Peer-Reviewed Publications
A complete list of publications
Underline: corresponding
- Brownstein NC, Chen YA. Predictive values, uncertainty, and interpretation of serology tests for the novel coronavirus. Sci Rep11, 5491 (2021). https://doi.org/10.1038/s41598-021-84173-1
- Phadke MS, Chen Z, Li J, Mohamed E, Davies MA, Smalley I, Duckett D, Palve V, Czerniecki BJ, Forsyth PA, Noyes D, Adeegbe DO, Eroglu Z, Nguyen KT, Tsai KY, Rix U, Burd CE, Chen YA, Rodriguez PC, Smalley KSM. Targeted therapy given after anti-PD-1 leads to prolonged responses in mouse melanoma models through sustained antitumor immunity. Cancer Immunol Res. 2021 Mar 2:canimm.CIR-20-0905-A.2020. doi: 10.1158/2326-6066.CIR-20-0905. Epub ahead of print. PMID: 33653716.
- Wang X, Yu X, Krauthammer M, Hugo W, Duan C, Kanetsky PA, Teer JK, Thompson ZJ, Kalos D, Smalley KSM, Tsai KY, Sondak VK, Chen YA, Conejo-Garcia JR. The association of MUC16 mutation with tumor mutation burden and its prognostic implications in cutaneous melanoma. Cancer Epidemiol Biomarkers Prev. 2020 Jul 1. PMID: 32611582.
- *Chen YA, Teer JK, Eroglu Z, Wu JY, Koomen JM, Karreth FA, Messina JL, Smalley KSM. Translational pathology, genomics and the development of systemic therapies for acral melanoma. Semin Cancer Biol. 2020 Apr;61:149-157. PMID: 31689494. *Co-corresponding author
- Garg SK, Ott MJ, Mostofa AGM, Chen Z, Chen YA, Kroeger J, Cao B, Mailloux AW, Agrawal A, Schaible BJ, Sarnaik A, Weber JS, Berglund AE, Mulé JJ, Markowitz J. Multi-Dimensional Flow Cytometry Analyses Reveal a Dichotomous Role for Nitric Oxide in Melanoma Patients Receiving Immunotherapy. Front Immunol. 2020;11:164.PMCID: PMC7052497.
- Li Q, Fisher K, Meng W, Fang B, Welsh E, Haura EB, Koomen JM, Eschrich SA, Fridley BL, Chen YA. GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. Bioinformatics. 2020 Jan 1;36(1):257-263. PMCID: PMC6956786.
- Prieto-Granada C, Castner N, Chen A, Li J, Yue B, Wong JY, Iyengar S, Sondak VK, Zager JS, Messina JL. Behavior of Cutaneous Adnexal Malignancies: a Single Institution Experience. Pathol Oncol Res. 2020 Jun 14. PMID: 29948620.
- McGraw KL, Cheng CH, Chen YA, Hou HA, Nilsson B, Genovese G, Cluzeau T, Pellagatti A, Przychodzen BP, Mallo M, Arenillas L, Mohamedali A, Adès L, Sallman DA, Padron E, Sokol L, Moreilhon C, Raynaud S, Tien HF, Boultwood J, Ebert BL, Sole F, Fenaux P, Mufti GJ, Maciejewski JP, Kanetsky PA, List AF. Non-del(5q) myelodysplastic syndromes-associated loci detected by SNP-array genome-wide association meta-analysis. Blood Adv. 2019 Nov 26;3(22):3579-3589. PMCID: PMC6880887.
- Smalley I, Kim E, Li J, Spence P, Wyatt CJ, Eroglu Z, Sondak VK, Messina JL, Babacan NA, Maria-Engler SS, De Armas L, Williams SL, Gatenby RA, *Chen YA, Anderson ARA, Smalley KSM. Leveraging transcriptional dynamics to improve BRAF inhibitor responses in melanoma. EBioMedicine. 2019 Oct;48:178-190. PMCID: PMC6838387. *Co-corresponding author
- Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Y Ann Chen , Koomen JM, Eschrich SA, Haura EB. Proteogenomic landscape of squamous cell lung cancer. Nat Commun. 2019 Aug 8;10(1):3578. PMCID: PMC6687710.
- Yu X, Chen YA, Conejo-Garcia JR, Chung CH, Wang X. Estimation of immune cell content in tumor using single-cell RNA-seq reference data. BMC Cancer. 2019 Jul 19;19(1):715. PMCID: PMC6642583.
