-
1
-
-
84964556059
-
Pooling across cells to normalize single-cell RNA sequencing data with many zero counts
-
Aaron, T. L. L., Bach, K., and Marioni, J. C. (2016). Pooling across cells to normalize single-cell RNA sequencing data with many zero counts. Genome Biol. 17:75. doi: 10.1186/s13059-016-0947-7
-
(2016)
Genome Biol
, vol.17
, pp. 75
-
-
Aaron, T.L.L.1
Bach, K.2
Marioni, J.C.3
-
2
-
-
84880280631
-
viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia
-
Amir, E. D., Davis, K. L., Tadmor, M. D., Simonds, E. F., Levine, J. H., and Bendall, S. C. (2013). viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nat. Biotechnol. 31, 545-552. doi: 10.1038/nbt.2594
-
(2013)
Nat. Biotechnol
, vol.31
, pp. 545-552
-
-
Amir, E.D.1
Davis, K.L.2
Tadmor, M.D.3
Simonds, E.F.4
Levine, J.H.5
Bendall, S.C.6
-
3
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biol. 11:R106. doi: 10.1186/gb-2010-11-10-r106
-
(2010)
Genome Biol
, vol.11
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
4
-
-
84928987900
-
HTSeq-a python framework to work with high-throughput sequencing data
-
Anders, S., Pyl, P. T., and Huber, W. (2014). HTSeq-a python framework to work with high-throughput sequencing data. Bioinformatics 31, 166-169. doi: 10.1093/bioinformatics/btu638
-
(2014)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
Pyl, P.T.2
Huber, W.3
-
6
-
-
0037016775
-
The isomap algorithm and topological stability
-
Balasubramanian, M., and Schwartz, E. L. (2002). The isomap algorithm and topological stability. Science 295:7. doi: 10.1126/science.295.5552.7a
-
(2002)
Science
, vol.295
, pp. 7
-
-
Balasubramanian, M.1
Schwartz, E.L.2
-
8
-
-
84899574465
-
Single-cell trajectory detection uncovers progression and regulatory coordination in human b cell development
-
Bendall, S. C., Davis, K. L., Amir, El-D, Tadmor, M. D., Simonds, E. F., Chen, T. J., et al. (2014). Single-cell trajectory detection uncovers progression and regulatory coordination in human b cell development. Cell 157, 714-725. doi: 10.1016/j.cell.2014.04.005
-
(2014)
Cell
, vol.157
, pp. 714-725
-
-
Bendall, S.C.1
Davis, K.L.2
Amir, E.-D.3
Tadmor, M.D.4
Simonds, E.F.5
Chen, T.J.6
-
9
-
-
84947205653
-
"When Is 'Nearest Neighbor' Meaningful?, "
-
(Jerusalem: Springer)
-
Beyer, K., Goldstein, J., Ramakrishnan, R., and Shaft, U. (1999). "When Is 'Nearest Neighbor' Meaningful?, " in DATABASE Theory-ICDT'99 (Jerusalem: Springer), 217-235.
-
(1999)
DATABASE Theory-ICDT'99
, pp. 217-235
-
-
Beyer, K.1
Goldstein, J.2
Ramakrishnan, R.3
Shaft, U.4
-
10
-
-
84905049901
-
Trimmomatic: a flexible trimmer for illumina sequence data
-
Bolger, A. M., Lohse, M., and Usadel, B. (2014). Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30, 2114-2120. doi: 10.1093/bioinformatics/btu170
-
(2014)
Bioinformatics
, vol.30
, pp. 2114-2120
-
-
Bolger, A.M.1
Lohse, M.2
Usadel, B.3
-
11
-
-
84939162152
-
Scalable microfluidics for single cell rna printing and sequencing
-
Bose, S., Wan, Z., Carr, A., Rizvi, A. H., Vieira, G., Pe'er, D., et al. (2015). Scalable microfluidics for single cell rna printing and sequencing. Genome Biol. 16:120. doi: 10.1186/s13059-015-0684-3
-
(2015)
Genome Biol
, vol.16
, pp. 120
-
-
Bose, S.1
Wan, Z.2
Carr, A.3
Rizvi, A.H.4
Vieira, G.5
Pe'er, D.6
-
12
-
-
84966283954
-
Near-optimal probabilistic RNA-seq quantification
-
Bray, N. L., Pimentel, H., Melsted, P., and Pachter, L. (2016). Near-optimal probabilistic RNA-seq quantification. Nat. Biotechnol. 34, 525-527. doi: 10.1038/nbt.3519
-
(2016)
Nat. Biotechnol
, vol.34
, pp. 525-527
-
-
Bray, N.L.1
Pimentel, H.2
Melsted, P.3
Pachter, L.4
-
13
-
-
84887109584
-
Accounting for technical noise in single-cell RNA-seq experiments
-
Brennecke, P., Anders, S., Kim, J. K., Kolodziejczyk, A. A., Zhang, X., Proserpio, V., et al. (2013). Accounting for technical noise in single-cell RNA-seq experiments. Nat. Methods 10, 1093-1095. doi: 10.1038/nmeth.2645
-
(2013)
Nat. Methods
, vol.10
, pp. 1093-1095
-
-
Brennecke, P.1
Anders, S.2
Kim, J.K.3
Kolodziejczyk, A.A.4
Zhang, X.5
Proserpio, V.6
-
14
-
-
84923292191
-
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
-
Buettner, F., Natarajan, K. N., Casale, F. P., Proserpio, V., Scialdone, A., Theis, F. J., et al. (2015). Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat. Biotechnol. 33, 55-160. doi: 10.1038/nbt.3102
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 55-160
-
-
Buettner, F.1
Natarajan, K.N.2
Casale, F.P.3
Proserpio, V.4
Scialdone, A.5
Theis, F.J.6
-
15
-
-
84866463531
-
A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
-
Buettner, F., and Theis, F. J. (2012). A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst. Bioinformatics 28, i626-i632. doi: 10.1093/bioinformatics/bts385
-
(2012)
Bioinformatics
, vol.28
, pp. i626-i632
-
-
Buettner, F.1
Theis, F.J.2
-
17
-
-
84886523027
-
"Benchmarking RNA-Seq quantification tools, "
-
(Osaka)
-
Chandramohan, R., Wu, P.-Y., Phan, J. H., and Wang, M. D. (2013). "Benchmarking RNA-Seq quantification tools, " in Engineering In Medicine and Biology Society (EMBC), 2013 35th Annual International Conference of the IEEE (Osaka), 647-650.
