Publications

1. Atiq MA, Balan J, Blackburn PR, Gross JM, Voss JS, Jin L, Fadra N, Davila JI, Pitel BA, Siqueira Parrilha Terra SB, Minn KT, Jackson RA, Hofich CD, Willkomm KS, Peterson BJ, Clausen SN, Rumilla KM, Gupta S, Lo YC, Ida CM, Molligan JF, Thangaiah JJ, Petersen MJ, Sukov WR, Guo R, Giannini C, Schoolmeester JK 2nd, Fritchie K, Inwards CY, Folpe AL, Oliveira AM, Torres-Mora J, Kipp BR, Halling KC. SARCP, a Clinical Next-Generation Sequencing Assay for the Detection of Gene Fusions in Sarcomas: A Description of the First 652 Cases. J Mol Diagn. 2024 Nov 7 Epub 2024 Nov 07
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2. Nguyen AJ, Fogarty ZC, Davila J, Markovic SN, Wang C, Guo R. Uncovering the hidden risk of metastatic cutaneous basal cell carcinoma by molecular profiling: A retrospective review. JAAD Int. 2024 Sep; 16:189-191 Epub 2024 May 24
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3. Chatzopoulos K, Davila JI, Fadra N, Jackson RA, Minn KT, Sotiriou S, Oliveira AM, Erickson LA, Halling KC, Rumilla KM, Rivera M. Transcriptomic and immunophenotypic characterization of two cases of adamantinoma-like Ewing sarcoma of the thyroid gland. Histopathology. 2023 Sep; 83 (3):426-434 Epub 2023 May 17
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4. Mitchell A, Ruiz M, Yang S, Wang C, Davila JI. Excerno: Using Mutational Signatures in Sequencing Data to Filter False Variants Caused by Clinical Archival. J Comput Biol. 2023 Apr; 30 (4):366-375 Epub 2022 Nov 02
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5. Van Treeck BJ, Moreira RK, Mounajjed T, Ferrell L, Xue Y, Jessen E, Davila J, Graham RP. Transcriptomic Analysis of Cirrhosis-Like Hepatocellular Carcinoma Reveals Distinct Molecular Characteristics and Pathologic Staging Implications. Am J Clin Pathol. 2022 Dec 1; 158 (6):750-758
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6. Zhao Y, Dimou A, Shen F, Zong N, Davila JI, Liu H, Wang C. PO2RDF: representation of real-world data for precision oncology using resource description framework. BMC Med Genomics. 2022 Jul 30; 15 (1):167 Epub 2022 July 30
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7. Tschumper RC, Hoelzinger DB, Walters DK, Davila JI, Osborne CA, Jelinek DF. Stage-Specific Non-Coding RNA Expression Patterns during In Vitro Human B Cell Differentiation into Antibody Secreting Plasma Cells. Noncoding RNA. 2022 Feb 05; 8(1).
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8. Ida CM, Johnson DR, Nair AA, Davila J, Kollmeyer TM, Minn K, Fadra NM, Balcom JR, Fung KA, Kim DK, Kaufmann TJ, Kipp BR, Halling KC, Jenkins RB, Giannini C. Polymorphous Low-Grade Neuroepithelial Tumor of the Young (PLNTY): Molecular Profiling Confirms Frequent MAPK Pathway Activation. J Neuropathol Exp Neurol. 2021 Sep 27; 80 (9):821-829
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9. Feng T, Davila JI, Liu Y, Lin S, Huang S, Wang C. Semi-Supervised Topological Analysis for Elucidating Hidden Structures in High-Dimensional Transcriptome Datasets. IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul-Aug; 18 (4):1620-1631 Epub 2021 Aug 06
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10. Davila JI, Chanana P, Sarangi V, Fogarty ZC, Weroha SJ, Guo R, Goode EL, Huang Y, Wang C. Frequent POLE-driven hypermutation in ovarian endometrioid cancer revealed by mutational signatures in RNA sequencing. BMC Med Genomics. 2021 Jun 22; 14 (1):165 Epub 2021 June 22
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11. DiGuardo MA, Davila JI, Jackson RA, Nair AA, Fadra N, Minn KT, Atiq MA, Zarei S, Blommel JH, Knight SM, Jen J, Eckloff BW, Voss JS, Rumilla KM, Kerr SE, Lam-Himlin DM, Bellizzi AM, Graham RP, Kipp BR, Jenkins RB, Halling KC. RNA-Seq Reveals Differences in Expressed Tumor Mutation Burden in Colorectal and Endometrial Cancers with and without Defective DNA-Mismatch Repair. J Mol Diagn. 2021 May; 23(5):555-564. Epub 2021 Feb 04.
