Dr. Kim-Anh Do, Ph.D.

Peer-Reviewed Articles

1. Long, JP, Yang, Y, Shimizu, S, Pham, T, Do, K. Causal models and prediction in cell line perturbation experiments. BMC Bioinformatics 26(1), 2025. e-Pub 2025. PMID: 39773352.
2. Chen, Y, Ballaro, R, Sans, M, Thege, F, Zuo, M, Dou, R, Min, J, Yip-Schneider, MT, Zhang, J, Wu, R, Irajizad, E, Makino, Y, Rajapakshe, K, Rudsari, HK, Hurd, MW, Leon Letelier, R, Katayama, H, Ostrin, EJ, Vykoukal, JV, Dennison, JB, Do, K, Hanash, S, Wolff, RA, Guerrero, PA, Kim, M, Schmidt, CM, Maitra, A, Fahrmann, JF. Long-chain sulfatide enrichment is an actionable metabolic vulnerability in intraductal papillary mucinous neoplasm (IPMN)-associated pancreatic cancers. Gut 74(10):1638-1652, 2025. e-Pub 2025. PMID: 40268349.
3. Liu, S, Chen, H, Gagea Iurascu, M, Federico, L, Zhang, F, Gomez, J, Do, K, Symmans, WF, Hortobagyi, GN, Mills, GB, González-Angulo, AM, Tripathy, D. ADAMs contribute to triple negative breast cancer via mTORC1 pathway. Cancer Letters 626, 2025. e-Pub 2025. PMID: 40339955.
4. Liu, C, Mosley, A, Irajizad, E, Yip-Schneider, MT, Wu, H, Smith-Kinnaman, WR, Tran, T, Long, JP, Do, K, Fahrmann, JF, Dewitt, J, Hanash, S, Schmidt, CM, Zhang, J. Cyst fluid proteins stratify malignant risk of intraductal papillary mucinous neoplasm of the pancreas. Cancer Letters 624, 2025. e-Pub 2025. PMID: 40300662.
5. Shi, Y, Zhang, L, Do, K, Jenq, RR, Peterson, CB. CAT. Briefings in bioinformatics 26(4), 2025. e-Pub 2025. PMID: 40641046.
6. Leon Letelier, R, Chen, Y, Dou, R, Irajizad, E, Yip-Schneider, MT, Wu, R, Ejaz, R, Rudsari, HK, Li, Y, Spencer, R, Ballaro, R, Vykoukal, JV, Hurd, MW, Dennison, JB, Do, K, Maitra, A, Zhang, J, Hanash, S, Schmidt, CM, Fahrmann, JF. Integrated Metabolomics and Spatial Transcriptomics of Cystic Pancreatic Cancer Precursors Reveals Dysregulated Polyamine Metabolism as a Biomarker of Progression. Clinical Cancer Research 31(12):2454-2465, 2025. e-Pub 2025. PMID: 40184234.
7. Ballaro, R, Wasylishen, A, Pieterman, CR, Olsen, C, Irajizad, E, Wu, R, Katayama, H, Liu, H, Cai, Y, Leon Letelier, R, Dennison, JB, Waguespack, SG, Do, K, Agarwal, SK, Walter, MF, Welch, JM, Weinstein, LS, Blau, J, Jha, S, Nilubol, N, Vriens, MR, Van Leeuwaarde, RS, Van Treijen, MJ, Valk, GD, Perrier, ND, Hanash, S, Fahrmann, JF. Elevated levels of circulating microbial-associated uremic toxins are associated with metastatic duodenopancreatic neuroendocrine tumors in patients with Multiple Endocrine Neoplasia Type 1. Cancer Letters 614, 2025. e-Pub 2025. PMID: 39924079.
8. Fahrmann, JF, Yip-Schneider, MT, Vykoukal, JV, Spencer, R, Dennison, JB, Do, K, Long, JP, Maitra, A, Zhang, J, Schmidt, CM, Hanash, S, Irajizad, E. Lead time trajectory of blood-based protein biomarkers for detection of pancreatic cancer based on repeat testing. Cancer Letters 612, 2025. e-Pub 2025. PMID: 39793753.
9. Ghasemi, SM, Gu, C, Fahrmann, JF, Hanash, S, Do, K, Long, JP, Irajizad, E. A Novel Sensitivity Maximization at a Given Specificity Method for Binary Classifications. Cancer Prevention Research 18(3):117-123, 2025. e-Pub 2025. PMID: 39618306.
10. Gu, C, Ghasemi, SM, Cai, Y, Fahrmann, JF, Long, JP, Katayama, H, Wu, C, Vykoukal, JV, Dennison, JB, Hanash, S, Do, K, Irajizad, E. Grape-Pi. Bioinformatics Advances 5(1), 2025. e-Pub 2025. PMID: 40406669.
11. Anfossi, S, Darbaniyan, F, Quinlan, J, Calin, S, Shimizu, M, Chen, M, Rausseo, P, Winters, M, Bogatenkova, E, Do, K, Martinez, I, Li, Z, Antal, L, Olariu, TR, Wistuba, II, Calin, GA. MicroRNAs are enriched at COVID-19 genomic risk regions, and their blood levels correlate with the COVID-19 prognosis of cancer patients infected by SARS-CoV-2. Molecular cancer 23(1), 2024. e-Pub 2024. PMID: 39434078.
12. Fahrmann JF, Ghasemi SM, Han CH, Wu R, Dennison JB, Vykoukal J, Celestino J, Lu K, Lu Z, Drescher C, K-A D, Hanash S, Bast RC, Irajizad E. A metabolite-based liquid biopsy for detection of ovarian cancer. In Press, Biomarker Research. Biomarker Research 12(1), 2024. e-Pub 2024. PMID: 39192316.
13. Song, L, Irajizad, E, Rundle, A, Sesso, HD, Gaziano, JM, Vykoukal, JV, Do, K, Dennison, JB, Ostrin, EJ, Fahrmann, JF, Perera, F, Hanash, S. Validation of a Blood-Based Protein Biomarker Panel for a Risk Assessment of Lethal Lung Cancer in the Physicians’ Health Study. Cancers 16(11), 2024. e-Pub 2024. PMID: 38893188.
14. Peterson CB, Saha S, Do KA. Analysis of Microbiome Data. Annu Rev Stat Appl 11(1):483-504, 2024. e-Pub 2024. PMID: 38962089.
