Peer-Reviewed Publications

  1. Li J, Smalley I, Schell MJ, Smalley K, Chen, YA. SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer, Bioinformatics, 2017 May. PMID:28472395
  2. Mullinax JE, Kroon HM, Thompson JF, Nath N, Mosca PJ, Farma JM, Bhati R, Hardmann D, Sileno S, O'Donoghue C, Perez M, Naqvi SM, Chen YA, Gonzalez RJ, Zager JS. Isolated Limb Infusion as a Limb Salvage Strategy for Locally Advanced Extremity Sarcoma. J Am Coll Surg. 2017 Feb 15. PMID: 28214556.
  3. Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen JM. Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics. 2017 Feb 14. PMID: 28195392.
  4. Reid BM, Permuth JB, Chen YA, Teer JK, Monteiro AN, Chen Z, Tyrer J, Berchuck A; Ovarian Cancer Association Consortium;., Chenevix-Trench G; Australian Ovarian Cancer Study Group and the Ovarian Cancer Association Consortium;., Doherty JA, Goode EL, Iverson ES, Lawrenson K, Pearce CL, Pharoah PD, Phelan CM, Ramus SJ, Rossing MA, Schildkraut JM, Cheng JQ, Gayther SA, Sellers TA; Ovarian Cancer Association Consortium. Integration of Population-Level Genotype Data with Functional Annotation Reveals Over-Representation of Long Noncoding RNAs at Ovarian Cancer Susceptibility Loci. Cancer Epidemiol Biomarkers Prev. 2017 Jan;26(1):116-125. PMID: 28035019. PMCID: PMC5312656.
  5. Brohl AS, Khushalani NI, Eroglu A, Markowitz J, Thapa R, Chen YA, Kudchadkar R, Weber JS. A phase IB study of ipilimumab with peginterferon alfa-2b in patients with unresectable melanoma. J ImmunoTher Cancer, In press.
  6. Lin HY, Cheng CH, Chen DT, Chen YA, Park JY. Coexpression and eQTL Analyses of the Angiogenesis Gene-Gene Interaction Network in Prostate Cancer. Transl Cancer Res. 2016 Oct; 5: S951-S963.
  7. Southey MC, Goldgar DE, Winqvist R, Pylkäs K, Couch F, Tischkowitz M, Foulkes WD, ..., Sellers TA, Chen YA, Tsai YY, Chen Z, Gentry-Maharaj A, Gayther SA, Ramus SJ, Menon U, Wu AH, Pearce CL, Van Den Berg D, Pike MC, Dansonka-Mieszkowska A, Plisiecka-Halasa J, Moes-Sosnowska J, Kupryjanczyk J, Pharoah PD, Song H, Winship I, Chenevix-Trench G, Giles GG, Tavtigian SV, Easton DF, Milne RL. PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS. J Med Genet. 2016 Dec;53(12):800-811. PMID: 27595995.  
  8. Zhang G, Scarborough H, Kim J, Rozhok AI, Chen YA, Zhang X, Song L, Bai Y, Fang B, Liu RZ, Koomen J, Tan AC, Degregori J, Haura EB. Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Sci Signal. 2016 Oct 18;9(450):rs12. PMID: 27811184.
  9. Fehringer G, Kraft P, Pharoah PD, Eeles RA, Chatterjee N, Schumacher FR, Schildkraut JM, ..., Chen YA, Tyrer JP, Christiani DC, Wei Y, Shen H, Hu Z, Shu XO, Shiraishi K, Takahashi A, Bossé Y, Obeidat M, Nickle D, Timens W, Freedman ML, Li Q, Seminara D, Chanock SJ, Gong J, Peters U, Gruber SB, Amos CI, Sellers TA, Easton DF, Hunter DJ, Haiman CA, Henderson BE, Hung RJ. Cross-cancer genome-wide analysis of lung, ovary, breast, prostate and colorectal cancer reveals novel pleiotropic associations. Cancer Res. 2016 Sep 1;76(17):5103-14. PMID: 27197191. PMCID: PMC5010493.
