Publications

  1. Qin Y, Wu CW, Taylor W, Sawas T, Burger KN, Mahoney DW, Sun Z, Yab TC, Lidgard GP, Allawi HT, Buttar NS, Smyrk TC, Iyer PG, Katzka D, Ahlquist DA, Kisiel JB. Discovery, validation, and application of novel methylated DNA markers for detection of esophageal cancer in plasma. Clin Cancer Res. 2019 Sep 16 Epub 2019 Sept 16
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  2. 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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  3. 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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  4. Braga-Neto MB, Gaballa JM, Bamidele AO, Sarmento OF, Phyllis S, Gonzalez M, Ramos GP, Sagstetter MR, Aseem S, 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. 2019 Jun 3 Epub 2019 June 03
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  5. 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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  6. 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. 2019 Feb 28 [Epub ahead of print]
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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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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  46. 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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  47. 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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  48. 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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  49. 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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  50. 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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  51. 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 4; 7:32 Epub 2014 June 04
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  52. 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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  53. 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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  54. 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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  55. Deng B, Sun Z, Jason W, Yang P. Increased BCAR1 predicts poor outcomes of non-small cell lung cancer in multiple-center patients. Ann Surg Oncol. 2013 Dec; 20 Suppl 3:S701-8 Epub 2013 Aug 01
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  56. Wang X, Wu G, Wang Y, Sun Z, Luo B. Gene variations of Epstein-Barr virus nuclear antigen 3A in nasopharyngeal carcinomas, gastric carcinomas and healthy carriers in northern China. Arch Virol. 2013 Oct; 158(10):2041-8. Epub 2013 Apr 21.
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  57. Borges S, Doppler H, Perez EA, Andorfer CA, Sun Z, Anastasiadis PZ, Thompson EA, Geiger XJ, Storz P. Pharmacologic reversion of epigenetic silencing of the PRKD1 promoter blocks breast tumor cell invasion and metastasis. Breast Cancer Res. 2013 Aug 23; 15(2):R66.
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  58. White WM, Brost B, Sun Z, Rose C, Craici I, Wagner SJ, Turner ST, Garovic VD. Genome-wide methylation profiling demonstrates hypermethylation in maternal leukocyte DNA in preeclamptic compared to normotensive pregnancies. Hypertens Pregnancy. 2013 Aug; 32 (3):257-69 Epub 2013 June 19
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  59. Huang X, Yuan T, Tschannen M, Sun Z, Jacob H, Du M, Liang M, Dittmar RL, Liu Y, Liang M, Kohli M, Thibodeau SN, Boardman L, Wang L. Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics. 2013 May 10; 14:319
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  60. Li Y, Tang H, Sun Z, Bungum AO, Edell ES, Lingle WL, Stoddard SM, Zhang M, Jen J, Yang P, Wang L. Network-based approach identified cell cycle genes as predictor of overall survival in lung adenocarcinoma patients. Lung Cancer. 2013 Apr; 80(1):91-8. Epub 2013 Jan 26.
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  61. Norton N, Sun Z, Asmann YW, Serie DJ, Necela BM, Bhagwate A, Jen J, Eckloff BW, Kalari KR, Thompson KJ, Carr JM, Kachergus JM, Geiger XJ, Perez EA, Thompson EA. Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors. PLoS One. 2013; 8 (11):e81925 Epub 2013 Nov 22
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  62. Sun Z, Asmann YW, Nair A, Zhang Y, Wang L, Kalari KR, Bhagwate AV, Baker TR, Carr JM, Kocher JP, Perez EA, Thompson EA. Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol. PLoS One. 2013; 8 (8):e71745 Epub 2013 Aug 19
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  63. Liu X, Wang Y, Wang X, Sun Z, Li L, Tao Q, Luo B. Epigenetic silencing of WNT5A in Epstein-Barr virus-associated gastric carcinoma. Arch Virol. 2013 Jan; 158(1):123-32. Epub 2012 Sep 23.