15. León-Letelier, RA, Dou, R, Vykoukal, J, Yip-Schneider, MT, Maitra, A, Irajizad, E, Wu, R, Dennison, JB, Do, KA, Zhang, J, Schmidt, CM. Contributions of the Microbiome-Derived Metabolome for Risk Assessment and Prognostication of Pancreatic Cancer, 2024. e-Pub 2024.
16. Ho IL, Li CY, Wang F, Zhao L, Liu J, Yen EY, Dyke CA, Shah R, Liu Z, Çetin AO, Chu Y, Citron F, Attanasio S, Corti D, Darbaniyan F, Del Poggetto E, Loponte S, Liu J, Soeung M, Chen Z, Jiang S, Jiang H, Inoue A, Gao S, Deem A, Feng N, Ying H, Kim M, Giuliani V, Genovese G, Zhang J, Futreal A, Maitra A, Heffernan T, Wang L, Do KA, Gargiulo G, Draetta G, Carugo A, Lin R, Viale A. Clonal dominance defines metastatic dissemination in pancreatic cancer. Sci Adv 10(11):eadd9342, 2024. e-Pub 2024. PMID: 38478609.
17. Arthur, JA, Edwards, T, Lu, Z, Amoateng, MD, Koom-Dadzie, K, Zhu, H, Long, JP, Do, K, Bruera, E. Healthcare provider perceptions and reported practices regarding opioid prescription for patients with chronic cancer pain. Supportive Care in Cancer 32(2), 2024. e-Pub 2024. PMID: 38252311.
18. Zhang L, San Valentin EMD, John TM, Jenq RR, Do KA, Hanna EY, Peterson CB, Reyes-Gibby CC. Influence of oral microbiome on longitudinal patterns of oral mucositis severity in patients with squamous cell carcinoma of the head and neck. Cancer 130(1):150-161, 2024. e-Pub 2024. PMID: 37688396.
19. Peterson CB, Satabdi S, K-A D. Analysis of Microbiome Data. To appear in Volume 11 of the Annual Review of Statistics and Its Application, 2024, 2024. e-Pub 2024.
20. Anfossi, Darbaniyan F, Quinlan J, Calin S, Shimizu M, Chen M, Rausseo P, Winters M, Bogatenkova E, K-A D, Martinez I, Li Z, Antal L, Olariu TR, Wistuba I, Calin GA. MicroRNAs are enriched at COVID-19 genomic risk regions, and their blood levels correlate with the COVID-19 prognosis of cancer patients infected by SARS-CoV-2, 2024. e-Pub 2024.
21. Shi Y, Zhang L, Do KA, Jenq RR, Peterson CB. survivalContour: visualizing predicted survival via colored contour plots. Bioinform Adv 4(1):vbae105, 2024. e-Pub 2024. PMID: 39086987.
22. Zhang X, Irajizad E, Hoffman KL, Fahrmann JF, Li F, Seo YD, Browman GJ, Dennison JB, Vykoukal J, Luna PN, Siu W, Wu R, Murage E, Ajami NJ, McQuade JL, Wargo JA, Long JP, Do KA, Lampe JW, Basen-Engquist KM, Okhuysen PC, Kopetz S, Hanash SM, Petrosino JF, Scheet P, Daniel CR. Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial. To appear in eBiomedicine , 2024. EBioMedicine 98:104873, 2023. e-Pub 2023. PMID: 38040541.
23. Fahrmann JF, Wasylishen AR, Pieterman CRC, Irajizad E, Vykoukal J, Wu R, Dennison JB, Peterson CB, Zhao H, Do KA, Halperin DM, Agarwal SK, Blau JE, Jha S, Rivero JD, Nilubol N, Walter MF, Welch JM, Weinstein LS, Vriens MR, van Leeuwaarde RS, van Treijen MJC, Valk GD, Perrier ND, Hanash SM, Katayama H. Blood-based Proteomic Signatures Associated With MEN1-related Duodenopancreatic Neuroendocrine Tumor Progression. J Clin Endocrinol Metab 108(12):3260-3271, 2023. e-Pub 2023. PMID: 37307230.
24. Jeske AH, Anderson A, Do KA, Ning J, Ma J, Bruera E. Patterns of opioid use among Texas dental practitioners during the COVID-19 pandemic. J Opioid Manag 19(6):523-532, 2023. e-Pub 2023. PMID: 38189194.
25. Arthur J, Edwards T, Lu Z, Amoateng DM, Koom-Dadzie K, Zhu H, Long J, Do KA, Bruera E. Healthcare provider perceptions and reported practices regarding opioid prescription for patients with chronic pain. Res Sq, 2023. e-Pub 2023. PMID: 37841840.
26. Irajizad E, Fahrmann JF, Marsh T, Vykoukal J, Dennison JB, Long JP, Do KA, Feng Z, Hanash S, Ostrin EJ. Mortality Benefit of a Blood-Based Biomarker Panel for Lung Cancer on the Basis of the Prostate, Lung, Colorectal, and Ovarian Cohort. J Clin Oncol 41(27):4360-4368, 2023. e-Pub 2023. PMID: 37379494.
27. Irajizad E, Kenney A, Tang T, Vykoukal J, Wu R, Murage E, Dennison JB, Sans M, Long JP, Loftus M, Chabot JA, Kluger MD, Kastrinos F, Brais L, Babic A, Jajoo K, Lee LS, Clancy TE, Ng K, Bullock A, Genkinger JM, Maitra A, Do KA, Yu B, Wolpin BM, Hanash S, Fahrmann JF. A blood-based metabolomic signature predictive of risk for pancreatic cancer. Cell Rep Med 4(9):101194, 2023. e-Pub 2023. PMID: 37729870.
28. Das P, Peterson CB, Ni Y, Reuben A, Zhang J, Zhang J, Do KA, Baladandayuthapani V. Bayesian hierarchical quantile regression with application to characterizing the immune architecture of lung cancer. Biometrics 79(3):2474-2488, 2023. e-Pub 2022. PMID: 36239535.
29. Huang L, Long JP, Irajizad E, Doecke JD, Do KA, Ha MJ. A unified mediation analysis framework for integrative cancer proteogenomics with clinical outcomes. Bioinformatics 39(1), 2023. e-Pub 2023. PMID: 36648331.
30. Class CA, Lukan CJ, Bristow CA, Do KA. Easy NanoString nCounter data analysis with the NanoTube. Bioinformatics 39(1), 2023. e-Pub 2023. PMID: 36440915.
