-
1
-
-
84893242996
-
RNA-seq differential expression studies: more sequence or more replication?
-
24319002, ():–.
-
Liu Y, Zhou J, White KP, (2014) RNA-seq differential expression studies: more sequence or more replication?Bioinformatics30: 301–304. doi: 10.1093/bioinformatics/btt68824319002
-
(2014)
Bioinformatics
, vol.30
, pp. 301-304
-
-
Liu, Y.1
Zhou, J.2
White, K.P.3
-
2
-
-
79960208246
-
Sequencing technology does not eliminate biological variability
-
21747377, ().:–.
-
Hansen KD, Wu Z, Irizarry RA, Leek JT, (2011) Sequencing technology does not eliminate biological variability. Nature Biotechnology29: 572–573. doi: 10.1038/nbt.191021747377
-
(2011)
Nature Biotechnology
, vol.29
, pp. 572-573
-
-
Hansen, K.D.1
Wu, Z.2
Irizarry, R.A.3
Leek, J.T.4
-
3
-
-
84866158885
-
Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing
-
22985019, . ().:.
-
Robles J, Qureshi S, Stephen S, Wilson S, Burden C, et al. (2012) Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing. BMC Genomics13: 484. doi: 10.1186/1471-2164-13-48422985019
-
(2012)
BMC Genomics
, vol.13
, pp. 484
-
-
Robles, J.1
Qureshi, S.2
Stephen, S.3
Wilson, S.4
Burden, C.5
-
4
-
-
84889049862
-
Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data
-
24314022, ().:.
-
Li C-I, Su P-F, Shyr Y, (2013) Sample size calculation based on exact test for assessing differential expression analysis in RNA-seq data. BMC Bioinformatics14: 357. doi: 10.1186/1471-2105-14-35724314022
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 357
-
-
Li, C.-I.1
Su, P.-F.2
Shyr, Y.3
-
5
-
-
84922578455
-
Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study
-
. ().:–.
-
Li S, Tighe SW, Nicolet CM, Grove D, Levy S, et al. (2014) Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nature Biotechnology32: 915–925. doi: 10.1038/nbt.2972
-
(2014)
Nature Biotechnology
, vol.32
, pp. 915-925
-
-
Li, S.1
Tighe, S.W.2
Nicolet, C.M.3
Grove, D.4
Levy, S.5
-
6
-
-
84909587930
-
Detecting and correcting systematic variation in large-scale RNA sequencing data
-
. ().:–.
-
Li S, Labaj PP, Zumbo P, Sykacek P, Shi W, et al. (2014) Detecting and correcting systematic variation in large-scale RNA sequencing data. Nature Biotechnology32: 888–895. doi: 10.1038/nbt.3000
-
(2014)
Nature Biotechnology
, vol.32
, pp. 888-895
-
-
Li, S.1
Labaj, P.P.2
Zumbo, P.3
Sykacek, P.4
Shi, W.5
-
7
-
-
84909644283
-
Normalization of RNA-seq data using factor analysis of control genes or samples
-
().:–.
-
Risso D, Ngai J, Speed TP, Dudoit S, (2014) Normalization of RNA-seq data using factor analysis of control genes or samples. Nature Biotechnology32: 896–902. doi: 10.1038/nbt.2931
-
(2014)
Nature Biotechnology
, vol.32
, pp. 896-902
-
-
Risso, D.1
Ngai, J.2
Speed, T.P.3
Dudoit, S.4
-
8
-
-
84912527013
-
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
-
. ().:–.
-
Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, et al. (2014) The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nature Biotechnology32: 926–932. doi: 10.1038/nbt.3001
-
(2014)
Nature Biotechnology
, vol.32
, pp. 926-932
-
-
Wang, C.1
Gong, B.2
Bushel, P.R.3
Thierry-Mieg, J.4
Thierry-Mieg, D.5
-
9
-
-
84920550975
-
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
-
().:–.
-
Consortium SM-I (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotech32: 903–914.
-
(2014)
Nat Biotech
, vol.32
, pp. 903-914
-
-
-
10
-
-
33644873184
-
BioGRID: a general repository for interaction datasets
-
16381927, . ().:–.