- Reid BM, Permuth JB, Chen YA, Fridley BL, Iversen ES, Chen Z, Jim H, Vierkant RA, Cunningham JM, Barnholtz-Sloan JS, Narod S, Risch H, Schildkraut JM, Goode EL, Monteiro AN, Sellers TA. Genome-wide Analysis of Common Copy Number Variation and Epithelial Ovarian Cancer Risk. Cancer Epidemiol Biomarkers Prev. 2019 Jul;28(7):1117-1126. Epub 2019 Apr 4. PMCID: PMC6606353.
- Emmons MF, Faião-Flores F, Sharma R, Thapa R, Messina JL, Becker JC, Schadendorf D, Seto E, Sondak VK, Koomen JM, Chen YA, Lau EK, Wan L, Licht JD, Smalley KSM. HDAC8 Regulates a Stress Response Pathway in Melanoma to Mediate Escape from BRAF Inhibitor Therapy. Cancer Res. 2019 Jun 1;79(11):2947-2961. Epub 2019 Apr 15. PMCID: PMC6548652.
- Srikumar T, Siegel EM, Gu Y, Balagurunathan Y, Garcia AL, Chen YA, Zhou JM, Zhao X, Gillies R, Clark W, Gamenthaler A, Choi J, Shibata D. Semiautomated Measure of Abdominal Adiposity Using Computed Tomography Scan Analysis. J Surg Res. 2019 May;237:12-21. Epub 2019 Jan 14. PMID: 30694786.
- Eroglu Z, Holmen SL, Chen Q, Khushalani NI, Amaravadi R, Thomas R, Ahmed KA, Tawbi H, Chandra S, Markowitz J, Smalley I, Liu JKC, Chen YA, Najjar YG, Karreth FA, Abate-Daga D, Glitza IC, Sosman JA, Sondak VK, Bosenberg M, Herlyn M, Atkins MB, Kluger H, Margolin K, Forsyth PA, Davies MA, Smalley KSM. Melanoma central nervous system metastases: An update to approaches, challenges, and opportunities. Pigment Cell Melanoma Res. 2019 May;32(3):458-469. PMID: 30712316.
- Buckley MA, Woods NT, Tyrer JP, Mendoza-Fandiño G, Lawrenson K, Hazelett DJ, Najafabadi HS, Gjyshi A, Carvalho RS, Lyra PC Jr, Coetzee SG, Shen HC, Yang AW, Earp MA, Yoder SJ, Risch H, Chenevix-Trench G, Ramus SJ, Phelan CM, Coetzee GA, Noushmehr H, Hughes TR, Sellers TA, Goode EL, Pharoah PD, Gayther SA, Monteiro ANA, Ovarian Cancer Association Consortium. Functional Analysis and Fine Mapping of the 9p22.2 Ovarian Cancer Susceptibility Locus. Cancer Res. 2019 Feb 1;79(3):467-481. PMCID: PMC6359979.
- Eroglu Z, Chen YA, Gibney GT, Weber JS, Kudchadkar RR, Khushalani NI, Markowitz J, Brohl AS, Tetteh LF, Ramadan H, Arnone G, Li J, Zhao X, Sharma R, Darville LNF, Fang B, Smalley I, Messina JL, Koomen JM, Sondak VK, Smalley KSM. Combined BRAF and HSP90 Inhibition in Patients with Unresectable BRAFV600E-Mutant Melanoma. Clin Cancer Res. 2018 Nov 15;24(22):5516-5524. PMCID: PMC6195480.
- Lu Y, Beeghly-Fadiel A, Wu L, Guo X, Li B, Schildkraut JM, Im HK, Chen YA, ...G, Sellers TA, Pharoah PDP, Zheng W, Long J. A transcriptome-wide association study among 97,898 women to identify candidate susceptibility genes for epithelial ovarian cancer risk. Cancer Res. 2018 Sep 15;78(18):5419-5430. PMID: 30054336. PMCID: PMC6139053.
- Sloot S, Chen YA, Zhao X, Weber J, Benedict JJ, Mule JJ, Smalley KS, Weber JS, Zager JS, Forsyth P, Sondak VK, Gibney GT. Reply to Improving the survival of patients with American Joint Committee on Cancer stage III and IV melanoma. Cancer. 2018 May 15;124(10):2254-2255. PMID:29543319
- Sloot S, Chen YA, Zhao X, Weber J, Benedict JJ, Mule JJ, Smalley KS, Weber JS, Zager JS, Forsyth P, Sondak VK, Gibney GT. Improved survival of patients with melanoma brain metastases in the era of targeted BRAF and immune checkpoint therapies. Cancer. 2018 Jan 15;124(2):297-305. PMID: 29023643.
