-
1
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W,. 2010. Differential expression analysis for sequence count data. Genome Biol 11: R106.
-
(2010)
Genome Biol
, vol.11
-
-
Anders, S.1
Huber, W.2
-
3
-
-
0035023305
-
Comparative gene expression profiles following UV exposure in wild type and SOS-deficient Escherichia coli
-
Courcelle J, Khodursky A, Peter B, Brown P, Hanawalt P,. 2001. Comparative gene expression profiles following UV exposure in wild type and SOS-deficient Escherichia coli. Genetics 158: 41-64.
-
(2001)
Genetics
, vol.158
, pp. 41-64
-
-
Courcelle, J.1
Khodursky, A.2
Peter, B.3
Brown, P.4
Hanawalt, P.5
-
4
-
-
84866368685
-
RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans
-
Dhamgaye S, Bernard M, Lelandais G, Sismeiro O, Lemoine S, Coppee JY, Le Crom S, Prasad R, Devaux F,. 2012. RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans. BMC Genomics 13: 396.
-
(2012)
BMC Genomics
, vol.13
, pp. 396
-
-
Dhamgaye, S.1
Bernard, M.2
Lelandais, G.3
Sismeiro, O.4
Lemoine, S.5
Coppee, J.Y.6
Le Crom, S.7
Prasad, R.8
Devaux, F.9
-
5
-
-
84887791432
-
A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis
-
Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, et al. 2013. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Brief Bioinform 14: 671-683.
-
(2013)
Brief Bioinform
, vol.14
, pp. 671-683
-
-
Dillies, M.A.1
Rau, A.2
Aubert, J.3
Hennequet-Antier, C.4
Jeanmougin, M.5
Servant, N.6
Keime, C.7
Marot, G.8
Castel, D.9
Estelle, J.10
-
6
-
-
78651486046
-
Identification of fusion genes in breast cancer by paired-end RNA-sequencing
-
Edgren H, Murumagi A, Kangaspeska S, Nicorici D, Hongisto V, Kleivi K, Rye IH, Nyberg S, Wolf M, Borresen-Dale AL, et al. 2011. Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol 12: R6.
-
(2011)
Genome Biol
, vol.12
-
-
Edgren, H.1
Murumagi, A.2
Kangaspeska, S.3
Nicorici, D.4
Hongisto, V.5
Kleivi, K.6
Rye, I.H.7
Nyberg, S.8
Wolf, M.9
Borresen-Dale, A.L.10
-
7
-
-
34250760229
-
On the generalized poisson regression model with an application to accidental data
-
Famoye F, Wulu J, Singh KP,. 2004. On the generalized poisson regression model with an application to accidental data. J Data Sci 2: 287-295.
-
(2004)
J Data Sci
, vol.2
, pp. 287-295
-
-
Famoye, F.1
Wulu, J.2
Singh, K.P.3
-
8
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-seq
-
Garber M, Grabherr MG, Guttman M, Trapnell C,. 2011. Computational methods for transcriptome annotation and quantification using RNA-seq. Nat Methods 8: 469-477.
-
(2011)
Nat Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
9
-
-
79960126958
-
FusionMap: Detecting fusion genes from next-generation sequencing data at base-pair resolution
-
Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W,. 2011. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics 27: 1922-1928.
-
(2011)
Bioinformatics
, vol.27
, pp. 1922-1928
-
-
Ge, H.1
Liu, K.2
Juan, T.3
Fang, F.4
Newman, M.5
Hoeck, W.6
-
10
-
-
77955298482
-
BaySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
-
Hardcastle TJ, Kelly KA,. 2010. baySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11: 422.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 422
-
-
Hardcastle, T.J.1
Kelly, K.A.2
-
11
-
-
80054003528
-
ChimeraScan: A tool for identifying chimeric transcription in sequencing data
-
Iyer MK, Chinnaiyan AM, Maher CA,. 2011. ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics 27: 2903-2904.
-
(2011)
Bioinformatics
, vol.27
, pp. 2903-2904
-
-
Iyer, M.K.1
Chinnaiyan, A.M.2
Maher, C.A.3
-
12
-
-
84873606413
-
SOAPfuse: An algorithm for identifying fusion transcripts from paired-end RNA-Seq data
-
Jia W, Qiu K, He M, Song P, Zhou Q, Zhou F, Yu Y, Zhu D, Nickerson ML, Wan S, et al. 2013. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data. Genome Biol 14: R12.
-
(2013)
Genome Biol
, vol.14
-
-
Jia, W.1
Qiu, K.2
He, M.3
Song, P.4
Zhou, Q.5
Zhou, F.6
Yu, Y.7
Zhu, D.8
Nickerson, M.L.9
Wan, S.10
-
13
-
-
80051507403
-
TopHat-Fusion: An algorithm for discovery of novel fusion transcripts
-
Kim D, Salzberg SL,. 2011. TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol 12: R72.
