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Aik Choon Tan, PhD

Academic Rank: Senior Member

Overview


Discipline

    • Biostatistics and Bioinformatics
    • Chemical Biology and Molecular Medicine Program

Education & Training

Fellowship:

  • University of Glasgow, PhD - Computer Science/Bioinformatics
  • Johns Hopkins University Whiting School of Engineering, - Computational Medicine
  • University of Colorado, - Computational Bioscience
  • Johns Hopkins University School of Medicine, - Gastrointenstinal Oncology
Research

  Dr. Tan’s research interests translational bioinformatics and cancer systems biology, primarily through the development of computational and statistical learning methods for the analysis and integration of highthroughput multi-omics data in understanding and overcoming treatment resistance mechanisms in cancer. Dr. Tan’s lab acts as a “connector” to provide seamless integration of computational and statistical methods in experimental and clinical research. Dr. Tan’s current research focus is drug repurposing, biomedical data science and precision oncology.

Publications

  • 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. Resistance to targeted therapies as a multifactorial, gradual adaptation to inhibitor specific selective pressures. Nat Commun. 2020 May.11(1):2393. Pubmedid: 32409712. Pmcid: PMC7224215.
  • Davis SL, Ionkina AA, Bagby SM, Orth JD, Gittleman B, Marcus JM, Lam ET, Corr BR, O'Bryant 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. 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. 2020 May.26(17):4633-4642. Pubmedid: 32414750.
  • 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. Inhibiting Translation Elongation with SVC112 Suppresses Cancer Stem Cells and Inhibits Growth in Head and Neck Squamous Carcinoma. Cancer Res. 2020 Mar.80(5):1183-1198. Pubmedid: 31911553. Pmcid: PMC7056512.
  • Schreiber AR, Kar A, Goodspeed AE, Pozdeyev N, Somerset H, Raeburn CD, Tan AC, Leong S, Wierman ME, Kiseljak-Vassiliades K. Leptomeningeal Metastasis from Adrenocortical Carcinoma: A Case Report. J Endocr Soc. 2020 Mar.4(3):bvaa017. Pubmedid: 32154490. Pmcid: PMC7053406.
  • 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. MCL1 inhibitors S63845/MIK665 plus Navitoclax synergistically kill difficult-to-treat melanoma cells. Cell Death Dis. 2020 Jun.11(6):443. Pubmedid: 32513939. Pmcid: PMC7280535.
  • 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. Induction of IRAK-M in melanoma induces caspase-3 dependent apoptosis by reducing TRAF6 and calpastatin levels. Commun Biol. 2020 Jun.3(1):306. Pubmedid: 32533049. Pmcid: PMC7293221.
  • Iwanaga R, Truong BT, Hsu JY, Lambert KA, Vyas R, Orlicky D, Shellman YG, Tan AC, Ceol C, Artinger KB. Loss of prdm1a accelerates melanoma onset and progression. Mol Carcinogen. 2020 Jun.59(9):1052-1063. Pubmedid: 32562448.
  • Kern JA, Kim J, Foster DG, Mishra R, Gardner EE, Poirier JT, Rivard C, Yu H, Finigan JH, Dowlati A, Rudin CM, Tan AC. Role of mTOR As an Essential Kinase in SCLC. J Thorac Oncol. 2020 Jun.15(9):1522-1534. Pubmedid: 32599072. Pmcid: PMC7483946.
  • 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. Pre-Treatment Mutational and Transcriptomic Landscape of Responding Metastatic Melanoma Patients to Anti-PD1 Immunotherapy. Cancers (Basel). 2020 Jul.12(7). Pubmedid: 32708981. Pmcid: PMC7409244.
  • 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. First-in-Class Inhibitors of Oncogenic CHD1L with Preclinical Activity against Colorectal Cancer. Mol Cancer Ther. 2020 Aug.19(8):1598-1612. Pubmedid: 32499299.
  • Nassar KW, Tan AC. The mutational landscape of mucosal melanoma. Semin Cancer Biol. 2020 Apr.61:139-148. Pubmedid: 31655118. Pmcid: PMC7078020.
  • Tan AC, Huang PH. Translational genomics for rare cancers: Challenges and opportunity. Semin Cancer Biol. 2020 Apr.61:iii-iiv. Pubmedid: 32092353.
  • 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. First-in-Class Phosphorylated-p68 Inhibitor RX-5902 Inhibits β-Catenin Signaling and Demonstrates Antitumor Activity in Triple-Negative Breast Cancer. Mol Cancer Ther. 2019 Sep.18(11):1916-1925. Pubmedid: 31488700. Pmcid: PMC6825586.
  • Aguado BA, Schuetze KB, Grim JC, Walker CJ, Cox AC, Ceccato TL, Tan AC, Sucharov CC, Leinwand LA, Taylor MRG, McKinsey TA, Anseth KS. Transcatheter aortic valve replacements alter circulating serum factors to mediate myofibroblast deactivation. Sci Transl Med. 2019 Sep.11(509). Pubmedid: 31511425. Pmcid: PMC6754739.
  • Samson JM, Ravindran Menon D, Smith DE, Baird E, Kitano T, Gao D, Tan AC, Fujita M. Clinical implications of ALDH1A1 and ALDH1A3 mRNA expression in melanoma subtypes. Chem Biol Interact. 2019 Sep.314:108822. Pubmedid: 31580832. Pmcid: PMC6916670.
  • Wilding CP, Elms ML, Judson I, Tan AC, Jones RL, Huang PH. The landscape of tyrosine kinase inhibitors in sarcomas: looking beyond pazopanib. Expert Rev Anticancer Ther. 2019 Nov.19(11):971-991. Pubmedid: 31665941. Pmcid: PMC6882314.
  • 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. Comprehensive Genetic Characterization of Human Thyroid Cancer Cell Lines: A Validated Panel for Preclinical Studies. Clin Cancer Res. 2019 May.25(10):3141-3151. Pubmedid: 30737244. Pmcid: PMC6522280.
  • Yoo M, Shin J, Kim H, Kim J, Kang J, Tan AC. Exploring the molecular mechanisms of Traditional Chinese Medicine components using gene expression signatures and connectivity map. Comput Methods Programs Biomed. 2019 Jun.174:33-40. Pubmedid: 29650251.
  • Rogers TJ, Christenson JL, Greene LI, O'Neill KI, Williams MM, Gordon MA, Nemkov T, D'Alessandro A, Degala GD, Shin J, Tan AC, Cittelly DM, Lambert JR, Richer JK. Reversal of Triple-Negative Breast Cancer EMT by miR-200c Decreases Tryptophan Catabolism and a Program of Immunosuppression. Mol Cancer Res. 2019 Jan.17(1):30-41. Pubmedid: 30213797. Pmcid: PMC6318067.
