Publications

1. Farris J, Khanna C, Smadbeck JB, Johnson SH, Bothun E, Kaplan T, Hoffman F, Polonis K, Oliver G, Reis LM, Semina EV, Rust L, Hoppman NL, Vasmatzis G, Marcou CA, Schimmenti LA, Klee EW. Complex balanced intrachromosomal rearrangement involving PITX2 identified as a cause of Axenfeld-Rieger Syndrome. Am J Med Genet A. 2024 May; 194 (5):e63542 Epub 2024 Jan 17
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2. Florio A, Johnson S, Salvatori R, Vasmatzis G. Monolayer culture alters EGFR inhibitor response through abrogation of microRNA-mediated feedback regulation. Sci Rep. 2024 Mar 27; 14 (1):7303
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3. Pezeshki A, Cheville JC, Florio AB, Leibovich BC, Vasmatzis G. Evaluation of tumor response to immune checkpoint inhibitors by a 3D immunotumoroid model. Front Immunol. 2024; 15:1356144 Epub 2024 Mar 28
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4. Gagnon MF, Penheiter AR, Harris F, Sadeghian D, Johnson SH, Karagouga G, McCune A, Zepeda-Mendoza C, Greipp PT, Xu X, Ketterling RP, McPhail ED, King RL, Peterson JF, Vasmatzis G, Baughn LB. Unraveling the genomic underpinnings of unbalanced MYC break-apart FISH results using whole genome sequencing analysis. Blood Cancer J 2023 Dec 19; 13 (1):190
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5. Lo YC, Rivera-Concepcion J, Vasmatzis G, Aubry MC, Leventakos K. Subtype of SCLC Is an Intrinsic and Persistent Feature Through Systemic Treatment. JTO Clin Res Rep. 2023 Sep; 4 (9):100561 Epub 2023 Aug 16
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6. Desai AP, Kosari F, Disselhorst M, Yin J, Agahi A, Peikert T, Udell J, Johnson SH, Smadbeck J, Murphy S, Karagouga G, McCune A, Schaefer-Klein J, Borad MJ, Cheville J, Vasmatzis G, Baas P, Mansfield A. Dynamics and survival associations of T cell receptor clusters in patients with pleural mesothelioma treated with immunotherapy. J Immunother Cancer. 2023 Jun; 11 (6)
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7. El Khoury LY, Lin WH, Smadbeck JB, Barrett MT, Sadeghian D, McCune AF, Karagouga G, Cheville JC, Harris FR, Kinsella LM, Feathers RW, Schafer Klein JL, Walther-Antonio MR, Johnson SH, Penheiter AR, Cucinella G, Schivardi G, Bhagwate A, Borad MJ, Mansfield AS, Murphy SJ, Mariani A, Vasmatzis G, Anastasiadis PZ, Weroha SJ, Larish AM. Epigenomics may begin to explain in vitro differential response to hypomethylating agents in MMR-D hypermethylated endometrial cancer. Epigenomics. 2023 Mar; 15 (5):283-292 Epub 2023 May 22
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8. Atkins TK, Solanki A, Vasmatzis G, Cornette J, Riedel M. Evaluating NetMHCpan performance on non-European HLA alleles not present in training data. Front Immunol 2023; 14:1288105 Epub 2024 Jan 16
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9. Dalland JC, Blackburn PR, Reichard KK, Johnson SH, Smadbeck JB, Vasmatzis G, Hoppman NL, Xu X, Greipp PT, Baughn LB, Peterson JF. A Novel USP25::PDGFRA Gene Fusion in a 78 Year Old Patient with a Myeloid Neoplasm. Lab Med. 2022 Sep 1; 53 (5):e134-e138
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10. Uson Junior PLS, DeLeon TT, Bogenberger JM, Pai RK, Kosiorek HE, Yin J, Ahn DH, Sonbol MB, Bekaii-Saab T, Mansfield AS, Buetow K, Gores GJ, Smoot R, Vasmatzis G, Kipp BR, Mahipal A, Baker AT, Babiker H, Barro O, Dumbauld C, Zhou Y, Aslam FN, Barrett M, Jacobs B, Meurice N, Arora M, Petit J, Elliott N, Nagalo B, Salomao MA, Borad MJ. FGFR2-IIIb Expression by Immunohistochemistry Has High Specificity in Cholangiocarcinoma with FGFR2 Genomic Alterations. Dig Dis Sci. 2022 Aug; 67(8):3797-3805. Epub 2021 Nov 13.
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11. Gagnon MF, Smadbeck JB, Vasmatzis G, Olteanu H, Wood AJ, Lewis DJ, Sharma N, Meyer RG, Greipp PT, Xu X, Hoppman NL, Baughn LB, Ketterling RP, Chiu A, Peterson JF. Identification of EWSR1 rearrangements in patients with immature hematopoietic neoplasms: A case series and review of literature. Ann Diagn Pathol. 2022 Jun; 58:151942 Epub 2022 Mar 23
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12. Kosari F, Disselhorst M, Yin J, Peikert T, Udell J, Johnson S, Smadbeck J, Murphy S, McCune A, Karagouga G, Desai A, Schaefer-Klein J, Borad MJ, Cheville J, Vasmatzis G, Baas P, Mansfield AS. Tumor Junction Burden and Antigen Presentation as Predictors of Survival in Mesothelioma Treated With Immune Checkpoint Inhibitors. J Thorac Oncol. 2022 Mar; 17 (3):446-454 Epub 2021 Nov 17
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13. Wen T, Barham W, Li Y, Zhang H, Gicobi JK, Hirdler JB, Liu X, Ham H, Peterson Martinez KE, Lucien F, Lavoie RR, Li H, Correia C, Monie DD, An Z, Harrington SM, Wu X, Guo R, Dronca RS, Mansfield AS, Yan Y, Markovic SN, Park SS, Sun J, Qin H, Liu MC, Vasmatzis G, Billadeau DD, Dong H. NKG7 Is a T-cell-Intrinsic Therapeutic Target for Improving Antitumor Cytotoxicity and Cancer Immunotherapy. Cancer Immunol Res. 2022 Feb; 10 (2):162-181 Epub 2021 Dec 15
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14. Kanakkanthara A, Hou X, Ekstrom TL, Zanfagnin V, Huehls AM, Kelly RL, Ding H, Larson MC, Vasmatzis G, Oberg AL, Kaufmann SH, Mansfield AS, Weroha SJ, Karnitz LM. Repurposing Ceritinib Induces DNA Damage and Enhances PARP Inhibitor Responses in High-Grade Serous Ovarian Carcinoma. Cancer Res. 2022 Jan 15; 82 (2):307-319 Epub 2021 Nov 22
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15. Koleilat A, McGarrah PW, Olteanu H, Van Dyke DL, Smadbeck JB, Johnson SH, Vasmatzis G, Hoppman NL, Xu X, Ketterling RP, Greipp PT, Baughn LB, Patnaik MS, Peterson JF. Utilizing next-generation sequencing to characterize a case of acute myeloid leukemia with t(4;12)(q12;p13) in the absence of ETV6/CHIC2 and ETV6/PDGFRA gene fusions. Cancer Genet. 2022 Jan; 260-261:1-5 Epub 2021 Nov 06
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16. Solanki A, Riedel M, Cornette J, Udell J, Vasmatzis G. Hydrophobicity identifies false positives and false negatives in peptide-MHC binding. Front Oncol. 2022; 12:1034810 Epub 2022 Nov 07
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17. Guenzel AJ, Smadbeck JB, Golden CL, Williamson CM, Benevides Demasi JC, Vasmatzis G, Pearce KE, Olteanu H, Xu X, Hoppman NL, Greipp PT, Baughn LB, Ketterling RP, Peterson JF. Clinical utility of next generation sequencing to detect IGH/IL3 rearrangements [t(5;14)(q31.1;q32.1)] in B-lymphoblastic leukemia/lymphoma. Ann Diagn Pathol. 2021 Aug; 53:151761 Epub 2021 May 10
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18. Dinoi G, Mariani A, Martinelli E, Ciucci A, Zannoni GF, Weaver AL, Keeney GL, Vasmatzis G, Anastasiadis PZ, Fanfani F, Scambia G, Gallo D. In search for biomarkers and potential drug targets for uterine serous endometrial cancer. J Cancer Res Clin Oncol. 2021 Jun; 147 (6):1647-1658 Epub 2021 Mar 23
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19. Freitag CE, Sukov WR, Bryce AH, Berg JV, Vanderbilt CM, Shen W, Smadbeck JB, Greipp PT, Ketterling RP, Jenkins RB, Herrera-Hernandez L, Costello BA, Thompson RH, Boorjian SA, Leibovich BC, Jimenez RE, Murphy SJ, Vasmatzis G, Cheville JC, Gupta S. Assessment of isochromosome 12p and 12p abnormalities in germ cell tumors using fluorescence in situ hybridization, single-nucleotide polymorphism arrays, and next-generation sequencing/mate-pair sequencing. Hum Pathol. 2021 Jun; 112:20-34 Epub 2021 Mar 31
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20. Berg HE, Blackburn PR, Smadbeck JB, Swanson KE, Rice CS, Webley MR, Johnson SH, Vasmatzis G, Xu X, Greipp PT, Hoppman NL, Ketterling RP, Baughn LB, Boston CH, Sutton LM, Peterson JF. Detection of a Cryptic EP300/ZNF384 Gene Fusion by Chromosomal Microarray and Next-Generation Sequencing Studies in a Pediatric Patient with B-Lymphoblastic Leukemia. Lab Med. 2021 May 4; 52 (3):297-302
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21. Ganguli A, Mostafa A, Saavedra C, Kim Y, Le P, Faramarzi V, Feathers RW, Berger J, Ramos-Cruz KP, Adeniba O, Diaz GJP, Drnevich J, Wright CL, Hernandez AG, Lin W, Smith AM, Kosari F, Vasmatzis G, Anastasiadis PZ, Bashir R. Three-dimensional microscale hanging drop arrays with geometric control for drug screening and live tissue imaging. Sci Adv. 2021 Apr; 7(17). Epub 2021 Apr 23.