-
Stark C, Breitkreutz B-J, Reguly T, Boucher L, Breitkreutz A, et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Research34: D535–D539. 16381927
-
(2006)
Nucleic Acids Research
, vol.34
, pp. D535-D539
-
-
Stark, C.1
Breitkreutz, B.-J.2
Reguly, T.3
Boucher, L.4
Breitkreutz, A.5
-
11
-
-
84859098571
-
The sva package for removing batch effects and other unwanted variation in high-throughput experiments
-
22257669, ().:–.
-
Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD, (2012) The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics28: 882–883. doi: 10.1093/bioinformatics/bts03422257669
-
(2012)
Bioinformatics
, vol.28
, pp. 882-883
-
-
Leek, J.T.1
Johnson, W.E.2
Parker, H.S.3
Jaffe, A.E.4
Storey, J.D.5
-
12
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in high-throughput data
-
. ().:
-
Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, et al. (2010) Tackling the widespread and critical impact of batch effects in high-throughput data. Nature reviews Genetics11: doi: 10.1038/nrg2825
-
(2010)
Nature reviews Genetics
, vol.11
-
-
Leek, J.T.1
Scharpf, R.B.2
Bravo, H.C.3
Simcha, D.4
Langmead, B.5
-
13
-
-
33645241407
-
The RIN: an RNA integrity number for assigning integrity values to RNA measurements
-
16448564, . ().:.
-
Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, et al. (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Molecular Biology7: 3. 16448564
-
(2006)
BMC Molecular Biology
, vol.7
, pp. 3
-
-
Schroeder, A.1
Mueller, O.2
Stocker, S.3
Salowsky, R.4
Leiber, M.5
-
14
-
-
84865074382
-
RSeQC: quality control of RNA-seq experiments
-
22743226, ().:–.
-
Wang L, Wang S, Li W, (2012) RSeQC: quality control of RNA-seq experiments. Bioinformatics28: 2184–2185. doi: 10.1093/bioinformatics/bts35622743226
-
(2012)
Bioinformatics
, vol.28
, pp. 2184-2185
-
-
Wang, L.1
Wang, S.2
Li, W.3
-
15
-
-
84861743958
-
RNA-SeQC: RNA-seq metrics for quality control and process optimization
-
22539670, . ().:–.
-
DeLuca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire M-D, et al. (2012) RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics28: 1530–1532. doi: 10.1093/bioinformatics/bts19622539670
-
(2012)
Bioinformatics
, vol.28
, pp. 1530-1532
-
-
DeLuca, D.S.1
Levin, J.Z.2
Sivachenko, A.3
Fennell, T.4
Nazaire, M.-D.5
-
17
-
-
84865757142
-
Landscape of transcription in human cells
-
22955620, . ().:–.
-
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, et al. (2012) Landscape of transcription in human cells. Nature489: 101–108. doi: 10.1038/nature1123322955620
-
(2012)
Nature
, vol.489
, pp. 101-108
-
-
Djebali, S.1
Davis, C.A.2
Merkel, A.3
Dobin, A.4
Lassmann, T.5
-
18
-
-
84866870523
-
SERE: single-parameter quality control and sample comparison for RNA-Seq
-
23033915, ().:.
-
Schulze SK, Kanwar R, Golzenleuchter M, Therneau TM, Beutler AS, (2012) SERE: single-parameter quality control and sample comparison for RNA-Seq. BMC Genomics13: 524. doi: 10.1186/1471-2164-13-52423033915
-
(2012)
BMC Genomics
, vol.13
, pp. 524
-
-
Schulze, S.K.1
Kanwar, R.2
Golzenleuchter, M.3
Therneau, T.M.4
Beutler, A.S.5
-
19
-
-
84903396895
-
Development of ERCC RNA Spike-In Control Mixes
-
. ().:–.
-
Lemire A, Lea K, Batten D, Jian Gu S, Whitley P, et al. (2011) Development of ERCC RNA Spike-In Control Mixes. Journal of Biomolecular Techniques: JBT22: S46–S46.
-
(2011)
Journal of Biomolecular Techniques: JBT
, vol.22
, pp. S46-S46
-
-
Lemire, A.1
Lea, K.2
Batten, D.3
Jian Gu, S.4
Whitley, P.5
-
21
-
-
50649089207
-
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
-
18550803, ().:–.