  • Jeon M, Park D, Lee J, Jeon H, Ko M, Kim S, Choi Y, Tan AC, Kang J. ReSimNet: drug response similarity prediction using Siamese neural networks. Bioinformatics. 2019 Dec.35(24):5249-5256. Pubmedid: 31116384.
  • Hinz TK, Kleczko EK, Singleton KR, Calhoun J, Marek LA, Kim J, Tan AC, Heasley LE. Functional RNAi Screens Define Distinct Protein Kinase Vulnerabilities in EGFR-Dependent HNSCC Cell Lines. Mol Pharmacol. 2019 Dec.96(6):862-870. Pubmedid: 31554698. Pmcid: PMC7385532.
  • de la Iglesia JV, Slebos RJ, 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 JJ, Harrison LB, Wenig B, Conejo-Garcia JR, Hernandez-Prera JC, Chung CH. Effects of Tobacco Smoking on the Tumor Immune Microenvironment in Head and Neck Squamous Cell Carcinoma. Clin Cancer Res. 2019 Dec.26(6):1474-1485. Pubmedid: 31848186. Pmcid: PMC7073297.
  • Gan CP, Sam KK, Yee PS, Zainal NS, Lee BKB, Abdul Rahman ZA, Patel V, Tan AC, Zain RB, Cheong SC. IFITM3 knockdown reduces the expression of CCND1 and CDK4 and suppresses the growth of oral squamous cell carcinoma cells. Cell Oncol (Dordr). 2019 Aug.42(4):477-490. Pubmedid: 30949979.
  • Kessler BE, Mishall KM, Kellett MD, Clark EG, Pugazhenthi U, Pozdeyev N, Kim J, Tan AC, Schweppe RE. 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. 2019 Apr.38(14):2565-2579. Pubmedid: 30531837. Pmcid: PMC6450711.
  • Parrish JK, McCann TS, Sechler M, Sobral LM, Ren W, Jones KL, Tan AC, Jedlicka P. 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. 2018 Sep.9(69):33110-33123. Pubmedid: 30237855. Pmcid: PMC6145692.
  • Suda K, Kim J, Murakami I, Rozeboom L, Shimoji M, Shimizu S, Rivard CJ, Mitsudomi T, Tan AC, Hirsch FR. Innate Genetic Evolution of Lung Cancers and Spatial Heterogeneity: Analysis of Treatment-Naïve Lesions. J Thorac Oncol. 2018 Oct.13(10):1496-1507. Pubmedid: 29933065. Pmcid: PMC6153034.
  • 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. 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. 2018 Oct.24(20):4949-4959. Pubmedid: 30084837.
  • Suda K, Murakami I, Yu H, Kim J, Tan AC, Mizuuchi H, Rozeboom L, Ellison K, Rivard CJ, Mitsudomi T, Hirsch FR. CD44 Facilitates Epithelial-to-Mesenchymal Transition Phenotypic Change at Acquisition of Resistance to EGFR Kinase Inhibitors in Lung Cancer. Mol Cancer Ther. 2018 Oct.17(10):2257-2265. Pubmedid: 30049789.
  • 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. Resistance to Radiotherapy and PD-L1 Blockade Is Mediated by TIM-3 Upregulation and Regulatory T-Cell Infiltration. Clin Cancer Res. 2018 Nov.24(21):5368-5380. Pubmedid: 30042205. Pmcid: PMC6886391.
  • Kim J, Yoo M, Shin J, Kim H, Kang J, Tan AC. Systems Pharmacology-Based Approach of Connecting Disease Genes in Genome-Wide Association Studies with Traditional Chinese Medicine. Int J Genomics. 2018 Mar.2018:7697356. Pubmedid: 29765977. Pmcid: PMC5885494.
  • 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. Salivary Gland Cancer Patient-Derived Xenografts Enable Characterization of Cancer Stem Cells and New Gene Events Associated with Tumor Progression. Clin Cancer Res. 2018 Jun.24(12):2935-2943. Pubmedid: 29555661. Pmcid: PMC6004240.
  • Powers RK, Goodspeed A, Pielke-Lombardo H, Tan AC, Costello JC. GSEA-InContext: identifying novel and common patterns in expression experiments. Bioinformatics. 2018 Jul.34(13):i555-i564. Pubmedid: 29950010. Pmcid: PMC6022535.
  • 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. GENIPAC: A Genomic Information Portal for Head and Neck Cancer Cell Systems. J Dent Res. 2018 Jul.97(8):909-916. Pubmedid: 29512401.
  • 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. Genetic Analysis of 779 Advanced Differentiated and Anaplastic Thyroid Cancers. Clin Cancer Res. 2018 Jul.24(13):3059-3068. Pubmedid: 29615459. Pmcid: PMC6030480.
  • 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. AMPK/FIS1-Mediated Mitophagy Is Required for Self-Renewal of Human AML Stem Cells. Cell Stem Cell. 2018 Jul.23(1):86-100.e6. Pubmedid: 29910151. Pmcid: PMC6035102.
  • Yue Z, Zheng Q, Neylon MT, Yoo M, Shin J, Zhao Z, Tan AC, Chen JY. PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. Nucleic Acids Res. 2018 Jan.46(D1):D668-D676. Pubmedid: 29126216. Pmcid: PMC5753198.
  • 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. ALK Inhibitor Response in Melanomas Expressing Fusions and Alternate Isoforms. Mol Cancer Ther. 2018 Jan.17(1):222-231. Pubmedid: 29054983. Pmcid: PMC5752582.
  • Kim S, Park D, Choi Y, Lee K, Kim B, Jeon M, Kim J, Tan AC, Kang J. A Pilot Study of Biomedical Text Comprehension using an Attention-Based Deep Neural Reader: Design and Experimental Analysis. JMIR Med Inform. 2018 Jan.6(1):e2. Pubmedid: 29305341. Pmcid: PMC5783222.
  • Lee K, Kim B, Choi Y, Kim S, Shin W, Lee S, Park S, Kim S, Tan AC, Kang J. Deep learning of mutation-gene-drug relations from the literature. BMC Bioinformatics. 2018 Jan.19(1):21. Pubmedid: 29368597. Pmcid: PMC5784504.
  • 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. Antitumor activity of the polo-like kinase inhibitor, TAK-960, against preclinical models of colorectal cancer. BMC Cancer. 2018 Feb.18(1):136. Pubmedid: 29402316. Pmcid: PMC5800287.
  • Pilling AB, Kim J, Estrada-Bernal A, Zhou Q, Le AT, Singleton KR, Heasley LE, Tan AC, DeGregori J, Doebele RC. ALK is a critical regulator of the MYC-signaling axis in ALK positive lung cancer. Oncotarget. 2018 Feb.9(10):8823-8835. Pubmedid: 29507657. Pmcid: PMC5823650.