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22. Murphy SJ, Levy MJ, Smadbeck JB, Karagouga G, McCune AF, Harris FR, Udell JB, Johnson SH, Kerr SE, Cheville JC, Kipp BR, Vasmatzis G, Gleeson FC. Theragnostic chromosomal rearrangements in treatment-naive pancreatic ductal adenocarcinomas obtained via endoscopic ultrasound. J Cell Mol Med. 2021 Apr; 25 (8):4110-4123 Epub 2021 Mar 11
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23. Murphy S, Smadbeck J, Eckloff B, Lee Y, Johnson S, Karagouga G, Serla V, Sharma A, Sikkink R, Voss J, Harris F, Kline JS, Kosari F, Feldman A, Wieben E, Aubry MC, Kipp B, Jen J, Cheville J, Vasmatzis G. Chromosomal Junction Detection from Whole-Genome Sequencing on Formalin-Fixed, Paraffin-Embedded Tumors. J Mol Diagn. 2021 Apr; 23 (4):375-388 Epub 2020 Dec 31
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24. Pitel BA, Sharma N, Zepeda-Mendoza C, Smadbeck JB, Pearce KE, Cook JM, Vasmatzis G, Sachs Z, Kanagal-Shamanna R, Viswanatha D, Xiao S, Jenkins RB, Xu X, Hoppman NL, Ketterling RP, Peterson JF, Greipp PT, Baughn LB. Myeloid malignancies with 5q and 7q deletions are associated with extreme genomic complexity, biallelic TP53 variants, and very poor prognosis. Blood Cancer J. 2021 Feb 8; 11(2):18.
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25. Pitel BA, Sharma N, Zepeda-Mendoza C, Smadbeck JB, Pearce KE, Cook JM, Vasmatzis G, Sachs Z, Kanagal-Shamanna R, Viswanatha D, Xiao S, Jenkins RB, Xu X, Hoppman NL, Ketterling RP, Peterson JF, Greipp PT, Baughn LB. Myeloid malignancies with 5q and 7q deletions are associated with extreme genomic complexity, biallelic TP53 variants, and very poor prognosis. Blood Cancer J 2021 Feb 8; 11 (2):18 Epub 2021 Feb 08
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26. Zepeda-Mendoza CJ, Essendrup A, Smoley SA, Johnson SH, Hoppman NL, Vasmatzis G, Jackson DL, Kearney HM, Baughn LB. Prenatal characterization of a novel inverted SMAD2 duplication by mate pair sequencing in a fetus with dextrocardia. Clin Case Rep. 2021 Feb; 9 (2):769-774 Epub 2020 Dec 10
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27. Berg HE, Blackburn PR, Baughn LB, Ketterling RP, Xu X, Greipp PT, Hoppman NL, Smadbeck JB, Vasmatzis G, Shi M, Reichard KK, Viswanatha DS, Jevremovic D, Maher GM, Peterson JF. Identification of a novel KMT2A/GIMAP8 gene fusion in a pediatric patient with acute undifferentiated leukemia. Genes Chromosomes Cancer. 2021 Feb; 60 (2):108-111 Epub 2020 Oct 21
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28. Vaubel R, Zschernack V, Tran QT, Jenkins S, Caron A, Milosevic D, Smadbeck J, Vasmatzis G, Kandels D, Gnekow A, Kramm C, Jenkins R, Kipp BR, Rodriguez FJ, Orr BA, Pietsch T, Giannini C. Biology and grading of pleomorphic xanthoastrocytoma-what have we learned about it? Brain Pathol. 2021 Jan; 31 (1):20-32 Epub 2020 Aug 04
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29. Grassi T, Harris FR, Smadbeck JB, Murphy SJ, Block MS, Multinu F, Schaefer Klein JL, Zhang P, Karagouga G, Liu MC, Larish A, Lemens MA, Sommerfield MKS, Cappuccio S, Cheville JC, Vasmatzis G, Mariani A. Personalized tumor-specific DNA junctions to detect circulating tumor in patients with endometrial cancer. PLoS One. 2021; 16 (6):e0252390 Epub 2021 June 10
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30. Bornschlegl S, Gustafson MP, Delivanis DA, Ryder M, Liu MC, Vasmatzis G, Hallemeier CL, Park SS, Roberts LR, Parney IF, Jelinek DF, Dietz AB. Categorisation of patients based on immune profiles: a new approach to identifying candidates for response to checkpoint inhibitors. Clin Transl Immunology. 2021; 10 (4):e1267 Epub 2021 Apr 29
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31. Murphy SJ, Harris FR, Smadbeck JB, Serla V, Karagouga G, Johnson SH, Kosari F, Pierson KE, Bungum AO, Edell ES, Mansfield AS, Wigle DA, Kipp BR, Vasmatzis G, Aubry MC. Optimizing clinical cytology touch preparations for next generation sequencing. Genomics. 2020 Nov; 112(6):5313-5323. Epub 2020 Nov 02.
