Aik Choon Tan

Aik Choon Tan, PhD

Languages spoken: English

Academic Information

Departments Primary - Oncological Sciences , Adjunct - Biomedical Informatics

Education History

Fellowship Johns Hopkins University School of Medicine
 Postdoctoral Research Fellow
Research Fellow Johns Hopkins Whiting School of Engineering
 Postdoctoral Research Fellow
Doctoral Training University of Glasgow
 PhD
Undergraduate University of Technology Malaysia
 BEng

Selected Publications

Journal Article

  1. Benej M, Hoyd R, Kreamer M, Wheeler CE, Grencewicz DJ, Choueiry F, Chan CHF, Zakharia Y, Ma Q, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Robinson LA, Singer EA, Ikeguchi AP, McCarter MD, Tinoco G, Husain M, Jin N, Tan AC, Osman AEG, Eljilany I, Riedlinger G, Schneider BP, Benejova K, Kery M, Papandreou I, Zhu J, Denko N, Spakowicz D (2024). The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer. Cancer Res Commun. (Read full article)
  2. Lambert KA, Clements CM, Mukherjee N, Pacheco TR, Shellman SX, Henen MA, Vgeli B, Goldstein NB, Birlea S, Hintzsche J, Caryotakis G, Tan AC, Zhao R, Norris DA, Robinson WA, Wang Y, VanTreeck JG, Shellman YG (2024). SASH1 S519N variant links skin hyperpigmentation and premature hair graying to dysfunction of melanocyte lineage. J Invest Dermatol. (Read full article)
  3. Quandt Z, Jacob S, Fadlullah MZH, Wu C, Wu C, Huppert L, Levine LS, Sison P, Tsai KK, Chow M, Kang JH, Hwang J, Lee J, Oglesby A, Venegas J, Brintz BJ, Tan AC, Anderson MS, Rosenblum, Young A, Daud AI (2024). Phase II trial of pembrolizumab, ipilimumab, and aspirin in melanoma: clinical outcomes and translational predictors of response. . BJC Reports.
  4. Fadlullah MZH, Lin CN, Coleman S, Young A, Naqash AR, Hu-Lieskovan S, Tan AC (2023). Exploring the Landscape of Immune Checkpoint Inhibitor-Induced Adverse Events Through Big Data Mining of Pan-Cancer Clinical Trials. Oncologist, 29(5), 415-421. (Read full article)
  5. Liu X, Gillis N, Jiang C, McCofie A, Shaw TI, Tan AC, Zhao B, Wan L, Duckett DR, Teng M (2024). An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. PLoS Comput Biol, 20(2), e1011873. (Read full article)
  6. Wang C, Ma A, Li Y, McNutt ME, Zhang S, Zhu J, Hoyd R, Wheeler CE, Robinson LA, Chan CHF, Zakharia Y, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Singer EA, Ikeguchi AP, McCarter MD, Denko N, Tinoco G, Husain M, Jin N, Osman AEG, Eljilany I, Tan AC, Coleman SS, Denko L, Riedlinger G, Schneider BP, Spakowicz D, Ma Q, exORIEN Consortium (2023). A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset. Cancer Res Commun, 4(2), 293-302. (Read full article)
  7. Kerepesi C, Abushukair HM, Ricciuti B, Nassar AH, Adib E, Alessi JV, Pecci F, Rakaee M, Fadlullah MZH, Tks AM, Rodig SJ, Awad MM, Tan AC, Bakacs T, Naqash AR (2024). Association of Baseline Tumor-Specific Neoantigens and CD8(+) T-Cell Infiltration With Immune-Related Adverse Events Secondary to Immune Checkpoint Inhibitors. JCO Precis Oncol, 8, e2300439. (Read full article)
  8. Xie M, Chaudhary R, Slebos RJC, Lee K, Song F, Poole MI, Hoening DS, Noel LC, Hernandez-Prera JC, Conejo-Garcia JR, Chung CH, Tan AC (2023). Immune landscape in molecular subtypes of human papillomavirus-negative head and neck cancer. Mol Carcinog, 63(1), 120-135. (Read full article)
  9. Walker V, Jin DX, Millis SZ, Nasri E, Corao-Uribe DA, Tan AC, Fridley BL, Chen JL, Seligson ND (2023). Gene partners of the EWSR1 fusion may represent molecularly distinct entities. Transl Oncol, 38, 101795. (Read full article)
  10. Manji GA, Lee S, Del Portillo A, May M, Ana SS, Alouani E, Sender N, Negri T, Gautier K, Ge L, Fan W, Xie M, Sethi A, Schrope B, Tan AC, Park H, Oberstein PE, Shah MA, Raufi AG (2024). Chemotherapy and Immune Checkpoint Blockade for Gastric and Gastroesophageal Junction Adenocarcinoma. JAMA Oncol, 9(12), 1702-1707. (Read full article)
  11. Ravindran Menon D, Hammerlindl H, Gimenez G, Hammerlindl S, Zuegner E, Torrano J, Bordag N, Emran AA, Giam M, Denil S, Pavelka N, Tan AC, Sturm RA, Haass NK, Rancati G, Herlyn M, Magnes C, Eccles MR, Fujita M, Schaider H (2023). H3K4me3 remodeling induced acquired resistance through O-GlcNAc transferase. Drug Resist Updat, 71, 100993. (Read full article)
  12. Wahdan-Alaswad RS, Edgerton SM, Kim HM, Tan AC, Haugen BR, Liu B, Thor AD (2023). Thyroid hormone enhances estrogen-mediated proliferation and cell cycle regulatory pathways in steroid receptor-positive breast Cancer. Cell Cycle, 1-20. (Read full article)
  13. Hu M, Coleman S, Fadlullah MZH, Spakowicz D, Chung CH, Tan AC (2023). Deciphering the Tumor-Immune-Microbe Interactions in HPV-Negative Head and Neck Cancer. Genes (Basel), 14(8). (Read full article)
  14. Thomas M, Li J, King K, Persaud AK, Duah E, Vangundy Z, Hofmeister CC, Lamba JK, Tan AC, Fridley BL, Poi MJ, Seligson ND (2023). PARP1 and POLD2 as prognostic biomarkers for multiple myeloma in autologous stem cell transplant. Haematologica, 108(8), 2155-2166. (Read full article)
  15. Florou V, Floudas CS, Maoz A, Naqash AR, Norton C, Tan AC, Sokol ES, Frampton G, Soares HP, Puri S, Swami U, Wilky B, Hosein P, Trent J, Lopes GL, Park W, Garrido-Laguna I (2023). Real-world pan-cancer landscape of frameshift mutations and their role in predicting responses to immune checkpoint inhibitors in cancers with low tumor mutational burden. J Immunother Cancer, 11(8). (Read full article)
  16. Lockhart JH, Ackerman HD, Lee K, Abdalah M, Davis AJ, Hackel N, Boyle TA, Saller J, Keske A, Hnggi K, Ruffell B, Stringfield O, Cress WD, Tan AC, Flores ER (2023). Grading of lung adenocarcinomas with simultaneous segmentation by artificial intelligence (GLASS-AI). NPJ Precis Oncol, 7(1), 68. (Read full article)
  17. Alem D, Yang X, Beato F, Sarcar B, Tassielli AF, Dai R, Hogenson TL, Park MA, Jiang K, Cai J, Yuan Y, Fernandez-Zapico ME, Tan AC, Fleming JB, Xie H (2023). Translational relevance of SOS1 targeting for KRAS-mutant colorectal cancer. Mol Carcinog, 62(7), 1025-1037. (Read full article)
  18. Obermayer AN, Chang D, Nobles G, Teng M, Tan AC, Wang X, Chen YA, Eschrich S, Rodriguez PC, Grass GD, Meshinchi S, Tarhini A, Chen DT, Shaw TI (2023). PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing. BMC Bioinformatics, 24(1), 266. (Read full article)
  19. Chaudhary R, Slebos RJC, Noel LC, Song F, Poole MI, Hoening DS, Hernandez-Prera JC, Conejo-Garcia JR, Guevara-Patino JA, Wang X, Xie M, Tan AC, Chung CH (2023). EGFR Inhibition by Cetuximab Modulates Hypoxia and IFN Response Genes in Head and Neck Squamous Cell Carcinoma. Cancer Res Commun, 3(5), 896-907. (Read full article)
  20. Saba NF, Steuer CE, Ekpenyong A, McCook-Veal A, Magliocca K, Patel M, Schmitt NC, Stokes W, Bates JE, Rudra S, Remick J, McDonald M, Abousaud M, Tan AC, Fadlullah MZH, Chaudhary R, Muzaffar J, Kirtane K, Liu Y, Chen GZ, Shin DM, Teng Y, Chung CH (2023). Pembrolizumab and cabozantinib in recurrent metastatic head and neck squamous cell carcinoma: a phase 2 trial. Nat Med, 29(4), 880-887. (Read full article)
  21. Lin CN, Chung CH, Tan AC (2023). NuKit: A deep learning platform for fast nucleus segmentation of histopathological images. J Bioinform Comput Biol, 21(1), 2350002. (Read full article)
  22. Rose MM, Espinoza VL, Hoff KJ, Pike LA, Sharma V, Hofmann MC, Tan AC, Pozdeyev N, Schweppe RE (2023). BCL2L11 Induction Mediates Sensitivity to Src and MEK1/2 Inhibition in Thyroid Cancer. Cancers (Basel), 15(2). (Read full article)
  23. Bian Y, Alem D, Beato F, Hogenson TL, Yang X, Jiang K, Cai J, Ma WW, Fernandez-Zapico M, Tan AC, Lawrence NJ, Fleming JB, Yuan Y, Xie H (2022). Development of SOS1 Inhibitor-Based Degraders to Target KRAS-Mutant Colorectal Cancer. J Med Chem, 65(24), 16432-16450. (Read full article)
  24. Boe DM, Hulsebus HJ, Najarro KM, Mullen JE, Kim H, Tan AC, McMahan RH, Kovacs EJ (2022). Advanced age is associated with changes in alveolar macrophages and their responses to the stress of traumatic injury. J Leukoc Biol, 112(6), 1371-1386. (Read full article)
  25. Thompson ZJ, Teer JK, Li J, Chen Z, Welsh EA, Zhang Y, Ayoubi N, Eroglu Z, Tan AC, Smalley KSM, Chen YA (2022). Drepmel-A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment. Cells, 11(18). (Read full article)
  26. Coleman S, Xie M, Tarhini AA, Tan AC (2022). Systematic evaluation of the predictive gene expression signatures of immune checkpoint inhibitors in metastatic melanoma. Mol Carcinog. (Read full article)
  27. Saad M, Lee SJ, Tan AC, El Naqa IM, Hodi FS, Butterfield LH, LaFramboise WA, Storkus W, Karunamurthy AD, Conejo-Garcia J, Hwu P, Streicher H, Sondak VK, Kirkwood JM, Tarhini AA (2022). Enhanced immune activation within the tumor microenvironment and circulation of female high-risk melanoma patients and improved survival with adjuvant CTLA4 blockade compared to males. J Transl Med, 20(1), 253. (Read full article)
