated patterns of gene expression in prostate cancer
-
Stuart, R. O. et al. In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc. Natl. Acad. Sci. 101, 615-620 (2004).
-
(2004)
Proc. Natl. Acad. Sci
, vol.101
, pp. 615-620
-
-
Stuart, R.O.1
-
3
-
-
84884368877
-
Influence of tumour micro-environment heterogeneity on therapeutic response
-
Junttila, M. R., de Sauvage, F. J. Influence of tumour micro-environment heterogeneity on therapeutic response. Nature 501, 346-354, doi: 10.1038/nature12626 (2013).
-
(2013)
Nature
, vol.501
, pp. 346-354
-
-
Junttila, M.R.1
De Sauvage, F.J.2
-
4
-
-
84873084388
-
Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer
-
doi: science.1227670
-
Kreso, A. et al. Variable clonal repopulation dynamics influence chemotherapy response in colorectal cancer. Science 339, 543-548, doi: science.1227670 (2013).
-
(2013)
Science
, vol.339
, pp. 543-548
-
-
Kreso, A.1
-
5
-
-
77951634577
-
Cell type-specific gene expression differences in complex tissues
-
Shen-Orr, S. S. et al. Cell type-specific gene expression differences in complex tissues. Nat Methods 7, 287-289, doi: 10.1038/nmeth.1439 (2010).
-
(2010)
Nat Methods
, vol.7
, pp. 287-289
-
-
Shen-Orr, S.S.1
-
6
-
-
80255135608
-
Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain
-
doi: nmeth. 1710
-
Kuhn, A., Thu, D., Waldvogel, H. J., Faull, R. L., Luthi-Carter, R. Population-specific expression analysis (PSEA) reveals molecular changes in diseased brain. Nat Methods 8, 945-947, doi: nmeth.1710 (2011).
-
(2011)
Nat Methods
, vol.8
, pp. 945-947
-
-
Kuhn, A.1
Thu, D.2
Waldvogel, H.J.3
Faull, R.L.4
Luthi-Carter, R.5
-
7
-
-
79951995151
-
PUGSVM: A caBIG analytical tool for multiclass gene selection and predictive classification
-
Yu, G. et al. PUGSVM: a caBIG analytical tool for multiclass gene selection and predictive classification. Bioinformatics 27, 736-738, doi: 10.1093/bioinformatics/btq721 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 736-738
-
-
Yu, G.1
-
8
-
-
84882455458
-
Single-cell sequencing-based technologies will revolutionize whole-organism science
-
Shapiro, E., Biezuner, T., Linnarsson, S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet 14, 618-630, doi: 10.1038/nrg3542 (2013).
-
(2013)
Nat Rev Genet
, vol.14
, pp. 618-630
-
-
Shapiro, E.1
Biezuner, T.2
Linnarsson, S.3
-
9
-
-
84868034841
-
Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling
-
doi: 4/157/157ra143
-
Yuan, Y. et al. Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling. Sci Transl Med 4, 157ra143, doi: 4/157/157ra143 (2012).
-
(2012)
Sci Transl Med
, vol.4
, pp. 157-163
-
-
Yuan, Y.1
-
10
-
-
0042838315
-
Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations
-
Lu, P., Nakorchevskiy, A., Marcotte, E. M. Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci USA 100, 10370-10375, doi: 10.1073/pnas.1832361100 (2003).
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 10370-10375
-
-
Lu, P.1
Nakorchevskiy, A.2
Marcotte, E.M.3
-
11
-
-
67749112023
-
Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus
-
Abbas, A. R., Wolslegel, K., Seshasayee, D., Modrusan, Z., Clark, H. F. Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PloS one 4, e6098, doi: 10.1371/journal.pone.0006098 (2009).
-
(2009)
PloS One
, vol.4
, pp. e6098
-
-
Abbas, A.R.1
Wolslegel, K.2
Seshasayee, D.3
Modrusan, Z.4
Clark, H.F.5
-
12
-
-
84883432733
-
A self-directed method for cell-type identification and separation of gene expression microarrays
-
Zuckerman, N. S., Noam, Y., Goldsmith, A. J., Lee, P. P. A self-directed method for cell-type identification and separation of gene expression microarrays. PLoS Comput Biol 9, e1003189, doi: 10.1371/journal.pcbi.1003189 (2013).
-
(2013)
PLoS Comput Biol
, vol.9
, pp. e1003189
-
-
Zuckerman, N.S.1
Noam, Y.2
Goldsmith, A.J.3
Lee, P.P.4
-
13
-
-
84860370062
-
Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study
-
Gaujoux, R., Seoighe, C. Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: a case study. Infect Genet Evol 12, 913-921 (2012).