-
(2011)
Genome Biol
, vol.12
-
-
Kim, D.1
Salzberg, S.L.2
-
14
-
-
84884684764
-
Insight into norfloxacin resistance of Acinetobacter oleivorans DR1: Target gene mutation, persister, and RNA-Seq analyses
-
Kim J, Noh J, Park W,. 2013. Insight into norfloxacin resistance of Acinetobacter oleivorans DR1: target gene mutation, persister, and RNA-Seq analyses. J Microbiol Biotechnol 23: 1293-1303.
-
(2013)
J Microbiol Biotechnol
, vol.23
, pp. 1293-1303
-
-
Kim, J.1
Noh, J.2
Park, W.3
-
15
-
-
84856241901
-
MicroRNA-mediated drug resistance in breast cancer
-
Kutanzi KR, Yurchenko OV, Beland FA, Checkhun VF, Pogribny IP,. 2011. MicroRNA-mediated drug resistance in breast cancer. Clin Epigenetics 2: 171-185.
-
(2011)
Clin Epigenetics
, vol.2
, pp. 171-185
-
-
Kutanzi, K.R.1
Yurchenko, O.V.2
Beland, F.A.3
Checkhun, V.F.4
Pogribny, I.P.5
-
16
-
-
84878893929
-
FusionQ: A novel approach for gene fusion detection and quantification from paired-end RNA-Seq
-
Liu C, Ma J, Chang CJ, Zhou X,. 2013. FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq. BMC Bioinformatics 14: 193.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 193
-
-
Liu, C.1
Ma, J.2
Chang, C.J.3
Zhou, X.4
-
17
-
-
62049085786
-
Transcriptome sequencing to detect gene fusions in cancer
-
Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM,. 2009. Transcriptome sequencing to detect gene fusions in cancer. Nature 458: 97-101.
-
(2009)
Nature
, vol.458
, pp. 97-101
-
-
Maher, C.A.1
Kumar-Sinha, C.2
Cao, X.3
Kalyana-Sundaram, S.4
Han, B.5
Jing, X.6
Sam, L.7
Barrette, T.8
Palanisamy, N.9
Chinnaiyan, A.M.10
-
18
-
-
79957829805
-
DeFuse: An algorithm for gene fusion discovery in tumor RNA-Seq data
-
McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N, et al. 2011. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol 7: e1001138.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
McPherson, A.1
Hormozdiari, F.2
Zayed, A.3
Giuliany, R.4
Ha, G.5
Sun, M.G.6
Griffith, M.7
Heravi Moussavi, A.8
Senz, J.9
Melnyk, N.10
-
19
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, 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
-
20
-
-
84890434867
-
Transcriptomic analysis by RNA-seq reveals AP-1 pathway as key regulator that green tea may rely on to inhibit lung tumorigenesis
-
Pan J, Zhang Q, Xiong D, Vedell P, Yan Y, Jiang H, Cui P, Ding F, Tichelaar JW, Wang Y, et al. 2014. Transcriptomic analysis by RNA-seq reveals AP-1 pathway as key regulator that green tea may rely on to inhibit lung tumorigenesis. Mol Carcinog 53: 19-29.
-
(2014)
Mol Carcinog
, vol.53
, pp. 19-29
-
-
Pan, J.1
Zhang, Q.2
Xiong, D.3
Vedell, P.4
Yan, Y.5
Jiang, H.6
Cui, P.7
Ding, F.8
Tichelaar, J.W.9
Wang, Y.10
-
21
-
-
0035999977
-
A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
-
Pan W,. 2002. A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments. Bioinformatics 18: 546-554.
-
(2002)
Bioinformatics
, vol.18
, pp. 546-554
-
-
Pan, W.1
-
22
-
-
60349098756
-
Assumption adequacy averaging as a concept to develop more robust methods for differential gene expression analysis
-
Pounds S, Rai SN,. 2009. Assumption adequacy averaging as a concept to develop more robust methods for differential gene expression analysis. Comput Stat Data Anal 53: 1604-1612.
-
(2009)
Comput Stat Data Anal
, vol.53
, pp. 1604-1612
-
-
Pounds, S.1
Rai, S.N.2
-
23
-
-
84879241018
-
Empirical bayesian selection of hypothesis testing procedures for analysis of sequence count expression data
-
Pounds SB, Gao CL, Zhang H,. 2012. Empirical bayesian selection of hypothesis testing procedures for analysis of sequence count expression data. Stat Appl Genet Mol Biol 11: 1544-6115.
-
(2012)
Stat Appl Genet Mol Biol
, vol.11
, pp. 1544-6115
-
-
Pounds, S.B.1
Gao, C.L.2
Zhang, H.3
-
24
-
-
84875451981
-
Development of strategies for SNP detection in RNA-seq data: Application to lymphoblastoid cell lines and evaluation using 1000 Genomes data
-
Quinn EM, Cormican P, Kenny EM, Hill M, Anney R, Gill M, Corvin AP, Morris DW,. 2013. Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data. PLoS ONE 8: e58815.
