Y. Ann Chen, PhD

Where You Are:
Y. Ann Chen, PhD

Assistant Member

Office  (813) 745-6890

Education And Training
  • PhD, Medical University of South Carolina, 2005 - Biostatistics, Bioinformatics, and Epidemiology
  • MS, University of Charleston, SC, 2001 - Marine Biology
  • BS, National Taiwan University, 1995 - Zoology


Dr. Chen’s research has focused on developing statistical methods and computational tools to incorporate multiple data sources, select biologically relevant markers, and predict clinical outcomes in a unified framework.  Her work on Bayesian methodological development of data integration for regulatory network inference and pathway and gene selection for breast cancer survival prediction facilitates the identification of deregulated pathways with therapeutic relevance in subsets of human cancer. She is working on developing statistical methods to simultaneously select relevant pathways and SNPs for cancer genome-wide association studies.  Dr. Chen’s work on nonparametric method improvement for the detection of nonlinear correlation has enabled the identification of key genes for the development of pathological conditions, which might have been missed by traditional methods to detect merely linear relationships. As a co-investigator for two studies using proteomics and other emerging technologies, two large-scale genomics studies, and one genetic epidemiology study, Dr. Chen also has works on identifying novel biomarker strategies to guide clinical decision making.  Working with Dr. Haura’s group, she is developing statistical models to integrate multiple data sources to infer the signaling network and guide treatment decision in lung cancer.

  • Remily-Wood ER, Benson K, Baz RC, Chen YA, Hussein M, Hartley-Brown MA, Sprung RW, Perez B, Liu RZ, Yoder S, Teer J, Eschrich SA, Koomen JM. Quantification of peptides from immunoglobulin constant and variable regions by LC-MRM MS for assessment of multiple myeloma patients. Proteom Clin Appl. 2014 Oct;8(10):783-795. Pubmedid: 24723328.
  • Yoshida T, Zhang G, Smith MA, Lopez AS, Bai Y, Li J, Fang B, Koomen JM, Rawal B, Fisher KJ, Chen YA, Kitano M, Morita Y, Yamaguchi H, Shibata K, Okabe T, Okamoto I, Nakagawa K, Haura EB. Tyrosine Phosphoproteomics Identifies Both Codrivers and Cotargeting Strategies for T790M-Related EGFR-TKI Resistance in Non-Small Cell Lung Cancer. Clin Cancer Res. 2014 Aug;20(15):4059-4074. Pubmedid: 24919575.
  • Wong J, Ann Chen Y, Fisher KJ, Beasley GM, Tyler DS, Zager JS. Resection of Residual Disease after Isolated Limb Infusion (ILI) Is Equivalent to a Complete Response after ILI-Alone in Advanced Extremity Melanoma. Ann Surg Oncol. 2014 Feb;21(2):650-655. Pubmedid: 24162840.
  • Weber JS, Kudchadkar RR, Yu B, Gallenstein D, Horak CE, Inzunza HD, Zhao X, Martinez AJ, Wang W, Gibney G, Kroeger J, Eysmans C, Sarnaik AA, Chen YA. Safety, efficacy, and biomarkers of nivolumab with vaccine in ipilimumab-refractory or -naive melanoma. J Clin Oncol. 2013 Dec;31(34):4311-4318. Pubmedid: 24145345. Pmcid: PMC3837092.
  • Clark W, Siegel EM, Chen YA, Zhao X, Parsons CM, Hernandez JM, Weber J, Thareja S, Choi J, Shibata D. Quantitative measures of visceral adiposity and body mass index in predicting rectal cancer outcomes after neoadjuvant chemoradiation. J Am Coll Surg. 2013 Jul;216(6):1070-1081. Pubmedid: 23523147.
  • Shan L, Chen YA, Davis L, Han G, Zhu W, Molina AD, Arango H, Lapolla JP, Hoffman MS, Sellers T, Kirby T, Nicosia SV, Sutphen R. Measurement of phospholipids may improve diagnostic accuracy in ovarian cancer. PLoS One. 2013 Apr;7(10):e46846. Pubmedid: 23082132. Pmcid: PMC3474784.