  28. Liu X, Zhao B, Shaw TI, Fridley BL, Duckett DR, Tan AC, Teng M (2022). Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers. Nucleic Acids Res, 50(6), 3115-3127. (Read full article)
  29. Brechbuhl HM, Xie M, Kopin EG, Han AL, Vinod-Paul K, Hagen J, Edgerton S, Owens P, Sams S, Elias A, Sartorius CA, Tan AC, Kabos P (2021). Neoadjuvant endocrine therapy expands stromal populations that predict poor prognosis in estrogen receptor-positive breast cancer. Mol Carcinog, 61(3), 359-371. (Read full article)
  30. Obermayer A, Dong L, Hu Q, Golden M, Noble JD, Rodriguez P, Robinson TJ, Teng M, Tan AC, Shaw TI (2022). DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets. Biology (Basel), 11(2). (Read full article)
  31. Napoli M, Wu SJ, Gore BL, Abbas HA, Lee K, Checker R, Dhar S, Rajapakshe K, Tan AC, Lee MG, Coarfa C, Flores ER (2022). ΔNp63 regulates a common landscape of enhancer associated genes in non-small cell lung cancer. Nat Commun, 13(1), 614. (Read full article)
  32. Tarhini AA, Lee SJ, Tan AC, El Naqa IM, Stephen Hodi F, Butterfield LH, LaFramboise WA, Storkus WJ, Karunamurthy AD, Conejo-Garcia JR, Hwu P, Streicher H, Sondak VK, Kirkwood JM (2021). Improved prognosis and evidence of enhanced immunogenicity in tumor and circulation of high-risk melanoma patients with unknown primary. J Immunother Cancer, 10(1). (Read full article)
  33. Chai AWY, Tan AC, Cheong SC (2021). Uncovering drug repurposing candidates for head and neck cancers: insights from systematic pharmacogenomics data analysis. Sci Rep, 11(1), 23933. (Read full article)
  34. Nassar KW, Hintzsche JD, Bagby SM, Espinoza V, Langout-Astri C, Amato CM, Chimed TS, Fujita M, Robinson W, Tan AC, Schweppe RE (2021). Targeting CDK4/6 Represents a Therapeutic Vulnerability in Acquired BRAF/MEK Inhibitor-Resistant Melanoma. Mol Cancer Ther, 20(10), 2049-2060. (Read full article)
  35. Xiong Z, Jeon M, Allaway RJ, Kang J, Park D, Lee J, Jeon H, Ko M, Jiang H, Zheng M, Tan AC, Guo X, Multi-Targeting Drug DREAM Challenge Community, Dang KK, Tropsha A, Hecht C, Das TK, Carlson HA, Abagyan R, Guinney J, Schlessinger A, Cagan R (2021). Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge. PLoS Comput Biol, 17(9), e1009302. (Read full article)
  36. de la Iglesia JV, Slebos RJC, Martin-Gomez L, Wang X, Teer JK, Tan AC, Gerke TA, Aden-Buie G, van Veen T, Masannat J, Chaudhary R, Song F, Fournier M, Siegel EM, Schabath MB, Wadsworth JT, Caudell J, Harrison L, Wenig BM, Conejo-Garcia J, Hernandez-Prera JC, Chung CH (2021). Correction: Effects of Tobacco Smoking On the Tumor Immune Microenvironment in Head and Neck Squamous Cell Carcinoma. Clin Cancer Res, 27(17), 4941. (Read full article)
  37. Pollyea DA, Kim HM, Stevens BM, Lee FF, Harris C, Hedin BR, Knapp JR, OConnor BP, Jordan CT, Pietras EM, Tan AC, Alper S (2020). MDS-associated SF3B1 mutations enhance proinflammatory gene expression in patient blast cells. J Leukoc Biol, 110(1), 197-205. (Read full article)
  38. Schubert L, Le AT, Estrada-Bernal A, Doak AE, Yoo M, Ferrara SE, Goodspeed A, Kinose F, Rix U, Tan AC, Doebele RC (2021). Novel Human-Derived RET Fusion NSCLC Cell Lines Have Heterogeneous Responses to RET Inhibitors and Differential Regulation of Downstream Signaling. Mol Pharmacol, 99(6), 435-447. (Read full article)
  39. Gurule NJ, McCoach CE, Hinz TK, Merrick DT, Van Bokhoven A, Kim J, Patil T, Calhoun J, Nemenoff RA, Tan AC, Doebele RC, Heasley LE (2021). A tyrosine kinase inhibitor-induced interferon response positively associates with clinical response in EGFR-mutant lung cancer. NPJ Precis Oncol, 5(1), 41. (Read full article)
  40. Eschrich SA, Teer JK, Reisman P, Siegel E, Challa C, Lewis P, Fellows K, Malpica E, Carvajal R, Gonzalez G, Cukras S, Betin-Montes M, Aden-Buie G, Avedon M, Manning D, Tan AC, Fridley BL, Gerke T, Van Looveren M, Blake A, Greenman J, Rollison DE (2021). Enabling Precision Medicine in Cancer Care Through a Molecular Data Warehouse: The Moffitt Experience. JCO Clin Cancer Inform, 5, 561-569. (Read full article)
  41. Xie M, Lee K, Lockhart JH, Cukras SD, Carvajal R, Beg AA, Flores ER, Teng M, Chung CH, Tan AC (2021). TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures. Bioinformatics. (Read full article)
  42. Tengesdal IW, Menon DR, Osborne DG, Neff CP, Powers NE, Gamboni F, Mauro AG, DAlessandro A, Stefanoni D, Henen MA, Mills TS, De Graaf DM, Azam T, Vogeli B, Palmer BE, Pietras EM, DeGregori J, Tan AC, Joosten LAB, Fujita M, Dinarello CA, Marchetti C (2021). Targeting tumor-derived NLRP3 reduces melanoma progression by limiting MDSCs expansion. Proc Natl Acad Sci U S A, 118(10). (Read full article)
  43. Miroshnychenko D, Baratchart E, Ferrall-Fairbanks MC, Velde RV, Laurie MA, Bui MM, Tan AC, Altrock PM, Basanta D, Marusyk A (2021). Spontaneous cell fusions as a mechanism of parasexual recombination in tumour cell populations. Nat Ecol Evol, 5(3), 379-391. (Read full article)
  44. Morton JJ, Alzofon N, Keysar SB, Chimed TS, Reisinger J, Perrenoud L, Le PN, Nieto C, Gomez K, Miller B, Yeager R, Gao D, Tan AC, Somerset H, Medina T, Wang XJ, Wang JH, Robinson W, Roop DR, Gonzalez R, Jimeno A (2020). Studying Immunotherapy Resistance in a Melanoma Autologous Humanized Mouse Xenograft. Mol Cancer Res, 19(2), 346-357. (Read full article)
  45. Chaudhary R, Slebos RJC, Song F, McCleary-Sharpe KP, Masannat J, Tan AC, Wang X, Amaladas N, Wu W, Hall GE, Conejo-Garcia JR, Hernandez-Prera JC, Chung CH (2020). Effects of checkpoint kinase 1 inhibition by prexasertib on the tumor immune microenvironment of head and neck squamous cell carcinoma. Mol Carcinog, 60(2), 138-150. (Read full article)
  46. Wahdan-Alaswad RS, Edgerton SM, Salem H, Kim HM, Tan AC, Finlay-Schultz J, Wellberg EA, Sartorius CA, Jacobsen BM, Haugen BR, Liu B, Thor AD (2020). Exogenous Thyroid Hormone Is Associated with Shortened Survival and Upregulation of High-Risk Gene Expression Profiles in Steroid Receptor-Positive Breast Cancers. Clin Cancer Res, 27(2), 585-597. (Read full article)
  47. He T, Wildey G, McColl K, Savadelis A, Spainhower K, McColl C, Kresak A, Tan AC, Yang M, Abbas A, Dowlati A (2020). Identification of RUNX1T1 as a potential epigenetic modifier in small-cell lung cancer. Mol Oncol, 15(1), 195-209. (Read full article)
  48. Lee WC, Reuben A, Hu X, McGranahan N, Chen R, Jalali A, Negrao MV, Hubert SM, Tang C, Wu CC, Lucas AS, Roh W, Suda K, Kim J, Tan AC, Peng DH, Lu W, Tang X, Chow CW, Fujimoto J, Behrens C, Kalhor N, Fukumura K, Coyle M, Thornton R, Gumbs C, Li J, Wu CJ, Little L, Roarty E, Song X, Lee JJ, Sulman EP, Rao G, Swisher S, Diao L, Wang J, Heymach JV, Huse JT, Scheet P, Wistuba II, Gibbons DL, Futreal PA, Zhang J, Gomez D, Zhang J (2020). Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity. Genome Biol, 21(1), 271. (Read full article)
  49. Chai AWY, Yee PS, Price S, Yee SM, Lee HM, Tiong VK, Gonalves E, Behan FM, Bateson J, Gilbert J, Tan AC, McDermott U, Garnett MJ, Cheong SC (2020). Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway. Elife, 9. (Read full article)
  50. Davis SL, Ionkina AA, Bagby SM, Orth JD, Gittleman B, Marcus JM, Lam ET, Corr BR, OBryant CL, Glode AE, Tan AC, Kim J, Tentler JJ, Capasso A, Lopez KL, Gustafson DL, Messersmith WA, Leong S, Eckhardt SG, Pitts TM, Diamond JR (2020). Preclinical and Dose-Finding Phase I Trial Results of Combined Treatment with a TORC1/2 Inhibitor (TAK-228) and Aurora A Kinase Inhibitor (Alisertib) in Solid Tumors. Clin Cancer Res, 26(17), 4633-4642. (Read full article)
  51. Iwanaga R, Truong BT, Hsu JY, Lambert KA, Vyas R, Orlicky D, Shellman YG, Tan AC, Ceol C, Artinger KB (2020). Loss of prdm1a accelerates melanoma onset and progression. Mol Carcinog, 59(9), 1052-1063. (Read full article)
  52. Kern JA, Kim J, Foster DG, Mishra R, Gardner EE, Poirier JT, Rivard C, Yu H, Finigan JH, Dowlati A, Rudin CM, Tan AC (2020). Role of mTOR As an Essential Kinase in SCLC. J Thorac Oncol, 15(9), 1522-1534. (Read full article)
  53. Abbott JM, Zhou Q, Esquer H, Pike L, Broneske TP, Rinaldetti S, Abraham AD, Ramirez DA, Lunghofer PJ, Pitts TM, Regan DP, Tan AC, Gustafson DL, Messersmith WA, LaBarbera DV (2020). First-in-Class Inhibitors of Oncogenic CHD1L with Preclinical Activity against Colorectal Cancer. Mol Cancer Ther, 19(8), 1598-1612. (Read full article)
  54. Amato CM, Hintzsche JD, Wells K, Applegate A, Gorden NT, Vorwald VM, Tobin RP, Nassar K, Shellman YG, Kim J, Medina TM, Rioth M, Lewis KD, McCarter MD, Gonzalez R, Tan AC, Robinson WA (2020). Pre-Treatment Mutational and Transcriptomic Landscape of Responding Metastatic Melanoma Patients to Anti-PD1 Immunotherapy. Cancers (Basel), 12(7). (Read full article)
