Publications

  1. Juran BD, McCauley BM, Atkinson EJ, Schlicht EM, Bianchi JK, Vollenweider JM, Ye H, LaRusso NF, Gores GJ, Sun Z, Lazaridis KN. Epigenetic disease markers in primary sclerosing cholangitis and primary biliary cholangitis-methylomics of cholestatic liver disease. Hepatol Commun. 2024 Aug 1; 8 (8) Epub 2024 July 18
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  2. Kosinsky RL, Gonzalez MM, Saul D, Barros LL, Sagstetter MR, Fedyshyn Y, Nair A, Sun Z, Hamdan FH, Gibbons HR, Perez Pachon ME, Druliner BR, Johnsen SA, Faubion WA. The FOXP3(+) Pro-Inflammatory T Cell: A Potential Therapeutic Target in Crohn's Disease. Gastroenterology. 2024 Apr; 166 (4):631-644.e17 Epub 2024 Jan 09
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  3. Grande J, Jones TL, Sun Z, Chanana P, Jaiswal I, Leontovich A, Carapanceanu N, Carapanceanu V, Saadalla A, Osman A, Famuyide AO, Daftary GS, Khan Z, Khazaie K. Corrigendum to "Host immunity and KLF 11 deficiency together promote fibrosis in a mouse model of endometriosis" [BBA - Mol. Basis of Dis. 1869 (2023) 166784]. Biochim Biophys Acta Mol Basis Dis. 2024 Mar; 1870 (3):166923 Epub 2023 Nov 08
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  4. Northrop-Albrecht EJ, Wu CW, Berger CK, Taylor WR, Foote PH, Doering KA, Gonser AM, Bhagwate A, Sun Z, Mahoney DW, Burger KN, Boardman LA, Kisiel JB. An investigation of plasma cell-free RNA for the detection of colorectal cancer: From transcriptome marker selection to targeted validation. PLoS One. 2024; 19 (8):e0308711 Epub 2024 Aug 15
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  5. Gao F, Hayashi Y, Saravanaperumal SA, Gajdos GB, Syed SA, Bhagwate AV, Ye Z, Zhong J, Zhang Y, Choi EL, Kvasha SM, Kaur J, Paradise BD, Cheng L, Simone BW, Wright AM, Kellogg TA, Kendrick ML, McKenzie TJ, Sun Z, Yan H, Yu C, Bharucha AE, Linden DR, Lee JH, Ordog T. Hypoxia-Inducible Factor 1alpha Stabilization Restores Epigenetic Control of Nitric Oxide Synthase 1 Expression and Reverses Gastroparesis in Female Diabetic Mice. Gastroenterology. 2023 Dec; 165 (6):1458-1474 Epub 2023 Aug 18
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  6. Sun Z, Braga-Neto MB, Xiong Y, Bhagwate AV, Gibbons HR, Sagstetter MR, Hamdan FH, Baheti S, Friton J, Nair A, Ye Z, Faubion WA. Hypomethylation and Overexpression of Th17-Associated Genes is a Hallmark of Intestinal CD4+ Lymphocytes in Crohn's Disease. J Crohns Colitis. 2023 Nov 24; 17 (11):1847-1857
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  7. Grande J, Jones TL, Sun Z, Chanana P, Jaiswal I, Leontovich A, Carapanceanu N, Carapanceanu V, Saadalla A, Osman A, Famuyide AO, Daftary GS, Khan Z, Khazaie K. Host immunity and KLF 11 deficiency together promote fibrosis in a mouse model of endometriosis. Biochim Biophys Acta Mol Basis Dis. 2023 Oct; 1869 (7):166784 Epub 2023 June 13
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  8. Ramos GP, Bamidele AO, Klatt EE, Sagstetter MR, Kurdi AT, Hamdan FH, Kosinsky RL, Gaballa JM, Nair A, Sun Z, Dasari S, Lanza IR, Rozeveld CN, Schott MB, Urrutia G, Westphal MS, Clarkson BD, Howe CL, Marietta EV, Luckey DH, Murray JA, Gonzalez M, Braga Neto MB, Gibbons HR, Smyrk TC, Johnsen S, Lomberk G, Faubion WA. G9a Modulates Lipid Metabolism in CD4 T Cells to Regulate Intestinal Inflammation. Gastroenterology. 2023 Feb; 164 (2):256-271.e10 Epub 2022 Oct 20