- Phadke M, Rix LLR, Smalley I, Bryant AT, Luo Y, Lawrence HR, Schaible BJ, Chen YA, Rix U, Smalley KSM. Dabrafenib inhibits the growth of BRAF-WT cancers through CDK16 and NEK9 inhibition. Mol Oncol. 2018 Jan;12(1):74-88. PMID: 29112787. PMCID: PMC5748485.
- Smith MA, Licata T, Lakhani A, Varella-Garcia M, Schildhaus HU, Vuaroqueaux V, Halmos B, Borczuk A, Chen YA, Creelan BC, Boyle TA, Haura EB. MET-GRB2 Signaling-Associated Complexes Correlate with Oncogenic MET Signaling and Sensitivity to MET Kinase Inhibitors. Clin Cancer Res. 2017 Nov 15;23(22):7084-7096. PMID: 28855353. PMCID: PMC5833309.
- Li J, Smalley I, Schell MJ, Smalley K, Chen YA. SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer. Bioinformatics. 2017 Sep 15;33(18):2951-2953. PMID: 28472395. PMCID: PMC5870537.
- 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 Apr;224(4):635-642. PMID: 28214556.
- 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 Mar;17(6). PMID: 28195392. PMCID: PMC5606153.
- Chen Y, Fisher KJ, Lloyd M, Wood ER, Coppola D, Siegel E, Shibata D, Chen YA, Koomen JM. Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins. Methods Mol Biol. 2017;1647:19-45. PMID: 28808993. PMCID: PMC5729929.
- 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.
- Brohl AS, Khushalani NI, Eroglu Z, 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. 2016 Dec 20;4:85. PMID: PMCID: PMC5170897.
- 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.
- Southey MC, Goldgar DE, Winqvist R, ..., 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. PMCID: PMC5200636.
- 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. PMCID: PMC5377910.
- Fehringer G, Kraft P, Pharoah PD, ..., 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.
- Permuth JB, Reid B, Earp M, Chen YA, ..., Goode EL, Sellers TA. Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility: results from a large-scale collaboration. Oncotarget. 2016 Nov 8;7(45):72381-72394. PMID: 27911851. PMCID: PMC5340123.
- Permuth JB, Pirie A, Chen YA, Lin HY, ..., 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 Aug 15;25(16):3600-3612. PMID: 27378695. PMCID: PMC5179948.
- 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 Nov 15;22(22):5605-5616. PMID: 27220961. PMCID: PMC5122466.
- Kim JY, Stewart PA Borne AL, Fang B, Welsh EA, Chen YA, 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. PMCID: PMC5217344.
- 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.
- 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.
- Winham SJ, Pirie A, Chen YA, ..., 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.
- 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.
- 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.
- 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, ...; Georgia Chenevix-Trench on behalf of the AOCS management group, Schildkraut JM, Ramus SJ, Goode EL, 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.
- 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, ..., 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.
- 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. 2015 Oct 27;6(33):34745-57. PMID: 26430965. PMCID: PMC4741487.
- Jim HS, Lin HY, Tyrer JP, Lawrenson K, Dennis J, Chornokur G, Chen Z, Chen AY, ..., 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.
- 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, ..., Monteiro A, Pharoah PD, 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.
- 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.
- 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, ..., 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.
- 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.
- Kuchenbaecker KB, Ramus SJ, Tyrer J, ..., 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.
- 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.
- Chornokur G, Lin HY, Tyrer JP, Lawrenson K, Dennis J, Amankwah EK, Qu X, Tsai YY, Jim HS, Chen Z, Chen AY, ..., 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.
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Permuth-Wey J, Lawrenson K, Shen HC, Velkova A, Tyrer JP, Chen Z, Lin HY, Chen YA, .., Iversen E, Schildkraut JM, Berchuck A, Fridley BL, Goode EL, Pharoah PD, Monteiro AN, 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.
- 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, ..., 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Goode EL, Chenevix-Trench G, Song H, ..., 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- Tsoi LC, Wolf B, Chen YA. The Promise of Genomic Studies on Human Diseases: From Basic Science to Clinical Application. Int J Genomics, vol. 2017, Article ID 5093167. 2017. PMCID: PMC5564070
- 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