-
1
-
-
0029852580
-
Use of a cDNA microarray to analyse gene expression patterns in human cancer
-
DeRisi J., Penland L., Brown P.O., Bittner M.L., Meltzer P.S., Ray M., Chen Y., Su Y.A., Trent J.M. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nature Genetics 1996, 14:457-460.
-
(1996)
Nature Genetics
, vol.14
, pp. 457-460
-
-
DeRisi, J.1
Penland, L.2
Brown, P.O.3
Bittner, M.L.4
Meltzer, P.S.5
Ray, M.6
Chen, Y.7
Su, Y.A.8
Trent, J.M.9
-
2
-
-
0031822837
-
Tissue microarrays for high-throughtput molecular profiling of tumor specimens
-
Kononen J., Bubendorf L., Kallionimeni A., Bärlund M., Schraml P., Leighton S., Torhorst J., Sauter G., Kallioniemi O.P. Tissue microarrays for high-throughtput molecular profiling of tumor specimens. Nature Medicine 1998, 4:844-847.
-
(1998)
Nature Medicine
, vol.4
, pp. 844-847
-
-
Kononen, J.1
Bubendorf, L.2
Kallionimeni, A.3
Bärlund, M.4
Schraml, P.5
Leighton, S.6
Torhorst, J.7
Sauter, G.8
Kallioniemi, O.P.9
-
3
-
-
0033569406
-
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring
-
Golub T.R., Slonim D.K., Tamayo P., Huard C., Gaasenbeek M., Mesiroy J.P., Coller H., Loh M.L., Downing J.R., Caligiuri M.A., Bloomfield C.D., Lander E.S. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286:531-537.
-
(1999)
Science
, vol.286
, pp. 531-537
-
-
Golub, T.R.1
Slonim, D.K.2
Tamayo, P.3
Huard, C.4
Gaasenbeek, M.5
Mesiroy, J.P.6
Coller, H.7
Loh, M.L.8
Downing, J.R.9
Caligiuri, M.A.10
Bloomfield, C.D.11
Lander, E.S.12
-
4
-
-
18244409687
-
Gene expression profiling predicts clinical outcome of breast cancer
-
van 't Veer L.J., Dai H., van de Vijver M.J., He Y.D., Hart A.A.M., Mao M., Peterse H.L., van der Kooy K., Marton M.J., Witteveen A.T., Schreiber G.J., Kerkhoven R.M., Roberts C., Linsley P.S., Bernards R., Friend S.H. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536.
-
(2002)
Nature
, vol.415
, pp. 530-536
-
-
van 't Veer, L.J.1
Dai, H.2
van de Vijver, M.J.3
He, Y.D.4
Hart, A.A.M.5
Mao, M.6
Peterse, H.L.7
van der Kooy, K.8
Marton, M.J.9
Witteveen, A.T.10
Schreiber, G.J.11
Kerkhoven, R.M.12
Roberts, C.13
Linsley, P.S.14
Bernards, R.15
Friend, S.H.16
-
5
-
-
84887614923
-
-
http://www.nature.com/news/2007/070205/full/news070205-7.html.
-
-
-
-
6
-
-
7444220147
-
Aberrant and alternative splicing in cancer
-
Venables J.P. Aberrant and alternative splicing in cancer. Cancer Research 2004, 64:7647-7654.
-
(2004)
Cancer Research
, vol.64
, pp. 7647-7654
-
-
Venables, J.P.1
-
8
-
-
53649106195
-
Next-generation DNA sequencing
-
Shendure J., Ji H. Next-generation DNA sequencing. Nature Biotechnology 2008, 26:1135-1145.
-
(2008)
Nature Biotechnology
, vol.26
, pp. 1135-1145
-
-
Shendure, J.1
Ji, H.2
-
9
-
-
67649406102
-
Mutation of FOXL2 in granulosa-cell tumors of the ovary
-
Shah S.P., Köbel M., Senz J., Morin R.D., Clarke B.A., Wiegand K.C., Leung G., Zayed A., Mehl E., Kalloger S.E., Sun M., Giuliany R., Yorida E., Jones S., Varhol R., Swenerton K.D., Miller D., Clement P.B., Crane C., Madore J., Provencher D., Leung P., DeFazio A., Khattra J., Turashvili G., Zhao Y., Zeng T., Glover J.N., Vanderhyden B., Zhao C., Parkinson C.A., Jimenez-Linan M., Bowtell D.D., Mes-Masson A.M., Brenton J.D., Aparicio S.A., Boyd N., Hirst M., Gilks C.B., Marra M., Huntsman D.G. Mutation of FOXL2 in granulosa-cell tumors of the ovary. The New England Journal of Medicine 2009, 360:2719-2729.
-
(2009)
The New England Journal of Medicine
, vol.360
, pp. 2719-2729
-
-
Shah, S.P.1
Köbel, M.2
Senz, J.3
Morin, R.D.4
Clarke, B.A.5
Wiegand, K.C.6
Leung, G.7
Zayed, A.8
Mehl, E.9
Kalloger, S.E.10
Sun, M.11
Giuliany, R.12
Yorida, E.13
Jones, S.14
Varhol, R.15
Swenerton, K.D.16
Miller, D.17
Clement, P.B.18
Crane, C.19
Madore, J.20
Provencher, D.21
Leung, P.22
DeFazio, A.23
Khattra, J.24
Turashvili, G.25
Zhao, Y.26
Zeng, T.27
Glover, J.N.28
Vanderhyden, B.29
Zhao, C.30
Parkinson, C.A.31
Jimenez-Linan, M.32
Bowtell, D.D.33
Mes-Masson, A.M.34
Brenton, J.D.35
Aparicio, S.A.36
Boyd, N.37
Hirst, M.38
Gilks, C.B.39
Marra, M.40
Huntsman, D.G.41
more..