31. Long, JP, Zhu, H, Do, K, Ha, MJ. Estimating causal effects with hidden confounding using instrumental variables and environments. Electronic Journal of Statistics 17(2):2849-2879, 2023. e-Pub 2023.
32. Santos DA, Zhang L, Do KA, Bednarski BK, Robinson Ledet C, Limmer A, Gibson H, You YN. Chemotherapy and Abdominal Wall Closure Technique Increase the Probability of Postoperative Ventral Incisional Hernia in Patients With Colon Cancer. Am Surg 89(1):31348211011149, 2023. e-Pub 2021. PMID: 33877925.
33. Shi Y, Zhang L, Do KA, Jenq R, Peterson CB. Sparse tree-based clustering of microbiome data to characterize microbiome heterogeneity in pancreatic cancer. J R Stat Soc Ser C Appl Stat 72(1):20-36, 2023. e-Pub 2023. PMID: 37034187.
34. Francisco DMA, Zhang L, Jiang Y, Olvera A, Adachi J, Guevara EY, Aitken SL, Garey KW, Peterson CB, Do KA, Dillon R, Obi EN, Jenq R, Okhuysen PC. Risk Factors Associated with Severe Clostridioides difficile Infection in Patients with Cancer. Infect Dis Ther 12(1):209-225, 2023. e-Pub 2023. PMID: 36443547.
35. Long JP, Zhu H, Do KA, Ha MJ. Estimating causal effects with hidden confounding using instrumental variables and environments. Electron J Stat 17(2):2849-2879, 2023. e-Pub 2023. PMID: 38957485.
36. Schwabkey ZI, Wiesnoski DH, Chang CC, Tsai WB, Pham D, Ahmed SS, Hayase T, Ortega Turrubiates MR, El-Himri RK, Sanchez CA, Hayase E, Frenk Oquendo AC, Miyama T, Halsey TM, Heckel BE, Brown AN, Jin Y, Raybaud M, Prasad R, Flores I, McDaniel L, Chapa V, Lorenzi PL, Warmoes MO, Tan L, Swennes AG, Fowler S, Conner M, McHugh K, Graf T, Jensen VB, Peterson CB, Do KA, Zhang L, Shi Y, Wang Y, Galloway-Pena JR, Okhuysen PC, Daniel-MacDougall CR, Shono Y, Burgos da Silva M, Peled JU, van den Brink MRM, Ajami N, Wargo JA, Reddy P, Valdivia RH, Davey L, Rondon G, Srour SA, Mehta RS, Alousi AM, Shpall EJ, Champlin RE, Shelburne SA, Molldrem JJ, Jamal MA, Karmouch JL, Jenq RR. Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment. Sci Transl Med 14(671):eabo3445, 2022. e-Pub 2022. PMID: 36383683.
37. Irajizad E, Han CY, Celestino J, Wu R, Murage E, Spencer R, Dennison JB, Vykoukal J, Long JP, Do KA, Drescher C, Lu K, Lu Z, Bast RC, Hanash S, Fahrmann JF. A Blood-Based Metabolite Panel for Distinguishing Ovarian Cancer from Benign Pelvic Masses. Clin Cancer Res 28(21):4669-4676, 2022. e-Pub 2022. PMID: 36037307.
38. Su X, Li Y, Müller P, Hsu CW, Pan H, Do KA. A semi-mechanistic dose-finding design in oncology using pharmacokinetic/pharmacodynamic modeling. Pharm Stat 21(6):1149-1166, 2022. e-Pub 2022. PMID: 35748220.
39. Darbaniyan F, Zheng H, Kanagal-Shamanna R, Lockyer P, Montalban-Bravo G, Estecio M, Lu Y, Soltysiak KA, Chien KS, Yang H, Sasaki K, Class C, Ganan-Gomez I, Do KA, Garcia-Manero G, Wei Y. Transcriptomic Signatures of Hypomethylating Agent Failure in Myelodysplastic Syndromes and Chronic Myelomonocytic Leukemia. Exp Hematol 115:44-53, 2022. e-Pub 2022. PMID: 36150563.
40. Li Z, Wang Y, Ganan-Gomez I, Colla S, Do KA. A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data. Bioinformatics 38(21):4885-4892, 2022. e-Pub 2022. PMID: 36083008.
41. Sasaki K, Jabbour E, Montalban-Bravo G, Darbaniyan F, Do KA, Class C, Short NJ, Kanagal-Shamana R, Kadia T, Borthakur G, Pemmaraju N, Cortes J, Ravandi F, Alvarado Y, Chien K, Komrokji R, Sekeres MA, Steensma DP, DeZern A, Roboz G, Soltysiak K, Yang H, Kantarjian HM, Garcia-Manero G. Low-Dose Decitabine versus Low-Dose Azacitidine in Lower-Risk MDS. NEJM Evid 1(10):EVIDoa2200034, 2022. e-Pub 2022. PMID: 38319837.
42. Wei Y, Zheng H, Lockyer PP, Darbaniyan F, Li Z, Kanagal-Shamanna R, Soltysiak KA, Yang H, Ganan-Gomez I, Montalban-Bravo G, Chien KS, Do KA, Daver N, Garcia-Manero G. MDM2 antagonist improves therapeutic activity of azacitidine in myelodysplastic syndromes and chronic myelomonocytic leukemia. Leuk Lymphoma:1-11. e-Pub 2022. PMID: 36059252.
43. Irajizad E, Fahrmann JF, Long JP, Vykoukal J, Kobayashi M, Capello M, Yu CY, Cai Y, Hsiao FC, Patel N, Park S, Peng Q, Dennison JB, Kato T, Tai MC, Taguchi A, Kadara H, Wistuba II, Katayama H, Do KA, Hanash SM, Ostrin EJ. A Comprehensive Search of Non-Canonical Proteins in Non-Small Cell Lung Cancer and Their Impact on the Immune Response. Int J Mol Sci 23(16), 2022. e-Pub 2022. PMID: 36012199.
44. Wei Y, Kanagal-Shamanna R, Zheng H, Bao N, Lockyer PP, Class CA, Darbaniyan F, Lu Y, Lin K, Yang H, Montalban-Bravo G, Ganan-Gomez I, Soltysiak KA, Do KA, Colla S, Garcia-Manero G. Cooperation between KDM6B overexpression and TET2 deficiency in the pathogenesis of chronic myelomonocytic leukemia. Leukemia 36(8):2097-2107, 2022. e-Pub 2022. PMID: 35697791.
