FusionSeq Papers - Revision history

Asboner: /* 2011 */

2012-03-08T19:46:39Z

2011

← Older revision		Revision as of 19:46, 8 March 2012
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	* Abate, F., A. Acquaviva, E. Ficarra, G. Paciello, E. Macii, A. Ferrarini, M. Delledonne, S. Soverini, and G. Martinelli. '''A Novel Framework for Chimeric Transcript Detection Based on Accurate Gene Fusion Model.''' 34–41. [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6112352&tag=1 IEEE, 2011]		* Abate, F., A. Acquaviva, E. Ficarra, G. Paciello, E. Macii, A. Ferrarini, M. Delledonne, S. Soverini, and G. Martinelli. '''A Novel Framework for Chimeric Transcript Detection Based on Accurate Gene Fusion Model.''' 34–41. [http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6112352&tag=1 IEEE, 2011]

			* Salzman, Julia, Robert J. Marinelli, Peter L. Wang, Ann E. Green, Julie S. Nielsen, Brad H. Nelson, Charles W. Drescher, and Patrick O. Brown. '''ESRRA-C11orf20 Is a Recurrent Gene Fusion in Serous Ovarian Carcinoma.''' PLoS Biol 9, no. 9 (2011): e1001156.

	* Asmann, Yan W, Asif Hossain, Brian M Necela, Sumit Middha, Krishna R Kalari, Zhifu Sun, High-Seng Chai, et al. “A Novel Bioinformatics Pipeline for Identification and Characterization of Fusion Transcripts in Breast Cancer and Normal Cell Lines.” Nucleic Acids Research 39, no. 15 (August 1, 2011): e100–e100.		* Asmann, Yan W, Asif Hossain, Brian M Necela, Sumit Middha, Krishna R Kalari, Zhifu Sun, High-Seng Chai, et al. “A Novel Bioinformatics Pipeline for Identification and Characterization of Fusion Transcripts in Breast Cancer and Normal Cell Lines.” Nucleic Acids Research 39, no. 15 (August 1, 2011): e100–e100.

			* Chen, William L., Burton A. Leland, Joseph L. Durant, David L. Grier, Bradley D. Christie, James G. Nourse, and Keith T. Taylor. '''Self-Contained Sequence Representation: Bridging the Gap Between Bioinformatics and Cheminformatics.''' J. Chem. Inf. Model. 51, no. 9 (2011): 2186–2208.

	* Kim, Daehwan, and Steven L Salzberg. '''TopHat-Fusion: An Algorithm for Discovery of Novel Fusion Transcripts.''' Genome Biology 12 (2011): R72.		* Kim, Daehwan, and Steven L Salzberg. '''TopHat-Fusion: An Algorithm for Discovery of Novel Fusion Transcripts.''' Genome Biology 12 (2011): R72.

Asboner: /* Scientific Papers */

2012-03-08T19:41:48Z

Scientific Papers

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 =Scientific Papers=
 ==2011==
-*McPherson, Andrew, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, and S. Cenk Sahinalp. '''Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data.''' [http://bioinformatics.oxfordjournals.org/content/early/2011/04/09/bioinformatics.btr184.abstract. Bioinformatics] (April 9, 2011).
+* Stein, Lincoln D. '''An Introduction to the Informatics of ‘Next‐Generation’ Sequencing''' In . John Wiley & Sons, Inc. [http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi1101s36/abstract Current Protocols in Bioinformatics]
-*Nacu, Serban, Wenlin Yuan, Zhengyan Kan, Deepali Bhatt, Celina Rivers, Jeremy Stinson, Brock Peters, et al. '''Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples.''' [http://www.biomedcentral.com/1755-8794/4/11 BMC Medical Genomics]  4, no. 1 (2011): 11.
+* Nacu, Serban, Wenlin Yuan, Zhengyan Kan, Deepali Bhatt, Celina Rivers, Jeremy Stinson, Brock Peters, et al. '''Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples.''' [http://www.biomedcentral.com/1755-8794/4/11 BMC Medical Genomics]  4, no. 1 (2011): 11.
 * Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin P, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, Rickman DS, Demichelis F, Gerstein MB, Rubin MA. '''Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing''' [http://www.genome.org/cgi/doi/10.1101/gr.110684.110 Genome Res]  2011; Vol. 21:56-67; Published in Advance October 29, 2010.  doi:[http://www.genome.org/cgi/doi/10.1101/gr.110684.110 10.1101/gr.110684.110]

Asboner at 13:37, 19 April 2011

2011-04-19T13:37:18Z

← Older revision		Revision as of 13:37, 19 April 2011
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	* Nov 2010: [http://www.genomeweb.com/sequencing/transcriptome-sequencing-25-prostate-cancer-tumors-ids-novel-gene-fusions GenomeWeb -- InSequence]		* Nov 2010: [http://www.genomeweb.com/sequencing/transcriptome-sequencing-25-prostate-cancer-tumors-ids-novel-gene-fusions GenomeWeb -- InSequence]
	* July/Aug 2010: [http://www.genomeweb.com/arrays/moving-away-microarrays?page=show GenomeWeb -- GenomeTechnology]		* July/Aug 2010: [http://www.genomeweb.com/arrays/moving-away-microarrays?page=show GenomeWeb -- GenomeTechnology]


	=Scientific Papers=		=Scientific Papers=
	==2011==		==2011==

	*McPherson, Andrew, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, and S. Cenk Sahinalp. '''Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data.''' [http://bioinformatics.oxfordjournals.org/content/early/2011/04/09/bioinformatics.btr184.abstract. Bioinformatics] (April 9, 2011).		*McPherson, Andrew, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, and S. Cenk Sahinalp. '''Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data.''' [http://bioinformatics.oxfordjournals.org/content/early/2011/04/09/bioinformatics.btr184.abstract. Bioinformatics] (April 9, 2011).