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12. Jessen E, Liu Y, Davila J, Kocher JP, Wang C. Determining mutational burden and signature using RNA-seq from tumor-only samples. BMC Med Genomics. 2021 Mar 1; 14 (1):65 Epub 2021 Mar 01
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13. Boland JM, Lee HE, Barr Fritcher EG, Voss JS, Jessen E, Davila JI, Kipp BR, Graham RP, Maleszewski JJ, Yi ES. Molecular Genetic Landscape of Sclerosing Pneumocytomas. Am J Clin Pathol. 2021 Feb 11; 155(3):397-404.
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14. Mujahed T, Tazelaar HD, Sukov WR, Halling KC, Davila JI, Glass C, Pavlisko EN, Strickland KC, Roggli V, Haque M, Mneimneh W, Carter E, Galateau-Salle F, Glidden D, Garcia-Kennedy R, Larsen BT. Malignant Peritoneal Mesothelioma Arising in Young Adults With Long-standing Indwelling Intra-abdominal Shunt Catheters. Am J Surg Pathol. 2021 Feb 1; 45 (2):255-262
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15. Van Treeck BJ, Mounajjed T, Moreira RK, Orujov M, Allende DS, Bellizzi AM, Lagana SM, Davila JI, Jessen E, Graham RP. Transcriptomic and Proteomic Analysis of Steatohepatitic Hepatocellular Carcinoma Reveals Novel Distinct Biologic Features. Am J Clin Pathol. 2021 Jan 4; 155 (1):87-96
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16. Pietrobono S, Anichini G, Sala C, Manetti F, Almada LL, Pepe S, Carr RM, Paradise BD, Sarkaria JN, Davila JI, Tofani L, Battisti I, Arrigoni G, Ying L, Zhang C, Li H, Meves A, Fernandez-Zapico ME, Stecca B. ST3GAL1 is a target of the SOX2-GLI1 transcriptional complex and promotes melanoma metastasis through AXL. Nat Commun. 2020 Nov 17; 11 (1):5865
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17. Van Treeck BJ, Lotfalla M, Czeczok TW, Mounajjed T, Moreira RK, Allende DS, Reid MD, Naini BV, Westerhoff M, Adsay NV, Kerr SE, Rizvi SH, I Ilyas SH, Smoot RL, Liu Y, Davila J, Graham RP. Molecular and Immunohistochemical Analysis of Mucinous Cystic Neoplasm of the Liver. Am J Clin Pathol. 2020 Nov 4; 154 (6):837-847
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18. Fritchie KJ, Torres-Mora J, Inwards C, Thway K, Vaiyapuri S, Jackson R, Minn K, Halling K, Arndt C, Houdek MT, Wenger DE, Curry R, Thirumala S, Fisher C, Davila J, Folpe AL. Xanthogranulomatous epithelial tumor: report of 6 cases of a novel, potentially deceptive lesion with a predilection for young women. Mod Pathol. 2020 Oct; 33 (10):1889-1895 Epub 2020 May 15
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19. Cheek EH, Fadra N, Jackson RA, Davila JI, Sukov WR, Uckerman MT, Clayton A, Keeney GL, Halling KC, Torres-Mora J, Schoolmeester JK. Uterine inflammatory myofibroblastic tumors in pregnant women with and without involvement of the placenta: a study of 6 cases with identification of a novel TIMP3-RET fusion. Hum Pathol. 2020 Mar; 97:29-39 Epub 2020 Jan 07
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20. Zhao Y, Yu H, Fu S, Shen F, Davila JI, Liu H, Wang C. Data-driven Sublanguage Analysis for Cancer Genomics Knowledge Modeling: Applications in Mining Oncological Genetics Information from Patients' Genetic Reports. AMIA Jt Summits Transl Sci Proc. 2020; 2020:720-729 Epub 2020 May 30