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  64. Hawse JR, Subramaniam M, Cicek M, Wu X, Gingery A, Grygo SB, Sun Z, Pitel KS, Lingle WL, Goetz MP, Ingle JN, Spelsberg TC. Endoxifen's molecular mechanisms of action are concentration dependent and different than that of other anti-estrogens. PLoS One. 2013; 8 (1):e54613 Epub 2013 Jan 28
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  65. Lanza IR, Zabielski P, Klaus KA, Morse DM, Heppelmann CJ, Bergen HR 3rd, Dasari S, Walrand S, Short KR, Johnson ML, Robinson MM, Schimke JM, Jakaitis DR, Asmann YW, Sun Z, Nair KS. Chronic caloric restriction preserves mitochondrial function in senescence without increasing mitochondrial biogenesis. Cell Metab. 2012 Dec 5; 16 (6):777-88
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  66. Niu N, Schaid DJ, Abo RP, Kalari K, Fridley BL, Feng Q, Jenkins G, Batzler A, Brisbin AG, Cunningham JM, Li L, Sun Z, Yang P, Wang L. Genetic association with overall survival of taxane-treated lung cancer patients - a genome-wide association study in human lymphoblastoid cell lines followed by a clinical association study. BMC Cancer. 2012 Sep 24; 12:422 Epub 2012 Sept 24
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  67. Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics. 2012 Aug 15; 28 (16):2180-1 Epub 2012 June 10
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  68. Jang JS, Jeon HS, Sun Z, Aubry MC, Tang H, Park CH, Rakhshan F, Schultz DA, Kolbert CP, Lupu R, Park JY, Harris CC, Yang P, Jen J. Increased miR-708 expression in NSCLC and its association with poor survival in lung adenocarcinoma from never smokers. Clin Cancer Res. 2012 Jul 1; 18 (13):3658-67 Epub 2012 May 09
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  69. White WM, Brost BC, Sun Z, Rose C, Craici I, Wagner SJ, Turner S, Garovic VD. Normal early pregnancy: a transient state of epigenetic change favoring hypomethylation. Epigenetics. 2012 Jul; 7 (7):729-34 Epub 2012 July 01
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  70. White W, Brost B, O'Brien J, Rose C, Davies N, Sun Z, Turner S, Garovic V. OS052. Preeclampsia candidate genes differentially methylated in maternal leukocyte DNA. Pregnancy Hypertens. 2012 Jul; 2(3):205. Epub 2012 Jun 13.
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  71. Wang Y, Wang XF, Sun ZF, Luo B. Unique variations of Epstein-Barr virus-encoded BARF1 gene in nasopharyngeal carcinoma biopsies. Virus Res. 2012 Jun; 166(1-2):23-30. Epub 2012 Mar 01.
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  72. Mahapatra S, Klee EW, Young CY, Sun Z, Jimenez RE, Klee GG, Tindall DJ, Donkena KV. Global methylation profiling for risk prediction of prostate cancer. Clin Cancer Res. 2012 May 15; 18(10):2882-95.
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  73. Dutta T, Chai HS, Ward LE, Ghosh A, Persson XM, Ford GC, Kudva YC, Sun Z, Asmann YW, Kocher JP, Nair KS. Concordance of changes in metabolic pathways based on plasma metabolomics and skeletal muscle transcriptomics in type 1 diabetes. Diabetes. 2012 May; 61: (5)1004-16.
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  74. de Andrade M, Li Y, Marks RS, Deschamps C, Scanlon PD, Olswold CL, Jiang R, Swensen SJ, Sun Z, Cunningham JM, Wampfler JA, Limper AH, Midthun DE, Yang P. Genetic variants associated with the risk of chronic obstructive pulmonary disease with and without lung cancer. Cancer Prev Res (Phila). 2012 Mar; 5 (3):365-73 Epub 2011 Nov 01
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  75. Luo B, Liu M, Chao Y, Wang Y, Jing Y, Sun Z. Characterization of Epstein-Barr virus gp350/220 gene variants in virus isolates from gastric carcinoma and nasopharyngeal carcinoma. Arch Virol. 2012 Feb; 157(2):207-16. Epub 2011 Oct 29.