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  9. Sun Z, Behati S, Wang P, Bhagwate A, McDonough S, Wang V, Taylor W, Cunningham J, Kisiel J. Performance comparisons of methylation and structural variants from low-input whole-genome methylation sequencing. Epigenomics. 2023 Jan; 15 (1):11-19 Epub 2023 Mar 15
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  10. He Y, Wei C, Sun Z, Cunningham JM, Wang L, Wei Z, Yang P. Genome-wide methylation profiling reveals differentially methylated genes in blood DNA of small-cell lung cancer patients. Precis Clin Med. 2022 Sep; 5 (3):pbac017 Epub 2022 June 22
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  11. Sun Z, Wang X, Vedell P, Kocher JP. DNA methylation signature predicts cancer response to demethylation agents from profiling diverse cancer cell lines. Cancer Commun (Lond) 2022 Aug; 42 (8):789-792 Epub 2022 June 18
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  12. Cheung AC, Juran BD, Schlicht EM, McCauley BM, Atkinson EJ, Moore R, Heimbach JK, Watt KD, Wu TT, LaRusso NF, Gores GJ, Sun Z, Lazaridis KN. DNA methylation profile of liver tissue in end-stage cholestatic liver disease. Epigenomics. 2022 Apr; 14 (8):481-497 Epub 2022 Apr 27
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  13. Aspros KGM, Carter JM, Hoskin TL, Suman VJ, Subramaniam M, Emch MJ, Ye Z, Sun Z, Sinnwell JP, Thompson KJ, Tang X, Rodman EPB, Wang X, Nelson AW, Chernukhin I, Hamdan FH, Bruinsma ES, Carroll JS, Fernandez-Zapico ME, Johnsen SA, Kalari KR, Huang H, Leon-Ferre RA, Couch FJ, Ingle JN, Goetz MP, Hawse JR. Estrogen receptor beta repurposes EZH2 to suppress oncogenic NFkappaB/p65 signaling in triple negative breast cancer. NPJ Breast Cancer. 2022 Feb 17; 8 (1):20
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  14. Kosinsky RL, Zerche M, Kutschat AP, Nair A, Ye Z, Saul D, von Heesen M, Friton JJ, Schwarzer AC, Paglilla N, Sheikh SZ, Wegwitz F, Sun Z, Ghadimi M, Newberry RD, Sartor RB, Faubion WA, Johnsen SA. RNF20 and RNF40 regulate vitamin D receptor-dependent signaling in inflammatory bowel disease. Cell Death Differ. 2021 Nov; 28 (11):3161-3175 Epub 2021 June 04
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  15. Deng T, Hu B, Jin C, Tong Y, Zhao J, Shi Z, Zhang T, Deng L, Sun Z, Chen G, Wang Y. A novel ferroptosis phenotype-related clinical-molecular prognostic signature for hepatocellular carcinoma. J Cell Mol Med. 2021 Jul; 25 (14):6618-6633 Epub 2021 June 04
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  16. Gonzalez MM, Bamidele AO, Svingen PA, Sagstetter MR, Smyrk TC, Gaballa JM, Hamdan FH, Kosinsky RL, Gibbons HR, Sun Z, Ye Z, Nair A, Ramos GP, Braga Neto MB, Wixom AQ, Mathison AJ, Johnsen SA, Urrutia R, Faubion WA Jr. BMI1 maintains the Treg epigenomic landscape to prevent inflammatory bowel disease. J Clin Invest. 2021 Jun 15; 131(12).
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  17. Chen X, Sun Z. Novel lincRNA Discovery and Tissue-Specific Gene Expression across 30 Normal Human Tissues. Genes (Basel). 2021 Apr 21; 12(5).
