BOOKS

1. Aik Choon Tan, Paul H. Huang (Eds). (2017) Kinase Signaling Networks. Methods in Molecular Biology, Volume 1636. Human Press, Springer. ISBN 978-1-4939-7154-1. [517 pages.] [WEBSITE] [BUY @AMAZON]

2. Junbai Wang, Aik Choon Tan, Tianhai Tian (Eds.) (2012) Next Generation Microarray Bioinformatics. Methods in Molecular Biology, Volume 802. Humana Press, Springer. ISBN 978-1-61778-399-8. [401 pages.] [WEBSITE] [READ] [BUY @AMAZON]

BOOK CHAPTERS

1. Hintzsche JD, Robinson WA, Tan AC. (2021). Variant Calling in Next Generation Sequencing Data. In: Systems Medicine: Integrative, Qualitative and Computational Approaches. (Olaf Wolkenhauer (ed)). Vol 1: pp: 129-140. Elsevier.

2. Bradshaw Pierce EL, Tan AC (2013). Integrating "Omics" Data for Quantitative and Systems Pharmacology in Translational Oncology. In: Micro and Nano Flow Systems for Bioanalysis. (Michael W. Collins and Carola S. Konig (eds)). pp. 187-206. Springer.

3. Tan AC, Leong S, Pitts TM, Tentler JJ, Eckhardt SG (2013). New Approaches to Integration of Personalized Medicine in Early Cancer Drug Development. In: Principles of Molecular Diagnostics and Personalized Cancer Medicine. (Dongfeng Tan and Henry Lynch (eds)). Lippincott Williams & Wilkins. p.659-673.

4. Kim J, Tan AC. (2012) BiNGS!SL-seq: a bioinformatics pipeline for the analysis and interpretation of deep sequencing genome-wide synthetic lethal screen. Methods Mol Biol. 802:389-398. [PMID: 22130895]

5. Tan AC. (2012) Employing gene set top scoring pairs to identify deregulated pathway-signatures in dilated cardiomyopathy from integrated microarray gene expression data. Methods Mol Biol. 802:345-361. [PMID: 22130892]

SPECIAL ISSUES

1. Ramin Homayouni, Prashanti Manda, Aik Choon Tan, Zhaohui Steve Qin. (2022). AI and Data Science in Drug Development and Public Health: Highlights from the MCBIOS 2022 Conference. Frontiers in Big Data. [READ]

2. Aik Choon Tan, Paul H. Huang. (Eds). (2020). Translational Genomics for Rare Cancers: Challenges and Opportunity. Seminars in Cancer Biology. Volume 61: 1-198. [READ]

PAPERS

Links to preprints are provided strictly for personal use only.

1. Fadlullah MZH, Lin CN, Coleman S, Young A, Naqash AR, Hu-Lieskovan S, Tan AC. (2024). Exploring the Landscape of Immune Checkpoint Inhibitor-Induced Adverse Events Through Big Data Mining of Pan-Cancer Clinical Trials. The Oncologist. [Epub ahead of print, Feb 8, 2024]. [PDF] [PMID: 38330451]

1. Lambert KA, et al. (2023). SASH1 interacts with TNKS2 and promotes human melanocyte stem cell maintenance. bioRxiv. doi: https://doi.org/10.1101/2023.09.26.559624 [Preprint: Sept 29, 2023] [PDF] [PMID: 37808724]

2. Williamson J, et al. (2023). Response to high dose ipilimumab plus temozolomide after progression on standard or low dose ipilimumab in advanced melanoma: a retrospective analysis. Research Square. rs.3.rs-2997157. [Preprint: June 1, 2023] [PDF] [PMID: 37398360]

3. Wheeler C, Coleman S, et al. (2023). The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors. bioRxiv. doi: https://doi.org/10.1101/2023.05.24.542123 [Preprint: May 25, 2023] [PDF] [PMID: 37292921]

4. Wang C, et al. (2023). A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset. bioRxiv. doi: https://doi.org/10.1101/2023.05.24.541982 [Preprint: May 24, 2023] [PDF] [PMID: 37292990]

5. Obemayer A, et al. (2023). DRPPM-PATH-SURVEIOR: Plug-and-Play Survival Analysis of Pathway-level Signatures and Immune Components. Research Square. rs.3.rs-2688545. [Preprint: Mar 14, 2023] [PDF] [PMID: 36993526]

6. Robertson-Tessi M, et al. (2023). Feasibility of an Evolutionary Tumor Board for Generating Novel Personalized Therapeutic Strategies. medRxiv. doi: https://doi.org/10.1101/2023.01.18.23284628 [Preprint: Jan 19, 2023] [PDF]

1. 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 Computational Biology. 20(2):e1011873. [PDF] [PMID:38335222]

2. Kerepesi C, Abushukair HM, Ricciuti B, Nassar AH, Adib E, Alessi JV, Pecci F, Rakaee M, Fadlullah MZH, Tőkés 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 Precision Oncology. 8:e2300439. [PDF] [PMID: 38330262]

3. 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 S, Denko L, Riedlinger G, Schneider BP, Spakowicz D, Ma Q; exORIEN Consortium. (2024). A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset. Cancer Research Communications. 4(2):293-302. [PDF] [PMID: 38259095]

4. 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. (2024). Immune landscape in molecular subtypes of human papillomavirus-negative head and neck cancer. Molecular Carcinogenesis. 63(1):120-135. [PDF] [PMID: 37750589]

1. Manji GA, Lee S, Del Portillo A, May M, Sta Ana S, 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. (2023). Chemotherapy and Immune Checkpoint Blockade for Gastric and Gastroesophageal Junction Adenocarcinoma JAMA Oncology. 9(12):1702-1707. [PDF] [PMID: 37856106]

2. 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. [Epub ahead of print, Sept 18, 2023] [PDF] [PMID: 37723865]

3. Walker V, Jin DX, Millis SZ, Nasri E, Corao-Uribe D, Tan AC, Fridley BF, Chen JL, Seligson ND. (2023). Gene partners of the EWSR1 fusion may represent molecularly distinct entities. Translational Oncology. 38:101795. [PDF] [PMID: 37797367]

4. 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 Resistance Update. 71:100993. [PDF] [PMID: 37639774]

5. 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. 14(8): 1599. [PDF] [PMID: 37628651]

6. 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. Journal for ImmunoTherapy of Cancer.. 11(8):e007440. [PDF] [PMID: 37586768]

7. Lockhart JH, Ackerman HD, Lee K, Abdalah M, Davis AJ, Hackel N, Boyle TA, Saller J, Keske A, Hanggi K, Ruffel B, Stringfield O, Cress WD, Tan AC, Flores ER. (2023). Grading of Lung Adenocarcinomas with Simultaneous Segmentation by Artificial Intelligence (GLASS-AI). npj Precision Oncology. 7(1):68. [PDF] [PMID: 37464050]

8. 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. [PDF] [PMID: 36861411]

9. 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. Molecular Carcinogenesis.62(7): 1025-1037. [PDF] [PMID: 37042566]

10. 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. [PDF] [PMID: 37380943]

11. 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 Research Communications. 3(5): 896-907. [PDF] [PMID: 37377902]

12. 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. Nature Medicine. 29(4):880-887. [PDF] [PMID: 37012550]

13. 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. Frontiers in Big Data. 6:1156811. [PDF] [PMID: 36923821]

14. Lin CN, Chung CH, Tan AC. (2023). NuKit: A Deep Learning Platform for Fast Nucleus Segmentation of Histopathological Images. Journal of Bioinformatics and Computational Biology. 21(1):2350002. [PDF] [PMID: 36958934]

15. 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. 15(2):378. [PDF] [PMID: 36672327]

16. Coleman S, Xie M, Tarhini AA, Tan AC. (2023). Systematic evaluation of the predictive gene expression signatures of immune checkpoint inhibitors in metastatic melanoma. Molecular Carcinogenesis. 62(1):77-89. [PDF] [PMID: 35781709]

1. 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. Journal of Medicinal Chemistry. 65(24):16432-16450. [PDF] [PMID: 36459180]

2. 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):2894. [PDF] [PMID: 36139469]

3. 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. Journal of Leukocyte Biology. 112(6):1371-1386. [PDF] [PMID: 36120937]

4. 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. Journal of Translational Medicine. 20(1):253. [PDF] [PMID: 35659704]

5. 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 Resaerch. 50(6):3115-3127. [PDF] [PMID: 35234924]

6. 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. Molecular Carcinogenesis. 61(3):359-371. [PDF] [PMID: 34856027] ^@Co-corresponding author.