45. Kanagal-Shamanna R, Orazi A, Hasserjian RP, Arber DA, Reichard K, Hsi ED, Bagg A, Rogers HJ, Geyer J, Darbaniyan F, Do KA, Devins KM, Pozdnyakova O, George TI, Cin PD, Greipp PT, Routbort MJ, Patel K, Garcia-Manero G, Verstovsek S, Medeiros LJ, Wang SA, Bueso-Ramos C. Correction to: Myelodysplastic/myeloproliferative neoplasms-unclassifiable with isolated isochromosome 17q represents a distinct clinico-biologic subset: a multi-institutional collaborative study from the Bone Marrow Pathology Group. Mod Pathol 35(5):705, 2022. e-Pub 2021. PMID: 34903824.
46. Shih DJH, Ruoxing L, Müller P, Zheng WJ, Do KA, Lin SY, Carter SL. CNGPLD: Case-control copy-number analysis using Gaussian process latent difference. Bioinformatics 38(8):2096-2101, 2022. e-Pub 2022. PMID: 35176131.
47. Kanagal-Shamanna R, Orazi A, Hasserjian RP, Arber DA, Reichard K, Hsi ED, Bagg A, Rogers HJ, Geyer J, Darbaniyan F, Do KA, Devins KM, Pozdnyakova O, George TI, Cin PD, Greipp PT, Routbort MJ, Patel K, Garcia-Manero G, Verstovsek S, Medeiros LJ, Wang SA, Bueso-Ramos C. Myelodysplastic/myeloproliferative neoplasms-unclassifiable with isolated isochromosome 17q represents a distinct clinico-biologic subset: a multi-institutional collaborative study from the Bone Marrow Pathology Group. Mod Pathol 35(4):470-479, 2022. e-Pub 2021. PMID: 34775472.
48. Fahrmann JF, Marsh T, Irajizad E, Patel N, Murage E, Vykoukal J, Dennison JB, Do KA, Ostrin E, Spitz MR, Lam S, Shete S, Meza R, Tammemägi MC, Feng Z, Hanash SM. Blood-Based Biomarker Panel for Personalized Lung Cancer Risk Assessment. J Clin Oncol 40(8):876-883, 2022. e-Pub 2022. PMID: 34995129.
49. Shi Y, Zhang L, Peterson CB, Do KA, Jenq RR. Performance determinants of unsupervised clustering methods for microbiome data. Microbiome 10(1):25, 2022. e-Pub 2022. PMID: 35120564.
50. Tanaka I, Dayde D, Tai MC, Mori H, Solis LM, Tripathi SC, Fahrmann JF, Unver N, Parhy G, Jain R, Parra ER, Murakami Y, Aguilar-Bonavides C, Mino B, Celiktas M, Dhillon D, Casabar JP, Nakatochi M, Stingo F, Baladandayuthapani V, Wang H, Katayama H, Dennison JB, Lorenzi PL, Do KA, Fujimoto J, Behrens C, Ostrin EJ, Rodriguez-Canales J, Hase T, Fukui T, Kajino T, Kato S, Yatabe Y, Hosoda W, Kawaguchi K, Yokoi K, Chen-Yoshikawa TF, Hasegawa Y, Gazdar AF, Wistuba II, Hanash S, Taguchi A. SRGN-Triggered Aggressive and Immunosuppressive Phenotype in a Subset of TTF-1-Negative Lung Adenocarcinomas. J Natl Cancer Inst 114(2):290-301, 2022. e-Pub 2021. PMID: 34524427.
51. Chen Y, Capello M, Rios Perez MV, Vykoukal JV, Roife D, Kang Y, Prakash LR, Katayama H, Irajizad E, Fleury A, Ferri-Borgogno S, Baluya DL, Dennison JB, Do KA, Fiehn O, Maitra A, Wang H, Chiao PJ, Katz MHG, Fleming JB, Hanash SM, Fahrmann JF. CES2 sustains HNF4α expression to promote pancreatic adenocarcinoma progression through an epoxide hydrolase-dependent regulatory loop. Mol Metab 56:101426, 2022. e-Pub 2021. PMID: 34971802.
52. Irajizad E, Wu R, Vykoukal J, Murage E, Spencer R, Dennison JB, Moulder S, Ravenberg E, Lim B, Litton J, Tripathym D, Valero V, Damodaran S, Rauch GM, Adrada B, Candelaria R, White JB, Brewster A, Arun B, Long JP, Do KA, Hanash S, Fahrmann JF. Application of Artificial Intelligence to Plasma Metabolomics Profiles to Predict Response to Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer. Front Artif Intell 5:876100, 2022. e-Pub 2022. PMID: 36034598.
53. Shih DJH, Chen MK, Yin J, McGrail DJ, Dai H, Wei R, Zhang J, Zheng WJ, Do KA, Yang L, Hung MC, Lin SY. Exploiting induced vulnerability to overcome PARPi resistance and clonal heterogeneity in BRCA mutant triple-negative inflammatory breast cancer. Am J Cancer Res 12(1):337-354, 2022. e-Pub 2022. PMID: 35141022.
54. Fahrmann JF, Wasylishen AR, Pieterman CRC, Irajizad E, Vykoukal J, Murage E, Wu R, Dennison JB, Krishna H, Peterson CB, Lozano G, Zhao H, Do KA, Halperin DM, Agarwal SK, Blau JE, Del Rivero J, Nilubol N, Walter MF, Welch JM, Weinstein LS, Vriens MR, van Leeuwaarde RS, van Treijen MJC, Valk GD, Perrier ND, Hanash SM. A blood-based polyamine signature associated with MEN1 duodenopancreatic neuroendocrine tumor progression. J Clin Endocrinol Metab 106(12):e4969-e4980, 2021. e-Pub 2021. PMID: 34318891.
55. Zhang L, Shi Y, Jenq RR, Do KA, Peterson CB. Bayesian compositional regression with structured priors for microbiome feature selection. Biometrics 77(3):824-838, 2021. e-Pub 2021. PMID: 32686846.
56. Karakas C, Francis AM, Ha MJ, Wingate HF, Meena RA, Yi M, Rasaputra KS, Barrera AMG, Arun B, Do KA, Sahin A, Keyomarsi K, Hunt KK. Cytoplasmic Cyclin E Expression Predicts for Response to Neoadjuvant Chemotherapy in Breast Cancer. Ann Surg 274(2):e150-e159, 2021. e-Pub 2021. PMID: 31436549.