  10. Permuth JB, Reid B, Earp M, Chen YA, Monteiro AN, Chen Z, ..., Sellers TA. Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility: results from a large-scale collaboration. Oncotarget. 2016 Jul 12;7(45):72381-72394. PMID: 27911851.      
  11. Permuth JB, Pirie A, Chen YA, Lin HY, Reid BM, Chen Z, Monteiro A, Dennis J, Mendoza-Fandino G; AOCS Study Group; Australian Cancer Study (Ovarian Cancer), Anton-Culver H, Bandera EV, Bisogna M, Brinton L, Brooks-Wilson A, Carney ME, Chenevix-Trench G, Cook LS, Cramer DW, Cunningham JM, Cybulski C, D'Aloisio AA, Doherty JA, Earp M, Edwards RP, Fridley BL, Gayther SA, Gentry-Maharaj A, Goodman MT, Gronwald J, Hogdall E, Iversen ES, Jakubowska A, Jensen A, Karlan BY, Kelemen LE, Kjaer SK, Kraft P, Le ND, Levine DA, Lissowska J, Lubinski J, Matsuo K, Menon U, Modugno R, Moysich KB, Nakanishi T, Ness RB, Olson S, Orlow I, Pearce CL, Pejovic T, Poole EM, Ramus SJ, Rossing MA, Sandler DP, Shu XO, Song H, Taylor JA, Teo SH, Terry KL, Thompson PJ, Tworoger SS, Webb PM, Wentzensen N, Wilkens LR, Winham S, Woo YL, Wu AH, Yang H, Zheng W, Ziogas A, Phelan CM, Schildkraut JM, Berchuck A, Goode EL, Pharoah PD, Sellers TA; Ovarian Cancer Association Consortium. Exome genotyping arrays to identify rare and low frequency variants associated with epithelial ovarian cancer risk. Hum Mol Genet. 2016 Jul 4. PMID: 27378695.
  12. Haake SM, Li J, Bai Y, Kinose F, Fang B, Welsh EA, Zent R, Dhillon J, Pow-Sang JM, Chen YA, Koomen JM, Rathmell WK, Fishman M, Haura EB. Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics. Clin Cancer Res. 2016 May 24. PMID: 27220961. PMCID: PMC5122466.
  13. Kim JY, Stewart PA Borne AL, Fang B, Welsh EA, Chen A, Eschrich S, Koomen JM, Haura EB. Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes. 2016 Apr; 4(2):16.
  14. Weber J, Gibney G, Kudchadkar R, Yu B, Cheng P, Martinez AJ, Kroeger J, Richards A, McCormick L, Moberg V, Cronin H, Zhao X, Schell M, Chen YA. Phase I/II Study of Metastatic Melanoma Patients Treated with Nivolumab Who Had Progressed after Ipilimumab. Cancer Immunol Res. 2016 Apr;4(4):345-53. PMID: 26873574. PMCID: PMC4818672.
  15. Fedorenko IV, Abel EV, Koomen JM, Fang B, Wood ER, Chen YA, Fisher KJ, Iyengar S, Dahlman KB, Wargo JA, Flaherty KT, Sosman JA, Sondak VK, Messina JL, Gibney GT, Smalley KS. Fibronectin induction abrogates the BRAF inhibitor response of BRAF V600E/PTEN-null melanoma cells. Oncogene. 2016 Mar 10;35(10):1225-35. PMID: 26073081. PMCID: PMC4679729.
