Aik Choon Tan

Aik Choon Tan, PhD

Languages spoken: English

Academic Information

Departments Adjunct - Biomedical Informatics , Primary - Oncological Sciences

Education History

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

Selected Publications

Journal Article

  1. Kim J, Tan A (2012). BiNGS!SL-seq: a bioinformatics pipeline for the analysis and interpretation of deep sequencing genome-wide synthetic lethal screen. Methods in molecular biology (Clifton, N.J.), 802, 389-98. (Read full article)
  2. Tan A (2012). Employing gene set top scoring pairs to identify deregulated pathway-signatures in dilated cardiomyopathy from integrated microarray gene expression data. Methods in molecular biology (Clifton, N.J.), 802, 345-61. (Read full article)
  3. Tan AC, Gilbert (2003). Ensemble machine learning on gene expression data for cancer classification. Applied bioinformatics, 2(3 Suppl), S75-83. (Read full article)
  4. Tan AC, Gilbert D, Deville (2003). Multi-class protein fold classification using a new ensemble machine learning approach. Genome informatics. International Conference on Genome Informatics, 14, 206-17. (Read full article)
  5. Ren T, Veeramalai M, Tan AC, Gilbert (2004). MSAT: a multiple sequence alignment tool based on TOPS. Applied bioinformatics, 3(2-3), 149-58. (Read full article)
  6. Tan AC, Naiman DQ, Xu L, Winslow RL, Geman (2005). Simple decision rules for classifying human cancers from gene expression profiles. Bioinformatics (Oxford, England), 21(20), 3896-904. (Read full article)
  7. Xu L, Tan AC, Naiman DQ, Geman D, Winslow R (2005). Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinformatics (Oxford, England), 21(20), 3905-11. (Read full article)
  8. 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 (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), 135-44. (Read full article)
  9. Xu L, Tan AC, Winslow RL, Geman (2008). Merging microarray data from separate breast cancer studies provides a robust prognostic test. BMC bioinformatics, 9, 125. (Read full article)
  10. 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 (2008). Coordinated epidermal growth factor receptor pathway gene overexpression predicts epidermal growth factor receptor inhibitor sensitivity in pancreatic cancer. Cancer research, 68(8), 2841-9. (Read full article)
  11. 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 (2008). Antitumor activity and molecular effects of the novel heat shock protein 90 inhibitor, IPI-504, in pancreatic cancer. Molecular cancer therapeutics, 7(10), 3275-84. (Read full article)
  12. 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 (2009). Identification of novel serological biomarkers for inflammatory bowel disease using Escherichia coli proteome chip. Molecular & cellular proteomics, 8(8), 1765-76. (Read full article)
  13. Tan AC, Jimeno A, Lin SH, Wheelhouse J, Chan F, Solomon A, Rajeshkumar NV, Rubio-Viqueira B, Hidalgo (2009). Characterizing DNA methylation patterns in pancreatic cancer genome. Molecular oncology, 3(5-6), 425-38. (Read full article)
  14. 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 (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), 1484-93. (Read full article)
  15. Rajeshkumar NV, Tan AC, De Oliveira E, Womack C, Wombwell H, Morgan S, Warren MV, Walker J, Green TP, Jimeno A, Messersmith WA, Hidalgo (2009). Antitumor effects and biomarkers of activity of AZD0530, a Src inhibitor, in pancreatic cancer. Clinical cancer research, 15(12), 4138-46. (Read full article)
  16. Tian Y, Tan AC, Sun X, Olson MT, Xie Z, Jinawath N, Chan DW, Shih IeM, Zhang Z, Zhang (2009). Quantitative proteomic analysis of ovarian cancer cells identified mitochondrial proteins associated with Paclitaxel resistance. Proteomics. Clinical applications, 3(11), 1288-95. (Read full article)
  17. Kent OA, Mullendore M, Wentzel EA, López-Romero P, Tan AC, Alvarez H, West K, Ochs MF, Hidalgo M, Arking DE, Maitra A, Mendell J (2009). A resource for analysis of microRNA expression and function in pancreatic ductal adenocarcinoma cells. Cancer biology & therapy, 8(21), 2013-24. (Read full article)
  18. Pitts TM, Tan AC, Kulikowski GN, Tentler JJ, Brown AM, Flanigan SA, Leong S, Coldren CD, Hirsch FR, Varella-Garcia M, Korch C, Eckhardt S (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), 3193-204. (Read full article)
  19. Gao D, Kim J, Kim H, Phang TL, Selby H, Tan AC, Tong (2010). A survey of statistical software for analysing RNA-seq data. Human genomics, 5(1), 56-60. (Read full article)
  20. Arcaroli JJ, Touban BM, Tan AC, Varella-Garcia M, Powell RW, Eckhardt SG, Elvin P, Gao D, Messersmith W (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), 4165-77. (Read full article)
  21. 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 (2010). Integrated preclinical and clinical development of mTOR inhibitors in pancreatic cancer. British journal of cancer, 103(5), 649-55. (Read full article)
  22. Deng Y, Liu J, Han G, Lu SL, Wang SY, Malkoski S, Tan AC, Deng C, Wang XJ, Zhang (2010). Redox-dependent Brca1 transcriptional regulation by an NADH-sensor CtBP1. Oncogene, 29(50), 6603-8. (Read full article)
  23. 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 S (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), 3351-62. (Read full article)
  24. Camidge DR, Kono SA, Flacco A, Tan AC, Doebele RC, Zhou Q, Crino L, Franklin WA, Varella-Garcia (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), 5581-90. (Read full article)
  25. Flanigan SA, Pitts TM, Eckhardt SG, Tentler JJ, Tan AC, Thorburn A, Leong (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), 5436-46. (Read full article)
  26. Jones LK, Zou F, Kheifets A, Rybnikov K, Berry D, Tan A (2011). Confident predictability: identifying reliable gene expression patterns for individualized tumor classification using a local minimax kernel algorithm. BMC medical genomics, 4, 10. (Read full article)
  27. 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 (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), 753-7. (Read full article)
  28. 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 C (2011). Caspase 3-mediated stimulation of tumor cell repopulation during cancer radiotherapy. Nature medicine, 17(7), 860-6. (Read full article)
  29. 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 (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), 5793-800. (Read full article)
  30. Lyons TR, O'Brien J, Borges VF, Conklin MW, Keely PJ, Eliceiri KW, Marusyk A, Tan AC, Schedin (2011). Postpartum mammary gland involution drives progression of ductal carcinoma in situ through collagen and COX-2. Nature medicine, 17(9), 1109-15. (Read full article)
  31. Khoo SK, Petillo D, Parida M, Tan AC, Resau JH, Obaro S (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. (Read full article)
  32. 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 C (2012). Direct reprogramming of human fibroblasts into dopaminergic neuron-like cells. Cell research, 22(2), 321-32. (Read full article)
