Y. Ann Chen

Y. Ann Chen, PhD

Languages spoken: Mandarin Chinese, English

Academic Information

Departments Primary - Internal Medicine , Adjunct - Population Health Sciences

Divisions: Epidemiology

Lab

Education History

Undergraduate National Taiwan University
 BS
Graduate Training University of Charleston
 MS
Doctoral Training Medical University of South Carolina
 PhD
Postdoctoral Training Texas A&M University
 Postdoctoral Research Fellow

Selected Publications

Journal Article

  1. Mandula JK, Chang S, Mohamed E, Jimenez R, Sierra-Mondragon RA, Chang DC, Obermayer AN, Moran-Segura CM, Das S, Vazquez-Martinez JA, Prieto K, Chen A, Smalley KSM, Czerniecki B, Forsyth P, Koya RC, Ruffell B, Cubillos-Ruiz JR, Munn DH, Shaw TI, Conejo-Garcia JR, Rodriguez P (2022). Ablation of the endoplasmic reticulum stress kinase PERK induces paraptosis and type I interferon to promote anti-tumor T cell responses. Cancer cell, 40(10), 1145-1160.e9. (Read full article)
  2. Thompson ZJ, Teer JK, Li J, Chen Z, Welsh EA, Zhang Y, Ayoubi N, Eroglu Z, Tan AC, Smalley KSM, Chen Y (2022). Drepmel-A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment. Cells, 11(18), (Read full article)
  3. Remsing Rix LL, Sumi NJ, Hu Q, Desai B, Bryant AT, Li X, Welsh EA, Fang B, Kinose F, Kuenzi BM, Chen YA, Antonia SJ, Lovly CM, Koomen JM, Haura EB, Marusyk A, Rix (2022). IGF-binding proteins secreted by cancer-associated fibroblasts induce context-dependent drug sensitization of lung cancer cells. Science signaling, 15(747), eabj5879. (Read full article)
  4. Mahajan S, Majumder A, Stewart PA, Chen YA, Adhikari E, Fang B, Yang Y, Lawrence H, Kinose F, Koomen JM, Haura E (2022). Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer. ACS chemical biology, 17(4), 776-784. (Read full article)
  5. Li J, Smalley I, Chen Z, Wu JY, Phadke MS, Teer JK, Nguyen T, Karreth FA, Koomen JM, Sarnaik AA, Zager JS, Khushalani NI, Tarhini AA, Sondak VK, Rodriguez PC, Messina JL, Chen YA, Smalley KS (2022). Single-cell Characterization of the Cellular Landscape of Acral Melanoma Identifies Novel Targets for Immunotherapy. Clinical cancer research, 28(10), 2131-2146. (Read full article)
  6. Yu X, Cen L, Chen YA, Markowitz J, Shaw TI, Tsai KY, Conejo-Garcia JR, Wang (2022). Tumor Expression Quantitative Trait Methylation Screening Reveals Distinct CpG Panels for Deconvolving Cancer Immune Signatures. Cancer research, 82(9), 1724-1735. (Read full article)
  7. Law V, Chen Z, Vena F, Smalley I, Macaulay R, Evernden BR, Tran N, Pina Y, Puskas J, Caceres G, Bayle S, Johnson J, Liu JKC, Etame A, Vogelbaum M, Rodriguez P, Duckett D, Czerniecki B, Chen A, Smalley KSM, Forsyth P (2022). A preclinical model of patient-derived cerebrospinal fluid circulating tumor cells for experimental therapeutics in leptomeningeal disease from melanoma. Neuro-oncology, 24(10), 1673-1686. (Read full article)
  8. Nakamura K, Reid BM, Chen A, Chen Z, Goode EL, Permuth JB, Teer JK, Tyrer J, Yu X, Kanetsky PA, Pharoah PD, Gayther SA, Sellers TA, Lawrenson K, Karreth F (2022). Functional analysis of the 1p34.3 risk locus implicates GNL2 in high-grade serous ovarian cancer. American journal of human genetics, 109(1), 116-135. (Read full article)
  9. Smalley I, Chen Z, Phadke M, Li J, Yu X, Wyatt C, Evernden B, Messina JL, Sarnaik A, Sondak VK, Zhang C, Law V, Tran N, Etame A, Macaulay RJB, Eroglu Z, Forsyth PA, Rodriguez PC, Chen YA, Smalley KS (2021). Single-Cell Characterization of the Immune Microenvironment of Melanoma Brain and Leptomeningeal Metastases. Clinical cancer research, 27(14), 4109-4125. (Read full article)