-
10
-
-
47949084846
-
Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing
-
Morin R., Bainbridge M., Fejes A., Hirst M., Krzywinski M., Pugh T., McDonald H., Varhol R., Jones S., Marra M. Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing. BioTechniques 2008, 45:81-94.
-
(2008)
BioTechniques
, vol.45
, pp. 81-94
-
-
Morin, R.1
Bainbridge, M.2
Fejes, A.3
Hirst, M.4
Krzywinski, M.5
Pugh, T.6
McDonald, H.7
Varhol, R.8
Jones, S.9
Marra, M.10
-
11
-
-
77950633122
-
Integrative analysis of the melanoma transcriptome
-
Berger M.F., Levin J.Z., Vijayendran K., Sivachenko A., Adiconis X., Maguire J., Johnson L.A., Robinson J., Verhaak R.G., Sougnez C., Onofrio R.C., Ziaugra L., Cibulskis K., Laine E., Barretina J., Winckler W., Fisher D.E., Getz G., Meyerson M., Jaffe D.B., Gabriel S.B., Lander E.S., Dummer R., Gnirke A., Nusbaum C., Garraway L.A. Integrative analysis of the melanoma transcriptome. Genome Research 2010, 20:413-427.
-
(2010)
Genome Research
, vol.20
, pp. 413-427
-
-
Berger, M.F.1
Levin, J.Z.2
Vijayendran, K.3
Sivachenko, A.4
Adiconis, X.5
Maguire, J.6
Johnson, L.A.7
Robinson, J.8
Verhaak, R.G.9
Sougnez, C.10
Onofrio, R.C.11
Ziaugra, L.12
Cibulskis, K.13
Laine, E.14
Barretina, J.15
Winckler, W.16
Fisher, D.E.17
Getz, G.18
Meyerson, M.19
Jaffe, D.B.20
Gabriel, S.B.21
Lander, E.S.22
Dummer, R.23
Gnirke, A.24
Nusbaum, C.25
Garraway, L.A.26
more..
-
12
-
-
79959331609
-
Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing
-
Kannan K., Wang L., Wang J., Ittmann M.M., Li W., Yen L. Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing. Proceedings of the National Academy of Sciences of the United States of America 2011, 108:9172-9177.
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, vol.108
, pp. 9172-9177
-
-
Kannan, K.1
Wang, L.2
Wang, J.3
Ittmann, M.M.4
Li, W.5
Yen, L.6
-
13
-
-
84870899165
-
Deep sequence analysis of non-small cell lung cancer: integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations
-
Kalari K.R., Rossell D., Necela B.M., Asmann Y.W., Nair A., Baheti S., Kachergus J.M., Younkin C.S., Baker T., Carr J.M., Tang X., Walsh M.P., Chai H.S., Sun Z., Hart S.N., Leontovich A.A., Hossain A., Kocher J.P., Perez E.A., Reisman D.N., Fields A.P., Thompson E.A. Deep sequence analysis of non-small cell lung cancer: integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations. Frontiers in Oncology 2012, 2:12.
-
(2012)
Frontiers in Oncology
, vol.2
, pp. 12
-
-
Kalari, K.R.1
Rossell, D.2
Necela, B.M.3
Asmann, Y.W.4
Nair, A.5
Baheti, S.6
Kachergus, J.M.7
Younkin, C.S.8
Baker, T.9
Carr, J.M.10
Tang, X.11
Walsh, M.P.12
Chai, H.S.13
Sun, Z.14
Hart, S.N.15
Leontovich, A.A.16
Hossain, A.17
Kocher, J.P.18
Perez, E.A.19
Reisman, D.N.20
Fields, A.P.21
Thompson, E.A.22
more..
-
14
-
-
84861142867
-
AMPKα modulation in cancer progression: multilayer integrative analysis of the whole transcriptome in Asian gastric cancer
-
Kim Y.H., Liang H., Liu X., Lee J.-S., Cho J.Y., Cheong J.H., Kim H., Li M., Downey T.J., Dyer M.D., Sun Y., Sun J., Beasley E.M., Chung H.C., Noh S.H., Weinstein J.N., Liu C.G., Powis G. AMPKα modulation in cancer progression: multilayer integrative analysis of the whole transcriptome in Asian gastric cancer. Cancer Research 2012, 72:2512-2521.
-
(2012)
Cancer Research
, vol.72
, pp. 2512-2521
-
-
Kim, Y.H.1
Liang, H.2
Liu, X.3
Lee, J.-S.4
Cho, J.Y.5
Cheong, J.H.6
Kim, H.7
Li, M.8
Downey, T.J.9
Dyer, M.D.10
Sun, Y.11
Sun, J.12
Beasley, E.M.13
Chung, H.C.14
Noh, S.H.15
Weinstein, J.N.16
Liu, C.G.17
Powis, G.18
-
15
-
-
84855320189
-
Accurate identification of A-to-I RNA editing in human by transcriptome sequencing
-
Bahn J.H., Lee J.H., Li G., Greer C., Peng G., Xiao X. Accurate identification of A-to-I RNA editing in human by transcriptome sequencing. Genome Research 2012, 22:142-150.
-
(2012)
Genome Research
, vol.22
, pp. 142-150
-
-
Bahn, J.H.1
Lee, J.H.2
Li, G.3
Greer, C.4
Peng, G.5
Xiao, X.6
-
16
-
-
84858682499
-
Canonical A-to-I and C-to-U RNA editing is enriched at 3'UTRs and microRNA target sites in multiple mouse tissues
-
Gu T., Buaas F.W., Simons A.K., Ackert-Bicknell C.L., Braun R.E., Hibbs M.A. Canonical A-to-I and C-to-U RNA editing is enriched at 3'UTRs and microRNA target sites in multiple mouse tissues. PLoS ONE 2012, 7:e33720.