  33. 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 S (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), 1051-62. (Read full article)
  34. 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 (2012). A DNA methylation fingerprint of 1628 human samples. Genome research, 22(2), 407-19. (Read full article)
  35. Haughian JM, Pinto MP, Harrell JC, Bliesner BS, Joensuu KM, Dye WW, Sartorius CA, Tan AC, Heikkilä P, Perou CM, Horwitz K (2012). Maintenance of hormone responsiveness in luminal breast cancers by suppression of Notch. Proceedings of the National Academy of Sciences of the United States of America, 109(8), 2742-7. (Read full article)
  36. Porter CC, Kim J, Fosmire S, Gearheart CM, van Linden A, Baturin D, Zaberezhnyy V, Patel PR, Gao D, Tan AC, DeGregori (2012). Integrated genomic analyses identify WEE1 as a critical mediator of cell fate and a novel therapeutic target in acute myeloid leukemia. Leukemia, 26(6), 1266-76. (Read full article)
  37. Smith AL, Iwanaga R, Drasin DJ, Micalizzi DS, Vartuli RL, Tan AC, Ford H (2012). The miR-106b-25 cluster targets Smad7, activates TGF-ß signaling, and induces EMT and tumor initiating cell characteristics downstream of Six1 in human breast cancer. Oncogene, 31(50), 5162-71. (Read full article)
  38. Arcaroli JJ, Powell RW, Varella-Garcia M, McManus M, Tan AC, Quackenbush KS, Pitts TM, Gao D, Spreafico A, Dasari A, Touban BM, Messersmith W (2012). ALDH+ tumor-initiating cells exhibiting gain in NOTCH1 gene copy number have enhanced regrowth sensitivity to a ¿-secretase inhibitor and irinotecan in colorectal cancer. Molecular oncology, 6(3), 370-81. (Read full article)
  39. 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 W (2012). Common PIK3CA mutants and a novel 3' UTR mutation are associated with increased sensitivity to saracatinib. Clinical cancer research, 18(9), 2704-14. (Read full article)
  40. Sullivan KD, Padilla-Just N, Henry RE, Porter CC, Kim J, Tentler JJ, Eckhardt SG, Tan AC, DeGregori J, Espinosa J (2012). ATM and MET kinases are synthetic lethal with nongenotoxic activation of p53. Nature chemical biology, 8(7), 646-54. (Read full article)
  41. Casás-Selves M, Kim J, Zhang Z, Helfrich BA, Gao D, Porter CC, Scarborough HA, Bunn PA Jr, Chan DC, Tan AC, DeGregori (2012). Tankyrase and the canonical Wnt pathway protect lung cancer cells from EGFR inhibition. Cancer research, 72(16), 4154-64. (Read full article)
  42. 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 W (2012). Biomarker-driven trial in metastatic pancreas cancer: feasibility in a multicenter study of saracatinib, an oral Src inhibitor, in previously treated pancreatic cancer. Cancer medicine, 1(2), 207-17. (Read full article)
  43. Giles ED, Wellberg EA, Astling DP, Anderson SM, Thor AD, Jindal S, Tan AC, Schedin PS, Maclean P (2012). Obesity and overfeeding affecting both tumor and systemic metabolism activates the progesterone receptor to contribute to postmenopausal breast cancer. Cancer research, 72(24), 6490-501. (Read full article)
  44. Khoo SK, Petillo D, Kang UJ, Resau JH, Berryhill B, Linder J, Forsgren L, Neuman LA, Tan A (2012). Plasma-based circulating MicroRNA biomarkers for Parkinson's disease. Journal of Parkinson's disease, 2(4), 321-31. (Read full article)
  45. Diamond JR, Eckhardt SG, Tan AC, Newton TP, Selby HM, Brunkow KL, Kachaeva MI, Varella-Garcia M, Pitts TM, Bray MR, Fletcher GC, Tentler J (2013). Predictive biomarkers of sensitivity to the aurora and angiogenic kinase inhibitor ENMD-2076 in preclinical breast cancer models. Clinical cancer research, 19(1), 291-303. (Read full article)
  46. Singleton KR, Kim J, Hinz TK, Marek LA, Casás-Selves M, Hatheway C, Tan AC, DeGregori J, Heasley L (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), 882-93. (Read full article)
  47. Bradshaw-Pierce EL, Pitts TM, Tan AC, McPhillips K, West M, Gustafson DL, Halsey C, Nguyen L, Lee NV, Kan JL, Murray BW, Eckhardt S (2013). Tumor P-Glycoprotein Correlates with Efficacy of PF-3758309 in in vitro and in vivo Models of Colorectal Cancer. Frontiers in pharmacology, 4, 22. (Read full article)
  48. 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 S (2013). Association of the epithelial-to-mesenchymal transition phenotype with responsiveness to the p21-activated kinase inhibitor, PF-3758309, in colon cancer models. Frontiers in pharmacology, 4, 35. (Read full article)
  49. Harvell DM, Kim J, O'Brien J, Tan AC, Borges VF, Schedin P, Jacobsen BM, Horwitz K (2013). Genomic signatures of pregnancy-associated breast cancer epithelia and stroma and their regulation by estrogens and progesterone. Hormones & cancer, 4(3), 140-53. (Read full article)
  50. Ware KE, Hinz TK, Kleczko E, Singleton KR, Marek LA, Helfrich BA, Cummings CT, Graham DK, Astling D, Tan AC, Heasley L (2013). A mechanism of resistance to gefitinib mediated by cellular reprogramming and the acquisition of an FGF2-FGFR1 autocrine growth loop. Oncogenesis, 2, e39. (Read full article)
  51. 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 D (2013). MERTK receptor tyrosine kinase is a therapeutic target in melanoma. The Journal of clinical investigation, 123(5), 2257-67. (Read full article)
  52. 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 (2013). A patient tumor transplant model of squamous cell cancer identifies PI3K inhibitors as candidate therapeutics in defined molecular bins. Molecular oncology, 7(4), 776-90. (Read full article)
  53. Andrysik Z, Kim J, Tan AC, Espinosa J (2013). A genetic screen identifies TCF3/E2A and TRIAP1 as pathway-specific regulators of the cellular response to p53 activation. Cell reports, 3(5), 1346-54. (Read full article)
  54. 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 S (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), 4149-62. (Read full article)
  55. Maller O, Hansen KC, Lyons TR, Acerbi I, Weaver VM, Prekeris R, Tan AC, Schedin (2013). Collagen architecture in pregnancy-induced protection from breast cancer. Journal of cell science, 126(Pt 18), 4108-10. (Read full article)
  56. 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 D (2013). Mer receptor tyrosine kinase is a therapeutic target in pre-B-cell acute lymphoblastic leukemia. Blood, 122(9), 1599-609. (Read full article)
  57. 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 W (2013). Tumours with elevated levels of the Notch and Wnt pathways exhibit efficacy to PF-03084014, a ¿-secretase inhibitor, in a preclinical colorectal explant model. British journal of cancer, 109(3), 667-75. (Read full article)
  58. 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 (2013). The dual pathway inhibitor rigosertib is effective in direct patient tumor xenografts of head and neck squamous cell carcinomas. Molecular cancer therapeutics, 12(10), 1994-2005. (Read full article)
  59. Khor GH, Froemming GR, Zain RB, Abraham MT, Omar E, Tan SK, Tan AC, Vincent-Chong VK, Thong K (2013). DNA methylation profiling revealed promoter hypermethylation-induced silencing of p16, DDAH2 and DUSP1 in primary oral squamous cell carcinoma. International journal of medical sciences, 10(12), 1727-39. (Read full article)