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  18. Punia S, Juran BD, Ali AH, Schlicht EM, Moore RM, Sun Z, Lazaridis KN. Evaluation of circulating cell-free DNA in cholestatic liver disease using liver-specific methylation markers. BMC Gastroenterol. 2021 Apr 01; 21(1):149.
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  19. Ho AM, Winham SJ, McCauley BM, Kundakovic M, Robertson KD, Sun Z, Ordog T, Webb LM, Frye MA, Veldic M. Plasma Cell-Free DNA Methylomics of Bipolar Disorder With and Without Rapid Cycling. Front Neurosci. 2021; 15:774037. Epub 2021 Nov 30.
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  20. Mars RAT, Yang Y, Ward T, Houtti M, Priya S, Lekatz HR, Tang X, Sun Z, Kalari KR, Korem T, Bhattarai Y, Zheng T, Bar N, Frost G, Johnson AJ, van Treuren W, Han S, Ordog T, Grover M, Sonnenburg J, D'Amato M, Camilleri M, Elinav E, Segal E, Blekhman R, Farrugia G, Swann JR, Knights D, Kashyap PC. Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. Cell. 2020 Sep 17; 182(6):1460-1473.e17. Epub 2020 Sep 10.
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  21. Moore RM, Sun Z, Juran BD, Lazaridis KN. Genome-wide resolution peripheral blood methylome profiling reveals signatures for cholestatic liver disease. Epigenomics. 2020 Aug; 12 (16):1363-1375 Epub 2020 Sept 11
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  22. Bos JM, Hebl VB, Oberg AL, Sun Z, Herman DS, Teekakirikul P, Seidman JG, Seidman CE, Dos Remedios CG, Maleszewski JJ, Schaff HV, Dearani JA, Noseworthy PA, Friedman PA, Ommen SR, Brozovich FV, Ackerman MJ. Marked Up-Regulation of ACE2 in Hearts of Patients With Obstructive Hypertrophic Cardiomyopathy: Implications for SARS-CoV-2-Mediated COVID-19. Mayo Clin Proc. 2020 Jul; 95 (7):1354-1368 Epub 2020 Apr 28
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  23. An Y, Wei N, Cheng X, Li Y, Liu H, Wang J, Xu Z, Sun Z, Zhang X. MCAM abnormal expression and clinical outcome associations are highly cancer dependent as revealed through pan-cancer analysis. Brief Bioinform. 2020 Mar 23; 21 (2):709-718
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  24. Braga-Neto MB, Gaballa JM, Bamidele AO, Sarmento OF, Svingen P, Gonzalez M, Ramos GP, Sagstetter MR, Aseem S, Aseem SO, Sun Z, Faubion WA. Deregulation of Long Intergenic Non-coding RNAs in CD4+ T Cells of Lamina Propria in Crohn's Disease Through Transcriptome Profiling. J Crohns Colitis. 2020 Jan 1; 14 (1):96-109
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  25. Liu H, Zhang B, Sun Z. Spectrum of EGFR aberrations and potential clinical implications: insights from integrative pan-cancer analysis. Cancer Commun (Lond). 2020 Jan; 40 (1):43-59 Epub 2020 Feb 18
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  26. Wei N, Song Y, Zhang F, Sun Z, Zhang X. Transcriptome Profiling of Acquired Gefitinib Resistant Lung Cancer Cells Reveals Dramatically Changed Transcription Programs and New Treatment Targets. Front Oncol. 2020; 10:1424 Epub 2020 Aug 14
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  27. Klein JP, Sun Z, Staff NP. Association between ALS and retroviruses: evidence from bioinformatics analysis. BMC Bioinformatics. 2019 Dec 20; 20 (Suppl 24):680
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  28. Qin Y, Wu CW, Taylor WR, Sawas T, Burger KN, Mahoney DW, Sun Z, Yab TC, Lidgard GP, Allawi HT, Buttar NS, Smyrk TC, Iyer PG, Katzka DA, Ahlquist DA, Kisiel JB. Discovery, Validation, and Application of Novel Methylated DNA Markers for Detection of Esophageal Cancer in Plasma. Clin Cancer Res. 2019 Dec 15; 25 (24):7396-7404 Epub 2019 Sept 16