  10. Smalley KSM, Teer JK, Chen YA, Wu JY, Yao J, Koomen JM, Chen WS, Rodriguez-Waitkus P, Karreth FA, Messina J (2021). A Mutational Survey of Acral Nevi. JAMA dermatology, 157(7), 831-835. (Read full article)
  11. Reid BM, Vyas S, Chen Z, Chen A, Kanetsky PA, Permuth JB, Sellers TA, Saglam (2021). Morphologic and molecular correlates of EZH2 as a predictor of platinum resistance in high-grade ovarian serous carcinoma. BMC cancer, 21(1), 714. (Read full article)
  12. Lin HY, Huang PY, Cheng CH, Tung HY, Fang Z, Berglund AE, Chen A, French-Kwawu J, Harris D, Pow-Sang J, Yamoah K, Cleveland JL, Awasthi S, Rounbehler RJ, Gerke T, Dhillon J, Eeles R, Kote-Jarai Z, Muir K, UKGPCS collaborators, Schleutker J, Pashayan N, APCB (Australian Prostate Cancer BioResource), Neal DE, Nielsen SF, Nordestgaard BG, Gronberg H, Wiklund F, Giles GG, Haiman CA, Travis RC, Stanford JL, Kibel AS, Cybulski C, Khaw KT, Maier C, Thibodeau SN, Teixeira MR, Cannon-Albright L, Brenner H, Kaneva R, Pandha H, PRACTICAL consortium, Srinivasan S, Clements J, Batra J, Park J (2021). KLK3 SNP-SNP interactions for prediction of prostate cancer aggressiveness. Scientific reports, 11(1), 9264. (Read full article)
  13. Lu Y, Beeghly-Fadiel A, Wu L, Guo X, Li B, Schildkraut JM, Im HK, Chen YA, Permuth JB, Reid BM, Teer JK, Moysich KB, Andrulis IL, Anton-Culver H, Arun BK, Bandera EV, Barkardottir RB, Barnes DR, Benitez J, Bjorge L, Brenton J, Butzow R, Caldes T, Caligo MA, Campbell I, Chang-Claude J, Claes KBM, Couch FJ, Cramer DW, Daly MB, deFazio A, Dennis J, Diez O, Domchek SM, Dörk T, Easton DF, Eccles DM, Fasching PA, Fortner RT, Fountzilas G, Friedman E, Ganz PA, Garber J, Giles GG, Godwin AK, Goldgar DE, Goodman MT, Greene MH, Gronwald J, Hamann U, Heitz F, Hildebrandt MAT, Høgdall CK, Hollestelle A, Hulick PJ, Huntsman DG, Imyanitov EN, Isaacs C, Jakubowska A, James P, Karlan BY, Kelemen LE, Kiemeney LA, Kjaer SK, Kwong A, Le ND, Leslie G, Lesueur F, Levine DA, Mattiello A, May T, McGuffog L, McNeish IA, Merritt MA, Modugno F, Montagna M, Neuhausen SL, Nevanlinna H, Nielsen FC, Nikitina-Zake L, Nussbaum RL, Offit K, Olah E, Olopade OI, Olson SH, Olsson H, Osorio A, Park SK, Parsons MT, Peeters PHM, Pejovic T, Peterlongo P, Phelan CM, Pujana MA, Ramus SJ, Rennert G, Risch H, Rodriguez GC, Rodríguez-Antona C, Romieu I, Rookus MA, Rossing MA, Rzepecka IK, Sandler DP, Schmutzler RK, Setiawan VW, Sharma P, Sieh W, Simard J, Singer CF, Song H, Southey MC, Spurdle AB, Sutphen R, Swerdlow AJ, Teixeira MR, Teo SH, Thomassen M, Tischkowitz M, Toland AE, Trichopoulou A, Tung N, Tworoger SS, van Rensburg EJ, Vanderstichele A, Vega A, Edwards DV, Webb PM, Weitzel JN, Wentzensen N, White E, Wolk A, Wu AH, Yannoukakos D, Zorn KK, Gayther SA, Antoniou AC, Berchuck A, Goode EL, Chenevix-Trench G, Sellers TA, Pharoah PDP, Zheng W, Long (2018). A Transcriptome-Wide Association Study Among 97,898 Women to Identify Candidate Susceptibility Genes for Epithelial Ovarian Cancer Risk. Cancer research, 78(18), 5419-5430. (Read full article)
  14. Phadke MS, Chen Z, Li J, Mohamed E, Davies MA, Smalley I, Duckett DR, 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 KS (2021). Targeted Therapy Given after Anti-PD-1 Leads to Prolonged Responses in Mouse Melanoma Models through Sustained Antitumor Immunity. Cancer immunology research, 9(5), 554-567. (Read full article)