  • Davis SL, Eckhardt SG, Diamond JR, Messersmith WA, Dasari A, Weekes CD, Lieu CH, Kane M, Choon Tan A, Pitts TM, Leong S. 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. 2018 Dec.23(12):1409-e140. Pubmedid: 30139840.
  • 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. CDK1 Interacts with Sox2 and Promotes Tumor Initiation in Human Melanoma. Cancer Res. 2018 Dec.78(23):6561-6574. Pubmedid: 30297536. Pmcid: PMC6279496.
  • Hintzsche JD, Yoo M, Kim J, Amato CM, Robinson WA, Tan AC. IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics. BMC Med Genomics. 2018 Apr.11(Suppl 2):26. Pubmedid: 29697364. Pmcid: PMC5918430.
  • 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. Molecular Analyses Reveal Inflammatory Mediators in the Solid Component and Cyst Fluid of Human Adamantinomatous Craniopharyngioma. J Neuropath Exp Neur. 2017 Sep.76(9):779-788. Pubmedid: 28859336. Pmcid: PMC6005018.
  • Zhang C, Liu Z, Bunker E, Ramirez A, Lee S, Peng Y, Tan AC, Eckhardt SG, Chapnick DA, Liu X. 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. 2017 Sep.292(36):15105-15120. Pubmedid: 28673964. Pmcid: PMC5592685.
  • 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. Evaluation of the efficacy of dasatinib, a Src/Abl inhibitor, in colorectal cancer cell lines and explant mouse model. PLoS One. 2017 Nov.12(11):e0187173. Pubmedid: 29091939. Pmcid: PMC5665512.
  • Harder B, Tian W, La Clair JJ, Tan AC, Ooi A, Chapman E, Zhang DD. Brusatol overcomes chemoresistance through inhibition of protein translation. Mol Carcinogen. 2017 May.56(5):1493-1500. Pubmedid: 28019675. Pmcid: PMC5404829.
  • Ionkina AA, Tentler JJ, Kim J, Capasso A, Pitts TM, Ryall KA, Howison RR, Kabos P, Sartorius CA, Tan AC, Eckhardt SG, Diamond JR. 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. 2017 May.7:94. Pubmedid: 28555173. Pmcid: PMC5430301.
  • Scarborough HA, Helfrich BA, Casás-Selves M, Schuller AG, Grosskurth SE, Kim J, Tan AC, Chan DC, Zhang Z, Zaberezhnyy V, Bunn PA, DeGregori J. 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. 2017 Mar.23(6):1531-1541. Pubmedid: 27663586. Pmcid: PMC5354947.
  • 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. Whole-exome sequencing identifies recurrent SF3B1 R625 mutation and comutation of NF1 and KIT in mucosal melanoma. Melanoma Res. 2017 Jun.27(3):189-199. Pubmedid: 28296713. Pmcid: PMC5470740.
  • Ohm AM, Tan AC, Heasley LE, Reyland ME. Co-dependency of PKCδ and K-Ras: inverse association with cytotoxic drug sensitivity in KRAS mutant lung cancer. Oncogene. 2017 Jul.36(30):4370-4378. Pubmedid: 28368426. Pmcid: PMC5532068.
  • Tan AC, Vyse S, Huang PH. Exploiting receptor tyrosine kinase co-activation for cancer therapy. Drug Discov Today. 2017 Jan.22(1):72-84. Pubmedid: 27452454. Pmcid: PMC5346155.
  • Murakami A, Wang L, Kalhorn S, Schraml P, Rathmell WK, Tan AC, Nemenoff R, Stenmark K, Jiang BH, Reyland ME, Heasley L, Hu CJ. Context-dependent role for chromatin remodeling component PBRM1/BAF180 in clear cell renal cell carcinoma. Oncogenesis. 2017 Jan.6(1):e287. Pubmedid: 28092369. Pmcid: PMC5294252.
  • Lee BK, Tiong KH, Chang JK, Liew CS, Abdul Rahman ZA, Tan AC, Khang TF, Cheong SC. DeSigN: connecting gene expression with therapeutics for drug repurposing and development. BMC Genomics. 2017 Jan.18(Suppl 1):934. Pubmedid: 28198666. Pmcid: PMC5310278.
  • 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. Kinase gene fusions in defined subsets of melanoma. Pigment Cell Melanoma Res. 2017 Jan.30(1):53-62. Pubmedid: 27864876. Pmcid: PMC5349025.
  • Hintzsche JD, Robinson WA, Tan AC. A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data. Int J Genomics. 2017 Jan.2016. Pubmedid: 28070503. Pmcid: PMC5192301.
  • 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. Targeting the protein ubiquitination machinery in melanoma by the NEDD8-activating enzyme inhibitor pevonedistat (MLN4924). Invest New Drugs. 2017 Feb.35(1):11-25. Pubmedid: 27783255. Pmcid: PMC5296256.
  • Nelson-Taylor SK, Le AT, Yoo M, Schubert L, Mishall KM, Doak A, Varella-Garcia M, Tan AC, Doebele RC. Resistance to RET-Inhibition in RET-Rearranged NSCLC Is Mediated By Reactivation of RAS/MAPK Signaling. Mol Cancer Ther. 2017 Aug.16(8):1623-1633. Pubmedid: 28500237. Pmcid: PMC5544556.
  • 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. Fibroblast Subtypes Regulate Responsiveness of Luminal Breast Cancer to Estrogen. Clin Cancer Res. 2017 Apr.23(7):1710-1721. Pubmedid: 27702820. Pmcid: PMC5378660.
  • Dimberg LY, Towers CG, Behbakht K, Hotz TJ, Kim J, Fosmire S, Porter CC, Tan AC, Thorburn A, Ford HL. A Genome-Wide Loss-of-Function Screen Identifies SLC26A2 as a Novel Mediator of TRAIL Resistance. Mol Cancer Res. 2017 Apr.15(4):382-394. Pubmedid: 28108622. Pmcid: PMC5380511.
  • Tan AC, Ryall KA, Huang PH. Expanding the computational toolbox for interrogating cancer kinomes. Pharmacogenomics. 2016 Sep.17(2):95-97. Pubmedid: 26666839.
  • Lee K, Shin W, Kim B, Lee S, Choi Y, Kim S, Jeon M, Tan AC, Kang J. HiPub: translating PubMed and PMC texts to networks for knowledge discovery. Bioinformatics. 2016 Sep.32(18):2886-2888. Pubmedid: 27485446. Pmcid: PMC5018380.
  • Bagby S, Messersmith WA, Pitts TM, Capasso A, Varella-Garcia M, Klauck PJ, Kim J, Tan AC, Eckhardt SG, Tentler JJ, Arcaroli J. Development and Maintenance of a Preclinical Patient Derived Tumor Xenograft Model for the Investigation of Novel Anti-Cancer Therapies. J Vis Exp. 2016 Sep.(115). Pubmedid: 27768028. Pmcid: PMC5092181.