-
(2012)
PLoS ONE
, vol.7
-
-
Gu, T.1
Buaas, F.W.2
Simons, A.K.3
Ackert-Bicknell, C.L.4
Braun, R.E.5
Hibbs, M.A.6
-
17
-
-
68149176840
-
Chimeric transcript discovery by paired-end transcriptome sequencing
-
Maher C.A., Palanisamy N., Brenner J.C., Cao X., Kalyana-Sundaram S., Luo S., Khrebtukova I., Barrette T.R., Grasso C., Yu J., Lonigro R.J., Schroth G., Kumar-Sinha C., Chinnaiyan A.M. Chimeric transcript discovery by paired-end transcriptome sequencing. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:12353-12358.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 12353-12358
-
-
Maher, C.A.1
Palanisamy, N.2
Brenner, J.C.3
Cao, X.4
Kalyana-Sundaram, S.5
Luo, S.6
Khrebtukova, I.7
Barrette, T.R.8
Grasso, C.9
Yu, J.10
Lonigro, R.J.11
Schroth, G.12
Kumar-Sinha, C.13
Chinnaiyan, A.M.14
-
18
-
-
62049085786
-
Transcriptome sequencing to detect gene fusions in cancer
-
Maher C.A., Kumar-Sinha C., Cao X., Kalyana-Sundaram S., Han B., Jing X., Sam L., Barrette T., Palanisamy N., Chinnaiyan A.M. Transcriptome sequencing to detect gene fusions in cancer. Nature 2009, 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
-
19
-
-
79952816655
-
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers
-
Steidl C., Shah S.P., Woolcock B.W., Rui L., Kawahara M., Farinha P., Johnson N.A., Zhao Y., Telenius A., Neriah S.B., McPherson A., Meissner B., Okoye U.C., Diepstra A., van den Berg A., Sun M., Leung G., Jones S.J., Connors J.M., Huntsman D.G., Savage K.J., Rimsza L.M., Horsman D.E., Staudt L.M., Steidl U., Marra M.A., Gascoyne R.D. MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature 2011, 471:377-381.
-
(2011)
Nature
, vol.471
, pp. 377-381
-
-
Steidl, C.1
Shah, S.P.2
Woolcock, B.W.3
Rui, L.4
Kawahara, M.5
Farinha, P.6
Johnson, N.A.7
Zhao, Y.8
Telenius, A.9
Neriah, S.B.10
McPherson, A.11
Meissner, B.12
Okoye, U.C.13
Diepstra, A.14
van den Berg, A.15
Sun, M.16
Leung, G.17
Jones, S.J.18
Connors, J.M.19
Huntsman, D.G.20
Savage, K.J.21
Rimsza, L.M.22
Horsman, D.E.23
Staudt, L.M.24
Steidl, U.25
Marra, M.A.26
Gascoyne, R.D.27
more..
-
20
-
-
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 I.H., Nyberg S., Wolf M., Borresen-Dale A.L., Kallioniemi O. Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biology 2011, 12:R6.
-
(2011)
Genome Biology
, 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
Kallioniemi, O.11
-
21
-
-
78651476339
-
Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing
-
Pflueger D., Terry S., Sboner A., Habegger L., Esgueva R., Lin P.C., Svensson M.A., Kitabayashi N., Moss B.J., MacDonald T.Y., Cao X., Barrette T., Tewari A.K., Chee M.S., Chinnaiyan A.M., Rickman D.S., Demichelis F., Gerstein M.B., Rubin M.A. Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Research 2011, 21:56-67.
-
(2011)
Genome Research
, vol.21
, pp. 56-67
-
-
Pflueger, D.1
Terry, S.2
Sboner, A.3
Habegger, L.4
Esgueva, R.5
Lin, P.C.6
Svensson, M.A.7
Kitabayashi, N.8
Moss, B.J.9
MacDonald, T.Y.10
Cao, X.11
Barrette, T.12
Tewari, A.K.13
Chee, M.S.14
Chinnaiyan, A.M.15
Rickman, D.S.16
Demichelis, F.17
Gerstein, M.B.18
Rubin, M.A.19
-
22
-
-
67650489112
-
N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer
-
Pflueger D., Rickman D.S., Sboner A., Perner S., Lafargue C.J., Svensson M.A., Moss B.J., Kitabayashi N., Pan Y., de la Taille A., Kuefer R., Tewari A.K., Demichelis F., Chee M.S., Gerstein M.B., Rubin M.A. N-myc downstream regulated gene 1 (NDRG1) is fused to ERG in prostate cancer. Neoplasia 2009, 11:804-811.
-
(2009)
Neoplasia
, vol.11
, pp. 804-811
-
-
Pflueger, D.1
Rickman, D.S.2
Sboner, A.3
Perner, S.4
Lafargue, C.J.5
Svensson, M.A.6
Moss, B.J.7
Kitabayashi, N.8
Pan, Y.9
de la Taille, A.10
Kuefer, R.11
Tewari, A.K.12
Demichelis, F.13
Chee, M.S.14
Gerstein, M.B.15
Rubin, M.A.16
-
23
-
-
75349100601
-
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
-
Levin J.Z., Berger M.F., Adiconis X., Rogov P., Melnikov A., Fennell T., Nusbaum C., Garraway L.A., Gnirke A. Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biology 2009, 10:R115.
-
(2009)
Genome Biology
, vol.10
-
-
Levin, J.Z.1
Berger, M.F.2
Adiconis, X.3
Rogov, P.4
Melnikov, A.5
Fennell, T.6
Nusbaum, C.7
Garraway, L.A.8
Gnirke, A.9
-
24
-
-
70449375354
-
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer
-
Wang X.S., Prensner J.R., Chen G., Cao Q., Han B., Dhanasekaran S.M., Ponnala R., Cao X., Varambally S., Thomas D.G., Giordano T.J., Beer D.G., Palanisamy N., Sartor M.A., Omenn G.S., Chinnaiyan A.M. An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer. Nature Biotechnology 2009, 27:1005-1011.