  15. Sloot S, Chen YA, Zhao X, Weber JL, Benedict JJ, Mulé JJ, Smalley KS, Weber JS, Zager JS, Forsyth PA, Sondak VK, Gibney G (2018). Improved survival of patients with melanoma brain metastases in the era of targeted BRAF and immune checkpoint therapies. Cancer, 124(2), 297-305. (Read full article)
  16. Phadke M, Remsing Rix LL, Smalley I, Bryant AT, Luo Y, Lawrence HR, Schaible BJ, Chen YA, Rix U, Smalley KS (2018). Dabrafenib inhibits the growth of BRAF-WT cancers through CDK16 and NEK9 inhibition. Molecular oncology, 12(1), 74-88. (Read full article)
  17. Smith MA, Licata T, Lakhani A, Garcia MV, Schildhaus HU, Vuaroqueaux V, Halmos B, Borczuk AC, Chen YA, Creelan BC, Boyle TA, Haura E (2017). MET-GRB2 Signaling-Associated Complexes Correlate with Oncogenic MET Signaling and Sensitivity to MET Kinase Inhibitors. Clinical cancer research, 23(22), 7084-7096. (Read full article)
  18. Wang X, Yu X, Krauthammer M, Hugo W, Duan C, Kanetsky PA, Teer JK, Thompson ZJ, Kalos D, Tsai KY, Smalley KSM, Sondak VK, Chen YA, Conejo-Garcia J (2020). The Association of MUC16 Mutation with Tumor Mutation Burden and Its Prognostic Implications in Cutaneous Melanoma. Cancer epidemiology, biomarkers & prevention, 29(9), 1792-1799. (Read full article)
  19. Li J, Smalley I, Schell MJ, Smalley KSM, Chen Y (2017). SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer. Bioinformatics (Oxford, England), 33(18), 2951-2953. (Read full article)
  20. Chen YA, Teer JK, Eroglu Z, Wu JY, Koomen JM, Karreth FA, Messina JL, Smalley KS (2020). Translational pathology, genomics and the development of systemic therapies for acral melanoma. Seminars in cancer biology, 61, 149-157. (Read full article)
  21. 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 J (2017). Isolated Limb Infusion as a Limb Salvage Strategy for Locally Advanced Extremity Sarcoma. Journal of the American College of Surgeons, 224(4), 635-642. (Read full article)
  22. Stewart PA, Fang B, Slebos RJ, Zhang G, Borne AL, Fellows K, Teer JK, Chen YA, Welsh E, Eschrich SA, Haura EB, Koomen J (2017). Relative protein quantification and accessible biology in lung tumor proteomes from four LC-MS/MS discovery platforms. Proteomics, 17(6), (Read full article)
  23. Chen Y, Fisher KJ, Lloyd M, Wood ER, Coppola D, Siegel E, Shibata D, Chen YA, Koomen J (2017). Multiplexed Liquid Chromatography-Multiple Reaction Monitoring Mass Spectrometry Quantification of Cancer Signaling Proteins. Methods in molecular biology (Clifton, N.J.), 1647, 19-45. (Read full article)
  24. 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 (2020). Multi-Dimensional Flow Cytometry Analyses Reveal a Dichotomous Role for Nitric Oxide in Melanoma Patients Receiving Immunotherapy. Frontiers in immunology, 11, 164. (Read full article)
  25. Reid BM, Permuth JB, Chen YA, Teer JK, Monteiro AN, Chen Z, Tyrer J, Berchuck A, Chenevix-Trench G, 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, Australian Ovarian Cancer Study Group and the Ovarian Cancer Association Consortium, Ovarian Cancer Association Consortiu (2017). Integration of Population-Level Genotype Data with Functional Annotation Reveals Over-Representation of Long Noncoding RNAs at Ovarian Cancer Susceptibility Loci. Cancer epidemiology, biomarkers & prevention, 26(1), 116-125. (Read full article)
  26. Brohl AS, Khushalani NI, Eroglu Z, Markowitz J, Thapa R, Chen YA, Kudchadkar R, Weber J (2016). A phase IB study of ipilimumab with peginterferon alfa-2b in patients with unresectable melanoma. Journal for immunotherapy of cancer, 4, 85. (Read full article)