  • Wong J, Chen YA, Fisher KJ, Zager JS. Isolated limb infusion in a series of over 100 infusions: a single-center experience. Ann Surg Oncol. 2013 Apr;20(4):1121-1127. Pubmedid: 23456376.
  • Xie Y, Dixon JF, Yee OM, Zhang J, Chen YA, Deangelo S, Yellowlees P, Hendren R, Schweitzer JB. A Study on the Effectiveness of Videoconferencing on Teaching Parent Training Skills to Parents of Children with ADHD. Telemed J E Health. 2013 Mar;19(3):192-199. Pubmedid: 23405952.
  • Deneve JL, Messina JL, Marzban SS, Gonzalez RJ, Walls BM, Fisher KJ, Ann Chen Y , Wayne Cruse C, Sondak VK, Zager JS. Merkel cell carcinoma of unknown primary origin. Ann Surg Oncol. 2012 Jul;19(7):2360-2366. Pubmedid: 22271206.
  • Kucera S, Centeno BA, Springett G, Malafa MP, Chen YA, Weber J, Klapman J. Cyst Fluid Carcinoembryonic Antigen Level Is not Predictive of Invasive Cancer in Patients with Intraductal Papillary Mucinous Neoplasm of the Pancreas. JOP. 2012 Jul;13(4):409-413. Pubmedid: 22797397.
  • Mahajan K, Coppola D, Rawal B, Chen YA, Lawrence HR, Engelman RW, Lawrence NJ, Mahajan NP. Ack1-mediated androgen receptor phosphorylation modulates radiation resistance in castration-resistant prostate cancer. J Biol Chem. 2012 Jun;287(26):22112-22122. Pubmedid: 22566699. Pmcid: PMC3381169.
  • Chai CY, Deneve JL, Beasley GM, Marzban SS, Chen YA, Rawal B, Grobmyer SR, Hochwald SN, Tyler DS, Zager JS. A multi-institutional experience of repeat regional chemotherapy for recurrent melanoma of extremities. Ann Surg Oncol. 2012 May;19(5):1637-1643. Pubmedid: 22143576.
  • Paraiso KH, Haarberg HE, Wood E, Rebecca VW, Chen YA, Xiang Y, Ribas A, Lo RS, Weber JS, Sondak VK, John JK, Sarnaik AA, Koomen JM, Smalley KS. The HSP90 inhibitor XL888 overcomes BRAF inhibitor resistance mediated through diverse mechanisms. Clin Cancer Res. 2012 May;18(9):2502-2514. Pubmedid: 22351686. Pmcid: PMC3398738.
  • Mahajan K, Coppola D, Chen YA, Zhu W, Lawrence HR, Lawrence NJ, Mahajan NP. Ack1 tyrosine kinase activation correlates with pancreatic cancer progression. Am J Pathol. 2012 Apr;180(4):1386-1393. Pubmedid: 22322295. Pmcid: PMC3349895.
  • Fridley BL, Jenkins GD, Tsai YY, Song H, Bolton KL, Fenstermacher D, Tyrer J, Ramus SJ, Cunningham JM, Vierkant RA, Chen Z, Chen YA, Iversen E, Menon U, Gentry-Maharaj A, Schildkraut J, Sutphen R, Gayther SA, Hartmann LC, Pharoah PD, Sellers TA, Goode EL. Gene set analysis of survival following ovarian cancer implicates macrolide binding and intracellular signaling genes. Cancer Epidemiol Biomarkers Prev. 2012 Mar;21(3):529-536. Pubmedid: 22302016. Pmcid: PMC3297690.
  • Sellers TA, Chen YA. New lung cancer susceptibility locus identified: significance and implications for other genome-wide association studies. Cancer Discov. 2012 Feb;2(2):110-111. Pubmedid: 22585853.
