Comparative assessment of methods for the fusion transcripts detection from RNA-Seq data
暂无分享,去创建一个
Hui Li | Shailesh Kumar | Angie Duy Vo | Fujun Qin | Shailesh Kumar | Fujun Qin | Hui Li
[1] Mukesh Jain,et al. NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data , 2012, PloS one.
[2] Martin Vingron,et al. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..
[3] Thomas R. Gingeras,et al. STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..
[4] J. Friedman. Special Invited Paper-Additive logistic regression: A statistical view of boosting , 2000 .
[5] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[6] O. Kallioniemi,et al. FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data , 2014, bioRxiv.
[7] Christopher A. Maher,et al. ChimeraScan: a tool for identifying chimeric transcription in sequencing data , 2011, Bioinform..
[8] Krishna R. Kalari,et al. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines , 2011, Nucleic acids research.
[9] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[10] S. Donatelli,et al. State-of-the-Art Fusion-Finder Algorithms Sensitivity and Specificity , 2013, BioMed research international.
[11] S. Redaelli,et al. FusionAnalyser: a new graphical, event-driven tool for fusion rearrangements discovery , 2012, Nucleic acids research.
[12] Krishna R. Kalari,et al. Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer. , 2012, Cancer research.
[13] J. Schalken,et al. Molecular diagnosis of prostate cancer: PCA3 and TMPRSS2:ERG gene fusion. , 2012, The Journal of urology.
[14] P. Marynen,et al. The NPM-ALK and the ATIC-ALK fusion genes can be detected in non-neoplastic cells. , 2001, The American journal of pathology.
[15] Brian P. Brunk,et al. Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM) , 2011, Bioinform..
[16] Aaron R. Quinlan,et al. BIOINFORMATICS APPLICATIONS NOTE , 2022 .
[17] Hui Li,et al. Chimeric RNAs generated by intergenic splicing in normal and cancer cells , 2014, Genes, chromosomes & cancer.
[18] Ching-Lai Hwang,et al. A new approach for multiple objective decision making , 1993, Comput. Oper. Res..
[19] Enrico Macii,et al. Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model , 2012, Bioinform..
[20] Jun Wang,et al. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data , 2013, Genome Biology.
[21] Tyson A. Clark,et al. Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing , 2015, Nucleic acids research.
[22] Fang Fang,et al. FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution , 2011, Bioinform..
[23] Derek Y. Chiang,et al. MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery , 2010, Nucleic acids research.
[24] Doron Lipson,et al. Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies , 2012, Nature Medicine.
[25] Lee T. Sam,et al. Transcriptome Sequencing to Detect Gene Fusions in Cancer , 2009, Nature.
[26] B. Williams,et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.
[27] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[28] Süleyman Cenk Sahinalp,et al. deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data , 2011, PLoS Comput. Biol..
[29] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[30] Denise Anderson,et al. FusionFinder: A Software Tool to Identify Expressed Gene Fusion Candidates from RNA-Seq Data , 2012, PloS one.
[31] Terrence S. Furey,et al. The UCSC Genome Browser Database , 2003, Nucleic Acids Res..
[32] E. Birney,et al. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.
[33] Nallasivam Palanisamy,et al. Recurrent reciprocal RNA chimera involving YPEL5 and PPP1CB in chronic lymphocytic leukemia , 2013, Proceedings of the National Academy of Sciences.
[34] Cole Trapnell,et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.
[35] Faraz Hach,et al. Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data , 2011, Bioinform..
[36] Marco Beccuti,et al. State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues? , 2013, BMC Bioinformatics.
[37] G. Weinstock,et al. TIGRA: A targeted iterative graph routing assembler for breakpoint assembly , 2014, Genome research.
[38] S. C. Sahinalp,et al. nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing , 2012, Genome research.
[39] Alberto Magi,et al. Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript , 2012, Bioinform..
[40] Jian Ma,et al. FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq , 2011, Bioinform..
[41] Hui Li,et al. Discovery of CTCF-Sensitive Cis-Spliced Fusion RNAs between Adjacent Genes in Human Prostate Cells , 2015, PLoS genetics.
[42] Steven J. M. Jones,et al. BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data , 2012, Bioinform..
[43] A. Oshlack,et al. JAFFA: High sensitivity transcriptome-focused fusion gene detection , 2015, bioRxiv.
[44] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.