-
(2013)
Engineering In Medicine and Biology Society (EMBC), 2013 35th Annual International Conference of the IEEE
, pp. 647-650
-
-
Chandramohan, R.1
Wu, P.-Y.2
Phan, J.H.3
Wang, M.D.4
-
18
-
-
84962023190
-
Pan-Cancer analyses reveal long intergenic non-coding rnas relevant to tumor diagnosis, subtyping and prognosis
-
Ching, T., Peplowska, K., Huang, S., Zhu, X., Shen, Y., Molnar, J., et al. (2016). Pan-Cancer analyses reveal long intergenic non-coding rnas relevant to tumor diagnosis, subtyping and prognosis. EBioMedicine 7, 62-72. doi: 10.1016/j.ebiom.2016.03.023
-
(2016)
EBioMedicine
, vol.7
, pp. 62-72
-
-
Ching, T.1
Peplowska, K.2
Huang, S.3
Zhu, X.4
Shen, Y.5
Molnar, J.6
-
19
-
-
77957151956
-
SolexaQA: at-a-glance quality assessment of illumina second-generation sequencing data
-
Cox, M. P., Peterson, D. A., and Biggs, P. J. (2010). SolexaQA: at-a-glance quality assessment of illumina second-generation sequencing data. BMC Bioinformatics 11:485. doi: 10.1186/1471-2105-11-485
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 485
-
-
Cox, M.P.1
Peterson, D.A.2
Biggs, P.J.3
-
20
-
-
57249084011
-
Visualizing data using T-SNE
-
der Maaten, L., and Hinton, G. (2008). Visualizing data using T-SNE. J. Mach. Learn. Res. 9, 2579-2605. Available online at: https://lvdmaaten.github.io/publications/papers/JMLR_2008.pdf
-
(2008)
J. Mach. Learn. Res
, vol.9
, pp. 2579-2605
-
-
der Maaten, L.1
Hinton, G.2
-
21
-
-
84924423596
-
Integrated genome and transcriptome sequencing of the same cell
-
Dey, S. S., Kester, L., Spanjaard, B., Bienko, M., and van Oudenaarden, A. (2015). Integrated genome and transcriptome sequencing of the same cell. Nat. Biotechnol. 33, 285-289. doi: 10.1038/nbt.3129
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 285-289
-
-
Dey, S.S.1
Kester, L.2
Spanjaard, B.3
Bienko, M.4
van Oudenaarden, A.5
-
22
-
-
84992322906
-
SCell: integrated analysis of single-cell RNA-Seq data
-
Diaz, A., Liu, S. J., Sandoval, C., Pollen, A., Nowakowski, T. J., Lim, D. A., et al. (2016). SCell: integrated analysis of single-cell RNA-Seq data. Bioinformatics 32, 2219-2220. doi: 10.1093/bioinformatics/btw201
-
(2016)
Bioinformatics
, vol.32
, pp. 2219-2220
-
-
Diaz, A.1
Liu, S.J.2
Sandoval, C.3
Pollen, A.4
Nowakowski, T.J.5
Lim, D.A.6
-
23
-
-
84936803955
-
Normalization and noise reduction for single cell RNA-Seq experiments
-
Ding, B., Zheng, L., Zhu, Y., Li, N., Jia, H., Ai, R., et al. (2015). Normalization and noise reduction for single cell RNA-Seq experiments. Bioinformatics 31, 2225-2227. doi: 10.1093/bioinformatics/btv122
-
(2015)
Bioinformatics
, vol.31
, pp. 2225-2227
-
-
Ding, B.1
Zheng, L.2
Zhu, Y.3
Li, N.4
Jia, H.5
Ai, R.6
-
24
-
-
85019897120
-
Mapping RNA-seq reads with STAR
-
11.14.1-11.14.19
-
Dobin, A., and Gingeras, T. R. (2015). Mapping RNA-seq reads with STAR. Curr. Protoc. Bioinform. 51, 11.14.1-11.14.19. doi: 10.1002/0471250953.bi1114s51
-
(2015)
Curr. Protoc. Bioinform
, vol.51
-
-
Dobin, A.1
Gingeras, T.R.2
-
25
-
-
84888861753
-
Systematic evaluation of spliced alignment programs for RNA-seq data
-
Engström, P. G., Steijger, T., Sipos, B., Grant, G. R., Kahles, A., Rätsch, G., et al. (2013). Systematic evaluation of spliced alignment programs for RNA-seq data. Nat. Methods 10, 1185-1191. doi: 10.1038/nmeth.2722
-
(2013)
Nat. Methods
, vol.10
, pp. 1185-1191
-
-
Engström, P.G.1
Steijger, T.2
Sipos, B.3
Grant, G.R.4
Kahles, A.5
Rätsch, G.6
-
26
-
-
84959189722
-
Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis
-
Fan, J.-B., Jean, J. J.-B., Salathia, N., Liu, R., Kaeser, G. E., Yung, Y. C., et al. (2016). Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. Nat. Methods 13, 241-244. doi: 10.1038/nmeth.3734
-
(2016)
Nat. Methods
, vol.13
, pp. 241-244
-
-
Fan, J.-B.1
Jean, J.J.-B.2
Salathia, N.3
Liu, R.4
Kaeser, G.E.5
Yung, Y.C.6
-
27
-
-
84951574149
-
MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data
-
Finak, G., McDavid, A., Yajima, M., Deng, J., Gersuk, V., Shalek, A. K., et al. (2015). MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biol. 16:278. doi: 10.1186/s13059-015-0844-5
-
(2015)
Genome Biol
, vol.16
, pp. 278
-
-
Finak, G.1
McDavid, A.2
Yajima, M.3
Deng, J.4
Gersuk, V.5
Shalek, A.K.6
-
28
-
-
84907500627
-
RNA-Seq gene profiling-a systematic empirical comparison
-
Fonseca, N. A., Marioni, J., and Brazma, A. (2014). RNA-Seq gene profiling-a systematic empirical comparison. PloS ONE 9:e107026. doi: 10.1371/journal.pone.0107026
-
(2014)
PloS ONE
, vol.9
-
-
Fonseca, N.A.1
Marioni, J.2
Brazma, A.3
-
29
-
-
74049087026
-
Community detection in graphs
-
Fortunato, S. (2010). Community detection in graphs. Phys. Rep. 486, 75-174. doi: 10.1016/j.physrep.2009.11.002
-
(2010)
Phys. Rep
, vol.486
, pp. 75-174
-
-
Fortunato, S.1
-
30
-
-
84961778087
-
Single-Cell RNA-seq reveals activation of unique gene groups as a consequence of stem cell-parenchymal cell fusion
-