  • Todd JR, Ryall KA, Vyse S, Wong JP, Natrajan RC, Yuan Y, Tan AC, Huang PH. Systematic analysis of tumour cell-extracellular matrix adhesion identifies independent prognostic factors in breast cancer. Oncotarget. 2016 Sep.7(39):62939-62953. Pubmedid: 27556857. Pmcid: PMC5325338.
  • 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. Regulation of Head and Neck Squamous Cancer Stem Cells by PI3K and SOX2. J Natl Cancer Inst. 2016 Sep.109(1). Pubmedid: 27634934. Pmcid: PMC5025278.
  • Zhang G, Scarborough H, Kim J, Rozhok AI, Chen YA, Zhang X, Song L, Bai Y, Fang B, Liu RZ, Koomen J, Tan AC, Degregori J, Haura EB. Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Sci Signal. 2016 Oct.9(450):rs12. Pubmedid: 27811184. Pmcid: PMC5377910.
  • Helfrich BA, Kim J, Gao D, Chan DC, Zhang Z, Tan AC, Bunn PA. Barasertib (AZD1152), a Small Molecule Aurora B Inhibitor, Inhibits the Growth of SCLC Cell Lines In Vitro and In Vivo. Mol Cancer Ther. 2016 Oct.15(10):2314-2322. Pubmedid: 27496133. Pmcid: PMC5050114.
  • Lee S, Kim D, Lee K, Choi J, Kim S, Jeon M, Lim S, Choi D, Kim S, Tan AC, Kang J. BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature. PLoS One. 2016 Oct.11(10):e0164680. Pubmedid: 27760149. Pmcid: PMC5070740.
  • 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. Dual Targeting of PDGFRα and FGFR1 Displays Synergistic Efficacy in Malignant Rhabdoid Tumors. Cell Rep. 2016 Oct.17(5):1265-1275. Pubmedid: 27783942. Pmcid: PMC5098123.
  • Gregory MA, D'Alessandro 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. ATM/G6PD-driven redox metabolism promotes FLT3 inhibitor resistance in acute myeloid leukemia. Proc Natl Acad Sci U S A. 2016 Oct.113(43):E6669-E6678. Pubmedid: 27791036. Pmcid: PMC5086999.
  • 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. Genetically-defined novel oral squamous cell carcinoma cell lines for the development of molecular therapies. Oncotarget. 2016 May.7(19):27802-27818. Pubmedid: 27050151. Pmcid: PMC5053689.
  • 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. IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. J Am Med Inform Assoc. 2016 Jul.23(4):721-730. Pubmedid: 27026619. Pmcid: PMC4926746.
  • 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. 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. 2016 Jan.138(1):195-205. Pubmedid: 26152787. Pmcid: PMC4618491.
  • 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. XactMice: humanizing mouse bone marrow enables microenvironment reconstitution in a patient-derived xenograft model of head and neck cancer. Oncogene. 2016 Jan.35(3):290-300. Pubmedid: 25893296. Pmcid: PMC4613815.
  • 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. A pilot study of cetuximab and the hedgehog inhibitor IPI-926 in recurrent/metastatic head and neck squamous cell carcinoma. Oral Oncol. 2016 Feb.53:74-79. Pubmedid: 26705064. Pmcid: PMC5676309.
  • Fornetti J, Flanders KC, Henson PM, Tan AC, Borges VF, Schedin P. Mammary epithelial cell phagocytosis downstream of TGF-β3 is characterized by adherens junction reorganization. Cell Death Differ. 2016 Feb.23(2):185-196. Pubmedid: 26113040. Pmcid: PMC4716300.
  • Cavalli G, Koenders M, Kalabokis V, Kim J, Tan AC, Garlanda C, Mantovani A, Dagna L, Joosten LA, Dinarello CA. Treating experimental arthritis with the innate immune inhibitor interleukin-37 reduces joint and systemic inflammation. Rheumatology (Oxford). 2016 Dec.55(12):2220-2229. Pubmedid: 27567100. Pmcid: PMC5144668.
  • Federer C, Yoo M, Tan AC. Big Data Mining and Adverse Event Pattern Analysis in Clinical Drug Trials. Assay Drug Dev Technol. 2016 Dec.14(10):557-566. Pubmedid: 27631620. Pmcid: PMC5175440.
  • 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. Antitumor activity of the aurora a selective kinase inhibitor, alisertib, against preclinical models of colorectal cancer. Oncotarget. 2016 Aug.7(31):50290-50301. Pubmedid: 27385211. Pmcid: PMC5226583.
  • Beadnell TC, Mishall KM, Zhou Q, Riffert SM, Wuensch KE, Kessler BE, Corpuz ML, Jing X, Kim J, Wang G, Tan AC, Schweppe RE. The Mitogen-Activated Protein Kinase Pathway Facilitates Resistance to the Src Inhibitor Dasatinib in Thyroid Cancer. Mol Cancer Ther. 2016 Aug.15(8):1952-1963. Pubmedid: 27222538. Pmcid: PMC4975658.
  • Pozdeyev N, Yoo M, Mackie R, Schweppe RE, Tan AC, Haugen BR. Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies. Oncotarget. 2016 Aug.7(32):51619-51625. Pubmedid: 27322211. Pmcid: PMC5239501.
  • Symonds JM, Ohm AM, Tan AC, Reyland ME. PKCδ regulates integrin αVβ3 expression and transformed growth of K-ras dependent lung cancer cells. Oncotarget. 2016 Apr.7(14):17905-17919. Pubmedid: 26918447. Pmcid: PMC4951259.
  • Lee K, Lee S, Park S, Kim S, Kim S, Choi K, Tan AC, Kang J. BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations. Database (Oxford). 2016 Apr.2016. Pubmedid: 27074804. Pmcid: PMC4830473.
  • Yoo M, Shin J, Kim J, Ryall KA, Lee K, Lee S, Jeon M, Kang J, Tan AC. DSigDB: drug signatures database for gene set analysis. Bioinformatics. 2015 Sep.31(18):3069-3071. Pubmedid: 25990557. Pmcid: PMC4668778.
  • Göke F, Franzen A, Hinz TK, Marek LA, Yoon P, Sharma R, Bode M, von Maessenhausen A, Lankat-Buttgereit B, Göke 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. FGFR1 Expression Levels Predict BGJ398 Sensitivity of FGFR1-Dependent Head and Neck Squamous Cell Cancers. Clin Cancer Res. 2015 Oct.21(19):4356-4364. Pubmedid: 26015511. Pmcid: PMC4592392.