-
(2009)
Nature Biotechnology
, vol.27
, pp. 1005-1011
-
-
Wang, X.S.1
Prensner, J.R.2
Chen, G.3
Cao, Q.4
Han, B.5
Dhanasekaran, S.M.6
Ponnala, R.7
Cao, X.8
Varambally, S.9
Thomas, D.G.10
Giordano, T.J.11
Beer, D.G.12
Palanisamy, N.13
Sartor, M.A.14
Omenn, G.S.15
Chinnaiyan, A.M.16
-
25
-
-
73549101052
-
Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins
-
Hegyi H., Buday L., Tompa P. Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins. PLoS Computational Biology 2009, 5:e1000552.
-
(2009)
PLoS Computational Biology
, vol.5
-
-
Hegyi, H.1
Buday, L.2
Tompa, P.3
-
26
-
-
33750370444
-
MicroRNA signatures in human cancers
-
Calin G.A., Croce C.M. MicroRNA signatures in human cancers. Nature Reviews Cancer 2006, 6:857-866.
-
(2006)
Nature Reviews Cancer
, vol.6
, pp. 857-866
-
-
Calin, G.A.1
Croce, C.M.2
-
27
-
-
82155186923
-
The emergence of lncRNAs in cancer biology
-
Prensner J.R., Chinnaiyan A.M. The emergence of lncRNAs in cancer biology. Cancer Discovery 2011, 1:391-407.
-
(2011)
Cancer Discovery
, vol.1
, pp. 391-407
-
-
Prensner, J.R.1
Chinnaiyan, A.M.2
-
28
-
-
78651397147
-
Large non-coding RNAs: missing links in cancer?
-
Huarte M., Rinn J.L. Large non-coding RNAs: missing links in cancer?. Human Molecular Genetics 2010, 19:R152-61.
-
(2010)
Human Molecular Genetics
, vol.19
-
-
Huarte, M.1
Rinn, J.L.2
-
29
-
-
78651394912
-
Identification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene
-
Persson H., Kvist A., Rego N., Staaf J., Vallon-Christersson J., Luts L., Loman N., Jonsson G., Naya H., Hoglund M., Borg A., Rovira C. Identification of new microRNAs in paired normal and tumor breast tissue suggests a dual role for the ERBB2/Her2 gene. Cancer Research 2011, 71:78-86.
-
(2011)
Cancer Research
, vol.71
, pp. 78-86
-
-
Persson, H.1
Kvist, A.2
Rego, N.3
Staaf, J.4
Vallon-Christersson, J.5
Luts, L.6
Loman, N.7
Jonsson, G.8
Naya, H.9
Hoglund, M.10
Borg, A.11
Rovira, C.12
-
30
-
-
79961202865
-
Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
-
Prensner J.R., Iyer M.K., Balbin O.A., Dhanasekaran S.M., Cao Q., Brenner J.C., Laxman B., Asangani I.A., Grasso C.S., Kominsky H.D., Cao X., Jing X., Wang X., Siddiqui J., Wei J.T., Robinson D., Iyer H.K., Palanisamy N., Maher C.A., Chinnaiyan A.M. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nature Biotechnology 2011, 29:742-749.
-
(2011)
Nature Biotechnology
, vol.29
, pp. 742-749
-
-
Prensner, J.R.1
Iyer, M.K.2
Balbin, O.A.3
Dhanasekaran, S.M.4
Cao, Q.5
Brenner, J.C.6
Laxman, B.7
Asangani, I.A.8
Grasso, C.S.9
Kominsky, H.D.10
Cao, X.11
Jing, X.12
Wang, X.13
Siddiqui, J.14
Wei, J.T.15
Robinson, D.16
Iyer, H.K.17
Palanisamy, N.18
Maher, C.A.19
Chinnaiyan, A.M.20
more..
-
31
-
-
84861881510
-
BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration
-
Flockhart R.J., Webster D.E., Qu K., Mascarenhas N., Kovalski J., Kretz M., Khavari P.A. BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Genome Research 2012, 22:1006-1014.
-
(2012)
Genome Research
, vol.22
, pp. 1006-1014
-
-
Flockhart, R.J.1
Webster, D.E.2
Qu, K.3
Mascarenhas, N.4
Kovalski, J.5
Kretz, M.6
Khavari, P.A.7
-
32
-
-
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 J.H., Yu Y., Yin C., Gao X., Cui Z., Zhang J., Yi K., Xu W., Chen C., Wang F., Guo X., Lu J., Yang J., Wei M., Tian Z., Guan Y., Tang L., Xu C., Wang L., Gao X., Tian W., Wang J., Yang H., Wang J., Sun Y. RNA-Seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings. Cell Research 2012, 22:806-821.
-
(2012)
Cell Research
, 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
Chen, C.11
Wang, F.12
Guo, X.13
Lu, J.14
Yang, J.15
Wei, M.16
Tian, Z.17
Guan, Y.18
Tang, L.19
Xu, C.20
Wang, L.21
Gao, X.22
Tian, W.23
Wang, J.24
Yang, H.25
Wang, J.26
Sun, Y.27
more..
-
35
-
-
1942454204
-
The impact of very short alternative splicing on protein structures and functions in the human genome
-
Wen F., Li F., Xia H., Lu X., Zhang X., Li Y. The impact of very short alternative splicing on protein structures and functions in the human genome. Trends in Genetics 2004, 20:232-236.
-
(2004)
Trends in Genetics
, vol.20
, pp. 232-236
-
-
Wen, F.1
Li, F.2
Xia, H.3
Lu, X.4
Zhang, X.5
Li, Y.6
-
36
-
-
12344250822
-
Function of alternative splicing
-
Stamm S., Ben-Ari S., Rafalska I., Tang Y., Zhang Z., Toiber D., Thanaraj T.A., Soreg H. Function of alternative splicing. Gene 2005, 344:1-20.