Freeman, B. T., Jung, J. P., and Ogle, B. M. (2016). Single-Cell RNA-seq reveals activation of unique gene groups as a consequence of stem cell-parenchymal cell fusion. Sci. Rep. 6:23270. doi: 10.1038/srep23270
-
(2016)
Sci. Rep
, vol.6
, pp. 23270
-
-
Freeman, B.T.1
Jung, J.P.2
Ogle, B.M.3
-
31
-
-
85021389457
-
Integrative single-cell transcriptomics reveals molecular networks defining neuronal maturation during postnatal neurogenesis
-
[Epub ahead of print]
-
Gao, Y., Wang, F., Eisinger, B. E., Kelnhofer, L. E., Jobe, E. M., and Zhao, X. (2016). Integrative single-cell transcriptomics reveals molecular networks defining neuronal maturation during postnatal neurogenesis. Cereb. Cortex. [Epub ahead of print]. doi: 10.1093/cercor/bhw040
-
(2016)
Cereb. Cortex
-
-
Gao, Y.1
Wang, F.2
Eisinger, B.E.3
Kelnhofer, L.E.4
Jobe, E.M.5
Zhao, X.6
-
32
-
-
84946226911
-
Design and analysis of single-cell sequencing experiments
-
Grün, D., and van Oudenaarden, A. (2015). Design and analysis of single-cell sequencing experiments. Cell 163, 799-810. doi: 10.1016/j.cell.2015.10.039
-
(2015)
Cell
, vol.163
, pp. 799-810
-
-
Grün, D.1
van Oudenaarden, A.2
-
33
-
-
84949293695
-
SINCERA: a Pipeline for Single-Cell RNA-Seq profiling analysis
-
Guo, M., Wang, H., Potter, S. S., Whitsett, J. A., and Xu, Y. (2015). SINCERA: a Pipeline for Single-Cell RNA-Seq profiling analysis. PLoS Comput. Biol. 11:e1004575. doi: 10.1371/journal.pcbi.1004575
-
(2015)
PLoS Comput. Biol
, vol.11
-
-
Guo, M.1
Wang, H.2
Potter, S.S.3
Whitsett, J.A.4
Xu, Y.5
-
34
-
-
84941753288
-
Diffusion maps for high-dimensional single-cell analysis of differentiation data
-
Haghverdi, L., Buettner, F., and Theis, F. J. (2015). Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics 31, 2989-2998. doi: 10.1093/bioinformatics/btv325
-
(2015)
Bioinformatics
, vol.31
, pp. 2989-2998
-
-
Haghverdi, L.1
Buettner, F.2
Theis, F.J.3
-
35
-
-
84923365432
-
Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform
-
Han, L., Zi, X., Garmire, L. X., Wu, Y., Weissman, S. M., Pan, X., et al. (2014). Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform. Sci. Rep. 4:6485. doi: 10.1038/srep06485
-
(2014)
Sci. Rep
, vol.4
, pp. 6485
-
-
Han, L.1
Zi, X.2
Garmire, L.X.3
Wu, Y.4
Weissman, S.M.5
Pan, X.6
-
36
-
-
84959475041
-
Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics
-
Handel, A. E., Chintawar, S., Lalic, T., Whiteley, E., Vowles, J., Giustacchini, A., et al. (2016). Assessing similarity to primary tissue and cortical layer identity in induced pluripotent stem cell-derived cortical neurons through single-cell transcriptomics. Hum. Mol. Genet. 25, 989-1000. doi: 10.1093/hmg/ddv637
-
(2016)
Hum. Mol. Genet
, vol.25
, pp. 989-1000
-
-
Handel, A.E.1
Chintawar, S.2
Lalic, T.3
Whiteley, E.4
Vowles, J.5
Giustacchini, A.6
-
37
-
-
84992028564
-
Molecular organization of CA1 interneuron classes
-
Harris, K., Magno, L., Katona, L., Lönnerberg, P., Muñoz Manchado, A. B., Somogyi, P., et al. (2015). Molecular organization of CA1 interneuron classes. bioRxiv 34595. doi: 10.1101/034595
-
(2015)
bioRxiv 34595
-
-
Harris, K.1
Magno, L.2
Katona, L.3
Lönnerberg, P.4
Muñoz Manchado, A.B.5
Somogyi, P.6
-
38
-
-
0034515528
-
A clustering algorithm based on graph connectivity
-
Hartuv, E., and Shamir, R. (2000). A clustering algorithm based on graph connectivity. Inf. Process. Lett. 76, 175-181. doi: 10.1016/S0020-0190(00)00142-3
-
(2000)
Inf. Process. Lett
, vol.76
, pp. 175-181
-
-
Hartuv, E.1
Shamir, R.2
-
39
-
-
84960091878
-
Single-Cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas
-
Hou, Y., Guo, H., Cao, C., Li, X., Hu, B., Zhu, P., et al. (2016). Single-Cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res. 26, 304-319. doi: 10.1038/cr.2016.23
-
(2016)
Cell Res
, vol.26
, pp. 304-319
-
-
Hou, Y.1
Guo, H.2
Cao, C.3
Li, X.4
Hu, B.5
Zhu, P.6
-
40
-
-
84958058589
-
Classification of low quality cells from single-cell RNA-seq data
-
Ilicic, T., Kim, J. K., Kolodziejczyk, A. A., Bagger, F. O., McCarthy, D. J., Marioni, J. C., et al. (2016). Classification of low quality cells from single-cell RNA-seq data. Genome Biol. 17:29. doi: 10.1186/s13059-016-0888-1
-
(2016)
Genome Biol
, vol.17
, pp. 29
-
-
Ilicic, T.1
Kim, J.K.2
Kolodziejczyk, A.A.3
Bagger, F.O.4
McCarthy, D.J.5
Marioni, J.C.6
-
41
-
-
84895069488
-
Quantitative single-Cell RNA-Seq with unique molecular identifiers
-
Islam, S., Zeisel, A., Joost, S., La Manno, G., Zajac, P., Kasper, M., et al. (2014). Quantitative single-Cell RNA-Seq with unique molecular identifiers. Nat. Methods 11, 163-166. doi: 10.1038/nmeth.2772
-
(2014)
Nat. Methods
, vol.11
, pp. 163-166
-
-
Islam, S.1
Zeisel, A.2
Joost, S.3
La Manno, G.4
Zajac, P.5
Kasper, M.6
-
42
-
-
84893905629
-
Massively parallel Single-Cell RNA-Seq for marker-free decomposition of tissues into cell types
-