  55. Geng D, Ciavattone N, Lasola JJ, Shrestha R, Sanchez A, Guo J, Vlk A, Younis R, Wang L, Brown AJ, Zhang Y, Velasco-Gonzalez C, Tan AC, Davila E (2020). Induction of IRAK-M in melanoma induces caspase-3 dependent apoptosis by reducing TRAF6 and calpastatin levels. Commun Biol, 3(1), 306. (Read full article)
  56. Mukherjee N, Skees J, Todd KJ, West DA, Lambert KA, Robinson WA, Amato CM, Couts KL, Van Gulick R, MacBeth M, Nassar K, Tan AC, Zhai Z, Fujita M, Bagby SM, Dart CR, Lambert JR, Norris DA, Shellman YG (2020). MCL1 inhibitors S63845/MIK665 plus Navitoclax synergistically kill difficult-to-treat melanoma cells. Cell Death Dis, 11(6), 443. (Read full article)
  57. Vander Velde R, Yoon N, Marusyk V, Durmaz A, Dhawan A, Miroshnychenko D, Lozano-Peral D, Desai B, Balynska O, Poleszhuk J, Kenian L, Teng M, Abazeed M, Mian O, Tan AC, Haura E, Scott J, Marusyk A (2020). Resistance to targeted therapies as a multifactorial, gradual adaptation to inhibitor specific selective pressures. Nat Commun, 11(1), 2393. (Read full article)
  58. de la Iglesia JV, Slebos RJC, Martin-Gomez L, Wang X, Teer JK, Tan AC, Gerke TA, Aden-Buie G, van Veen T, Masannat J, Chaudhary R, Song F, Fournier M, Siegel EM, Schabath MB, Wadsworth JT, Caudell J, Harrison L, Wenig BM, Conejo-Garcia J, Hernandez-Prera JC, Chung CH (2019). Effects of Tobacco Smoking on the Tumor Immune Microenvironment in Head and Neck Squamous Cell Carcinoma. Clin Cancer Res, 26(6), 1474-1485. (Read full article)
  59. Keysar SB, Gomes N, Miller B, Jackson BC, Le PN, Morton JJ, Reisinger J, Chimed TS, Gomez KE, Nieto C, Frederick B, Pronk GJ, Somerset HL, Tan AC, Wang XJ, Raben D, Su TT, Jimeno A (2020). Inhibiting Translation Elongation with SVC112 Suppresses Cancer Stem Cells and Inhibits Growth in Head and Neck Squamous Carcinoma. Cancer Res, 80(5), 1183-1198. (Read full article)
  60. Schreiber AR, Kar A, Goodspeed AE, Pozdeyev N, Somerset H, Raeburn CD, Tan AC, Leong S, Wierman ME, Kiseljak-Vassiliades K (2020). Leptomeningeal Metastasis from Adrenocortical Carcinoma: A Case Report. J Endocr Soc, 4(3), bvaa017. (Read full article)
  61. Jeon M, Park D, Lee J, Jeon H, Ko M, Kim S, Choi Y, Tan AC, Kang J (2018). ReSimNet: drug response similarity prediction using Siamese neural networks. Bioinformatics, 35(24), 5249-5256. (Read full article)
  62. Hinz TK, Kleczko EK, Singleton KR, Calhoun J, Marek LA, Kim J, Tan AC, Heasley LE (2019). Functional RNAi Screens Define Distinct Protein Kinase Vulnerabilities in EGFR-Dependent HNSCC Cell Lines. Mol Pharmacol, 96(6), 862-870. (Read full article)
  63. Samson JM, Ravindran Menon D, Smith DE, Baird E, Kitano T, Gao D, Tan AC, Fujita M (2019). Clinical implications of ALDH1A1 and ALDH1A3 mRNA expression in melanoma subtypes. Chem Biol Interact, 314, 108822. (Read full article)
  64. Capasso A, Bagby SM, Dailey KL, Currimjee N, Yacob BW, Ionkina A, Frank JG, Kim DJ, George C, Lee YB, Benaim E, Gittleman B, Hartman SJ, Tan AC, Kim J, Pitts TM, Eckhardt SG, Tentler JJ, Diamond JR (2019). First-in-Class Phosphorylated-p68 Inhibitor RX-5902 Inhibits β-Catenin Signaling and Demonstrates Antitumor Activity in Triple-Negative Breast Cancer. Mol Cancer Ther, 18(11), 1916-1925. (Read full article)
  65. Aguado BA, Schuetze KB, Grim JC, Walker CJ, Cox AC, Ceccato TL, Tan AC, Sucharov CC, Leinwand LA, Taylor MRG, McKinsey TA, Anseth KS (2018). Transcatheter aortic valve replacements alter circulating serum factors to mediate myofibroblast deactivation. Sci Transl Med, 11(509). (Read full article)
  66. Gan CP, Sam KK, Yee PS, Zainal NS, Lee BKB, Abdul Rahman ZA, Patel V, Tan AC, Zain RB, Cheong SC (2019). IFITM3 knockdown reduces the expression of CCND1 and CDK4 and suppresses the growth of oral squamous cell carcinoma cells. Cell Oncol (Dordr), 42(4), 477-490. (Read full article)
  67. Yoo M, Shin J, Kim H, Kim J, Kang J, Tan AC (2018). Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map. Comput Methods Programs Biomed, 174, 33-40. (Read full article)
  68. Landa I, Pozdeyev N, Korch C, Marlow LA, Smallridge RC, Copland JA, Henderson YC, Lai SY, Clayman GL, Onoda N, Tan AC, Garcia-Rendueles MER, Knauf JA, Haugen BR, Fagin JA, Schweppe RE (2019). Comprehensive Genetic Characterization of Human Thyroid Cancer Cell Lines: A Validated Panel for Preclinical Studies. Clin Cancer Res, 25(10), 3141-3151. (Read full article)
  69. Kessler BE, Mishall KM, Kellett MD, Clark EG, Pugazhenthi U, Pozdeyev N, Kim J, Tan AC, Schweppe RE (2018). Resistance to Src inhibition alters the BRAF-mutant tumor secretome to promote an invasive phenotype and therapeutic escape through a FAK>p130Cas>c-Jun signaling axis. Oncogene, 38(14), 2565-2579. (Read full article)
  70. Rogers TJ, Christenson JL, Greene LI, ONeill KI, Williams MM, Gordon MA, Nemkov T, DAlessandro A, Degala GD, Shin J, Tan AC, Cittelly DM, Lambert JR, Richer JK (2018). Reversal of Triple-Negative Breast Cancer EMT by miR-200c Decreases Tryptophan Catabolism and a Program of Immunosuppression. Mol Cancer Res, 17(1), 30-41. (Read full article)
  71. Brown P, RELISH Consortium, Zhou Y (2019). Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database (Oxford), 2019. (Read full article)
  72. Davis SL, Eckhardt SG, Diamond JR, Messersmith WA, Dasari A, Weekes CD, Lieu CH, Kane M, Choon Tan A, Pitts TM, Leong S (2018). A Phase I Dose-Escalation Study of Linsitinib (OSI-906), a Small-Molecule Dual Insulin-Like Growth Factor-1 Receptor/Insulin Receptor Kinase Inhibitor, in Combination with Irinotecan in Patients with Advanced Cancer. Oncologist, 23(12), 1409-e140. (Read full article)
  73. Ravindran Menon D, Luo Y, Arcaroli JJ, Liu S, KrishnanKutty LN, Osborne DG, Li Y, Samson JM, Bagby S, Tan AC, Robinson WA, Messersmith WA, Fujita M (2018). CDK1 Interacts with Sox2 and Promotes Tumor Initiation in Human Melanoma. Cancer Res, 78(23), 6561-6574. (Read full article)
  74. Oweida A, Hararah MK, Phan A, Binder D, Bhatia S, Lennon S, Bukkapatnam S, Van Court B, Uyanga N, Darragh L, Kim HM, Raben D, Tan AC, Heasley L, Clambey E, Nemenoff R, Karam SD (2018). Resistance to Radiotherapy and PD-L1 Blockade Is Mediated by TIM-3 Upregulation and Regulatory T-Cell Infiltration. Clin Cancer Res, 24(21), 5368-5380. (Read full article)
  75. Karam SD, Reddy K, Blatchford PJ, Waxweiler T, DeLouize AM, Oweida A, Somerset H, Marshall C, Young C, Davies KD, Kane M, Tan AC, Wang XJ, Jimeno A, Aisner DL, Bowles DW, Raben D (2018). Final Report of a Phase I Trial of Olaparib with Cetuximab and Radiation for Heavy Smoker Patients with Locally Advanced Head and Neck Cancer. Clin Cancer Res, 24(20), 4949-4959. (Read full article)
  76. Suda K, Kim J, Murakami I, Rozeboom L, Shimoji M, Shimizu S, Rivard CJ, Mitsudomi T, Tan AC, Hirsch FR (2018). Innate Genetic Evolution of Lung Cancers and Spatial Heterogeneity: Analysis of Treatment-Naïve Lesions. J Thorac Oncol, 13(10), 1496-1507. (Read full article)
  77. Suda K, Murakami I, Yu H, Kim J, Tan AC, Mizuuchi H, Rozeboom L, Ellison K, Rivard CJ, Mitsudomi T, Hirsch FR (2018). CD44 Facilitates Epithelial-to-Mesenchymal Transition Phenotypic Change at Acquisition of Resistance to EGFR Kinase Inhibitors in Lung Cancer. Mol Cancer Ther, 17(10), 2257-2265. (Read full article)
  78. Parrish JK, McCann TS, Sechler M, Sobral LM, Ren W, Jones KL, Tan AC, Jedlicka P (2018). The Jumonji-domain histone demethylase inhibitor JIB-04 deregulates oncogenic programs and increases DNA damage in Ewing Sarcoma, resulting in impaired cell proliferation and survival, and reduced tumor growth. Oncotarget, 9(69), 33110-33123. (Read full article)
  79. Pei S, Minhajuddin M, Adane B, Khan N, Stevens BM, Mack SC, Lai S, Rich JN, Inguva A, Shannon KM, Kim H, Tan AC, Myers JR, Ashton JM, Neff T, Pollyea DA, Smith CA, Jordan CT (2018). AMPK/FIS1-Mediated Mitophagy Is Required for Self-Renewal of Human AML Stem Cells. Cell Stem Cell, 23(1), 86-100.e6. (Read full article)
  80. Lee BKB, Gan CP, Chang JK, Tan JL, Fadlullah MZ, Abdul Rahman ZA, Prime SS, Gutkind JS, Liew CS, Khang TF, Tan AC, Cheong SC (2018). GENIPAC: A Genomic Information Portal for Head and Neck Cancer Cell Systems. J Dent Res, 97(8), 909-916. (Read full article)
  81. Pozdeyev N, Gay LM, Sokol ES, Hartmaier R, Deaver KE, Davis S, French JD, Borre PV, LaBarbera DV, Tan AC, Schweppe RE, Fishbein L, Ross JS, Haugen BR, Bowles DW (2018). Genetic Analysis of 779 Advanced Differentiated and Anaplastic Thyroid Cancers. Clin Cancer Res, 24(13), 3059-3068. (Read full article)
  82. Powers RK, Goodspeed A, Pielke-Lombardo H, Tan AC, Costello JC (2018). GSEA-InContext: identifying novel and common patterns in expression experiments. Bioinformatics, 34(13), i555-i564. (Read full article)
