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Items: 1 to 20 of 83


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.


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.


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.


Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.

BMC Genomics. 2009 Jan 21;10:37. doi: 10.1186/1471-2164-10-37.


Paired-end genomic signature tags: a method for the functional analysis of genomes and epigenomes.

Dunn JJ, McCorkle SR, Everett L, Anderson CW.

Genet Eng (N Y). 2007;28:159-73. Review.


A global map of p53 transcription-factor binding sites in the human genome.

Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T, Shahab A, Yong HC, Fu Y, Weng Z, Liu J, Zhao XD, Chew JL, Lee YL, Kuznetsov VA, Sung WK, Miller LD, Lim B, Liu ET, Yu Q, Ng HH, Ruan Y.

Cell. 2006 Jan 13;124(1):207-19.


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.


Chromatin Interaction Analysis with Paired-End Tag Sequencing (ChIA-PET) for mapping chromatin interactions and understanding transcription regulation.

Goh Y, Fullwood MJ, Poh HM, Peh SQ, Ong CT, Zhang J, Ruan X, Ruan Y.

J Vis Exp. 2012 Apr 30;(62). pii: 3770. doi: 10.3791/3770.


Chromatin interaction analysis using paired-end tag sequencing.

Fullwood MJ, Han Y, Wei CL, Ruan X, Ruan Y.

Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. doi: 10.1002/0471142727.mb2115s89.


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.


Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

Yao F, Ariyaratne PN, Hillmer AM, Lee WH, Li G, Teo AS, Woo XY, Zhang Z, Chen JP, Poh WT, Zawack KF, Chan CS, Leong ST, Neo SC, Choi PS, Gao S, Nagarajan N, Thoreau H, Shahab A, Ruan X, Cacheux-Rataboul V, Wei CL, Bourque G, Sung WK, Liu ET, Ruan Y.

PLoS One. 2012;7(9):e46152. doi: 10.1371/journal.pone.0046152. Epub 2012 Sep 28.


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.


Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB.

PLoS Comput Biol. 2009 Jul;5(7):e1000432. doi: 10.1371/journal.pcbi.1000432. Epub 2009 Jul 10.


ChIA-PET analysis of transcriptional chromatin interactions.

Zhang J, Poh HM, Peh SQ, Sia YY, Li G, Mulawadi FH, Goh Y, Fullwood MJ, Sung WK, Ruan X, Ruan Y.

Methods. 2012 Nov;58(3):289-99. doi: 10.1016/j.ymeth.2012.08.009. Epub 2012 Aug 25.


ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing.

Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK.

Genome Biol. 2010;11(2):R22. doi: 10.1186/gb-2010-11-2-r22. Epub 2010 Feb 25.


The use of multiple displacement amplification to amplify complex DNA libraries.

Fullwood MJ, Tan JJ, Ng PW, Chiu KP, Liu J, Wei CL, Ruan Y.

Nucleic Acids Res. 2008 Mar;36(5):e32. doi: 10.1093/nar/gkn074. Epub 2008 Feb 19.


Paired-end sequencing of Fosmid libraries by Illumina.

Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK, Jaffe DB, Nusbaum C, Gnirke A.

Genome Res. 2012 Nov;22(11):2241-9. doi: 10.1101/gr.138925.112. Epub 2012 Jul 16.


Assessing the feasibility of GS FLX Pyrosequencing for sequencing the Atlantic salmon genome.

Quinn NL, Levenkova N, Chow W, Bouffard P, Boroevich KA, Knight JR, Jarvie TP, Lubieniecki KP, Desany BA, Koop BF, Harkins TT, Davidson WS.

BMC Genomics. 2008 Aug 28;9:404. doi: 10.1186/1471-2164-9-404.


Targeted high-throughput sequencing of tagged nucleic acid samples.

Meyer M, Stenzel U, Myles S, Prüfer K, Hofreiter M.

Nucleic Acids Res. 2007;35(15):e97. Epub 2007 Aug 1.


Preparing a re-sequencing DNA library of 2 cancer candidate genes using the ligation-by-amplification protocol by two PCR reactions.

Su Y, Lin L, Tian G, Chen C, Liu T, Xu X, Qi X, Zhang X, Yang H.

Sci China C Life Sci. 2009 May;52(5):483-91. doi: 10.1007/s11427-009-0066-8. Epub 2009 May 27.

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