-
1
-
-
20444397431
-
Identification of bronchioalveolar stem cells in normal lung and lung cancer
-
Kim, C. F. B. et al. Identification of bronchioalveolar stem cells in normal lung and lung cancer. Cell 121, 823-835 (2005).
-
(2005)
Cell
, vol.121
, pp. 823-835
-
-
Kim, C.F.B.1
-
2
-
-
61549143051
-
Molecular staging of epithelial maturation using secretory cell-specific genes as markers
-
Zemke, A. C. et al. Molecular staging of epithelial maturation using secretory cell-specific genes as markers. Am. J. Respir. Cell Mol. Biol. 40, 340-348 (2009).
-
(2009)
Am. J. Respir. Cell Mol. Biol.
, vol.40
, pp. 340-348
-
-
Zemke, A.C.1
-
3
-
-
84864510497
-
Neuroepithelial body microenvironment is a niche for a distinct subset of Clara-like precursors in the developing airways
-
Guha, A. et al. Neuroepithelial body microenvironment is a niche for a distinct subset of Clara-like precursors in the developing airways. Proc. Natl Acad. Sci. USA 109, 12592-12597 (2012).
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 12592-12597
-
-
Guha, A.1
-
4
-
-
11144342766
-
Freshly isolated rat alveolar type i cells, type II cells, and cultured type II cells have distinct molecular phenotypes
-
Gonzalez, R. et al. Freshly isolated rat alveolar type I cells, type II cells, and cultured type II cells have distinct molecular phenotypes. Am. J. Physiol. Lung Cell. Mol. Physiol. 288, L179-L189 (2005).
-
(2005)
Am. J. Physiol. Lung Cell. Mol. Physiol.
, vol.288
-
-
Gonzalez, R.1
-
5
-
-
84865197613
-
Transcriptional programs controlling perinatal lung maturation
-
Xu, Y. et al. Transcriptional programs controlling perinatal lung maturation. PLoS ONE 7, e37046 (2012).
-
(2012)
PLoS ONE
, vol.7
-
-
Xu, Y.1
-
6
-
-
84896319764
-
Alveolar progenitor and stem cells in lung development, renewal and cancer
-
Desai, T. J., Brownfield, D. G.& Krasnow, M. A. Alveolar progenitor and stem cells in lung development, renewal and cancer. Nature 507, 190-194 (2014).
-
(2014)
Nature
, vol.507
, pp. 190-194
-
-
Desai, T.J.1
Brownfield, D.G.2
Krasnow, M.A.3
-
7
-
-
84893910301
-
Quantitative assessment of single-cell RNA-sequencing methods
-
Wu, A. R. et al. Quantitative assessment of single-cell RNA-sequencing methods. Nature Methods 11, 41-46 (2013).
-
(2013)
Nature Methods
, vol.11
, pp. 41-46
-
-
Wu, A.R.1
-
8
-
-
79959403670
-
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
-
Islam, S. et al. Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq. Genome Res. 21, 1160-1167 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1160-1167
-
-
Islam, S.1
-
9
-
-
84859621573
-
Highly multiplexed and strand-specific single-cell RNA 59 end sequencing
-
Islam, S. et al. Highly multiplexed and strand-specific single-cell RNA 59 end sequencing. Nature Protocols 7, 813-828 (2012).
-
(2012)
Nature Protocols
, vol.7
, pp. 813-828
-
-
Islam, S.1
-
10
-
-
84878997106
-
Single-cell transcriptomics reveals bimodality inexpression and splicing in immune cells
-
Shalek, A. K. et al. Single-cell transcriptomics reveals bimodality inexpression and splicing in immune cells. Nature 498, 236-240 (2013).
-
(2013)
Nature
, vol.498
, pp. 236-240
-
-
Shalek, A.K.1
-
11
-
-
84876085773
-
Quartz-Seq: A highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity
-
Sasagawa, Y. et al. Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity. Genome Biol. 14, R31 (2013).
-
(2013)
Genome Biol.
, vol.14
-
-
Sasagawa, Y.1
-
12
-
-
55249089662
-
Whole genome amplification by T7-based linear amplification of DNA (TLAD). II. Second-strand synthesis and in vitro transcription
-
Liu, C. L., Bernstein, B. E. & Schreiber, S. L. Whole genome amplification by T7-based linear amplification of DNA (TLAD). II. Second-strand synthesis and in vitro transcription. CSH Protocols, http://dx.doi.org/10.1101/ pdb.prot5003 (2008).