  27. Li Q, Fisher K, Meng W, Fang B, Welsh E, Haura EB, Koomen JM, Eschrich SA, Fridley BL, Chen Y (2020). GMSimpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. Bioinformatics (Oxford, England), 36(1), 257-263. (Read full article)
  28. Prieto-Granada C, Castner N, Chen A, Li J, Yue B, Wong JY, Iyengar S, Sondak VK, Zager JS, Messina J (2020). Behavior of Cutaneous Adnexal Malignancies: a Single Institution Experience. Pathology oncology research, 26(1), 239-244. (Read full article)
  29. 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 A (2019). Non-del(5q) myelodysplastic syndromes-associated loci detected by SNP-array genome-wide association meta-analysis. Blood advances, 3(22), 3579-3589. (Read full article)
  30. Southey MC, Goldgar DE, Winqvist R, Pylkäs K, Couch F, Tischkowitz M, Foulkes WD, Dennis J, Michailidou K, van Rensburg EJ, Heikkinen T, Nevanlinna H, Hopper JL, Dörk T, Claes KB, Reis-Filho J, Teo ZL, Radice P, Catucci I, Peterlongo P, Tsimiklis H, Odefrey FA, Dowty JG, Schmidt MK, Broeks A, Hogervorst FB, Verhoef S, Carpenter J, Clarke C, Scott RJ, Fasching PA, Haeberle L, Ekici AB, Beckmann MW, Peto J, Dos-Santos-Silva I, Fletcher O, Johnson N, Bolla MK, Sawyer EJ, Tomlinson I, Kerin MJ, Miller N, Marme F, Burwinkel B, Yang R, Guénel P, Truong T, Menegaux F, Sanchez M, Bojesen S, Nielsen SF, Flyger H, Benitez J, Zamora MP, Perez JI, Menéndez P, Anton-Culver H, Neuhausen S, Ziogas A, Clarke CA, Brenner H, Arndt V, Stegmaier C, Brauch H, Brüning T, Ko YD, Muranen TA, Aittomäki K, Blomqvist C, Bogdanova NV, Antonenkova NN, Lindblom A, Margolin S, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Spurdle AB, Investigators K, Australian Ovarian Cancer Study Group, Wauters E, Smeets D, Beuselinck B, Floris G, Chang-Claude J, Rudolph A, Seibold P, Flesch-Janys D, Olson JE, Vachon C, Pankratz VS, McLean C, Haiman CA, Henderson BE, Schumacher F, Le Marchand L, Kristensen V, Alnæs GG, Zheng W, Hunter DJ, Lindstrom S, Hankinson SE, Kraft P, Andrulis I, Knight JA, Glendon G, Mulligan AM, Jukkola-Vuorinen A, Grip M, Kauppila S, Devilee P, Tollenaar RA, Seynaeve C, Hollestelle A, Garcia-Closas M, Figueroa J, Chanock SJ, Lissowska J, Czene K, Darabi H, Eriksson M, Eccles DM, Rafiq S, Tapper WJ, Gerty SM, Hooning MJ, Martens JW, Collée JM, Tilanus-Linthorst M, Hall P, Li J, Brand JS, Humphreys K, Cox A, Reed MW, Luccarini C, Baynes C, Dunning AM, Hamann U, Torres D, Ulmer HU, Rüdiger T, Jakubowska A, Lubinski J, Jaworska K, Durda K, Slager S, Toland AE, Ambrosone CB, Yannoukakos D, Swerdlow A, Ashworth A, Orr N, Jones M, González-Neira A, Pita G, Alonso MR, Álvarez N, Herrero D, Tessier DC, Vincent D, Bacot F, Simard J, Dumont M, Soucy P, Eeles R, Muir K, Wiklund F, Gronberg H, Schleutker J, Nordestgaard BG, Weischer M, Travis RC, Neal D, Donovan JL, Hamdy FC, Khaw KT, Stanford JL, Blot WJ, Thibodeau S, Schaid DJ, Kelley JL, Maier C, Kibel AS, Cybulski C, Cannon-Albright L, Butterbach K, Park J, Kaneva R, Batra J, Teixeira MR, Kote-Jarai Z, Olama AA, Benlloch S, Renner SP, Hartmann A, Hein A, Ruebner M, Lambrechts D, Van Nieuwenhuysen E, Vergote I, Lambretchs S, Doherty JA, Rossing MA, Nickels S, Eilber U, Wang-Gohrke S, Odunsi K, Sucheston-Campbell LE, Friel G, Lurie G, Killeen JL, Wilkens LR, Goodman MT, Runnebaum I, Hillemanns PA, Pelttari LM, Butzow R, Modugno F, Edwards RP, Ness RB, Moysich KB, du