-
(2012)
Infect Genet Evol
, vol.12
, pp. 913-921
-
-
Gaujoux, R.1
Seoighe, C.2
-
14
-
-
76949086352
-
Applying unmixing to gene expression data for tumor phylogeny inference
-
Schwartz, R., Shackney, S. E. Applying unmixing to gene expression data for tumor phylogeny inference. BMC Bioinformatics 11, 42, doi: 10.1186/1471-2105-11-42 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 42
-
-
Schwartz, R.1
Shackney, S.E.2
-
15
-
-
84923850454
-
Inferring biological tasks using Pareto analysis of high-dimensional data
-
Hart, Y. et al. Inferring biological tasks using Pareto analysis of high-dimensional data. Nat Methods 12, 233-235, doi: 10.1038/nmeth.3254 (2015).
-
(2015)
Nat Methods
, vol.12
, pp. 233-235
-
-
Hart, Y.1
-
16
-
-
84863012015
-
Gene expression deconvolution in linear space
-
author reply 9
-
Zhong, Y., Liu, Z. Gene expression deconvolution in linear space. Nat Methods 9, 8-9; author reply 9, doi: 10.1038/nmeth.1830 (2012).
-
(2012)
Nat Methods
, vol.9
, pp. 8-9
-
-
Zhong, Y.1
Liu, Z.2
-
17
-
-
0021892197
-
Detection of signals by information theoretic criteria
-
Wax, M., Kailath, T. Detection of signals by information theoretic criteria. IEEE Trans Acoustics, Speech, and Signal Processing 33, 387-392 (1985).
-
(1985)
IEEE Trans Acoustics, Speech, and Signal Processing
, vol.33
, pp. 387-392
-
-
Wax, M.1
Kailath, T.2
-
18
-
-
0031742022
-
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization
-
Spellman, P. T. et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-3297 (1998).
-
(1998)
Mol Biol Cell
, vol.9
, pp. 3273-3297
-
-
Spellman, P.T.1
-
19
-
-
61449172037
-
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
-
Huang da, W., Sherman, B. T., Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4, 44-57, doi: 10.1038/nprot.2008.211 (2009).
-
(2009)
Nat Protoc
, vol.4
, pp. 44-57
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
20
-
-
84868651389
-
Cell population-specific expression analysis of human cerebellum
-
Kuhn, A. et al. Cell population-specific expression analysis of human cerebellum. BMC Genomics 13, 610, doi: 10.1186/1471-2164-13-610 (2012).
-
(2012)
BMC Genomics
, vol.13
, pp. 610
-
-
Kuhn, A.1
-
21
-
-
84955617987
-
Prognostic imaging biomarkers in glioblastoma: Development and independent validation on the basis of multiregion and quantitative analysis of mr images
-
Cui, Y. et al. Prognostic Imaging Biomarkers in Glioblastoma: Development and Independent Validation on the Basis of Multiregion and Quantitative Analysis of MR Images. Radiology, 150358, doi: 10.1148/radiol.2015150358 (2015).
-
(2015)
Radiology
, pp. 150358
-
-
Cui, Y.1
-
22
-
-
77949836282
-
Nonnegative least-correlated component analysis for separation of dependent sources by volume maximization
-
Wang, F. Y., Chi, C. Y., Chan, T. H., Wang, Y. Nonnegative least-correlated component analysis for separation of dependent sources by volume maximization. IEEE Trans Pattern Anal Mach Intell 32, 875-888, doi: 10.1109/TPAMI.2009.72 (2010).
-
(2010)
IEEE Trans Pattern Anal Mach Intell
, vol.32
, pp. 875-888
-
-
Wang, F.Y.1
Chi, C.Y.2
Chan, T.H.3
Wang, Y.4
-
23
-
-
84885670924
-
The CAM software for nonnegative blind source separation in R-Java
-
Wang, N. et al. The CAM software for nonnegative blind source separation in R-Java. J. Machine Learning Research 14, 2899-2903 (2013).