Asboner: /* 2010 */

2011-04-19T13:36:35Z

2010

← Older revision		Revision as of 13:36, 19 April 2011
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	==2010==		=News=
	* Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin P, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, Rickman DS, Demichelis F, Gerstein MB, Rubin MA. '''Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing'''. ''Genome Res'' Published in Advance October 29, 2010. doi:[http://www.genome.org/cgi/doi/10.1101/gr.110684.110 10.1101/gr.110684.110]		* Nov 2010: [http://www.genomeweb.com/sequencing/transcriptome-sequencing-25-prostate-cancer-tumors-ids-novel-gene-fusions GenomeWeb -- InSequence]
			* July/Aug 2010: [http://www.genomeweb.com/arrays/moving-away-microarrays?page=show GenomeWeb -- GenomeTechnology]

			=Scientific Papers=
			==2011==

			*McPherson, Andrew, Chunxiao Wu, Iman Hajirasouliha, Fereydoun Hormozdiari, Faraz Hach, Anna Lapuk, Stanislav Volik, Sohrab Shah, Colin Collins, and S. Cenk Sahinalp. '''Comrad: a novel algorithmic framework for the integrated analysis of RNA-Seq and WGSS data.''' [http://bioinformatics.oxfordjournals.org/content/early/2011/04/09/bioinformatics.btr184.abstract. Bioinformatics] (April 9, 2011).

			*Nacu, Serban, Wenlin Yuan, Zhengyan Kan, Deepali Bhatt, Celina Rivers, Jeremy Stinson, Brock Peters, et al. '''Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples.''' [http://www.biomedcentral.com/1755-8794/4/11 BMC Medical Genomics] 4, no. 1 (2011): 11.

			* Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin P, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, Rickman DS, Demichelis F, Gerstein MB, Rubin MA. '''Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing''' [http://www.genome.org/cgi/doi/10.1101/gr.110684.110 Genome Res] 2011; Vol. 21:56-67; Published in Advance October 29, 2010. doi:[http://www.genome.org/cgi/doi/10.1101/gr.110684.110 10.1101/gr.110684.110]

Asboner at 00:40, 1 November 2010

2010-11-01T00:40:35Z

← Older revision		Revision as of 00:40, 1 November 2010
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	Here is a list of papers citing:		Here is a list of papers citing:
	* Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB. '''FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data.''' ''Genome Biol'' 21 Oct. 2010; '''11''':R104 doi: [http://dx.doi.org/10.1186/gb-2010-11-10-r104 10.1186/gb-2010-11-10-r104]		* Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB. '''FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data.''' ''Genome Biol'' 21 Oct. 2010; '''11''':R104 doi:[http://dx.doi.org/10.1186/gb-2010-11-10-r104 10.1186/gb-2010-11-10-r104]


	==2010==		==2010==
	* Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin P, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, Rickman DS, Demichelis F, Gerstein MB, Rubin MA. '''Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing'''. ''Genome Res'' Published in Advance October 29, 2010. doi:[http://www.genome.org/cgi/doi/10.1101/gr.110684.110 10.1101/gr.110684.110]		* Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin P, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, Rickman DS, Demichelis F, Gerstein MB, Rubin MA. '''Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing'''. ''Genome Res'' Published in Advance October 29, 2010. doi:[http://www.genome.org/cgi/doi/10.1101/gr.110684.110 10.1101/gr.110684.110]

Asboner: Created page with '{{FusionSeqHeader}} Here is a list of papers citing: * Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F,…'

2010-11-01T00:39:13Z

Created page with '{{FusionSeqHeader}} Here is a list of papers citing: * Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F,…'

New page

{{FusionSeqHeader}}

Here is a list of papers citing:
* Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB. '''FusionSeq: a modular framework for finding gene fusions by analyzing Paired-End RNA-Sequencing data.''' ''Genome Biol'' 21 Oct. 2010; '''11''':R104 doi: [http://dx.doi.org/10.1186/gb-2010-11-10-r104 10.1186/gb-2010-11-10-r104]

==2010==
* Pflueger D, Terry S, Sboner A, Habegger L, Esgueva R, Lin P, Svensson MA, Kitabayashi N, Moss BJ, MacDonald TY, Cao X, Barrette T, Tewari AK, Chee MS, Chinnaiyan AM, Rickman DS, Demichelis F, Gerstein MB, Rubin MA. '''Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing'''. ''Genome Res'' Published in Advance October 29, 2010. doi:[http://www.genome.org/cgi/doi/10.1101/gr.110684.110 10.1101/gr.110684.110]