Bois A, Heitz F, Harter P, Kommoss S, Karlan BY, Walsh C, Lester J, Jensen A, Kjaer SK, Høgdall E, Peissel B, Bonanni B, Bernard L, Goode EL, Fridley BL, Vierkant RA, Cunningham JM, Larson MC, Fogarty ZC, Kalli KR, Liang D, Lu KH, Hildebrandt MA, Wu X, Levine DA, Dao F, Bisogna M, Berchuck A, Iversen ES, Marks JR, Akushevich L, Cramer DW, Schildkraut J, Terry KL, Poole EM, Stampfer M, Tworoger SS, Bandera EV, Orlow I, Olson SH, Bjorge L, Salvesen HB, van Altena AM, Aben KK, Kiemeney LA, Massuger LF, Pejovic T, Bean Y, Brooks-Wilson A, Kelemen LE, Cook LS, Le ND, Górski B, Gronwald J, Menkiszak J, Høgdall CK, Lundvall L, Nedergaard L, Engelholm SA, Dicks E, Tyrer J, Campbell I, McNeish I, Paul J, Siddiqui N, Glasspool R, Whittemore AS, Rothstein JH, McGuire V, Sieh W, Cai H, Shu XO, Teten RT, Sutphen R, McLaughlin JR, Narod SA, Phelan CM, Monteiro AN, Fenstermacher D, Lin HY, Permuth JB, 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 R (2016). PALB2, CHEK2 and ATM rare variants and cancer risk: data from COGS. Journal of medical genetics, 53(12), 800-811. (Read full article)
  31. 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 E (2016). Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Science signaling, 9(450), rs12. (Read full article)
  32. 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 KS (2019). Leveraging transcriptional dynamics to improve BRAF inhibitor responses in melanoma. EBioMedicine, 48, 178-190. (Read full article)
  33. Fehringer G, Kraft P, Pharoah PD, Eeles RA, Chatterjee N, Schumacher FR, Schildkraut JM, Lindström S, Brennan P, Bickeböller H, Houlston RS, Landi MT, Caporaso N, Risch A, Amin Al Olama A, Berndt SI, Giovannucci EL, Grönberg H, Kote-Jarai Z, Ma J, Muir K, Stampfer MJ, Stevens VL, Wiklund F, Willett WC, Goode EL, Permuth JB, Risch HA, Reid BM, Bezieau S, Brenner H, Chan AT, Chang-Claude J, Hudson TJ, Kocarnik JK, Newcomb PA, Schoen RE, Slattery ML, White E, Adank MA, Ahsan H, Aittomäki K, Baglietto L, Blomquist C, Canzian F, Czene K, Dos-Santos-Silva I, Eliassen AH, Figueroa JD, Flesch-Janys D, Fletcher O, Garcia-Closas M, Gaudet MM, Johnson N, Hall P, Hazra A, Hein R, Hofman A, Hopper JL, Irwanto A, Johansson M, Kaaks R, Kibriya MG, Lichtner P, Liu J, Lund E, Makalic E, Meindl A, Müller-Myhsok B, Muranen TA, Nevanlinna H, Peeters PH, Peto J, Prentice RL, Rahman N, Sanchez MJ, Schmidt DF, Schmutzler RK, Southey MC, Tamimi R, Travis RC, Turnbull C, Uitterlinden AG, Wang Z, Whittemore AS, Yang XR, Zheng W, Buchanan DD, Casey G, Conti DV, Edlund CK, Gallinger S, Haile RW, Jenkins M, Le Marchand L, Li L, Lindor NM, Schmit SL, Thibodeau SN, Woods MO, Rafnar T, Gudmundsson J, Stacey SN, Stefansson K, Sulem P, 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, Ovarian Cancer Association Consortium (OCAC), PRACTICAL Consortium, Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON), Colorectal Transdisciplinary (CORECT) Study, African American Breast Cancer Consortium (AABC) and African Ancestry Prostate Cancer Consortium (AAPC (2016). Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations. Cancer research, 76(17), 5103-14. (Read full article)