  • Singleton KR, Hinz TK, Kleczko EK, Marek LA, Kwak J, Harp T, Kim J, Tan AC, Heasley LE. Kinome RNAi Screens Reveal Synergistic Targeting of MTOR and FGFR1 Pathways for Treatment of Lung Cancer and HNSCC. Cancer Res. 2015 Oct.75(20):4398-4406. Pubmedid: 26359452. Pmcid: PMC4609283.
  • 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. Antitumor activity of a potent MEK inhibitor, TAK-733, against colorectal cancer cell lines and patient derived xenografts. Oncotarget. 2015 Oct.6(33):34561-34572. Pubmedid: 26439693. Pmcid: PMC4741473.
  • Drasin DJ, Guarnieri AL, Neelakantan D, Kim J, Cabrera JH, Wang CA, Zaberezhnyy V, Gasparini P, Cascione L, Huebner K, Tan AC, Ford HL. TWIST1-Induced miR-424 Reversibly Drives Mesenchymal Programming while Inhibiting Tumor Initiation. Cancer Res. 2015 May.75(9):1908-1921. Pubmedid: 25716682. Pmcid: PMC4417413.
  • Tentler JJ, Ionkina AA, Tan AC, Newton TP, Pitts TM, Glogowska MJ, Kabos P, Sartorius CA, Sullivan KD, Espinosa JM, Eckhardt SG, Diamond JR. p53 Family Members Regulate Phenotypic Response to Aurora Kinase A Inhibition in Triple-Negative Breast Cancer. Mol Cancer Ther. 2015 May.14(5):1117-1129. Pubmedid: 25758253. Pmcid: PMC4425647.
  • Kleczko EK, Kim J, Keysar SB, Heasley LR, Eagles JR, Simon M, Marshall ME, Singleton KR, Jimeno A, Tan AC, Heasley LE. An Inducible TGF-β2-TGFβR Pathway Modulates the Sensitivity of HNSCC Cells to Tyrosine Kinase Inhibitors Targeting Dominant Receptor Tyrosine Kinases. PLoS One. 2015 May.10(5):e0123600. Pubmedid: 25946135. Pmcid: PMC4422719.
  • Yonekawa T, Gamez G, Kim J, Tan AC, Thorburn J, Gump J, Thorburn A, Morgan MJ. RIP1 negatively regulates basal autophagic flux through TFEB to control sensitivity to apoptosis. EMBO Rep. 2015 Jun.16(6):700-708. Pubmedid: 25908842. Pmcid: PMC4467854.
  • Davis EM, Kim J, Menasche BL, Sheppard J, Liu X, Tan AC, Shen J. Comparative Haploid Genetic Screens Reveal Divergent Pathways in the Biogenesis and Trafficking of Glycophosphatidylinositol-Anchored Proteins. Cell Rep. 2015 Jun.11(11):1727-1736. Pubmedid: 26074080. Pmcid: PMC4481156.
  • 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. Combined inhibition of MEK and Aurora A kinase in KRAS/PIK3CA double-mutant colorectal cancer models. Front Pharmacol. 2015 Jun.6:120. Pubmedid: 26136684. Pmcid: PMC4468631.
  • Saha A, Jeon M, Tan AC, Kang J. iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data. PLoS One. 2015 Jul.10(7):e0131656. Pubmedid: 26147457. Pmcid: PMC4492968.
  • Micel LN, Tentler JJ, Tan AC, Selby HM, Brunkow KL, Robertson KM, Davis SL, Klauck PJ, Pitts TM, Gangolli E, Fabrey R, O'Connell SM, Vincent PW, Eckhardt SG. Antitumor activity of the MEK inhibitor TAK-733 against melanoma cell lines and patient-derived tumor explants. Mol Cancer Ther. 2015 Feb.14(2):317-325. Pubmedid: 25376610. Pmcid: PMC4671492.
  • Ryall KA, Tan AC. Systems biology approaches for advancing the discovery of effective drug combinations. J Cheminform. 2015 Feb.7:7. Pubmedid: 25741385. Pmcid: PMC4348553.
  • 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. An integrated bioinformatics analysis to dissect kinase dependency in triple negative breast cancer. BMC Genomics. 2015 Dec.16 Suppl 12:S2. Pubmedid: 26681397. Pmcid: PMC4682411.
  • Ryall KA, Shin J, Yoo M, Hinz TK, Kim J, Kang J, Heasley LE, Tan AC. Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data. Bioinformatics. 2015 Dec.31(23):3799-3806. Pubmedid: 26206305. Pmcid: PMC4675831.
  • Henry CJ, Casás-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. Aging-associated inflammation promotes selection for adaptive oncogenic events in B cell progenitors. J Clin Invest. 2015 Dec.125(12):4666-4680. Pubmedid: 26551682. Pmcid: PMC4665776.
  • 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. The Six1 oncoprotein downregulates p53 via concomitant regulation of RPL26 and microRNA-27a-3p. Nat Commun. 2015 Dec.6:10077. Pubmedid: 26687066. Pmcid: PMC4703841.
  • 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. Potent antitumor activity of cabozantinib, a c-MET and VEGFR2 inhibitor, in a colorectal cancer patient-derived tumor explant model. Int J Cancer. 2015 Apr.136(8):1967-1975. Pubmedid: 25242168. Pmcid: PMC4323738.
  • Fleenor CJ, Rozhok AI, Zaberezhnyy V, Mathew D, Kim J, Tan AC, Bernstein ID, DeGregori J. Contrasting roles for C/EBPα and Notch in irradiation-induced multipotent hematopoietic progenitor cell defects. Stem Cells. 2015 Apr.33(4):1345-1358. Pubmedid: 25546133. Pmcid: PMC4376650.
  • 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. Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy. Bioinformatics. 2014 Sep.30(17):2393-2398. Pubmedid: 24812339. Pmcid: PMC4147888.
  • Seelenfreund E, Robinson WA, Amato CM, Tan AC, Kim J, Robinson SE. Long term storage of dry versus frozen RNA for next generation molecular studies. PLoS One. 2014 Nov.9(11):e111827. Pubmedid: 25380187. Pmcid: PMC4224406.
  • 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. Dual pharmacological targeting of the MAP kinase and PI3K/mTOR pathway in preclinical models of colorectal cancer. PLoS One. 2014 Nov.9(11):e113037. Pubmedid: 25401499. Pmcid: PMC4234626.
  • 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. 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. 2014 Mar.20(6):1656-1665. Pubmedid: 24493827. Pmcid: PMC4160109.
  • Morrison JA, Pike LA, Sams SB, Sharma V, Zhou Q, Severson JJ, Tan AC, Wood WM, Haugen BR. Thioredoxin interacting protein (TXNIP) is a novel tumor suppressor in thyroid cancer. Mol Cancer. 2014 Mar.13:62. Pubmedid: 24645981. Pmcid: PMC3995095.