  16. Winham SJ, Pirie A, Chen YA, Larson MC, Fogarty ZC, Earp MA, Anton-Culver H, Bandera EV, Cramer D, Doherty JA, Goodman MT, Gronwald J, Karlan BY, Kjaer SK, Levine DA, Menon U, Ness RB, Pearce CL, Pejovic T, Rossing MA, Wentzensen N, Bean YT, Bisogna M, Brinton LA, Carney ME, Cunningham JM, Cybulski C, deFazio A, Dicks EM, Edwards RP, Gayther SA, Gentry-Maharaj A, Gore M, Iversen ES, Jensen A, Johnatty SE, Lester J, Lin HY, Lissowska J, Lubinski J, Menkiszak J, Modugno F, Moysich KB, Orlow I, Pike MC, Ramus SJ, Song H, Terry KL, Thompson PJ, Tyrer JP, van den Berg DJ, Vierkant RA, Vitonis AF, Walsh C, Wilkens LR, Wu AH, Yang H, Ziogas A, Berchuck A, Georgia Chenevix-Trench on behalf of Australian Ovarian Cancer Study G, Schildkraut JM, Permuth-Wey J, Phelan CM, Pharoah PD, Fridley BL, Sellers TA, Goode EL. Investigation of Exomic Variants Associated with Overall Survival in Ovarian Cancer. Cancer Epidemiol Biomarkers Prev. 2016 Mar;25(3):446-54. PMID: 26747452. PMCID: PMC4779669. 
  17. Earp M, Winham SJ, Larson N, Permuth JB, Sicotte H, Chien J, Anton-Culver H, Bandera EV, Berchuck A, Cook LS, Cramer D, Doherty JA, Goodman MT, Levine DA, Monteiro AN, Ness RB, Pearce CL, Rossing MA, Tworoger SS, Wentzensen N, Bisogna M, Brinton L, Brooks-Wilson A, Carney ME, Cunningham JM, Edwards RP, Fogarty ZC, Iversen ES, Kraft P, Larson MC, Le ND, Lin HY, Lissowska J, Modugno F, Moysich KB, Olson SH, Pike MC, Poole EM, Rider DN, Terry KL, Thompson PJ, van den Berg D, Vierkant RA, Vitonis AF, Wilkens LR, Wu AH, Yang HP, Ziogas A, Phelan CM, Schildkraut JM, Chen YA, Sellers TA, Fridley BL, Goode EL. A targeted genetic association study of epithelial ovarian cancer susceptibility. Oncotarget. 2016 Feb 16;7(7):7381-9. PMID: 26848776. PMCID: PMC4884925.
  18. Li J, Fang B, Kinose F, Bai Y, Kim JY, Chen YA, Rix U, Koomen JM, Haura EB. Target Identification in Small Cell Lung Cancer Via Integrated Phenotypic Screening and Activity-Based Protein Profiling. Mol Cancer Ther. 2016 Feb;15(2):334-42. PMID: 26772203. PMCID: PMC4747823.
  19. Amankwah EK, Lin HY, Tyrer JP, Lawrenson K, Dennis J, Chornokur G, Aben KK, Anton-Culver H, Antonenkova N, Bruinsma F, Bandera EV, Bean YT, Beckmann MW, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bunker CH, Butzow R, Campbell IG, Carty K, Chen Z, Chen YA, ..., Monteiro AN, Gayther SA, Narod SA, Pharoah PD, Sellers TA, Phelan CM. Epithelial-Mesenchymal Transition (EMT) Gene Variants and Epithelial Ovarian Cancer (EOC) Risk. Genet Epidemiol. 2015 Dec;39(8):689-97. PMID: 26399219. PMCID: PMC4721602.
  20. Lawrenson K, Iversen ES, Tyrer J, Weber RP, Concannon P, Hazelett DJ, Li Q, Marks JR, Berchuck A, Lee JM, Aben KK, Anton-Culver H, Antonenkova N, Australian Cancer S, Australian Ovarian Cancer Study G, Bandera EV, Bean Y, Beckmann MW, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bruinsma F, Butzow R, Campbell IG, Carty K, Chang-Claude J, Chenevix-Trench G, Chen A, Chen Z, ..., Freedman ML, Monteiro AN, Moes-Sosnowska J, Kupryjanczyk J, Pharoah PD, Gayther SA, Schildkraut JM. Common Variants at the Chek2 Gene Locus and Risk of Epithelial Ovarian Cancer. Carcinogenesis. 2015 Nov;36(11):1341-53. PMID: 26424751. PMCID: PMC4635670.