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32. Blackburn PR, Smadbeck JB, Znoyko I, Webley MR, Pitel BA, Vasmatzis G, Xu X, Greipp PT, Hoppman NL, Ketterling RP, Baughn LB, Lindsey KG, Schandl CA, Wolff DJ, Peterson JF. Cryptic and atypical KMT2A-USP2 and KMT2A-USP8 rearrangements identified by mate pair sequencing in infant and childhood leukemia. Genes Chromosomes Cancer. 2020 Jul; 59 (7):422-427 Epub 2020 Mar 26
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33. Chalmers SJ, Murphy SJ, Thompson LL, Hoppman NL, Smadbeck JB, Balcom JR, Harris FR, Frantz RP, Vasmatzis G, E Wylam M. Mate-pair sequencing identifies a cryptic BMPR2 mutation in hereditary pulmonary arterial hypertension. Pulm Circ. 2020 Jul-Sep; 10 (3):2045894020933081 Epub 2021 July 12
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34. Polonis K, Schultz MJ, Olteanu H, Smadbeck JB, Johnson SH, Vasmatzis G, Xu X, Greipp PT, Ketterling RP, Hoppman NL, Baughn LB, Peterson JF. Detection of cryptic CCND1 rearrangements in mantle cell lymphoma by next generation sequencing. Ann Diagn Pathol. 2020 Jun; 46:151533 Epub 2020 May 06
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35. Lopes JL, Webley M, Pitel BA, Pearce KE, Smadbeck JB, Johnson SH, Vasmatzis G, Sukov WR, Greipp PT, Hoppman NL, Ketterling RP, Baughn LB, Finn L, Peterson JF. Characterizing false-positive fluorescence in situ hybridization results by mate-pair sequencing in a patient with chronic myeloid leukemia and progression to myeloid blast crisis. Cancer Genet. 2020 May; 243:48-51 Epub 2020 Mar 17
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36. Schultz MJ, Blackburn PR, Cogbill CH, Pitel BA, Smadbeck JB, Johnson SH, Vasmatzis G, Rech KL, Sukov WR, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP, Peterson JF. Characterization of a cryptic PML-RARA fusion by mate-pair sequencing in a case of acute promyelocytic leukemia with a normal karyotype and negative RARA FISH studies. Leuk Lymphoma 2020 Apr; 61 (4):975-978 Epub 2019 Dec 06
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37. Mansfield AS, Peikert T, Vasmatzis G. Chromosomal rearrangements and their neoantigenic potential in mesothelioma. Transl Lung Cancer Res. 2020 Feb; 9 (Suppl 1):S92-S99
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38. Blackburn PR, Huang L, Dalovisio A, Pitel BA, Chen D, Oliveira JL, Wood AJ, Smadbeck JB, Johnson SH, Vasmatzis G, Haferlach C, Greipp PT, Hoppman NL, Ketterling RP, Baughn LB, Peterson JF. Secondary acquisition of BCR-ABL1 fusion in de novo GATA2-MECOM positive acute myeloid leukemia with subsequent emergence of a rare KMT2A-ASXL2 fusion. Cancer Genet 2020 Feb; 241:67-71 Epub 2019 Dec 26
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39. Vasmatzis G, Liu MC, Reganti S, Feathers RW, Smadbeck J, Johnson SH, Schaefer Klein JL, Harris FR, Yang L, Kosari F, Murphy SJ, Borad MJ, Thompson EA, Cheville JC, Anastasiadis PZ. Integration of Comprehensive Genomic Analysis and Functional Screening of Affected Molecular Pathways to Inform Cancer Therapy. Mayo Clin Proc. 2020 Feb; 95 (2):306-318 Epub 2019 Nov 02
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40. Parney IF, Gustafson MP, Solseth M, Bulur P, Peterson TE, Smadbeck JB, Johnson SH, Murphy SJ, Vasmatzis G, Dietz AB. Novel strategy for manufacturing autologous dendritic cell/allogeneic tumor lysate vaccines for glioblastoma. Neurooncol Adv. 2020 Jan-Dec; 2 (1):vdaa105 Epub 2020 Aug 26
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41. Perez-Rodriguez D, Kalyva M, Leija-Salazar M, Lashley T, Tarabichi M, Chelban V, Gentleman S, Schottlaender L, Franklin H, Vasmatzis G, Houlden H, Schapira AHV, Warner TT, Holton JL, Jaunmuktane Z, Proukakis C. Investigation of somatic CNVs in brains of synucleinopathy cases using targeted SNCA analysis and single cell sequencing. Acta Neuropathol Commun. 2019 Dec 23; 7 (1):219
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42. Smadbeck J, Peterson JF, Pearce KE, Pitel BA, Figueroa AL, Timm M, Jevremovic D, Shi M, Stewart AK, Braggio E, Riggs DL, Bergsagel PL, Vasmatzis G, Kearney HM, Hoppman NL, Ketterling RP, Kumar S, Rajkumar SV, Greipp PT, Baughn LB. Mate pair sequencing outperforms fluorescence in situ hybridization in the genomic characterization of multiple myeloma. Blood Cancer J. 2019 Dec 16; 9 (12):103
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43. Rowsey RA, Smoley SA, Williamson CM, Vasmatzis G, Smadbeck JB, Ning Y, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP, Peterson JF. Characterization of TCF3 rearrangements in pediatric B-lymphoblastic leukemia/lymphoma by mate-pair sequencing (MPseq) identifies complex genomic rearrangements and a novel TCF3/TEF gene fusion. Blood Cancer J. 2019 Oct 1; 9 (10):81 Epub 2019 Oct 01
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44. Murphy SJ, Harris FR, Kosari F, Barreto Siqueira Parrilha Terra S, Nasir A, Johnson SH, Serla V, Smadbeck JB, Halling GC, Karagouga G, Sukov WR, Leventakos K, Yang P, Peikert T, Mansfield AS, Wigle DA, Yi ES, Kipp BR, Vasmatzis G, Aubry MC. Using Genomics to Differentiate Multiple Primaries From Metastatic Lung Cancer. J Thorac Oncol. 2019 Sep; 14 (9):1567-1582 Epub 2019 May 16
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45. Peterson JF, He RR, Nayer H, Cuevo RS, Smadbeck JB, Vasmatzis G, Greipp PT, Ketterling RP, Hoppman NL, Baughn LB. Characterization of a rarely reported STAT5B/RARA gene fusion in a young adult with newly diagnosed acute promyelocytic leukemia with resistance to ATRA therapy. Cancer Genet. 2019 Sep; 237:51-54 Epub 2019 June 12
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46. Peterson JF, Meyer RG, Smoley SA, Webley M, Smadbeck JB, Vasmatzis G, Pearce K, Greipp PT, Ketterling RP, Craig FE, Stewart AK, Baughn LB. Whole Genome Mate-pair Sequencing of Plasma Cell Neoplasm as a Novel Diagnostic Strategy: A Case of Unrecognized t(2;11) Structural Variation. Clin Lymphoma Myeloma Leuk. 2019 Sep; 19 (9):598-602 Epub 2019 June 18
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47. Peterson JF, Sukov WR, Pitel BA, Smoley SA, Pearce KE, Meyer RG, Williamson CM, Smadbeck JB, Vasmatzis G, Hoppman NL, Greipp PT, Baughn LB, Ketterling RP. Acute leukemias harboring KMT2A/MLLT10 fusion: a 10-year experience from a single genomics laboratory. Genes Chromosomes Cancer. 2019 Aug; 58 (8):567-577 Epub 2019 Mar 19
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48. Muppa P, Parrilha Terra SBS, Sharma A, Mansfield AS, Aubry MC, Bhinge K, Asiedu MK, de Andrade M, Janaki N, Murphy SJ, Nasir A, Van Keulen V, Vasmatzis G, Wigle DA, Yang P, Yi ES, Peikert T, Kosari F. Immune Cell Infiltration May Be a Key Determinant of Long-Term Survival in Small Cell Lung Cancer. J Thorac Oncol. 2019 Jul; 14 (7):1286-1295 Epub 2019 May 09
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49. Peterson JF, Pitel BA, Smoley SA, Smadbeck JB, Johnson SH, Vasmatzis G, Kearney HM, Greipp PT, Hoppman NL, Baughn LB, Ketterling RP. Use of mate-pair sequencing to characterize a complex cryptic BCR/ABL1 rearrangement observed in a newly diagnosed case of chronic myeloid leukemia. Hum Pathol. 2019 Jul; 89:109-114 Epub 2018 Sept 26
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50. Peterson JF, Blackburn PR, Webley MR, Pearce KE, Williamson CM, Vasmatzis G, Smadbeck JB, Bieliauskas SL, Reichard KK, Ketterling RP, Baughn LB, Greipp PT. Identification of a Novel ZBTB20-JAK2 Fusion by Mate-Pair Sequencing in a Young Adult With B-Lymphoblastic Leukemia/Lymphoma. Mayo Clin Proc 2019 Jul; 94 (7):1381-1384
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51. Peterson JF, Pitel BA, Smoley SA, Vasmatzis G, Smadbeck JB, Greipp PT, Ketterling RP, Macon WR, Baughn LB. Elucidating a false-negative MYC break-apart fluorescence in situ hybridization probe study by next-generation sequencing in a patient with high-grade B-cell lymphoma with IGH/MYC and IGH/BCL2 rearrangements. Cold Spring Harb Mol Case Stud. 2019 Jun; 5 (3) Epub 2019 June 03