Jaitin, D. A., Kenigsberg, E., Keren-Shaul, H., Elefant, N., Paul, F., Zaretsky, I., et al. (2014). Massively parallel Single-Cell RNA-Seq for marker-free decomposition of tissues into cell types. Science 343, 776-779. doi: 10.1126/science.1247651
-
(2014)
Science
, vol.343
, pp. 776-779
-
-
Jaitin, D.A.1
Kenigsberg, E.2
Keren-Shaul, H.3
Elefant, N.4
Paul, F.5
Zaretsky, I.6
-
43
-
-
84982806105
-
TSCAN: pseudo-time reconstruction and evaluation in Single-Cell RNA-Seq analysis
-
Ji, Z., and Ji, H. (2016). TSCAN: pseudo-time reconstruction and evaluation in Single-Cell RNA-Seq analysis. Nucl. Acids Res. 44:e117. doi: 10.1093/nar/gkw430
-
(2016)
Nucl. Acids Res
, vol.44
-
-
Ji, Z.1
Ji, H.2
-
44
-
-
84976875133
-
GiniClust: detecting rare cell types from single-cell gene expression data with gini index
-
Jiang, L., Chen, H., Pinello, L., and Yuan, G.-C. (2016). GiniClust: detecting rare cell types from single-cell gene expression data with gini index. Genome Biol. 17:144. doi: 10.1186/s13059-016-1010-4
-
(2016)
Genome Biol
, vol.17
, pp. 144
-
-
Jiang, L.1
Chen, H.2
Pinello, L.3
Yuan, G.-C.4
-
45
-
-
84983372594
-
Quality control of Single-Cell RNA-seq by SinQC
-
[Epub ahead of print]
-
Jiang, P., Thomson, J. A, and Stewart, R. (2016). Quality control of Single-Cell RNA-seq by SinQC. Bioinformatics. [Epub ahead of print]. doi: 10.1093/bioinformatics/btw176
-
(2016)
Bioinformatics
-
-
Jiang, P.1
Thomson, J.A.2
Stewart, R.3
-
46
-
-
33845432928
-
Adjusting batch effects in microarray expression data using empirical bayes methods
-
Johnson, W. E., Li, C., and Rabinovic, A. (2007). Adjusting batch effects in microarray expression data using empirical bayes methods. Biostatistics 8, 118-127. doi: 10.1093/biostatistics/kxj037
-
(2007)
Biostatistics
, vol.8
, pp. 118-127
-
-
Johnson, W.E.1
Li, C.2
Rabinovic, A.3
-
47
-
-
84890060756
-
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization
-
Katayama, S., Töhönen, V., Linnarsson, S., and Kere, J. (2013). SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization. Bioinformatics 29, 2943-2945. doi: 10.1093/bioinformatics/btt511
-
(2013)
Bioinformatics
, vol.29
, pp. 2943-2945
-
-
Katayama, S.1
Töhönen, V.2
Linnarsson, S.3
Kere, J.4
-
48
-
-
84992094812
-
Radiotranscriptomics: a synergy of imaging and transcriptomics in clinical assessment
-
Katrib, A., Hsu, W., Bui, A., and Xing, Y. (2016). Radiotranscriptomics: a synergy of imaging and transcriptomics in clinical assessment. Quant. Biol. 4, 1-12. doi: 10.1007/s40484-016-0061-6
-
(2016)
Quant. Biol
, vol.4
, pp. 1-12
-
-
Katrib, A.1
Hsu, W.2
Bui, A.3
Xing, Y.4
-
49
-
-
84903574951
-
Bayesian approach to single-cell differential expression analysis
-
Kharchenko, P. V., Silberstein, L., and Scadden, D. T. (2014). Bayesian approach to single-cell differential expression analysis. Nat. Methods 11, 740-742. doi: 10.1038/nmeth.2967
-
(2014)
Nat. Methods
, vol.11
, pp. 740-742
-
-
Kharchenko, P.V.1
Silberstein, L.2
Scadden, D.T.3
-
50
-
-
84926519013
-
HISAT: a fast spliced aligner with low memory requirements
-
Kim, D., Langmead, B., and Salzberg, S. L. (2015). HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357-360. doi: 10.1038/nmeth.3317
-
(2015)
Nat. Methods
, vol.12
, pp. 357-360
-
-
Kim, D.1
Langmead, B.2
Salzberg, S.L.3
-
51
-
-
84876996918
-
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
-
Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., Salzberg, S. L., et al. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14:R36. doi: 10.1186/gb-2013-14-4-r36
-
(2013)
Genome Biol
, vol.14
, pp. R36
-
-
Kim, D.1
Pertea, G.2
Trapnell, C.3
Pimentel, H.4
Kelley, R.5
Salzberg, S.L.6
-
52
-
-
84937573360
-
Single-Cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
-
Kim, K. T., Lee, H. W., Lee, H. O., Kim, S. C., Seo, Y. J., Chung, W., et al. (2015). Single-Cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells. Genome Biol. 16:127. doi: 10.1186/s13059-015-0692-3
-
(2015)
Genome Biol
, vol.16
, pp. 127
-
-
Kim, K.T.1
Lee, H.W.2
Lee, H.O.3
Kim, S.C.4
Seo, Y.J.5
Chung, W.6
-
53
-
-
84954562766
-
A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages
-
Kimmerling, R. J., Szeto, G. L., Li, J. W., Genshaft, A. S., Kazer, S. W., Payer, K. R., et al. (2016). A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages. Nat. Commun. 7:10220. doi: 10.1038/ncomms10220
-
(2016)
Nat. Commun
, vol.7
, pp. 10220
-
-
Kimmerling, R.J.1
Szeto, G.L.2
Li, J.W.3
Genshaft, A.S.4
Kazer, S.W.5
Payer, K.R.6
-
54
-
-
84923188586
-
Deconstructing transcriptional heterogeneity in pluripotent stem cells
-
Kumar, R. M., Cahan, P., Shalek, A. K., Satija, R., DaleyKeyser, A. J., Li, H., et al. (2014). Deconstructing transcriptional heterogeneity in pluripotent stem cells. Nature 516, 56-61. doi: 10.1038/nature13920
-
(2014)
Nature
, vol.516
, pp. 56-61
-
-
Kumar, R.M.1
Cahan, P.2
Shalek, A.K.3
Satija, R.4
DaleyKeyser, A.J.5
Li, H.6
-
55
-
-
84983542835
-
Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring
-