  • Wynes MW, Hinz TK, Gao D, Martini M, Marek LA, Ware KE, Edwards MG, Böhm D, Perner S, Helfrich BA, Dziadziuszko R, Jassem J, Wojtylak S, Sejda A, Gozgit JM, Bunn PA, Camidge DR, Tan AC, Hirsch FR, Heasley LE. FGFR1 mRNA and protein expression, not gene copy number, predict FGFR TKI sensitivity across all lung cancer histologies. Clin Cancer Res. 2014 Jun.20(12):3299-3309. Pubmedid: 24771645. Pmcid: PMC4062100.
  • Jeon M, Lee S, Lee K, Tan AC, Kang J. BEReX: Biomedical Entity-Relationship eXplorer. Bioinformatics. 2014 Jan.30(1):135-136. Pubmedid: 24149052.
  • Saha A, Tan AC, Kang J. Automatic context-specific subnetwork discovery from large interaction networks. PLoS One. 2014 Jan.9(1):e84227. Pubmedid: 24392115. Pmcid: PMC3877685.
  • Wang CA, Drasin D, Pham C, Jedlicka P, Zaberezhnyy V, Guney M, Li H, Nemenoff R, Costello JC, Tan AC, Ford HL. Homeoprotein Six2 promotes breast cancer metastasis via transcriptional and epigenetic control of E-cadherin expression. Cancer Res. 2014 Dec;74(24):7357-7370. Pubmedid: 25348955. Pmcid: PMC4268359.
  • Maller O, Hansen KC, Lyons TR, Acerbi I, Weaver VM, Prekeris R, Tan AC, Schedin P. Collagen architecture in pregnancy-induced protection from breast cancer. J Cell Sci. 2013 Sep.126(Pt 18):4108-4110. Pubmedid: 23843613. Pmcid: PMC3772386.
  • Kim J, Yoo M, Kang J, Tan AC. K-Map: connecting kinases with therapeutics for drug repurposing and development. Hum Genomics. 2013 Sep.7:20. Pubmedid: 24060470. Pmcid: PMC3868238.
  • 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. The dual pathway inhibitor rigosertib is effective in direct patient tumor xenografts of head and neck squamous cell carcinomas. Mol Cancer Ther. 2013 Oct.12(10):1994-2005. Pubmedid: 23873848. Pmcid: PMC3796006.
  • Lieu CH, Tan AC, Leong S, Diamond JR, Eckhardt SG. From bench to bedside: lessons learned in translating preclinical studies in cancer drug development. J Natl Cancer Inst. 2013 Oct.105(19):1441-1456. Pubmedid: 24052618. Pmcid: PMC3787906.
  • Khor GH, Froemming GR, Zain RB, Abraham MT, Omar E, Tan SK, Tan AC, Vincent-Chong VK, Thong KL. DNA methylation profiling revealed promoter hypermethylation-induced silencing of p16, DDAH2 and DUSP1 in primary oral squamous cell carcinoma. Int J Med Sci. 2013 Oct.10(12):1727-1739. Pubmedid: 24155659. Pmcid: PMC3805925.
  • Flanigan SA, Pitts TM, Newton TP, Kulikowski GN, Tan AC, McManus MC, Spreafico A, Kachaeva MI, Selby HM, Tentler JJ, Eckhardt SG, Leong S. Overcoming IGF1R/IR resistance through inhibition of MEK signaling in colorectal cancer models. Clin Cancer Res. 2013 Nov.19(22):6219-6229. Pubmedid: 24045180. Pmcid: PMC3843359.
  • 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. MERTK receptor tyrosine kinase is a therapeutic target in melanoma. J Clin Invest. 2013 May.123(5):2257-2267. Pubmedid: 23585477. Pmcid: PMC3639697.
  • Andrysik Z, Kim J, Tan AC, Espinosa JM. A genetic screen identifies TCF3/E2A and TRIAP1 as pathway-specific regulators of the cellular response to p53 activation. Cell Rep. 2013 May.3(5):1346-1354. Pubmedid: 23684607. Pmcid: PMC3733554.
  • 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. Tumor P-Glycoprotein Correlates with Efficacy of PF-3758309 in in vitro and in vivo Models of Colorectal Cancer. Front Pharmacol. 2013 Mar.4:22. Pubmedid: 23524533. Pmcid: PMC3605511.
  • 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. Association of the epithelial-to-mesenchymal transition phenotype with responsiveness to the p21-activated kinase inhibitor, PF-3758309, in colon cancer models. Front Pharmacol. 2013 Mar.4:35. Pubmedid: 23543898. Pmcid: PMC3610060.
  • Ware KE, Hinz TK, Kleczko E, Singleton KR, Marek LA, Helfrich BA, Cummings CT, Graham DK, Astling D, Tan AC, Heasley LE. A mechanism of resistance to gefitinib mediated by cellular reprogramming and the acquisition of an FGF2-FGFR1 autocrine growth loop. Oncogenesis. 2013 Mar.2:e39. Pubmedid: 23552882. Pmcid: PMC3641357.
  • Harvell DM, Kim J, O'Brien J, Tan AC, Borges VF, Schedin P, Jacobsen BM, Horwitz KB. Genomic signatures of pregnancy-associated breast cancer epithelia and stroma and their regulation by estrogens and progesterone. Horm Cancer. 2013 Jun.4(3):140-153. Pubmedid: 23479404. Pmcid: PMC3810166.
  • 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. Predictive biomarkers of sensitivity to the aurora and angiogenic kinase inhibitor ENMD-2076 in preclinical breast cancer models. Clin Cancer Res. 2013 Jan.19(1):291-303. Pubmedid: 23136197. Pmcid: PMC3537923.
  • Davies KD, Mahale S, Astling DP, Aisner DL, Le AT, Hinz TK, Vaishnavi A, Bunn PA, Heasley LE, Tan AC, Camidge DR, Varella-Garcia M, Doebele RC. Resistance to ROS1 inhibition mediated by EGFR pathway activation in non-small cell lung cancer. PLoS One. 2013 Dec.8(12):e82236. Pubmedid: 24349229. Pmcid: PMC3862576.
  • 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. A patient tumor transplant model of squamous cell cancer identifies PI3K inhibitors as candidate therapeutics in defined molecular bins. Mol Oncol. 2013 Aug.7(4):776-790. Pubmedid: 23607916. Pmcid: PMC3760013.
  • 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. Rational combination of a MEK inhibitor, selumetinib, and the Wnt/calcium pathway modulator, cyclosporin A, in preclinical models of colorectal cancer. Clin Cancer Res. 2013 Aug.19(15):4149-4162. Pubmedid: 23757356. Pmcid: PMC3905307.
  • Linger RM, Lee-Sherick AB, DeRyckere D, Cohen RA, Jacobsen KM, McGranahan A, Brandão LN, Winges A, Sawczyn KK, Liang X, Keating AK, Tan AC, Earp HS, Graham DK. Mer receptor tyrosine kinase is a therapeutic target in pre-B-cell acute lymphoblastic leukemia. Blood. 2013 Aug.122(9):1599-1609. Pubmedid: 23861246. Pmcid: PMC3757372.