  60. Flanigan SA, Pitts TM, Newton TP, Kulikowski GN, Tan AC, McManus MC, Spreafico A, Kachaeva MI, Selby HM, Tentler JJ, Eckhardt SG, Leong (2013). Overcoming IGF1R/IR resistance through inhibition of MEK signaling in colorectal cancer models. Clinical cancer research, 19(22), 6219-29. (Read full article)
  61. Kim J, Yoo M, Kang J, Tan A (2013). K-Map: connecting kinases with therapeutics for drug repurposing and development. Human genomics, 7, 20. (Read full article)
  62. 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 R (2013). Resistance to ROS1 inhibition mediated by EGFR pathway activation in non-small cell lung cancer. PloS one, 8(12), e82236. (Read full article)
  63. Jeon M, Lee S, Lee K, Tan AC, Kang (2014). BEReX: Biomedical Entity-Relationship eXplorer. Bioinformatics (Oxford, England), 30(1), 135-6. (Read full article)
  64. Saha A, Tan AC, Kang (2014). Automatic context-specific subnetwork discovery from large interaction networks. PloS one, 9(1), e84227. (Read full article)
  65. 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 (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. Clinical cancer research, 20(6), 1656-65. (Read full article)
  66. Morrison JA, Pike LA, Sams SB, Sharma V, Zhou Q, Severson JJ, Tan AC, Wood WM, Haugen B (2014). Thioredoxin interacting protein (TXNIP) is a novel tumor suppressor in thyroid cancer. Molecular cancer, 13, 62. (Read full article)
  67. 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 Jr, Camidge DR, Tan AC, Hirsch FR, Heasley L (2014). FGFR1 mRNA and protein expression, not gene copy number, predict FGFR TKI sensitivity across all lung cancer histologies. Clinical cancer research, 20(12), 3299-309. (Read full article)
  68. 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 A (2014). Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy. Bioinformatics (Oxford, England), 30(17), 2393-8. (Read full article)
  69. Wang CA, Drasin D, Pham C, Jedlicka P, Zaberezhnyy V, Guney M, Li H, Nemenoff R, Costello JC, Tan AC, Ford H (2014). Homeoprotein Six2 promotes breast cancer metastasis via transcriptional and epigenetic control of E-cadherin expression. Cancer research, 74(24), 7357-70. (Read full article)
  70. Seelenfreund E, Robinson WA, Amato CM, Tan AC, Kim J, Robinson S (2014). Long term storage of dry versus frozen RNA for next generation molecular studies. PloS one, 9(11), e111827. (Read full article)
  71. 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 (2014). Dual pharmacological targeting of the MAP kinase and PI3K/mTOR pathway in preclinical models of colorectal cancer. PloS one, 9(11), e113037. (Read full article)
  72. 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 J (2015). Potent antitumor activity of cabozantinib, a c-MET and VEGFR2 inhibitor, in a colorectal cancer patient-derived tumor explant model. International journal of cancer, 136(8), 1967-75. (Read full article)
  73. 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 S (2015). Antitumor activity of the MEK inhibitor TAK-733 against melanoma cell lines and patient-derived tumor explants. Molecular cancer therapeutics, 14(2), 317-25. (Read full article)
  74. Fleenor CJ, Rozhok AI, Zaberezhnyy V, Mathew D, Kim J, Tan AC, Bernstein ID, DeGregori (2015). Contrasting roles for C/EBP¿ and Notch in irradiation-induced multipotent hematopoietic progenitor cell defects. Stem cells (Dayton, Ohio), 33(4), 1345-58. (Read full article)
  75. Ryall KA, Tan A (2015). Systems biology approaches for advancing the discovery of effective drug combinations. Journal of cheminformatics, 7, 7. (Read full article)
  76. Drasin DJ, Guarnieri AL, Neelakantan D, Kim J, Cabrera JH, Wang CA, Zaberezhnyy V, Gasparini P, Cascione L, Huebner K, Tan AC, Ford H (2015). TWIST1-Induced miR-424 Reversibly Drives Mesenchymal Programming while Inhibiting Tumor Initiation. Cancer research, 75(9), 1908-21. (Read full article)
  77. Tentler JJ, Ionkina AA, Tan AC, Newton TP, Pitts TM, Glogowska MJ, Kabos P, Sartorius CA, Sullivan KD, Espinosa JM, Eckhardt SG, Diamond J (2015). p53 Family Members Regulate Phenotypic Response to Aurora Kinase A Inhibition in Triple-Negative Breast Cancer. Molecular cancer therapeutics, 14(5), 1117-29. (Read full article)
  78. Kleczko EK, Kim J, Keysar SB, Heasley LR, Eagles JR, Simon M, Marshall ME, Singleton KR, Jimeno A, Tan AC, Heasley L (2015). An Inducible TGF-ß2-TGFßR Pathway Modulates the Sensitivity of HNSCC Cells to Tyrosine Kinase Inhibitors Targeting Dominant Receptor Tyrosine Kinases. PloS one, 10(5), e0123600. (Read full article)
  79. Yonekawa T, Gamez G, Kim J, Tan AC, Thorburn J, Gump J, Thorburn A, Morgan M (2015). RIP1 negatively regulates basal autophagic flux through TFEB to control sensitivity to apoptosis. EMBO reports, 16(6), 700-8. (Read full article)
  80. Yoo M, Shin J, Kim J, Ryall KA, Lee K, Lee S, Jeon M, Kang J, Tan A (2015). DSigDB: drug signatures database for gene set analysis. Bioinformatics (Oxford, England), 31(18), 3069-71. (Read full article)
  81. 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 (2015). FGFR1 Expression Levels Predict BGJ398 Sensitivity of FGFR1-Dependent Head and Neck Squamous Cell Cancers. Clinical cancer research, 21(19), 4356-64. (Read full article)
  82. Davis EM, Kim J, Menasche BL, Sheppard J, Liu X, Tan AC, Shen (2015). Comparative Haploid Genetic Screens Reveal Divergent Pathways in the Biogenesis and Trafficking of Glycophosphatidylinositol-Anchored Proteins. Cell reports, 11(11), 1727-36. (Read full article)
  83. 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 S (2015). Combined inhibition of MEK and Aurora A kinase in KRAS/PIK3CA double-mutant colorectal cancer models. Frontiers in pharmacology, 6, 120. (Read full article)
  84. Saha A, Jeon M, Tan AC, Kang (2015). iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data. PloS one, 10(7), e0131656. (Read full article)
  85. 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 A (2015). An integrated bioinformatics analysis to dissect kinase dependency in triple negative breast cancer. BMC genomics, 16 Suppl 12, S2. (Read full article)
  86. Ryall KA, Shin J, Yoo M, Hinz TK, Kim J, Kang J, Heasley LE, Tan A (2015). Identifying kinase dependency in cancer cells by integrating high-throughput drug screening and kinase inhibition data. Bioinformatics (Oxford, England), 31(23), 3799-806. (Read full article)
  87. Singleton KR, Hinz TK, Kleczko EK, Marek LA, Kwak J, Harp T, Kim J, Tan AC, Heasley L (2015). Kinome RNAi Screens Reveal Synergistic Targeting of MTOR and FGFR1 Pathways for Treatment of Lung Cancer and HNSCC. Cancer research, 75(20), 4398-406. (Read full article)
  88. 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 S (2015). Antitumor activity of a potent MEK inhibitor, TAK-733, against colorectal cancer cell lines and patient derived xenografts. Oncotarget, 6(33), 34561-72. (Read full article)