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  29. Ankam S, Rovini A, Baheti S, Hrstka R, Wu Y, Schmidt K, Wang H, Madigan N, Koenig LS, Stelzig K, Resch Z, Klein CJ, Sun Z, Staff NP. DNA methylation patterns in human iPSC-derived sensory neuronal differentiation. Epigenetics. 2019 Sep; 14 (9):927-937 Epub 2019 June 06
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  30. Zheng D, Trynda J, Sun Z, Li Z. NUCLIZE for quantifying epigenome: generating histone modification data at single-nucleosome resolution using genuine nucleosome positions. BMC Genomics. 2019 Jul 2; 20 (1):541 Epub 2019 July 02
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  31. Le-Rademacher JG, Rowland K, Atherton PJ, Dakhil C, Sun Z, Tan A, Schmidt L, Nguyen PL, Radecki Breitkopf C, Pittelkow M, Tindall D, Menon S, Jatoi A. Androgen Mediation-and Antiandrogens Mitigation-of the Epidermal Growth Factor Receptor (EGFR) Inhibitor-Induced Rash: Results From a Pilot Randomized Trial and Small Translational Case Series. Am J Hosp Palliat Care. 2019 Jun; 36 (6):519-525 Epub 2019 Jan 02
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  32. Wang X, Sun Z, Zimmermann MT, Bugrim A, Kocher JP. Predict drug sensitivity of cancer cells with pathway activity inference. BMC Med Genomics. 2019 Jan 31; 12 (Suppl 1):15
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  33. McDonough SJ, Bhagwate A, Sun Z, Wang C, Zschunke M, Gorman JA, Kopp KJ, Cunningham JM. Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods. PLoS One. 2019; 14 (4):e0211400 Epub 2019 Apr 11
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  34. Song YA, Ma T, Zhang XY, Cheng XS, Olajuyin AM, Sun ZF, Zhang XJ. Apatinib preferentially inhibits PC9 gefitinib-resistant cancer cells by inducing cell cycle arrest and inhibiting VEGFR signaling pathway. Cancer Cell Int. 2019; 19:117 Epub 2019 May 02
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  35. Luchtel RA, Dasari S, Oishi N, Pedersen MB, Hu G, Rech KL, Ketterling RP, Sidhu J, Wang X, Katoh R, Dogan A, Kip NS, Cunningham JM, Sun Z, Baheti S, Porcher JC, Said JW, Jiang L, Hamilton-Dutoit SJ, Moller MB, Norgaard P, Bennani NN, Chng WJ, Huang G, Link BK, Facchetti F, Cerhan JR, d'Amore F, Ansell SM, Feldman AL. Molecular profiling reveals immunogenic cues in anaplastic large cell lymphomas with DUSP22 rearrangements. Blood. 2018 Sep 27; 132 (13):1386-1398 Epub 2018 Aug 09
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  36. Prodduturi N, Bhagwate A, Kocher JA, Sun Z. Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine. BMC Med Genomics. 2018 Sep 14; 11 (Suppl 3):67 Epub 2018 Sept 14
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  37. Xie D, Allen MS, Marks R, Jiang G, Sun Z, Nichols F, Zhang M, Chen C, Aubry MC, Jatoi A, Garces YI, Mansfield A, Wigle D, Molina J, Deschamps C, Yang P. Nomogram prediction of overall survival for patients with non-small-cell lung cancer incorporating pretreatment peripheral blood markers. Eur J Cardiothorac Surg. 2018 Jun 1; 53 (6):1214-1222
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  38. Lomberk G, Blum Y, Nicolle R, Nair A, Gaonkar KS, Marisa L, Mathison A, Sun Z, Yan H, Elarouci N, Armenoult L, Ayadi M, Ordog T, Lee JH, Oliver G, Klee E, Moutardier V, Gayet O, Bian B, Duconseil P, Gilabert M, Bigonnet M, Garcia S, Turrini O, Delpero JR, Giovannini M, Grandval P, Gasmi M, Secq V, De Reynies A, Dusetti N, Iovanna J, Urrutia R. Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes. Nat Commun. 2018 May 17; 9 (1):1978
