-
1
-
-
42749087226
-
Highly integrated single-base resolution maps of the epigenome in Arabidopsis
-
Lister,R., O’Malley,R.C., Tonti-Filippini,J., Gregory,B.D., Berry,C.C., Millar,A.H. and Ecker,J.R. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell, 133, 523–536.
-
(2008)
Cell
, vol.133
, pp. 523-536
-
-
Lister, R.1
O’Malley, R.C.2
Tonti-Filippini, J.3
Gregory, B.D.4
Berry, C.C.5
Millar, A.H.6
Ecker, J.R.7
-
2
-
-
45549088326
-
The transcriptional landscape of the yeast genome defined by RNA sequencing
-
Nagalakshmi,U., Wang,Z., Waern,K., Shou,C., Raha,D., Gerstein,M. and Snyder,M. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344–1349.
-
(2008)
SCIENCE
, vol.320
, pp. 1344-1349
-
-
Nagalakshmi, U.1
Wang, Z.2
Waern, K.3
Shou, C.4
Raha, D.5
Gerstein, M.6
Snyder, M.7
-
3
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi,A., Williams,B.A., McCue,K., Schaeffer,L. and Wold,B. (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods, 5, 621–628.
-
(2008)
Nat. Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
4
-
-
78651301328
-
The sequence read archive
-
Leinonen,R., Sugawara,H. and Shumway,M. (2011) The sequence read archive. Nucleic Acids Res., 39, D19–D21.
-
(2011)
Nucleic Acids Res
, vol.39
, pp. D19-D21
-
-
Leinonen, R.1
Sugawara, H.2
Shumway, M.3
-
5
-
-
84877768911
-
RNA sequencing of cancer reveals novel splicing alterations
-
Eswaran,J., Horvath,A., Godbole,S., Reddy,S.D., Mudvari,P., Ohshiro,K., Cyanam,D., Nair,S., Fuqua,S.A.W., Polyak,K. et al. (2013) RNA sequencing of cancer reveals novel splicing alterations. Scientific Rep., 3, 1689.
-
(2013)
Scientific Rep
, vol.3
, pp. 1689
-
-
Eswaran, J.1
Horvath, A.2
Godbole, S.3
Reddy, S.D.4
Mudvari, P.5
Ohshiro, K.6
Cyanam, D.7
Nair, S.8
Fuqua, S.A.W.9
Polyak, K.10
-
6
-
-
84891437638
-
An integrated model of the transcriptome of HER2-positive breast cancer
-
Kalari,K.R., Necela,B.M., Tang,X., Thompson,K.J., Lau,M., Eckel-Passow,J.E., Kachergus,J.M., Anderson,S.K., Sun,Z., Baheti,S. et al. (2013) An integrated model of the transcriptome of HER2-positive breast cancer. PLOS ONE, 8, e79298.
-
(2013)
PLoS One
, vol.8
-
-
Kalari, K.R.1
Necela, B.M.2
Tang, X.3
Thompson, K.J.4
Lau, M.5
Eckel-Passow, J.E.6
Kachergus, J.M.7
Anderson, S.K.8
Sun, Z.9
Baheti, S.10
-
7
-
-
85014052295
-
Flexible expressed region analysis for RNA-seq with derfinder
-
Collado-Torres,L., Nellore,A., Frazee,A.C., Wilks,C., Love,M.I., Langmead,B., Irizarry,R.A., Leek,J.T. and Jaffe,A.E. (2017) Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Res., 45, e9.
-
(2017)
Nucleic Acids Res
, vol.45
, pp. e9
-
-
Collado-Torres, L.1
Nellore, A.2
Frazee, A.C.3
Wilks, C.4
Love, M.I.5
Langmead, B.6
Irizarry, R.A.7
Leek, J.T.8
Jaffe, A.E.9
-
8
-
-
85014594340
-
Don’t let useful data go to waste
-
Denk,F. (2017) Don’t let useful data go to waste. Nat. News, 543, 7.