  • Lin HY, Chen YA, Tsai YY, Qu X, Tseng TS, Park JY. TRM: a powerful two-stage machine learning approach for identifying SNP-SNP interactions. Ann Hum Genet. 2012 Jan;76(1):53-62. Pubmedid: 22150548. Pmcid: PMC3243917.
  • Permuth-Wey J, Thompson RC, Burton Nabors L, Olson JJ, Browning JE, Madden MH, Ann Chen Y, Egan KM. A functional polymorphism in the pre-miR-146a gene is associated with risk and prognosis in adult glioma. J Neurooncol. 2011 Dec;105(3):639-646. Pubmedid: 21744077. Pmcid: PMC3217154.
  • Egan KM, Thompson RC, Nabors LB, Olson JJ, Brat DJ, Larocca RV, Brem S, Moots PL, Madden MH, Browning JE, Chen YA. Erratum to: Cancer susceptibility variants and the risk of adult glioma in a US case-control study. J Neurooncol. 2011 Sep;104(2):543. Pubmedid: 21286782.
  • Egan KM, Thompson RC, Nabors LB, Olson JJ, Brat DJ, Larocca RV, Brem S, Moots PL, Madden MH, Browning JE, Ann Chen Y. Cancer susceptibility variants and the risk of adult glioma in a US case-control study. J Neurooncol. 2011 Sep;104(2):535-542. Pubmedid: 21203894. Pmcid: PMC3138895.
  • Permuth-Wey J, Chen Z, Tsai YY, Lin HY, Chen YA, Barnholtz-Sloan J, Birrer MJ, Chanock SJ, Cramer DW, Cunningham JM, Fenstermacher D, Fridley BL, Garcia-Closas M, Gayther SA, Gentry-Maharaj A, Gonzalez-Bosquet J, Iversen E, Jim H, McLaughlin J, Menon U, Narod SA, Phelan CM, Ramus SJ, Risch H, Song H, Sutphen R, Terry KL, Tyrer J, Vierkant RA, Wentzensen N, Lancaster JM, Cheng JQ, Berchuck A, Pharoah PD, Schildkraut JM, Goode EL, Sellers TA. MicroRNA processing and binding site polymorphisms are not replicated in the Ovarian Cancer Association Consortium. Cancer Epidemiol Biomarkers Prev. 2011 Aug;20(8):1793-1797. Pubmedid: 21636674. Pmcid: PMC3153581.
  • Permuth-Wey J, Chen YA, Tsai YY, Chen Z, Qu X, Lancaster JM, Stockwell H, Dagne G, Iversen E, Risch H, Barnholtz-Sloan J, Cunningham JM, Vierkant RA, Fridley BL, Sutphen R, McLaughlin J, Narod SA, Goode EL, Schildkraut JM, Fenstermacher D, Phelan CM, Sellers TA. Inherited variants in mitochondrial biogenesis genes may influence epithelial ovarian cancer risk. Cancer Epidemiol Biomarkers Prev. 2011 Jun;20(6):1131-1145. Pubmedid: 21447778. Pmcid: PMC3111851.
  • Permuth-Wey J, Kim D, Tsai YY, Lin HY, Chen YA, Barnholtz-Sloan J, Birrer MJ, Bloom G, Chanock SJ, Chen Z, Cramer DW, Cunningham JM, Dagne G, Ebbert-Syfrett J, Fenstermacher D, Fridley BL, Garcia-Closas M, Gayther SA, Ge W, Gentry-Maharaj A, Gonzalez-Bosquet J, Goode EL, Iversen E, Jim H, Kong W, McLaughlin J, Menon U, Monteiro AN, Narod SA, Pharoah PD, Phelan CM, Qu X, Ramus SJ, Risch H, Schildkraut JM, Song H, Stockwell H, Sutphen R, Terry KL, Tyrer J, Vierkant RA, Wentzensen N, Lancaster JM, Cheng JQ, Sellers TA. LIN28B polymorphisms influence susceptibility to epithelial ovarian cancer. Cancer Res. 2011 Jun;71(11):3896-3903. Pubmedid: 21482675. Pmcid: PMC3107389.