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52. Gupta S, Sosa CP, Kosari F, Folpe A, Bhinge KN, Yang L, Agahi A, Johnson SH, Frank I, Boorjian SA, Hansel DE, Al-Ahmadie HA, Reuter VE, Vasmatzis G, Jimenez RE, Herrera-Hernandez L, Cheville JC. A comparison of adult rhabdomyosarcoma and high-grade neuroendocrine carcinoma of the urinary bladder reveals novel PPP1R12A fusions in rhabdomyosarcoma. Hum Pathol. 2019 Jun; 88:48-59 Epub 2019 Apr 01
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53. King RL, McPhail ED, Meyer RG, Vasmatzis G, Pearce K, Smadbeck JB, Ketterling RP, Smoley SA, Greipp PT, Hoppman NL, Peterson JF, Baughn LB. False-negative rates for MYC fluorescence in situ hybridization probes in B-cell neoplasms. Haematologica 2019 Jun; 104 (6):e248-e251 Epub 2018 Dec 06
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54. Peterson JF, Baughn LB, Ketterling RP, Pitel BA, Smoley SA, Vasmatzis G, Smadbeck JB, Greipp PT, Mangaonkar AA, Thompson CA, Parikh SA, Chen D, Viswanatha DS. Characterization of a cryptic IGH/CCND1 rearrangement in a case of mantle cell lymphoma with negative CCND1 FISH studies. Blood Adv. 2019 Apr 23; 3 (8):1298-1302
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55. Peterson JF, Pitel BA, Smoley SA, Smadbeck JB, Johnson SH, Vasmatzis G, Koon SJ, Webley MR, McGrath M, Bayerl MG, Baughn LB, Rowsey RA, Ketterling RP, Greipp PT, Hoppman NL. Detection of a cryptic NUP214/ABL1 gene fusion by mate-pair sequencing (MPseq) in a newly diagnosed case of pediatric T-lymphoblastic leukemia. Cold Spring Harb Mol Case Stud. 2019 Apr; 5 (2) Epub 2019 Apr 01
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56. Bryce AH, Egan JB, Smadbeck JB, Johnson SH, Murphy SJ, Harris FR, Halling GC, Terra SBSP, Cheville J, Pagliaro L, Leibovich B, Costello BA, Vasmatzis G. Shared and unique genomic structural variants of different histological components within testicular germ cell tumours identified with mate pair sequencing. Sci Rep. 2019 Mar 5; 9 (1):3586 Epub 2019 Mar 05
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57. Rusheen AE, Smadbeck JB, Schimmenti LA, Klee EW, Link MJ, Vasmatzis G, Carlson ML. Proposal for Modification of Cahan's Criteria Utilizing Molecular Genetic Analyses for Cases without Baseline Histopathology: A Unique Method Applicable to Primary Radiosurgery. J Neurol Surg B Skull Base. 2019 Feb; 80 (1):10-17 Epub 2018 May 31
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58. Mansfield AS, Peikert T, Smadbeck JB, Udell JBM, Garcia-Rivera E, Elsbernd L, Erskine CL, Van Keulen VP, Kosari F, Murphy SJ, Ren H, Serla VV, Schaefer Klein JL, Karagouga G, Harris FR, Sosa C, Johnson SH, Nevala W, Markovic SN, Bungum AO, Edell ES, Dong H, Cheville JC, Aubry MC, Jen J, Vasmatzis G. Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma. J Thorac Oncol. 2019 Feb; 14 (2):276-287 Epub 2018 Oct 10
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59. Harris FR, Zhang P, Yang L, Hou X, Leventakos K, Weroha SJ, Vasmatzis G, Kovtun IV. Targeting HER2 in patient-derived xenograft ovarian cancer models sensitizes tumors to chemotherapy. Mol Oncol. 2019 Feb; 13 (2):132-152 Epub 2018 Dec 21
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60. Vasmatzis G, Kosari F, Murphy SJ, Terra S, Kovtun IV, Harris FR, Zarei S, Smadbeck JB, Johnson SH, Gaitatzes AG, Therneau TM, Rangel LJ, Knudson RA, Greipp P, Sukov WR, Knutson DL, Kloft-Nelson SM, Karnes RJ, Cheville JC. Large Chromosomal Rearrangements Yield Biomarkers to Distinguish Low-Risk From Intermediate- and High-Risk Prostate Cancer. Mayo Clin Proc. 2019 Jan; 94(1):27-36.
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61. Peterson JF, Pitel BA, Smoley SA, Smadbeck JB, Johnson SH, Vasmatzis G, Pearce KE, He R, Kelemen K, Al-Mondhiry HAB, Lamparella NE, Hoppman NL, Kearney HM, Baughn LB, Ketterling RP, Greipp PT. Constitutional chromosome rearrangements that mimic the 2017 world health organization "acute myeloid leukemia with recurrent genetic abnormalities": A study of three cases and review of the literature. Cancer Genet. 2019 Jan; 230:37-46 Epub 2018 Nov 20
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62. Aypar U, Smoley SA, Pitel BA, Pearce KE, Zenka RM, Vasmatzis G, Johnson SH, Smadbeck JB, Peterson JF, Geiersbach KB, Van Dyke DL, Thorland EC, Jenkins RB, Ketterling RP, Greipp PT, Kearney HM, Hoppman NL, Baughn LB. Mate pair sequencing improves detection of genomic abnormalities in acute myeloid leukemia. Eur J Haematol. 2019 Jan; 102 (1):87-96 Epub 2018 Nov 22
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63. Hussain S, Bedekovics T, Liu Q, Hu W, Jeon H, Johnson SH, Vasmatzis G, May DG, Roux KJ, Galardy PJ. UCH-L1 bypasses mTOR to promote protein biosynthesis and is required for MYC-driven lymphomagenesis in mice. Blood. 2018 Dec 13; 132 (24):2564-2574 Epub 2018 Sept 26
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64. Liu Y, Le P, Lim SJ, Ma L, Sarkar S, Han Z, Murphy SJ, Kosari F, Vasmatzis G, Cheville JC, Smith AM. Enhanced mRNA FISH with compact quantum dots. Nat Commun. 2018 Oct 26; 9 (1):4461
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65. Carlson ML, Smadbeck JB, Link MJ, Klee EW, Vasmatzis G, Schimmenti LA. Next Generation Sequencing of Sporadic Vestibular Schwannoma: Necessity of Biallelic NF2 Inactivation and Implications of Accessory Non-NF2 Variants. Otol Neurotol. 2018 Oct; 39 (9):e860-e871
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66. Sugihara T, Werneburg NW, Hernandez MC, Yang L, Kabashima A, Hirsova P, Yohanathan L, Sosa C, Truty MJ, Vasmatzis G, Gores GJ, Smoot RL. YAP Tyrosine Phosphorylation and Nuclear Localization in Cholangiocarcinoma Cells Are Regulated by LCK and Independent of LATS Activity. Mol Cancer Res. 2018 Oct; 16 (10):1556-1567 Epub 2018 June 14
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67. Smadbeck JB, Johnson SH, Smoley SA, Gaitatzes A, Drucker TM, Zenka RM, Kosari F, Murphy SJ, Hoppman N, Aypar U, Sukov WR, Jenkins RB, Kearney HM, Feldman AL, Vasmatzis G. Copy number variant analysis using genome-wide mate-pair sequencing. Genes Chromosomes Cancer. 2018 Sep; 57 (9):459-470 Epub 2018 July 30
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68. Vasmatzis G, Wang X, Smadbeck JB, Murphy SJ, Geiersbach KB, Johnson SH, Gaitatzes AG, Asmann YW, Kosari F, Borad MJ, Serie DJ, McLaughlin SA, Kachergus JM, Necela BM, Thompson EA. Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples. BMC Cancer. 2018 Jul 13; 18(1):738.
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69. Gaitatzes A, Johnson SH, Smadbeck JB, Vasmatzis G. Genome U-Plot: a whole genome visualization. Bioinformatics. 2018 May 15; 34 (10):1629-1634
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70. Zhang P, Schaefer-Klein J, Cheville JC, Vasmatzis G, Kovtun IV. Frequently rearranged and overexpressed delta-catenin is responsible for low sensitivity of prostate cancer cells to androgen receptor and beta-catenin antagonists. Oncotarget. 2018 May 11; 9 (36):24428-24442
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71. Asiedu MK, Thomas CF Jr, Dong J, Schulte SC, Khadka P, Sun Z, Kosari F, Jen J, Molina J, Vasmatzis G, Kuang R, Aubry MC, Yang P, Wigle DA. Pathways Impacted by Genomic Alterations in Pulmonary Carcinoid Tumors. Clin Cancer Res. 2018 Apr 1; 24 (7):1691-1704 Epub 2018 Jan 19
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72. DeLeon TT, Ahn DH, Bogenberger JM, Anastasiadis PZ, Arora M, Ramanathan RK, Aqel BA, Vasmatzis G, Truty MJ, Oklu R, Bekaii-Saab TS, Borad MJ. Novel targeted therapy strategies for biliary tract cancers and hepatocellular carcinoma. Future Oncol. 2018 Mar; 14 (6):553-566 Epub 2018 Feb 20
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73. H Chang, A Ikram, Farhad Kosari, George Vasmatzis, A Bhunia, R Bashir. Electrical characterization of micro-organisms using microfabricated devices Journal of Vacuum Science & Technology B. 2018.