-
(2005)
Gene
, vol.344
, pp. 1-20
-
-
Stamm, S.1
Ben-Ari, S.2
Rafalska, I.3
Tang, Y.4
Zhang, Z.5
Toiber, D.6
Thanaraj, T.A.7
Soreg, H.8
-
37
-
-
0035252410
-
Alternative splicing: increasing diversity in the proteomic world
-
Graveley B.R. Alternative splicing: increasing diversity in the proteomic world. Trends in Genetics 2001, 17:100-107.
-
(2001)
Trends in Genetics
, vol.17
, pp. 100-107
-
-
Graveley, B.R.1
-
38
-
-
0036337915
-
A genomic view of alternative splicing
-
Modrek B., Lee C. A genomic view of alternative splicing. Nature Genetics 2002, 30:13-19.
-
(2002)
Nature Genetics
, vol.30
, pp. 13-19
-
-
Modrek, B.1
Lee, C.2
-
39
-
-
70350569286
-
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches
-
Chen M., Manley J.L. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nature Reviews Molecular Cell Biology 2009, 10:741-754.
-
(2009)
Nature Reviews Molecular Cell Biology
, vol.10
, pp. 741-754
-
-
Chen, M.1
Manley, J.L.2
-
40
-
-
56549101959
-
Alternative isoform regulation in human tissue transcriptomes
-
Wang E.T., Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., Kingsmore S.F., Schroth G.P., Burge C.B. Alternative isoform regulation in human tissue transcriptomes. Nature 2008, 456:470-476.
-
(2008)
Nature
, vol.456
, pp. 470-476
-
-
Wang, E.T.1
Sandberg, R.2
Luo, S.3
Khrebtukova, I.4
Zhang, L.5
Mayr, C.6
Kingsmore, S.F.7
Schroth, G.P.8
Burge, C.B.9
-
41
-
-
56749098074
-
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing
-
Pan Q., Shai O., Lee L.J., Frey B.J., Blencowe B.J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics 2008, 40:1413-1415.
-
(2008)
Nature Genetics
, vol.40
, pp. 1413-1415
-
-
Pan, Q.1
Shai, O.2
Lee, L.J.3
Frey, B.J.4
Blencowe, B.J.5
-
43
-
-
0043136678
-
Alternative splicing disrupts a nuclear localization signal in spleen kyrosine kinase that is required for invasion suppression in breast cancer
-
Wang L., Duke L., Zhang P.S., Arlinghaus R.B., Symmans W.F., Sahin A., Mendez R., Dai J.L. Alternative splicing disrupts a nuclear localization signal in spleen kyrosine kinase that is required for invasion suppression in breast cancer. Cancer Research 2003, 63:4724-4730.
-
(2003)
Cancer Research
, vol.63
, pp. 4724-4730
-
-
Wang, L.1
Duke, L.2
Zhang, P.S.3
Arlinghaus, R.B.4
Symmans, W.F.5
Sahin, A.6
Mendez, R.7
Dai, J.L.8
-
44
-
-
0035811561
-
Spleen tyrosine kinase (Syk) deficiency in childhood pro-B cell acute lymphoblastic leukemia
-
Goodman P.A., Wood C.M., Vassilev A., Mao C., Uckun F.M. Spleen tyrosine kinase (Syk) deficiency in childhood pro-B cell acute lymphoblastic leukemia. Oncogene 2001, 20:3969-3978.
-
(2001)
Oncogene
, vol.20
, pp. 3969-3978
-
-
Goodman, P.A.1
Wood, C.M.2
Vassilev, A.3
Mao, C.4
Uckun, F.M.5
-
45
-
-
33646119178
-
Clinical significance of nuclear expression of spleen tyrosine kinase (Syk) in gastric cancer
-
Nakashima H., Natsugoe S., Ishigami S., Okumura H., Matsumoto M., Hokita S., Aikou T. Clinical significance of nuclear expression of spleen tyrosine kinase (Syk) in gastric cancer. Cancer Letters 2006, 236:89-94.
-
(2006)
Cancer Letters
, vol.236
, pp. 89-94
-
-
Nakashima, H.1
Natsugoe, S.2
Ishigami, S.3
Okumura, H.4
Matsumoto, M.5
Hokita, S.6
Aikou, T.7
-
46
-
-
79958812227
-
Alternative splicing of SYK regulates mitosis and cell survival
-
Prinos P., Garneau D., Lucier J.F., Gendron D., Couture S., Boivin M., Brosseau J.P., Lapointe E., Thibault P., Durand M., Tremblay K., Gervais-Bird J., Nwilati H., Klinck R., Chabot B., Perreault J.P., Wellinger R.J., Elela S.A. Alternative splicing of SYK regulates mitosis and cell survival. Nature Structural and Molecular Biology 2011, 18:673-679.
-
(2011)
Nature Structural and Molecular Biology
, vol.18
, pp. 673-679
-
-
Prinos, P.1
Garneau, D.2
Lucier, J.F.3
Gendron, D.4
Couture, S.5
Boivin, M.6
Brosseau, J.P.7
Lapointe, E.8
Thibault, P.9
Durand, M.10
Tremblay, K.11
Gervais-Bird, J.12
Nwilati, H.13
Klinck, R.14
Chabot, B.15
Perreault, J.P.16
Wellinger, R.J.17
Elela, S.A.18
-
47
-
-
34447106755
-
Alternative splicing in cancer: noise, functional, or systematic?
-
Skotheim R.I., Nees M. Alternative splicing in cancer: noise, functional, or systematic?. The International Journal of Biochemistry and Cell Biology 2007, 39:1432-1449.
-
(2007)
The International Journal of Biochemistry and Cell Biology
, vol.39
, pp. 1432-1449
-
-
Skotheim, R.I.1
Nees, M.2
-
48
-
-
33646364024
-
Profiling alternatively spliced mRNA isoforms for prostate cancer classification
-
Zhang C., Li H.R., Fan J.B., Wang-Rodriguez J., Downs T., Fu X.D., Zhang M.Q. Profiling alternatively spliced mRNA isoforms for prostate cancer classification. BMC Bioinformatics 2006, 7:202.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 202
-
-
Zhang, C.1
Li, H.R.2
Fan, J.B.3
Wang-Rodriguez, J.4
Downs, T.5
Fu, X.D.6
Zhang, M.Q.7
-
49
-
-
33846467191
-
Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array
-
Gardina P.J., Clark T.A., Shimada B., Staples M.K., Yang Q., Veitch J., Schweitzer A., Awad T., Sugnet C., Dee S., Davies C., Williams A., Turpaz Y. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array. BMC Genomics 2006, 7:325.