7. Obermayer AN, 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. 11(2): 260. [PDF] [PMID: 35205126]

8. Napoli M, Wu SJ, Gore B, Abbas H, 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. Nature Communications. 13(1):614. [PDF] [PMID: 35105868]

9. Tarhini AA, 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. (2022). Improved prognosis and evidence of enhanced immunogenicity in tumor and circulation of high-risk melanoma patients with unknown primary. Journal of ImmunoTherapy for Cancer.10:e004310. [PDF] [PMID: 35074904]

1. Chai AWY, Tan AC, Cheong SC. (2021). Uncovering drug repurposing candidates for head and neck cancers: insights from systematic pharmacogenomics data analysis. Scientific Reports 11(1): 23933. [PDF] [PMID: 34907286]

2. 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. 37(20): 3681-3683. [PDF] [PMID: 33901274] [TIMEx]

3. Nassar KW, Hintzsche JD, Bagby SM, Espinoza V, Langouët-Astrié 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. Molecular Cancer Therapeutics. 20(10): 2049-2060. [PDF] [PMID: 34376578] ^@Co-corresponding author.

4. Lee K*, Lockhart JH*, Xie M, Chaudhary R, Slebos RJ, Flores ER, Chung CH, Tan AC. (2021). Deep Learning of Histopathology Images at the Single Cell Level. Frontiers in Artificial Intelligence 4: 754641. [PDF] [PMID: 34568816]

5. Xiong Z*, Jeon M*, Allaway RJ*, Kang J, Park D, Lee J, Jeon H, Ko M, Jiang H, Zheng M, Tan AC, Guo X, The 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 Computational Biology 17(9): e1009302. [PDF] [PMID: 34520464]

6. Schubert L, Le A, Estrada-Bernal A, Doak A, Yoo M, Ferrara S, Goodspeed A, Kimose 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. Molecular Pharmacology 99(6): 435-447. [PDF] [PMID: 33795352]

7. 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 Precision Oncology. 5(1):41. [PDF] [PMID: 34001994]

8. 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 D. (2021). Enabling Precision Medicine in Cancer Care Through a Molecular Data Warehouse: The Moffitt Experience. JCO Clinical Cancer Informatics. 5:561-569. [PDF] [PMID: 33989014]

9. Pollyea DA, Kim HM, Stevens BM, Lee FF, Harris C, Hedin BR, Knapp JR, O'Connor BP, Jordan CT, Pietras EM, Tan AC, Alper S. (2021). MDS-associated SF3B1 mutations enhance proinflammatory gene expression in patient blast cells. Journal of Leukocyte Biology. 110(1):197-205. [PDF] [PMID: 33155727]

10. Tengesdal IW, Menon DR, Osborne DG, Neff CP, Powers NE, Gamboni F, Mauro AG, D'Alessandro 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. Proceedings of the National Academy of Sciences USA. 118(10):e2000915118. [PDF] [PMID: 33649199]

11. 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. Nature Ecology & Evolution. 5(3):379-391. [PDF] [PMID: 33462489] [COVER]

12. 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. (2021). Effects of checkpoint kinase 1 inhibition by prexasertib on the tumor immune microenvironment of head and neck squamous cell carcinoma. Molecular Carcinogenesis. 60(2):138-150. [PDF] [PMID: 33378592] [COVER]

13. Morton JJ, Alzofon N, Keysar SB, Chimed T-S, Reisinger J, Perrenoud L, Le PN, Nieto C, Gomez KE, Miller B, Yeager R, Gao D, Tan AC, Somerset H, Medina T, Wang XJ, Wang JH, Robinson W, Roop DR, Gonzalez R, Jimeno A. (2021). Studying immunotherapy resistance in a melanoma autologous humanized mouse xenograft. Molecular Cancer Research. 19(2):346-357. [PDF] [PMID: 33087417]

14. Wahdan-Alaswad R, Edgerton SM, Salem H, Kim H, Tan AC, Finlay-Schultz J, Wellberg E, Sartorius CA, Jacobsen BM, Haugen BR, Liu B, Thor AD. (2021). Exogenous Thyroid Hormone is Associated with Shortened Survival and Upregulation of High Risk Gene Expression Profiles in Steroid Receptor Positive Breast Cancers. Clinical Cancer Research. 27(2):585-597. [PDF] [PMID: 33097494]

15. He T, Wildey G, McColl K, Savedelis A, Spainhower K, McColl C, Kresak A, Tan AC, Yang M, Abbas A, Dowlati A. (2021). Identification of RUNX1T1 as a potential epigenetic modifier in small cell lung cancer. Molecular Oncology. 15(1):195-209. [PDF] [PMID: 33084222]

1. 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 Biology. 21(1):271. [PDF] [PMID: 33148332]

2. Chai AWY, Yee PS, Price S, Yee SM, Lee HM, Tiong VK, Gonçalves 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:e57761. [Epub ahead of print, Sept 29, 2020] [PDF] [PMID: 32990596]

3. 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. Journal of Thoracic Oncology. 15(9):1522-1534. [Epub ahead of print, June 26, 2020] [PDF] [PMID: 32599072]

4. 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. 12(7):1943. [PDF] [PMID: 32708981]

5. Iwanaga R, Truong BT, Hsu JY, Lambert KA, Vyas R, Orlicky D, Shellman YG, Tan AC, Ceol C, Artinger KB. (2020). Loss of prdm1a accelerastes melanoma onset and progression. Molecular Carcinogenesis. 59(9):1052-1063. [Epub ahead of print, Jun 20, 2020] [PDF] [PMID: 32562448]

6. 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. Molecular Cancer Therapeutics. 19(8):1598-1612. [Epub ahead of print, Jun 4, 2020] [PDF] [PMID: 32499299]

7. Davis SL, Ionkina A, 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. (2020). Preclinical and Dose-Finding Phase 1 Trial Results of Combined Treatment with a TORC1/2 Inhibitor (TAK-228) and Aurora A Kinase Inhibitor (Alisertib) in Solid Tumors. Clinical Cancer Research. 26(17):4633-4642. [PDF] [PMID: 32499299] [ClinicalTrials.gov ID: NCT02719691]

8. 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. Communications Biology. 3(1):306. [PDF] [PMID: 32533049]

9. 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 and Diseases. 11(6):443. [PDF] [PMID: 32513939]

10. 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. Nature Communications. 11(1):2393. [PDF] [PMID: 32409712]