  83. Keysar SB, Eagles JR, Miller B, Jackson BC, Chowdhury FN, Reisinger J, Chimed TS, Le PN, Morton JJ, Somerset HL, Varella-Garcia M, Tan AC, Song JI, Bowles DW, Reyland ME, Jimeno A (2018). Salivary Gland Cancer Patient-Derived Xenografts Enable Characterization of Cancer Stem Cells and New Gene Events Associated with Tumor Progression. Clin Cancer Res, 24(12), 2935-2943. (Read full article)
  84. Hintzsche JD, Yoo M, Kim J, Amato CM, Robinson WA, Tan AC (2018). IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics. BMC Med Genomics, 11(Suppl 2), 26. (Read full article)
  85. Kim J, Yoo M, Shin J, Kim H, Kang J, Tan AC (2018). Systems Pharmacology-Based Approach of Connecting Disease Genes in Genome-Wide Association Studies with Traditional Chinese Medicine. Int J Genomics, 2018, 7697356. (Read full article)
  86. Klauck PJ, Bagby SM, Capasso A, Bradshaw-Pierce EL, Selby HM, Spreafico A, Tentler JJ, Tan AC, Kim J, Arcaroli JJ, Purkey A, Messersmith WA, Kuida K, Eckhardt SG, Pitts TM (2018). Antitumor activity of the polo-like kinase inhibitor, TAK-960, against preclinical models of colorectal cancer. BMC Cancer, 18(1), 136. (Read full article)
  87. Lee K, Kim B, Choi Y, Kim S, Shin W, Lee S, Park S, Kim S, Tan AC, Kang J (2018). Deep learning of mutation-gene-drug relations from the literature. BMC Bioinformatics, 19(1), 21. (Read full article)
  88. Pilling AB, Kim J, Estrada-Bernal A, Zhou Q, Le AT, Singleton KR, Heasley LE, Tan AC, DeGregori J, Doebele RC (2018). ALK is a critical regulator of the MYC-signaling axis in ALK positive lung cancer. Oncotarget, 9(10), 8823-8835. (Read full article)
  89. Kim S, Park D, Choi Y, Lee K, Kim B, Jeon M, Kim J, Tan AC, Kang J (2018). A Pilot Study of Biomedical Text Comprehension using an Attention-Based Deep Neural Reader: Design and Experimental Analysis. JMIR Med Inform, 6(1), e2. (Read full article)
  90. Yue Z, Zheng Q, Neylon MT, Yoo M, Shin J, Zhao Z, Tan AC, Chen JY (2017). PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. Nucleic Acids Res, 46(D1), D668-D676. (Read full article)
  91. Couts KL, Bemis J, Turner JA, Bagby SM, Murphy D, Christiansen J, Hintzsche JD, Le A, Pitts TM, Wells K, Applegate A, Amato C, Multani P, Chow-Maneval E, Tentler JJ, Shellman YG, Rioth MJ, Tan AC, Gonzalez R, Medina T, Doebele RC, Robinson WA (2017). ALK Inhibitor Response in Melanomas Expressing EML4-ALK Fusions and Alternate ALK Isoforms. Mol Cancer Ther, 17(1), 222-231. (Read full article)
  92. Cavalli G, Koenders M, Kalabokis V, Kim J, Choon Tan A, Garlanda C, Mantovani A, Dagna L, Joosten LAB, Dinarello CA (2017). Treating experimental arthritis with the innate immune inhibitor interleukin-37 reduces joint and systemic inflammation. Rheumatology (Oxford), 56(12), 2256. (Read full article)
  93. Scott AJ, Song EK, Bagby S, Purkey A, McCarter M, Gajdos C, Quackenbush KS, Cross B, Pitts TM, Tan AC, Eckhardt SG, Fenton H, Arcaroli J, Messersmith WA (2017). Evaluation of the efficacy of dasatinib, a Src/Abl inhibitor, in colorectal cancer cell lines and explant mouse model. PLoS One, 12(11), e0187173. (Read full article)
  94. Zhang C, Liu Z, Bunker E, Ramirez A, Lee S, Peng Y, Tan AC, Eckhardt SG, Chapnick DA, Liu X (2017). Sorafenib targets the mitochondrial electron transport chain complexes and ATP synthase to activate the PINK1-Parkin pathway and modulate cellular drug response. J Biol Chem, 292(36), 15105-15120. (Read full article)
  95. Donson AM, Apps J, Griesinger AM, Amani V, Witt DA, Anderson RCE, Niazi TN, Grant G, Souweidane M, Johnston JM, Jackson EM, Kleinschmidt-DeMasters BK, Handler MH, Tan AC, Gore L, Virasami A, Gonzalez-Meljem JM, Jacques TS, Martinez-Barbera JP, Foreman NK, Hankinson TC, Advancing Treatment for Pediatric Craniopharyngioma Consortium (2017). Molecular Analyses Reveal Inflammatory Mediators in the Solid Component and Cyst Fluid of Human Adamantinomatous Craniopharyngioma. J Neuropathol Exp Neurol, 76(9), 779-788. (Read full article)
  96. Nelson-Taylor SK, Le AT, Yoo M, Schubert L, Mishall KM, Doak A, Varella-Garcia M, Tan AC, Doebele RC (2017). Resistance to RET-Inhibition in RET-Rearranged NSCLC Is Mediated By Reactivation of RAS/MAPK Signaling. Mol Cancer Ther, 16(8), 1623-1633. (Read full article)
  97. Ohm AM, Tan AC, Heasley LE, Reyland ME (2017). Co-dependency of PKCδ and K-Ras: inverse association with cytotoxic drug sensitivity in KRAS mutant lung cancer. Oncogene, 36(30), 4370-4378. (Read full article)
  98. Hintzsche JD, Gorden NT, Amato CM, Kim J, Wuensch KE, Robinson SE, Applegate AJ, Couts KL, Medina TM, Wells KR, Wisell JA, McCarter MD, Box NF, Shellman YG, Gonzalez RC, Lewis KD, Tentler JJ, Tan AC, Robinson WA (2017). Whole-exome sequencing identifies recurrent SF3B1 R625 mutation and comutation of NF1 and KIT in mucosal melanoma. Melanoma Res, 27(3), 189-199. (Read full article)
  99. Ionkina AA, Tentler JJ, Kim J, Capasso A, Pitts TM, Ryall KA, Howison RR, Kabos P, Sartorius CA, Tan AC, Eckhardt SG, Diamond JR (2017). Efficacy and Molecular Mechanisms of Differentiated Response to the Aurora and Angiogenic Kinase Inhibitor ENMD-2076 in Preclinical Models of p53-Mutated Triple-Negative Breast Cancer. Front Oncol, 7, 94. (Read full article)
  100. Harder B, Tian W, La Clair JJ, Tan AC, Ooi A, Chapman E, Zhang DD (2017). Brusatol overcomes chemoresistance through inhibition of protein translation. Mol Carcinog, 56(5), 1493-1500. (Read full article)
  101. Brechbuhl HM, Finlay-Schultz J, Yamamoto TM, Gillen AE, Cittelly DM, Tan AC, Sams SB, Pillai MM, Elias AD, Robinson WA, Sartorius CA, Kabos P (2016). Fibroblast Subtypes Regulate Responsiveness of Luminal Breast Cancer to Estrogen. Clin Cancer Res, 23(7), 1710-1721. (Read full article)
  102. Dimberg LY, Towers CG, Behbakht K, Hotz TJ, Kim J, Fosmire S, Porter CC, Tan AC, Thorburn A, Ford HL (2017). A Genome-Wide Loss-of-Function Screen Identifies SLC26A2 as a Novel Mediator of TRAIL Resistance. Mol Cancer Res, 15(4), 382-394. (Read full article)
  103. Scarborough HA, Helfrich BA, Cass-Selves M, Schuller AG, Grosskurth SE, Kim J, Tan AC, Chan DC, Zhang Z, Zaberezhnyy V, Bunn PA, DeGregori J (2016). AZ1366: An Inhibitor of Tankyrase and the Canonical Wnt Pathway that Limits the Persistence of Non-Small Cell Lung Cancer Cells Following EGFR Inhibition. Clin Cancer Res, 23(6), 1531-1541. (Read full article)
  104. Wong KM, Micel LN, Selby HM, Tan AC, Pitts TM, Bagby SM, Spreafico A, Klauck PJ, Blakemore SJ, Smith PF, McDonald A, Berger A, Tentler JJ, Eckhardt SG (2016). Targeting the protein ubiquitination machinery in melanoma by the NEDD8-activating enzyme inhibitor pevonedistat (MLN4924). Invest New Drugs, 35(1), 11-25. (Read full article)
  105. Lee BK, Tiong KH, Chang JK, Liew CS, Abdul Rahman ZA, Tan AC, Khang TF, Cheong SC (2017). DeSigN: connecting gene expression with therapeutics for drug repurposing and development. BMC Genomics, 18(Suppl 1), 934. (Read full article)
  106. Murakami A, Wang L, Kalhorn S, Schraml P, Rathmell WK, Tan AC, Nemenoff R, Stenmark K, Jiang BH, Reyland ME, Heasley L, Hu CJ (2017). Context-dependent role for chromatin remodeling component PBRM1/BAF180 in clear cell renal cell carcinoma. Oncogenesis, 6(1), e287. (Read full article)
  107. Turner J, Couts K, Sheren J, Saichaemchan S, Ariyawutyakorn W, Avolio I, Cabral E, Glogowska M, Amato C, Robinson S, Hintzsche J, Applegate A, Seelenfreund E, Gonzalez R, Wells K, Bagby S, Tentler J, Tan AC, Wisell J, Varella-Garcia M, Robinson W (2016). Kinase gene fusions in defined subsets of melanoma. Pigment Cell Melanoma Res, 30(1), 53-62. (Read full article)
  108. Cavalli G, Koenders M, Kalabokis V, Kim J, Tan AC, Garlanda C, Mantovani A, Dagna L, Joosten LA, Dinarello CA (2016). Treating experimental arthritis with the innate immune inhibitor interleukin-37 reduces joint and systemic inflammation. Rheumatology (Oxford), 55(12), 2220-2229. (Read full article)
  109. Federer C, Yoo M, Tan AC (2016). Big Data Mining and Adverse Event Pattern Analysis in Clinical Drug Trials. Assay Drug Dev Technol, 14(10), 557-566. (Read full article)
  110. Wong JP, Todd JR, Finetti MA, McCarthy F, Broncel M, Vyse S, Luczynski MT, Crosier S, Ryall KA, Holmes K, Payne LS, Daley F, Wai P, Jenks A, Tanos B, Tan AC, Natrajan RC, Williamson D, Huang PH (2016). Dual Targeting of PDGFRα and FGFR1 Displays Synergistic Efficacy in Malignant Rhabdoid Tumors. Cell Rep, 17(5), 1265-1275. (Read full article)
  111. Gregory MA, DAlessandro A, Alvarez-Calderon F, Kim J, Nemkov T, Adane B, Rozhok AI, Kumar A, Kumar V, Pollyea DA, Wempe MF, Jordan CT, Serkova NJ, Tan AC, Hansen KC, DeGregori J (2016). ATM/G6PD-driven redox metabolism promotes FLT3 inhibitor resistance in acute myeloid leukemia. Proc Natl Acad Sci U S A, 113(43), E6669-E6678. (Read full article)