    
74. Johnson SH, Smadbeck JB, Smoley SA, Gaitatzes A, Murphy SJ, Harris FR, Drucker TM, Zenka RM, Pitel BA, Rowsey RA, Hoppman NL, Aypar U, Sukov WR, Jenkins RB, Feldman AL, Kearney HM, Vasmatzis G. SVAtools for junction detection of genome-wide chromosomal rearrangements by mate-pair sequencing (MPseq). Cancer Genet. 2018 Feb; 221:1-18 Epub 2017 Dec 02
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75. Rizvi S, Fischbach SR, Bronk SF, Hirsova P, Krishnan A, Dhanasekaran R, Smadbeck JB, Smoot RL, Vasmatzis G, Gores GJ. YAP-associated chromosomal instability and cholangiocarcinoma in mice. Oncotarget. 2018 Jan 19; 9 (5):5892-5905 Epub 2017 Dec 22
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76. Penheiter AR, Deelchand DK, Kittelson E, Damgard SE, Murphy SJ, O'Brien DR, Bamlet WR, Passow MR, Smyrk TC, Couch FJ, Vasmatzis G, Port JD, Marjanska M, Carlson SK. Identification of a pyruvate-to-lactate signature in pancreatic intraductal papillary mucinous neoplasms. Pancreatology. 2018 Jan; 18 (1):46-53 Epub 2017 Nov 14
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77. Murphy SJ, Kosari F, Karnes RJ, Nasir A, Johnson SH, Gaitatzes AG, Smadbeck JB, Rangel LJ, Vasmatzis G, Cheville JC. Retention of Interstitial Genes between TMPRSS2 and ERG Is Associated with Low-Risk Prostate Cancer. Cancer Res. 2017 Nov 15; 77 (22):6157-6167 Epub 2017 Nov 10
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78. Murphy SJ, Terra SB, Harris FR, Nasir A, Voss JS, Smadbeck JB, Johnson SH, Serla V, Ryu JH, Yi ES, Kipp BR, Vasmatzis G, Carmona EM. Genomic rearrangements in sporadic lymphangioleiomyomatosis: an evolving genetic story. Mod Pathol. 2017 Sep; 30 (9):1223-1233 Epub 2017 June 23
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79. Leventakos K, Peikert T, Midthun DE, Molina JR, Blackmon S, Nichols FC, Garces YI, Hallemeier CL, Murphy SJ, Vasmatzis G, Kratz SL, Holland WP, Thomas CF, Mullon JJ, Shen KR, Cassivi SD, Marks RS, Aubry MC, Adjei AA, Yang P, Allen MS, Edell ES, Wigle D, Mansfield AS. Management of Multifocal Lung Cancer: Results of a Survey. J Thorac Oncol. 2017 Sep; 12 (9):1398-1402 Epub 2017 June 03
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80. Catic A, Kurtovic-Kozaric A, Johnson SH, Vasmatzis G, Pins MR, Kogan J. A novel cytogenetic and molecular characterization of renal metanephric adenoma: Identification of partner genes involved in translocation t(9;15)(p24;q24). Cancer Genet. 2017 Aug; 214-215:9-15 Epub 2017 Mar 16
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81. Gupta S, Johnson SH, Vasmatzis G, Porath B, Rustin JG, Rao P, Costello BA, Leibovich BC, Thompson RH, Cheville JC, Sukov WR. TFEB-VEGFA (6p21.1) co-amplified renal cell carcinoma: a distinct entity with potential implications for clinical management. Mod Pathol. 2017 Jul; 30 (7):998-1012 Epub 2017 Mar 24
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82. Ali MF, Dasari H, Van Keulen VP, Cornec D, Vasmatzis G, Peikert T, Carmona EM. Microbial Antigens Stimulate Metalloprotease-7 Secretion in Human B-Lymphocytes Using mTOR-Dependent and Independent Pathways. Sci Rep. 2017 Jun 20; 7 (1):3869 Epub 2017 June 20
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83. Menke JR, Vasmatzis G, Murphy S, Yang L, Menke DM, Tun HW, King RL, Smoley SA, Ketterling RP, Sukov WR. Mantle cell lymphoma with a novel t(11;12)(q13;p11.2): a proposed alternative mechanism of CCND1 up-regulation. Hum Pathol. 2017 Jun; 64:207-212 Epub 2017 Jan 27
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84. Bhinge K, Yang L, Terra S, Nasir A, Muppa P, Aubry MC, Yi J, Janaki N, Kovtun IV, Murphy SJ, Halling G, Rahi H, Mansfield A, de Andrade M, Yang P, Vasmatzis G, Peikert T, Kosari F. EGFR mediates activation of RET in lung adenocarcinoma with neuroendocrine differentiation characterized by ASCL1 expression. Oncotarget. 2017 Apr 18; 8 (16):27155-27165
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85. Gao G, Johnson SH, Vasmatzis G, Pauley CE, Tombers NM, Kasperbauer JL, Smith DI. Common fragile sites (CFS) and extremely large CFS genes are targets for human papillomavirus integrations and chromosome rearrangements in oropharyngeal squamous cell carcinoma. Genes Chromosomes Cancer. 2017 Jan; 56 (1):59-74 Epub 2016 Nov 01
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86. Wieben ED, Aleff RA, Tang X, Butz ML, Kalari KR, Highsmith EW, Jen J, Vasmatzis G, Patel SV, Maguire LJ, Baratz KH, Fautsch MP. Trinucleotide Repeat Expansion in the Transcription Factor 4 (TCF4) Gene Leads to Widespread mRNA Splicing Changes in Fuchs' Endothelial Corneal Dystrophy. Invest Ophthalmol Vis Sci. 2017 Jan 1; 58 (1):343-352
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87. Gleeson FC, Kerr SE, Kipp BR, Voss JS, Minot DM, Tu ZJ, Henry MR, Vasmatzis G, Cheville JC, Lazaridis KN, Levy MJ. Molecular cytology genotyping of primary and metastatic GI stromal tumors by using a custom two-gene targeted next-generation sequencing panel with therapeutic intent. Gastrointest Endosc. 2016 Dec; 84 (6):950-958.e3 Epub 2016 Apr 23
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88. Mansfield AS, Murphy SJ, Harris FR, Robinson SI, Marks RS, Johnson SH, Smadbeck JB, Halling GC, Yi ES, Wigle D, Vasmatzis G, Jen J. Chromoplectic TPM3-ALK rearrangement in a patient with inflammatory myofibroblastic tumor who responded to ceritinib after progression on crizotinib. Ann Oncol. 2016 Nov; 27 (11):2111-2117 Epub 2016 Oct 14
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89. Jang JS, Wang X, Vedell PT, Wen J, Zhang J, Ellison DW, Evans JM, Johnson SH, Yang P, Sukov WR, Oliveira AM, Vasmatzis G, Sun Z, Jen J, Yi ES. Custom Gene Capture and Next-Generation Sequencing to Resolve Discordant ALK Status by FISH and IHC in Lung Adenocarcinoma. J Thorac Oncol. 2016 Nov; 11 (11):1891-1900 Epub 2016 June 22
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90. 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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91. Gleeson FC, Kerr SE, Kipp BR, Voss JS, Minot DM, Tu ZJ, Henry MR, Graham RP, Vasmatzis G, Cheville JC, Lazaridis KN, Levy MJ. Targeted next generation sequencing of endoscopic ultrasound acquired cytology from ampullary and pancreatic adenocarcinoma has the potential to aid patient stratification for optimal therapy selection. Oncotarget. 2016 Aug 23; 7 (34):54526-54536
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92. Harris FR, Kovtun IV, Smadbeck J, Multinu F, Jatoi A, Kosari F, Kalli KR, Murphy SJ, Halling GC, Johnson SH, Liu MC, Mariani A, Vasmatzis G. Quantification of Somatic Chromosomal Rearrangements in Circulating Cell-Free DNA from Ovarian Cancers. Sci Rep. 2016 Jul 20; 6:29831 Epub 2016 July 20
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93. Mansfield AS, Murphy SJ, Peikert T, Yi ES, Vasmatzis G, Wigle DA, Aubry MC. Heterogeneity of Programmed Cell Death Ligand 1 Expression in Multifocal Lung Cancer. Clin Cancer Res. 2016 May 1; 22 (9):2177-82 Epub 2015 Dec 14
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94. Shim S, Shim J, Taylor WR, Kosari F, Vasmatzis G, Ahlquist DA, Bashir R. Magnetophoretic-based microfluidic device for DNA Concentration. Biomed Microdevices. 2016 Apr; 18: (2)28.
