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Global and unbiased detection of splice junctions from RNA-seq data
Adam Ameur, Anna Wetterbom, Lars Feuk, Ulf Gyllensten
Genome Biol. 2010; 11(3): R34. Published online 2010 March 17. doi: 10.1186/gb-2010-11-3-r34
PMCID:
PMC2864574
Abstract Full Text PDF–725K Supplementary Material

Is Cited by the Following 15 Articles in this Archive:

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm
Onur Sakarya, Heinz Breu, Milan Radovich, Yongzhi Chen, Yulei N. Wang, Catalin Barbacioru, Sowmi Utiramerur, Penn P. Whitley, Joel P. Brockman, Paolo Vatta, Zheng Zhang, Liviu Popescu, Matthew W. Muller, Vidya Kudlingar, Nriti Garg, Chieh-Yuan Li, Benjamin S. Kong, John P. Bodeau, Robert C. Nutter, Jian Gu, Kelli S. Bramlett, Jeffrey K. Ichikawa, Fiona C. Hyland, Asim S. Siddiqui
PLoS Comput Biol. 2012 April; 8(4): e1002464. Published online 2012 April 5. doi: 10.1371/journal.pcbi.1002464
PMCID:
PMC3320572
Abstract Full Text PDF–701K Supplementary Material
Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia
I Iacobucci, A Ferrarini, M Sazzini, E Giacomelli, A Lonetti, L Xumerle, A Ferrari, C Papayannidis, G Malerba, D Luiselli, A Boattini, P Garagnani, A Vitale, S Soverini, F Pane, M Baccarani, M Delledonne, G Martinelli
Blood Cancer J. 2012 March; 2(3): e61. Published online 2012 March 9. doi: 10.1038/bcj.2012.6
PMCID:
PMC3317525
Abstract Full Text PDF–351K Supplementary Material
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
Daehwan Kim, Steven L Salzberg
Genome Biol. 2011; 12(8): R72. Published online 2011 August 11. doi: 10.1186/gb-2011-12-8-r72
PMCID:
PMC3245612
Abstract Full Text PDF–456K Supplementary Material
Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits
Ghazal Zaboli, Adam Ameur, Wilmar Igl, Åsa Johansson, Caroline Hayward, Veronique Vitart, Susan Campbell, Lina Zgaga, Ozren Polasek, Gerd Schmitz, Cornelia van Duijn, Ben Oostra, Peter Pramstaller, Andrew Hicks, Tomas Meitinger, Igor Rudan, Alan Wright, James F Wilson, Harry Campbell, Ulf Gyllensten
Eur J Hum Genet. 2012 January; 20(1): 77–83. Published online 2011 August 3. doi: 10.1038/ejhg.2011.138
PMCID:
PMC3234506
Free in PMC on 2013/01/01
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length
Shao-Ke Lou, Jing-Woei Li, Hao Qin, Aldrin Kay-Yuen Yim, Leung-Yau Lo, Bing Ni, Kwong-Sak Leung, Stephen Kwok-Wing Tsui, Ting-Fung Chan
BMC Bioinformatics. 2011; 12(Suppl 5): S2. Published online 2011 July 27. doi: 10.1186/1471-2105-12-S5-S2
PMCID:
PMC3226252
Abstract Full Text PDF–1.0M Supplementary Material
Ultra-Deep Sequencing of Mouse Mitochondrial DNA: Mutational Patterns and Their Origins
Adam Ameur, James B. Stewart, Christoph Freyer, Erik Hagström, Max Ingman, Nils-Göran Larsson, Ulf Gyllensten
PLoS Genet. 2011 March; 7(3): e1002028. Published online 2011 March 24. doi: 10.1371/journal.pgen.1002028
PMCID:
PMC3063763
Abstract Full Text PDF–331K Supplementary Material
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs
Marcus Kinsella, Olivier Harismendy, Masakazu Nakano, Kelly A. Frazer, Vineet Bafna
Bioinformatics. 2011 April 15; 27(8): 1068–1075. Published online 2011 February 16. doi: 10.1093/bioinformatics/btr085
PMCID:
PMC3072550
Abstract Full Text PDF–369K Supplementary Material
Detecting structural variations in the human genome using next generation sequencing
Ruibin Xi, Tae-Min Kim, Peter J. Park
Brief Funct Genomics. 2010 December; 9(5-6): 405–415. Published online 2011 January 6. doi: 10.1093/bfgp/elq025
PMCID:
PMC3080742
Abstract Full Text PDF–344K
RNA sequencing: advances, challenges and opportunities
Fatih Ozsolak, Patrice M. Milos
Nat Rev Genet. Author manuscript; available in PMC 2011 May 1.
Published in final edited form as: Nat Rev Genet. 2011 February; 12(2): 87–98. Published online 2010 December 30. doi: 10.1038/nrg2934
PMCID:
PMC3031867
Abstract Full Text PDF–633K
From RNA-seq reads to differential expression results
Alicia Oshlack, Mark D Robinson, Matthew D Young
Genome Biol. 2010; 11(12): 220. Published online 2010 December 22. doi: 10.1186/gb-2010-11-12-220
PMCID:
PMC3046478
Abstract Full Text PDF–435K
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping
Shao-Ke Lou, Bing Ni, Leung-Yau Lo, Stephen Kwok-Wing Tsui, Ting-Fung Chan, Kwong-Sak Leung
Bioinformatics. 2011 February 1; 27(3): 421–422. Published online 2010 December 17. doi: 10.1093/bioinformatics/btq656
PMCID:
PMC3031031
Abstract Full Text PDF–168K Supplementary Material
Noisy Splicing Drives mRNA Isoform Diversity in Human Cells
Joseph K. Pickrell, Athma A. Pai, Yoav Gilad, Jonathan K. Pritchard
PLoS Genet. 2010 December; 6(12): e1001236. Published online 2010 December 9. doi: 10.1371/journal.pgen.1001236
PMCID:
PMC3000347
Abstract Full Text PDF–1.2M Supplementary Material
HMMSplicer: A Tool for Efficient and Sensitive Discovery of Known and Novel Splice Junctions in RNA-Seq Data
Michelle T. Dimon, Katherine Sorber, Joseph L. DeRisi
PLoS One. 2010; 5(11): e13875. Published online 2010 November 8. doi: 10.1371/journal.pone.0013875
PMCID:
PMC2975632
Abstract Full Text PDF–1.0M
FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data
Andrea Sboner, Lukas Habegger, Dorothee Pflueger, Stephane Terry, David Z Chen, Joel S Rozowsky, Ashutosh K Tewari, Naoki Kitabayashi, Benjamin J Moss, Mark S Chee, Francesca Demichelis, Mark A Rubin, Mark B Gerstein
Genome Biol. 2010; 11(10): R104. Published online 2010 October 21. doi: 10.1186/gb-2010-11-10-r104
PMCID:
PMC3218660
Abstract Full Text PDF–1.3M Supplementary Material
Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing
Anna Wetterbom, Adam Ameur, Lars Feuk, Ulf Gyllensten, Lucia Cavelier
Genome Biol. 2010; 11(7): R78. Published online 2010 July 23. doi: 10.1186/gb-2010-11-7-r78
PMCID:
PMC2926789
Abstract Full Text PDF–2.3M Supplementary Material
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