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A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA. Asmann YW, et al. Among authors: kocher jp. Nucleic Acids Res. 2011 Aug;39(15):e100. doi: 10.1093/nar/gkr362. Epub 2011 May 27. Nucleic Acids Res. 2011. PMID: 21622959 Free PMC article.
PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data.
Wang C, Evans JM, Bhagwate AV, Prodduturi N, Sarangi V, Middha M, Sicotte H, Vedell PT, Hart SN, Oliver GR, Kocher JP, Maurer MJ, Novak AJ, Slager SL, Cerhan JR, Asmann YW. Wang C, et al. Among authors: kocher jp. Bioinformatics. 2014 Sep 15;30(18):2678-80. doi: 10.1093/bioinformatics/btu363. Epub 2014 May 29. Bioinformatics. 2014. PMID: 24876377 Free PMC article.
MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing.
Kalari KR, Nair AA, Bhavsar JD, O'Brien DR, Davila JI, Bockol MA, Nie J, Tang X, Baheti S, Doughty JB, Middha S, Sicotte H, Thompson AE, Asmann YW, Kocher JP. Kalari KR, et al. Among authors: kocher jp. BMC Bioinformatics. 2014 Jun 27;15:224. doi: 10.1186/1471-2105-15-224. BMC Bioinformatics. 2014. PMID: 24972667 Free PMC article.
RVboost: RNA-seq variants prioritization using a boosting method.
Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW. Wang C, et al. Among authors: kocher jp. Bioinformatics. 2014 Dec 1;30(23):3414-6. doi: 10.1093/bioinformatics/btu577. Epub 2014 Aug 27. Bioinformatics. 2014. PMID: 25170027 Free PMC article.
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.
Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. Yan H, et al. Among authors: kocher jp. BMC Bioinformatics. 2014 Aug 15;15(1):280. doi: 10.1186/1471-2105-15-280. BMC Bioinformatics. 2014. PMID: 25128017 Free PMC article.
164 results