Software
Software available at: https://github.com/ChrisMaherLab/
DANSR: A tool for the detection of annotated and novel small RNAs.
Zhang J, Eteleeb AM, Rozycki EB, Inkman MJ, Ly A, Scharf RE, Jayachandran K, Krasnick BA, Mazur T, White NM, Fields RC, Maher CA. DANSR: A Tool for the Detection of Annotated and Novel Small RNAs. Noncoding RNA. 2022 Jan 13;8(1):9. doi: 10.3390/ncrna8010009. PMID: 35076605; PMCID: PMC8788476.
SV-HotSpot: A tool for detection and visualization of genome hotspots targeted by recurrent structural variants associated with gene expression.
Eteleeb AM, Quigley DA, Zhao SG, Pham D, Yang R, Dehm SM, Luo J, Feng FY, Dang HX, Maher CA. SV-HotSpot: detection and visualization of hotspots targeted by structural variants associated with gene expression. Sci Rep. 2020 Sep 28;10(1):15890. doi: 10.1038/s41598-020-71168-7. PMID: 32985524; PMCID: PMC7522247.
ClonEvol: A tool for inferring and visualizing clonal evolution in multiple samples.
Dang HX, White BS, Foltz SM, Miller CA, Luo J, Fields RC, Maher CA. ClonEvol: clonal ordering and visualization in cancer sequencing. Ann Oncol. 2017 Dec 1;28(12):3076-3082. doi: 10.1093/annonc/mdx517. PMID: 28950321; PMCID: PMC5834020.
INTEGRATE-Vis: A gene fusion visualization tool.
Zhang J, Gao T, Maher CA. INTEGRATE-Vis: a tool for comprehensive gene fusion visualization. Sci Rep. 2017 Dec 19;7(1):17808. doi: 10.1038/s41598-017-18257-2. PMID: 29259323; PMCID: PMC5736641.
INTEGRATE-Neo: A tool for gene fusion neoantigen discovery using next-generation sequencing data.
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Zhang J, Mardis ER, Maher CA. INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery. Bioinformatics. 2016 Oct 24. pii: btw674. [Epub ahead of print] PubMed PMID: 27797777.
INTEGRATE: A tool for calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data.
Zhang J, White NM, Schmidt HK, Fulton RS, Tomlinson C, Warren WC, Wilson RK, Maher CA. INTEGRATE: gene fusion discovery using whole genome and transcriptome data. Genome Res. 2016 Jan;26(1):108-18. doi: 10.1101/gr.186114.114. Epub 2015 Nov 10. PubMed PMID: 26556708; PubMed Central PMCID: PMC4691743.
ChimeraScan: A tool for discovery of chimeric transcripts in high-throughput sequencing data.
Iyer MK, Chinnaiyan AM, Maher CA. ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011 Oct 15;27(20):2903-4. doi: 10.1093/bioinformatics/btr467. Epub 2011 Aug 11. PubMed PMID: 21840877; PubMed Central PMCID: PMC3187648.
Data Resources
PepTransDB: A database for peptides encoded by long and circular noncoding RNAs.
Othoum G, Coonrod E, Zhao S, Dang HX, Maher CA. Pan-cancer proteogenomic analysis reveals long and circular noncoding RNAs encoding peptides. NAR Cancer. 2020 September;2(3). doi: 10.1093/narcan/zcaa015. Epub 2020 Aug 12.