11. Nassar KW, Tan AC. (2020). The Mutational Landscape of Mucosal Melanoma. Seminars in Cancer Biology. 61:139-148. [PDF] [PMID: 31655118]

12. Tan AC, Huang PH. (2020). Translational Genomics for Rare Cancers: Challenges and Opportunity. Seminars in Cancer Biology. 61:iii-iv. [PDF] [PMID: 32092353]

13. 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 JJ, Harrison LB, Wenig B, Conejo-Garcia JR, Hernandez-Prera JC, Chung CH. (2020). Effects of tobacco smoking on the tumor immune microenvironment in head and neck squamous cell carcinoma. Clinical Cancer Research. 26(6):1474-1485. [PDF] [PMID: 31848186]

14. Schreiber AR, Kar A, Goodspped AE, Pozdeyev N, Somerset H, Raeburn CD, Tan AC, Leong S, Wierman MW, Kiseljak-Vassiliades K. (2020). Leptomeningeal Metastasis from Adrenocortical Carcinoma: A Case Report. Journal of the Endocrine Society. 4(3):bvaa017. [PDF] [PMID: 32154490]

15. Keysar SB, Gomes N, Miller B, Jackson BC, Le PN, Morton JJ, Reisinger J, Chimed T-S, 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 Research. 80(5): 1183-1198. [PDF] [PMID: 31911553]

1. Jeon M*, Park D*, Lee J,, Jeon H, Ko M, Kim S, Choi Y, Tan AC, Kang J. (2019). ReSimNet: Drug Response Similarity Prediction using Siamese Neural Networks. Bioinformatics. 35(24):5249-5256. [PDF] [PMID: 31116384]

2. 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. Molecular Pharmacology. 96(6):862-870. [PDF] [PMID: 31554698]

3. Wilding CP*, Elms ML*, Judson I, Tan AC, Jones RL, Huang PH. (2019). The Landscape of Tyrosine Kinase Inhibitors in Sarcoma - looking beyond Pazopanib. Expert Review of Anticancer Therapy 19(11):971-991. [PDF] [PMID: 31665941]

4. 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. Chemico-Biological Interactions. 314: 108822. [PDF] [PMID: 31580832]

5. Capasso A, Bagby S, 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 anti-tumor activity in triple-negative breast cancer. Molecular Cancer Therapeutics. 18(11):1916-1925. [PDF] [PMID: 31488700] [ClinicalTrials.gov ID: NCT02003092]

6. Lee BKB, Cheong SC, Tan AC. (2019). Expanding the Connectivity Map Concept as the Functional Look-Up Table for Systems Biology. Advances in Molecular Pathology. 2: 201-213. [PDF]

7. Brown P, RELISH Consortium (Tan AC et al), Zhou Y. (2019). Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database. 2019: baz085. [PDF] [PMID: 33326193] [RELISH]

8. Aguado BA, Schuetze KB, Grim JC, Walker CJ, Cox AC, Ceccato TL, Tan AC, Sucharov CC, Leinwand LA, Taylor MRG, McKinsey TA, Anseth KS. (2019). Transcatheter aortic valve replacements alter circulating serum factors to mediate myofibroblast deactivation. Science Translational Medicine. 11(509). pii: eaav3233. [PDF] [PMID: 31511425]

9. Gan CP, Sam KK, Yee PS, Zainal NS, Lee BKB, Rahman ZAA, Patel V, Tan AC, Zain RB, Cheong SC. (2019). IFITM3 knockdown reduces the expression of CCND1 and CDK4 to suppress the growth of oral squamous cell carcinoma. Cellular Oncology 42(4):477-490. [Epub ahead of print, Apr 4, 2019] [PDF] [PMID: 30949979]

10. Yoo M, Shin J, Kim H, Kim J, Kang J, Tan AC. (2019). Exploring the molecular mechanisms of Traditional Chinese Medicine Components using Gene Expression Signatures and Connectivity Map. Computer Methods and Programs in Biomedicine. 174:33-40. [Epub ahead of print, Apr 4, 2018] [PDF] [PMID: 29650251] [TCM Hub]

11. 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. Clinical Cancer Research. 25(10):3141-3151. [Epub ahead of print, Feb 8, 2019] [PDF]` [PMID: 30737244]

12. Kessler B, Mishall K, Kellett M, Clark E, Pugazhenthi U, Pozdeyev N, Kim J, Tan AC, Schweppe R. (2019). 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. [Epub ahead of print, Dec 10, 2018] [PDF] [PMID: 30531837]

13. 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. (2019). Reversal of Triple-negative Breast Cancer EMT by miR-200c Decreases Tryptophan Catabolism and a Program of Immune-Suppression. Molecular Cancer Research. 17(1):30-41. [Epub ahead of print, Sept 13, 2018] [PDF] [PMID: 30213797]

1. Davis SL, Eckhardt SG, Diamond JR, Messersmith WA, Dasari A, Weekes CD, Lieu CH, Kane M, Tan AC, 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. [Epub ahead of print, Aug 23, 2018]. [PDF] [PMID: 30139840] [ClinicalTrials.gov ID: NCT01016860]

2. 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 Research. 78(23):6561-6574. [Epub ahead of print, Oct 8, 2018] [PDF] [PMID: 30297536]

3. Oweida A, Hararah MK, Phan A, Binder D, Bhatia S, Lennon S, Bukkapatnam S, Van Court B, Uyanga N, Darragh L, Kim H, 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. Clinical Cancer Research. 24(21): 5368-5380. [PDF] [PMID: 30042205]

4. 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. Molecular Cancer Therapeutics. 17(10):2257-2265. [Epub ahead of print, July 26, 2018] [PDF] [PMID: 30049789]

5. 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. Clinical Cancer Research. 24(20):4949-4959. [PDF] [PMID: 30084837] [ClinicalTrials.gov ID: NCT01758731]

6. 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 naive lesions. Journal of Thoracic Oncology. 13(10): 1496-1507. [PDF] [PMID: 29933065] [COVER]

7. Parrish JK, McCann TS, Sechler M, Sobral LM, Ren WH, 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. [PDF] [PMID: 30237855]

8. Powers R, Goodspeed A, Pielke-Lombardo H, Tan AC, Costello J. (2018). GSEA-InContext: Identifying novel and common patterns in expression experiments. Bioinformatics. 34(13):i555-i564. [PDF] [PMID: 29950010]

9. Pei S, Minhajuddin M, Adane B, Khan N, Stevens BM, Mack SC, Lai S, Rick 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. [Epub ahead of print, June 14, 2018] [PDF] [PMID: 29910151]

10. Pozdeyev N, Gay LM, Sokol E, Hartmaier R, Deaver KE, Davis S, French JD, Vanden Borre P, LaBarbera DV, Tan AC, Schweppe RE, Fishbain L, Ross JS, Haugan BR, Bowles DW. (2018). Genetic analysis of 779 advanced differentiated and anaplastic thyroid cancers. Clinical Cancer Research. 24(13):3059-3068. [Epub ahead of print, Apr 3, 2018] [PDF] [PMID: 29615459]

11. Keysar SB*, Eagles JR*, Miller B, Jackson BC, Chowdhury FN, Reisinger J, Chimed T-S, Le PH, 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 fusions associated with tumor progression. Clinical Cancer Research. 24(12):2935-2943. [Epub ahead of print, Mar 19, 2018] [PDF] [PMID: 29555661]

12. 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. Journal of Dental Research. 97(8):909-916. [Epub ahead of print, Mar 1, 2018] [PDF] [PMID: 29512401] [GENIPAC]

13. 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 Medical Genomics. 11(Suppl 2): 26. [PDF] [PMID: 29697364] [IMPACT]

14. 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. International Journal of Genomics. 2018: 7697356. [PDF] [PMID: 29765977] [TCM Hub]

15. 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: 136. [PDF] [PMID: 29402316]

16. Pilling A, Kim J, Estrada-bernal A, Zhou Q, Le A, Singleton K, 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. [PDF] [PMID: 29507657]

17. 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. 19:21. [PDF] [PMID: 29368597] [VarDrugPub] [^@Co-corresponding authors.]