-
(2017)
Nat. News
, vol.543
, pp. 7
-
-
Denk, F.1
-
9
-
-
85017363752
-
Reproducible RNA-seq analysis using recount2
-
Collado-Torres,L., Nellore,A., Kammers,K., Ellis,S.E., Taub,M.A., Hansen,K.D., Jaffe,A.E., Langmead,B. and Leek,J.T. (2017) Reproducible RNA-seq analysis using recount2. Nat. Biotechnol., 35, 319–321.
-
(2017)
Nat. Biotechnol.
, vol.35
, pp. 319-321
-
-
Collado-Torres, L.1
Nellore, A.2
Kammers, K.3
Ellis, S.E.4
Taub, M.A.5
Hansen, K.D.6
Jaffe, A.E.7
Langmead, B.8
Leek, J.T.9
-
10
-
-
85044381193
-
Rail-RNA: Scalable analysis of RNA-seq splicing and coverage
-
Nellore,A., Collado-Torres,L., Jaffe,A.E., Alquicira-Hernández,J., Wilks,C., Pritt,J., Morton,J., Leek,J.T. and Langmead,B. (2017) Rail-RNA: Scalable analysis of RNA-seq splicing and coverage. Bioinformatics, 33, 4033–4040.
-
(2017)
Bioinformatics
, vol.33
, pp. 4033-4040
-
-
Nellore, A.1
Collado-Torres, L.2
Jaffe, A.E.3
Alquicira-Hernández, J.4
Wilks, C.5
Pritt, J.6
Morton, J.7
Leek, J.T.8
Langmead, B.9
-
11
-
-
34848914038
-
Capturing heterogeneity in gene expression studies by surrogate variable analysis
-
Leek,J.T. and Storey,J.D. (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet., 3, 1724–1735.
-
(2007)
PLoS Genet.
, vol.3
, pp. 1724-1735
-
-
Leek, J.T.1
Storey, J.D.2
-
12
-
-
84878682420
-
The Genotype-Tissue Expression (GTEx) project
-
Lonsdale,J., Thomas,J., Salvatore,M., Phillips,R., Lo,E., Shad,S., Hasz,R., Walters,G., Garcia,F., Young,N. et al. (2013) The genotype-tissue expression (GTEx) project. Nat. Genet., 45, 580–585.
-
(2013)
Nat. Genet.
, vol.45
, pp. 580-585
-
-
Lonsdale, J.1
Thomas, J.2
Salvatore, M.3
Phillips, R.4
Lo, E.5
Shad, S.6
Hasz, R.7
Walters, G.8
Garcia, F.9
Young, N.10
-
13
-
-
84929001104
-
The Genotype-Tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans
-
Consortium,T.G. (2015) The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science, 348, 648–660.
-
(2015)
SCIENCE
, vol.348
, pp. 648-660
-
-
Consortium, T.G.1
-
14
-
-
85029793308
-
MetaSRA: Normalized human sample-specific metadata for the Sequence Read Archive
-
Bernstein,M.N., Doan,A. and Dewey,C.N. (2017) MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive. Bioinformatics, 33, 2914–2923.
-
(2017)
Bioinformatics
, vol.33
, pp. 2914-2923
-
-
Bernstein, M.N.1
Doan, A.2
Dewey, C.N.3
-
15
-
-
78649903173
-
Sex bias in neuroscience and biomedical research
-
Beery,A.K. and Zucker,I. (2011) Sex bias in neuroscience and biomedical research. Neurosci. Biobehav. Rev., 35, 565–572.
-
(2011)
Neurosci Biobehav Rev
, vol.35
, pp. 565-572
-
-
Beery, A.K.1
Zucker, I.2
-
16
-
-
84958904696
-
Twenty years and still counting: Including women as participants and studying sex and gender in biomedical research
-
Mazure,C.M. and Jones,D.P. (2015) Twenty years and still counting: including women as participants and studying sex and gender in biomedical research. BMC Women’s Health, 15, 94.