-
Marioni J, Mason C, Mane S, Stephens M, Gilad Y, (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Research18: 1509–1517. doi: 10.1101/gr.079558.10818550803
-
(2008)
Genome Research
, vol.18
, pp. 1509-1517
-
-
Marioni, J.1
Mason, C.2
Mane, S.3
Stephens, M.4
Gilad, Y.5
-
22
-
-
79952759697
-
Human transcriptome array for high-throughput clinical studies
-
. ().:–.
-
Xu W, Seok J, Mindrinos MN, Schweitzer AC, Jiang H, et al. (2011) Human transcriptome array for high-throughput clinical studies. Proceedings of the National Academy of Sciences108: 3707–3712.
-
(2011)
Proceedings of the National Academy of Sciences
, vol.108
, pp. 3707-3712
-
-
Xu, W.1
Seok, J.2
Mindrinos, M.N.3
Schweitzer, A.C.4
Jiang, H.5
-
23
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
16964229, ().:–.
-
(2006) The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology24: 1151–1161. 16964229
-
(2006)
Nature Biotechnology
, vol.24
, pp. 1151-1161
-
-
-
24
-
-
0001165055
-
Frequency distribution of the values of the correlation coefficient in samples from an indefinitely large population
-
().:–.
-
Fisher RA, (1915) Frequency distribution of the values of the correlation coefficient in samples from an indefinitely large population. Biometrika: 507–521.
-
(1915)
Biometrika
, pp. 507-521
-
-
Fisher, R.A.1
-
25
-
-
0032441150
-
Cluster analysis and display of genome-wide expression patterns
-
9843981, ().:–.
-
Eisen MB, Spellman PT, Brown PO, Botstein D, (1998) Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America95: 14863–14868. 9843981
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, pp. 14863-14868
-
-
Eisen, M.B.1
Spellman, P.T.2
Brown, P.O.3
Botstein, D.4
-
26
-
-
0141993704
-
A gene-coexpression network for global discovery of conserved genetic modules
-
12934013, ().:–.
-
Stuart JM, Segal E, Koller D, Kim SK, (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science302: 249–255. 12934013
-
(2003)
Science
, vol.302
, pp. 249-255
-
-
Stuart, J.M.1
Segal, E.2
Koller, D.3
Kim, S.K.4
-
27
-
-
84936817216
-
Guidance for RNA-seq co-expression network construction and analysis: safety in numbers
-
25717192, ().:–.
-
Ballouz S, Verleyen W, Gillis J, (2015) Guidance for RNA-seq co-expression network construction and analysis: safety in numbers. Bioinformatics31: 2123–2130. doi: 10.1093/bioinformatics/btv11825717192
-
(2015)
Bioinformatics
, vol.31
, pp. 2123-2130
-
-
Ballouz, S.1
Verleyen, W.2
Gillis, J.3
-
28
-
-
0034682504
-
Fundamental patterns underlying gene expression profiles: Simplicity from complexity
-
. ().:–.
-
Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, et al. (2000) Fundamental patterns underlying gene expression profiles: Simplicity from complexity. Proceedings of the National Academy of Sciences97: 8409–8414.
-
(2000)
Proceedings of the National Academy of Sciences
, vol.97
, pp. 8409-8414
-
-
Holter, N.S.1
Mitra, M.2
Maritan, A.3
Cieplak, M.4
Banavar, J.R.5
-
29
-
-
84923292191
-
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
-
25599176, . ().:–.
-
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, et al. (2015) Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature Biotechnology33: 155–160. doi: 10.1038/nbt.310225599176
-
(2015)
Nature Biotechnology
, vol.33
, pp. 155-160
-
-
Buettner, F.1
Natarajan, K.N.2
Casale, F.P.3
Proserpio, V.4
Scialdone, A.5
-
30
-
-
84961371413
-
Lean Big Data integration in systems biology and systems pharmacology
-
25109570, . ().:–.
