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Items: 1 to 20 of 81

1.

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs).

Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan KG, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL.

Genome Res. 2007 Jun;17(6):828-38.

2.

Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer.

Bärlund M, Monni O, Weaver JD, Kauraniemi P, Sauter G, Heiskanen M, Kallioniemi OP, Kallioniemi A.

Genes Chromosomes Cancer. 2002 Dec;35(4):311-7.

PMID:
12378525
3.

Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation.

Ng P, Wei CL, Sung WK, Chiu KP, Lipovich L, Ang CC, Gupta S, Shahab A, Ridwan A, Wong CH, Liu ET, Ruan Y.

Nat Methods. 2005 Feb;2(2):105-11. Epub 2005 Jan 9.

PMID:
15782207
4.

Transcriptional consequences of genomic structural aberrations in breast cancer.

Inaki K, Hillmer AM, Ukil L, Yao F, Woo XY, Vardy LA, Zawack KF, Lee CW, Ariyaratne PN, Chan YS, Desai KV, Bergh J, Hall P, Putti TC, Ong WL, Shahab A, Cacheux-Rataboul V, Karuturi RK, Sung WK, Ruan X, Bourque G, Ruan Y, Liu ET.

Genome Res. 2011 May;21(5):676-87. doi: 10.1101/gr.113225.110. Epub 2011 Apr 5.

5.

PET-Tool: a software suite for comprehensive processing and managing of Paired-End diTag (PET) sequence data.

Chiu KP, Wong CH, Chen Q, Ariyaratne P, Ooi HS, Wei CL, Sung WK, Ruan Y.

BMC Bioinformatics. 2006 Aug 25;7:390.

6.

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses.

Fullwood MJ, Wei CL, Liu ET, Ruan Y.

Genome Res. 2009 Apr;19(4):521-32. doi: 10.1101/gr.074906.107. Review.

7.

Decoding the fine-scale structure of a breast cancer genome and transcriptome.

Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins C.

Genome Res. 2006 Mar;16(3):394-404. Epub 2006 Feb 3.

8.

The der(17)t(X;17)(p11;q25) of human alveolar soft part sarcoma fuses the TFE3 transcription factor gene to ASPL, a novel gene at 17q25.

Ladanyi M, Lui MY, Antonescu CR, Krause-Boehm A, Meindl A, Argani P, Healey JH, Ueda T, Yoshikawa H, Meloni-Ehrig A, Sorensen PH, Mertens F, Mandahl N, van den Berghe H, Sciot R, Dal Cin P, Bridge J.

Oncogene. 2001 Jan 4;20(1):48-57.

9.

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

Ng P, Tan JJ, Ooi HS, Lee YL, Chiu KP, Fullwood MJ, Srinivasan KG, Perbost C, Du L, Sung WK, Wei CL, Ruan Y.

Nucleic Acids Res. 2006 Jul 13;34(12):e84.

10.

Novel transcripts discovered by mining genomic DNA from defined regions of bovine chromosome 6.

Weikard R, Goldammer T, Eberlein A, Kuehn C.

BMC Genomics. 2009 Apr 24;10:186. doi: 10.1186/1471-2164-10-186.

11.

Identification and characterization of JMJD2 family genes in silico.

Katoh M, Katoh M.

Int J Oncol. 2004 Jun;24(6):1623-8.

PMID:
15138608
12.

A transcriptional sketch of a primary human breast cancer by 454 deep sequencing.

Guffanti A, Iacono M, Pelucchi P, Kim N, Soldà G, Croft LJ, Taft RJ, Rizzi E, Askarian-Amiri M, Bonnal RJ, Callari M, Mignone F, Pesole G, Bertalot G, Bernardi LR, Albertini A, Lee C, Mattick JS, Zucchi I, De Bellis G.

BMC Genomics. 2009 Apr 20;10:163. doi: 10.1186/1471-2164-10-163.

13.

Paired-end diTagging for transcriptome and genome analysis.

Ng P, Wei CL, Ruan Y.

Curr Protoc Mol Biol. 2007 Jul;Chapter 21:Unit 21.12. doi: 10.1002/0471142727.mb2112s79.

PMID:
18265396
14.

Retrotransposition as a source of new promoters.

Okamura K, Nakai K.

Mol Biol Evol. 2008 Jun;25(6):1231-8. doi: 10.1093/molbev/msn071. Epub 2008 Mar 25.

15.

[DNA sequence analysis of a novel variate type of PML/RAR alpha fusion gene transcript].

Wang GP, Chen FP, Jian ZF.

Hunan Yi Ke Da Xue Xue Bao. 2001 Dec 28;26(6):581-2. Chinese. No abstract available.

PMID:
12536551
16.

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.

Hillmer AM, Yao F, Inaki K, Lee WH, Ariyaratne PN, Teo AS, Woo XY, Zhang Z, Zhao H, Ukil L, Chen JP, Zhu F, So JB, Salto-Tellez M, Poh WT, Zawack KF, Nagarajan N, Gao S, Li G, Kumar V, Lim HP, Sia YY, Chan CS, Leong ST, Neo SC, Choi PS, Thoreau H, Tan PB, Shahab A, Ruan X, Bergh J, Hall P, Cacheux-Rataboul V, Wei CL, Yeoh KG, Sung WK, Bourque G, Liu ET, Ruan Y.

Genome Res. 2011 May;21(5):665-75. doi: 10.1101/gr.113555.110. Epub 2011 Apr 5.

17.

Multiplex parallel pair-end-ditag sequencing approaches in system biology.

Ruan Y, Wei CL.

Wiley Interdiscip Rev Syst Biol Med. 2010 Mar-Apr;2(2):224-34. doi: 10.1002/wsbm.40. Review.

PMID:
20836024
18.

Identification of human-specific transcript variants induced by DNA insertions in the human genome.

Kim DS, Hahn Y.

Bioinformatics. 2011 Jan 1;27(1):14-21. doi: 10.1093/bioinformatics/btq612. Epub 2010 Oct 29.

19.

A novel cryptic translocation t(12;17)(p13;p12-p13) in a secondary acute myeloid leukemia results in a fusion of the ETV6 gene and the antisense strand of the PER1 gene.

Murga Penas EM, Cools J, Algenstaedt P, Hinz K, Seeger D, Schafhausen P, Schilling G, Marynen P, Hossfeld DK, Dierlamm J.

Genes Chromosomes Cancer. 2003 May;37(1):79-83.

PMID:
12661008
20.

nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing.

McPherson A, Wu C, Wyatt AW, Shah S, Collins C, Sahinalp SC.

Genome Res. 2012 Nov;22(11):2250-61. doi: 10.1101/gr.136572.111. Epub 2012 Jun 28.

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