-
(2015)
BMC Womens Health
, vol.15
, pp. 94
-
-
Mazure, C.M.1
Jones, D.P.2
-
17
-
-
84902690266
-
Differential expression analysis of RNA-seq data at single-base resolution
-
Frazee,A.C., Sabunciyan,S., Hansen,K.D., Irizarry,R.A. and Leek,J.T. (2014) Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics (England), 15, 413–426.
-
(2014)
Biostatistics (England)
, vol.15
, pp. 413-426
-
-
Frazee, A.C.1
Sabunciyan, S.2
Hansen, K.D.3
Irizarry, R.A.4
Leek, J.T.5
-
18
-
-
84901358543
-
BWTool: A tool for bigwig files
-
Pohl,A. and Beato,M. (2014) bwtool: a tool for bigWig files. Bioinformatics, 30, 1618–1619.
-
(2014)
Bioinformatics
, vol.30
, pp. 1618-1619
-
-
Pohl, A.1
Beato, M.2
-
19
-
-
84926507971
-
Limma powers differential expression analyses for RNA-sequencing and microarray studies
-
Ritchie,M.E., Phipson,B., Wu,D., Hu,Y., Law,C.W., Shi,W. and Smyth,G.K. (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res., 43, e47.
-
(2015)
Nucleic Acids Res
, vol.43
, pp. e47
-
-
Ritchie, M.E.1
Phipson, B.2
Wu, D.3
Hu, Y.4
Law, C.W.5
Shi, W.6
Smyth, G.K.7
-
20
-
-
84897548625
-
Minfi: A flexible and comprehensive bioconductor package for the analysis of infinium DNA methylation microarrays
-
Aryee,M.J., Jaffe,A.E., Corrada-Bravo,H., Ladd-Acosta,C., Feinberg,A.P., Hansen,K.D. and Irizarry,R.A. (2014) Minfi: a flexible and comprehensive bioconductor package for the analysis of infinium DNA methylation microarrays. Bioinformatics, 30, 1363–1369.
-
(2014)
Bioinformatics
, vol.30
, pp. 1363-1369
-
-
Aryee, M.J.1
Jaffe, A.E.2
Corrada-Bravo, H.3
Ladd-Acosta, C.4
Feinberg, A.P.5
Hansen, K.D.6
Irizarry, R.A.7
-
21
-
-
84860637797
-
DNA methylation arrays as surrogate measures of cell mixture distribution
-
Houseman,E.A., Accomando,W.P., Koestler,D.C., Christensen,B.C., Marsit,C.J., Nelson,H.H., Wiencke,J.K. and Kelsey,K.T. (2012) DNA methylation arrays as surrogate measures of cell mixture distribution. BMC Bioinformatics, 13, 86.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 86
-
-
Houseman, E.A.1
Accomando, W.P.2
Koestler, D.C.3
Christensen, B.C.4
Marsit, C.J.5
Nelson, H.H.6
Wiencke, J.K.7
Kelsey, K.T.8
-
22
-
-
84893772701
-
RNA sequencing identifies multiple fusion transcripts, differentially expressed genes, and reduced expression of immune function genes in BRAF (V600E) mutant vs BRAF wild-type papillary thyroid carcinoma
-
Smallridge,R.C., Chindris,A.-M., Asmann,Y.W., Casler,J.D., Serie,D.J., Reddi,H.V., Cradic,K.W., Rivera,M., Grebe,S.K., Necela,B.M. et al. (2014) RNA sequencing identifies multiple fusion transcripts, differentially expressed genes, and reduced expression of immune function genes in BRAF (V600E) mutant vs BRAF wild-type papillary thyroid carcinoma. J. Clin. Endocrinol. Metab., 99, E338–E347.