  89. 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 (2015). Aging-associated inflammation promotes selection for adaptive oncogenic events in B cell progenitors. The Journal of clinical investigation, 125(12), 4666-80. (Read full article)
  90. 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 H (2015). The Six1 oncoprotein downregulates p53 via concomitant regulation of RPL26 and microRNA-27a-3p. Nature communications, 6, 10077. (Read full article)
  91. 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 W (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. International journal of cancer, 138(1), 195-205. (Read full article)
  92. 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 (2016). A pilot study of cetuximab and the hedgehog inhibitor IPI-926 in recurrent/metastatic head and neck squamous cell carcinoma. Oral oncology, 53, 74-9. (Read full article)
  93. Fornetti J, Flanders KC, Henson PM, Tan AC, Borges VF, Schedin (2016). Mammary epithelial cell phagocytosis downstream of TGF-ß3 is characterized by adherens junction reorganization. Cell death and differentiation, 23(2), 185-96. (Read full article)
  94. 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 (2016). XactMice: humanizing mouse bone marrow enables microenvironment reconstitution in a patient-derived xenograft model of head and neck cancer. Oncogene, 35(3), 290-300. (Read full article)
  95. Symonds JM, Ohm AM, Tan AC, Reyland M (2016). PKC¿ regulates integrin ¿Vß3 expression and transformed growth of K-ras dependent lung cancer cells. Oncotarget, 7(14), 17905-19. (Read full article)
  96. Lee K, Lee S, Park S, Kim S, Kim S, Choi K, Tan AC, Kang (2016). BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations. Database, 2016, (Read full article)
  97. 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 A (2016). IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples. Journal of the American Medical Informatics Association, 23(4), 721-30. (Read full article)
  98. 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 S (2016). Genetically-defined novel oral squamous cell carcinoma cell lines for the development of molecular therapies. Oncotarget, 7(19), 27802-18. (Read full article)
  99. 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 S (2016). Antitumor activity of the aurora a selective kinase inhibitor, alisertib, against preclinical models of colorectal cancer. Oncotarget, 7(31), 50290-50301. (Read full article)
  100. Beadnell TC, Mishall KM, Zhou Q, Riffert SM, Wuensch KE, Kessler BE, Corpuz ML, Jing X, Kim J, Wang G, Tan AC, Schweppe R (2016). The Mitogen-Activated Protein Kinase Pathway Facilitates Resistance to the Src Inhibitor Dasatinib in Thyroid Cancer. Molecular cancer therapeutics, 15(8), 1952-63. (Read full article)
  101. Pozdeyev N, Yoo M, Mackie R, Schweppe RE, Tan AC, Haugen B (2016). Integrating heterogeneous drug sensitivity data from cancer pharmacogenomic studies. Oncotarget, 7(32), 51619-51625. (Read full article)
  102. Lee K, Shin W, Kim B, Lee S, Choi Y, Kim S, Jeon M, Tan AC, Kang (2016). HiPub: translating PubMed and PMC texts to networks for knowledge discovery. Bioinformatics (Oxford, England), 32(18), 2886-8. (Read full article)
  103. Helfrich BA, Kim J, Gao D, Chan DC, Zhang Z, Tan AC, Bunn PA J (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. (Read full article)
  104. Bagby S, Messersmith WA, Pitts TM, Capasso A, Varella-Garcia M, Klauck PJ, Kim J, Tan AC, Eckhardt SG, Tentler JJ, Arcaroli (2016). Development and Maintenance of a Preclinical Patient Derived Tumor Xenograft Model for the Investigation of Novel Anti-Cancer Therapies. Journal of visualized experiments, (115), (Read full article)
  105. Todd JR, Ryall KA, Vyse S, Wong JP, Natrajan RC, Yuan Y, Tan AC, Huang P (2016). Systematic analysis of tumour cell-extracellular matrix adhesion identifies independent prognostic factors in breast cancer. Oncotarget, 7(39), 62939-62953. (Read full article)
  106. Lee S, Kim D, Lee K, Choi J, Kim S, Jeon M, Lim S, Choi D, Kim S, Tan AC, Kang (2016). BEST: Next-Generation Biomedical Entity Search Tool for Knowledge Discovery from Biomedical Literature. PloS one, 11(10), e0164680. (Read full article)
  107. 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 P (2016). Dual Targeting of PDGFR¿ and FGFR1 Displays Synergistic Efficacy in Malignant Rhabdoid Tumors. Cell reports, 17(5), 1265-1275. (Read full article)
  108. 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 (2016). ATM/G6PD-driven redox metabolism promotes FLT3 inhibitor resistance in acute myeloid leukemia. Proceedings of the National Academy of Sciences of the United States of America, 113(43), E6669-E6678. (Read full article)
  109. Zhang G, Scarborough H, Kim J, Rozhok AI, Chen YA, Zhang X, Song L, Bai Y, Fang B, Liu RZ, Koomen J, Tan AC, Degregori J, Haura E (2016). Coupling an EML4-ALK-centric interactome with RNA interference identifies sensitizers to ALK inhibitors. Science signaling, 9(450), rs12. (Read full article)
  110. Cavalli G, Koenders M, Kalabokis V, Kim J, Tan AC, Garlanda C, Mantovani A, Dagna L, Joosten LA, Dinarello C (2016). Treating experimental arthritis with the innate immune inhibitor interleukin-37 reduces joint and systemic inflammation. Rheumatology (Oxford, England), 55(12), 2220-2229. (Read full article)
  111. Federer C, Yoo M, Tan A (2016). Big Data Mining and Adverse Event Pattern Analysis in Clinical Drug Trials. Assay and drug development technologies, 14(10), 557-566. (Read full article)
  112. Murakami A, Wang L, Kalhorn S, Schraml P, Rathmell WK, Tan AC, Nemenoff R, Stenmark K, Jiang BH, Reyland ME, Heasley L, Hu C (2017). Context-dependent role for chromatin remodeling component PBRM1/BAF180 in clear cell renal cell carcinoma. Oncogenesis, 6(1), e287. (Read full article)
  113. Lee BK, Tiong KH, Chang JK, Liew CS, Abdul Rahman ZA, Tan AC, Khang TF, Cheong S (2017). DeSigN: connecting gene expression with therapeutics for drug repurposing and development. BMC genomics, 18(Suppl 1), 934. (Read full article)
  114. 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 (2016). Regulation of Head and Neck Squamous Cancer Stem Cells by PI3K and SOX2. Journal of the National Cancer Institute, 109(1), (Read full article)
  115. 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 (2017). Kinase gene fusions in defined subsets of melanoma. Pigment cell & melanoma research, 30(1), 53-62. (Read full article)
  116. 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 S (2017). Targeting the protein ubiquitination machinery in melanoma by the NEDD8-activating enzyme inhibitor pevonedistat (MLN4924). Investigational new drugs, 35(1), 11-25. (Read full article)
  117. Scarborough HA, Helfrich BA, Casás-Selves M, Schuller AG, Grosskurth SE, Kim J, Tan AC, Chan DC, Zhang Z, Zaberezhnyy V, Bunn PA, DeGregori (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. (Read full article)