  • Balasis ME, Forinash KD, Chen YA, Fulp WJ, Coppola D, Hamilton AD, Cheng JQ, Sebti SM. Combination of farnesyltransferase and Akt inhibitors is synergistic in breast cancer cells and causes significant breast tumor regression in ErbB2 transgenic mice. Clin Cancer Res. 2011 May;17(9):2852-2862. Pubmedid: 21536547. Pmcid: PMC3156694.
  • Paraiso KH, Xiang Y, Rebecca VW, Abel EV, Chen YA, Munko AC, Wood E, Fedorenko IV, Sondak VK, Anderson AR, Ribas A, Palma MD, Nathanson KL, Koomen JM, Messina JL, Smalley KS. PTEN loss confers BRAF inhibitor resistance to melanoma cells through the suppression of BIM expression. Cancer Res. 2011 Apr;71(7):2750-2760. Pubmedid: 21317224. Pmcid: PMC3070772.
  • Mahajan K, Coppola D, Challa S, Fang B, Chen YA, Zhu W, Lopez AS, Koomen J, Engelman RW, Rivera C, Muraoka-Cook RS, Cheng JQ, Schönbrunn E, Sebti SM, Earp HS, Mahajan NP. Ack1 mediated AKT/PKB tyrosine 176 phosphorylation regulates its activation. PLoS One. 2011 Jan;5(3):e9646. Pubmedid: 20333297. Pmcid: PMC2841635.
  • Goode EL, Chenevix-Trench G, Song H, Ramus SJ, Notaridou M, Lawrenson K, Widschwendter M, Vierkant RA, Larson MC, Kjaer SK, Birrer MJ, Berchuck A, Schildkraut J, Tomlinson I, Kiemeney LA, Cook LS, Gronwald J, Garcia-Closas M, Gore ME, Campbell I, Whittemore AS, Sutphen R, Phelan C, Anton-Culver H, Pearce CL, Lambrechts D, Rossing MA, Chang-Claude J, Moysich KB, Goodman MT, Dörk T, Nevanlinna H, Ness RB, Rafnar T, Hogdall C, Hogdall E, Fridley BL, Cunningham JM, Sieh W, McGuire V, Godwin AK, Cramer DW, Hernandez D, Levine D, Lu K, Iversen ES, Palmieri RT, Houlston R, van Altena AM, Aben KK, Massuger LF, Brooks-Wilson A, Kelemen LE, Le ND, Jakubowska A, Lubinski J, Medrek K, Stafford A, Easton DF, Tyrer J, Bolton KL, Harrington P, Eccles D, Chen A, Molina AN, Davila BN, Arango H, Tsai YY, Chen Z, Risch HA, McLaughlin J, Narod SA, Ziogas A, Brewster W, Gentry-Maharaj A, Menon U, Wu AH, Stram DO, Pike MC, Beesley J, Webb PM, Chen X, Ekici AB, Thiel FC, Beckmann MW, Yang H, Wentzensen N, Lissowska J, Fasching PA, Despierre E, Amant F, Vergote I, Doherty J, Hein R, Wang-Gohrke S, Lurie G, Carney ME, Thompson PJ, Runnebaum I, Hillemanns P, Dürst M, Antonenkova N, Bogdanova N, Leminen A, Butzow R, Heikkinen T, Stefansson K, Sulem P, Besenbacher S, Sellers TA, Gayther SA, Pharoah PD. A genome-wide association study identifies susceptibility loci for ovarian cancer at 2q31 and 8q24. Nat Genetics. 2010 Oct;42(10):874-879. Pubmedid: 20852632. Pmcid: PMC3020231.
  • Mahajan K, Challa S, Coppola D, Lawrence H, Luo Y, Gevariya H, Zhu W, Chen YA, Lawrence NJ, Mahajan NP. Effect of Ack1 tyrosine kinase inhibitor on ligand-independent androgen receptor activity. Prostate. 2010 Sep;70(12):1274-1285. Pubmedid: 20623637. Pmcid: PMC3953126.