Kvastad, L., Solnestam, B. W., Johansson, E., Nygren, A. O., Laddach, N., Sahlén, P., et al. (2015). Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring. Sci. Rep. 5:16519. doi: 10.1038/srep16519
-
(2015)
Sci. Rep
, vol.5
, pp. 16519
-
-
Kvastad, L.1
Solnestam, B.W.2
Johansson, E.3
Nygren, A.O.4
Laddach, N.5
Sahlén, P.6
-
56
-
-
84925226706
-
Svaseq: removing batch effects and other unwanted noise from sequencing data
-
Leek, J. T. (2014). Svaseq: removing batch effects and other unwanted noise from sequencing data. Nucleic Acids Res. 42. doi: 10.1093/nar/gku864
-
(2014)
Nucleic Acids Res
, pp. 42
-
-
Leek, J.T.1
-
57
-
-
84962711132
-
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data
-
Leng, N., Choi, J., Chu, L. F., Thomson, J. A., Kendziorski, C., and Stewart, R. (2016). OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data. Bioinformatics 32, 1408-1410. doi: 10.1093/bioinformatics/btw004
-
(2016)
Bioinformatics
, vol.32
, pp. 1408-1410
-
-
Leng, N.1
Choi, J.2
Chu, L.F.3
Thomson, J.A.4
Kendziorski, C.5
Stewart, R.6
-
58
-
-
84959122613
-
Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments
-
Leng, N., Chu, L. F., Barry, C., Li, Y., Choi, J., Li, X., et al. (2015). Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments. Nat. Methods 12, 947-950. doi: 10.1038/nmeth.3549
-
(2015)
Nat. Methods
, vol.12
, pp. 947-950
-
-
Leng, N.1
Chu, L.F.2
Barry, C.3
Li, Y.4
Choi, J.5
Li, X.6
-
59
-
-
84934442835
-
Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis
-
Levine, J. H., Simonds, E. F., Bendall, S. C., Davis, K. L., Amir el, A. D., Tadmor, M. D., et al. (2015). Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell 162, 184-197. doi: 10.1016/j.cell.2015.05.047
-
(2015)
Cell
, vol.162
, pp. 184-197
-
-
Levine, J.H.1
Simonds, E.F.2
Bendall, S.C.3
Davis, K.L.4
Amir el, A.D.5
Tadmor, M.D.6
-
60
-
-
79961123152
-
RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome
-
Li, B., and Dewey, C. N. (2011). RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome. BMC Bioinformatics 12:323. doi: 10.1186/1471-2105-12-323
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 323
-
-
Li, B.1
Dewey, C.N.2
-
61
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., et al. (2009). The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078-2079. doi: 10.1093/bioinformatics/btp352
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
-
62
-
-
84886557480
-
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-seq data
-
Li, J., and Tibshirani, R. (2013). Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-seq data. Stat. Methods Med. Res. 22, 519-536. doi: 10.1177/0962280211428386
-
(2013)
Stat. Methods Med. Res
, vol.22
, pp. 519-536
-
-
Li, J.1
Tibshirani, R.2
-
63
-
-
84897397058
-
featurecounts: an efficient general purpose program for assigning sequence reads to genomic features
-
Liao, Y., Smyth, G. K., and Shi, W. (2013). featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. doi: 10.1093/bioinformatics/btt656
-
(2013)
Bioinformatics
-
-
Liao, Y.1
Smyth, G.K.2
Shi, W.3
-
64
-
-
84900333051
-
Whole exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
-
Lohr, J. G., Adalsteinsson, V. A., Cibulskis, K., Choudhury, A. D., Rosenberg, M., Cruz-Gordillo, P., et al. (2014). Whole exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer. Nat. Biotechnol. 32:479. doi: 10.1038/nbt.2892
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 479
-
-
Lohr, J.G.1
Adalsteinsson, V.A.2
Cibulskis, K.3
Choudhury, A.D.4
Rosenberg, M.5
Cruz-Gordillo, P.6
-
65
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M. I., Huber, W., and Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 1-21. doi: 10.1101/002832
-
(2014)
Genome Biol
, vol.15
, pp. 1-21
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
66
-
-
84930178333
-
G&T-Seq: parallel sequencing of single-cell genomes and transcriptomes
-
Macaulay, I. C., Haerty, W., Kumar, P., Li, Y. I., Hu, T. X., Teng, M. J., et al. (2015). G&T-Seq: parallel sequencing of single-cell genomes and transcriptomes. Nat. Methods 12, 519-522. doi: 10.1038/nmeth.3370
-
(2015)
Nat. Methods
, vol.12
, pp. 519-522
-
-
Macaulay, I.C.1
Haerty, W.2
Kumar, P.3
Li, Y.I.4
Hu, T.X.5
Teng, M.J.6
-
67
-
-
84924365758
-
Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape
-
Marco, M., Karp, R. L., Guo, G., Robson, P., Hart, A. H., Trippa, L., et al. (2014). Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape. Proc. Natl. Acad. Sci. 111, E5643-E5650. doi: 10.1073/pnas.1408993111
-
(2014)
Proc. Natl. Acad. Sci
, vol.111
, pp. E5643-E5650
-
-
Marco, M.1
Karp, R.L.2
Guo, G.3
Robson, P.4
Hart, A.H.5
Trippa, L.6
-
68
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads
-
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. J. 17:10. doi: 10.14806/ej.17.1.200
-
(2011)
EMBnet. J
, vol.17
, pp. 10
-
-
Martin, M.1
-
69
-
-
84964786844
-
