FusionSeq Papers

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=Scientific Papers=
=Scientific Papers=
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==2012==
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* Pierron, Gaëlle, Franck Tirode, Carlo Lucchesi, Stéphanie Reynaud, Stelly Ballet, Sarah Cohen-Gogo, Virginie Perrin, Jean-Michel Coindre, and Olivier Delattre. '''A New Subtype of Bone Sarcoma Defined by BCOR-CCNB3 Gene Fusion.'''  [http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.1107.html Nature Genetics]  (March 4, 2012).
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* Barbieri, Christopher E, Francesca Demichelis, and Mark A Rubin. '''Molecular Genetics of Prostate Cancer: Emerging Appreciation of Genetic Complexity.''' Histopathology 60, no. 1 (January 1, 2012): 187–198.
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* Chng, Kern Rei, Shin Chet Chuah, and Edwin Cheung eds. '''Stem Cells and Human Diseases.''' 175–196  [http://www.springerlink.com/content/g101v26672v450uk/abstract/ Springer Netherlands 2012].
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==2011==
==2011==
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*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).  
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* 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]
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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]
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* 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.
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* Kim, Daehwan, and Steven L Salzberg. '''TopHat-Fusion: An Algorithm for Discovery of Novel Fusion Transcripts.''' Genome Biology 12 (2011): R72.
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* McPherson, Andrew, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G. F. Sun, Malachi Griffith, et al. '''deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data.''' PLoS Comput Biol 7, no. 5 (May 19, 2011): e1001138.
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* Ge, Huanying, Kejun Liu, Todd Juan, Fang Fang, Matthew Newman, and Wolfgang Hoeck. “FusionMap: Detecting Fusion Genes from Next-generation Sequencing Data at Base-pair Resolution.” [http://bioinformatics.oxfordjournals.org/content/early/2011/05/18/bioinformatics.btr310.abstract Bioinformatics] (May 18, 2011).
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* Li, Yang, Jeremy Chien, David I. Smith, and Jian Ma. '''FusionHunter: Identifying Fusion Transcripts in Cancer Using Paired-end RNA-seq.''' [http://bioinformatics.oxfordjournals.org/content/early/2011/05/05/bioinformatics.btr265.abstract Bioinformatics] (May 5, 2011).
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* 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).  
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*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.
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* 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]
* 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]

Revision as of 19:41, 8 March 2012

FusionSeq main web page
User documentation main

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:10.1186/gb-2010-11-10-r104


Contents

News


Scientific Papers

2012

  • Pierron, Gaëlle, Franck Tirode, Carlo Lucchesi, Stéphanie Reynaud, Stelly Ballet, Sarah Cohen-Gogo, Virginie Perrin, Jean-Michel Coindre, and Olivier Delattre. A New Subtype of Bone Sarcoma Defined by BCOR-CCNB3 Gene Fusion. Nature Genetics (March 4, 2012).
  • Barbieri, Christopher E, Francesca Demichelis, and Mark A Rubin. Molecular Genetics of Prostate Cancer: Emerging Appreciation of Genetic Complexity. Histopathology 60, no. 1 (January 1, 2012): 187–198.

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. IEEE, 2011
  • 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.
  • Kim, Daehwan, and Steven L Salzberg. TopHat-Fusion: An Algorithm for Discovery of Novel Fusion Transcripts. Genome Biology 12 (2011): R72.
  • McPherson, Andrew, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G. F. Sun, Malachi Griffith, et al. deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data. PLoS Comput Biol 7, no. 5 (May 19, 2011): e1001138.
  • Ge, Huanying, Kejun Liu, Todd Juan, Fang Fang, Matthew Newman, and Wolfgang Hoeck. “FusionMap: Detecting Fusion Genes from Next-generation Sequencing Data at Base-pair Resolution.” Bioinformatics (May 18, 2011).
  • Li, Yang, Jeremy Chien, David I. Smith, and Jian Ma. FusionHunter: Identifying Fusion Transcripts in Cancer Using Paired-end RNA-seq. Bioinformatics (May 5, 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. 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. 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 Genome Res 2011; Vol. 21:56-67; Published in Advance October 29, 2010. doi:10.1101/gr.110684.110
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