  34. Permuth JB, Reid B, Earp M, Chen YA, Monteiro AN, Chen Z, AOCS Study Group, Chenevix-Trench G, Fasching PA, Beckmann MW, Lambrechts D, Vanderstichele A, Van Niewenhuyse E, Vergote I, Rossing MA, Doherty JA, Chang-Claude J, Moysich K, Odunsi K, Goodman MT, Shvetsov YB, Wilkens LR, Thompson PJ, Dörk T, Bogdanova N, Butzow R, Nevanlinna H, Pelttari L, Leminen A, Modugno F, Edwards RP, Ness RB, Kelley J, Heitz F, Karlan B, Lester J, Kjaer SK, Jensen A, Giles G, Hildebrandt M, Liang D, Lu KH, Wu X, Levine DA, Bisogna M, Berchuck A, Cramer DW, Terry KL, Tworoger SS, Poole EM, Bandera EV, Fridley B, Cunningham J, Winham SJ, Olson SH, Orlow I, Bjorge L, Kiemeney LA, Massuger L, Pejovic T, Moffitt M, Le N, Cook LS, Brooks-Wilson A, Kelemen LE, Gronwald J, Lubinski J, Wentzensen N, Brinton LA, Lissowska J, Yang H, Hogdall E, Hogdall C, Lundvall L, Pharoah PD, Song H, Campbell I, Eccles D, McNeish I, Whittemore A, McGuire V, Sieh W, Rothstein J, Phelan CM, Risch H, Narod S, McLaughlin J, Anton-Culver H, Ziogas A, Menon U, Gayther S, Ramus SJ, Gentry-Maharaj A, Pearce CL, Wu AH, Kupryjanczyk J, Dansonka-Mieszkowska A, Schildkraut JM, Cheng JQ, Goode EL, Sellers T (2016). Inherited variants affecting RNA editing may contribute to ovarian cancer susceptibility: results from a large-scale collaboration. Oncotarget, 7(45), 72381-72394. (Read full article)
  35. 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, Ann Chen Y, Koomen JM, Eschrich SA, Haura E (2019). Proteogenomic landscape of squamous cell lung cancer. Nature communications, 10(1), 3578. (Read full article)
  36. 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 E (2016). Tyrosine Kinase Signaling in Clear Cell and Papillary Renal Cell Carcinoma Revealed by Mass Spectrometry-Based Phosphotyrosine Proteomics. Clinical cancer research, 22(22), 5605-5616. (Read full article)
  37. Kim JY, Stewart PA, Borne AL, Fang B, Welsh EA, Chen YA, Eschrich SA, Koomen JM, Haura E (2016). Activity-Based Proteomics Reveals Heterogeneous Kinome and ATP-Binding Proteome Responses to MEK Inhibition in KRAS Mutant Lung Cancer. Proteomes, 4(2), 16. (Read full article)
  38. 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 Y (2016). Phase I/II Study of Metastatic Melanoma Patients Treated with Nivolumab Who Had Progressed after Ipilimumab. Cancer immunology research, 4(4), 345-53. (Read full article)
  39. 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 K (2016). Fibronectin induction abrogates the BRAF inhibitor response of BRAF V600E/PTEN-null melanoma cells. Oncogene, 35(10), 1225-35. (Read full article)
  40. Yu X, Chen YA, Conejo-Garcia JR, Chung CH, Wang (2019). Estimation of immune cell content in tumor using single-cell RNA-seq reference data. BMC cancer, 19(1), 715. (Read full article)
  41. 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, Chenevix-Trench G, Schildkraut JM, Permuth-Wey J, Phelan CM, Pharoah PD, Fridley BL, Sellers TA, Goode EL, Australian Ovarian Cancer Study Grou (2016). Investigation of Exomic Variants Associated with Overall Survival in Ovarian Cancer. Cancer epidemiology, biomarkers & prevention, 25(3), 446-54. (Read full article)
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  67. Clark W, Siegel EM, Chen YA, Zhao X, Parsons CM, Hernandez JM, Weber J, Thareja S, Choi J, Shibata (2013). Quantitative measures of visceral adiposity and body mass index in predicting rectal cancer outcomes after neoadjuvant chemoradiation. Journal of the American College of Surgeons, 216(6), 1070-81. (Read full article)
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  71. Xie Y, Dixon JF, Yee OM, Zhang J, Chen YA, Deangelo S, Yellowlees P, Hendren R, Schweitzer J (2013). A study on the effectiveness of videoconferencing on teaching parent training skills to parents of children with ADHD. Telemedicine journal and e-health, 19(3), 192-9. (Read full article)