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21. Zong N, Sharma DK, Yu Y, Egan JB, Davila JI, Wang C, Jiang G. Developing a FHIR-based Framework for Phenome Wide Association Studies: A Case Study with A Pan-Cancer Cohort. AMIA Jt Summits Transl Sci Proc. 2020; 2020:750-759 Epub 2020 May 30
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22. Blessing MM, Blackburn PR, Krishnan C, Harrod VL, Barr Fritcher EG, Zysk CD, Jackson RA, Milosevic D, Nair AA, Davila JI, Balcom JR, Jenkins RB, Halling KC, Kipp BR, Nageswara Rao AA, Laack NN, Daniels DJ, Macon WR, Ida CM. Desmoplastic Infantile Ganglioglioma: A MAPK Pathway-Driven and Microglia/Macrophage-Rich Neuroepithelial Tumor. J Neuropathol Exp Neurol. 2019 Nov 1; 78 (11):1011-1021
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23. Bhagwate AV, Liu Y, Winham SJ, McDonough SJ, Stallings-Mann ML, Heinzen EP, Davila JI, Vierkant RA, Hoskin TL, Frost M, Carter JM, Radisky DC, Cunningham JM, Degnim AC, Wang C. Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples. BMC Genomics. 2019 Sep 2; 20 (1):689 Epub 2019 Sept 02
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24. Blackburn PR, Davila JI, Jackson RA, Fadra N, Atiq MA, Pitel BA, Nair AA, VanDeWalker TJ, Hessler MG, Hovel SK, Wehrs RN, Fritchie KJ, Jenkins RB, Halling KC, Geiersbach KB. RNA sequencing identifies a novel USP9X-USP6 promoter swap gene fusion in a primary aneurysmal bone cyst. Genes Chromosomes Cancer. 2019 Aug; 58(8):589-594. Epub 2019 Mar 06.
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25. Ainsworth AJ, Dashti NK, Mounajjed T, Fritchie KJ, Davila J, Mopuri R, Jackson RA, Halling KC, Bakkum-Gamez JN, Schoolmeester JK. Leiomyoma with KAT6B-KANSL1 fusion: case report of a rapidly enlarging uterine mass in a postmenopausal woman. Diagn Pathol. 2019 Apr 25; 14 (1):32
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26. Liu Y, Chanana P, Davila JI, Hou X, Zanfagnin V, McGehee CD, Goode EL, Polley EC, Haluska P, Weroha SJ, Wang C. Gene expression differences between matched pairs of ovarian cancer patient tumors and patient-derived xenografts. Sci Rep. 2019 Apr 19; 9 (1):6314
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27. Mangaonkar AA, Patnaik MM, Oliver GR, Rao KW, Kaiser-Rogers K, Davila JI, Fadra N, Wehrs RN, Elliott MA, Greipp PT, Halling KC, Van Dyke DL. Multiple isodicentric Y chromosomes in myeloid malignancies: a unique cytogenetic entity and potential therapeutic target. Leuk Lymphoma 2019 Mar; 60 (3):821-824 Epub 2018 Aug 30
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28. Ren H, Hou X, Eiken PW, Zhang J, Pierson KE, Nair AA, Davila JI, Kovarikova H, Jang JS, Johnson SH, Molina JR, Marks RS, Yang P, Yi JE, Mansfield AS, Jen J. Identification and Development of a Lung Adenocarcinoma PDX Model With STRN-ALK Fusion. Clin Lung Cancer. 2019 Mar; 20(2):e142-e147. Epub 2018 Nov 20.
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29. Dashti NK, Wehrs RN, Thomas BC, Nair A, Davila J, Buckner JC, Martinez AP, Sukov WR, Halling KC, Howe BM, Folpe AL. Spindle cell rhabdomyosarcoma of bone with FUS-TFCP2 fusion: confirmation of a very recently described rhabdomyosarcoma subtype. Histopathology. 2018 Sep; 73(3):514-520. Epub 2018 Jun 29.