  112. Lee S, Kim D, Lee K, Choi J, Kim S, Jeon M, Lim S, Choi D, Kim S, Tan AC, Kang J (2016). BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature. PLoS One, 11(10), e0164680. (Read full article)
  113. 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 (2016). Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Sci Signal, 9(450), rs12. (Read full article)
  114. Helfrich BA, Kim J, Gao D, Chan DC, Zhang Z, Tan AC, Bunn PA Jr (2016). Barasertib (AZD1152), a Small Molecule Aurora B Inhibitor, Inhibits the Growth of SCLC Cell Lines In Vitro and In Vivo. Mol Cancer Ther, 15(10), 2314-2322. (Read full article)
  115. Bagby S, Messersmith WA, Pitts TM, Capasso A, Varella-Garcia M, Klauck PJ, Kim J, Tan AC, Eckhardt SG, Tentler JJ, Arcaroli J (2016). Development and Maintenance of a Preclinical Patient Derived Tumor Xenograft Model for the Investigation of Novel Anti-Cancer Therapies. J Vis Exp, (115). (Read full article)
  116. Todd JR, Ryall KA, Vyse S, Wong JP, Natrajan RC, Yuan Y, Tan AC, Huang PH (2016). Systematic analysis of tumour cell-extracellular matrix adhesion identifies independent prognostic factors in breast cancer. Oncotarget, 7(39), 62939-62953. (Read full article)
  117. Lee K, Shin W, Kim B, Lee S, Choi Y, Kim S, Jeon M, Tan AC, Kang J (2016). HiPub: translating PubMed and PMC texts to networks for knowledge discovery. Bioinformatics, 32(18), 2886-8. (Read full article)
  118. Keysar SB, Le PN, Miller B, Jackson BC, Eagles JR, Nieto C, Kim J, Tang B, Glogowska MJ, Morton JJ, Padilla-Just N, Gomez K, Warnock E, Reisinger J, Arcaroli JJ, Messersmith WA, Wakefield LM, Gao D, Tan AC, Serracino H, Vasiliou V, Roop DR, Wang XJ, Jimeno A (2016). Regulation of Head and Neck Squamous Cancer Stem Cells by PI3K and SOX2. J Natl Cancer Inst, 109(1). (Read full article)
  119. Pozdeyev N, Yoo M, Mackie R, Schweppe RE, Tan AC, Haugen BR (2016). Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies. Oncotarget, 7(32), 51619-51625. (Read full article)
  120. Pitts TM, Bradshaw-Pierce EL, Bagby SM, Hyatt SL, Selby HM, Spreafico A, Tentler JJ, McPhillips K, Klauck PJ, Capasso A, Diamond JR, Davis SL, Tan AC, Arcaroli JJ, Purkey A, Messersmith WA, Ecsedy JA, Eckhardt SG (2016). Antitumor activity of the aurora a selective kinase inhibitor, alisertib, against preclinical models of colorectal cancer. Oncotarget, 7(31), 50290-50301. (Read full article)
  121. Beadnell TC, Mishall KM, Zhou Q, Riffert SM, Wuensch KE, Kessler BE, Corpuz ML, Jing X, Kim J, Wang G, Tan AC, Schweppe RE (2016). The Mitogen-Activated Protein Kinase Pathway Facilitates Resistance to the Src Inhibitor Dasatinib in Thyroid Cancer. Mol Cancer Ther, 15(8), 1952-63. (Read full article)
  122. Hintzsche J, Kim J, Yadav V, Amato C, Robinson SE, Seelenfreund E, Shellman Y, Wisell J, Applegate A, McCarter M, Box N, Tentler J, De S, Robinson WA, Tan AC (2016). IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. J Am Med Inform Assoc, 23(4), 721-30. (Read full article)
  123. Fadlullah MZ, Chiang IK, Dionne KR, Yee PS, Gan CP, Sam KK, Tiong KH, Ng AK, Martin D, Lim KP, Kallarakkal TG, Mustafa WM, Lau SH, Abraham MT, Zain RB, Rahman ZA, Molinolo A, Patel V, Gutkind JS, Tan AC, Cheong SC (2015). Genetically-defined novel oral squamous cell carcinoma cell lines for the development of molecular therapies. Oncotarget, 7(19), 27802-18. (Read full article)
  124. Lee K, Lee S, Park S, Kim S, Kim S, Choi K, Tan AC, Kang J (2016). BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations. Database (Oxford), 2016. (Read full article)
  125. Symonds JM, Ohm AM, Tan AC, Reyland ME (2016). PKCδ regulates integrin αVβ3 expression and transformed growth of K-ras dependent lung cancer cells. Oncotarget, 7(14), 17905-19. (Read full article)
  126. Fornetti J, Flanders KC, Henson PM, Tan AC, Borges VF, Schedin P (2015). Mammary epithelial cell phagocytosis downstream of TGF-β3 is characterized by adherens junction reorganization. Cell Death Differ, 23(2), 185-96. (Read full article)
  127. Bowles DW, Keysar SB, Eagles JR, Wang G, Glogowska MJ, McDermott JD, Le PN, Gao D, Ray CE, Rochon PJ, Roop DR, Tan AC, Serracino HS, Jimeno A (2015). A pilot study of cetuximab and the hedgehog inhibitor IPI-926 in recurrent/metastatic head and neck squamous cell carcinoma. Oral Oncol, 53, 74-9. (Read full article)
  128. Morton JJ, Bird G, Keysar SB, Astling DP, Lyons TR, Anderson RT, Glogowska MJ, Estes P, Eagles JR, Le PN, Gan G, McGettigan B, Fernandez P, Padilla-Just N, Varella-Garcia M, Song JI, Bowles DW, Schedin P, Tan AC, Roop DR, Wang XJ, Refaeli Y, Jimeno A (2015). XactMice: humanizing mouse bone marrow enables microenvironment reconstitution in a patient-derived xenograft model of head and neck cancer. Oncogene, 35(3), 290-300. (Read full article)
  129. Arcaroli JJ, Tai WM, McWilliams R, Bagby S, Blatchford PJ, Varella-Garcia M, Purkey A, Quackenbush KS, Song EK, Pitts TM, Gao D, Lieu C, McManus M, Tan AC, Zheng X, Zhang Q, Ozeck M, Olson P, Jiang ZQ, Kopetz S, Jimeno A, Keysar S, Eckhardt G, Messersmith WA (2015). A NOTCH1 gene copy number gain is a prognostic indicator of worse survival and a predictive biomarker to a Notch1 targeting antibody in colorectal cancer. Int J Cancer, 138(1), 195-205. (Read full article)
  130. Towers CG, Guarnieri AL, Micalizzi DS, Harrell JC, Gillen AE, Kim J, Wang CA, Oliphant MUJ, Drasin DJ, Guney MA, Kabos P, Sartorius CA, Tan AC, Perou CM, Espinosa JM, Ford HL (2015). The Six1 oncoprotein downregulates p53 via concomitant regulation of RPL26 and microRNA-27a-3p. Nat Commun, 6, 10077. (Read full article)
  131. Ryall KA, Shin J, Yoo M, Hinz TK, Kim J, Kang J, Heasley LE, Tan AC (2015). Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data. Bioinformatics, 31(23), 3799-806. (Read full article)
  132. Henry CJ, Cass-Selves M, Kim J, Zaberezhnyy V, Aghili L, Daniel AE, Jimenez L, Azam T, McNamee EN, Clambey ET, Klawitter J, Serkova NJ, Tan AC, Dinarello CA, DeGregori J (2015). Aging-associated inflammation promotes selection for adaptive oncogenic events in B cell progenitors. J Clin Invest, 125(12), 4666-80. (Read full article)
  133. Lieu CH, Klauck PJ, Henthorn PK, Tentler JJ, Tan AC, Spreafico A, Selby HM, Britt BC, Bagby SM, Arcaroli JJ, Messersmith WA, Pitts TM, Eckhardt SG (2015). Antitumor activity of a potent MEK inhibitor, TAK-733, against colorectal cancer cell lines and patient derived xenografts. Oncotarget, 6(33), 34561-72. (Read full article)
  134. Singleton KR, Hinz TK, Kleczko EK, Marek LA, Kwak J, Harp T, Kim J, Tan AC, Heasley LE (2015). Kinome RNAi Screens Reveal Synergistic Targeting of MTOR and FGFR1 Pathways for Treatment of Lung Cancer and HNSCC. Cancer Res, 75(20), 4398-406. (Read full article)
  135. Gke F, Franzen A, Hinz TK, Marek LA, Yoon P, Sharma R, Bode M, von Maessenhausen A, Lankat-Buttgereit B, Gke A, Golletz C, Kirsten R, Boehm D, Vogel W, Kleczko EK, Eagles JR, Hirsch FR, Van Bremen T, Bootz F, Schroeck A, Kim J, Tan AC, Jimeno A, Heasley LE, Perner S (2015). FGFR1 Expression Levels Predict BGJ398 Sensitivity of FGFR1-Dependent Head and Neck Squamous Cell Cancers. Clin Cancer Res, 21(19), 4356-64. (Read full article)
  136. Yoo M, Shin J, Kim J, Ryall KA, Lee K, Lee S, Jeon M, Kang J, Tan AC (2015). DSigDB: drug signatures database for gene set analysis. Bioinformatics, 31(18), 3069-71. (Read full article)
  137. Saha A, Jeon M, Tan AC, Kang J (2015). iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data. PLoS One, 10(7), e0131656. (Read full article)
  138. Davis EM, Kim J, Menasche BL, Sheppard J, Liu X, Tan AC, Shen J (2015). Comparative Haploid Genetic Screens Reveal Divergent Pathways in the Biogenesis and Trafficking of Glycophosphatidylinositol-Anchored Proteins. Cell Rep, 11(11), 1727-36. (Read full article)
  139. Davis SL, Robertson KM, Pitts TM, Tentler JJ, Bradshaw-Pierce EL, Klauck PJ, Bagby SM, Hyatt SL, Selby HM, Spreafico A, Ecsedy JA, Arcaroli JJ, Messersmith WA, Tan AC, Eckhardt SG (2015). Combined inhibition of MEK and Aurora A kinase in KRAS/PIK3CA double-mutant colorectal cancer models. Front Pharmacol, 6, 120. (Read full article)
  140. Yonekawa T, Gamez G, Kim J, Tan AC, Thorburn J, Gump J, Thorburn A, Morgan MJ (2015). RIP1 negatively regulates basal autophagic flux through TFEB to control sensitivity to apoptosis. EMBO Rep, 16(6), 700-8. (Read full article)
  141. Kleczko EK, Kim J, Keysar SB, Heasley LR, Eagles JR, Simon M, Marshall ME, Singleton KR, Jimeno A, Tan AC, Heasley LE (2015). An Inducible TGF-β2-TGFβR Pathway Modulates the Sensitivity of HNSCC Cells to Tyrosine Kinase Inhibitors Targeting Dominant Receptor Tyrosine Kinases. PLoS One, 10(5), e0123600. (Read full article)