  118. Brechbuhl HM, Finlay-Schultz J, Yamamoto TM, Gillen AE, Cittelly DM, Tan AC, Sams SB, Pillai MM, Elias AD, Robinson WA, Sartorius CA, Kabos (2017). Fibroblast Subtypes Regulate Responsiveness of Luminal Breast Cancer to Estrogen. Clinical cancer research, 23(7), 1710-1721. (Read full article)
  119. Dimberg LY, Towers CG, Behbakht K, Hotz TJ, Kim J, Fosmire S, Porter CC, Tan AC, Thorburn A, Ford H (2017). A Genome-Wide Loss-of-Function Screen Identifies SLC26A2 as a Novel Mediator of TRAIL Resistance. Molecular cancer research, 15(4), 382-394. (Read full article)
  120. Harder B, Tian W, La Clair JJ, Tan AC, Ooi A, Chapman E, Zhang D (2017). Brusatol overcomes chemoresistance through inhibition of protein translation. Molecular carcinogenesis, 56(5), 1493-1500. (Read full article)
  121. 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 W (2017). Whole-exome sequencing identifies recurrent SF3B1 R625 mutation and comutation of NF1 and KIT in mucosal melanoma. Melanoma research, 27(3), 189-199. (Read full article)
  122. Ionkina AA, Tentler JJ, Kim J, Capasso A, Pitts TM, Ryall KA, Howison RR, Kabos P, Sartorius CA, Tan AC, Eckhardt SG, Diamond J (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, 94. (Read full article)
  123. Nelson-Taylor SK, Le AT, Yoo M, Schubert L, Mishall KM, Doak A, Varella-Garcia M, Tan AC, Doebele R (2017). Resistance to RET-Inhibition in RET-Rearranged NSCLC Is Mediated By Reactivation of RAS/MAPK Signaling. Molecular cancer therapeutics, 16(8), 1623-1633. (Read full article)
  124. Ohm AM, Tan AC, Heasley LE, Reyland M (2017). Co-dependency of PKC¿ and K-Ras: inverse association with cytotoxic drug sensitivity in KRAS mutant lung cancer. Oncogene, 36(30), 4370-4378. (Read full article)
  125. Donson AM, Apps J, Griesinger AM, Amani V, Witt DA, Anderson RCE, Niazi TN, Grant G, Souweidane M, Johnston JM, Jackson EM, Kleinschmidt-DeMasters BK, Handler MH, Tan AC, Gore L, Virasami A, Gonzalez-Meljem JM, Jacques TS, Martinez-Barbera JP, Foreman NK, Hankinson TC, Advancing Treatment for Pediatric Craniopharyngioma Consortium (2017). Molecular Analyses Reveal Inflammatory Mediators in the Solid Component and Cyst Fluid of Human Adamantinomatous Craniopharyngioma. Journal of neuropathology and experimental neurology, 76(9), 779-788. (Read full article)
  126. Zhang C, Liu Z, Bunker E, Ramirez A, Lee S, Peng Y, Tan AC, Eckhardt SG, Chapnick DA, Liu (2017). Sorafenib targets the mitochondrial electron transport chain complexes and ATP synthase to activate the PINK1-Parkin pathway and modulate cellular drug response. The Journal of biological chemistry, 292(36), 15105-15120. (Read full article)
  127. 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 W (2017). Evaluation of the efficacy of dasatinib, a Src/Abl inhibitor, in colorectal cancer cell lines and explant mouse model. PloS one, 12(11), e0187173. (Read full article)
  128. Yue Z, Zheng Q, Neylon MT, Yoo M, Shin J, Zhao Z, Tan AC, Chen J (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. (Read full article)
  129. 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 W (2018). ALK Inhibitor Response in Melanomas Expressing EML4-ALK Fusions and Alternate ALK Isoforms. Molecular cancer therapeutics, 17(1), 222-231. (Read full article)
  130. Kim S, Park D, Choi Y, Lee K, Kim B, Jeon M, Kim J, Tan AC, Kang (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. (Read full article)
  131. Lee K, Kim B, Choi Y, Kim S, Shin W, Lee S, Park S, Kim S, Tan AC, Kang (2018). Deep learning of mutation-gene-drug relations from the literature. BMC bioinformatics, 19(1), 21. (Read full article)
  132. Pilling AB, Kim J, Estrada-Bernal A, Zhou Q, Le AT, Singleton KR, Heasley LE, Tan AC, DeGregori J, Doebele R (2018). ALK is a critical regulator of the MYC-signaling axis in ALK positive lung cancer. Oncotarget, 9(10), 8823-8835. (Read full article)
  133. 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 T (2018). Antitumor activity of the polo-like kinase inhibitor, TAK-960, against preclinical models of colorectal cancer. BMC cancer, 18(1), 136. (Read full article)
  134. Kim J, Yoo M, Shin J, Kim H, Kang J, Tan A (2018). Systems Pharmacology-Based Approach of Connecting Disease Genes in Genome-Wide Association Studies with Traditional Chinese Medicine. International journal of genomics, 2018, 7697356. (Read full article)
  135. Hintzsche JD, Yoo M, Kim J, Amato CM, Robinson WA, Tan A (2018). IMPACT web portal: oncology database integrating molecular profiles with actionable therapeutics. BMC medical genomics, 11(Suppl 2), 26. (Read full article)
  136. Lee BKB, Gan CP, Chang JK, Tan JL, Fadlullah MZ, Abdul Rahman ZA, Prime SS, Gutkind JS, Liew CS, Khang TF, Tan AC, Cheong S (2018). GENIPAC: A Genomic Information Portal for Head and Neck Cancer Cell Systems. Journal of dental research, 97(8), 909-916. (Read full article)
  137. Powers RK, Goodspeed A, Pielke-Lombardo H, Tan AC, Costello J (2018). GSEA-InContext: identifying novel and common patterns in expression experiments. Bioinformatics (Oxford, England), 34(13), i555-i564. (Read full article)
  138. 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 (2018). Salivary Gland Cancer Patient-Derived Xenografts Enable Characterization of Cancer Stem Cells and New Gene Events Associated with Tumor Progression. Clinical cancer research, 24(12), 2935-2943. (Read full article)
  139. 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 D (2018). Genetic Analysis of 779 Advanced Differentiated and Anaplastic Thyroid Cancers. Clinical cancer research, 24(13), 3059-3068. (Read full article)
  140. 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 C (2018). AMPK/FIS1-Mediated Mitophagy Is Required for Self-Renewal of Human AML Stem Cells. Cell stem cell, 23(1), 86-100.e6. (Read full article)
  141. Parrish JK, McCann TS, Sechler M, Sobral LM, Ren W, Jones KL, Tan AC, Jedlicka (2018). The Jumonji-domain histone demethylase inhibitor JIB-04 deregulates oncogenic programs and increases DNA damage in Ewing Sarcoma, resulting in impaired cell proliferation and survival, and reduced tumor growth. Oncotarget, 9(69), 33110-33123. (Read full article)
  142. Suda K, Kim J, Murakami I, Rozeboom L, Shimoji M, Shimizu S, Rivard CJ, Mitsudomi T, Tan AC, Hirsch F (2018). Innate Genetic Evolution of Lung Cancers and Spatial Heterogeneity: Analysis of Treatment-Naïve Lesions. Journal of thoracic oncology, 13(10), 1496-1507. (Read full article)
  143. 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 (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. (Read full article)
  144. 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 S (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. (Read full article)
  145. Suda K, Murakami I, Yu H, Kim J, Tan AC, Mizuuchi H, Rozeboom L, Ellison K, Rivard CJ, Mitsudomi T, Hirsch F (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. (Read full article)
  146. Davis SL, Eckhardt SG, Diamond JR, Messersmith WA, Dasari A, Weekes CD, Lieu CH, Kane M, Choon Tan A, Pitts TM, Leong (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. The oncologist, 23(12), 1409-e140. (Read full article)
