These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
2. INTEGRATE: gene fusion discovery using whole genome and transcriptome data. Zhang J; White NM; Schmidt HK; Fulton RS; Tomlinson C; Warren WC; Wilson RK; Maher CA Genome Res; 2016 Jan; 26(1):108-18. PubMed ID: 26556708 [TBL] [Abstract][Full Text] [Related]
3. Case Study: Systematic Detection and Prioritization of Gene Fusions in Cancer by RNA-Seq: A DIY Toolkit. Vats P; Chinnaiyan AM; Kumar-Sinha C Methods Mol Biol; 2020; 2079():69-79. PubMed ID: 31728962 [TBL] [Abstract][Full Text] [Related]
4. Systematic discovery of gene fusions in pediatric cancer by integrating RNA-seq and WGS. van Belzen IAEM; Cai C; van Tuil M; Badloe S; Strengman E; Janse A; Verwiel ETP; van der Leest DFM; Kester L; Molenaar JJ; Meijerink J; Drost J; Peng WC; Kerstens HHD; Tops BBJ; Holstege FCP; Kemmeren P; Hehir-Kwa JY BMC Cancer; 2023 Jul; 23(1):618. PubMed ID: 37400763 [TBL] [Abstract][Full Text] [Related]
5. Identification of Fusion Transcripts from Unaligned RNA-Seq Reads Using ChimeRScope. Vellichirammal NN; Albahrani A; Li Y; Guda C Methods Mol Biol; 2020; 2079():13-25. PubMed ID: 31728959 [TBL] [Abstract][Full Text] [Related]
6. Fast and sensitive validation of fusion transcripts in whole-genome sequencing data. Hafstað V; Häkkinen J; Persson H BMC Bioinformatics; 2023 Sep; 24(1):359. PubMed ID: 37741966 [TBL] [Abstract][Full Text] [Related]
7. RNA-seq Fusion Detection in Clinical Oncology. Hedges DJ Adv Exp Med Biol; 2022; 1361():163-175. PubMed ID: 35230688 [TBL] [Abstract][Full Text] [Related]
8. InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data. Okonechnikov K; Imai-Matsushima A; Paul L; Seitz A; Meyer TF; Garcia-Alcalde F PLoS One; 2016; 11(12):e0167417. PubMed ID: 27907167 [TBL] [Abstract][Full Text] [Related]
9. LongGF: computational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing. Liu Q; Hu Y; Stucky A; Fang L; Zhong JF; Wang K BMC Genomics; 2020 Dec; 21(Suppl 11):793. PubMed ID: 33372596 [TBL] [Abstract][Full Text] [Related]
10. Identification of Chimeric RNAs Using RNA-Seq Reads and Protein-Protein Interactions of Translated Chimeras. Frenkel-Morgenstern M Methods Mol Biol; 2020; 2079():27-40. PubMed ID: 31728960 [TBL] [Abstract][Full Text] [Related]
12. Plasmid Reconstruction from Next-Gen Data: A Detailed Protocol for the Use of PLACNETw for the Reconstruction of Plasmids from WGS Datasets. de Toro M; Lanza VF; Vielva L; Redondo-Salvo S; de la Cruz F Methods Mol Biol; 2020; 2075():323-339. PubMed ID: 31584173 [TBL] [Abstract][Full Text] [Related]
13. Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers. Tsang ES; Grisdale CJ; Pleasance E; Topham JT; Mungall K; Reisle C; Choo C; Carreira M; Bowlby R; Karasinska JM; MacMillan D; Williamson LM; Chuah E; Moore RA; Mungall AJ; Zhao Y; Tessier-Cloutier B; Ng T; Sun S; Lim HJ; Schaeffer DF; Renouf DJ; Yip S; Laskin J; Marra MA; Jones SJM; Loree JM Clin Cancer Res; 2021 Jan; 27(2):522-531. PubMed ID: 33148671 [TBL] [Abstract][Full Text] [Related]
14. Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines. Gioiosa S; Bolis M; Flati T; Massini A; Garattini E; Chillemi G; Fratelli M; Castrignanò T Gigascience; 2018 Oct; 7(10):. PubMed ID: 29860514 [TBL] [Abstract][Full Text] [Related]
15. ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data. Rodríguez-Martín B; Palumbo E; Marco-Sola S; Griebel T; Ribeca P; Alonso G; Rastrojo A; Aguado B; Guigó R; Djebali S BMC Genomics; 2017 Jan; 18(1):7. PubMed ID: 28049418 [TBL] [Abstract][Full Text] [Related]
16. Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Latysheva NS; Babu MM Nucleic Acids Res; 2016 Jun; 44(10):4487-503. PubMed ID: 27105842 [TBL] [Abstract][Full Text] [Related]
17. NGS-QC Generator: A Quality Control System for ChIP-Seq and Related Deep Sequencing-Generated Datasets. Mendoza-Parra MA; Saleem MA; Blum M; Cholley PE; Gronemeyer H Methods Mol Biol; 2016; 1418():243-65. PubMed ID: 27008019 [TBL] [Abstract][Full Text] [Related]
18. Analysis and Visualization of ChIP-Seq and RNA-Seq Sequence Alignments Using ngs.plot. Loh YH; Shen L Methods Mol Biol; 2016; 1415():371-83. PubMed ID: 27115642 [TBL] [Abstract][Full Text] [Related]
19. Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data. Bai Y; Kinne J; Donham B; Jiang F; Ding L; Hassler JR; Kaufman RJ BMC Genomics; 2016 Aug; 17 Suppl 7(Suppl 7):503. PubMed ID: 27556805 [TBL] [Abstract][Full Text] [Related]
20. GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression. Lopes R; Agami R; Korkmaz G Methods Mol Biol; 2017; 1543():45-55. PubMed ID: 28349421 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]