Dnmt3a haploinsufficiency transforms Flt3-ITD myeloproliferative disease into a rapid, spontaneous, and fully-penetrant acute myeloid leukemia
-
Meyer, S. E., Qin, T., Muench, D. E., Masuda, K., Venkatasubramanian, M., Orr, E., et al. (2016). Dnmt3a haploinsufficiency transforms Flt3-ITD myeloproliferative disease into a rapid, spontaneous, and fully-penetrant acute myeloid leukemia. Cancer Discov. 6, 501-515. doi: 10.1158/2159-8290.CD-16-0008
-
(2016)
Cancer Discov
, vol.6
, pp. 501-515
-
-
Meyer, S.E.1
Qin, T.2
Muench, D.E.3
Masuda, K.4
Venkatasubramanian, M.5
Orr, E.6
-
70
-
-
84942904757
-
RNA-seq of single prostate CTCs implicates noncanonical wnt signaling in antiandrogen resistance
-
Miyamoto, D. T., Zheng, Y., Wittner, B. S., Lee, R. J., Zhu, H., Broderick, K. T., et al. (2015). RNA-seq of single prostate CTCs implicates noncanonical wnt signaling in antiandrogen resistance. Science 349, 1351-1356. doi: 10.1126/science.aab0917
-
(2015)
Science
, vol.349
, pp. 1351-1356
-
-
Miyamoto, D.T.1
Zheng, Y.2
Wittner, B.S.3
Lee, R.J.4
Zhu, H.5
Broderick, K.T.6
-
71
-
-
84924353105
-
Decoding the regulatory network of early blood development from single-cell gene expression measurements
-
Moignard, V., Woodhouse, S., Haghverdi, L., Lilly, A. J., Tanaka, Y., Wilkinson, A. C., et al. (2015). Decoding the regulatory network of early blood development from single-cell gene expression measurements. Nat. Biotechnol. 33, 269-276. doi: 10.1038/nbt.3154
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 269-276
-
-
Moignard, V.1
Woodhouse, S.2
Haghverdi, L.3
Lilly, A.J.4
Tanaka, Y.5
Wilkinson, A.C.6
-
72
-
-
79953766940
-
Tumour evolution inferred by single-cell sequencing
-
Navin, N., Kendall, J., Troge, J., Andrews, P., Rodgers, L., McIndoo, J., et al. (2011). Tumour evolution inferred by single-cell sequencing. Nature 472, 90-94. doi: 10.1038/nature09807
-
(2011)
Nature
, vol.472
, pp. 90-94
-
-
Navin, N.1
Kendall, J.2
Troge, J.3
Andrews, P.4
Rodgers, L.5
McIndoo, J.6
-
73
-
-
84969856092
-
Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts
-
Ntranos, V., Kamath, G. M., Zhang, J. M., Pachter, L., and Tse, D. N. (2016). Fast and accurate single-cell RNA-seq analysis by clustering of transcript-compatibility counts. bioRxiv. 17:112. doi: 10.1186/s13059-016-0970-8
-
(2016)
bioRxiv
, vol.17
, pp. 112
-
-
Ntranos, V.1
Kamath, G.M.2
Zhang, J.M.3
Pachter, L.4
Tse, D.N.5
-
74
-
-
84902668801
-
Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma
-
Patel, A. P., Tirosh, I., Trombetta, J. J., Shalek, A. K., Gillespie, S. M., Wakimoto, H., et al. (2014). Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science 344, 1396-1401. doi: 10.1126/science.1254257
-
(2014)
Science
, vol.344
, pp. 1396-1401
-
-
Patel, A.P.1
Tirosh, I.2
Trombetta, J.J.3
Shalek, A.K.4
Gillespie, S.M.5
Wakimoto, H.6
-
75
-
-
84962688754
-
Single-cell RNA-seq reveals lineage and x chromosome dynamics in human preimplantation embryos
-
Petropoulos, S., Edsgärd, D., Reinius, B., Deng, Q., Panula, S. P, Codeluppi, S., et al. (2016). Single-cell RNA-seq reveals lineage and x chromosome dynamics in human preimplantation embryos. Cell 165, 1012-1026. doi: 10.1016/j.cell.2016.03.023
-
(2016)
Cell
, vol.165
, pp. 1012-1026
-
-
Petropoulos, S.1
Edsgärd, D.2
Reinius, B.3
Deng, Q.4
Panula, S.P.5
Codeluppi, S.6
-
76
-
-
84907587700
-
Identifying cell types from spatially referenced single-cell expression datasets
-
Pettit, J.-B., Tomer, R, Achim, K, Richardson, S, Azizi, L., and Marioni, J. (2014). Identifying cell types from spatially referenced single-cell expression datasets. PLoS Comput Biol 10:e1003824. doi: 10.1371/journal.pcbi.1003824
-
(2014)
PLoS Comput Biol
, vol.10
-
-
Pettit, J.-B.1
Tomer, R.2
Achim, K.3
Richardson, S.4
Azizi, L.5
Marioni, J.6
-
77
-
-
84955706109
-
ZIFA: dimensionality reduction for zero-inflated single-cell gene expression analysis
-
Pierson, E., and Yau, C. (2015). ZIFA: dimensionality reduction for zero-inflated single-cell gene expression analysis. Genome Biol. 16, 1-10. doi: 10.1186/s13059-015-0805-z
-
(2015)
Genome Biol
, vol.16
, pp. 1-10
-
-
Pierson, E.1
Yau, C.2
-
78
-
-
84922321862
-
Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex
-
Pollen, A. A., Nowakowski, T. J., Shuga, J., Wang, X., Leyrat, A. A, Lui, J. H., et al. (2014). Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat. Biotechnol. 32, 1053-1058. doi: 10.1038/nbt.2967
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 1053-1058
-
-
Pollen, A.A.1
Nowakowski, T.J.2
Shuga, J.3
Wang, X.4
Leyrat, A.A.5
Lui, J.H.6
-
79
-
-
84992108405
-
"Dirichlet process mixture model for correcting technical variation in single-cell gene expression data."
-
(New York, NY)
-
Prabhakaran, S., Azizi, E., and Pe'er, D. (2016). "Dirichlet process mixture model for correcting technical variation in single-cell gene expression data." in Proceedings of The 33rd International Conference on Machine Learning (New York, NY), 1070-1079.