  147. 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 (2018). CDK1 Interacts with Sox2 and Promotes Tumor Initiation in Human Melanoma. Cancer research, 78(23), 6561-6574. (Read full article)
  148. Yoo M, Shin J, Kim H, Kim J, Kang J, Tan A (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. (Read full article)
  149. 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 J (2019). Reversal of Triple-Negative Breast Cancer EMT by miR-200c Decreases Tryptophan Catabolism and a Program of Immunosuppression. Molecular cancer research, 17(1), 30-41. (Read full article)
  150. 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 R (2019). Comprehensive Genetic Characterization of Human Thyroid Cancer Cell Lines: A Validated Panel for Preclinical Studies. Clinical cancer research, 25(10), 3141-3151. (Read full article)
  151. Kessler BE, Mishall KM, Kellett MD, Clark EG, 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. (Read full article)
  152. Gan CP, Sam KK, Yee PS, Zainal NS, Lee BKB, Abdul Rahman ZA, Patel V, Tan AC, Zain RB, Cheong S (2019). IFITM3 knockdown reduces the expression of CCND1 and CDK4 and suppresses the growth of oral squamous cell carcinoma cells. Cellular oncology (Dordrecht, Netherlands), 42(4), 477-490. (Read full article)
  153. Aguado BA, Schuetze KB, Grim JC, Walker CJ, Cox AC, Ceccato TL, Tan AC, Sucharov CC, Leinwand LA, Taylor MRG, McKinsey TA, Anseth K (2019). Transcatheter aortic valve replacements alter circulating serum factors to mediate myofibroblast deactivation. Science translational medicine, 11(509), (Read full article)
  154. Brown P, RELISH Consortium ., Zhou (2019). Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database, 2019, (Read full article)
  155. Samson JM, Ravindran Menon D, Smith DE, Baird E, Kitano T, Gao D, Tan AC, Fujita (2019). Clinical implications of ALDH1A1 and ALDH1A3 mRNA expression in melanoma subtypes. Chemico-biological interactions, 314, 108822. (Read full article)
  156. 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 J (2019). First-in-Class Phosphorylated-p68 Inhibitor RX-5902 Inhibits ß-Catenin Signaling and Demonstrates Antitumor Activity in Triple-Negative Breast Cancer. Molecular cancer therapeutics, 18(11), 1916-1925. (Read full article)
  157. Hinz TK, Kleczko EK, Singleton KR, Calhoun J, Marek LA, Kim J, Tan AC, Heasley L (2019). Functional RNAi Screens Define Distinct Protein Kinase Vulnerabilities in EGFR-Dependent HNSCC Cell Lines. Molecular pharmacology, 96(6), 862-870. (Read full article)
  158. Jeon M, Park D, Lee J, Jeon H, Ko M, Kim S, Choi Y, Tan AC, Kang (2019). ReSimNet: drug response similarity prediction using Siamese neural networks. Bioinformatics (Oxford, England), 35(24), 5249-5256. (Read full article)
  159. de la Iglesia JV, Slebos RJC, Martin-Gomez L, Wang X, Teer JK, Tan AC, Gerke TA, Aden-Buie G, van Veen T, Masannat J, Chaudhary R, Song F, Fournier M, Siegel EM, Schabath MB, Wadsworth JT, Caudell J, Harrison L, Wenig BM, Conejo-Garcia J, Hernandez-Prera JC, Chung C (2020). Effects of Tobacco Smoking on the Tumor Immune Microenvironment in Head and Neck Squamous Cell Carcinoma. Clinical cancer research, 26(6), 1474-1485. (Read full article)
  160. 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 (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. (Read full article)
  161. Schreiber AR, Kar A, Goodspeed AE, Pozdeyev N, Somerset H, Raeburn CD, Tan AC, Leong S, Wierman ME, Kiseljak-Vassiliades (2020). Leptomeningeal Metastasis from Adrenocortical Carcinoma: A Case Report. Journal of the Endocrine Society, 4(3), bvaa017. (Read full article)
  162. 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 (2020). Resistance to targeted therapies as a multifactorial, gradual adaptation to inhibitor specific selective pressures. Nature communications, 11(1), 2393. (Read full article)
  163. 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 Y (2020). MCL1 inhibitors S63845/MIK665 plus Navitoclax synergistically kill difficult-to-treat melanoma cells. Cell death & disease, 11(6), 443. (Read full article)
  164. 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 (2020). Induction of IRAK-M in melanoma induces caspase-3 dependent apoptosis by reducing TRAF6 and calpastatin levels. Communications biology, 3(1), 306. (Read full article)
  165. 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 D (2020). First-in-Class Inhibitors of Oncogenic CHD1L with Preclinical Activity against Colorectal Cancer. Molecular cancer therapeutics, 19(8), 1598-1612. (Read full article)
  166. Iwanaga R, Truong BT, Hsu JY, Lambert KA, Vyas R, Orlicky D, Shellman YG, Tan AC, Ceol C, Artinger K (2020). Loss of prdm1a accelerates melanoma onset and progression. Molecular carcinogenesis, 59(9), 1052-1063. (Read full article)
  167. 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 W (2020). Pre-Treatment Mutational and Transcriptomic Landscape of Responding Metastatic Melanoma Patients to Anti-PD1 Immunotherapy. Cancers, 12(7), (Read full article)
  168. Kern JA, Kim J, Foster DG, Mishra R, Gardner EE, Poirier JT, Rivard C, Yu H, Finigan JH, Dowlati A, Rudin CM, Tan A (2020). Role of mTOR As an Essential Kinase in SCLC. Journal of thoracic oncology, 15(9), 1522-1534. (Read full article)
  169. 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 S (2020). Genome-wide CRISPR screens of oral squamous cell carcinoma reveal fitness genes in the Hippo pathway. eLife, 9, (Read full article)
  170. 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 (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. (Read full article)
  171. He T, Wildey G, McColl K, Savadelis A, Spainhower K, McColl C, Kresak A, Tan AC, Yang M, Abbas A, Dowlati (2021). Identification of RUNX1T1 as a potential epigenetic modifier in small-cell lung cancer. Molecular oncology, 15(1), 195-209. (Read full article)
  172. Wahdan-Alaswad RS, Edgerton SM, Salem H, Kim HM, Tan AC, Finlay-Schultz J, Wellberg EA, Sartorius CA, Jacobsen BM, Haugen BR, Liu B, Thor A (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. (Read full article)
  173. 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 C (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. (Read full article)
  174. Morton JJ, Alzofon N, Keysar SB, Chimed TS, Reisinger J, Perrenoud L, Le PN, Nieto C, Gomez K, Miller B, Yeager R, Gao D, Tan AC, Somerset H, Medina T, Wang XJ, Wang JH, Robinson W, Roop DR, Gonzalez R, Jimeno (2021). Studying Immunotherapy Resistance in a Melanoma Autologous Humanized Mouse Xenograft. Molecular cancer research, 19(2), 346-357. (Read full article)
  175. Miroshnychenko D, Baratchart E, Ferrall-Fairbanks MC, Velde RV, Laurie MA, Bui MM, Tan AC, Altrock PM, Basanta D, Marusyk (2021). Spontaneous cell fusions as a mechanism of parasexual recombination in tumour cell populations. Nature ecology & evolution, 5(3), 379-391. (Read full article)