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  39. Zhang Y, Baheti S, Sun Z. Statistical method evaluation for differentially methylated CpGs in base resolution next-generation DNA sequencing data. Brief Bioinform. 2018 May 1; 19 (3):374-386
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  40. 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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  41. 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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  42. Li Y, Wang Z, Nair A, Song W, Yang P, Zhang X, Sun Z. Comprehensive Profiling of lincRNAs in Lung Adenocarcinoma of Never Smokers Reveals Their Roles in Cancer Development and Prognosis. Genes (Basel). 2017 Nov 13; 8 (11)
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  43. Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher JA. Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. Brief Bioinform. 2017 Nov 1; 18 (6):973-983
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  44. Baheti S, Singh P, Zhang Y, Evans J, Jensen MD, Somers VK, Kocher JA, Sun Z, Chakkera HA. Adipose tissue DNA methylome changes in development of new-onset diabetes after kidney transplantation. Epigenomics. 2017 Nov; 9 (11):1423-1435 Epub 2017 Oct 02
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  45. Sun Z, Nair A, Chen X, Prodduturi N, Wang J, Kocher JP. UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq. Sci Rep. 2017 Oct 27; 7(1):14196.
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  46. Wang J, Liu Q, Yuan S, Xie W, Liu Y, Xiang Y, Wu N, Wu L, Ma X, Cai T, Zhang Y, Sun Z, Li Y. Genetic predisposition to lung cancer: comprehensive literature integration, meta-analysis, and multiple evidence assessment of candidate-gene association studies. Sci Rep. 2017 Aug 21; 7 (1):8371
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  47. 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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  48. Sarmento OF, Svingen PA, Xiong Y, Sun Z, Bamidele AO, Mathison AJ, Smyrk TC, Nair AA, Gonzalez MM, Sagstetter MR, Baheti S, McGovern DP, Friton JJ, Papadakis KA, Gautam G, Xavier RJ, Urrutia RA, Faubion WA. The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD). J Biol Chem. 2017 Jan 13; 292 (2):706-722 Epub 2016 Dec 01
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  49. 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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  50. Xie W, Yuan S, Sun Z, Li Y. Long noncoding and circular RNAs in lung cancer: advances and perspectives. Epigenomics. 2016 Sep; 8 (9):1275-87 Epub 2016 Sept 02
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  51. Yan H, Tian S, Slager SL, Sun Z. ChIP-seq in studying epigenetic mechanisms of disease and promoting precision medicine: progresses and future directions. Epigenomics. 2016 Sep; 8 (9):1239-58 Epub 2016 June 20
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  52. White WM, Sun Z, Borowski KS, Brost BC, Davies NP, Rose CH, Garovic VD. Preeclampsia/Eclampsia candidate genes show altered methylation in maternal leukocytes of preeclamptic women at the time of delivery. Hypertens Pregnancy. 2016 Aug; 35 (3):394-404 Epub 2016 Apr 11
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  53. Allen M, Burgess JD, Ballard T, Serie D, Wang X, Younkin CS, Sun Z, Kouri N, Baheti S, Wang C, Carrasquillo MM, Nguyen T, Lincoln S, Malphrus K, Murray M, Golde TE, Price ND, Younkin SG, Schellenberg GD, Asmann Y, Ordog T, Crook J, Dickson D, Ertekin-Taner N. Gene expression, methylation and neuropathology correlations at progressive supranuclear palsy risk loci. Acta Neuropathol. 2016 Aug; 132(2):197-211. Epub 2016 Apr 26.