  21. Richards EJ, Permuth-Wey J, Li Y, Chen YA, Coppola D, Reid BM, Lin HY, Teer JK, Berchuck A, Birrer MJ, Lawrenson K, Monteiro AN, Schildkraut JM, Goode EL, Gayther SA, Sellers TA, Cheng JQ. A functional variant in HOXA11-AS, a novel long non-coding RNA, inhibits the oncogenic phenotype of epithelial ovarian cancer. Oncotarget. 2015 Oct 27;6(33):34745-57. PMID: 26430965. PMCID: PMC4741487.
  22. Jim HS, Lin HY, Tyrer JP, Lawrenson K, Dennis J, Chornokur G, Chen Z, Chen AY, ..., Pharoah PD, Sellers TA, Phelan CM. Common Genetic Variation in Circadian Rhythm Genes and Risk of Epithelial Ovarian Cancer (EOC). J Genet Genome Res. 2015;2(2). pii: 017. PMID: 26807442. PMCID: PMC4722961.
  23. Lawrenson K, Li Q, Kar S, Seo JH, Tyrer J, Spindler TJ, Lee J, Chen Y, Karst A, Drapkin R, Aben KK, Anton-Culver H, Antonenkova N, Australian Ovarian Cancer Study G, Baker H, Bandera EV, Bean Y, Beckmann MW, Berchuck A, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Bruinsma F, Butzow R, Campbell IG, Carty K, Chang-Claude J, Chenevix-Trench G, Chen A, ..., Gayther SA, Freedman ML. Cis-Eqtl Analysis and Functional Validation of Candidate Susceptibility Genes for High-Grade Serous Ovarian Cancer. Nat Commun. 2015 Sep 22;6:8234. PMID: 26391404. PMCID: PMC4580986.
  24. Ovarian Cancer Association C, Australian Cancer S, Australian Ovarian Cancer Study G. Genome-wide significant risk associations for mucinous ovarian carcinoma. Nat Genet. Aug 2015;47(8):888-97. PMID: 26075790. PMCID: PMC4520768. 
  25. Kar SP, Tyrer JP, Li Q, Lawrenson K, Aben KK, Anton-Culver H, Antonenkova N, Chenevix-Trench G, Baker H, Bandera E, Bean YT, Beckmann MW, Berchuck A, Bisogna M, Bjorge L, Bogdanova N, Brinton LA, Brooks-Wilson A, Butzow R, Campbell I, Carty K, Chang-Claude J, Chen YA, Chen Z, ..., Sellers TA, Monteiro AN, Freedman ML, Gayther SA, Pharoah PD. Network-based integration of GWAS and gene expression identifies a HOX-centric network associated with serous ovarian cancer risk. Cancer Epidemiol Biomarkers Prev. 2015 Oct;24(10):1574-84. PMID: 26209509. PMCID: PMC4592449.
  26. Phadke M, Gibney GT, Rich CJ, Fedorenko IV, Chen YA, Kudchadkar RR, Sondak VK, Weber J, Messina JL, Smalley KS. XL888 Limits Vemurafenib-Induced Proliferative Skin Events by Suppressing Paradoxical MAPK Activation. J Invest Dermatol. 2015 Oct;135(10):2542-4. PMID: 26039542. PMCID: PMC4567904.