18. 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 Medical Informatics. 6(1): e2. [PDF] [PMID: 29305341]

19. 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. (2018). ALK Inhibitor Response in Melanomas Expressing EML4-ALK Fusions and Alternate ALK Isoforms. Molecular Cancer Therapeutics. 17(1); 222-231. [Epub ahead of print, Oct 20, 2017] [PDF] [PMID: 29054983] [Highlights]

20. Yue Z, Zheng Q, Neylon MT, Yoo M, Shin J, Zhao Z, Tan AC, Chen JY. (2018). PAGER 2.0: An update to the pathway, annotated-list, and gene-signature electronic repository for Human Network Biology. Nucleic Acids Research. 46(D1): D668-D676. [Epub ahead of print, Nov 8, 2017]. [PDF] [PMID: 29126216] [PAGER 2.0]

1. 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. [PDF] [PMID: 29091939]

2. 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. Journal of Biological Chemistry. 292(36): 15105-15120. [Epub ahead of Print, Jul 3, 2017] [PMID: 28673964]

3. Donson A, Apps J, Griesinger AM, Amani VA, Witt DA, Anderson RCE, Niazi TN, Grant G, Souweidane M, Johnston JM, Jackson EM, Kleinschmidt-DeMasters BK, Handler MH, Tan AC, Gore L, Virasemi A, Gonzalez-Meljem JM, Jacques TS, Martinez-Barbera JP, Foreman NK, Hankinson TC. (2017). Molecular analyses reveal inflammatory mediators in the solid component and cyst fluid of human adamantinomatous craniopharyngioma. Journal of Neuropathology and Experimental Neurology. 76(9): 779-788. [PMID: 28859336]

4. 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. Molecular Cancer Therapeutics. 16(8):1623-1633. [Epub ahead of Print, May 12, 2017] [PDF] [PMID: 28500237]

5. 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. [Epub ahead of print, April 3, 2017] [PDF] [PMID: 28368426]

6. 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. Frontiers in Oncology. 7: Article 94. [PDF] [PMID: 28555173]

7. 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 Co-Mutation of NF1 and KIT in Mucosal Melanoma. Melanoma Research. 27(3):189-199. [Epub ahead of print, Mar 14, 2017]. [PDF] [PMID: 28296713] [^@Co-corresponding authors.]

8. 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. Molecular Cancer Research. 15(4): 382-394. [Epub ahead of print, Jan 20, 2017]. [PDF] [PMID: 28108622]

9. Harder B, Tian W, La Clair JJ, Tan AC, Ooi A, Chapman E, Zhang DD. (2017). Brusatol overcomes chemoresistance through inhibition of protein translation. Molecular Carcinogenesis. 56(5): 1493-1500. [Epub ahead of print, Dec 26, 2016]. [PDF] [PMID: 28019675]

10. Smith Jr BJ, Hintzsche JD, Amato CM, Tan AC, Wells KR, Applegate AJ, Gonzalez RT, Barr JR, Robinson WA. (2017). Systematic Analysis of Whole Exome Sequencing Determines RET G691S Polymorphis, as Germline Variant in Melanoma. Marshall Journal of Medicine. 3(2): Article 10. [PDF]

11. Brechbuhl HM, Finlay-Schultz J, Yamamoto TM, Gillen AE, Cittelly DM, Tan AC, Sams S, Pillai MM, Elias AD, Robinson WA, Sartorius CA, Kabos P. (2017). Fibroblast Subtypes Regulate Responsiveness of Luminal Breast Cancer to Estrogen. Clinical Cancer Research. 23(7): 1710-1721. [Epub ahead of print, Oct 4, 2016] [PDF] [PMID: 27702820] [COVER]

12. Scarborough HA, Helfrich BA, Casas-Selves M, Schuller AG, Grosskurth SE, Kim J, Tan AC, Chan DC, Zhang Z, Zaberezhnyy V, Bunn PA, DeGregori J. (2017). AZ1366: An inhibitor of tankyrase and the canonical Wnt pathway that limits the persistence of non-small cell lung cancer cells following EGFR inhibition. Clinical Cancer Research. 23(6): 1531-1541. [Epub ahead of print, Sept 23, 2016] [PDF]. [PMID: 27663586]

13. Wong KM, Micel L, Selby H, Tan AC, Pitts TM, Bagby S, Spreafico A, Klauck P, Blakemore S, Smith P, McDonald A, Berger A, Tentler J, Eckhardt SG. (2017). Targeting the Protein Ubiquitination Machinery in Melanoma by the NEDD8-Activating Enzyme Inhibitor Pevonedistat (MLN4924). Investigational New Drugs. 35(1): 11-25. [Epub ahead of print, Oct 25, 2016] [PDF]. [PMID: 27783255]

14. 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 WA. (2017). Kinase Gene Fusions in Defined Subsets of Melanoma. Pigment Cell & Melanoma Research. 30(1):53-62. [Epub ahead of print, Nov 19, 2016]. [PDF] [PMID: 27864876]

15. Keysar SB, Le PH, 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. (2017). Regulation of Head and Neck Squamous Cancer Stem Cells by PI3K and SOX2. Journal of the National Cancer Institute. 109(1): djw189. [Epub ahead of print, Sept 15, 2016] [PDF] [PMID: 27634934]

16. Lee BKB, 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. [PDF] [PMID: 28198666 [DESIGN]

17. 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: e287. [PDF] [PMID: 28092369]

18. Tan AC, Vyse S, Huang PH. (2017). Exploiting Receptor Tyrosine Kinase Co-activation for Cancer Therapy. Drug Discovery Today. 22(1): 72-84. [Epub ahead of print, July 21, 2016]. [PDF] [PMID: 27452454]

1. Wuensch KE, Tan AC. (2016). Trunk or Branch? Identifying and Targeting Intratumoral Heterogeneity in Hepatocellular Carcinoma using Genomics and Patient Derived Primary Cancer Cells. Translational Cancer Research. 5 (Suppl 7): S1383 - S1386. [PDF]

2. Federer C*, Yoo M*, Tan AC. (2016). Big Data Mining and Adverse Event Pattern Analysis in Clinical Drug Trials. ASSAY and Drug Development Technologies. 14(10): 557-566. [PDF] [PMID: 27631620] (*contributed equally). [COVER]

3. Hintzsche JD, Robinson WA, Tan AC. (2016). A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data. International Journal of Genomics. 2016:7983236. [PDF] [PMID: 28070503]

4. Cavalli G, Koenders M, Kalabokis V, Kim J, Tan AC, Mantovani A, Garlanda C, Dagna L, Joosten LAB, Dinarello CA. (2016). Treating experimental arthritis with the innate inflammation inhibitor IL 37 reduces joint and systemic inflammation. Rheumatology. 55(12):2220-2229. [Epub ahead of print, Aug 26, 2016] [PDF]. [PMID: 27567100]

5. 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 tumours. Cell Reports. 17(5):1265-1275. [PDF] [PMID: 27783942]