  • 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. 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. Brit J Cancer. 2013 Aug.109(3):667-675. Pubmedid: 23868008. Pmcid: PMC3738122.
  • Singleton KR, Kim J, Hinz TK, Marek LA, Casás-Selves M, Hatheway C, Tan AC, DeGregori J, Heasley LE. 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 ne. Mol Pharmacol. 2013 Apr.83(4):882-893. Pubmedid: 23371912. Pmcid: PMC3608435.
  • 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. Common PIK3CA mutants and a novel 3' UTR mutation are associated with increased sensitivity to saracatinib. Clin Cancer Res. 2012 May.18(9):2704-2714. Pubmedid: 22553375. Pmcid: PMC3836589.
  • Porter CC, Kim J, Fosmire S, Gearheart CM, van Linden A, Baturin D, Zaberezhnyy V, Patel PR, Gao D, Tan AC, DeGregori J. Integrated genomic analyses identify WEE1 as a critical mediator of cell fate and a novel therapeutic target in acute myeloid leukemia. Leukemia. 2012 Jun.26(6):1266-1276. Pubmedid: 22289989. Pmcid: PMC3678731.
  • 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. 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. 2012 Jun.6(3):370-381. Pubmedid: 22521243. Pmcid: PMC4033713.
  • Sullivan KD, Padilla-Just N, Henry RE, Porter CC, Kim J, Tentler JJ, Eckhardt SG, Tan AC, DeGregori J, Espinosa JM. ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53. Nat Chem Biol. 2012 Jul.8(7):646-654. Pubmedid: 22660439. Pmcid: PMC3430605.
  • 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. Direct reprogramming of human fibroblasts into dopaminergic neuron-like cells. Cell Res. 2012 Feb.22(2):321-332. Pubmedid: 22105488. Pmcid: PMC3271588.
  • 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. Preclinical activity of the rational combination of selumetinib (AZD6244) in combination with vorinostat in KRAS-mutant colorectal cancer models. Clin Cancer Res. 2012 Feb.18(4):1051-1062. Pubmedid: 22173548. Pmcid: PMC3876277.
  • 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, Graña O, Perez-Jurado L, Mora J, Puig S, Prat J, Badimon L, Puca AA, Meltzer SJ, Lengauer T, Bridgewater J, Bock C, Esteller M. A DNA methylation fingerprint of 1628 human samples. Genome Res. 2012 Feb.22(2):407-419. Pubmedid: 21613409. Pmcid: PMC3266047.
  • Haughian JM, Pinto MP, Harrell JC, Bliesner BS, Joensuu KM, Dye WW, Sartorius CA, Tan AC, Heikkilä P, Perou CM, Horwitz KB. Maintenance of hormone responsiveness in luminal breast cancers by suppression of Notch. Proc Natl Acad Sci U S A. 2012 Feb.109(8):2742-2747. Pubmedid: 21969591. Pmcid: PMC3287001.
  • Smith AL, Iwanaga R, Drasin DJ, Micalizzi DS, Vartuli RL, Tan AC, Ford HL. 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. 2012 Dec.31(50):5162-5171. Pubmedid: 22286770. Pmcid: PMC3342483.
  • Khoo SK, Petillo D, Kang UJ, Resau JH, Berryhill B, Linder J, Forsgren L, Neuman LA, Tan AC. Plasma-based circulating MicroRNA biomarkers for Parkinson's disease. J Parkinsons Dis. 2012 Dec.2(4):321-331. Pubmedid: 23938262.
  • Casás-Selves M, Kim J, Zhang Z, Helfrich BA, Gao D, Porter CC, Scarborough HA, Bunn PA, Chan DC, Tan AC, DeGregori J. Tankyrase and the canonical Wnt pathway protect lung cancer cells from EGFR inhibition. Cancer Res. 2012 Aug.72(16):4154-4164. Pubmedid: 22738915. Pmcid: PMC3673784.
  • Kim J, Tan AC. BiNGS!SL-seq: a bioinformatics pipeline for the analysis and interpretation of deep sequencing genome-wide synthetic lethal screen. Methods Mol Biol. 2012 Apr.802:389-398. Pubmedid: 22130895.
  • Tan AC. Employing gene set top scoring pairs to identify deregulated pathway-signatures in dilated cardiomyopathy from integrated microarray gene expression data. Methods Mol Biol. 2012 Apr.802:345-361. Pubmedid: 22130892.
  • Tentler JJ, Tan AC, Weekes CD, Jimeno A, Leong S, Pitts TM, Arcaroli JJ, Messersmith WA, Eckhardt SG. Patient-derived tumour xenografts as models for oncology drug development. Nat Rev Clin Oncol. 2012 Apr.9(6):338-350. Pubmedid: 22508028. Pmcid: PMC3928688.
  • 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. 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. 2011 Sep.17(17):5793-5800. Pubmedid: 21742805. Pmcid: PMC3210576.
  • Khoo SK, Petillo D, Parida M, Tan AC, Resau JH, Obaro SK. Host response transcriptional profiling reveals extracellular components and ABC (ATP-binding cassette) transporters gene enrichment in typhoid fever-infected Nigerian children. BMC Infect Dis. 2011 Sep.11:241. Pubmedid: 21914192. Pmcid: PMC3189140.
  • 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. MIR29B regulates expression of MLLT11 (AF1Q), an MLL fusion partner, and low MIR29B expression associates with adverse cytogenetics and poor overall survival in AML. Brit J Haematol. 2011 Jun.153(6):753-757. Pubmedid: 21496004. Pmcid: PMC3896048.
  • Huang Q, Li F, Liu X, Li W, Shi W, Liu FF, O'Sullivan 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. Caspase 3-mediated stimulation of tumor cell repopulation during cancer radiotherapy. Nat Med. 2011 Jul.17(7):860-866. Pubmedid: 21725296. Pmcid: PMC3132290.
  • Kim H, Kim J, Selby H, Gao D, Tong T, Phang TL, Tan AC. A short survey of computational analysis methods in analysing ChIP-seq data. Hum Genomics. 2011 Jan.5(2):117-123. Pubmedid: 21296745. Pmcid: PMC3525234.
  • Jones LK, Zou F, Kheifets A, Rybnikov K, Berry D, Tan AC. Confident predictability: identifying reliable gene expression patterns for individualized tumor classification using a local minimax kernel algorithm. BMC Med Genomics. 2011 Jan.4:10. Pubmedid: 21261972. Pmcid: PMC3038886.