  27. Kuchenbaecker KB, Ramus SJ, Tyrer J, Lee A, Shen HC, Beesley J, Lawrenson K, ...AS, Rothstein JH, McGuire V, Sieh W, Ji BT, Zheng W, Shu XO, Gao YT, Rosen B, Risch HA, McLaughlin JR, Narod SA, Monteiro AN, Chen A, Lin HY, Permuth-Wey J, Sellers TA, Tsai YY, Chen Z, Ziogas A, Anton-Culver H, Gentry-Maharaj A, Menon U, Harrington P, Lee AW, Wu AH, Pearce CL, Coetzee G, Pike MC, Dansonka-Mieszkowska A, Timorek A, Rzepecka IK, Kupryjanczyk J, Freedman M, Noushmehr H, Easton DF, Offit K, Couch FJ, Gayther S, Pharoah PP, Antoniou AC, Chenevix-Trench G. Identification of six new susceptibility loci for invasive epithelial ovarian cancer. Nat Genet. Feb 2015;47(2):164-71. PMID: 25581431. PMCID: PMC4445140.
  28. Permuth-Wey J, Chen YA, Fisher K, McCarthy S, Qu X, Lloyd MC, Kasprzak A, Fournier M, Williams VL, Ghia KM, Yoder SJ, Hall L, Georgeades C, Olaoye F, Husain K, Springett GM, Chen DT, Yeatman T, Centeno BA, Klapman J, Coppola D, Malafa M. A Genome-Wide Investigation of MicroRNA Expression Identifies Biologically-Meaningful MicroRNAs That Distinguish between High-Risk and Low-Risk Intraductal Papillary Mucinous Neoplasms of the Pancreas. PLoS One. 2015;10(1):e0116869. PMID: 25607660. PMCID: PMC4301643 
  29. Chornokur G, Lin HY, Tyrer JP, Lawrenson K, Dennis J, Amankwah EK, Qu X, Tsai YY, Jim HS, Chen Z, Chen AY, ..., Pharoah PD, Sellers TA, Phelan CM. Common Genetic Variation In Cellular Transport Genes and Epithelial Ovarian Cancer (EOC) Risk. PLoS One. 2015;10(6):e0128106. PMID: 26091520. PMCID: PMC4474865.
  30. Smith MA, Hall R, Fisher K, Haake SM, Khalil F, Schabath MB, Vuaroqueaux V, Fiebig HH, Altiok S, Chen YA, Haura EB. Annotation of human cancers with EGFR signaling-associated protein complexes using proximity ligation assays. Sci Signal. Jan 13 2015;8(359):ra4. PMID: 25587191. PMCID: PMC4440040. 
  31. Bai Y, Kim JY, Watters JM, Fang B, Kinose F, Song L, Koomen JM, Teer JK, Fisher K, Chen YA, Rix U, Haura EB. Adaptive responses to dasatinib-treated lung squamous cell cancer cells harboring DDR2 mutations. Cancer Res. Dec 15 2014;74(24):7217-28. PMID: 25348954. PMCID: PMC4326029.
  32. Chen YA, Eschrich SA. (2014). Computational methods and opportunities for phosphorylation network medicine. Transl Cancer Res. 3(3): 266-278. PMID: 25530950. PMCID: PMC4271781. Editor’s Choice   
  33. Yoshida T, Zhang G, Smith MA, Lopez AS, Bai Y, Li J, Fang B, Koomen J, Rawal B, Fisher KJ, Chen YA, Kitano M, Morita Y, Yamaguchi H, Shibata K, Okabe T, Okamoto I, Nakagawa K, Haura EB. (2014). 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 1;20(15):4059-74. PMID: 24919575. PMCID: PMC4119578.
  34. Remily-Wood E, Benson K, Baz R, Chen Y, Hussein M, Hartley-Brown M, Liu R, Sprung R, Perez B, Yoder S, Teer J, Eschrich S, Koomen J. Quantification of Peptides from Immunoglobulin Constant and Variable Regions by Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry for Assessment of Multiple Myeloma Patients. Proteomics Clin Appl. 2014 Oct;8(9-10):783-95. PMID: 24723328. PMCID: PMC4302417.
  35. Wong J, Chen YA, 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. Feb 2014;21(2):650-5. PMID: 24162840. PMCID: PMC4504422.
  36. 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. Dec 1 2013;31(34):4311-8. PMID: 24145345. PMCID: PMC3837092. 