  142. Drasin DJ, Guarnieri AL, Neelakantan D, Kim J, Cabrera JH, Wang CA, Zaberezhnyy V, Gasparini P, Cascione L, Huebner K, Tan AC, Ford HL (2015). TWIST1-Induced miR-424 Reversibly Drives Mesenchymal Programming while Inhibiting Tumor Initiation. Cancer Res, 75(9), 1908-21. (Read full article)
  143. Tentler JJ, Ionkina AA, Tan AC, Newton TP, Pitts TM, Glogowska MJ, Kabos P, Sartorius CA, Sullivan KD, Espinosa JM, Eckhardt SG, Diamond JR (2015). p53 Family Members Regulate Phenotypic Response to Aurora Kinase A Inhibition in Triple-Negative Breast Cancer. Mol Cancer Ther, 14(5), 1117-29. (Read full article)
  144. Song EK, Tai WM, Messersmith WA, Bagby S, Purkey A, Quackenbush KS, Pitts TM, Wang G, Blatchford P, Yahn R, Kaplan J, Tan AC, Atreya CE, Eckhardt G, Kelley RK, Venook A, Kwak EL, Ryan D, Arcaroli JJ (2014). Potent antitumor activity of cabozantinib, a c-MET and VEGFR2 inhibitor, in a colorectal cancer patient-derived tumor explant model. Int J Cancer, 136(8), 1967-75. (Read full article)
  145. Fleenor CJ, Rozhok AI, Zaberezhnyy V, Mathew D, Kim J, Tan AC, Bernstein ID, DeGregori J (2014). Contrasting roles for C/EBPα and Notch in irradiation-induced multipotent hematopoietic progenitor cell defects. Stem Cells, 33(4), 1345-58. (Read full article)
  146. Ryall KA, Tan AC (2015). Systems biology approaches for advancing the discovery of effective drug combinations. J Cheminform, 7, 7. (Read full article)
  147. Micel LN, Tentler JJ, Tan AC, Selby HM, Brunkow KL, Robertson KM, Davis SL, Klauck PJ, Pitts TM, Gangolli E, Fabrey R, OConnell SM, Vincent PW, Eckhardt SG (2014). Antitumor activity of the MEK inhibitor TAK-733 against melanoma cell lines and patient-derived tumor explants. Mol Cancer Ther, 14(2), 317-25. (Read full article)
  148. Ryall KA, Kim J, Klauck PJ, Shin J, Yoo M, Ionkina A, Pitts TM, Tentler JJ, Diamond JR, Eckhardt SG, Heasley LE, Kang J, Tan AC (2015). An integrated bioinformatics analysis to dissect kinase dependency in triple negative breast cancer. BMC Genomics, 16 Suppl 12, S2. (Read full article)
  149. Wang CA, Drasin D, Pham C, Jedlicka P, Zaberezhnyy V, Guney M, Li H, Nemenoff R, Costello JC, Tan AC, Ford HL (2014). Homeoprotein Six2 promotes breast cancer metastasis via transcriptional and epigenetic control of E-cadherin expression. Cancer Res, 74(24), 7357-70. (Read full article)
  150. Pitts TM, Newton TP, Bradshaw-Pierce EL, Addison R, Arcaroli JJ, Klauck PJ, Bagby SM, Hyatt SL, Purkey A, Tentler JJ, Tan AC, Messersmith WA, Eckhardt SG, Leong S (2014). Dual pharmacological targeting of the MAP kinase and PI3K/mTOR pathway in preclinical models of colorectal cancer. PLoS One, 9(11), e113037. (Read full article)
  151. Seelenfreund E, Robinson WA, Amato CM, Tan AC, Kim J, Robinson SE (2014). Long term storage of dry versus frozen RNA for next generation molecular studies. PLoS One, 9(11), e111827. (Read full article)
  152. Kim J, Vasu VT, Mishra R, Singleton KR, Yoo M, Leach SM, Farias-Hesson E, Mason RJ, Kang J, Ramamoorthy P, Kern JA, Heasley LE, Finigan JH, Tan AC (2014). Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy. Bioinformatics, 30(17), 2393-8. (Read full article)
  153. Wynes MW, Hinz TK, Gao D, Martini M, Marek LA, Ware KE, Edwards MG, Bhm D, Perner S, Helfrich BA, Dziadziuszko R, Jassem J, Wojtylak S, Sejda A, Gozgit JM, Bunn PA Jr, Camidge DR, Tan AC, Hirsch FR, Heasley LE (2014). FGFR1 mRNA and protein expression, not gene copy number, predict FGFR TKI sensitivity across all lung cancer histologies. Clin Cancer Res, 20(12), 3299-309. (Read full article)
  154. Morrison JA, Pike LA, Sams SB, Sharma V, Zhou Q, Severson JJ, Tan AC, Wood WM, Haugen BR (2014). Thioredoxin interacting protein (TXNIP) is a novel tumor suppressor in thyroid cancer. Mol Cancer, 13, 62. (Read full article)
  155. Bowles DW, Diamond JR, Lam ET, Weekes CD, Astling DP, Anderson RT, Leong S, Gore L, Varella-Garcia M, Vogler BW, Keysar SB, Freas E, Aisner DL, Ren C, Tan AC, Wilhelm F, Maniar M, Eckhardt SG, Messersmith WA, Jimeno A (2014). Phase I study of oral rigosertib (ON 01910.Na), a dual inhibitor of the PI3K and Plk1 pathways, in adult patients with advanced solid malignancies. Clin Cancer Res, 20(6), 1656-65. (Read full article)
  156. Jeon M, Lee S, Lee K, Tan AC, Kang J (2013). BEReX: Biomedical Entity-Relationship eXplorer. Bioinformatics, 30(1), 135-6. (Read full article)
  157. Saha A, Tan AC, Kang J (2014). Automatic context-specific subnetwork discovery from large interaction networks. PLoS One, 9(1), e84227. (Read full article)
  158. Davies KD, Mahale S, Astling DP, Aisner DL, Le AT, Hinz TK, Vaishnavi A, Bunn PA Jr, Heasley LE, Tan AC, Camidge DR, Varella-Garcia M, Doebele RC (2013). Resistance to ROS1 inhibition mediated by EGFR pathway activation in non-small cell lung cancer. PLoS One, 8(12), e82236. (Read full article)
  159. Flanigan SA, Pitts TM, Newton TP, Kulikowski GN, Tan AC, McManus MC, Spreafico A, Kachaeva MI, Selby HM, Tentler JJ, Eckhardt SG, Leong S (2013). Overcoming IGF1R/IR resistance through inhibition of MEK signaling in colorectal cancer models. Clin Cancer Res, 19(22), 6219-29. (Read full article)
  160. Khor GH, Froemming GR, Zain RB, Abraham MT, Omar E, Tan SK, Tan AC, Vincent-Chong VK, Thong KL (2013). DNA methylation profiling revealed promoter hypermethylation-induced silencing of p16, DDAH2 and DUSP1 in primary oral squamous cell carcinoma. Int J Med Sci, 10(12), 1727-39. (Read full article)
  161. Anderson RT, Keysar SB, Bowles DW, Glogowska MJ, Astling DP, Morton JJ, Le P, Umpierrez A, Eagles-Soukup J, Gan GN, Vogler BW, Sehrt D, Takimoto SM, Aisner DL, Wilhelm F, Frederick BA, Varella-Garcia M, Tan AC, Jimeno A (2013). The dual pathway inhibitor rigosertib is effective in direct patient tumor xenografts of head and neck squamous cell carcinomas. Mol Cancer Ther, 12(10), 1994-2005. (Read full article)
  162. Kim J, Yoo M, Kang J, Tan AC (2013). K-Map: connecting kinases with therapeutics for drug repurposing and development. Hum Genomics, 7, 20. (Read full article)
  163. Maller O, Hansen KC, Lyons TR, Acerbi I, Weaver VM, Prekeris R, Tan AC, Schedin P (2013). Collagen architecture in pregnancy-induced protection from breast cancer. J Cell Sci, 126(Pt 18), 4108-10. (Read full article)
  164. Linger RM, Lee-Sherick AB, DeRyckere D, Cohen RA, Jacobsen KM, McGranahan A, Brando LN, Winges A, Sawczyn KK, Liang X, Keating AK, Tan AC, Earp HS, Graham DK (2013). Mer receptor tyrosine kinase is a therapeutic target in pre-B-cell acute lymphoblastic leukemia. Blood, 122(9), 1599-609. (Read full article)
  165. Arcaroli JJ, Quackenbush KS, Purkey A, Powell RW, Pitts TM, Bagby S, Tan AC, Cross B, McPhillips K, Song EK, Tai WM, Winn RA, Bikkavilli K, Vanscoyk M, Eckhardt SG, Messersmith WA (2013). Tumours with elevated levels of the Notch and Wnt pathways exhibit efficacy to PF-03084014, a γ-secretase inhibitor, in a preclinical colorectal explant model. Br J Cancer, 109(3), 667-75. (Read full article)
  166. Keysar SB, Astling DP, Anderson RT, Vogler BW, Bowles DW, Morton JJ, Paylor JJ, Glogowska MJ, Le PN, Eagles-Soukup JR, Kako SL, Takimoto SM, Sehrt DB, Umpierrez A, Pittman MA, Macfadden SM, Helber RM, Peterson S, Hausman DF, Said S, Leem TH, Goddard JA, Arcaroli JJ, Messersmith WA, Robinson WA, Hirsch FR, Varella-Garcia M, Raben D, Wang XJ, Song JI, Tan AC, Jimeno A (2013). A patient tumor transplant model of squamous cell cancer identifies PI3K inhibitors as candidate therapeutics in defined molecular bins. Mol Oncol, 7(4), 776-90. (Read full article)
  167. Spreafico A, Tentler JJ, Pitts TM, Tan AC, Gregory MA, Arcaroli JJ, Klauck PJ, McManus MC, Hansen RJ, Kim J, Micel LN, Selby HM, Newton TP, McPhillips KL, Gustafson DL, Degregori JV, Messersmith WA, Winn RA, Eckhardt SG (2013). Rational combination of a MEK inhibitor, selumetinib, and the Wnt/calcium pathway modulator, cyclosporin A, in preclinical models of colorectal cancer. Clin Cancer Res, 19(15), 4149-62. (Read full article)
  168. Harvell DM, Kim J, OBrien J, Tan AC, Borges VF, Schedin P, Jacobsen BM, Horwitz KB (2013). Genomic signatures of pregnancy-associated breast cancer epithelia and stroma and their regulation by estrogens and progesterone. Horm Cancer, 4(3), 140-53. (Read full article)
  169. Andrysik Z, Kim J, Tan AC, Espinosa JM (2013). A genetic screen identifies TCF3/E2A and TRIAP1 as pathway-specific regulators of the cellular response to p53 activation. Cell Rep, 3(5), 1346-54. (Read full article)
