-
1
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
Encode Project Consortium
-
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
2
-
-
84920550975
-
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the sequencing quality control consortium
-
SEQC/MAQC-III Consortium
-
SEQC/MAQC-III Consortium. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the sequencing quality control consortium. Nat. Biotechnol. 32, 903-914 (2014).
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 903-914
-
-
-
3
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang, Z., Gerstein, M. & Snyder, M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10, 57-63 (2009).
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
4
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNASeq
-
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNASeq. Nat. Methods 5, 621-628 (2008).
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
5
-
-
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 (2013).
-
(2013)
Nat. Rev. Genet.
, vol.14
, pp. 618-630
-
-
Shapiro, E.1
Biezuner, T.2
Linnarsson, S.3
-
6
-
-
85038874186
-
Comparative analysis of single-cell RNA-sequencing methods
-
doi: 10.1101/035758
-
Ziegenhain, C. et al. Comparative analysis of single-cell RNA-sequencing methods. bioRxiv doi: 10.1101/035758 (2016).
-
(2016)
BioRxiv
-
-
Ziegenhain, C.1
-
7
-
-
84929687805
-
The technology and biology of single-cell RNA sequencing
-
Kolodziejczyk, A. A., Kim, J. K., Svensson, V., Marioni, J. C. & Teichmann, S. A. The technology and biology of single-cell RNA sequencing. Mol. Cell 58, 610-620 (2015).
-
(2015)
Mol. Cell
, vol.58
, pp. 610-620
-
-
Kolodziejczyk, A.A.1
Kim, J.K.2
Svensson, V.3
Marioni, J.C.4
Teichmann, S.A.5
-
8
-
-
84906228597
-
Single-cell RNA-seq: Advances and future challenges
-
Saliba, A.-E., Westermann, A. J., Gorski, S. A. & Vogel, J. Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res. 42, 8845-8860 (2014).
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 8845-8860
-
-
Saliba, A.-E.1
Westermann, A.J.2
Gorski, S.A.3
Vogel, J.4
-
9
-
-
63949083912
-
Amplification-free illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes
-
Kozarewa, I. et al. Amplification-free illumina sequencing-library preparation facilitates improved mapping and assembly of (G + C)-biased genomes. Nat. Methods 6, 291-295 (2009).
-
(2009)
Nat. Methods
, vol.6
, pp. 291-295
-
-
Kozarewa, I.1
-
10
-
-
77449147610
-
FRT-seq: Amplification-free, strand-specific transcriptome sequencing
-
Mamanova, L. et al. FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat. Methods 7, 130-132 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 130-132
-
-
Mamanova, L.1
-
11
-
-
84911861819
-
IVT-seq reveals extreme bias in RNA sequencing
-
Lahens, N. F. et al. IVT-seq reveals extreme bias in RNA sequencing. Genome Biol. 15, R86 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. R86
-
-
Lahens, N.F.1
-
12
-
-
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. Nat. Biotechnol. 30, 777-782 (2012).
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 777-782
-
-
Ramskold, D.1
-
13
-
-
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. Nat. Methods 10, 1096-1098 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 1096-1098
-
-
Picelli, S.1
-
14
-
-
84879692466
-
Comparative analysis of RNA sequencing methods for degraded or low-input samples
-
Adiconis, X. et al. Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat. Methods 10, 623-629 (2013).
-
(2013)
Nat. Methods
, vol.10
, pp. 623-629
-
-
Adiconis, X.1
-
15
-
-
84941201582
-
Single-cell messenger RNA sequencing reveals rare intestinal cell types
-
Grn, D. et al. Single-cell messenger RNA sequencing reveals rare intestinal cell types. Nature 525, 251-255 (2015).
-
(2015)
Nature
, vol.525
, pp. 251-255
-
-
Grn, D.1
-
16
-
-
84969812139
-
Characterization of directed differentiation by high-throughput single-cell RNA-Seq
-
doi: 10.1101/003236
-
Soumillon, M. et al. Characterization of directed differentiation by high-throughput single-cell RNA-Seq. bioRxiv doi: 10.1101/003236 (2014).
-
(2014)
BioRxiv
-
-
Soumillon, M.1
-
17
-
-
27144548491
-
The external RNA controls consortium: A progress report
-
Baker, S. C. et al. The external RNA controls consortium: a progress report. Nat. Methods 2, 731-734 (2005).
-
(2005)
Nat. Methods
, vol.2
, pp. 731-734
-
-
Baker, S.C.1
-
18
-
-
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
-
19
-
-
84928981375
-
PROPER: Comprehensive power evaluation for differential expression using RNA-seq
-
Wu, H., Wang, C. & Wu, Z. PROPER: comprehensive power evaluation for differential expression using RNA-seq. Bioinformatics 31, 233-241 (2015).
