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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: davila ji. 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: davila ji. Bioinformatics. 2014 Dec 1;30(23):3414-6. doi: 10.1093/bioinformatics/btu577. Epub 2014 Aug 27. Bioinformatics. 2014. PMID: 25170027 Free PMC article.
TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer.
Chien J, Sicotte H, Fan JB, Humphray S, Cunningham JM, Kalli KR, Oberg AL, Hart SN, Li Y, Davila JI, Baheti S, Wang C, Dietmann S, Atkinson EJ, Asmann YW, Bell DA, Ota T, Tarabishy Y, Kuang R, Bibikova M, Cheetham RK, Grocock RJ, Swisher EM, Peden J, Bentley D, Kocher JP, Kaufmann SH, Hartmann LC, Shridhar V, Goode EL. Chien J, et al. Among authors: davila ji. Nucleic Acids Res. 2015 Aug 18;43(14):6945-58. doi: 10.1093/nar/gkv111. Epub 2015 Apr 27. Nucleic Acids Res. 2015. PMID: 25916844 Free PMC article.
Integrated mate-pair and RNA sequencing identifies novel, targetable gene fusions in peripheral T-cell lymphoma.
Boddicker RL, Razidlo GL, Dasari S, Zeng Y, Hu G, Knudson RA, Greipp PT, Davila JI, Johnson SH, Porcher JC, Smadbeck JB, Eckloff BW, Billadeau DD, Kurtin PJ, McNiven MA, Link BK, Ansell SM, Cerhan JR, Asmann YW, Vasmatzis G, Feldman AL. Boddicker RL, et al. Among authors: davila ji. Blood. 2016 Sep 1;128(9):1234-45. doi: 10.1182/blood-2016-03-707141. Epub 2016 Jun 13. Blood. 2016. PMID: 27297792 Free PMC article. Clinical Trial.
Impact of RNA degradation on fusion detection by RNA-seq.
Davila JI, Fadra NM, Wang X, McDonald AM, Nair AA, Crusan BR, Wu X, Blommel JH, Jen J, Rumilla KM, Jenkins RB, Aypar U, Klee EW, Kipp BR, Halling KC. Davila JI, et al. BMC Genomics. 2016 Oct 20;17(1):814. doi: 10.1186/s12864-016-3161-9. BMC Genomics. 2016. PMID: 27765019 Free PMC article.
Gastroblastoma harbors a recurrent somatic MALAT1-GLI1 fusion gene.
Graham RP, Nair AA, Davila JI, Jin L, Jen J, Sukov WR, Wu TT, Appelman HD, Torres-Mora J, Perry KD, Zhang L, Kloft-Nelson SM, Knudson RA, Greipp PT, Folpe AL. Graham RP, et al. Among authors: davila ji. Mod Pathol. 2017 Oct;30(10):1443-1452. doi: 10.1038/modpathol.2017.68. Epub 2017 Jul 21. Mod Pathol. 2017. PMID: 28731043 Free article.
59 results