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95. Murphy SJ, Karnes RJ, Kosari F, Castellar BE, Kipp BR, Johnson SH, Terra S, Harris FR, Halling GC, Klein JL, Nasir A, Bergstrahl E, Rangel LJ, Sukov WR, Vasmatzis G, Cheville JC. Integrated analysis of the genomic instability of PTEN in clinically insignificant and significant prostate cancer. Mod Pathol. 2016 Feb; 29 (2):143-56 Epub 2015 Nov 27
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96. Murphy SJ, Hart SN, Halling GC, Johnson SH, Smadbeck JB, Drucker T, Lima JF, Rohakhtar FR, Harris FR, Kosari F, Subramanian S, Petersen GM, Wiltshire TD, Kipp BR, Truty MJ, McWilliams RR, Couch FJ, Vasmatzis G. Integrated Genomic Analysis of Pancreatic Ductal Adenocarcinomas Reveals Genomic Rearrangement Events as Significant Drivers of Disease. Cancer Res. 2016 Feb 1; 76 (3):749-61 Epub 2015 Dec 16
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97. Kovtun IV, Murphy SJ, Johnson SH, Cheville JC, Vasmatzis G. Chromosomal catastrophe is a frequent event in clinically insignificant prostate cancer. Oncotarget. 2015 Oct 6; 6 (30):29087-96
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98. An J, Ren S, Murphy SJ, Dalangood S, Chang C, Pang X, Cui Y, Wang L, Pan Y, Zhang X, Zhu Y, Wang C, Halling GC, Cheng L, Sukov WR, Karnes RJ, Vasmatzis G, Zhang Q, Zhang J, Cheville JC, Yan J, Sun Y, Huang H. Truncated ERG Oncoproteins from TMPRSS2-ERG Fusions Are Resistant to SPOP-Mediated Proteasome Degradation. Mol Cell. 2015 Sep 17; 59 (6):904-16 Epub 2015 Sept 03
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99. Aubry MC, Roden A, Murphy SJ, Vasmatzis G, Johnson SH, Harris FR, Halling G, Knudson RA, Ketterling RP, Feldman AL. Chromosomal rearrangements and copy number abnormalities of TP63 correlate with p63 protein expression in lung adenocarcinoma. Mod Pathol. 2015 Mar; 28 (3):359-66 Epub 2014 Sept 05
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100. Lu J, Lonergan PE, Nacusi LP, Wang L, Schmidt LJ, Sun Z, Van der Steen T, Boorjian SA, Kosari F, Vasmatzis G, Klee GG, Balk SP, Huang H, Wang C, Tindall DJ. The cistrome and gene signature of androgen receptor splice variants in castration resistant prostate cancer cells. J Urol. 2015 Feb; 193 (2):690-8 Epub 2014 Aug 14
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101. Schaefer-Klein JL, Murphy SJ, Johnson SH, Vasmatzis G, Kovtun IV. Topoisomerase 2 Alpha Cooperates with Androgen Receptor to Contribute to Prostate Cancer Progression. PLoS One. 2015; 10 (11):e0142327 Epub 2015 Nov 11
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102. Shim J, Kim Y, Humphreys GI, Nardulli AM, Kosari F, Vasmatzis G, Taylor WR, Ahlquist DA, Myong S, Bashir R. Nanopore-based assay for detection of methylation in double-stranded DNA fragments. ACS nano. 2015; 9(1):290-300.
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103. Penheiter AR, Erdogan S, Murphy SJ, Hart SN, Felipe Lima J, Rakhshan Rohakhtar F, O'Brien DR, Bamlet WR, Wuertz RE, Smyrk TC, Couch FJ, Vasmatzis G, Bender CE, Carlson SK. Transcriptomic and Immunohistochemical Profiling of SLC6A14 in Pancreatic Ductal Adenocarcinoma. Biomed Res Int. 2015; 2015:593572 Epub 2015 May 27
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104. Murphy SJ, Aubry MC, Harris FR, Halling GC, Johnson SH, Terra S, Drucker TM, Asiedu MK, Kipp BR, Yi ES, Peikert T, Yang P, Vasmatzis G, Wigle DA. Identification of independent primary tumors and intrapulmonary metastases using DNA rearrangements in non-small-cell lung cancer. J Clin Oncol. 2014 Dec 20; 32 (36):4050-8 Epub 2014 Nov 10
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105. Parrilla Castellar ER, Jaffe ES, Said JW, Swerdlow SH, Ketterling RP, Knudson RA, Sidhu JS, Hsi ED, Karikehalli S, Jiang L, Vasmatzis G, Gibson SE, Ondrejka S, Nicolae A, Grogg KL, Allmer C, Ristow KM, Wilson WH, Macon WR, Law ME, Cerhan JR, Habermann TM, Ansell SM, Dogan A, Maurer MJ, Feldman AL. ALK-negative anaplastic large cell lymphoma is a genetically heterogeneous disease with widely disparate clinical outcomes. Blood. 2014 Aug 28; 124(9):1473-80. Epub 2014 Jun 03.
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106. Graham RP, Barr Fritcher EG, Pestova E, Schulz J, Sitailo LA, Vasmatzis G, Murphy SJ, McWilliams RR, Hart SN, Halling KC, Roberts LR, Gores GJ, Couch FJ, Zhang L, Borad MJ, Kipp BR. Fibroblast growth factor receptor 2 translocations in intrahepatic cholangiocarcinoma. Hum Pathol. 2014 Aug; 45(8):1630-8. Epub 2014 Apr 13.
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107. Kosari F, Ida CM, Aubry MC, Yang L, Kovtun IV, Klein JL, Li Y, Erdogan S, Tomaszek SC, Murphy SJ, Bolette LC, Kolbert CP, Yang P, Wigle DA, Vasmatzis G. ASCL1 and RET expression defines a clinically relevant subgroup of lung adenocarcinoma characterized by neuroendocrine differentiation. Oncogene. 2014 Jul 17; 33 (29):3776-83 Epub 2013 Sept 16
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108. Murphy SJ, Wigle DA, Lima JF, Harris FR, Johnson SH, Halling G, Asiedu MK, Seto CT, Terra S, Kosari F, Peikert T, Yang P, Aubry MC, Vasmatzis G. Genomic rearrangements define lineage relationships between adjacent lepidic and invasive components in lung adenocarcinoma. Cancer Res. 2014 Jun 1; 74 (11):3157-67
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109. Drucker TM, Johnson SH, Murphy SJ, Cradic KW, Therneau TM, Vasmatzis G. BIMA V3: an aligner customized for mate pair library sequencing. Bioinformatics. 2014 Jun 1; 30 (11):1627-9 Epub 2014 Feb 12
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110. Gao G, Johnson SH, Kasperbauer JL, Eckloff BW, Tombers NM, Vasmatzis G, Smith DI. Mate pair sequencing of oropharyngeal squamous cell carcinomas reveals that HPV integration occurs much less frequently than in cervical cancer. J Clin Virol. 2014 Mar; 59(3):195-200. Epub 2013 Dec 28.
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111. Ansell SM, Hodge LS, Secreto FJ, Manske M, Braggio E, Price-Troska T, Ziesmer S, Li Y, Johnson SH, Hart SN, Kocher JP, Vasmatzis G, Chanan-Kahn A, Gertz M, Fonseca R, Dogan A, Cerhan JR, Novak AJ. Activation of TAK1 by MYD88 L265P drives malignant B-cell Growth in non-Hodgkin lymphoma. Blood Cancer J. 2014 Feb 14; 4:e183
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112. Cradic KW, Murphy SJ, Drucker TM, Sikkink RA, Eberhardt NL, Neuhauser C, Vasmatzis G, Grebe SK. A simple method for gene phasing using mate pair sequencing. BMC Med Genet. 2014 Feb 6; 15:19 Epub 2014 Feb 06
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113. Deng B, Molina J, Aubry MC, Sun Z, Wang L, Eckloff BW, Vasmatzis G, You M, Wieben ED, Jen J, Wigle DA, Yang P. Clinical biomarkers of pulmonary carcinoid tumors in never smokers via profiling miRNA and target mRNA. Cell Biosci. 2014; 4:35 Epub 2014 July 09
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114. 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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115. Murphy SJ, Hart SN, Lima JF, Kipp BR, Klebig M, Winters JL, Szabo C, Zhang L, Eckloff BW, Petersen GM, Scherer SE, Gibbs RA, McWilliams RR, Vasmatzis G, Couch FJ. Genetic alterations associated with progression from pancreatic intraepithelial neoplasia to invasive pancreatic tumor. Gastroenterology. 2013 Nov; 145 (5):1098-1109.e1 Epub 2013 Aug 02
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116. Lasho T, Johnson SH, Smith DI, Crispino JD, Pardanani A, Vasmatzis G, Tefferi A. Identification of submicroscopic genetic changes and precise breakpoint mapping in myelofibrosis using high resolution mate-pair sequencing. Am J Hematol. 2013 Sep; 88(9):741-6. Epub 2013 Aug 01.