  37. 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. Jun 2013;216(6):1070-81. PMID: 23523147. PMCID: PMC4621808. 
  38. 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. Apr 2013;20(4):1121-7. PMID: 23456376. PMCID: PMC4504423.
  39. Permuth-Wey J, Lawrenson K, Shen HC, Velkova A, Tyrer JP, Chen Z, Lin HY, Chen YA,..., Sellers TA, Gayther SA. Identification and molecular characterization of a new ovarian cancer susceptibility locus at 17q21.31. Nat Commun. 2013;4:1627. PMID: 23535648. PMCID: PMC3709460.
  40. 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, Dork T, du Bois A, Durst 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, Hogdall E, Hogdall 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, Lubinski 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, Southey MC, Spellman P, Tajima K, Teo SH, Terry KL, Thompson PJ, Timorek A, Tworoger SS, van Altena AM, van den Berg D, Vergote I, Vierkant RA, Vitonis AF, Wang-Gohrke S, Wentzensen N, Whittemore AS, Wik E, Winterhoff B, Woo YL, Wu AH, Yang HP, Zheng W, Ziogas A, Zulkifli F, Goodman MT, Hall P, Easton DF, Pearce CL, Berchuck A, Chenevix-Trench G, Iversen E, Monteiro AN, Gayther SA, Schildkraut JM, Sellers TA. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer. Nat Genet. Apr 2013;45(4):362-70, 70e1-2. PMID: 23535730. PMCID: PMC3693183. 
  41. 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. Mar 2013;19(3):192-9. PMID: 23405952.
  42. Day R, Joo H, Chavan AC, Lennox KP, Chen YA, Dahl DB, Vannucci M, Tsai JW. Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment. Comput Biol Chem. Feb 2013;42:40-8. PMID: 23266765. PMCID: PMC3867305.
  43. 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. 2012;7(10):e46846. (*with equal contribution) PMID: 23082132. PMCID: PMC3474784. 
  44. 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. Jul 2012;13(4):409-13. PMID: 22797397.
  45. Deneve JL, Messina JL, Marzban SS, Gonzalez RJ, Walls BM, Fisher KJ, Chen YA, Cruse CW, Sondak VK, Zager JS. Merkel cell carcinoma of unknown primary origin. Ann Surg Oncol. Jul 2012;19(7):2360-6. PMID: 22271206. PMCID: PMC4504007.
  46. 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. Jun 22 2012;287(26):22112-22. PMID: 22566699. PMCID: PMC3381169.
  47. 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. May 2012;19(5):1637-43. PMID: 22143576. PMCID: PMC4515968.
  48. Raska P, Iversen E, Chen A, Chen Z, Fridley BL, Permuth-Wey J, Tsai YY, Vierkant RA, Goode EL, Risch H, Schildkraut JM, Sellers TA, Barnholtz-Sloan J. European American stratification in ovarian cancer case control data: the utility of genome-wide data for inferring ancestry. PLoS One. 2012;7(5):e35235. PMID: 22590501. PMCID: PMC3348917 
  49. 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. May 1 2012;18(9):2502-14. PMID: 22351686. PMCID: PMC3398738.
  50. 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. Apr 2012;180(4):1386-93. PMID: 22322295. PMCID: PMC3349895. 
  51. 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. Mar 2012;21(3):529-36. PMID: 22302016. PMCID: PMC3297690.
  52. Xie Y, Chen YA, De Bellis MD. The relationship of age, gender, and IQ with the brainstem and thalamus in healthy children and adolescents: a magnetic resonance imaging volumetric study. J Child Neurol. Mar 2012;27(3):325-31. PMID: 21954432. PMCID: PMC3252469.
  53. 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. Jan 2012;76(1):53-62. PMID: 22150548. PMCID: PMC3243917. 
  54. Stingo FC, Chen YA, Tadesse MG, Vannucci M. Incorporating Biological Information into Linear Models: A Bayesian Approach to the Selection of Pathways and Genes. Ann Appl Stat. Sep 1 2011;5(3):1978-2002. PMID: 23667412. PMCID: PMC3650864.