  170. Schlegel J, Sambade MJ, Sather S, Moschos SJ, Tan AC, Winges A, DeRyckere D, Carson CC, Trembath DG, Tentler JJ, Eckhardt SG, Kuan PF, Hamilton RL, Duncan LM, Miller CR, Nikolaishvili-Feinberg N, Midkiff BR, Liu J, Zhang W, Yang C, Wang X, Frye SV, Earp HS, Shields JM, Graham DK (2013). MERTK receptor tyrosine kinase is a therapeutic target in melanoma. J Clin Invest, 123(5), 2257-67. (Read full article)
  171. Singleton KR, Kim J, Hinz TK, Marek LA, Cass-Selves M, Hatheway C, Tan AC, DeGregori J, Heasley LE (2013). A receptor tyrosine kinase network composed of fibroblast growth factor receptors, epidermal growth factor receptor, v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, and hepatocyte growth factor receptor drives growth and survival of head and neck squamous carcinoma cell lines. Mol Pharmacol, 83(4), 882-93. (Read full article)
  172. Pitts TM, Kulikowski GN, Tan AC, Murray BW, Arcaroli JJ, Tentler JJ, Spreafico A, Selby HM, Kachaeva MI, McPhillips KL, Britt BC, Bradshaw-Pierce EL, Messersmith WA, Varella-Garcia M, Eckhardt SG (2013). Association of the epithelial-to-mesenchymal transition phenotype with responsiveness to the p21-activated kinase inhibitor, PF-3758309, in colon cancer models. Front Pharmacol, 4, 35. (Read full article)
  173. Ware KE, Hinz TK, Kleczko E, Singleton KR, Marek LA, Helfrich BA, Cummings CT, Graham DK, Astling D, Tan AC, Heasley LE (2013). A mechanism of resistance to gefitinib mediated by cellular reprogramming and the acquisition of an FGF2-FGFR1 autocrine growth loop. Oncogenesis, 2, e39. (Read full article)
  174. Bradshaw-Pierce EL, Pitts TM, Tan AC, McPhillips K, West M, Gustafson DL, Halsey C, Nguyen L, Lee NV, Kan JL, Murray BW, Eckhardt SG (2013). Tumor P-Glycoprotein Correlates with Efficacy of PF-3758309 in in vitro and in vivo Models of Colorectal Cancer. Front Pharmacol, 4, 22. (Read full article)
  175. Diamond JR, Eckhardt SG, Tan AC, Newton TP, Selby HM, Brunkow KL, Kachaeva MI, Varella-Garcia M, Pitts TM, Bray MR, Fletcher GC, Tentler JJ (2012). Predictive biomarkers of sensitivity to the aurora and angiogenic kinase inhibitor ENMD-2076 in preclinical breast cancer models. Clin Cancer Res, 19(1), 291-303. (Read full article)
  176. Giles ED, Wellberg EA, Astling DP, Anderson SM, Thor AD, Jindal S, Tan AC, Schedin PS, Maclean PS (2012). Obesity and overfeeding affecting both tumor and systemic metabolism activates the progesterone receptor to contribute to postmenopausal breast cancer. Cancer Res, 72(24), 6490-501. (Read full article)
  177. Smith AL, Iwanaga R, Drasin DJ, Micalizzi DS, Vartuli RL, Tan AC, Ford HL (2012). The miR-106b-25 cluster targets Smad7, activates TGF-β signaling, and induces EMT and tumor initiating cell characteristics downstream of Six1 in human breast cancer. Oncogene, 31(50), 5162-71. (Read full article)
  178. Arcaroli J, Quackenbush K, Dasari A, Powell R, McManus M, Tan AC, Foster NR, Picus J, Wright J, Nallapareddy S, Erlichman C, Hidalgo M, Messersmith WA (2012). Biomarker-driven trial in metastatic pancreas cancer: feasibility in a multicenter study of saracatinib, an oral Src inhibitor, in previously treated pancreatic cancer. Cancer Med, 1(2), 207-17. (Read full article)
  179. Cass-Selves M, Kim J, Zhang Z, Helfrich BA, Gao D, Porter CC, Scarborough HA, Bunn PA Jr, Chan DC, Tan AC, DeGregori J (2012). Tankyrase and the canonical Wnt pathway protect lung cancer cells from EGFR inhibition. Cancer Res, 72(16), 4154-64. (Read full article)
  180. Sullivan KD, Padilla-Just N, Henry RE, Porter CC, Kim J, Tentler JJ, Eckhardt SG, Tan AC, DeGregori J, Espinosa JM (2012). ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53. Nat Chem Biol, 8(7), 646-54. (Read full article)
  181. Porter CC, Kim J, Fosmire S, Gearheart CM, van Linden A, Baturin D, Zaberezhnyy V, Patel PR, Gao D, Tan AC, DeGregori J (2012). Integrated genomic analyses identify WEE1 as a critical mediator of cell fate and a novel therapeutic target in acute myeloid leukemia. Leukemia, 26(6), 1266-76. (Read full article)
  182. Arcaroli JJ, Powell RW, Varella-Garcia M, McManus M, Tan AC, Quackenbush KS, Pitts TM, Gao D, Spreafico A, Dasari A, Touban BM, Messersmith WA (2012). ALDH+ tumor-initiating cells exhibiting gain in NOTCH1 gene copy number have enhanced regrowth sensitivity to a γ-secretase inhibitor and irinotecan in colorectal cancer. Mol Oncol, 6(3), 370-81. (Read full article)
  183. Arcaroli JJ, Quackenbush KS, Powell RW, Pitts TM, Spreafico A, Varella-Garcia M, Bemis L, Tan AC, Reinemann JM, Touban BM, Dasari A, Eckhardt SG, Messersmith WA (2012). Common PIK3CA mutants and a novel 3' UTR mutation are associated with increased sensitivity to saracatinib. Clin Cancer Res, 18(9), 2704-14. (Read full article)
  184. Haughian JM, Pinto MP, Harrell JC, Bliesner BS, Joensuu KM, Dye WW, Sartorius CA, Tan AC, Heikkil P, Perou CM, Horwitz KB (2011). Maintenance of hormone responsiveness in luminal breast cancers by suppression of Notch. Proc Natl Acad Sci U S A, 109(8), 2742-7. (Read full article)
  185. Morelli MP, Tentler JJ, Kulikowski GN, Tan AC, Bradshaw-Pierce EL, Pitts TM, Brown AM, Nallapareddy S, Arcaroli JJ, Serkova NJ, Hidalgo M, Ciardiello F, Eckhardt SG (2011). Preclinical activity of the rational combination of selumetinib (AZD6244) in combination with vorinostat in KRAS-mutant colorectal cancer models. Clin Cancer Res, 18(4), 1051-62. (Read full article)
  186. Fernandez AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, Yamamoto H, Hidalgo M, Tan AC, Galm O, Ferrer I, Sanchez-Cespedes M, Villanueva A, Carmona J, Sanchez-Mut JV, Berdasco M, Moreno V, Capella G, Monk D, Ballestar E, Ropero S, Martinez R, Sanchez-Carbayo M, Prosper F, Agirre X, Fraga MF, Graa O, Perez-Jurado L, Mora J, Puig S, Prat J, Badimon L, Puca AA, Meltzer SJ, Lengauer T, Bridgewater J, Bock C, Esteller M (2011). A DNA methylation fingerprint of 1628 human samples. Genome Res, 22(2), 407-19. (Read full article)
  187. Liu X, Li F, Stubblefield EA, Blanchard B, Richards TL, Larson GA, He Y, Huang Q, Tan AC, Zhang D, Benke TA, Sladek JR, Zahniser NR, Li CY (2011). Direct reprogramming of human fibroblasts into dopaminergic neuron-like cells. Cell Res, 22(2), 321-32. (Read full article)
  188. Tan AC (2011). Employing gene set top scoring pairs to identify deregulated pathway-signatures in dilated cardiomyopathy from integrated microarray gene expression data. Methods Mol Biol, 802, 345-61. (Read full article)
  189. Kim J, Tan AC (2011). BiNGS!SL-seq: a bioinformatics pipeline for the analysis and interpretation of deep sequencing genome-wide synthetic lethal screen. Methods Mol Biol, 802, 389-98. (Read full article)
  190. Khoo SK, Petillo D, Kang UJ, Resau JH, Berryhill B, Linder J, Forsgren L, Neuman LA, Tan AC (2013). Plasma-based circulating MicroRNA biomarkers for Parkinson's disease. J Parkinsons Dis, 2(4), 321-31. (Read full article)
  191. Khoo SK, Petillo D, Parida M, Tan AC, Resau JH, Obaro SK (2011). Host response transcriptional profiling reveals extracellular components and ABC (ATP-binding cassette) transporters gene enrichment in typhoid fever-infected Nigerian children. BMC Infect Dis, 11, 241. (Read full article)
  192. Garrido-Laguna I, Uson M, Rajeshkumar NV, Tan AC, de Oliveira E, Karikari C, Villaroel MC, Salomon A, Taylor G, Sharma R, Hruban RH, Maitra A, Laheru D, Rubio-Viqueira B, Jimeno A, Hidalgo M (2011). Tumor engraftment in nude mice and enrichment in stroma- related gene pathways predict poor survival and resistance to gemcitabine in patients with pancreatic cancer. Clin Cancer Res, 17(17), 5793-800. (Read full article)
  193. Lyons TR, OBrien J, Borges VF, Conklin MW, Keely PJ, Eliceiri KW, Marusyk A, Tan AC, Schedin P (2011). Postpartum mammary gland involution drives progression of ductal carcinoma in situ through collagen and COX-2. Nat Med, 17(9), 1109-15. (Read full article)
  194. Huang Q, Li F, Liu X, Li W, Shi W, Liu FF, OSullivan B, He Z, Peng Y, Tan AC, Zhou L, Shen J, Han G, Wang XJ, Thorburn J, Thorburn A, Jimeno A, Raben D, Bedford JS, Li CY (2011). Caspase 3-mediated stimulation of tumor cell repopulation during cancer radiotherapy. Nat Med, 17(7), 860-6. (Read full article)
  195. Xiong Y, Li Z, Ji M, Tan AC, Bemis J, Tse JV, Huang G, Park J, Ji C, Chen J, Bemis LT, Bunting KD, Tse W (2011). MIR29B regulates expression of MLLT11 (AF1Q), an MLL fusion partner, and low MIR29B expression associates with adverse cytogenetics and poor overall survival in AML. Br J Haematol, 153(6), 753-7. (Read full article)
  196. Jones LK, Zou F, Kheifets A, Rybnikov K, Berry D, Tan AC (2011). Confident predictability: identifying reliable gene expression patterns for individualized tumor classification using a local minimax kernel algorithm. BMC Med Genomics, 4, 10. (Read full article)