-
(2013)
PLoS ONE
, vol.8
-
-
Quinn, E.M.1
Cormican, P.2
Kenny, E.M.3
Hill, M.4
Anney, R.5
Gill, M.6
Corvin, A.P.7
Morris, D.W.8
-
25
-
-
84862777104
-
RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings
-
Ren S, Peng Z, Mao JH, Yu Y, Yin C, Gao X, Cui Z, Zhang J, Yi K, Xu W, et al. 2012. RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell Res 22: 806-821.
-
(2012)
Cell Res
, vol.22
, pp. 806-821
-
-
Ren, S.1
Peng, Z.2
Mao, J.H.3
Yu, Y.4
Yin, C.5
Gao, X.6
Cui, Z.7
Zhang, J.8
Yi, K.9
Xu, W.10
-
26
-
-
41149085992
-
Small-sample estimation of negative binomial dispersion, with applications to SAGE data
-
Robinson MD, Smyth GK,. 2008. Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 9: 321-332.
-
(2008)
Biostatistics
, vol.9
, pp. 321-332
-
-
Robinson, M.D.1
Smyth, G.K.2
-
27
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson MD, McCarthy DJ, Smyth GK,. 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
-
28
-
-
85052549687
-
A two-parameter generalized Poisson model to improve the analysis of RNA-seq data
-
Srivastava S, Chen L,. 2010. A two-parameter generalized Poisson model to improve the analysis of RNA-seq data. Nucleic Acids Res 38: e170.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Srivastava, S.1
Chen, L.2
-
29
-
-
57749195712
-
RNA-Seq: A revolutionary tool for transcriptomics
-
Wang Z, Gerstein M, Snyder M,. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
-
(2009)
Nat Rev Genet
, vol.10
, pp. 57-63
-
-
Wang, Z.1
Gerstein, M.2
Snyder, M.3
-
30
-
-
77957969261
-
Targeting miRNAs involved in cancer stem cell and EMT regulation: An emerging concept in overcoming drug resistance
-
Wang Z, Li Y, Ahmad A, Azmi AS, Kong D, Banerjee S, Sarkar FH,. 2010. Targeting miRNAs involved in cancer stem cell and EMT regulation: an emerging concept in overcoming drug resistance. Drug Resist Update 13: 109-118.
-
(2010)
Drug Resist Update
, vol.13
, pp. 109-118
-
-
Wang, Z.1
Li, Y.2
Ahmad, A.3
Azmi, A.S.4
Kong, D.5
Banerjee, S.6
Sarkar, F.H.7
-
31
-
-
84896718888
-
Changes in the expression of miR-381 and miR-495 are inversely associated with the expression of the MDR1 gene and development of multi-drug resistance
-
Xu Y, Ohms SJ, Li Z, Wang Q, Gong G, Hu Y, Mao Z, Shannon MF, Fan JY,. 2013. Changes in the expression of miR-381 and miR-495 are inversely associated with the expression of the MDR1 gene and development of multi-drug resistance. PLoS ONE 8: e82062.
-
(2013)
PLoS ONE
, vol.8
-
-
Xu, Y.1
Ohms, S.J.2
Li, Z.3
Wang, Q.4
Gong, G.5
Hu, Y.6
Mao, Z.7
Shannon, M.F.8
Fan, J.Y.9
-
32
-
-
84894254382
-
Abnormal gene expression and gene fusion in lung adenocarcinoma with high-throughput RNA sequencing
-
Yang ZH, Zheng R, Gao Y, Zhang Q, Zhang H,. 2014. Abnormal gene expression and gene fusion in lung adenocarcinoma with high-throughput RNA sequencing. Cancer Gene Ther 21: 74-82.
-
(2014)
Cancer Gene Ther
, vol.21
, pp. 74-82
-
-
Yang, Z.H.1
Zheng, R.2
Gao, Y.3
Zhang, Q.4
Zhang, H.5
-
33
-
-
84864631640
-
A new look at the difference between the GEE and the GLMM when modeling longitudinal count responses
-
Zhang H, Yu Q, Feng C, Gunzler D, Wu P, Tu XM,. 2012. A new look at the difference between the GEE and the GLMM when modeling longitudinal count responses. J Appl Stat 39: 2067-2079.
-
(2012)
J Appl Stat
, vol.39
, pp. 2067-2079
-
-
Zhang, H.1
Yu, Q.2
Feng, C.3
Gunzler, D.4
Wu, P.5
Tu, X.M.6
-
34
-
-
84872852142
-
Genome-wide analysis of miRNA signature differentially expressed in doxorubicin-resistant and parental human hepatocellular carcinoma cell lines
-
Zhang J, Wang Y, Zhen P, Luo X, Zhang C, Zhou L, Lu Y, Yang Y, Zhang W, Wan J,. 2013. Genome-wide analysis of miRNA signature differentially expressed in doxorubicin-resistant and parental human hepatocellular carcinoma cell lines. PLoS ONE 8: e54111.
-
(2013)
PLoS ONE
, vol.8
-
-
Zhang, J.1
Wang, Y.2
Zhen, P.3
Luo, X.4
Zhang, C.5
Zhou, L.6
Lu, Y.7
Yang, Y.8
Zhang, W.9
Wan, J.10
|