  176. 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 (2021). Targeting tumor-derived NLRP3 reduces melanoma progression by limiting MDSCs expansion. Proceedings of the National Academy of Sciences of the United States of America, 118(10), (Read full article)
  177. Pollyea DA, Kim HM, Stevens BM, Lee FF, Harris C, Hedin BR, Knapp JR, O'Connor BP, Jordan CT, Pietras EM, Tan AC, Alper (2021). MDS-associated SF3B1 mutations enhance proinflammatory gene expression in patient blast cells. Journal of leukocyte biology, 110(1), 197-205. (Read full article)
  178. Gurule NJ, McCoach CE, Hinz TK, Merrick DT, Van Bokhoven A, Kim J, Patil T, Calhoun J, Nemenoff RA, Tan AC, Doebele RC, Heasley L (2021). A tyrosine kinase inhibitor-induced interferon response positively associates with clinical response in EGFR-mutant lung cancer. NPJ precision oncology, 5(1), 41. (Read full article)
  179. Schubert L, Le AT, Estrada-Bernal A, Doak AE, Yoo M, Ferrara SE, Goodspeed A, Kinose F, Rix U, Tan AC, Doebele R (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. (Read full article)
  180. 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. (Read full article)
  181. Xiong Z, Jeon M, Allaway RJ, Kang J, Park D, Lee J, Jeon H, Ko M, Jiang H, Zheng M, Tan AC, Guo X, Multi-Targeting Drug DREAM Challenge Community., Dang KK, Tropsha A, Hecht C, Das TK, Carlson HA, Abagyan R, Guinney J, Schlessinger A, Cagan (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. (Read full article)
  182. Xie M, Lee K, Lockhart JH, Cukras SD, Carvajal R, Beg AA, Flores ER, Teng M, Chung CH, Tan A (2021). TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures. Bioinformatics (Oxford, England), (Read full article)
  183. Nassar KW, Hintzsche JD, Bagby SM, Espinoza V, Langouët-Astrié C, Amato CM, Chimed TS, Fujita M, Robinson W, Tan AC, Schweppe R (2021). Targeting CDK4/6 Represents a Therapeutic Vulnerability in Acquired BRAF/MEK Inhibitor-Resistant Melanoma. Molecular cancer therapeutics, 20(10), 2049-2060. (Read full article)
  184. Chai AWY, Tan AC, Cheong S (2021). Uncovering drug repurposing candidates for head and neck cancers: insights from systematic pharmacogenomics data analysis. Scientific reports, 11(1), 23933. (Read full article)
  185. Tarhini AA, Lee SJ, Tan AC, El Naqa IM, Stephen Hodi F, Butterfield LH, LaFramboise WA, Storkus WJ, Karunamurthy AD, Conejo-Garcia JR, Hwu P, Streicher H, Sondak VK, Kirkwood J (2022). Improved prognosis and evidence of enhanced immunogenicity in tumor and circulation of high-risk melanoma patients with unknown primary. Journal for immunotherapy of cancer, 10(1), (Read full article)
  186. Napoli M, Wu SJ, Gore BL, Abbas HA, Lee K, Checker R, Dhar S, Rajapakshe K, Tan AC, Lee MG, Coarfa C, Flores E (2022). ¿Np63 regulates a common landscape of enhancer associated genes in non-small cell lung cancer. Nature communications, 13(1), 614. (Read full article)
  187. 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 (2022). Neoadjuvant endocrine therapy expands stromal populations that predict poor prognosis in estrogen receptor-positive breast cancer. Molecular carcinogenesis, 61(3), 359-371. (Read full article)
  188. Liu X, Zhao B, Shaw TI, Fridley BL, Duckett DR, Tan AC, Teng (2022). Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers. Nucleic acids research, 50(6), 3115-3127. (Read full article)
  189. Obermayer A, Dong L, Hu Q, Golden M, Noble JD, Rodriguez P, Robinson TJ, Teng M, Tan AC, Shaw T (2022). DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets. Biology, 11(2), (Read full article)
  190. Coleman S, Xie M, Tarhini AA, Tan A (2022). Systematic evaluation of the predictive gene expression signatures of immune checkpoint inhibitors in metastatic melanoma. Molecular carcinogenesis, (Read full article)
  191. 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 A (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. (Read full article)
  192. Wang C, Ma A, Li Y, McNutt ME, Zhang S, Zhu J, Hoyd R, Wheeler CE, Robinson LA, Chan CHF, Zakharia Y, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Singer EA, Ikeguchi AP, McCarter MD, Denko N, Tinoco G, Husain M, Jin N, Osman AEG, Eljilany I, Tan AC, Coleman SS, Denko L, Riedlinger G, Schneider BP, Spakowicz D, Ma Q, exORIEN Consortiu (2024). A Bioinformatics Tool for Identifying Intratumoral Microbes from the ORIEN Dataset. Cancer research communications, 4(2), 293-302. (Read full article)
  193. Kerepesi C, Abushukair HM, Ricciuti B, Nassar AH, Adib E, Alessi JV, Pecci F, Rakaee M, Fadlullah MZH, T'kés AM, Rodig SJ, Awad MM, Tan AC, Bakacs T, Naqash A (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. (Read full article)
  194. 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 A (2024). Immune landscape in molecular subtypes of human papillomavirus-negative head and neck cancer. Molecular carcinogenesis, 63(1), 120-135. (Read full article)
  195. Manji GA, Lee S, Del Portillo A, May M, Ana SS, Alouani E, Sender N, Negri T, Gautier K, Ge L, Fan W, Xie M, Sethi A, Schrope B, Tan AC, Park H, Oberstein PE, Shah MA, Raufi A (2023). Chemotherapy and Immune Checkpoint Blockade for Gastric and Gastroesophageal Junction Adenocarcinoma. JAMA oncology, 9(12), 1702-1707. (Read full article)
  196. Walker V, Jin DX, Millis SZ, Nasri E, Corao-Uribe DA, Tan AC, Fridley BL, Chen JL, Seligson N (2023). Gene partners of the EWSR1 fusion may represent molecularly distinct entities. Translational oncology, 38, 101795. (Read full article)
  197. 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 (2023). H3K4me3 remodeling induced acquired resistance through O-GlcNAc transferase. Drug resistance updates, 71, 100993. (Read full article)
  198. Wahdan-Alaswad RS, Edgerton SM, Kim HM, Tan AC, Haugen BR, Liu B, Thor A (2023). Thyroid hormone enhances estrogen-mediated proliferation and cell cycle regulatory pathways in steroid receptor-positive breast Cancer. Cell cycle (Georgetown, Tex.), 1-20. (Read full article)
  199. Hu M, Coleman S, Fadlullah MZH, Spakowicz D, Chung CH, Tan A (2023). Deciphering the Tumor-Immune-Microbe Interactions in HPV-Negative Head and Neck Cancer. Genes, 14(8), (Read full article)
  200. 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 (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), (Read full article)
  201. Thomas M, Li J, King K, Persaud AK, Duah E, Vangundy Z, Hofmeister CC, Lamba JK, Tan AC, Fridley BL, Poi MJ, Seligson N (2023). PARP1 and POLD2 as prognostic biomarkers for multiple myeloma in autologous stem cell transplant. Haematologica, 108(8), 2155-2166. (Read full article)
  202. Lockhart JH, Ackerman HD, Lee K, Abdalah M, Davis AJ, Hackel N, Boyle TA, Saller J, Keske A, Hänggi K, Ruffell B, Stringfield O, Cress WD, Tan AC, Flores E (2023). Grading of lung adenocarcinomas with simultaneous segmentation by artificial intelligence (GLASS-AI). NPJ precision oncology, 7(1), 68. (Read full article)