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117. Kovtun IV, Cheville JC, Murphy SJ, Johnson SH, Zarei S, Kosari F, Sukov WR, Karnes RJ, Vasmatzis G. Lineage relationship of Gleason patterns in Gleason score 7 prostate cancer. Cancer Res. 2013 Jun 1; 73 (11):3275-84 Epub 2013 May 21
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118. Gomez CR, Kosari F, Munz JM, Schreiber CA, Knutson GJ, Ida CM, El Khattouti A, Karnes RJ, Cheville JC, Vasmatzis G, Vuk-Pavlovic S. Prognostic value of discs large homolog 7 transcript levels in prostate cancer. PLoS One. 2013; 8 (12):e82833 Epub 2013 Dec 09
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119. Shim J, Humphreys GI, Venkatesan BM, Munz JM, Zou X, Sathe C, Schulten K, Kosari F, Nardulli AM, Vasmatzis G, Bashir R. Detection and quantification of methylation in DNA using solid-state nanopores. Sci Rep. 2013; 3:1389.
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120. Zhang Y, Foreman O, Wigle DA, Kosari F, Vasmatzis G, Salisbury JL, van Deursen J, Galardy PJ. USP44 regulates centrosome positioning to prevent aneuploidy and suppress tumorigenesis. J Clin Invest. 2012 Dec; 122 (12):4362-74 Epub 2012 Nov 26
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121. Murphy SJ, Cheville JC, Zarei S, Johnson SH, Sikkink RA, Kosari F, Feldman AL, Eckloff BW, Karnes RJ, Vasmatzis G. Mate pair sequencing of whole-genome-amplified DNA following laser capture microdissection of prostate cancer. DNA Res. 2012 Oct; 19 (5):395-406 Epub 2012 Sept 18
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122. Vasmatzis G, Johnson SH, Knudson RA, Ketterling RP, Braggio E, Fonseca R, Viswanatha DS, Law ME, Kip NS, Ozsan N, Grebe SK, Frederick LA, Eckloff BW, Thompson EA, Kadin ME, Milosevic D, Porcher JC, Asmann YW, Smith DI, Kovtun IV, Ansell SM, Dogan A, Feldman AL. Genome-wide analysis reveals recurrent structural abnormalities of TP63 and other p53-related genes in peripheral T-cell lymphomas. Blood. 2012 Sep 13; 120 (11):2280-9 Epub 2012 Aug 01
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123. Kosari F, Cheville JC, Ida CM, Karnes RJ, Leontovich AA, Sebo TJ, Erdogan S, Rodriguez E, Murphy SJ, Vasmatzis G. Shared gene expression alterations in prostate cancer and histologically benign prostate from patients with prostate cancer. Am J Pathol. 2012 Jul; 181 (1):34-42 Epub 2012 May 26
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124. Feldman AL, Dogan A, Smith DI, Law ME, Ansell SM, Johnson SH, Porcher JC, Ozsan N, Wieben ED, Eckloff BW, Vasmatzis G. Discovery of recurrent t(6;7)(p25.3;q32.3) translocations in ALK-negative anaplastic large cell lymphomas by massively parallel genomic sequencing. Blood. 2011 Jan 20; 117 (3):915-9 Epub 2010 Oct 28
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125. Karnes RJ, Cheville JC, Ida CM, Sebo TJ, Nair AA, Tang H, Munz JM, Kosari F, Vasmatzis G. The ability of biomarkers to predict systemic progression in men with high-risk prostate cancer treated surgically is dependent on ERG status. Cancer Res. 2010 Nov 15; 70 (22):8994-9002 Epub 2010 Nov 09
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126. Li Y, Sheu CC, Ye Y, de Andrade M, Wang L, Chang SC, Aubry MC, Aakre JA, Allen MS, Chen F, Cunningham JM, Deschamps C, Jiang R, Lin J, Marks RS, Pankratz VS, Su L, Li Y, Sun Z, Tang H, Vasmatzis G, Harris CC, Spitz MR, Jen J, Wang R, Zhang ZF, Wang R, Christiani DC, Wu X, Yang P. Genetic variants and risk of lung cancer in never smokers: a genome-wide association study. Lancet Oncol. 2010 Apr; 11 (4):321-30 Epub 2010 Mar 19
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127. Shin S, Kim TD, Jin F, van Deursen JM, Dehm SM, Tindall DJ, Grande JP, Munz JM, Vasmatzis G, Janknecht R. Induction of prostatic intraepithelial neoplasia and modulation of androgen receptor by ETS variant 1/ETS-related protein 81. Cancer Res. 2009 Oct 15; 69(20):8102-10. Epub 2009 Sep 29
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128. Boland JM, Erdogan S, Vasmatzis G, Yang P, Tillmans LS, Johnson MR, Wang X, Peterson LM, Halling KC, Oliveira AM, Aubry MC, Yi ES. Anaplastic lymphoma kinase immunoreactivity correlates with ALK gene rearrangement and transcriptional up-regulation in non-small cell lung carcinomas. Hum Pathol. 2009 Aug; 40 (8):1152-8 Epub 2009 Apr 22
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129. Savci-Heijink CD, Kosari F, Aubry MC, Caron BL, Sun Z, Yang P, Vasmatzis G. The role of desmoglein-3 in the diagnosis of squamous cell carcinoma of the lung. Am J Pathol. 2009 May; 174 (5):1629-37 Epub 2009 Mar 26
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130. Klee EW, Erdogan S, Tillmans L, Kosari F, Sun Z, Wigle DA, Yang P, Aubry MC, Vasmatzis G. Impact of sample acquisition and linear amplification on gene expression profiling of lung adenocarcinoma: laser capture micro-dissection cell-sampling versus bulk tissue-sampling. BMC Med Genomics. 2009 Mar 9; 2:13 Epub 2009 Mar 09
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131. Cheville JC, Karnes RJ, Therneau TM, Kosari F, Munz JM, Tillmans L, Basal E, Rangel LJ, Bergstralh E, Kovtun IV, Savci-Heijink CD, Klee EW, Vasmatzis G. Gene panel model predictive of outcome in men at high-risk of systemic progression and death from prostate cancer after radical retropubic prostatectomy. J Clin Oncol. 2008 Aug 20; 26 (24):3930-6
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132. Kosari F, Munz JM, Savci-Heijink CD, Spiro C, Klee EW, Kube DM, Tillmans L, Slezak J, Karnes RJ, Cheville JC, Vasmatzis G. Identification of prognostic biomarkers for prostate cancer. Clin Cancer Res. 2008 Mar 15; 14 (6):1734-43
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133. Vasmatzis G, Klee EW, Kube DM, Therneau TM, Kosari F. Quantitating tissue specificity of human genes to facilitate biomarker discovery. Bioinformatics. 2007 Jun 1; 23(11):1348-55. Epub 2007 Mar 23.
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134. Kube DM, Savci-Heijink CD, Lamblin AF, Kosari F, Vasmatzis G, Cheville JC, Connelly DP, Klee GG. Optimization of laser capture microdissection and RNA amplification for gene expression profiling of prostate cancer. BMC Mol Biol. 2007 Mar 21; 8:25
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135. Finlay JA, Klee EW, McDonald C, Attewell JR, Hebrink D, Dyer R, Love B, Vasmatzis G, Li TM, Beechem JM, Klee GG. A systematic method for selection of promising serum protein biomarkers to improve prostate cancer (PCa1) detection. Clin Chem. 2006 Nov; 52(11):2159-62.
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136. Klee EW, Finlay JA, McDonald C, Attewell JR, Hebrink D, Dyer R, Hebrink D, Love B, Vasmatzis G, Li TM, Beechem JM, Klee GG. Bioinformatics methods for prioritizing serum biomarker candidates. Clin Chem. 2006 Nov; 52 (11):2162-4
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137. Chang H, Venkatesan BM, Iqbal SM, Andreadakis G, Kosari F, Vasmatzis G, Peroulis D, Bashir R. DNA counterion current and saturation examined by a MEMS-based solid state nanopore sensor. Biomed Microdevices. 2006 Sep; 8(3):263-9.
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138. Wang X, Zheng L, Zeng Z, Zhou G, Chien J, Qian C, Vasmatzis G, Shridhar V, Chen L, Liu W. DIXDC1 isoform, l-DIXDC1, is a novel filamentous actin-binding protein. Biochem Biophys Res Commun. 2006 Aug 18; 347(1):22-30. Epub 2006 Jun 19.