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  76. Li L, Schaid DJ, Fridley BL, Kalari KR, Jenkins GD, Abo RP, Batzler A, Moon I, Pelleymounter L, Eckloff BW, Wieben ED, Sun Z, Yang P, Wang L. Gemcitabine metabolic pathway genetic polymorphisms and response in patients with non-small cell lung cancer. Pharmacogenet Genomics. 2012 Feb; 22 (2):105-16
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  77. Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics. 2012 Jan 15; 28 (2):277-8 Epub 2011 Nov 15
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  78. Wang X, Wang Y, Wu G, Chao Y, Sun Z, Luo B. Sequence analysis of Epstein-Barr virus EBNA-2 gene coding amino acid 148-487 in nasopharyngeal and gastric carcinomas. Virol J. 2012; 9:49. Epub 2012 Feb 21.
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  79. Fridley BL, Chalise P, Tsai YY, Sun Z, Vierkant RA, Larson MC, Cunningham JM, Iversen ES, Fenstermacher D, Barnholtz-Sloan J, Asmann Y, Risch HA, Schildkraut JM, Phelan CM, Sutphen R, Sellers TA, Goode EL. Germline copy number variation and ovarian cancer survival. Front Genet. 2012; 3:142 Epub 2012 Aug 08
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  80. Kalari KR, Rossell D, Necela BM, Asmann YW, Nair A, Baheti S, Kachergus JM, Younkin CS, Baker T, Carr JM, Tang X, Walsh MP, Chai HS, Sun Z, Hart SN, Leontovich AA, Hossain A, Kocher JP, Perez EA, Reisman DN, Fields AP, Thompson EA. Deep Sequence Analysis of Non-Small Cell Lung Cancer: Integrated Analysis of Gene Expression, Alternative Splicing, and Single Nucleotide Variations in Lung Adenocarcinomas with and without Oncogenic KRAS Mutations. Front Oncol. 2012; 2:12 Epub 2012 Feb 10
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  81. Sun Z, Chai HS, Wu Y, White WM, Donkena KV, Klein CJ, Garovic VD, Therneau TM, Kocher JP. Batch effect correction for genome-wide methylation data with Illumina Infinium platform. BMC Med Genomics. 2011 Dec 16; 4:84
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  82. Yang JD, Seol SY, Leem SH, Kim YH, Sun Z, Lee JS, Thorgeirsson SS, Chu IS, Roberts LR, Kang KJ. Genes associated with recurrence of hepatocellular carcinoma: integrated analysis by gene expression and methylation profiling. J Korean Med Sci. 2011 Nov; 26 (11):1428-38 Epub 2011 Oct 27
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  83. Tan XL, Moyer AM, Fridley BL, Schaid DJ, Niu N, Batzler AJ, Jenkins GD, Abo RP, Li L, Cunningham JM, Sun Z, Yang P, Wang L. Genetic variation predicting cisplatin cytotoxicity associated with overall survival in lung cancer patients receiving platinum-based chemotherapy. Clin Cancer Res. 2011 Sep 1; 17 (17):5801-11 Epub 2011 July 20
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  84. Pankratz VS, Sun Z, Aakre J, Li Y, Johnson C, Garces YI, Aubry MC, Molina JR, Wigle DA, Yang P. Systematic evaluation of genetic variants in three biological pathways on patient survival in low-stage non-small cell lung cancer. J Thorac Oncol. 2011 Sep; 6(9):1488-95.
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  85. Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JP, Perez EA, Thompson EA. A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res. 2011 Aug; 39 (15):e100 Epub 2011 May 27
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  86. Li Y, Sun Z, Cunningham JM, Aubry MC, Wampfler JA, Croghan GA, Johnson C, Wu D, Aakre JA, Molina J, Wang L, Pankratz VS, Yang P. Genetic variations in multiple drug action pathways and survival in advanced stage non-small cell lung cancer treated with chemotherapy. Clin Cancer Res. 2011 Jun 1; 17(11):3830-40.
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  87. Wu X, Subramaniam M, Grygo SB, Sun Z, Negron V, Lingle WL, Goetz MP, Ingle JN, Spelsberg TC, Hawse JR. Estrogen receptor-beta sensitizes breast cancer cells to the anti-estrogenic actions of endoxifen. Breast Cancer Res. 2011 Mar 10; 13 (2):R27
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