-
(2008)
CSH Protocols
-
-
Liu, C.L.1
Bernstein, B.E.2
Schreiber, S.L.3
-
13
-
-
84866953427
-
CEL-Seq:single-cell RNA-Seq by multiplexed linear amplification
-
Hashimshony, T., Wagner, F., Sher, N. & Yanai, I. CEL-Seq: single-cell RNA-Seq by multiplexed linear amplification. Cell Rep. 2, 666-673 (2012).
-
(2012)
Cell Rep.
, vol.2
, pp. 666-673
-
-
Hashimshony, T.1
Wagner, F.2
Sher, N.3
Yanai, I.4
-
14
-
-
84864880991
-
Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells
-
Ramskold, D. et al. Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells. Nature Biotechnol. 30, 777-782 (2012).
-
(2012)
Nature Biotechnol
, vol.30
, pp. 777-782
-
-
Ramskold, D.1
-
15
-
-
80054053911
-
Whole-transcriptome RNAseq analysis from minute amount of total RNA
-
Tariq, M. A., Kim, H. J., Jejelowo, O. & Pourmand, N. Whole-transcriptome RNAseq analysis from minute amount of total RNA. Nucleic Acids Res. 39, e120 (2011).
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Tariq, M.A.1
Kim, H.J.2
Jejelowo, O.3
Pourmand, N.4
-
16
-
-
84887101406
-
Smart-seq2 for sensitive full-length transcriptome profiling in single cells
-
Picelli, S. et al.Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nature Methods 10, 1096-1098 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 1096-1098
-
-
Picelli, S.1
-
17
-
-
84887109584
-
Accounting for technical noise in single-cell RNA-seq experiments
-
Brennecke, P. et al. Accounting for technical noise in single-cell RNA-seq experiments. Nature Methods 10, 1093-1095 (2013).
-
(2013)
Nature Methods
, vol.10
, pp. 1093-1095
-
-
Brennecke, P.1
-
18
-
-
67349146589
-
MRNA-Seq whole-transcriptome analysis of a single cell
-
Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nature Methods 6, 377-382 (2009).
-
(2009)
Nature Methods
, vol.6
, pp. 377-382
-
-
Tang, F.1
-
19
-
-
77749323185
-
RNA-Seq analysis to capture the transcriptomelandscape of a single cell
-
Tang, F. et al.RNA-Seq analysis to capture the transcriptomelandscape of a single cell. Nature Protocols 5, 516-535 (2010).
-
(2010)
Nature Protocols
, vol.5
, pp. 516-535
-
-
Tang, F.1
-
20
-
-
77956412152
-
Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis
-
Tang, F. et al. Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis. Cell Stem Cell 6, 468-478 (2010).
-
(2010)
Cell Stem Cell
, vol.6
, pp. 468-478
-
-
Tang, F.1
-
21
-
-
61449172037
-
Systematic and integrative analysis of large genelists usingDAVIDbioinformatics resources
-
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large genelists usingDAVIDbioinformatics resources.Nature Protocols 4,44-57 (2009).
-
(2009)
Nature Protocols
, vol.4
, pp. 44-57
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
22
-
-
33746617492
-
Hop functions downstream of Nkx2.1 and GATA6 to mediate HDAC-dependent negative regulation of pulmonary gene expression
-
Yin, Z. et al. Hop functions downstream of Nkx2.1 and GATA6 to mediate HDAC-dependent negative regulation of pulmonary gene expression. Am. J. Physiol. Lung Cell. Mol. Physiol. 291, L191-L199 (2006).
-
(2006)
Am. J. Physiol. Lung Cell. Mol. Physiol
, vol.291
-
-
Yin, Z.1
-
23
-
-
3242670531
-
Gene targeting reveals a widespread role for the high-mobility-group transcription factor Sox11 in tissue remodeling
-
Sock, E. et al. Gene targeting reveals a widespread role for the high-mobility-group transcription factor Sox11 in tissue remodeling. Mol. Cell. Biol. 24, 6635-6644 (2004).
-
(2004)
Mol. Cell. Biol.