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  54. Zhang T, Guo L, Creighton CJ, Lu Q, Gibbons DL, Yi ES, Deng B, Molina JR, Sun Z, Yang P, Yang Y. A genetic cell context-dependent role for ZEB1 in lung cancer. Nat Commun. 2016 Jul 26; 7:12231 Epub 2016 July 26
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  55. Lee S, She J, Deng B, Kim J, de Andrade M, Na J, Sun Z, Wampfler JA, Cunningham JM, Wu Y, Limper AH, Aubry MC, Wendt C, Biterman P, Yang P, Lou Z. Multiple-level validation identifies PARK2 in the development of lung cancer and chronic obstructive pulmonary disease. Oncotarget. 2016 Jul 12; 7 (28):44211-44223
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  56. Baheti S, Kanwar R, Goelzenleuchter M, Kocher JP, Beutler AS, Sun Z. Targeted alignment and end repair elimination increase alignment and methylation measure accuracy for reduced representation bisulfite sequencing data. BMC Genomics. 2016 Feb 27; 17:149
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  57. Chen J, Just AC, Schwartz J, Hou L, Jafari N, Sun Z, Kocher JP, Baccarelli A, Lin X. CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. Bioinformatics. 2016 Feb 1; 32 (3):469-71 Epub 2015 Oct 07
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  58. Yan H, Tian S, Slager SL, Sun Z, Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016 Jan 15; 183: (2)96-109.
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  59. Wang D, Ding L, Wang L, Zhao Y, Sun Z, Karnes RJ, Zhang J, Huang H. LncRNA MALAT1 enhances oncogenic activities of EZH2 in castration-resistant prostate cancer. Oncotarget. 2015 Dec 1; 6 (38):41045-55
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  60. Liu S, Wang X, Shu J, Zhao Z, Sun Z, Luo B. Sequence analysis of EBV immune evasion gene BNLF2a in EBV associated tumors and healthy individuals from nasopharyngeal carcinoma endemic and non-endemic regions of China. J Med Virol. 2015 Nov; 87 (11):1946-52 Epub 2015 June 02
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  61. Kisiel JB, Raimondo M, Taylor WR, Yab TC, Mahoney DW, Sun Z, Middha S, Baheti S, Zou H, Smyrk TC, Boardman LA, Petersen GM, Ahlquist DA. New DNA Methylation Markers for Pancreatic Cancer: Discovery, Tissue Validation, and Pilot Testing in Pancreatic Juice. Clin Cancer Res. 2015 Oct 1; 21 (19):4473-81 Epub 2015 May 28
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  62. Sun Z, Prodduturi N, Sun SY, Thompson EA, Kocher JP. Chromosome X genomic and epigenomic aberrations and clinical implications in breast cancer by base resolution profiling. Epigenomics. 2015 Oct; 7: (7)1099-110.
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  63. Sun Z, Cunningham J, Slager S, Kocher JP. Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis. Epigenomics. 2015 Aug; 7 (5):813-28 Epub 2015 Sept 14
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  64. Jang JS, Lee A, Li J, Liyanage H, Yang Y, Guo L, Asmann YW, Li PW, Erickson-Johnson M, Sakai Y, Sun Z, Jeon HS, Hwang H, Bungum AO, Edell ES, Simon VA, Kopp KJ, Eckloff B, Oliveira AM, Wieben E, Aubry MC, Yi E, Wigle D, Diasio RB, Yang P, Jen J. Common Oncogene Mutations and Novel SND1-BRAF Transcript Fusion in Lung Adenocarcinoma from Never Smokers. Sci Rep. 2015 May 18; 5:9755
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  65. Mansfield AS, Wang L, Cunningham JM, Jen J, Kolbert CP, Sun Z, Yang P. DNA methylation and RNA expression profiles in lung adenocarcinomas of never-smokers. Cancer Genet. 2015 May; 208 (5):253-60 Epub 2014 Dec 31
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  66. Han L, Sun LL, Zhao ZZ, Chao Y, Sun ZF, Li H, Luo B. Sequence variation of epstein-barr virus (ebv) bcrf1 in lymphomas in non-endemic areas of nasopharyngeal carcinoma. Arch Virol. 2015 Feb; 160(2):441-5.