6. Zhang G, Scarborough HA, 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. Science Signaling. 9(450): rs12. [PDF]. [PMID: 27811184]

7. 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. (2016). ATM/G6PD-driven redox metabolism promotes FLT3 inhibitor resistance in acute myeloid leukemia. Proceedings of the National Academy of Sciences USA. 113(43):E6669-E6678. [Epub ahead of print, Oct 10, 2016]. [PDF] [PMID: 27791036]

8. 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. [PDF]. [PMID: 27760149] [BEST]

9. Helfrich BA, Kim J, Gao D, Chan DC, Zhang Z, Tan AC, Bunn Jr PA. (2016). Barasertib (AZD1152), a small molecule Aurora B inhibitor, inhibits the growth of SCLC cell lines in vitro and in vivo. Molecular Cancer Therapeutics 15(10): 2314-2322. [Epub ahead of print, Aug 5, 2016] [PDF]. [PMID: 27496133]

10. Bagby S, Messersmith WA, Pitts TM, Capasso A, Varella-Garcia M, Klauck P, Kim J, Tan AC, Eckhardt SG, Tentler JJ, Arcaroli JJ. (2016). Development and Maintenance of a Preclinical Patient Derived Tumor Xenograft Model for the Investigation of Novel Anti-Cancer Therapies. The Journal of Visualized Experiments.115: e54393. doi:10.3791/54393. [PDF] [PMID: 27768028] [VIDEO]

11. 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. [Epub ahead of print, Aug 17, 2016] [PDF]. [PMID: 27556857] (*contributed equally).

12. 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): 2886-2888. [Epub ahead of print, Aug 2, 2016] [PDF] [PMID: 27485446] [HiPub] [^@Co-corresponding authors.]

13. 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. [Epub ahead of print, June 14, 2016]. [PDF]. [QAPC] [PMID: 27322211] (*Co-senior authors)

14. Beadnell TC, Mishall KM, Zhou Q, Riffert SM, Wuensch KE, Kessler BE, Corpus 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. Molecular Cancer Therapeutics. 15(8): 1952-1963. [Epub ahead of print, May 24, 2016]. [PMID: 27222538].

15. Pitts TM, Bradshaw-Pierce E, Bagby S, Hyatt S, Selby H, Spreafico A, Tentler J, McPhillips K, Klauck P, Capasso A, Diamond JR, Davis SL, Tan AC, Arcaroli J, Purkey A, Messersmith WA, Ecsedy J, Eckhardt SG. (2016). Antitumor Activity of the Aurora A Selective Kinase Inhibitor, Alisertib, Against Preclinical Models of Colorectal Cancer. Oncotarget. 7(31): 50308-50319. [Epub ahead of print, July 1, 2016]. [PDF] [PMID: 27385211]

16. 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: Whole-Exome Sequencing Analysis Pipeline of Integrating Molecular Profiles with Actionable Therapeutics in Clinical Samples. Journal of the American Medical Informatics Association. 23(4): 721-730. [Epub ahead of print, Mar 28, 2016]. [PDF] [PMID: 27026619]. [PRESS RELEASE] [IMPACT]

17. Hidayatullah Fadlullah MZ, Chiang IK, Dionne KR, Yee PS, Gan CP, Sam KK, Tiong KH, Wen Ng AK, Martin D, Lim KP, Kallarakkal TG, Wan Mustafa WM, Lau SH, Abraham MT, Zain RB, Abdul Rahman ZA, Molinolo A, Patel V, Gutkind JS, Tan AC, Cheong SC. (2016). Genetically-defined novel oral squamous cell carcinoma cell lines for the development of molecular therapies. Oncotarget. 7(19):27802-27818. [Epub ahead of print, Apr 1, 2016]. [PDF] [PMID: 27050151].

18. 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. 2016:baw043. [Epub ahead of print, Apr 13, 2016]. [PDF] [PMID: 27074804]. [BRONCO] [^@Co-corresponding authors.]

19. 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): 17905-17919. [Epub ahead of print, Feb 21, 2016]. [PDF] [PMID: 26918447].

20. 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. (2016). XactMice: humanizing mouse bone marrow enables microenvironment reconstitution in a patient-derived xenograft model of head and neck cancer. Oncogene. 35: 290-300. [Epub ahead of print, Apr 20, 2015]. [PDF] [PMID: 25893296].

21. Fornetti J, Flanders K, Henson PM, Tan AC, Borges V, Schedin P. (2016). Mammary epithelial cell phagocytosis downstream of TGF-B3 is characterized by adherens junction reorganization. Cell Death and Differentiation. 23(2):185-196. [Epub ahead of print, Jun 26, 2015] [PDF] [PMID: 26113040].

22. 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. (2016). A pilot study of cetuximab and the hedgehog inhibitor IPI-926 in recurrent/metastatic head and neck squamous cell carcinoma. Oral Oncology. 53: 74-79. [Epub ahead of print, Dec 15, 2015] [PDF] [PMID: 26705064]. [ClinicalTrials.gov ID: NCT01255800]

23. Tan AC, Ryall KA, Huang PH. (2016). Expanding the Computational Toolbox for Interrogating Cancer Kinomes. Pharmacogenomics. 17(2):95-97. [Epub ahead of print, Dec 15, 2015] [PDF] [PMID: 26666839].

24. 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. (2016). 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. [Epub ahead of print, July 7, 2015]. [PDF] [PMID: 26152787].

1. 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-27-a-3p. Nature Communications. 6:10077. [PDF] [PMID: 26687066].

2. 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. [PDF] (Proceedings of the 1st Joint GIW/InCoB Conference, Tokyo, Japan). [PMID: 26681397].

3. Henry C, Casas-Selves M, Kim J, Zaberezhnvv 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. The Journal of Clinical Investigation. 125(12):4666-4680. [Epub ahead of print, Nov 9, 2015] [PMID: 26551682].

4. 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):3799-3806. [Epub ahead of print, July 23, 2015]. [PDF]. [PMID: 26206305]. [PRESS RELEASE] [Download KAR]

5. Lieu CH, Klauck PJ, Henthron 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):34561-34572. [Epub ahead of print, Oct 1, 2015]. [PDF] [PMID: 26439693].

6. 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 Research. 75(20): 4398-4406. [Epub ahead of print, Sept 10, 2015]. [PMID: 26359452].

7. Göke F, Franzen A, Hinz TK, Marek LA, Yoon P, Sharma R, Bode M, von Mäessenhausen 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, Schröck 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. Clinical Cancer Research. 21(19): 4356-4364. [Epub ahead of print, May 26, 2015]. [PMID: 26015511].

8. 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): 3069-3071. [Epub ahead of print, May 19, 2015]. [PDF] [DSigDB] [PMID: 25990557].

9. 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. [PMID: 26147457]. [PDF].