-
(2016)
Proceedings of The 33rd International Conference on Machine Learning
, pp. 1070-1079
-
-
Prabhakaran, S.1
Azizi, E.2
Pe'er, D.3
-
80
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
-
Ramsköld, D., Luo, S., Wang, Y.-C., Li, R., Deng, Q., Faridani, O. R., et al. (2012). Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nat. Biotechnol. 30, 777-782. doi: 10.1038/nbt.2282
-
(2012)
Nat. Biotechnol
, vol.30
, pp. 777-782
-
-
Ramsköld, D.1
Luo, S.2
Wang, Y.-C.3
Li, R.4
Deng, Q.5
Faridani, O.R.6
-
81
-
-
75249087100
-
edgeR: a bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J, and Smyth, G. K. (2010). edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140. doi: 10.1093/bioinformatics/btp616
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
82
-
-
84946545109
-
Single-Cell ChIP-seq reveals cell subpopulations defined by chromatin state
-
Rotem, A., Ram, O., Shoresh, N., Sperling, R. A., Goren, A., Weitz, D. A., et al. (2015). Single-Cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat. Biotechnol. 33, 1165-1172. doi: 10.1038/nbt.3383
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 1165-1172
-
-
Rotem, A.1
Ram, O.2
Shoresh, N.3
Sperling, R.A.4
Goren, A.5
Weitz, D.A.6
-
83
-
-
84929151009
-
Spatial reconstruction of single-cell gene expression data
-
Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., and Regev, A. (2015). Spatial reconstruction of single-cell gene expression data. Nat. Biotechnol. 33, 495-502. doi: 10.1038/nbt.3192
-
(2015)
Nat. Biotechnol
, vol.33
, pp. 495-502
-
-
Satija, R.1
Farrell, J.A.2
Gennert, D.3
Schier, A.F.4
Regev, A.5
-
84
-
-
84970949920
-
How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
-
Schurch, N. J., Schofield, P., Gierlinski, M., Cole, C., Sherstnev, A., Singh, V., et al. (2016). How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA 22, 839-851. doi: 10.1261/rna.053959.115
-
(2016)
RNA
, vol.22
, pp. 839-851
-
-
Schurch, N.J.1
Schofield, P.2
Gierlinski, M.3
Cole, C.4
Sherstnev, A.5
Singh, V.6
-
85
-
-
84891956083
-
Automatic classification of cellular expression by nonlinear stochastic embedding (ACCENSE)
-
Shekhar, K., Brodin, P., Davis, M. M., and Chakraborty, A. K. (2014). Automatic classification of cellular expression by nonlinear stochastic embedding (ACCENSE). Proc. Natl. Acad. Sci.U.S.A. 111, 202-207. doi: 10.1073/pnas.1321405111
-
(2014)
Proc. Natl. Acad. Sci.U.S.A
, vol.111
, pp. 202-207
-
-
Shekhar, K.1
Brodin, P.2
Davis, M.M.3
Chakraborty, A.K.4
-
86
-
-
84941010341
-
Single-Cell RNA-Seq with waterfall reveals molecular cascades underlying adult neurogenesis
-
Shin, J., Berg, D. A., Zhu, Y., Shin, J. Y., Song, J., Bonaguidi, M. A., et al. (2015). Single-Cell RNA-Seq with waterfall reveals molecular cascades underlying adult neurogenesis. Cell Stem Cell 17, 360-372. doi: 10.1016/j.stem.2015.07.013
-
(2015)
Cell Stem Cell
, vol.17
, pp. 360-372
-
-
Shin, J.1
Berg, D.A.2
Zhu, Y.3
Shin, J.Y.4
Song, J.5
Bonaguidi, M.A.6
-
87
-
-
77956412152
-
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-seq analysis
-
Tang, F., Barbacioru, C., Bao, S., Lee, C., Nordman, E., Wang, X., et al. (2010). Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-seq analysis. Cell Stem Cell 6, 468-478. doi: 10.1016/j.stem.2010.03.015
-
(2010)
Cell Stem Cell
, vol.6
, pp. 468-478
-
-
Tang, F.1
Barbacioru, C.2
Bao, S.3
Lee, C.4
Nordman, E.5
Wang, X.6
-
88
-
-
0034704229
-
A global geometric framework for nonlinear dimensionality reduction
-
Tenenbaum, J. B., De Silva, V., and Langford, J. C. (2000). A global geometric framework for nonlinear dimensionality reduction. Science 290, 2319-2323. doi: 10.1126/science.290.5500.2319
-
(2000)
Science
, vol.290
, pp. 2319-2323
-
-
Tenenbaum, J.B.1
De Silva, V.2
Langford, J.C.3
-
89
-
-
84907414338
-
Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells
-
Ting, D. T., Wittner, B. S., Ligorio, M., Jordan, N. V, Shah, A. M., Miyamoto, D. T., et al. (2014). Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells. Cell Rep. 8, 1905-1918. doi: 10.1016/j.celrep.2014.08.029
-
(2014)
Cell Rep
, vol.8
, pp. 1905-1918
-
-
Ting, D.T.1
Wittner, B.S.2
Ligorio, M.3
Jordan, N.V.4
Shah, A.M.5
Miyamoto, D.T.6
-
90
-
-
84963614956
-
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
-
Tirosh, I., Izar, B., Prakadan, S. M., Wadsworth, M. H., Treacy, D., Trombetta, J. J., et al. (2016). Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science 352, 189-196. doi: 10.1126/science.aad0501
-
(2016)
Science
, vol.352
, pp. 189-196
-
-
Tirosh, I.1
Izar, B.2
Prakadan, S.M.3
Wadsworth, M.H.4
Treacy, D.5
Trombetta, J.J.6
-
91
-
-
84900873950
-
Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions
-
Trapnell, C., Cacchiarelli, D., Grimsby, J., Pokharel, P., Li, S., Morse, M., et al. (2014). Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions. Nat. Biotechnol. 32, 381. doi: 10.1038/nbt.2859
-
(2014)
Nat. Biotechnol
, vol.32
, pp. 381
-
-
Trapnell, C.1
Cacchiarelli, D.2
Grimsby, J.3
Pokharel, P.4
Li, S.5
Morse, M.6
-
92
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-seq
-
Trapnell, C., Pachter, L., and Salzberg, S. L. (2009). TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105-1111. doi: 10.1093/bioinformatics/btp120
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
93
-
-
77952123055
-
Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., Van Baren, M. J., et al. (2010). Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511-515. doi: 10.1038/nbt.1621
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
Van Baren, M.J.6
-
94
-
-
84951287682
-
Non-coding yet non-trivial: a review on the computational genomics of lincRNAs
-
Travers, C., Masaki, J., Weirather, J., Garmire, L. X., Ching, T., Masaki, J., et al. (2015). Non-coding yet non-trivial: a review on the computational genomics of lincRNAs. BioData Min. 8:44. doi: 10.1186/s13040-015-0075-z
-
(2015)
BioData Min
, vol.8
, pp. 44
-
-
Travers, C.1
Masaki, J.2
Weirather, J.3
Garmire, L.X.4
Ching, T.5
Masaki, J.6
-
95
-
-
84900529199
-
Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
-
