Software
Software available at: https://github.com/ChrisMaherLab/
INTEGRATE-Circ: A tool for unbiased, genome-wide discovery of fusion-derived circRNAs.
Webster J, Mai H, Ly A, Maher C. INTEGRATE-Circ and INTEGRATE-Vis: Unbiased Detection and Visualization of Fusion-Derived Circular RNA. Bioinformatics. 2023 Sep 14:btad569. doi: 10.1093/bioinformatics/btad569. Epub ahead of print. PMID: 37707537.
PACT: A standardized pipeline for detecting somatic variants using targeted sequencing of circulating tumor DNA.
Webster J, Dang HX, Chauhan PS, Feng W, Shiang A, Harris PK, Pachynski RK, Chaudhuri AA, Maher CA. PACT: a pipeline for analysis of circulating tumor DNA. Bioinformatics. 2023 Aug 1;39(8):btad489. doi: 10.1093/bioinformatics/btad489. PMID: 37549060; PMCID: PMC10415172.
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.
Webster J, Mai H, Ly A, Maher C. INTEGRATE-Circ and INTEGRATE-Vis: Unbiased Detection and Visualization of Fusion-Derived Circular RNA. Bioinformatics. 2023 Sep 14:btad569. doi: 10.1093/bioinformatics/btad569. Epub ahead of print. PMID: 37707537.
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
PDACLncDB: A database for lncRNAs associated with intra-tumoral heterogeneity and the tumor microenvironment (TME) in pancreatic ductal adenocarcinoma.
Dang HX, Saha D, Jayasinghe R, Zhao S, Coonrod E, Mudd J, Goedegebuure SP, Fields R, Ding L, Maher CA. Single-cell transcriptomics reveals long noncoding RNAs associated with tumor biology and the microenvironment in pancreatic cancer. NAR Cancer. 2023 Nov 22;5(4):zcad055. doi: 10.1093/narcan/zcad055. PMID: 38023733; PMCID: PMC10664695.
CrypticProteinDB: A database for proteome and immunopeptidome derived non-canonical cancer proteins.
Othoum G, Maher CA. CrypticProteinDB: an integrated database of proteome and immunopeptidome derived non-canonical cancer proteins. NAR Cancer. 2023 Jun 1;5(2):zcad024. doi: 10.1093/narcan/zcad024. PMID: 37275273; PMCID: PMC10233886.
TMECircDB: A database for cell-type specificity of circRNAs in metastatic colorectal cancer.
Zhao S, Ly A, Mudd JL, Rozycki EB, Webster J, Coonrod E, Othoum G, Luo J, Dang HX, Fields RC, Maher CA. Characterization of cell-type specific circular RNAs associated with colorectal cancer metastasis. NAR Cancer. 2023 May 19;5(2):zcad021. doi: 10.1093/narcan/zcad021. PMID: 37213253; PMCID: PMC10198730.
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.