-
(2013)
J. Machine Learning Research
, vol.14
, pp. 2899-2903
-
-
Wang, N.1
-
24
-
-
80052768992
-
CAM-CM: A signal deconvolution tool for in vivo dynamic contrast-enhanced imaging of complex tissues
-
doi: btr436
-
Chen, L. et al. CAM-CM: a signal deconvolution tool for in vivo dynamic contrast-enhanced imaging of complex tissues. Bioinformatics 27, 2607-2609, doi: btr436 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 2607-2609
-
-
Chen, L.1
-
25
-
-
54749083549
-
A convex analysis framework for blind separation of Non-Negative sources
-
Chan, T.-H., Ma, W.-K., Chi, C.-Y., Wang, Y. A Convex Analysis Framework for Blind Separation of Non-Negative Sources. IEEE Trans Signal Processing 56, 5120-5134 (2008).
-
(2008)
IEEE Trans Signal Processing
, vol.56
, pp. 5120-5134
-
-
Chan, T.-H.1
Ma, W.-K.2
Chi, C.-Y.3
Wang, Y.4
-
26
-
-
82455189646
-
Tissue-specific compartmental analysis for dynamic contrast-enhanced MR imaging of complex tumors
-
Chen, L. et al. Tissue-specific compartmental analysis for dynamic contrast-enhanced MR imaging of complex tumors. IEEE Trans Med Imaging 30, 2044-2058, doi: 10.1109/TMI.2011.2160276 (2011).
-
(2011)
IEEE Trans Med Imaging
, vol.30
, pp. 2044-2058
-
-
Chen, L.1
-
27
-
-
84954494648
-
-
arXiv:1406.7349v2 [stat.ML]
-
Zhu, Y., Wang, N., Miller, D. J., Wang, Y. Convex Analysis of Mixtures for Separating Non-negative Well-grounded Sources. arXiv:1406.7349v2 [stat.ML] (2015).
-
(2015)
Convex Analysis of Mixtures for Separating Non-negative Well-grounded Sources
-
-
Zhu, Y.1
Wang, N.2
Miller, D.J.3
Wang, Y.4
-
28
-
-
84915749669
-
Unsupervised deconvolution of dynamic imaging reveals intratumor vascular heterogeneity and repopulation dynamics
-
Chen, L. et al. Unsupervised Deconvolution of Dynamic Imaging Reveals Intratumor Vascular Heterogeneity and Repopulation Dynamics. PloS one 9, e112143, doi: 10.1371/journal.pone.0112143 (2014).
-
(2014)
PloS One
, vol.9
, pp. e112143
-
-
Chen, L.1
-
29
-
-
84922353869
-
UNDO: A Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples
-
Wang, N. et al. UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples. Bioinformatics 31, 137-139, doi: 10.1093/bioinformatics/btu607 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 137-139
-
-
Wang, N.1
-
30
-
-
84923292191
-
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
-
Buettner, F. et al. Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol 33, 155-160 (2015).
-
(2015)
Nat Biotechnol
, vol.33
, pp. 155-160
-
-
Buettner, F.1
-
32
-
-
33847172327
-
Clustering by passing messages between data points
-
Frey, B. J., Dueck, D. Clustering by Passing Messages Between Data Points. Science 315, 972-976, doi: 10.1126/science.1136800 (2007).
-
(2007)
Science
, vol.315
, pp. 972-976
-
-
Frey, B.J.1
Dueck, D.2
-
34
-
-
0032112293
-
A genome-wide transcriptional analysis of the mitotic cell cycle
-
Cho, R. J. et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell 2, 65-73 (1998).
-
(1998)
Mol Cell
, vol.2
, pp. 65-73
-
-
Cho, R.J.1
-
35
-
-
41949124936
-
Are we overestimating the number of cell-cycling genes the impact of background models on timeseries analysis
-
Futschik, M. E., Herzel, H. Are we overestimating the number of cell-cycling genes The impact of background models on timeseries analysis. Bioinformatics 24, 1063-1069, doi: 10.1093/bioinformatics/btn072 (2008).
-
(2008)
Bioinformatics
, vol.24
, pp. 1063-1069
-
-
Futschik, M.E.1
Herzel, H.2
-
36
-
-
14844285655
-
Comparison of computational methods for the identification of cell cycle-regulated genes
-
de Lichtenberg, U. et al. Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 21, 1164-1171, doi: 10.1093/bioinformatics/bti093 (2005).
-
(2005)
Bioinformatics
, vol.21
, pp. 1164-1171
-
-
De Lichtenberg, U.1
-
37
-
-
84883194790
-
Measuring cell-type specific differential methylation in human brain tissue
-
Montano, C. M. et al. Measuring cell-type specific differential methylation in human brain tissue. Genome Biol 14, R94, doi: 10.1186/gb-2013-14-8-r94 (2013).
-
(2013)
Genome Biol
, vol.14
, pp. R94
-
-
Montano, C.M.1
|