Treutlein, B., Brownfield, D. G., Wu, A. R., Neff, N. F., Mantalas, G. L., Espinoza, F. H., et al. (2014). Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq. Nature 509, 371-375. doi: 10.1038/nature13173
-
(2014)
Nature
, vol.509
, pp. 371-375
-
-
Treutlein, B.1
Brownfield, D.G.2
Wu, A.R.3
Neff, N.F.4
Mantalas, G.L.5
Espinoza, F.H.6
-
96
-
-
19544387813
-
Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices
-
Tsafrir, D., Tsafrir, I., Ein-Dor, L., Zuk, O., Notterman, D. A., and Domany, E. (2005). Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices. Bioinformatics 21, 2301-2308. doi: 10.1093/bioinformatics/bti329
-
(2005)
Bioinformatics
, vol.21
, pp. 2301-2308
-
-
Tsafrir, D.1
Tsafrir, I.2
Ein-Dor, L.3
Zuk, O.4
Notterman, D.A.5
Domany, E.6
-
97
-
-
84953226880
-
BASiCS: Bayesian analysis of single-cell sequencing data
-
Vallejos, C. A., Marioni, J. C., and Richardson, S. (2015). BASiCS: Bayesian analysis of single-cell sequencing data. PLoS Comput. Biol. 11:e1004333. doi: 10.1371/journal.pcbi.1004333
-
(2015)
PLoS Comput. Biol
, vol.11
-
-
Vallejos, C.A.1
Marioni, J.C.2
Richardson, S.3
-
98
-
-
84984845042
-
Beta-poisson model for single-cell RNA-seq data analyses
-
Vu, T. N., Wills, Q. F., Kalari, K. R., Niu, N., Wang, L., Rantalainen, M., et al. (2016). Beta-poisson model for single-cell RNA-seq data analyses. Bioinformatics 32, 2128-2135. doi: 10.1093/bioinformatics/btw202
-
(2016)
Bioinformatics
, vol.32
, pp. 2128-2135
-
-
Vu, T.N.1
Wills, Q.F.2
Kalari, K.R.3
Niu, N.4
Wang, L.5
Rantalainen, M.6
-
99
-
-
85029436397
-
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning
-
Wang, B., Zhu, J., Pierson, E., and Batzoglou, S. (2016). Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. bioRxiv. 52225. doi: 10.1101/052225
-
(2016)
bioRxiv 52225
-
-
Wang, B.1
Zhu, J.2
Pierson, E.3
Batzoglou, S.4
-
100
-
-
84869109105
-
Multiple graph regularized protein domain ranking
-
Wang, J.-Y., Bensmail, H., and Gao, X. (2012). Multiple graph regularized protein domain ranking. BMC Bioinformatics 13:307. doi: 10.1186/1471-2105-13-307
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 307
-
-
Wang, J.-Y.1
Bensmail, H.2
Gao, X.3
-
101
-
-
78649345104
-
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery
-
Wang, K., Singh, D., Zeng, Z., Coleman, S. J., Huang, Y., Savich, G. L., et al. (2010). MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res. 38:e178. doi: 10.1093/nar/gkq622
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Wang, K.1
Singh, D.2
Zeng, Z.3
Coleman, S.J.4
Huang, Y.5
Savich, G.L.6
-
102
-
-
84969505817
-
SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data
-
Welch, J. D., Hartemink, A. J., and Prins, J. F. (2016). SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. Genome Biol. 17:106. doi: 10.1186/s13059-016-0975-3
-
(2016)
Genome Biol
, vol.17
, pp. 106
-
-
Welch, J.D.1
Hartemink, A.J.2
Prins, J.F.3
-
103
-
-
84961618446
-
GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality
-
Wu, T. D., Reeder, J., Lawrence, M., Becker, G., and Brauer, M. J. (2016). GMAP and GSNAP for genomic sequence alignment: enhancements to speed, accuracy, and functionality. Stat. Genomics Methods Protoc. 1418, 283-334. doi: 10.1007/978-1-4939-3578-9_15
-
(2016)
Stat. Genomics Methods Protoc
, vol.1418
, pp. 283-334
-
-
Wu, T.D.1
Reeder, J.2
Lawrence, M.3
Becker, G.4
Brauer, M.J.5
-
104
-
-
84931072284
-
Identification of cell types from single-cell transcriptomes using a novel clustering method
-
Xu, C., and Su, Z. (2015). Identification of cell types from single-cell transcriptomes using a novel clustering method. Bioinformatics 31, 1974-1980. doi: 10.1093/bioinformatics/btv088
-
(2015)
Bioinformatics
, vol.31
, pp. 1974-1980
-
-
Xu, C.1
Su, Z.2
-
105
-
-
84883743509
-
Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells
-
Yan, L., Yang, M., Guo, H., Yang, L., Wu, J., Li, R., et al. (2013). Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1131-1139. doi: 10.1038/nsmb.2660
-
(2013)
Nat. Struct. Mol. Biol
, vol.20
, pp. 1131-1139
-
-
Yan, L.1
Yang, M.2
Guo, H.3
Yang, L.4
Wu, J.5
Li, R.6
-
106
-
-
84873041419
-
HTQC: a fast quality control toolkit for illumina sequencing data
-
Yang, X., Liu, D., Liu, F., Wu, J., Zou, J., Xiao, X., et al. (2013). HTQC: a fast quality control toolkit for illumina sequencing data. BMC Bioinformatics 14:33. doi: 10.1186/1471-2105-14-33
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 33
-
-
Yang, X.1
Liu, D.2
Liu, F.3
Wu, J.4
Zou, J.5
Xiao, X.6
-
107
-
-
84924565530
-
Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq
-
Zeisel, A., Muñoz-Manchado, A. B., Codeluppi, S., Lönnerberg, P., Manno, G. L., Juréus, A., et al. (2015). Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science 347, 1138-1142. doi: 10.1126/science.aaa1934
-
(2015)
Science
, vol.347
, pp. 1138-1142
-
-
Zeisel, A.1
Muñoz-Manchado, A.B.2
Codeluppi, S.3
Lönnerberg, P.4
Manno, G.L.5
Juréus, A.6
-
108
-
-
84863054719
-
BIGpre: a quality assessment package for next-generation sequencing data
-
Zhang, T., Luo, Y., Liu, K., Pan, L., Zhang, B., Yu, J., et al. (2011). BIGpre: a quality assessment package for next-generation sequencing data. Genomics, Proteomics Bioinformatics 9, 238-244. doi: 10.1016/S1672-0229(11)60027-2
-
(2011)
Genomics, Proteomics Bioinformatics
, vol.9
, pp. 238-244
-
-
Zhang, T.1
Luo, Y.2
Liu, K.3
Pan, L.4
Zhang, B.5
Yu, J.6
-
109
-
-
84960877099
-
Constructing 3D interaction maps from 1D epigenomes
-
Zhu, Z., Chen, Z., Zhang, K., Wang, M., Medovoy, D., Whitaker, J. W., et al. (2016). Constructing 3D interaction maps from 1D epigenomes. Nat. Commun. 7:10812. doi: 10.1038/ncomms10812
-
(2016)
Nat. Commun
, vol.7
, pp. 10812
-
-
Zhu, Z.1
Chen, Z.2
Zhang, K.3
Wang, M.4
Medovoy, D.5
Whitaker, J.W.6
-
110
-
-
84977499231
-
pcaReduce: hierarchical clustering of single cell transcriptional profiles
-
Zurauskiene, J., and Yau, C. (2015). pcaReduce: hierarchical clustering of single cell transcriptional profiles. bioRxiv. 26385. doi: 10.1186/s12859-016-0984-y
-
(2015)
bioRxiv 26385
-
-
Zurauskiene, J.1
Yau, C.2
|