  55. Egan KM, Thompson RC, Nabors LB, Olson JJ, Brat DJ, Larocca RV, Brem S, Moots PL, Madden MH, Browning JE, Chen YA. Cancer susceptibility variants and the risk of adult glioma in a US case-control study. J Neurooncol. Sep 2011;104(2):535-42. PMID: 21203894. PMCID: PMC3138895. 
  56. 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. Aug 2011;20(8):1793-7. PMID: 21636674. PMCID: PMC3153581. 
  57. Pharoah PD, Palmieri RT, Ramus SJ, Gayther SA, Andrulis IL, Anton-Culver H, Antonenkova N, Antoniou AC, Goldgar D, Beattie MS, Beckmann MW, Birrer MJ, Bogdanova N, Bolton KL, Brewster W, Brooks-Wilson A, Brown R, Butzow R, Caldes T, Caligo MA, Campbell I, Chang-Claude J, Chen YA, Cook LS, Couch FJ, Cramer DW, Cunningham JM, Despierre E, Doherty JA, Dork T, Durst M, Eccles DM, Ekici AB, Easton D, Fasching PA, de Fazio A, Fenstermacher DA, Flanagan JM, Fridley BL, Friedman E, Gao B, Sinilnikova O, Gentry-Maharaj A, Godwin AK, Goode EL, Goodman MT, Gross J, Hansen TV, Harnett P, Rookus M, Heikkinen T, Hein R, Hogdall C, Hogdall E, Iversen ES, Jakubowska A, Johnatty SE, Karlan BY, Kauff ND, Kaye SB, Chenevix-Trench G, Kelemen LE, Kiemeney LA, Kjaer SK, Lambrechts D, Lapolla JP, Lazaro C, Le ND, Leminen A, Leunen K, Levine DA, Lu Y, Lundvall L, Macgregor S, Marees T, Massuger LF, McLaughlin JR, Menon U, Montagna M, Moysich KB, Narod SA, Nathanson KL, Nedergaard L, Ness RB, Nevanlinna H, Nickels S, Osorio A, Paul J, Pearce CL, Phelan CM, Pike MC, Radice P, Rossing MA, Schildkraut JM, Sellers TA, Singer CF, Song H, Stram DO, Sutphen R, Lindblom A, Terry KL, Tsai YY, van Altena AM, Vergote I, Vierkant RA, Vitonis AF, Walsh C, Wang-Gohrke S, Wappenschmidt B, Wu AH, Ziogas A, Berchuck A, Risch HA. The role of KRAS rs61764370 in invasive epithelial ovarian cancer: implications for clinical testing. Clin Cancer Res. Jun 1 2011;17(11):3742-50. PMID: 21385923. PMCID: PMC3107901.
  58. 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. Jun 1 2011;71(11):3896-903. PMID: 21482675. PMCID: PMC3107389.
  59. 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. Jun 2011;20(6):1131-45. PMID: 21447778. PMCID: PMC3111851. 
  60. 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. May 1 2011;17(9):2852-62. PMID: 21536547. PMCID: PMC3156694.
  61. Permuth-Wey J, Thompson RC, Nabors LB, Olson JJ, Browning JE, Madden MH, Chen YA, Egan KM. A functional polymorphism in the pre-miR-146a gene is associated with risk and prognosis in adult glioma. J Neurooncol. 2011;105(3):639-46. PMID: 21744077. PMCID: PMC3217154.
  62. 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. Apr 1 2011;71(7):2750-60. PMID: 21317224. PMCID: PMC3070772. 
  63. Stingo FC, Chen YA, Vannucci M, Barrier M, Mirkes PE. A Bayesian Graphical Modeling Approach to MicroRNA Regulatory Network Inference. Ann Appl Stat. 2010;4(4):2024-48. PMID: 23946863. PMCID: PMC3740979. 