10. Davis EM, Kim J, Menasche B, Sheppard J, Liu X, Tan AC, Shen J. (2015). Comparative haploid genetic screens reveal divergent pathways in the biogenesis of glycophosphatidylinositol-anchored proteins. Cell Reports. 11(11):1727-1736. [Epub ahead of print, Jun 10, 2015]. [PMID: 26074080]. [PMCID: PMC4481156] [PDF]

11. 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. Frontiers in Pharmacology. 6:120. [PMID: 26136684]. [PMCID: PMC4468631] [PDF]

12. 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 Reports. 16:700-708. [Epub ahead of print, Apr 23, 2015] [PMID: 25908842]. [PMCID: PMC4467854] [PDF]

13. Kleczko EK, Kim J, Keysar SB, Heasley LR, Eagles-Soukup J, Simon M, Marshall ME, Singleton KR, Jimeno A, Tan AC, Heasley LE. (2015). An Inducible TGFB2-TGFBR Pathway Modulates the Sensitivity of HNSCC Cells to Tyrosine Kinase Inhibitors Targeting Dominant Receptor Tyrosine Kinases. PLoS ONE. 10(5):e0123600. [PMID: 25946135]. [PMCID: PMC4422719] [PDF]

14. Tentler JJ, Ionkina A, Tan AC, Newton TP, Pitts TM, Glogowska MJ, Kabos P, Sartorius CA, Sullivan KD, Espinosa JM, Eckhardt SG, Diamond JD. (2015). p53 Family Members Regulate Phenotypic Response to Aurora Kinase A Inhibition in Triple-Negative Breast Cancer. Molecular Cancer Therapeutics. 14(5):1117 - 1129. [Epub ahead of print, Mar 10, 2015]. [PMID: 25758253]. [PMCID: PMC4425647]

15. Drasin DJ, Guarnier AL, Neelakantan D, Kim J, Cabrera JH, Wang CA, Zaberezhnyy V, Gasparini P, Cascione L, Huebner K, Tan AC, Ford HL. (2015). Twist1-induced microRNA-424 reversibly drives mesenchymal programming while inhibiting tumor initiation. Cancer Research. 75(9): 1908-1921. [Epub ahead of print Feb 25, 2015]. [PMID: 25716682]. [PMCID: PMC4417413]

16. Fleenor CJ, Rozhok AI, Zaberezhnyy V, Mathew D, Kim J, Tan AC, Bernstein ID, DeGregori J. (2015). Contrasting Roles for C/EBPalpha and Notch in Irradiation-Induced Multipotent Hematopoietic Progenitor Cell Defects. Stem Cells. 33(4):1345-1358. [Epub ahead of print Dec 27, 2014]. [PMID: 25546133]. [PMCID: PMC4376650]

17. Ryall KA, Tan AC. (2015). Systems Biology Approaches For Advancing The Discovery Of Effective Drug Combinations. J. Cheminformatics. 7:7. [PDF] [PMID: 25741385]. [PMCID: PMC4348553]

18. Song EK, Tai W, 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. (2015). 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 - 1975. [Epub ahead of print, Sept 20, 2014]. [PMID: 25242168]. [PMCID: PMC4323738]

19. 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. (2015). Antitumor Activity of the MEK Inhibitor TAK-733 Against Melanoma Cell Lines and Patient-Derived Tumor Explants. Molecular Cancer Therapeutics. 14(2): 317-325. [Epud ahead of print Nov 5, 2014]. [PMID: 25376610].

20. Petillo D, Orey S, Tan AC, Forsgren L, Khoo SK. (2015). Parkinson's Disease-related Circulating microRNA Biomarkers - a Validation Study. AIMS Medical Science. 2(1): 7-14. [PDF]
    This research is supported by the Michael J. Fox Foundation for Parkinson's Research Rapid Response Innovation Award (PI: SKK and ACT).

1. 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. [PMID: 25401499]. [PMCID: PMC4234626]

2. 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. [PMID: 25380187]. [PMCID: PMC4224406]

3. 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 Research. 74(24):7357-7370. [Epub ahead of print, Oct 27, 2014]. [PMID: 25348955]. [PMCID: PMC4268359]

4. 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 over-coming EGFR-mutant lung cancer resistance to EGFR therapy. Bioinformatics. 30(17):2393-2398. [Epub ahead of print, May 7, 2014]. [PDF] [PMID: 24812339] [PMCID: PMC4147888] . [PRESS RELEASE]

5. Wynes MW, Hinz TK, Gao D, Martini M, Marek L, Ware KE, Edwards MG, Böhm 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): 3299-3309. [Epub ahead of print, Apr 25, 2014]. [PMID: 24771645] [PMCID: PMC4062100]

6. 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. [PMID: 24645981] [PMCID: PMC3995095]

7. 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: 1656 - 1665. [PDF] [PMID: 24493827] [PMCID: PMC4160109] [ClinicalTrials.gov ID: NCT01168011]

8. Saha A, Tan AC, Kang J. (2014). Automiatic Context-Specific Subnetwork Discovery from Large Interaction Networks. PLos ONE. 9(1):e84227. [PMID: 24392115] [PMCID: PMC3877685]

9. Jeon M, Lee S, Lee K, Tan AC, Kang J. (2014). BEReX: Biomedical Entity-Relationship eXplorer. Bioinformatics. 30(1):135-136. [Epub ahead of print, Oct 21, 2013]. [PDF] [PMID: 24149052] [BEReX page]

1. 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. [PMID:24349229] [PMCID: PMC3862576]

2. Kim J*, Yoo M*, Kang J, Tan AC. (2013). K-Map: connecting kinases with therapeutics for drug repurposing and development. Hum Genomics. 7(1):20. [Epud ahead of print, Sep 23, 2013]. [PMID: 24060470] [PMCID: PMC3868238] [PDF] [K-Map page]

3. 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. J. Natl. Cancer Inst. 105(19):1441 - 1456. [Epud ahead of print, Sep 19, 2013]. [PMID: 24052618] [PMCID: PMC3787906] [PDF]

4. Khor GH, Froemming GRA, 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 - 1739. [PMID:24155659] [PMCID: PMC3805925] [PDF]

5. 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):6219-6229. [Epub ahead of print, Sep 17, 2013]. [PMID: 24045180] [PMCID: PMC3843359]

6. Anderson RT, Keysar SB, Bowles DW, Glogowska MJ, Astling DP, Morton JJ, Le P, Umpierrez A, Eagles-Soukup J, Gan GN, Vogler BW, Sehrt DB, Takimoto SM, Aisner DL, Wilhem 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. [Epub ahead of print, Jul 23, 2013]. [PMID: 23873848] [PMCID: PMC3796006]

7. 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 - 675. [doi: 10.1038/bjc.2013.361. Epub 2013 Jul 18.] [PMID: 23868008] [PMCID: PMC3738122]

8. Linger RM, Lee-Sherick AB, Deryckere D, Cohen RA, Jacobsen KM, McGranahan A, Brandao 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 - 1609. [doi: 10.1182/blood-2013-01-478156. Epub 2013 Jul 16.] [PMID: 23861246] [PMCID: PMC3757372]

9. 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 - 4110. [Epub ahead of print, Jul 10, 2013] [PMID: 23843613] [PMCID: PMC3772386]

10. 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 K, 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. Clinical Cancer Research 19(15):4149 - 4162. [Epub ahead of print, Jun 11, 2013] [PMID: 23757356] [PMCID: PMC3905307]
    TRANSLATIONAL CANCER RESEARCH: This research is translated into a NCI CTEP approved clinical trial "Phase I/IB Study of the Combination of Selumetinib (AZD6244) and Cyclosporin A (CsA) in Patients with Advanced Solid Tumors with an Expansion Cohort in Metastatic KRAS Mutant Colorectal Cancer" (PI: Christopher Lieu) . [ClinicalTrials.gov ID: NCT02188264]

11. 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 Reports 3(5):1346-1354. [doi: 10.1016/j.celrep.2013.04.014. Epub 2013 May 16.] [PMID:23684607] [PMCID: PMC3733554] [PDF]

12. 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. Molecular Oncology. 7(4): 776-790. [doi: 10.1016/j.molonc.2013.03.004. , Epub ahead of print April 4, 2013] [PMID:23607916] [PMCID: PMC3760013] [PDF]