  • Chen YA, Almeida JS, Richards AJ, Müller P, Carroll RJ, Rohrer B. A nonparametric approach to detect nonlinear correlation in gene expression. J Comput Graph Stat. 2010 Sep;19(3):552-568. Pubmedid: 20877445. Pmcid: PMC2945392.
  • Hosako H, Martin GS, Barrier M, Chen YA, Ivanov IV, Mirkes PE. Gene and microRNA expression in p53-deficient day 8.5 mouse embryos. Birth Defects Res A Clin Mol Teratol. 2009 Jun;85(6):546-555. Pubmedid: 19229884.
  • Chen X, Bai F, Sokol L, Zhou J, Ren A, Painter JS, Liu J, Sallman DA, Chen YA, Yoder JA, Djeu JY, Loughran TP, Epling-Burnette PK, Wei S. A critical role for DAP10 and DAP12 in CD8+ T cell-mediated tissue damage in large granular lymphocyte leukemia. Blood. 2009 Apr;113(14):3226-3234. Pubmedid: 19075187. Pmcid: PMC2665892.
  • Robalino J, Almeida J, McKillen D, Colglazier J, Trent HF 3rd, Chen Y, PeckME, Browdy C, Chapman R, Warr G, Gross P. Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge. Physiol Genomics. 2007 Mar;29(1):44-56. Pubmedid: 17148689.
  • Mancia A, Lundqvist M, Romano T, Peden-Adams M, Fair P, Kindy M, EllisBC, Gattoni-Celli S, McKillen D, Trent H, Chen Y, Almeida J, Gross P, Chapman R, Warr G. A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions. Dev Comp Immunol. 2007;31(5):520-529. Pubmedid: 17084893.
  • Jenny M, Chapman R, Mancia A, Chen Y, Warr G, et al. A cDNA microarray for Crassostrea virginica and C. gigas. Marine Biotechnology. 2007;1:15-15.
  • Chen Y, Chou C, Lu X, Slate E, Peck K, Xu W, Voit E, Almeida J. A multivariate prediction model for microarray cross-hybridization. Bmc Bioinformatics. 2006 Mar;7:101-101. Pubmedid: 16509965.
  • McKillen D, Chen Y, Chen C, Jenny M, Trent HF 3rd, Robalino J, McLean DCJr, Gross P, Chapman R, Warr G, Almeida J. Marine genomics: a clearing-house for genomic and transcriptomic data of marineorganisms. Bmc Genomics. 2005 Mar;6(1):34-34. Pubmedid: 15760464.
  • Almeida J, McKillen D, Chen Y, Gross P, Chapman R, Warr G. Design and calibration of microarrays as universal transcriptomic environmentalbiosensors. Comp Funct Genomics. 2005;6(3):132-137. Pubmedid: 18629225.
  • Chen Y, McKillen D, Wu S, Jenny M, Chapman R, Gross P, Warr G, AlmeidaJS. Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. Bmc Bioinformatics. 2004 Dec;5(1):191-191. Pubmedid: 15585062.
  • Wenner E, Sanger D, Arendt M, Holland F, Chen Y. Variability in dissolved oxygen and other water quality variables within the National Estuarine Research Reserve System. Journal Of Coastal Research. 2004;45:17-38. Pubmedid: noPMID.