  197. Deng Y, Liu J, Han G, Lu SL, Wang SY, Malkoski S, Tan AC, Deng C, Wang XJ, Zhang Q (2010). Redox-dependent Brca1 transcriptional regulation by an NADH-sensor CtBP1. Oncogene, 29(50), 6603-8. (Read full article)
  198. Tentler JJ, Nallapareddy S, Tan AC, Spreafico A, Pitts TM, Morelli MP, Selby HM, Kachaeva MI, Flanigan SA, Kulikowski GN, Leong S, Arcaroli JJ, Messersmith WA, Eckhardt SG (2010). Identification of predictive markers of response to the MEK1/2 inhibitor selumetinib (AZD6244) in K-ras-mutated colorectal cancer. Mol Cancer Ther, 9(12), 3351-62. (Read full article)
  199. Flanigan SA, Pitts TM, Eckhardt SG, Tentler JJ, Tan AC, Thorburn A, Leong S (2010). The insulin-like growth factor I receptor/insulin receptor tyrosine kinase inhibitor PQIP exhibits enhanced antitumor effects in combination with chemotherapy against colorectal cancer models. Clin Cancer Res, 16(22), 5436-46. (Read full article)
  200. Camidge DR, Kono SA, Flacco A, Tan AC, Doebele RC, Zhou Q, Crino L, Franklin WA, Varella-Garcia M (2010). Optimizing the detection of lung cancer patients harboring anaplastic lymphoma kinase (ALK) gene rearrangements potentially suitable for ALK inhibitor treatment. Clin Cancer Res, 16(22), 5581-90. (Read full article)
  201. Gao D, Kim J, Kim H, Phang TL, Selby H, Tan AC, Tong T (2010). A survey of statistical software for analysing RNA-seq data. Hum Genomics, 5(1), 56-60. (Read full article)
  202. Garrido-Laguna I, Tan AC, Uson M, Angenendt M, Ma WW, Villaroel MC, Zhao M, Rajeshkumar NV, Jimeno A, Donehower R, Iacobuzio-Donahue C, Barrett M, Rudek MA, Rubio-Viqueira B, Laheru D, Hidalgo M (2010). Integrated preclinical and clinical development of mTOR inhibitors in pancreatic cancer. Br J Cancer, 103(5), 649-55. (Read full article)
  203. Arcaroli JJ, Touban BM, Tan AC, Varella-Garcia M, Powell RW, Eckhardt SG, Elvin P, Gao D, Messersmith WA (2010). Gene array and fluorescence in situ hybridization biomarkers of activity of saracatinib (AZD0530), a Src inhibitor, in a preclinical model of colorectal cancer. Clin Cancer Res, 16(16), 4165-77. (Read full article)
  204. Pitts TM, Tan AC, Kulikowski GN, Tentler JJ, Brown AM, Flanigan SA, Leong S, Coldren CD, Hirsch FR, Varella-Garcia M, Korch C, Eckhardt SG (2010). Development of an integrated genomic classifier for a novel agent in colorectal cancer: approach to individualized therapy in early development. Clin Cancer Res, 16(12), 3193-204. (Read full article)
  205. Tan AC, Jimeno A, Lin SH, Wheelhouse J, Chan F, Solomon A, Rajeshkumar NV, Rubio-Viqueira B, Hidalgo M (2009). Characterizing DNA methylation patterns in pancreatic cancer genome. Mol Oncol, 3(5-6), 425-38. (Read full article)
  206. Kent OA, Mullendore M, Wentzel EA, Lpez-Romero P, Tan AC, Alvarez H, West K, Ochs MF, Hidalgo M, Arking DE, Maitra A, Mendell JT (2009). A resource for analysis of microRNA expression and function in pancreatic ductal adenocarcinoma cells. Cancer Biol Ther, 8(21), 2013-24. (Read full article)
  207. Tian Y, Tan AC, Sun X, Olson MT, Xie Z, Jinawath N, Chan DW, Shih IeM, Zhang Z, Zhang H (2010). Quantitative proteomic analysis of ovarian cancer cells identified mitochondrial proteins associated with Paclitaxel resistance. Proteomics Clin Appl, 3(11), 1288-95. (Read full article)
  208. Chen CS, Sullivan S, Anderson T, Tan AC, Alex PJ, Brant SR, Cuffari C, Bayless TM, Talor MV, Burek CL, Wang H, Li R, Datta LW, Wu Y, Winslow RL, Zhu H, Li X (2009). Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. Mol Cell Proteomics, 8(8), 1765-76. (Read full article)
  209. Rajeshkumar NV, Tan AC, De Oliveira E, Womack C, Wombwell H, Morgan S, Warren MV, Walker J, Green TP, Jimeno A, Messersmith WA, Hidalgo M (2009). Antitumor effects and biomarkers of activity of AZD0530, a Src inhibitor, in pancreatic cancer. Clin Cancer Res, 15(12), 4138-46. (Read full article)
  210. Messersmith WA, Rajeshkumar NV, Tan AC, Wang XF, Diesl V, Choe SE, Follettie M, Coughlin C, Boschelli F, Garcia-Garcia E, Lopez-Rios F, Jimeno A, Hidalgo M (2009). Efficacy and pharmacodynamic effects of bosutinib (SKI-606), a Src/Abl inhibitor, in freshly generated human pancreas cancer xenografts. Mol Cancer Ther, 8(6), 1484-93. (Read full article)
  211. Song D, Chaerkady R, Tan AC, Garca-Garca E, Nalli A, Surez-Gauthier A, Lpez-Ros F, Zhang XF, Solomon A, Tong J, Read M, Fritz C, Jimeno A, Pandey A, Hidalgo M (2008). Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Mol Cancer Ther, 7(10), 3275-84. (Read full article)
  212. Jimeno A, Tan AC, Coffa J, Rajeshkumar NV, Kulesza P, Rubio-Viqueira B, Wheelhouse J, Diosdado B, Messersmith WA, Iacobuzio-Donahue C, Maitra A, Varella-Garcia M, Hirsch FR, Meijer GA, Hidalgo M (2008). Coordinated epidermal growth factor receptor pathway gene overexpression predicts epidermal growth factor receptor inhibitor sensitivity in pancreatic cancer. Cancer Res, 68(8), 2841-9. (Read full article)
  213. Xu L, Tan AC, Winslow RL, Geman D (2008). Merging microarray data from separate breast cancer studies provides a robust prognostic test. BMC Bioinformatics, 9, 125. (Read full article)
  214. Tan AC, Fan JB, Karikari C, Bibikova M, Garcia EW, Zhou L, Barker D, Serre D, Feldmann G, Hruban RH, Klein AP, Goggins M, Couch FJ, Hudson TJ, Winslow RL, Maitra A, Chakravarti A (2007). Allele-specific expression in the germline of patients with familial pancreatic cancer: an unbiased approach to cancer gene discovery. Cancer Biol Ther, 7(1), 135-44. (Read full article)
  215. Tan AC, Naiman DQ, Xu L, Winslow RL, Geman D (2005). Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics, 21(20), 3896-904. (Read full article)
  216. Xu L, Tan AC, Naiman DQ, Geman D, Winslow RL (2005). Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinformatics, 21(20), 3905-11. (Read full article)
  217. Ren T, Veeramalai M, Tan AC, Gilbert D (2005). MSAT: a multiple sequence alignment tool based on TOPS. Appl Bioinformatics, 3(2-3), 149-58. (Read full article)
  218. Tan AC, Gilbert D (2004). Ensemble machine learning on gene expression data for cancer classification. Appl Bioinformatics, 2(3 Suppl), S75-83. (Read full article)
  219. Tan AC, Gilbert D, Deville Y (2005). Multi-class protein fold classification using a new ensemble machine learning approach. Genome Inform, 14, 206-17. (Read full article)

Review

  1. Lee K, Lockhart JH, Xie M, Chaudhary R, Slebos RJC, Flores ER, Chung CH, Tan AC (2021). Deep Learning of Histopathology Images at the Single Cell Level. [Review]. Front Artif Intell, 4, 754641. (Read full article)
  2. Nassar KW, Tan AC (2019). The mutational landscape of mucosal melanoma. [Review]. Semin Cancer Biol, 61, 139-148. (Read full article)
  3. Wilding CP, Elms ML, Judson I, Tan AC, Jones RL, Huang PH (2019). The landscape of tyrosine kinase inhibitors in sarcomas: looking beyond pazopanib. [Review]. Expert Rev Anticancer Ther, 19(11), 971-991. (Read full article)
  4. Tan AC, Vyse S, Huang PH (2016). Exploiting receptor tyrosine kinase co-activation for cancer therapy. [Review]. Drug Discov Today, 22(1), 72-84. (Read full article)
  5. Hintzsche JD, Robinson WA, Tan AC (2016). A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data. [Review]. Int J Genomics, 2016, 7983236. (Read full article)
  6. Lieu CH, Tan AC, Leong S, Diamond JR, Eckhardt SG (2013). From bench to bedside: lessons learned in translating preclinical studies in cancer drug development. [Review]. J Natl Cancer Inst, 105(19), 1441-56. (Read full article)
  7. Tentler JJ, Tan AC, Weekes CD, Jimeno A, Leong S, Pitts TM, Arcaroli JJ, Messersmith WA, Eckhardt SG (2012). Patient-derived tumour xenografts as models for oncology drug development. [Review]. Nat Rev Clin Oncol, 9(6), 338-50. (Read full article)
  8. Kim H, Kim J, Selby H, Gao D, Tong T, Phang TL, Tan AC (2011). A short survey of computational analysis methods in analysing ChIP-seq data. [Review]. Hum Genomics, 5(2), 117-23. (Read full article)
  9. Leong S, Messersmith WA, Tan AC, Eckhardt SG (2010). Novel agents in the treatment of metastatic colorectal cancer. [Review]. Cancer J, 16(3), 273-82. (Read full article)

Editorial

  1. Homayouni R, Manda P, Tan AC, Qin ZS (2023). Editorial: AI and data science in drug development and public health: Highlights from the MCBIOS 2022 conference. Front Big Data, 6, 1156811. (Read full article)
  2. Tan AC, Huang PH (2020). Translational genomics for rare cancers: Challenges and opportunity. Semin Cancer Biol, 61, iii-iv. (Read full article)
  3. Tan AC, Ryall KA, Huang PH (2015). Expanding the computational toolbox for interrogating cancer kinomes. Pharmacogenomics, 17(2), 95-7. (Read full article)

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