57. Giuliani V, Miller MA, Liu CY, Hartono SR, Class CA, Bristow CA, Suzuki E, Sanz LA, Gao G, Gay JP, Feng N, Rose JL, Tomihara H, Daniele JR, Peoples MD, Bardenhagen JP, Geck Do MK, Chang QE, Vangamudi B, Vellano C, Ying H, Deem AK, Do KA, Genovese G, Marszalek JR, Kovacs JJ, Kim M, Fleming JB, Guccione E, Viale A, Maitra A, Emilia Di Francesco M, Yap TA, Jones P, Draetta G, Carugo A, Chedin F, Heffernan TP. PRMT1-dependent regulation of RNA metabolism and DNA damage response sustains pancreatic ductal adenocarcinoma. Nat Commun 12(1):4626, 2021. e-Pub 2021. PMID: 34330913.
58. Dayde D, Gunther J, Hirayama Y, Weksberg DC, Boutin A, Parhy G, Aguilar-Bonavides C, Wang H, Katayama H, Abe Y, Do KA, Hara K, Kinoshita T, Komori K, Shimizu Y, Tajika M, Niwa Y, Wang YA, DePinho R, Hanash S, Krishnan S, Taguchi A. Identification of Blood-Based Biomarkers for the Prediction of the Response to Neoadjuvant Chemoradiation in Rectal Cancer. Cancers (Basel) 13(14), 2021. e-Pub 2021. PMID: 34298853.
59. Montalban-Bravo G, Kanagal-Shamanna R, Darbaniyan F, Siddiqui MT, Sasaki K, Wei Y, Yang H, Chien KS, Naqvi K, Jabbour E, Kadia TM, Daver N, DiNardo C, Ravandi F, Pemmaraju N, Bose P, Verstovsek S, Pierce S, Bueso-Ramos C, Patel K, Do KA, Kantarjian H, Garcia-Manero G. Clinical, genomic, and transcriptomic differences between myelodysplastic syndrome/myeloproliferative neoplasm with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T) and myelodysplastic syndrome with ring sideroblasts (MDS-RS). Am J Hematol 96(7):E246-E249, 2021. e-Pub 2021. PMID: 33811786.
60. Shu H, Chiang T, Wei P, Do KA, Lesslie MD, Cohen EO, Srinivasan A, Moseley TW, Chang Sen LQ, Leung JWT, Dennison JB, Hanash SM, Weaver OO. A Deep Learning Approach to Re-create Raw Full-Field Digital Mammograms for Breast Density and Texture Analysis. Radiol Artif Intell 3(4):e200097, 2021. e-Pub 2021. PMID: 34350403.
61. Zhang L, Shi Y, Do KA, Peterson CB, Jenq RR. ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries. BMC Bioinformatics 22(1):126, 2021. e-Pub 2021. PMID: 33731016.
62. Kanagal-Shamanna R, Montalban-Bravo G, Katsonis P, Sasaki K, Class CA, Jabbour E, Sallman D, Hunter AM, Benton C, Chien KS, Luthra R, Bueso-Ramos CE, Kadia T, Andreeff M, Komrokji RS, Al Ali NH, Short N, Daver N, Routbort MJ, Khoury JD, Patel K, Ganan-Gomez I, Wei Y, Borthakur G, Ravandi F, Do KA, Soltysiak KA, Lichtarge O, Medeiros LJ, Kantarjian H, Garcia-Manero G. Evolutionary action score identifies a subset of TP53 mutated myelodysplastic syndrome with favorable prognosis. Blood Cancer J 11(3):52, 2021. e-Pub 2021. PMID: 33677472.
63. Fahrmann JF, Schmidt CM, Mao X, Irajizad E, Loftus M, Zhang J, Patel N, Vykoukal J, Dennison JB, Long JP, Do KA, Zhang J, Chabot JA, Kluger MD, Kastrinos F, Brais L, Babic A, Jajoo K, Lee LS, Clancy TE, Ng K, Bullock A, Genkinger J, Yip-Schneider MT, Maitra A, Wolpin BM, Hanash S. Lead-time trajectory of CA19-9 as an anchor marker for pancreatic cancer early detection. Gastroenterology 160(4):1373-1383.e6, 2021. e-Pub 2021. PMID: 33333055.
64. Fahrmann JF, Irajizad E, Kobayashi M, Vykoukal J, Dennison JB, Murage E, Wu R, Long JP, Do KA, Celestino J, Lu KH, Lu Z, Bast RC, Hanash S. A MYC-Driven Plasma Polyamine Signature for Early Detection of Ovarian Cancer. Cancers (Basel) 13(4), 2021. e-Pub 2021. PMID: 33671595.
65. Montalban-Bravo G, Darbaniyan F, Kanagal-Shamanna R, Ganan-Gomez I, Class CA, Sasaki K, Naqvi K, Wei Y, Yang H, Soltysiak KA, Chien KS, Bueso-Ramos C, Do KA, Kantarjian H, Garcia-Manero G. Type I Interferon Upregulation and Deregulation of Genes Involved in Monopoiesis in Chronic Myelomonocytic Leukemia. Leuk Res 101:106511, 2021. e-Pub 2021. PMID: 33517186.
66. Kim J, Zhu H, Wang X, Do KA. Scalable network estimation with L (0) penalty. Stat Anal Data Min 14(1):18-30, 2021. e-Pub 2021. PMID: 35027990.
67. Ha MJ, Kim J, Galloway-Peña J, Do KA, Peterson CB. Compositional zero-inflated network estimation for microbiome data. BMC Bioinformatics 21(Suppl 21):581, 2020. e-Pub 2020. PMID: 33371887.
68. Abi Jaoude J, Kouzy R, Minsky BD, Fuller CD, Yuan Y, Do KA, Taniguchi CM, Ludmir EB. Sponsor-involved statistical analyses in Phase III cancer clinical trials. Int J Cancer 147(12):3579-3581, 2020. e-Pub 2020. PMID: 32621758.
69. Reyes-Gibby CC, Wang J, Zhang L, Peterson CB, Do KA, Jenq RR, Shelburne S, Shah DP, Chambers MS, Hanna EY, Yeung SJ, Shete S. Oral microbiome and onset of oral mucositis in patients with squamous cell carcinoma of the head and neck. Cancer 126(23):5124-5136, 2020. e-Pub 2020. PMID: 32888342.