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30. Winters JL, Davila JI, McDonald AM, Nair AA, Fadra N, Wehrs RN, Thomas BC, Balcom JR, Jin L, Wu X, Voss JS, Klee EW, Oliver GR, Graham RP, Neff JL, Rumilla KM, Aypar U, Kipp BR, Jenkins RB, Jen J, Halling KC. Development and Verification of an RNA Sequencing (RNA-Seq) Assay for the Detection of Gene Fusions in Tumors. J Mol Diagn. 2018 Jul; 20(4):495-511. Epub 2018 Jun 19.
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31. Sharma A, Oishi N, Boddicker RL, Hu G, Benson HK, Ketterling RP, Greipp PT, Knutson DL, Kloft-Nelson SM, He R, Eckloff BW, Jen J, Nair AA, Davila JI, Dasari S, Lazaridis KN, Bennani NN, Wu TT, Nowakowski GS, Murray JA, Feldman AL. Recurrent STAT3-JAK2 fusions in indolent T-cell lymphoproliferative disorder of the gastrointestinal tract. Blood 2018 May 17; 131 (20):2262-2266 Epub 2018 Mar 28
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32. Sharma A, Oishi N, Boddicker RL, Hu G, Benson HK, Ketterling RP, Greipp PT, Knutson DL, Kloft-Nelson SM, He R, Eckloff BW, Jen J, Nair AA, Davila JI, Dasari S, Lazaridis KN, Bennani NN, Wu TT, Nowakowski GS, Murray JA, Feldman AL. Recurrent STAT3-JAK2 fusions in indolent T-cell lymphoproliferative disorder of the gastrointestinal tract. Blood. 2018 May 17; 131(20):2262-2266. Epub 2018 Mar 28.
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33. Mansfield AS, Ren H, Sutor S, Sarangi V, Nair A, Davila J, Elsbernd LR, Udell JB, Dronca RS, Park S, Markovic SN, Sun Z, Halling KC, Nevala WK, Aubry MC, Dong H, Jen J. Contraction of T cell richness in lung cancer brain metastases. Sci Rep. 2018 Feb 1; 8 (1):2171 Epub 2018 Feb 01
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34. Perry KD, Al-Lbraheemi A, Rubin BP, Jen J, Ren H, Jang JS, Nair A, Davila J, Pambuccian S, Horvai A, Sukov W, Tazelaar HD, Folpe AL. Composite hemangioendothelioma with neuroendocrine marker expression: an aggressive variant. Mod Pathol. 2017 Nov; 30 (11):1589-1602 Epub 2017 July 21
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35. Larson NB, McDonnell SK, Fogarty Z, Larson MC, Cheville J, Riska S, Baheti S, Weber AM, Nair AA, Wang L, O'Brien D, Davila J, Schaid DJ, Thibodeau SN. Network-directed cis-mediator analysis of normal prostate tissue expression profiles reveals downstream regulatory associations of prostate cancer susceptibility loci. Oncotarget. 2017 Oct 17; 8 (49):85896-85908 Epub 2017 Sept 08
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36. 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. Gastroblastoma harbors a recurrent somatic MALAT1-GLI1 fusion gene. Mod Pathol. 2017 Oct; 30(10):1443-1452. Epub 2017 Jul 21.
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37. Davila JI, Starr JS, Attia S, Wang C, Knudson RA, Necela BM, Sarangi V, Sun Z, Ren Y, Casler JD, Menke DM, Oliver GR, Joseph RW, Copland JA, Parker AS, Kocher JA, Thompson EA, Smallridge RC, Asmann YW. Comprehensive Genomic Profiling of a Rare Thyroid Follicular Dendritic Cell Sarcoma. Rare Tumors. 2017 Jul 3; 9 (2):6834 Epub 2017 Sept 15
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38. 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. Impact of RNA degradation on fusion detection by RNA-seq. BMC Genomics. 2016 Oct 20; 17(1):814.