-
Ma’ayan A, Rouillard AD, Clark NR, Wang Z, Duan Q, et al. (2014) Lean Big Data integration in systems biology and systems pharmacology. Trends in Pharmacological Sciences35: 450–460. doi: 10.1016/j.tips.2014.07.00125109570
-
(2014)
Trends in Pharmacological Sciences
, vol.35
, pp. 450-460
-
-
Ma’ayan, A.1
Rouillard, A.D.2
Clark, N.R.3
Wang, Z.4
Duan, Q.5
-
31
-
-
0034960264
-
Missing value estimation methods for DNA microarrays
-
11395428, . ().:–.
-
Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, et al. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics17: 520–525. 11395428
-
(2001)
Bioinformatics
, vol.17
, pp. 520-525
-
-
Troyanskaya, O.1
Cantor, M.2
Sherlock, G.3
Brown, P.4
Hastie, T.5
-
32
-
-
84855897445
-
MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis
-
22116060, ().:.
-
Kang DD, Sibille E, Kaminski N, Tseng GC, (2012) MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. Nucleic Acids Research40: e15. doi: 10.1093/nar/gkr107122116060
-
(2012)
Nucleic Acids Research
, vol.40
, pp. e15
-
-
Kang, D.D.1
Sibille, E.2
Kaminski, N.3
Tseng, G.C.4
-
33
-
-
84942322190
-
Systematic noise degrades gene co-expression signals but can be corrected
-
().:–.
-
Freytag S, Gagnon-Bartsch J, Speed TP, Bahlo M, (2015) Systematic noise degrades gene co-expression signals but can be corrected. BMC Bioinformatics16: 1–17.
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 1-17
-
-
Freytag, S.1
Gagnon-Bartsch, J.2
Speed, T.P.3
Bahlo, M.4
-
34
-
-
79955550445
-
A User's Guide to the Encyclopedia of DNA Elements (ENCODE)
-
21526222, ().:.
-
The EPC (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biology9: e1001046. doi: 10.1371/journal.pbio.100104621526222
-
(2011)
PLoS Biology
, vol.9
, pp. e1001046
-
-
-
35
-
-
84964715312
-
-
(2011) BrainSpan: Atlas of the Developing Human Brain [Internet].
-
(2011) BrainSpan: Atlas of the Developing Human Brain [Internet].
-
-
-
-
36
-
-
84964795779
-
-
()[Internet].:.
-
(2010) SRA Handbook[Internet]. Bethesda (MD): National Center for Biotechnology Information (US).
-
(2010)
SRA Handbook
-
-
-
37
-
-
84859210032
-
Fast gapped-read alignment with Bowtie 2
-
22388286, ().:–.
-
Langmead B, Salzberg SL, (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods9: 357–359. doi: 10.1038/nmeth.192322388286
-
(2012)
Nature Methods
, vol.9
, pp. 357-359
-
-
Langmead, B.1
Salzberg, S.L.2
-
38
-
-
78651426148
-
RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries
-
21134889, . ().:–.
-
Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, et al. (2011) RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics27: 281–283. doi: 10.1093/bioinformatics/btq64321134889
-
(2011)
Bioinformatics
, vol.27
, pp. 281-283
-
-
Habegger, L.1
Sboner, A.2
Gianoulis, T.A.3
Rozowsky, J.4
Agarwal, A.5
-
39
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
22383036, . ().:–.
-
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols7: 562–578. doi: 10.1038/nprot.2012.01622383036
-
(2012)
Nature Protocols
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Goff, L.3
Pertea, G.4
Kim, D.5
-
40
-
-
84865543515
-
Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data
-
22782548, . ().:–.
-
Zoubarev A, Hamer KM, Keshav KD, McCarthy EL, Santos JRC, et al. (2012) Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinformatics28: 2272–2273. doi: 10.1093/bioinformatics/bts43022782548
-
(2012)
Bioinformatics
, vol.28
, pp. 2272-2273
-
-
Zoubarev, A.1
Hamer, K.M.2
Keshav, K.D.3
McCarthy, E.L.4
Santos, J.R.C.5
-
41
-
-
79961123152
-
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
-
().:–.
-
Li B, Dewey CN, (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics12: 1–16.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 1-16
-
-
Li, B.1
Dewey, C.N.2
-
42
-
-
0034069495
-
Gene Ontology: tool for the unification of biology
-
10802651, . ().:–.
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. Nature Genetics25: 25–29. 10802651
-
(2000)
Nature Genetics
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
|