70. Capello M, Fahrmann JF, Rios Perez MV, Vykoukal JV, Irajizad E, Tripathi SC, Roife D, Bantis LE, Kang Y, Kundnani DL, Xu H, Prakash LR, Long JP, Katayama H, Fleury A, Ferri-Borgogno S, Baluya DL, Dennison JB, Aguilar-Bonavides C, Casabar JP, Celiktas M, Do KA, Fiehn O, Maitra A, Wang H, Feng Z, Chiao PJ, Katz MH, Fleming JB, Hanash SM. CES2 Expression in Pancreatic Adenocarcinoma Is Predictive of Response to Irinotecan and Is Associated With Type 2 Diabetes. JCO Precis Oncol 4:426-436, 2020. e-Pub 2020. PMID: 35050739.
71. Shi Y, Zhang L, Do KA, Peterson CB, Jenq RR. aPCoA: covariate adjusted principal coordinates analysis. Bioinformatics 36(13):4099-4101, 2020. e-Pub 2020. PMID: 32339223.
72. Fahrmann JF, Vykoukal J, Fleury A, Tripathi S, Dennison JB, Murage E, Wang P, Yu CY, Capello M, Creighton CJ, Do KA, Long JP, Irajizad E, Peterson C, Katayama H, Disis ML, Arun B, Hanash S. Association between plasma diacetylspermine and tumor spermine synthase with outcome in triple negative breast cancer. J Natl Cancer Inst 112(6):607-616, 2020. e-Pub 2020. PMID: 31503278.
73. Chien KS, Class CA, Montalban-Bravo G, Wei Y, Sasaki K, Naqvi K, Ganan-Gomez I, Yang H, Soltysiak KA, Kanagal-Shamanna R, Do KA, Kantarjian HM, Garcia-Manero G. LILRB4 Expression in Chronic Myelomonocytic Leukemia and Myelodysplastic Syndrome Based on Response to Hypomethylating Agents. Leuk Lymphoma 61(6):1493-1499, 2020. e-Pub 2020. PMID: 32036728.
74. Galloway-Peña JR, Shi Y, Peterson CB, Sahasrabhojane P, Gopalakrishnan V, Brumlow CE, Daver NG, Alfayez M, Boddu PC, Khan MAW, Wargo JA, Do KA, Jenq RR, Kontoyiannis DP, Shelburne SA. Gut Microbiome Signatures are Predictive of Infectious Risk Following Induction Therapy for Acute Myeloid Leukemia. Clin Infect Dis 71(1):63-71, 2020. e-Pub 2020. PMID: 31436833.
75. Montalban-Bravo G, Kanagal-Shamanna R, Class CA, Sasaki K, Ravandi F, Cortes JE, Daver N, Takahashi K, Short NJ, DiNardo CD, Jabbour E, Borthakur G, Naqvi K, Issa GC, Konopleva M, Khoury JD, Routbort M, Pierce S, Do KA, Bueso-Ramos C, Patel K, Kantarjian H, Garcia-Manero G, Kadia TM. Outcomes of acute myeloid leukemia with myelodysplasia related changes depend on diagnostic criteria and therapy. Am J Hematol 95(6):612-622, 2020. e-Pub 2020. PMID: 32112433.
76. Chekouo T, Stingo FC, Class CA, Yan Y, Bohannan Z, Wei Y, Garcia-Manero G, Hanash S, Do KA. Investigating protein patterns in human leukemia cell line experiments: A Bayesian approach for extremely small sample sizes. Stat Methods Med Res 29(4):1181-1196, 2020. e-Pub 2020. PMID: 31172886.
77. Montalban-Bravo G, Class CA, Ganan-Gomez I, Kanagal-Shamanna R, Sasaki K, Richard-Carpentier G, Naqvi K, Wei Y, Yang H, Soltysiak KA, Chien K, Bueso-Ramos C, Do KA, Kantarjian H, Garcia-Manero G. Transcriptomic analysis implicates necroptosis in disease progression and prognosis in myelodysplastic syndromes. Leukemia 34(3):872-881, 2020. e-Pub 2020. PMID: 31719677.
78. Das P, Peterson CB, Do KA, Akbani R, Baladandayuthapani V. NExUS: Bayesian simultaneous network estimation across unequal sample sizes. Bioinformatics 36(3):798-804, 2020. e-Pub 2020. PMID: 31504175.
79. Kobayashi M, Katayama H, Irajizad E, Vykoukal JV, Fahrmann JF, Kundnani DL, Yu CY, Cai Y, Hsiao FC, Yang WL, Lu Z, Celestino J, Long JP, Do KA, Lu KH, Ladd JJ, Urban N, Bast RC, Hanash SM. Proteome Profiling Uncovers an Autoimmune Response Signature That Reflects Ovarian Cancer Pathogenesis. Cancers (Basel) 12(2), 2020. e-Pub 2020. PMID: 32092936.
80. Fahrmann JF, Rios Perez MV, Vykoukal JV, Irajizad E, Tripathi SC, Roife D, Bantis LE, Kang Y, Kundnani DL, Xu H, Prakash LR, Long JP, Katayama H, Fleury A, Ferri-Borgogno S, Baluya DL, Dennison JB, Aguilar-Bonavides C, Casabar JP, Celiktas M, K-A D, Fiehn O, Maitra A, Wang H, Feng Z, Chiao PJ, Matthew, Fleming JB, Hanash SM. CES2 Expression in Pancreatic Adenocarcinoma Is Predictive of Response to Irinotecan and Is Associated With Type 2 Diabetes. JCO Precision Oncology 2020 4:426-436, 2020. e-Pub 2020.
81. Riquelme E, Zhang Y, Zhang L, Montiel M, Zoltan M, Dong W, Quesada P, Sahin I, Chandra V, San Lucas A, Scheet P, Xu H, Hanash SM, Feng L, Burks JK, Do KA, Peterson CB, Nejman D, Tzeng CD, Kim MP, Sears CL, Ajami N, Petrosino J, Wood LD, Maitra A, Straussman R, Katz M, White JR, Jenq R, Wargo J, McAllister F. Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes. Cell 178(4):795-806.e12, 2019. e-Pub 2019. PMID: 31398337.
82. Riquelme E, Zhang Y, Zhang L, Montiel M, Zoltan M, Dong W, Quesada P, Sahin I, Chandra V, San Lucas A, Scheet P, Xu H, Hanash SM, Feng L, Burks JK, Do KA, Peterson CB, Nejman D, Tzeng CD, Kim MP, Sears CL, Ajami N, Petrosino J, Wood LD, Maitra A, Straussman R, Katz M, White JR, Jenq R, Wargo J, McAllister F. Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes. Cell 178(4):795-806, 2019. e-Pub 2019.