-
(2006)
BMC Genomics
, vol.7
, pp. 325
-
-
Gardina, P.J.1
Clark, T.A.2
Shimada, B.3
Staples, M.K.4
Yang, Q.5
Veitch, J.6
Schweitzer, A.7
Awad, T.8
Sugnet, C.9
Dee, S.10
Davies, C.11
Williams, A.12
Turpaz, Y.13
-
50
-
-
47849097478
-
Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis
-
Thorsen K., Sørensen K.D., Brems-eskildsen A.S., Modin C., Gaustadnes M., Hein A.M., Kruhøffer M., Laurberg S., Borre M., Wang K., Brunak S., Krainer A.R., Tørring N., Dyrskjøt L., Andersen C.L., Orntoft T.F. Alternative splicing in colon, bladder, and prostate cancer identified by exon array analysis. Molecular and Cellular Proteomics 2008, 7:1214-1224.
-
(2008)
Molecular and Cellular Proteomics
, vol.7
, pp. 1214-1224
-
-
Thorsen, K.1
Sørensen, K.D.2
Brems-eskildsen, A.S.3
Modin, C.4
Gaustadnes, M.5
Hein, A.M.6
Kruhøffer, M.7
Laurberg, S.8
Borre, M.9
Wang, K.10
Brunak, S.11
Krainer, A.R.12
Tørring, N.13
Dyrskjøt, L.14
Andersen, C.L.15
Orntoft, T.F.16
-
51
-
-
56649083778
-
Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer
-
Xi L., Feber A., Gupta V., Wu M., Bergemann A.D., Landreneau R.J., Litle V.R., Pennathur A., Luketich J.D., Godfrey T.E. Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer. Nucleic Acids Research 2008, 36:6535-6547.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 6535-6547
-
-
Xi, L.1
Feber, A.2
Gupta, V.3
Wu, M.4
Bergemann, A.D.5
Landreneau, R.J.6
Litle, V.R.7
Pennathur, A.8
Luketich, J.D.9
Godfrey, T.E.10
-
52
-
-
77955463831
-
Exon-level microarray analyses identify alternative splicing programs in breast cancer
-
Lapuk A., Marr H., Jakkula L., Pedro H., Bhattacharya S., Purdom E., Hu Z., Simpson K., Pachter L., Durinck S., Wang N., Parvin B., Fontenay G., Speed T., Garbe J., Stampfer M., Bayandorian H., Dorton S., Clark T.A., Schweitzer A., Wyrobek A., Feiler H., Spellman P., Conboy J., Gray J.W. Exon-level microarray analyses identify alternative splicing programs in breast cancer. Molecular Cancer Research 2010, 8:961-974.
-
(2010)
Molecular Cancer Research
, vol.8
, pp. 961-974
-
-
Lapuk, A.1
Marr, H.2
Jakkula, L.3
Pedro, H.4
Bhattacharya, S.5
Purdom, E.6
Hu, Z.7
Simpson, K.8
Pachter, L.9
Durinck, S.10
Wang, N.11
Parvin, B.12
Fontenay, G.13
Speed, T.14
Garbe, J.15
Stampfer, M.16
Bayandorian, H.17
Dorton, S.18
Clark, T.A.19
Schweitzer, A.20
Wyrobek, A.21
Feiler, H.22
Spellman, P.23
Conboy, J.24
Gray, J.W.25
more..
-
53
-
-
47649124124
-
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
-
Sultan M., Schulz M.H., Richard H., Magen A., Klingenhoff A., Scherf M., Seifert M., Borodina T., Soldatov A., Parkhomchuk D., Schmidt D., O'Keeffe S., Haas S., Vingron M., Lehrach H., Yaspo M.L. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science 2008, 321:956-960.
-
(2008)
Science
, vol.321
, pp. 956-960
-
-
Sultan, M.1
Schulz, M.H.2
Richard, H.3
Magen, A.4
Klingenhoff, A.5
Scherf, M.6
Seifert, M.7
Borodina, T.8
Soldatov, A.9
Parkhomchuk, D.10
Schmidt, D.11
O'Keeffe, S.12
Haas, S.13
Vingron, M.14
Lehrach, H.15
Yaspo, M.L.16
-
54
-
-
46249106990
-
Mapping and quantifying mammalian transcriptomes by RNA-Seq
-
Mortazavi A., Williams B.A., Mccue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods 2008, 5:621-628.
-
(2008)
Nature Methods
, vol.5
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
Mccue, K.3
Schaeffer, L.4
Wold, B.5
-
55
-
-
67349146589
-
MRNA-Seq whole-transcriptome analysis of a single cell
-
Tang F., Barbacioru C., Wang Y., Nordman E., Lee C., Xu N., Wang X., Bodeau J., Tuch B.B., Siddiqui A., Lao K., Surani M.A. mRNA-Seq whole-transcriptome analysis of a single cell. Nature Method 2009, 6:377-382.
-
(2009)
Nature Method
, vol.6
, pp. 377-382
-
-
Tang, F.1
Barbacioru, C.2
Wang, Y.3
Nordman, E.4
Lee, C.5
Xu, N.6
Wang, X.7
Bodeau, J.8
Tuch, B.B.9
Siddiqui, A.10
Lao, K.11
Surani, M.A.12
-
56
-
-
84864660437
-
Transcriptome profiling of the cancer, adjacent non-tumor and distant normal tissues from a colorectal cancer patient by deep sequencing
-
Wu Y., Wang X., Wu F., Huang R., Xue F., Liang G., Tao M., Cai P., Huang Y. Transcriptome profiling of the cancer, adjacent non-tumor and distant normal tissues from a colorectal cancer patient by deep sequencing. PLoS ONE 2012, 7:e41001.