  • Lyons TR, O'Brien J, Borges VF, Conklin MW, Keely PJ, Eliceiri KW, Marusyk A, Tan AC, Schedin P. Postpartum mammary gland involution drives progression of ductal carcinoma in situ through collagen and COX-2. Nat Med. 2011 Aug;17(9):1109-1115. Pubmedid: 21822285. Pmcid: PMC3888478.
  • Gao D, Kim J, Kim H, Phang TL, Selby H, Tan AC, Tong T. A survey of statistical software for analysing RNA-seq data. Hum Genomics. 2010 Oct.5(1):56-60. Pubmedid: 21106489. Pmcid: PMC3500157.
  • Camidge DR, Kono SA, Flacco A, Tan AC, Doebele RC, Zhou Q, Crino L, Franklin WA, Varella-Garcia M. Optimizing the detection of lung cancer patients harboring anaplastic lymphoma kinase (ALK) gene rearrangements potentially suitable for ALK inhibitor treatment. Clin Cancer Res. 2010 Nov.16(22):5581-5590. Pubmedid: 21062932. Pmcid: PMC3395226.
  • Flanigan SA, Pitts TM, Eckhardt SG, Tentler JJ, Tan AC, Thorburn A, Leong S. 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. 2010 Nov.16(22):5436-5446. Pubmedid: 20943761. Pmcid: PMC3119523.
  • Leong S, Messersmith WA, Tan AC, Eckhardt SG. Novel agents in the treatment of metastatic colorectal cancer. Cancer J. 2010 May.16(3):273-282. Pubmedid: 20526106.
  • 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. Development of an integrated genomic classifier for a novel agent in colorectal cancer: approach to individualized therapy in early development. Clin Cancer Res. 2010 Jun.16(12):3193-3204. Pubmedid: 20530704. Pmcid: PMC2889230.
  • Deng Y, Liu J, Han G, Lu SL, Wang SY, Malkoski S, Tan AC, Deng C, Wang XJ, Zhang Q. Redox-dependent Brca1 transcriptional regulation by an NADH-sensor CtBP1. Oncogene. 2010 Dec.29(50):6603-6608. Pubmedid: 20818429. Pmcid: PMC3081720.
  • 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. Identification of predictive markers of response to the MEK1/2 inhibitor selumetinib (AZD6244) in K-ras-mutated colorectal cancer. Mol Cancer Ther. 2010 Dec.9(12):3351-3362. Pubmedid: 20923857. Pmcid: PMC3931013.
  • Arcaroli JJ, Touban BM, Tan AC, Varella-Garcia M, Powell RW, Eckhardt SG, Elvin P, Gao D, Messersmith WA. 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. 2010 Aug.16(16):4165-4177. Pubmedid: 20682712. Pmcid: PMC3805460.
  • 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. Integrated preclinical and clinical development of mTOR inhibitors in pancreatic cancer. Brit J Cancer. 2010 Aug.103(5):649-655. Pubmedid: 20664591. Pmcid: PMC2938261.
  • Tian Y, Tan AC, Sun X, Olson MT, Xie Z, Jinawath N, Chan DW, Shih IeM, Zhang Z, Zhang H. Quantitative proteomic analysis of ovarian cancer cells identified mitochondrial proteins associated with Paclitaxel resistance. Proteom Clin Appl. 2009 Nov.3(11):1288-1295. Pubmedid: 21113235. Pmcid: PMC2989613.
  • Kent OA, Mullendore M, Wentzel EA, López-Romero P, Tan AC, Alvarez H, West K, Ochs MF, Hidalgo M, Arking DE, Maitra A, Mendell JT. A resource for analysis of microRNA expression and function in pancreatic ductal adenocarcinoma cells. Cancer Biol Ther. 2009 Nov.8(21):2013-2024. Pubmedid: 20037478. Pmcid: PMC2824894.
  • 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. Efficacy and pharmacodynamic effects of bosutinib (SKI-606), a Src/Abl inhibitor, in freshly generated human pancreas cancer xenografts. Mol Cancer Ther. 2009 Jun.8(6):1484-1493. Pubmedid: 19509264.
  • 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. Antitumor effects and biomarkers of activity of AZD0530, a Src inhibitor, in pancreatic cancer. Clin Cancer Res. 2009 Jun.15(12):4138-4146. Pubmedid: 19509160.
  • Tan AC, Jimeno A, Lin SH, Wheelhouse J, Chan F, Solomon A, Rajeshkumar NV, Rubio-Viqueira B, Hidalgo M. Characterizing DNA methylation patterns in pancreatic cancer genome. Mol Oncol. 2009 Dec.3(5-6):425-438. Pubmedid: 19497796. Pmcid: PMC5527529.
  • 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. Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. Mol Cell Proteomics. 2009 Aug.8(8):1765-1776. Pubmedid: 19357087. Pmcid: PMC2722769.
  • Song D, Chaerkady R, Tan AC, García-García E, Nalli A, Suárez-Gauthier A, López-Ríos F, Zhang XF, Solomon A, Tong J, Read M, Fritz C, Jimeno A, Pandey A, Hidalgo M. Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Mol Cancer Ther. 2008 Oct.7(10):3275-3284. Pubmedid: 18852131.
  • 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. Allele-specific expression in the germline of patients with familial pancreatic cancer: an unbiased approach to cancer gene discovery. Cancer Biol Ther. 2008 Jan.7(1):135-144. Pubmedid: 18059179. Pmcid: PMC4104667.
  • Xu L, Tan AC, Winslow RL, Geman D. Merging microarray data from separate breast cancer studies provides a robust prognostic test. BMC Bioinformatics. 2008 Feb.9:125. Pubmedid: 18304324. Pmcid: PMC2409450.
  • 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. Coordinated epidermal growth factor receptor pathway gene overexpression predicts epidermal growth factor receptor inhibitor sensitivity in pancreatic cancer. Cancer Res. 2008 Apr.68(8):2841-2849. Pubmedid: 18413752.
  • Tan AC, Naiman DQ, Xu L, Winslow RL, Geman D. Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics. 2005 Oct.21(20):3896-3904. Pubmedid: 16105897. Pmcid: PMC1987374.
  • Xu L, Tan AC, Naiman DQ, Geman D, Winslow RL. Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinformatics. 2005 Oct.21(20):3905-3911. Pubmedid: 16131522.
  • Ren T, Veeramalai M, Tan AC, Gilbert D. MSAT: a multiple sequence alignment tool based on TOPS. Appl Bioinformatics. 2004 Dec.3(2-3):149-158. Pubmedid: 15693740.
  • Tan AC, Gilbert D. Ensemble machine learning on gene expression data for cancer classification. Appl Bioinformatics. 2003 Dec.2(3 Suppl):S75-S83. Pubmedid: 15130820.
  • Tan AC, Gilbert D, Deville Y. Multi-class protein fold classification using a new ensemble machine learning approach. Genome Inform. 2003 Dec.14:206-217. Pubmedid: 15706535.