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139. Parker AS, Kosari F, Lohse CM, Houston Thompson R, Kwon ED, Murphy L, Riehle DL, Blute ML, Leibovich BC, Vasmatzis G, Cheville JC. High expression levels of survivin protein independently predict a poor outcome for patients who undergo surgery for clear cell renal cell carcinoma. Cancer. 2006 Jul 1; 107 (1):37-45
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140. Murillo H, Schmidt LJ, Karter M, Hafner KA, Kondo Y, Ballman KV, Vasmatzis G, Jenkins RB, Tindall DJ. Prostate cancer cells use genetic and epigenetic mechanisms for progression to androgen independence. Genes Chromosomes Cancer. 2006 Jul; 45(7):702-16.
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141. Kosari F, Parker AS, Kube DM, Lohse CM, Leibovich BC, Blute ML, Cheville JC, Vasmatzis G. Clear cell renal cell carcinoma: gene expression analyses identify a potential signature for tumor aggressiveness. Clin Cancer Res. 2005 Jul 15; 11 (14):5128-39
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142. Sun Z, Yang P, Aubry MC, Kosari F, Endo C, Molina J, Vasmatzis G. Can gene expression profiling predict survival for patients with squamous cell carcinoma of the lung? Mol Cancer. 2004 Dec 3; 3 (1):35 Epub 2004 Dec 03
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143. Yang P, Sun Z, Aubry MC, Kosari F, Bamlet W, Endo C, Molina JR, Vasmatzis G. Study design considerations in clinical outcome research of lung cancer using microarray analysis. Lung Cancer. 2004 Nov; 46(2):215-26.
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144. Chang H, Kosari F, Andreadakis G, Alam MA, Vasmatzis G, Bashir R. DNA-mediated fluctuations in ionic current through silicon oxide nanopore channels. Nano lett. 2004 Aug; 4(8):1551-6.
     
145. Bergen HR 3rd, Vasmatzis G, Cliby WA, Johnson KL, Oberg AL, Muddiman DC. Discovery of ovarian cancer biomarkers in serum using NanoLC electrospray ionization TOF and FT-ICR mass spectrometry. Dis Markers. 2003-2004; 19(4-5):239-49.
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146. Kosari F, Asmann YW, Cheville JC, Vasmatzis G. Cysteine-rich secretory protein-3: a potential biomarker for prostate cancer. Cancer Epidemiol Biomarkers Prev. 2002 Nov; 11(11):1419-26.
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147. Chang H, Ikram A, Geng T, Kosari F, Vasmatzis G, Bhunia A, Bashir R. Electrical characterization of microorganisms using microfabricated devices. J VAC SCI TECHNOL B. 2002 SEP-OCT; 20(5):2058-64.
     
148. Chang H, Ikram A, Kosari F, Vasmatzis G, Bhunia A, Bashir R. Electrical characterization of micro-organisms using microfabricated devices. Journal of Vacuum Science & Technology B. 2002 Sep-Oct; 20(5):2058-64.
     
149. Asmann YW, Kosari F, Wang K, Cheville JC, Vasmatzis G. Identification of differentially expressed genes in normal and malignant prostate by electronic profiling of expressed sequence tags. Cancer Res. 2002 Jun 1; 62 (11):3308-14
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150. Geanacopoulos M, Vasmatzis G, Zhurkin VB, Adhya S. Gal repressosome contains an antiparallel DNA loop. Nat Struct Biol. 2001 May; 8(5):432-6.
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151. Yerushalmi N, Keppler-Hafkemeyer A, Vasmatzis G, Liu XF, Olsson P, Bera TK, Duray P, Lee B, Pastan I. ERGL, a novel gene related to ERGIC-53 that is highly expressed in normal and neoplastic prostate and several other tissues. Gene. 2001 Mar; 265(1-2):55-60.
     
152. Geanacopoulos M, Vasmatzis G, Zhurkin V, Adhya S. Structure-based genetic analysis of Gal repressosome: GalR tetramer and the DNA loop it forms. Nat Struct Biol. 2001 May; 8(5):432-6.
     
153. Onda M, Kreitman RJ, Vasmatzis G, Lee B, Pastan I. Reduction of the nonspecific toxicity of immunotoxin anti-Tac(Fv)-PE38 (LMB-2) by mutations in the Fv which lower the isoelectric point. Blood. 1999; 94: (10)1246.
     
154. Liu XF, Essand M, Vasmatzis G, Lee B, Pastan I. Identification of three new alternate human kallikrein 2 transcripts: Evidence of long transcript and alternative splicing. Biochem Biophys Res Commun. 1999; 264(3):833-9.
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155. Essand M, Vasmatzis G, Brinkmann U, Lee B, Pastan I. High expression of a specific T-cell receptor gamma transcript in epithelial cells of the prostate. Proc Natl Acad Sci USA. 1999; 96(16):9287-92.
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156. Vasmatzis G, Brinkmann U, Lee B, Pastan I. Novel genes in the PAGE and GAGE family of tumor antigens found by homology walking in the EST database. Cancer Res. 1999; 59(7):1445-8.
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157. Pastan L, Vasmatzis G, Essand M, Olsson P, Liu XF, Iavarone C, Ailey B, Duray P, Bera T, Lee B. Discovery of new targets for prostate cancer immunotherapy by EST database analysis. Clin Cancer Res Suppl S. 1999 Nov; 5:3869S-3869.
     
158. Geanacopoulos M, Vasmatzis G, Lewis DEA, Roy S, Lee B, Adhya S. GalR mutants diffective in repressosome formation. Genes & Development. 1999; 13:1251-62.
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159. Almog O, Benhar I, Vasmatzis G, Tordova M, Lee B, Pastan I, Gilliland GL. Crystal structure of the disulfide-stabilized Fv fragment of anticancer antibody B1: conformational influence of an engineered disulfide bond. Proteins. 1998 May 1; 31(2):128-38.
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160. Nambiar MP, Vasmatzis G, Lee BK, FitzGerald DJ, Pastan IH. Production of stable scFv by mutation of the unusual amino acids at the framework region. FASEB J. 1998 Apr 24; 12(8 Suppl S):683.
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161. Brinkmann U, Vasmatzis G, Lee B, Yerushalmi N, Essand M, Pastan I. PAGE-1, an X chromosome-linked GAGE-like gene that is expressed in normal and neoplastic prostate, testis, and uterus. Proc Natl Acad Sci USA. 1998; 95(18):10757-62.
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162. Chowdhury PS, Vasmatzis G, Beers R, Lee B, Pastan I. Improvement of the stability and yield of scFv immunotoxins by molecular modeling and protein engineering. FASEB J. 1998; 12(8):681 Suppl S.
     
163. Chowdhury PS, Vasmatzis G, Beers R, Lee B, Pastan I. Improvement of the stability and yield of K1 scFv immunotoxin by computer design and protein engineering. J Mol Biol. 1998; 281(5):917-28.
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164. Vasmatzis G, Essand M, Brinkmann U, Lee B, Pastan I. Discovery of three new genes specifically expressed in human prostate by expressed sequence tag database analysis. Proc Natl Acad Sci USA. 1998; 95(1):300-4.
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165. Lee B, Vasmatzis G. Stabilization of protein structure. Curr Opin Biotechnol. 1997; 8(4):423-8.
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166. Brinkmann U, Carlo AD, Vasmatzis G, Kurochkina N, Beers R, Lee B, Pastan I. Stabilization of a recombinant Fv fragment by base-loop interconnection and v(h)-v(l) permutation. J Mol Biol. 1997; 268(1):107-17.
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167. Zhang C, Vasmatzis G, Cornette J, DeLisi C. Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol. 1997; 267(3):707-26.
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168. Vasmatzis G, Zhang C, Cornette J, DeLisi C. Computational of side chain specificity for pockets in class I MHC molecules. Mol Immunol. 1996; 33(16):1231-9.
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169. Vasmatzis G, Cornette J, Sezerman U, DeLisi C. TcR recognition of the MHC-peptide dimer: Structural properties of a ternary complex. J Mol Biol. 1996; 261(1):72-89.
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170. Vasmatzis G, Brower RC, DeLisi C. Predicting immunoglobulin-like hypervariable loops. Biopolymers. 1994; 34:1669-80.
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171. Brower RC, Vasmatzis G, Siverman M, DeLisi C. Peptide conformations on a lattice by exhaustive search and simulated annealing. Biopolymers. 1993; 33:329-34.
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