-
(2012)
PLoS ONE
, vol.7
-
-
Wu, Y.1
Wang, X.2
Wu, F.3
Huang, R.4
Xue, F.5
Liang, G.6
Tao, M.7
Cai, P.8
Huang, Y.9
-
57
-
-
80054771709
-
RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma
-
Huang Q., Lin B., Liu H., Ma X., Mo F., Yu W., Li L., Li H., Tian T., Wu D., Shen F., Xing J., Chen Z.N. RNA-Seq analyses generate comprehensive transcriptomic landscape and reveal complex transcript patterns in hepatocellular carcinoma. PLoS ONE 2011, 6:e26168.
-
(2011)
PLoS ONE
, vol.6
-
-
Huang, Q.1
Lin, B.2
Liu, H.3
Ma, X.4
Mo, F.5
Yu, W.6
Li, L.7
Li, H.8
Tian, T.9
Wu, D.10
Shen, F.11
Xing, J.12
Chen, Z.N.13
-
58
-
-
80052322960
-
An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype
-
Shapiro I.M., Cheng A.W., Flytzanis N.C., Balsamo M., Condeelis J.S., Oktay M.H., Burge C.B., Gertler F.B. An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genetics 2011, 7:e1002218.
-
(2011)
PLoS Genetics
, vol.7
-
-
Shapiro, I.M.1
Cheng, A.W.2
Flytzanis, N.C.3
Balsamo, M.4
Condeelis, J.S.5
Oktay, M.H.6
Burge, C.B.7
Gertler, F.B.8
-
59
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
60
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B., Trapnell C., Pop M., Salzberg S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009, 10:R25.
-
(2009)
Genome Biology
, vol.10
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
61
-
-
40049104732
-
SOAP: short oligonucleotide alignment program
-
Li R., Li Y., Kristiansen K., Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008, 24:713-714.
-
(2008)
Bioinformatics
, vol.24
, pp. 713-714
-
-
Li, R.1
Li, Y.2
Kristiansen, K.3
Wang, J.4
-
62
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li H., Ruan J., Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 2008, 18:1851-1858.
-
(2008)
Genome Research
, vol.18
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
63
-
-
65449136284
-
TopHat: discovering splice junctions with RNA-Seq
-
Trapnell C., Pachter L., Salzberg S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 2009, 25:1105-1111.
-
(2009)
Bioinformatics
, vol.25
, pp. 1105-1111
-
-
Trapnell, C.1
Pachter, L.2
Salzberg, S.L.3
-
64
-
-
77955443472
-
Detection of splice junctions from paired-end RNA-Seq data by SpliceMap
-
Au K.F., Jiang H., Lin L., Xing Y., Wong W.H. Detection of splice junctions from paired-end RNA-Seq data by SpliceMap. Nucleic Acids Research 2010, 38:4570-4578.
-
(2010)
Nucleic Acids Research
, vol.38
, pp. 4570-4578
-
-
Au, K.F.1
Jiang, H.2
Lin, L.3
Xing, Y.4
Wong, W.H.5
-
65
-
-
79957894499
-
Observations on novel splice junctions from RNA sequencing data
-
Wang L., Wang X., Wang X., Liang Y., Zhang X. Observations on novel splice junctions from RNA sequencing data. Biochemical and Biophysical Research Communications 2011, 409:299-303.
-
(2011)
Biochemical and Biophysical Research Communications
, vol.409
, pp. 299-303
-
-
Wang, L.1
Wang, X.2
Wang, X.3
Liang, Y.4
Zhang, X.5
-
66
-
-
64549119707
-
Statistical inferences for isoform expression in RNA-Seq
-
Jiang H., Wong W.H. Statistical inferences for isoform expression in RNA-Seq. Bioinformatics 2009, 25:1026-1032.
-
(2009)
Bioinformatics
, vol.25
, pp. 1026-1032
-
-
Jiang, H.1
Wong, W.H.2
-
67
-
-
78650004236
-
Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-Seq
-
Wang X., Wu Z., Zhang X. Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-Seq. Journal of Bioinformatics and Computational Biology 2010, 8:177.
-
(2010)
Journal of Bioinformatics and Computational Biology
, vol.8
, pp. 177
-
-
Wang, X.1
Wu, Z.2
Zhang, X.3
-
68
-
-
77952123055
-
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
-
Trapnell C., Williams B.A., Pertea G., Mortazavi A., Kwan G., van Baren M.J., Salzberg S.L., Word B.J., Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 2010, 28:511-515.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 511-515
-
-
Trapnell, C.1
Williams, B.A.2
Pertea, G.3
Mortazavi, A.4
Kwan, G.5
van Baren, M.J.6
Salzberg, S.L.7
Word, B.J.8
Pachter, L.9
-
69
-
-
78649714014
-
Analysis and design of RNA sequencing experiments for identifying isoform regulation
-
Katz Y., Wang E.T., Airoldi E.M., Burge C.B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nature Methods 2010, 7:1009-1015.
-
(2010)
Nature Methods
, vol.7
, pp. 1009-1015
-
-
Katz, Y.1
Wang, E.T.2
Airoldi, E.M.3
Burge, C.B.4
-
70
-
-
79951522882
-
Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq
-
Wu Z., Wang X., Zhang X. Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq. Bioinformatics 2011, 27:502-508.
-
(2011)
Bioinformatics
, vol.27
, pp. 502-508
-
-
Wu, Z.1
Wang, X.2
Zhang, X.3
-
71
-
-
77949507153
-
RNA-Seq gene expression estimation with read mapping uncertainty
-
Li B., Ruotti V., Stewart R.M., Thomson J.A., Dewey C.N. RNA-Seq gene expression estimation with read mapping uncertainty. Bioinformatics 2010, 26:493-500.