  203. 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 (2023). Translational relevance of SOS1 targeting for KRAS-mutant colorectal cancer. Molecular carcinogenesis, 62(7), 1025-1037. (Read full article)
  204. 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 T (2023). PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing. BMC bioinformatics, 24(1), 266. (Read full article)
  205. 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 C (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. (Read full article)
  206. 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 C (2023). Pembrolizumab and cabozantinib in recurrent metastatic head and neck squamous cell carcinoma: a phase 2 trial. Nature medicine, 29(4), 880-887. (Read full article)
  207. Lin CN, Chung CH, Tan A (2023). NuKit: A deep learning platform for fast nucleus segmentation of histopathological images. Journal of bioinformatics and computational biology, 21(1), 2350002. (Read full article)
  208. Rose MM, Espinoza VL, Hoff KJ, Pike LA, Sharma V, Hofmann MC, Tan AC, Pozdeyev N, Schweppe R (2023). BCL2L11 Induction Mediates Sensitivity to Src and MEK1/2 Inhibition in Thyroid Cancer. Cancers, 15(2), (Read full article)
  209. 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 (2022). Development of SOS1 Inhibitor-Based Degraders to Target KRAS-Mutant Colorectal Cancer. Journal of medicinal chemistry, 65(24), 16432-16450. (Read full article)
  210. Boe DM, Hulsebus HJ, Najarro KM, Mullen JE, Kim H, Tan AC, McMahan RH, Kovacs E (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. (Read full article)
  211. Thompson ZJ, Teer JK, Li J, Chen Z, Welsh EA, Zhang Y, Ayoubi N, Eroglu Z, Tan AC, Smalley KSM, Chen Y (2022). Drepmel-A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment. Cells, 11(18), (Read full article)
  212. de la Iglesia JV, Slebos RJC, Martin-Gomez L, Wang X, Teer JK, Tan AC, Gerke TA, Aden-Buie G, van Veen T, Masannat J, Chaudhary R, Song F, Fournier M, Siegel EM, Schabath MB, Wadsworth JT, Caudell J, Harrison L, Wenig BM, Conejo-Garcia J, Hernandez-Prera JC, Chung C (2021). Correction: Effects of Tobacco Smoking On the Tumor Immune Microenvironment in Head and Neck Squamous Cell Carcinoma. Clinical cancer research, 27(17), 4941. (Read full article)
  213. 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 J (2020). Preclinical and Dose-Finding Phase I Trial Results of Combined Treatment with a TORC1/2 Inhibitor (TAK-228) and Aurora A Kinase Inhibitor (Alisertib) in Solid Tumors. Clinical cancer research, 26(17), 4633-4642. (Read full article)
  214. Cavalli G, Koenders M, Kalabokis V, Kim J, Choon Tan A, Garlanda C, Mantovani A, Dagna L, Joosten LAB, Dinarello C (2017). Treating experimental arthritis with the innate immune inhibitor interleukin-37 reduces joint and systemic inflammation. Rheumatology (Oxford, England), 56(12), 2256. (Read full article)
  215. Lambert KA, Clements CM, Mukherjee N, Pacheco TR, Shellman SX, Henen MA, Vögeli B, Goldstein NB, Birlea S, Hintzsche J, Caryotakis G, Tan AC, Zhao R, Norris DA, Robinson WA, Wang Y, VanTreeck JG, Shellman Y (2024). SASH1 S519N variant links skin hyperpigmentation and premature hair graying to dysfunction of melanocyte lineage. The Journal of investigative dermatology, (Read full article)
  216. Liu X, Gillis N, Jiang C, McCofie A, Shaw TI, Tan AC, Zhao B, Wan L, Duckett DR, Teng (2024). An Epigenomic fingerprint of human cancers by landscape interrogation of super enhancers at the constituent level. PLoS computational biology, 20(2), e1011873. (Read full article)
  217. Fadlullah MZH, Lin CN, Coleman S, Young A, Naqash AR, Hu-Lieskovan S, Tan A (2024). Exploring the Landscape of Immune Checkpoint Inhibitor-Induced Adverse Events Through Big Data Mining of Pan-Cancer Clinical Trials. The oncologist, 29(5), 415-421. (Read full article)
  218. Benej M, Hoyd R, Kreamer M, Wheeler CE, Grencewicz DJ, Choueiry F, Chan CHF, Zakharia Y, Ma Q, Dodd RD, Ulrich CM, Hardikar S, Churchman ML, Tarhini AA, Robinson LA, Singer EA, Ikeguchi AP, McCarter MD, Tinoco G, Husain M, Jin N, Tan AC, Osman AEG, Eljilany I, Riedlinger G, Schneider BP, Benejova K, Kery M, Papandreou I, Zhu J, Denko N, Spakowicz (2024). The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer. Cancer research communications, 4(7), 1690-1701. (Read full article)
  219. Quandt Z, Jacob S, Fadlullah MZH, Wu C, Wu C, Huppert L, Levine LS, Sison P, Tsai KK, Chow M, Kang JH, Hwang J, Lee J, Oglesby A, Venegas J, Brintz BJ, Tan AC, Anderson MS, Rosenblum, Young A, Daud A (2024). Phase II trial of pembrolizumab, ipilimumab, and aspirin in melanoma: clinical outcomes and translational predictors of response. . BJC Reports,

Review

  1. Leong S, Messersmith WA, Tan AC, Eckhardt S (2010). Novel agents in the treatment of metastatic colorectal cancer. Cancer journal (Sudbury, Mass.), 16(3), 273-82. (Read full article)
  2. Kim H, Kim J, Selby H, Gao D, Tong T, Phang TL, Tan A (2011). A short survey of computational analysis methods in analysing ChIP-seq data. Human genomics, 5(2), 117-23. (Read full article)
  3. Tentler JJ, Tan AC, Weekes CD, Jimeno A, Leong S, Pitts TM, Arcaroli JJ, Messersmith WA, Eckhardt S (2012). Patient-derived tumour xenografts as models for oncology drug development. Nature reviews. Clinical oncology, 9(6), 338-50. (Read full article)
  4. Lieu CH, Tan AC, Leong S, Diamond JR, Eckhardt S (2013). From bench to bedside: lessons learned in translating preclinical studies in cancer drug development. Journal of the National Cancer Institute, 105(19), 1441-56. (Read full article)
  5. Hintzsche JD, Robinson WA, Tan A (2016). A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data. International journal of genomics, 2016, 7983236. (Read full article)
  6. Tan AC, Vyse S, Huang P (2017). Exploiting receptor tyrosine kinase co-activation for cancer therapy. Drug discovery today, 22(1), 72-84. (Read full article)
  7. Wilding CP, Elms ML, Judson I, Tan AC, Jones RL, Huang P (2019). The landscape of tyrosine kinase inhibitors in sarcomas: looking beyond pazopanib. Expert review of anticancer therapy, 19(11), 971-991. (Read full article)
  8. Nassar KW, Tan A (2020). The mutational landscape of mucosal melanoma. Seminars in cancer biology, 61, 139-148. (Read full article)
  9. Lee K, Lockhart JH, Xie M, Chaudhary R, Slebos RJC, Flores ER, Chung CH, Tan A (2021). Deep Learning of Histopathology Images at the Single Cell Level. Frontiers in artificial intelligence, 4, 754641. (Read full article)

Editorial

  1. Tan AC, Ryall KA, Huang P (2016). Expanding the computational toolbox for interrogating cancer kinomes. Pharmacogenomics, 17(2), 95-7. (Read full article)
  2. Tan AC, Huang P (2020). Translational genomics for rare cancers: Challenges and opportunity. Seminars in cancer biology, 61, iii-iv. (Read full article)
  3. Homayouni R, Manda P, Tan AC, Qin Z (2023). Editorial: AI and data science in drug development and public health: Highlights from the MCBIOS 2022 conference. Frontiers in big data, 6, 1156811. (Read full article)

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