-
(2015)
Bioinformatics
, vol.31
, pp. 233-241
-
-
Wu, H.1
Wang, C.2
Wu, Z.3
-
20
-
-
84893910301
-
Quantitative assessment of single-cell RNA-sequencing methods
-
Wu, A. R. et al. Quantitative assessment of single-cell RNA-sequencing methods. Nat. Methods 11, 41-46 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 41-46
-
-
Wu, A.R.1
-
21
-
-
78649773164
-
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
-
Adey, A. et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol. 11, R119 (2010).
-
(2010)
Genome Biol.
, vol.11
, pp. R119
-
-
Adey, A.1
-
22
-
-
84924629414
-
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
-
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
23
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011).
-
(2011)
Nat. Genet.
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
-
24
-
-
84861964081
-
Systematic evaluation of factors influencing ChIP-seq fidelity
-
Chen, Y. et al. Systematic evaluation of factors influencing ChIP-seq fidelity. Nat. Methods 9, 609-614 (2012).
-
(2012)
Nat. Methods
, vol.9
, pp. 609-614
-
-
Chen, Y.1
-
25
-
-
0345548600
-
ChipCheck -A program predicting total hybridization equilibria for DNA binding to small oligonucleotide microarrays
-
Siegmund, K. H., Steiner, U. E. & Richert, C. ChipCheck -a program predicting total hybridization equilibria for DNA binding to small oligonucleotide microarrays. J. Chem. Inf. Comput. Sci. 43, 2153-2162 (2003).
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 2153-2162
-
-
Siegmund, K.H.1
Steiner, U.E.2
Richert, C.3
-
26
-
-
8844237589
-
Correcting log ratios for signal saturation in cDNA microarrays
-
Dodd, L. E., Korn, E. L., McShane, L. M., Chandramouli, G. V. R. & Chuang, E. Y. Correcting log ratios for signal saturation in cDNA microarrays. Bioinformatics 20, 2685-2693 (2004).
-
(2004)
Bioinformatics
, vol.20
, pp. 2685-2693
-
-
Dodd, L.E.1
Korn, E.L.2
McShane, L.M.3
Chandramouli, G.V.R.4
Chuang, E.Y.5
-
27
-
-
0036161083
-
Correcting for signal saturation errors in the analysis of microarray data
-
Hsiao, L. L. et al. Correcting for signal saturation errors in the analysis of microarray data. Biotechniques 32, 330-2, 334, 336 (2002).
-
(2002)
Biotechniques
, vol.32
, Issue.330-332
, pp. 334-336
-
-
Hsiao, L.L.1
-
28
-
-
84901831004
-
Validation of noise models for single-cell transcriptomics
-
Grn, D., Kester, L. & van Oudenaarden, A. Validation of noise models for single-cell transcriptomics. Nat. Methods 11, 637-640 (2014).
-
(2014)
Nat. Methods
, vol.11
, pp. 637-640
-
-
Grn, D.1
Kester, L.2
Van Oudenaarden, A.3
-
29
-
-
84871809302
-
STAR: Ultrafast universal RNA-seq aligner
-
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
-
30
-
-
84885997727
-
NextGenMap: Fast and accurate read mapping in highly polymorphic genomes
-
Sedlazeck, F. J., Rescheneder, P. & von Haeseler, A. NextGenMap: fast and accurate read mapping in highly polymorphic genomes. Bioinformatics 29, 2790-2791 (2013).
-
(2013)
Bioinformatics
, vol.29
, pp. 2790-2791
-
-
Sedlazeck, F.J.1
Rescheneder, P.2
Von Haeseler, A.3
-
31
-
-
84897397058
-
Featurecounts: An efficient general purpose program for assigning sequence reads to genomic features
-
Liao, Y., Smyth, G. K. & Shi, W. featurecounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930 (2014).
-
(2014)
Bioinformatics
, vol.30
, pp. 923-930
-
-
Liao, Y.1
Smyth, G.K.2
Shi, W.3
-
32
-
-
85055457123
-
PWMEnrich: PWM enrichment analysis
-
Cambridge Systems Biology Institute University of Cambridge, UK. URL
-
Stojnic, R. & Diez, D. PWMEnrich: PWM enrichment analysis. R package version 4.6.0. Cambridge Systems Biology Institute, University of Cambridge, UK. URL https://www.bioconductor.org/packages/release/bioc/html/PWMEnrich.html (2015).
-
(2015)
R Package Version 4.6.0
-
-
Stojnic, R.1
Diez, D.2
|