83. Xing Y, Lin NU, Maurer MA, Chen H, Mahvash A, Sahin A, Akcakanat A, Li Y, Abramson V, Litton J, Chavez-MacGregor M, Valero V, Piha-Paul SA, Hong D, Do KA, Tarco E, Riall D, Eterovic AK, Wulf GM, Cantley LC, Mills GB, Doyle LA, Winer E, Hortobagyi GN, Gonzalez-Angulo AM, Meric-Bernstam F. Phase II trial of AKT inhibitor MK-2206 in patients with advanced breast cancer who have tumors with PIK3CA or AKT mutations, and/or PTEN loss/PTEN mutation. Breast Cancer Res 21(1):78, 2019. e-Pub 2019. PMID: 31277699.
84. Yan Y, Sun N, Wang H, Kobayashi M, Ladd JJ, Long JP, Lo KC, Patel J, Sullivan E, Albert T, Goodman GE, Do KA, Hanash SM. Whole genome-derived tiled peptide arrays detect pre-diagnostic autoantibody signatures in non-small cell lung cancer. Cancer Res 79(7):1549-1557, 2019. e-Pub 2019. PMID: 30723114.
85. Wang Y, Hu J, Do KA, Hobbs BP. An Efficient Nonparametric Estimate for Spatially Correlated Functional Data. Statistics in Biosciences 11(1):162-183, 2019. e-Pub 2019.
86. Thomas PS, Class CA, Gandhi TR, Bambhroliya A, Do KA, Brewster AM. Demographic, clinical, and geographical factors associated with lack of receipt of physician recommended chemotherapy in women with breast cancer in Texas. Cancer Causes Control 30(4):409-415, 2019. e-Pub 2019.
87. Thomas PS, Class CA, Gandhi TR, Bambhroliya A, Do KA, Brewster AM. Demographic, clinical, and geographical factors associated with lack of receipt of physician recommended chemotherapy in women with breast cancer in Texas. Cancer Causes Control 30(4):409-415, 2019. e-Pub 2019. PMID: 30868330.
88. Kim J, Do KA, Ha MJ, Peterson CB. Bayesian inference of hub nodes across multiple networks. Biometrics 75(1):172-182, 2019. e-Pub 2019. PMID: 30051914.
89. Gaudreau PO, Clairefond S, Class CA, Boulay PL, Chrobak P, Allard B, Azzi F, Pommey S, Do KA, Saad F, Trudel D, Young M, Stagg J. WISP1 is associated to advanced disease, EMT and an inflamed tumor microenvironment in multiple solid tumors. Oncoimmunology 8(5):e1581545, 2019. e-Pub 2019. PMID: 31069142.
90. Liu S, Li S, Wang B, Liu W, Gagea M, Chen H, Sohn J, Parinyanitikul N, Primeau T, Do KA, Vande Woude GF, Mendelsohn J, Ueno NT, Mills GB, Tripathy D, Gonzalez-Angulo AM. Cooperative Effect of Oncogenic MET and PIK3CA in an HGF-Dominant Environment in Breast Cancer. Mol Cancer Ther 18(2):399-412, 2019. e-Pub 2019. PMID: 30518672.
91. Liu S, Li S, Wang B, Liu W, Gagea M, Chen H, Sohn J, Parinyanitikul N, Primeau T, Do KA, Vande Woude GF, Mendelsohn J, Ueno NT, Mills GB, Tripathy D, Gonzalez-Angulo AM. Cooperative effect of oncogenic MET and PIK3CA in an HGF-dominant environment in breast cancer. Mol Cancer Ther 18(2):399-412, 2019. e-Pub 2019.
92. Nguyen K, Yan Y, Yuan B, Dasgupta A, Sun J, Mu H, Do KA, Ueno NT, Andreeff M, Battula VL. ST8SIA1 regulates tumor growth and metastasis in TNBC by activating the FAK-AKT-mTOR signaling pathway. Mol Cancer Ther 17(12):2689-2701, 2018. e-Pub 2018. PMID: 30237308.
93. Jiang ZD, Jenq RR, Ajami NJ, Petrosino JF, Alexander AA, Ke S, Iqbal T, DuPont AW, Muldrew K, Shi Y, Peterson C, Do KA, DuPont HL. Safety and preliminary efficacy of orally administered lyophilized fecal microbiota product compared with frozen product given by enema for recurrent Clostridium difficile infection: A randomized clinical trial. PLoS One 13(11):e0205064, 2018. e-Pub 2018. PMID: 30388112.
94. Wei Y, Zheng H, Bao N, Jiang S, Bueso-Ramos CE, Khoury J, Class C, Lu Y, Lin K, Yang H, Ganan-Gomez I, Starczynowski DT, Do KA, Colla S, Garcia-Manero G. KDM6B overexpression activates innate immune signaling and impairs hematopoiesis in mice. Blood Adv 2(19):2491-2504, 2018. e-Pub 2018. PMID: 30275007.
95. Ha MJ, Banerjee S, Akbani R, Liang L, Mills GB, Do KA, Baladandayuthapani V. Personalized Integrated Network Modeling of the Cancer Proteome Atlas. Sci Rep 8(1):14924, 2018. e-Pub 2018. PMID: 30297783.
96. Brewster AM, Thomas P, Brown P, Coyne R, Yan Y, Checka C, Middleton L, Do KA, Bevers T. A System-Level Approach to Improve the Uptake of Antiestrogen Preventive Therapy among Women with Atypical Hyperplasia and Lobular Cancer In Situ. Cancer Prev Res (Phila) 11(5):295-302, 2018. e-Pub 2018. PMID: 29618460.
97. Takahashi K, Hu B, Wang F, Yan Y, Kim E, Vitale C, Patel KP, Strati P, Gumbs C, Little L, Tippen S, Song X, Zhang J, Jain N, Thompson P, Garcia-Manero G, Kantarjian H, Estrov Z, Do KA, Keating M, Burger JA, Wierda WG, Futreal PA, Ferrajoli A. Clinical Implicationsof Cancer Gene Mutations in Patients with Chronic Lymphocytic Leukemia Treated with Lenalidomide. Blood 131(16):1820-1832, 2018. e-Pub 2018. PMID: 29358183.
98. Class CA, Ha MJ, Baladandayuthapani V, Do KA. iDINGO - Integrative Differential Network Analysis in Genomics with Shiny Application. Bioinformatics 34(7):1243-1245, 2018. e-Pub 2018. PMID: 29194470.