13. 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. Journal of Clinical Investigation. 23(5):2257-2267. [doi:10.1172/JCI67816. Epub ahead of print April 15, 2013] [PMID:23585477] [PMCID: PMC3639697] [PDF]

14. 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. [doi:10.1038/oncsis.2013.4] [PMID: 23552882] [PMCID: PMC3641357] [PDF]

15. 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 (EMT) Phenotype with Responsiveness to the p21-Activated Kinase Inhibitor, PF-3758309, in Colon Cancer Models. Front. Pharmacol. 4:35. [PMID:23543898] [PMCID: PMC3610010] [PDF]

16. Bradshaw-Pierce EL, Pitts TM, Tan AC, McPhillips K, West M, Gustafson DL, Halsey C, Nguyen L, Lee NV, Kan JLC, 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. [PMID:23524533] [PMCID: PMC3605511] [PDF]

17. Harvell DM, Kim J, O'Brien 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):140-153. [Epub ahead of print, Mar 12, 2013] [PMID:23479404] [PMCID: PMC3810166]

18. Singleton KR, Kim J, Hinz TK, Marek LA, Casas-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. Molecular Pharmacology. 83(4):882-893. [published ahead of print January 31, 2013, doi:10.1124/mol.112.084111] [PMID: 23371912] [PMCID: PMC3608435]

19. 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. (2013). Predictive Biomarkers of Sensitivity to the Aurora and Angiogenic Kinase Inhibitor ENMD-2076 in Preclinical Breast Cancer Models. Clinical Cancer Research. 19(1): 19:291-303. [Epub ahead of print, Nov 7, 2012]. [PMID: 23136197] [PMCID: PMC3537923] [COVER ARTICLE]
    TRANSLATIONAL CANCER RESEARCH: This research is translated into a clinical trial. "A Phase II Study of the Aurora and Angiogenic Kinase Inhibitor ENMD-2076 in Previously Treated Locally Advanced and Metastatic Triple-Negative Breast Cancer" (PI: Jennifer R. Diamond) . [ClinicalTrials.gov ID: NCT01639248]

1. Khoo SK*, Petillo D, Kang UJ, Resau JH, Berryhill B, Linder J, Forsgren L, Neuman LA, Tan AC*. (2012). Plasma-Based Circulating MicroRNA Biomarkers for Parkinson's Disease. Journal of Parkinson's Disease. 2(4): 321-331. [PMID: 23938262] [PDF] [IOS Press Release]
   This research is supported by the Michael J. Fox Foundation for Parkinson's Research 2010 Rapid Response Innovation Award (PI: SKK and ACT).

2. 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 Research 72(24): 6490-6501. [Epub ahead of print, Dec 7, 2012]. [PMID: 23222299] [PMCID: PMC4010325] [PDF] [AACR Press Release] [COVER ARTICLE]

3. 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 Multi-Center Study of Saracatinib, an Oral Src Inhibitor, in Previously Treated Pancreatic Cancer. Cancer Medicine. 1(2):207-217. [PMID:23342270] [PMCID: PMC354442] [PDF]
   TRANSLATIONAL BIOINFORMATICS RESEARCH: This is the results of a Phase II clinical trial (ClinicalTrials.gov ID: NCT00735917) based on the predictive biomarkers identified from preclinical models (Rajeshkumar NV, Tan AC, et al Clin. Can. Res. 2009; Arcaroli J., et al Clin. Can. Res. 2012) for saracatinib (AZD0530) in pancreatic cancer.

4. Casas-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 Research.72(16):4154-4164. [Epub ahead of print, Jun 27, 2012]. [PMID: 22738915] [PMCID: PMC3673784] [PDF]

5. 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. Nature Chemical Biology. 8(7): 646-654. [PMID: 22660439] [PMCID: PMC3430605] [PDF]

6. 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. Clinical Cancer Research. 18(9):2704-2714. [PMID: 22553375] [PMCID: PMC3836589] [PDF]

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. Nature Reviews Clinical Oncology. 9(6):338-350. [PMID: 22508028] [PMCID: PMC3928688] [PDF] [COVER ARTICLE]

8. 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 gamma-secretase inhibitor and irinotecan in colorecta cancer. Molecular Oncology. 6(3):370-381. [Available Online 28 March 2012.] [PMID: 22521243] [PMCID: PMC4033713] [PDF]

9. Smith AL, Iwanaga R, Drasin DJ, Micalizzi DS, Vartuli RL, Tan AC, Ford HL. (2012). The miR-106b-25 cluster targets Smad7, activates TGF-&beta signaling, and induces EMT and tumor initiating cell characteristics downstream of Six1 in human breast cancer. Oncogene. 31(50): 5162-5171 [2012 Jan 30. Epub ahead of print; doi:10.1038/onc.2012.11] [PMID: 22286770] [PMCID: PMC3342483] [PDF]

10. 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):1266-1276. [advance online publication, January 13, 2012; doi:10.1038/leu.2011.392] [PMID: 22289989] [PMCID: PMC3678731] [PDF]

11. 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. (2012) Preclinical Activity of the Rational Combination of Selumetinib (AZD6244) in Combination with Vorinostat in KRAS Mutant Colorectal Cancer Models. Clinical Cancer Research. 18(4):1051-1062 [2011 Dec 15. Epub ahead of print] [PMID: 22173548] [PMCID: PMC3876277] [PDF]

12. Haughian JM, Pinto MP, Harrell JC, Bliesner BS, Joensuu KM, Dye WW, Sartorius CA, Tan AC, Heikkilä P, Perou CM, Horwitz KB. (2012) Maintenance of hormone responsiveness in luminal breast cancers by suppression of Notch. Proc Natl Acad Sci U S A. 109(8):2742-2747 [2011 Oct 3. Epub ahead of print] [PMID: 21969591] [PMCID: PMC3287001] [PDF]

13. 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. (2012) A DNA methylation fingerprint of 1628 human samples. Genome Research. 22:407-419 [2011 May 25. Epub ahead of print] [PMID: 21613409] [PMCID: PMC3266047] [PDF]

14. 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. (2012) Direct reprogramming of human fibroblasts into dopaminergic neuron-like cells. Cell Research. 22:321-332. [2011 Nov 22. doi: 10.1038/cr.2011.181. Epub ahead of print] [PMID: 22105488] [PMCID: PMC3271588] [PDF]

1. 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 Infectious Diseases. 11:241. [PMID: 21914192] [PMCID: PMC3189140] [PDF]

2. Lyons TR, O'Brien 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. Nature Medicine. 17(9):1109-1115. [doi: 10.1038/nm.2416.] [PMID: 21822285] [PMCID: PMC388478] [PDF] [COVER ARTICLE]

3. 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. Clinical Cancer Research. 17(17):5793-5800. [Epub 2011 Jul 8]. [PMID: 21742805] [PMCID: PMC3210576] [PDF]

4. 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. (2011) Caspase 3-mediated stimulation of tumor cell repopulation during cancer radiotherapy. Nature Medicine. 17(7):860-866. [doi: 10.1038/nm.2385.] [PMID: 21725296] [PMCID: PMC3132290] [PDF]

5. 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. British Journal of Haematology. 153(6):753-757. [doi: 10.1111/j.1365-2141.2011.08662.x. Epub 2011 Apr 18.] [PMID: 21496004] [PMCID: PMC3896048] [PDF]

6. 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. Human Genomics. 5(2):117-123. [PMID: 21296745] [PMCID: PMC3525234] [PDF]

7. 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 Medical Genomics. 4:10. [PMID: 21261972] [PMCID: PMC3038886] [PDF]