  72. Day R, Joo H, Chavan AC, Lennox KP, Chen YA, Dahl DB, Vannucci M, Tsai J (2013). Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment. Computational biology and chemistry, 42, 40-8. (Read full article)
  73. 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 (2012). Measurement of phospholipids may improve diagnostic accuracy in ovarian cancer. PloS one, 7(10), e46846. (Read full article)
  74. Kucera S, Centeno BA, Springett G, Malafa MP, Chen YA, Weber J, Klapman (2012). Cyst fluid carcinoembryonic antigen level is not predictive of invasive cancer in patients with intraductal papillary mucinous neoplasm of the pancreas. JOP, 13(4), 409-13. (Read full article)
  75. Deneve JL, Messina JL, Marzban SS, Gonzalez RJ, Walls BM, Fisher KJ, Chen YA, Cruse CW, Sondak VK, Zager J (2012). Merkel cell carcinoma of unknown primary origin. Annals of surgical oncology, 19(7), 2360-6. (Read full article)
  76. Mahajan K, Coppola D, Rawal B, Chen YA, Lawrence HR, Engelman RW, Lawrence NJ, Mahajan N (2012). Ack1-mediated androgen receptor phosphorylation modulates radiation resistance in castration-resistant prostate cancer. The Journal of biological chemistry, 287(26), 22112-22. (Read full article)
  77. Chai CY, Deneve JL, Beasley GM, Marzban SS, Chen YA, Rawal B, Grobmyer SR, Hochwald SN, Tyler DS, Zager J (2012). A multi-institutional experience of repeat regional chemotherapy for recurrent melanoma of extremities. Annals of surgical oncology, 19(5), 1637-43. (Read full article)
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  79. 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 K (2012). The HSP90 inhibitor XL888 overcomes BRAF inhibitor resistance mediated through diverse mechanisms. Clinical cancer research, 18(9), 2502-14. (Read full article)
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  82. Xie Y, Chen YA, De Bellis M (2012). The relationship of age, gender, and IQ with the brainstem and thalamus in healthy children and adolescents: a magnetic resonance imaging volumetric study. Journal of child neurology, 27(3), 325-31. (Read full article)
  83. Lin HY, Chen YA, Tsai YY, Qu X, Tseng TS, Park J (2012). TRM: a powerful two-stage machine learning approach for identifying SNP-SNP interactions. Annals of human genetics, 76(1), 53-62. (Read full article)
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  86. 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, Ovarian Cancer Association Consortium (OCAC (2011). MicroRNA processing and binding site polymorphisms are not replicated in the Ovarian Cancer Association Consortium. Cancer epidemiology, biomarkers & prevention, 20(8), 1793-7. (Read full article)
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  90. Balasis ME, Forinash KD, Chen YA, Fulp WJ, Coppola D, Hamilton AD, Cheng JQ, Sebti S (2011). Combination of farnesyltransferase and Akt inhibitors is synergistic in breast cancer cells and causes significant breast tumor regression in ErbB2 transgenic mice. Clinical cancer research, 17(9), 2852-62. (Read full article)
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  117. Phadke MS, Li J, Sriramareddy S, Rodriguez PC, Ruffell B, Luca VC, Tran TTT, Chen YA, Smalley KS (2025). Identification of anti-TIM-3 based checkpoint inhibitor combinations with activity in immunotherapy refractory melanoma models. Journal for immunotherapy of cancer, 13(8), (Read full article)