-
(2010)
Bioinformatics
, vol.26
, pp. 493-500
-
-
Li, B.1
Ruotti, V.2
Stewart, R.M.3
Thomson, J.A.4
Dewey, C.N.5
-
72
-
-
79952709611
-
Improving RNA-Seq expression estimates by correcting for fragment bias
-
Roberts A., Trapnell C., Donaghey J., Rinn J.L., Pachter L. Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biology 2011, 12:R22.
-
(2011)
Genome Biology
, vol.12
-
-
Roberts, A.1
Trapnell, C.2
Donaghey, J.3
Rinn, J.L.4
Pachter, L.5
-
73
-
-
67149098194
-
Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes
-
Blencowe B.J., Ahmad S., Lee L.J. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. Genes and Development 2009, 23:1379-1386.
-
(2009)
Genes and Development
, vol.23
, pp. 1379-1386
-
-
Blencowe, B.J.1
Ahmad, S.2
Lee, L.J.3
-
74
-
-
75249095274
-
DEGseq: an R package for identifying differentially expressed genes from RNA-Seq data
-
Wang L., Feng Z., Wang X., Wang X., Zhang X. DEGseq: an R package for identifying differentially expressed genes from RNA-Seq data. Bioinformatics 2010, 26:136-138.
-
(2010)
Bioinformatics
, vol.26
, pp. 136-138
-
-
Wang, L.1
Feng, Z.2
Wang, X.3
Wang, X.4
Zhang, X.5
-
75
-
-
75249087100
-
EdgeR: a bioconductor package for differential expression analysis of digital gene expression data
-
Robinson M.D., McCarthy D.J., Smyth G.K. edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26:139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
76
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S., Huber W. Differential expression analysis for sequence count data. Genome Biology 2010, 11:R106.
-
(2010)
Genome Biology
, vol.11
-
-
Anders, S.1
Huber, W.2
-
77
-
-
77955298482
-
BaySeq: empirical Bayesian methods for identifying differential expression in sequence count data
-
Hardcastle T.J., Kelly K.A. BaySeq: empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 2010, 11:422.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 422
-
-
Hardcastle, T.J.1
Kelly, K.A.2
-
78
-
-
78650552020
-
Statistical tests for detecting differential RNA-transcript expression from read counts
-
Stegle O., Drewe P., Bohnert R., Borgwardt K.M., Gunnar R. Statistical tests for detecting differential RNA-transcript expression from read counts. Nature Proceedings 2010, 1-11. 10.1038/npre.2010.4437.1.
-
(2010)
Nature Proceedings
, pp. 1-11
-
-
Stegle, O.1
Drewe, P.2
Bohnert, R.3
Borgwardt, K.M.4
Gunnar, R.5
-
79
-
-
80053435328
-
FDM: a graph-based statistical method to detect differential transcription using RNA-Seq data
-
Singh D., Orellana C.F., Hu Y., Jones C.D., Liu Y., Chiang D.Y., Liu J., Prins J.F. FDM: a graph-based statistical method to detect differential transcription using RNA-Seq data. Bioinformatics 2011, 27:2633-2640.
-
(2011)
Bioinformatics
, vol.27
, pp. 2633-2640
-
-
Singh, D.1
Orellana, C.F.2
Hu, Y.3
Jones, C.D.4
Liu, Y.5
Chiang, D.Y.6
Liu, J.7
Prins, J.F.8
-
80
-
-
84860385776
-
MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data
-
Shen S., Park J.W., Huang J., Dittmar K.A., Lu Z., Zhou Q., Carstens R.P., Xing Y. MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data. Nucleic Acids Research 2012, 40:e61.
-
(2012)
Nucleic Acids Research
, vol.40
-
-
Shen, S.1
Park, J.W.2
Huang, J.3
Dittmar, K.A.4
Lu, Z.5
Zhou, Q.6
Carstens, R.P.7
Xing, Y.8
-
81
-
-
84875374758
-
Identifying differentially spliced genes from two groups of RNA-Seq samples
-
W. Wang, Z. Qin, Z. Feng, X. Wang, X. Zhang, Identifying differentially spliced genes from two groups of RNA-Seq samples, Gene (2012). http://dx.doi.org/10.1016/j.gene.2012.11.045.
-
(2012)
Gene
-
-
Wang, W.1
Qin, Z.2
Feng, Z.3
Wang, X.4
Zhang, X.5
-
82
-
-
77952148742
-
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
-
Guttman M., Garber M., Levin J.Z., Donaghey J., Robinson J., Adiconis X., Fan L., Kiziol M.J., Gnirke A., Nusbaum C., Rinn J.L., Lander E.S., Regev A. Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology 2010, 28:503-510.
-
(2010)
Nature Biotechnology
, vol.28
, pp. 503-510
-
-
Guttman, M.1
Garber, M.2
Levin, J.Z.3
Donaghey, J.4
Robinson, J.5
Adiconis, X.6
Fan, L.7
Kiziol, M.J.8
Gnirke, A.9
Nusbaum, C.10
Rinn, J.L.11
Lander, E.S.12
Regev, A.13
-
83
-
-
79957842166
-
Computational methods for transcriptome annotation and quantification using RNA-Seq
-
Garber M., Grabherr M.G., Guttman M., Trapnell C. Computational methods for transcriptome annotation and quantification using RNA-Seq. Nature Methods 2011, 8:469-477.
-
(2011)
Nature Methods
, vol.8
, pp. 469-477
-
-
Garber, M.1
Grabherr, M.G.2
Guttman, M.3
Trapnell, C.4
-
84
-
-
68549104404
-
1000 Genome project data processing subgroup, the sequence alignment/map (SAM) format and SAMtools
-
Li H., Handsaker B., Wysoker A., Fennel T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. 1000 Genome project data processing subgroup, the sequence alignment/map (SAM) format and SAMtools. Bioinformatics 2009, 25:2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennel, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
|