, vol.24
, pp. 6635-6644
-
-
Sock, E.1
-
24
-
-
78649613797
-
Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma
-
Wang, X. et al. Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma. PLoS ONE 5, e14085 (2010).
-
(2010)
PLoS ONE
, vol.5
-
-
Wang, X.1
-
25
-
-
65449136284
-
TopHat: Discovering splice junctions with RNA-Seq
-
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
26
-
-
83255177150
-
Single-cell dissection of transcriptional heterogeneity in human colon tumors
-
Dalerba, P. et al. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nature Biotechnol. 29, 1120-1127 (2011).
-
(2011)
Nature Biotechnol.
, vol.29
, pp. 1120-1127
-
-
Dalerba, P.1
-
28
-
-
79959946669
-
Integrin a6b4 identifies an adult distal lung epithelial population with regenerative potential in mice
-
Chapman, H. A. et al. Integrin a6b4 identifies an adult distal lung epithelial population with regenerative potential in mice. J. Clin. Invest. 121, 2855-2862 (2011).
-
(2011)
J. Clin. Invest.
, vol.121
, pp. 2855-2862
-
-
Chapman, H.A.1
-
29
-
-
83255193921
-
Interconversion between intestinal stem cell populations in distinct niches
-
Takeda, N. et al. Interconversion between intestinal stem cell populations in distinct niches. Science 334, 1420-1424 (2011).
-
(2011)
Science
, vol.334
, pp. 1420-1424
-
-
Takeda, N.1
-
30
-
-
84900562880
-
-
Babraham Institute Babraham Bioinformatics
-
Babraham Institute. Babraham Bioinformatics. FASTQC. http://www. bioinformatics.bbsrc.ac.uk/projects/fastqc.
-
FASTQC
-
-
-
31
-
-
80255127234
-
Cutadapt removes adapter sequences from high-throughput sequencing reads EMBnet
-
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10-12 (2011).
-
(2011)
Journal
, vol.17
, pp. 10-12
-
-
Martin, M.1
-
32
-
-
79952422304
-
Quality control and preprocessing of metagenomic datasets
-
Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 863-864
-
-
Schmieder, R.1
Edwards, R.2
-
33
-
-
62349130698
-
Ultrafastandmemory-efficient alignment of short DNA sequences to the human genome
-
Langmead,B.,Trapnell, C.,Pop,M.&Salzberg,S.Ultrafastandmemory- efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
-
(2009)
Genome Biol.
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.4
-
34
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nature Methods 9, 357-359 (2012).
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
35
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
36
-
-
27144548491
-
The External RNA Controls Consortium: A progress report
-
Baker, S. C. et al. The External RNA Controls Consortium: a progress report. Nature Methods 2, 731-734 (2005).
-
(2005)
Nature Methods
, vol.2
, pp. 731-734
-
-
Baker, S.C.1
-
37
-
-
80052521697
-
Synthetic spike-in standards for RNA-seq experiments
-
Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543-1551 (2011).
-
(2011)
Genome Res.
, vol.21
, pp. 1543-1551
-
-
Jiang, L.1
-
38
-
-
84862198697
-
AnimalTFDB: A comprehensive animal transcription factor database
-
Zhang, H.-M. et al. AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res. 40, D144-D149 (2012).
-
(2012)
Nucleic Acids Res.
, vol.40
-
-
Zhang, H.-M.1
-
39
-
-
0033452362
-
Prediction of gene function by genome-scale expression analysis: Prostate cancer-associated genes
-
Walker, M. G., Volkmuth, W., Sprinzak, E., Hodgson, D. & Klingler, T. Prediction of gene function by genome-scale expression analysis: prostate cancer-associated genes. Genome Res. 9, 1198-1203 (1999).
-
(1999)
Genome Res.
, vol.9
, pp. 1198-1203
-
-
Walker, M.G.1
Volkmuth, W.2
Sprinzak, E.3
Hodgson, D.4
Klingler, T.5
-
40
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37, 1-13 (2009).
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 1-13
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
41
-
-
84866053210
-
Radial construction of an arterial wall
-
Greif, D. M. et al. Radial construction of an arterial wall. Dev. Cell 23, 482-493 (2012).
-
(2012)
Dev. Cell
, vol.23
, pp. 482-493
-
-
Greif, D.M.1
|