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  67. 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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  68. Sun L, Zhao Z, Liu S, Liu X, Sun Z, Luo B. Sequence Variation Analysis of Epstein-Barr Virus Nuclear Antigen 1 Gene in the Virus Associated Lymphomas of Northern China. PLoS One. 2015; 10 (10):e0140529 Epub 2015 Oct 13
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  69. Wu G, Liu X, Liu S, Shu J, Sun Z, Luo B. Epstein-Barr Virus EBNA-2 Polymorphic Patterns in Nasopharyngeal Carcinoma in Southern China. Intervirology. 2015; 58: (6)386-92.
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  70. Huang X, Yuan T, Liang M, Du M, Xia S, Dittmar R, Wang D, See W, Costello BA, Quevedo F, Tan W, Nandy D, Bevan GH, Longenbach S, Sun Z, Lu Y, Wang T, Thibodeau SN, Boardman L, Kohli M, Wang L. Exosomal miR-1290 and miR-375 as prognostic markers in castration-resistant prostate cancer. Eur Urol. 2015 Jan; 67 (1):33-41 Epub 2014 Aug 14
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  71. Necela BM, Crozier JA, Andorfer CA, Lewis-Tuffin L, Kachergus JM, Geiger XJ, Kalari KR, Serie DJ, Sun Z, Moreno-Aspitia A, O'Shannessy DJ, Maltzman JD, McCullough AE, Pockaj BA, Cunliffe HE, Ballman KV, Thompson EA, Perez EA. Folate receptor-alpha (FOLR1) expression and function in triple negative tumors. PLoS One. 2015; 10 (3):e0122209 Epub 2015 Mar 27
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  72. Walker DL, Bhagwate AV, Baheti S, Smalley RL, Hilker CA, Sun Z, Cunningham JM. DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip. Epigenomics. 2015; 7: (8)1287-302.
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  73. Necela BM, Crozier JA, Andorfer CA, Lewis-Tuffin L, Kachergus JM, Geiger XJ, Kalari KR, Serie DJ, Sun Z, Moreno-Aspitia A, O'Shannessy DJ, Maltzman JD, McCullough AE, Pockaj BA, Cunliffe HE, Ballman KV, Thompson EA, Perez EA. Correction: Folate receptor-alpha (FOLR1) expression and function in triple negative tumors. PLoS One. 2015; 10 (4):e0127133 Epub 2015 Apr 30
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  74. Wang L, Chen J, Wang C, Uuskula-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Nov 10; 42 (20):e156 Epub 2014 Sept 23
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  75. Yang Y, Jia YP, Wang Y, Wang XF, Sun ZF, Luo B. Sequence analysis of ebv immediate-early gene bzlf1 and brlf1 in lymphomas. J Med Virol. 2014 Oct; 86(10):1788-95.
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  76. Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP. HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data. BMC Bioinformatics. 2014 Aug 15; 15:280
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  77. Sun Z, Wu Y, Ordog T, Baheti S, Nie J, Duan X, Hojo K, Kocher JP, Dyck PJ, Klein CJ. Aberrant signature methylome by DNMT1 hot spot mutation in hereditary sensory and autonomic neuropathy 1E. Epigenetics. 2014 Aug; 9 (8):1184-93 Epub 2014 July 07
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  78. Sun Z, Wang L, Eckloff BW, Deng B, Wang Y, Wampfler JA, Jang J, Wieben ED, Jen J, You M, Yang P. Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers. BMC Med Genomics. 2014 Jun 04; 7:32.
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  79. Sun Z, Evans J, Bhagwate A, Middha S, Bockol M, Yan H, Kocher JP. CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data. BMC Genomics. 2014 Jun 3; 15:423 Epub 2014 June 03
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  80. Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics. 2014 Apr 1; 30 (7):1006-7 Epub 2013 Dec 18
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  81. 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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