Review

  1. Kar SP, Tyrer JP, Li Q, Lawrenson K, Aben KK, Anton-Culver H, Antonenkova N, Chenevix-Trench G, Australian Cancer Study, Australian Ovarian Cancer Study Group, Baker H, Bandera EV, Bean YT, Beckmann MW, Berchuck A, Bisogna M, Bjørge L, Bogdanova N, Brinton L, Brooks-Wilson A, Butzow R, Campbell I, Carty K, Chang-Claude J, Chen YA, Chen Z, Cook LS, Cramer D, Cunningham JM, Cybulski C, Dansonka-Mieszkowska A, Dennis J, Dicks E, Doherty JA, Dörk T, du Bois A, Dürst M, Eccles D, Easton DF, Edwards RP, Ekici AB, Fasching PA, Fridley BL, Gao YT, Gentry-Maharaj A, Giles GG, Glasspool R, Goode EL, Goodman MT, Grownwald J, Harrington P, Harter P, Hein A, Heitz F, Hildebrandt MA, Hillemanns P, Hogdall E, Hogdall CK, Hosono S, Iversen ES, Jakubowska A, Paul J, Jensen A, Ji BT, Karlan BY, Kjaer SK, Kelemen LE, Kellar M, Kelley J, Kiemeney LA, Krakstad C, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le ND, Lee AW, Lele S, Leminen A, Lester J, Levine DA, Liang D, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger L, Matsuo K, McGuire V, McLaughlin JR, McNeish IA, Menon U, Modugno F, Moysich KB, Narod SA, Nedergaard L, Ness RB, Nevanlinna H, Odunsi K, Olson SH, Orlow I, Orsulic S, Weber RP, Pearce CL, Pejovic T, Pelttari LM, Permuth-Wey J, Phelan CM, Pike MC, Poole EM, Ramus SJ, Risch HA, Rosen B, Rossing MA, Rothstein JH, Rudolph A, Runnebaum IB, Rzepecka IK, Salvesen HB, Schildkraut JM, Schwaab I, Shu XO, Shvetsov YB, Siddiqui N, Sieh W, Song H, Southey MC, Sucheston-Campbell LE, Tangen IL, Teo SH, Terry KL, Thompson PJ, Timorek A, Tsai YY, Tworoger SS, van Altena AM, Van Nieuwenhuysen E, Vergote I, Vierkant RA, Wang-Gohrke S, Walsh C, Wentzensen N, Whittemore AS, Wicklund KG, Wilkens LR, Woo YL, Wu X, Wu A, Yang H, Zheng W, Ziogas A, Sellers TA, Monteiro AN, Freedman ML, Gayther SA, Pharoah P (2015). Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk. Cancer epidemiology, biomarkers & prevention, 24(10), 1574-84. (Read full article)
  2. Cheng OJ, Tran TTT, Chen YA, Tan A (2025). Harnessing Single-Cell RNA-Seq for Computational Drug Repurposing in Cancer Immunotherapy. Pharmaceuticals (Basel, Switzerland), 18(11), (Read full article)

Editorial

  1. Tsoi LC, Wolf B, Chen Y (2017). The Promise of Genomic Studies on Human Diseases: From Basic Science to Clinical Application. International journal of genomics, 2017, 5093167. (Read full article)

Letter

  1. Malachowski SJ, Moy A, Messina J, Chen YA, Sun J, Sokol L, Seminario-Vidal (2022). Mapping cutaneous T-cell lymphoma in the state of Florida: A retrospective exploratory spatial analysis of incidence patterns. Journal of the American Academy of Dermatology, 86(1), 186-188. (Read full article)
  2. Sloot S, Chen YA, Zhao X, Weber JL, Benedict JJ, Mulé JJ, Smalley KS, Weber JS, Zager JS, Forsyth PA, Sondak VK, Gibney G (2018). Reply to Improving the survival of patients with American Joint Committee on Cancer stage III and IV melanoma. Cancer, 124(10), 2254-2255. (Read full article)
  3. Phadke M, Gibney GT, Rich CJ, Fedorenko IV, Chen YA, Kudchadkar RR, Sondak VK, Weber J, Messina JL, Smalley KS (2015). XL888 Limits Vemurafenib-Induced Proliferative Skin Events by Suppressing Paradoxical MAPK Activation. The Journal of investigative dermatology, 135(10), 2542-2544. (Read full article)