-
(2014)
J Clin Endocrinol Metab
, vol.99
, pp. E338-E347
-
-
Smallridge, R.C.1
Chindris, A.-M.2
Asmann, Y.W.3
Casler, J.D.4
Serie, D.J.5
Reddi, H.V.6
Cradic, K.W.7
Rivera, M.8
Grebe, S.K.9
Necela, B.M.10
-
23
-
-
84911961534
-
A nineteen gene-based risk score classifier predicts prognosis of colorectal cancer patients
-
Kim,S.-K., Kim,S.-Y., Kim,J.-H., Roh,S.A., Cho,D.-H., Kim,Y.S. and Kim,J.C. (2014) A nineteen gene-based risk score classifier predicts prognosis of colorectal cancer patients. Mol. Oncol., 8, 1653–1666.
-
(2014)
Mol Oncol
, vol.8
, pp. 1653-1666
-
-
Kim, S.-K.1
Kim, S.-Y.2
Kim, J.-H.3
Roh, S.A.4
Cho, D.-H.5
Kim, Y.S.6
Kim, J.C.7
-
24
-
-
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.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
25
-
-
46049110099
-
TiGER: A database for tissue-specific gene expression and regulation
-
Liu,X., Yu,X., Zack,D.J., Zhu,H. and Qian,J. (2008) TiGER: A database for tissue-specific gene expression and regulation. BMC Bioinformatics, 9, 271.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 271
-
-
Liu, X.1
Yu, X.2
Zack, D.J.3
Zhu, H.4
Qian, J.5
-
27
-
-
85010952398
-
Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies
-
Toker,L., Feng,M. and Pavlidis,P. (2016) Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies. F1000Research, 5, 2103.
-
(2016)
F1000Research
, vol.5
, pp. 2103
-
-
Toker, L.1
Feng, M.2
Pavlidis, P.3
-
28
-
-
84920550975
-
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium
-
Seqc/Maqc-Iii Consortium. (2014) A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat. Biotechnol., 32, 903–914.
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 903-914
-
-
-
29
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
Irizarry,R.A., Warren,D., Spencer,F., Kim,I.F., Biswal,S., Frank,B.C., Gabrielson,E., Garcia,J.G.N., Geoghegan,J., Germino,G. et al. (2005) Multiple-laboratory comparison of microarray platforms. Nat. Methods, 2, 345–350.
-
(2005)
Nat Methods
, vol.2
, pp. 345-350
-
-
Irizarry, R.A.1
Warren, D.2
Spencer, F.3
Kim, I.F.4
Biswal, S.5
Frank, B.C.6
Gabrielson, E.7
Garcia, J.G.N.8
Geoghegan, J.9
Germino, G.10
-
30
-
-
84954548507
-
Tumor-derived cell lines as molecular models of cancer pharmacogenomics
-
Goodspeed,A., Heiser,L.M., Gray,J.W. and Costello,J.C. (2016) Tumor-derived cell lines as molecular models of cancer pharmacogenomics. Mol. Cancer Res.: MCR, 14, 3–13.
-
(2016)
Mol. Cancer Res.: MCR
, vol.14
, pp. 3-13
-
-
Goodspeed, A.1
Heiser, L.M.2
Gray, J.W.3
Costello, J.C.4
-
31
-
-
84979649916
-
A landscape of pharmacogenomic interactions in cancer
-
Iorio,F., Knijnenburg,T.A., Vis,D.J., Bignell,G.R., Menden,M.P., Schubert,M., Aben,N., Gonçalves,E., Barthorpe,S., Lightfoot,H. et al. (2016) A landscape of pharmacogenomic interactions in cancer. Cell, 166, 740–754.
-
(2016)
Cell
, vol.166
, pp. 740-754
-
-
Iorio, F.1
Knijnenburg, T.A.2
Vis, D.J.3
Bignell, G.R.4
Menden, M.P.5
Schubert, M.6
Aben, N.7
Goncalves, E.8
Barthorpe, S.9
Lightfoot, H.10
|