  64. 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, Dork 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, Durst 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 Genet. Oct 2010;42(10):874-9. PMID: 20852632. PMCID: PMC3020231.
  65. 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. Sep 1 2010;70(12):1274-85. PMID: 20623637. PMCID: PMC3953126.
  66. Chen YA, Almeida JS, Richards AJ, Muller P, Carroll RJ, Rohrer B. A nonparametric approach to detect nonlinear correlation in gene expression. J Comput Graph Stat. Sep 1 2010;19(3):552-68. (Featured Article) PMID: 20877445. PMCID: PMC2945392.  
  67. 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, Schonbrunn E, Sebti SM, Earp HS, Mahajan NP. Ack1 mediated AKT/PKB tyrosine 176 phosphorylation regulates its activation. PLoS One. 2010;5(3):e9646. PMID: 20333297. PMCID: PMC2841635.
  68. 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. Jun 2009;85(6):546-55. PMID: 19229884. 
  69. 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. Apr 2 2009;113(14):3226-34. PMID: 19075187. PMCID: PMC2665892. 
  70. Mancia A, Lundqvist ML, Romano TA, Peden-Adams MM, Fair PA, Kindy MS, Ellis BC, Gattoni-Celli S, McKillen DJ, Trent HF, Chen YA, Almeida JS, Gross PS, Chapman RW, Warr GW. A dolphin peripheral blood leukocyte cDNA microarray for studies of immune function and stress reactions. Dev Comp Immunol. 2007;31(5):520-9. PMID: 17084893.
  71. Jenny MJ, Chapman RW, Mancia A, Chen YA, McKillen DJ, Trent H, Lang P, Escoubas JM, Bachere E, Boulo V, Liu ZJ, Gross PS, Cunningham C, Cupit PM, Tanguy A, Guo X, Moraga D, Boutet I, Huvet A, De Guise S, Almeida JS, Warr GW. A cDNA microarray for Crassostrea virginica and C. gigas. Mar Biotechnol (NY). Sep-Oct 2007;9(5):577-91. PMID: 17668266.
  72. Robalino J, Almeida JS, McKillen D, Colglazier J, Trent HF, 3rd, Chen YA, Peck ME, Browdy CL, Chapman RW, Warr GW, Gross PS. Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge. Physiol Genomics. Mar 14 2007;29(1):44-56. PMID: 17148689. 
  73. Chen YA, Chou CC, Lu X, Slate EH, Peck K, Xu W, Voit EO, Almeida JS. A multivariate prediction model for microarray cross-hybridization. BMC Bioinformatics. 2006;7:101. (Highly accessed) PMID: 16509965. PMCID: PMC1409802. 
  74. Almeida JS, McKillen DJ, Chen YA, Gross PS, Chapman RW, Warr G. Design and calibration of microarrays as universal transcriptomic environmental biosensors. Comp Funct Genomics. 2005;6(3):132-7. PMID: 18629225. PMCID: PMC2447521.
  75. McKillen DJ, Chen YA, Chen C, Jenny MJ, Trent HF, 3rd, Robalino J, McLean DC, Jr., Gross PS, Chapman RW, Warr GW, Almeida JS. Marine genomics: a clearing-house for genomic and transcriptomic data of marine organisms. BMC Genomics. 2005;6:34. (Highly accessed) PMID: 15760464. PMCID: PMC1079820. 
  76. Wenner E, Sanger D, Arendt M, Holland AF, 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.   
  77. Chen YA, McKillen DJ, Wu S, Jenny MJ, Chapman R, Gross PS, Warr GW, Almeida JS. Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information. BMC Bioinformatics. Dec 7 2004;5:191. PMID: 15585062. PMCID: PMC539232.

Invited Publications

 

  1. Sellers TA, Chen YA. New lung cancer susceptibility locus identified: significance and implications for other genome-wide association studies. Cancer Discov. Feb 2012;2(2):110-1. PMID: 22585853