1. 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. Human Genomics. 5(1):56-60. [PMID: 21106489] [PMCID: PMC3500157] [PDF]

2. 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. Clinical Cancer Research. 16(22):5581-5590. [Epub 2010 Nov 9.] [PMID: 21062932] [PMCID: PMC3395226] [PDF]

3. 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. Clinical Cancer Research. 16(22):5436-5446. [Epub 2010 Oct 13.] [PMID: 20943761] [PMCID: PMC3119523] [PDF]
   TRANSLATIONAL BIOINFORMATICS RESEARCH: This research is translated into a clinical trial. "A Phase I/IB Study of OSI-906 and Irinotecan in Patients With Advanced Cancer With Expanded Cohorts of Patients With Colorectal Cancer Stratified by the OSI-906 Integrated Classifier" (PI: Stephen Leong) . [ClinicalTrials.gov ID: NCT01016860]

4. 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. Molecular Cancer Therapeutics. 9(12):3351-3362. [Epub 2010 Oct 5.] [PMID: 20923857] [PMCID: PMC3931013] [PDF]

5. 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):6603-6608. [Epub 2010 Sep 6.] [PMID:20818429] [PMCID: PMC3081720] [PDF]

6. 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. Clinical Cancer Research. 16(16):4165-4177. [Epub 2010 Aug 3.] [PMID: 20682712] [PMCID: PMC3805460] [PDF]

7. 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. British Journal of Cancer. 103(5):649-655. [Epub 2010 Jul 27.] [PMID: 20664591] [PMCID: PMC2938261] [PDF]

8. 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. Clinical Cancer Research. 16(12):3193-3204. [Epub 2010 Jun 8.] [PMID: 20530704] [PMCID: PMC2889230] [PDF]
   TRANSLATIONAL BIOINFORMATICS RESEARCH: This research is translated into a clinical trial. "A Phase I/IB Study of OSI-906 and Irinotecan in Patients With Advanced Cancer With Expanded Cohorts of Patients With Colorectal Cancer Stratified by the OSI-906 Integrated Classifier" (PI: Stephen Leong) . [ClinicalTrials.gov ID: NCT01016860]

9. Leong S, Messersmith WA, Tan AC, Eckhardt SG. (2010) Novel agents in the treatment of metastatic colorectal cancer. Cancer J. 16(3):273-282. [PMID: 20526106] [PDF]

1. Tian Y, Tan AC, Sun X, Olson MT, Xie Z, Jinawath N, Chan DW, Shih IM, Zhang Z, Zhang H. (2009) Quantitative proteomic analysis of ovarian cancer cells identified mitochondrial proteins associated with Paclitaxel resistance. Proteomics Clinical Applications 3(11):1288-1295. [PMID: 21113235] [PMCID: PMC2989613] [PDF]

2. Kent OA, Mullendore M, Wentzel EA, Lopez-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 Biology Therapy. 8(21):2013-2024. [PMID: 20037478] [PMCID: PMC2824894] [PDF]

3. 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. Molecular Cancer Therapeutics. 8(6):1484-1493. [Epub 2009 Jun 9.] [PMID: 19509264] [PDF]

4. 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. Clinical Cancer Research. 15(12):4138-4146. [Epub 2009 Jun 9.] [PMID: 19509160] [PDF]
   TRANSLATIONAL BIOINFORMATICS RESEARCH: The classifier is being evaluated in a clinical trial. "A Phase II Trial of AZD0530 in Previously Treated Metastatic Pancreatic Cancer" (PI: Wells A. Messersmith) . [ClinicalTrials.gov ID: NCT00735917]

5. 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. Molecular Oncology. 3(5-6):425-438. [Epub 2009 Apr 22.] [PMID: 19497796] [PDF]

6. 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):1765-1776. [Epub 2009 Apr 7.] [PMID: 19357087] [PMCID: PMC2722769] [PDF]

1. Song D, Chaerkady R, Tan AC, Garcia-Garcia E, Nalli A, Suarez-Gauthier A, Lopez-Rios 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. Molecular Cancer Therapeutics. 7(10):3275-3284. [PMID: 18852131] [PDF]

2. Geman D, Bahman A, Tan AC, Naiman DQ. (2008). Microarray classification from several two-gene expression comparisons. In Proceedings of the Seventh International Conference on Machine Learning and Applications (ICMLA 08). (eds. M.A. Wani, X.-w. Chen, D. Casasent, L. Kurgan, T. Hu, and K. Hafeez) p. 583- 585. IEEE Computer Society. [PDF]

3. 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 Research. 68(8):2841-2849. [PMID: 18413752] [PDF]

4. 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. [PMID: 18304324] [PMCID: PMC2409450] [PDF]

5. 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. (2008) Allele-specific expression in the germline of patients with familial pancreatic cancer: an unbiased approach to cancer gene discovery. Cancer Biology Therapy. 7(1):135-144. [Epub 2007 Oct 19.] [PMID: 18059179] [PMCID: PMC4104667] [PDF]

1. 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):3905-3911. [Epub 2005 Aug 30.] [PMID:16131522] [PDF]

2. 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):3896-3904. [Epub 2005 Aug 16.] [PMID: 16105897] [PMCID: PMC1987374] [PDF]

1. Ren T, Veeramalai M, Tan AC, Gilbert D. (2004) MSAT: a multiple sequence alignment tool based on TOPS. Applied Bioinformatics. 3(2-3):149-158. [PMID:15693740] [PDF]

2. Al-Shahib A, He C, Tan AC, Girolami M, Gilbert D. (2004). An assessment of feature relevance in predicting protein function from sequence. In Proceedings of the Fifth Interntaional Conference on Intelligent Data Engineering and Automated Learning (IDEAL 04). (eds. R.L. Yang, R. Everson, and H. Yin). Lecture Notes in Computer Science. 3177: 52-57. Springer-Verlag, Exeter, UK. [PDF]

1. Tan AC, Gilbert D, Deville Y. (2003) Multi-class protein fold classification using a new ensemble machine learning approach. Genome Informatics. 14:206-217. [PMID: 15706535] [PDF]

2. Ren T, Veeramalai M, Tan AC, Gilbert D. (2003). MSAT: a Multiple Sequence Alignment tool based on TOPS. In Proceedings of the Biological Language Conference (BLC 2003). (eds. J. Klein-Seetharaman, R. Rosenfeld, and R. Reddy), pp. 286-301, Pittsburgh, USA. [PDF]

3. Tan AC, Gilbert D, Deville Y. (2003). Integrative machine learning approach for multi-class SCOP protein fold classification. In Proceedings of the German Conference on Bioinformatics (GCB2003). (eds. H.-W. Mewes, D. Frishman, V. Heun, and S. Kramer), pp. 153-159, Munich, Germany. [PDF]

4. Tan AC, Gilbert D. (2003) Ensemble machine learning on gene expression data for cancer classification. Applied Bioinformatics. 2(3 Suppl):S75-S83. [PMID: 15130820] [PDF]

5. Tan AC, Gilbert D. (2003). An empirical comparison of supervised machine learning techniques in bioinformatics. In Proceedings of the 1st Asia Pacific Bioinformatics Conference (APBC 2003). (ed. Y.-P. Chen, P.), pp. 219-222. [PDF]

1. Tan AC, Gilbert D, Tuson A. (2002). Characterisation of FAD-family Folds using a Machine Learning Approach. In Proceedings of the International Conference on Bioinformatics (InCoB 2002), Bangkok, Thailand. [PDF]