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39. 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. Integrated mate-pair and RNA sequencing identifies novel, targetable gene fusions in peripheral T-cell lymphoma. Blood. 2016 Sep 1; 128 (9):1234-45 Epub 2016 June 13
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40. 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. TP53 mutations, tetraploidy and homologous recombination repair defects in early stage high-grade serous ovarian cancer. Nucleic Acids Res. 2015 Aug 18; 43 (14):6945-58 Epub 2015 Apr 27
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41. De Assuncao TM, Sun Y, Jalan-Sakrikar N, Drinane MC, Huang BQ, Li Y, Davila JI, Wang R, O'Hara SP, Lomberk GA, Urrutia RA, Ikeda Y, Huebert RC. Development and characterization of human-induced pluripotent stem cell-derived cholangiocytes. Lab Invest. 2015 Jun; 95 (6):684-96 Epub 2015 Apr 13
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42. Yamada D, Ilyas SI, Razumilava N, Bronk SF, Davila JI, Champion MD, Borad MJ, Bezerra JA, Chen X, Gores GJ. IL-33 facilitates oncogene-induced cholangiocarcinoma in mice by an interleukin-6-sensitive mechanism. Hepatology. 2015 May; 61 (5):1627-42 Epub 2015 Mar 20
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43. Dasari S, Theis JD, Vrana JA, Meureta OM, Quint PS, Muppa P, Zenka RM, Tschumper RC, Jelinek DF, Davila JI, Sarangi V, Kurtin PJ, Dogan A. Proteomic detection of immunoglobulin light chain variable region peptides from amyloidosis patient biopsies. J Proteome Res. 2015 Apr 3; 14 (4):1957-67 Epub 2015 Mar 20
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44. Du J, Aleff RA, Soragni E, Kalari K, Nie J, Tang X, Davila J, Kocher JP, Patel SV, Gottesfeld JM, Baratz KH, Wieben ED. RNA toxicity and missplicing in the common eye disease fuchs endothelial corneal dystrophy. J Biol Chem. 2015 Mar 6; 290 (10):5979-90 Epub 2015 Jan 15
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45. Couch FJ, Hart SN, Sharma P, Toland AE, Wang X, Miron P, Olson JE, Godwin AK, Pankratz VS, Olswold C, Slettedahl S, Hallberg E, Guidugli L, Davila JI, Beckmann MW, Janni W, Rack B, Ekici AB, Slamon DJ, Konstantopoulou I, Fostira F, Vratimos A, Fountzilas G, Pelttari LM, Tapper WJ, Durcan L, Cross SS, Pilarski R, Shapiro CL, Klemp J, Yao S, Garber J, Cox A, Brauch H, Ambrosone C, Nevanlinna H, Yannoukakos D, Slager SL, Vachon CM, Eccles DM, Fasching PA. Inherited mutations in 17 breast cancer susceptibility genes among a large triple-negative breast cancer cohort unselected for family history of breast cancer. J Clin Oncol. 2015 Feb 1; 33 (4):304-11 Epub 2014 Dec 01
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46. Wang C, Davila JI, Baheti S, Bhagwate AV, Wang X, Kocher JP, Slager SL, Feldman AL, Novak AJ, Cerhan JR, Thompson EA, Asmann YW. RVboost: RNA-seq variants prioritization using a boosting method. Bioinformatics. 2014 Dec 1; 30 (23):3414-6 Epub 2014 Aug 27
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47. 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. MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing. BMC Bioinformatics. 2014 Jun 27; 15:224 Epub 2014 June 27
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48. Sakuma T, Davila JI, Malcolm JA, Kocher JP, Tonne JM, Ikeda Y. Murine leukemia virus uses NXF1 for nuclear export of spliced and unspliced viral transcripts. J Virol. 2014 Apr; 88 (8):4069-82 Epub 2014 Jan 29
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49. Feldman AL, Vasmatzis G, Asmann YW, Davila J, Middha S, Eckloff BW, Johnson SH, Porcher JC, Ansell SM, Caride A. Novel TRAF1-ALK fusion identified by deep RNA sequencing of anaplastic large cell lymphoma. Genes Chromosomes Cancer. 2013 Nov; 52 (11):1097-102 Epub 2013 Sept 02
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