  • Pharoah PD, Tsai YY, Ramus SJ, Phelan CM, Goode EL, Lawrenson K, Buckley M, Fridley BL, Tyrer JP, Shen H, Weber R, Karevan R, Larson MC, Song H, Tessier DC, Bacot F, Vincent D, Cunningham JM, Dennis J, Dicks E, Aben KK, Anton-Culver H, Antonenkova N, Armasu SM, Baglietto L, Bandera EV, Beckmann MW, Birrer MJ, Bloom G, Bogdanova N, Brenton JD, Brinton LA, Brooks-Wilson A, Brown R, Butzow R, Campbell I, Carney ME, Carvalho RS, Chang-Claude J, Chen YA, Chen Z, Chow WH, Cicek MS, Coetzee G, Cook LS, Cramer DW, Cybulski C, Dansonka-Mieszkowska A, Despierre E, Doherty JA, Dörk T, du Bois A, Dürst M, Eccles D, Edwards R, Ekici AB, Fasching PA, Fenstermacher D, Flanagan J, Gao YT, Garcia-Closas M, Gentry-Maharaj A, Giles G, Gjyshi A, Gore M, Gronwald J, Guo Q, Halle MK, Harter P, Hein A, Heitz F, Hillemanns P, Hoatlin M, Høgdall E, Høgdall CK, Hosono S, Jakubowska A, Jensen A, Kalli KR, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Konecny GE, Krakstad C, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee N, Lee J, Leminen A, Lim BK, Lissowska J, Lubiński J, Lundvall L, Lurie G, Massuger LF, Matsuo K, McGuire V, McLaughlin JR, Menon U, Modugno F, Moysich KB, Nakanishi T, Narod SA, Ness RB, Nevanlinna H, Nickels S, Noushmehr H, Odunsi K, Olson S, Orlow I, Paul J, Pejovic T, Pelttari LM, Permuth-Wey J, Pike MC, Poole EM, Qu X, Risch HA, Rodriguez-Rodriguez L, Rossing MA, Rudolph A, Runnebaum I, Rzepecka IK, Salvesen HB, Schwaab I, Severi G, Shen H, Shridhar V, Shu XO, Sieh W, ...
  • Permuth-Wey J, Lawrenson K, Shen HC, Velkova A, Tyrer JP, Chen Z, Lin HY, Ann Chen Y, Tsai YY, Qu X, Ramus SJ, Karevan R, Lee J, Lee N, Larson MC, Aben KK, Anton-Culver H, Antonenkova N, Antoniou AC, Armasu SM, Bacot F, Baglietto L, Bandera EV, Barnholtz-Sloan J, Beckmann MW, Birrer MJ, Bloom G, Bogdanova N, Brinton LA, Brooks-Wilson A, Brown R, Butzow R, Cai Q, Campbell I, Chang-Claude J, Chanock S, Chenevix-Trench G, Cheng JQ, Cicek MS, Coetzee GA, Cook LS, Couch FJ, Cramer DW, Cunningham JM, Dansonka-Mieszkowska A, Despierre E, Doherty JA, Dörk T, du Bois A, Dürst M, Easton DF, Eccles D, Edwards R, Ekici AB, Fasching PA, Fenstermacher DA, Flanagan JM, Garcia-Closas M, Gentry-Maharaj A, Giles GG, Glasspool RM, Gonzalez-Bosquet J, Goodman MT, Gore M, Górski B, Gronwald J, Hall P, Halle MK, Harter P, Heitz F, Hillemanns P, Hoatlin M, Høgdall CK, Høgdall E, Hosono S, Jakubowska A, Jensen A, Jim H, Kalli KR, Karlan BY, Kaye SB, Kelemen LE, Kiemeney LA, Kikkawa F, Konecny GE, Krakstad C, Krüger Kjaer S, Kupryjanczyk J, Lambrechts D, Lambrechts S, Lancaster JM, Le ND, Leminen A, Levine DA, Liang D, Kiong Lim B, Lin J, Lissowska J, Lu KH, Lubiński J, Lurie G, Massuger LF, Matsuo K, McGuire V, McLaughlin JR, Menon U, Modugno F, Moysich KB, Nakanishi T, Narod SA, Nedergaard L, Ness RB, Nevanlinna H, Nickels S, Noushmehr H, Odunsi K, Olson SH, Orlow I, Paul J, Pearce CL, Pejovic T, Pelttari LM, Pike MC, Poole EM, Raska P, Renner SP, Risch HA, Rodriguez-Rodriguez L, Anne Rossing ...
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