99. Stagg J, Gaudreau PO, Clairefond S, Class CA, Boulay PL, Chrobak P, Allard B, Azzi F, Pommey S, K-A D, Saad F, Trudel D, Young M. WISP1 iss associated to advanced disease, EMT and an inflamed tumor microenvironment in multiple solid tumors. OncoImmunology 8(5), 2018. e-Pub 2018.
100. Tayob N, Stingo F, Do KA, Lok ASF, Feng Z. A Bayesian Screening Approach for Hepatocellular Carcinoma using Multiple Longitudinal Biomarkers. Biometrics 74(1):249-259, 2018. e-Pub 2018. PMID: 28482112.
101. Hunt KK, Karakas C, Ha MJ, Biernacka A, Yi M, Sahin AA, Adjapong O, Hortobagyi GN, Bondy M, Thompson P, Cheung KL, Ellis IO, Bacus S, Symmans WF, Do KA, Keyomarsi K. Cytoplasmic Cyclin E Predicts Recurrence in Patients with Breast Cancer. Clin Cancer Res 23(12):2991-3002, 2017. e-Pub 2017. PMID: 27881578.
102. Chekouo T, Stingo FC, Doecke JD, Do KA. A Bayesian integrative approach for multi-platform genomic data: A kidney cancer case study. Biometrics 73(2):615-624, 2017. e-Pub 2017. PMID: 27669160.
103. Jonasch E, Hasanov E, Corn PG, Moss T, Shaw KR, Stovall S, Marcott V, Gan B, Bird S, Wang X, Do KA, Altamirano PF, Zurita AJ, Doyle LA, Lara PN, Tannir NM. A randomized phase 2 study of MK-2206 versus everolimus in refractory renal cell carcinoma. Ann Oncol 28(4):804-808, 2017. e-Pub 2017. PMID: 28049139.
104. Çeliktas M, Tanaka I, Tripathi SC, Fahrmann JF, Aguilar-Bonavides C, Villalobos P, Delgado O, Dhillon D, Dennison JB, Ostrin EJ, Wang H, Behrens C, Do KA, Gazdar AF, Hanash SM, Taguchi A. Role of CPS1 in Cell Growth, Metabolism, and Prognosis in LKB1-Inactivated Lung Adenocarcinoma. J Natl Cancer Inst 109(3):1-9, 2017. e-Pub 2017. PMID: 28376202.
105. Yang Q, Chen LS, Ha MJ, Do KA, Neelapu SS, Gandhi V. Idelalisib Impacts Cell Growth through Inhibiting Translation-Regulatory Mechanisms in Mantle Cell Lymphoma. Clin Cancer Res 23(1):181-192, 2017. e-Pub 2017. PMID: 27342398.
106. An X, Hu J, Do KA. SIFORM: shared informative factor models for integration of multi-platform bioinformatic data. Bioinformatics 32(21):3279-3290, 2016. e-Pub 2016. PMID: 27381342.
107. Jiang Y, Chen HC, Su X, Thompson PA, Liu X, Do KA, Wierda W, Keating MJ, Plunkett W. ATM function and its relationship with ATM gene mutations in chronic lymphocytic leukemia with the recurrent deletion (11q22.3-23.2). Blood Cancer J 6(6, e465):e465, 2016. e-Pub 2016. PMID: 27588518.
108. Kebriaei P, Singh H, Huls MH, Figliola MJ, Bassett R, Olivares S, Jena B, Dawson MJ, Kumaresan PR, Su S, Maiti S, Dai J, Moriarity B, Forget MA, Senyukov V, Orozco A, Liu T, McCarty J, Jackson RN, Moyes JS, Rondon G, Qazilbash M, Ciurea S, Alousi A, Nieto Y, Rezvani K, Marin D, Popat U, Hosing C, Shpall EJ, Kantarjian H, Keating M, Wierda W, Do KA, Largaespada DA, Lee DA, Hackett PB, Champlin RE, Cooper LJ. Phase I trials using Sleeping Beauty to generate CD19-specific CAR T cells. J Clin Invest 126(9):3363-76, 2016. e-Pub 2016. PMID: 27482888.
109. Tayob N, Do KA, Feng Z. Unbiased estimation of biomarker panel performance when combining training and testing data in a group sequential design. Biometrics 72(3):888-96, 2016. e-Pub 2016. PMID: 26845527.
110. Caruso HG, Torikai H, Zhang L, Maiti S, Dai J, Do KA, Singh H, Huls H, Lee DA, Champlin RE, Heimberger AB, Cooper LJ. Redirecting T-Cell Specificity to EGFR Using mRNA to Self-limit Expression of Chimeric Antigen Receptor. J Immunother 39(5):205-17, 2016. e-Pub 2016. PMID: 27163741.
111. Kim J, Davis JW, Klein EA, Magi-Galluzzi C, Lotan Y, Ward JF, Pisters LL, Basler JW, Pettaway CA, Stephenson A, Li Ning Tapia EM, Efstathiou E, Wang X, Do KA, Lee JJ, Gorlov IP, Vornik LA, Hoque AM, Prokhorova IN, Parnes HL, Lippman SM, Thompson IM, Brown PH, Logothetis CJ, Troncoso P. Tissue Effects in a Randomized Controlled Trial of Short-term Finasteride in Early Prostate Cancer. EBioMedicine 7:85-93, 2016. e-Pub 2016. PMID: 27322462.
112. Tayob N, Lok AS, Do KA, Feng Z. Improved Detection of Hepatocellular Carcinoma by Using a Longitudinal Alpha-Fetoprotein Screening Algorithm. Clin Gastroenterol Hepatol 14(3):469-475, 2016. e-Pub 2016. PMID: 26260109.
113. Tambaro FP, Garcia-Manero G, O'Brien SM, Faderl SH, Ferrajoli A, Burger JA, Pierce S, Wang X, Do KA, Kantarjian HM, Keating MJ, Wierda WG. Outcomes for patients with chronic lymphocytic leukemia and acute leukemia or myelodysplastic syndrome. Leukemia 30(2):325-30, 2016. e-Pub 2016. PMID: 26290497.
114. Powell E, Shao J, Yuan Y, Chen HC, Cai S, Echeverria GV, Mistry N, Decker KF, Schlosberg C, Do KA, Edwards JR, Liang H, Piwnica-Worms D, Piwnica-Worms H. p53 deficiency linked to B cell translocation gene 2 (BTG2) loss enhances metastatic potential by promoting tumor growth in primary and metastatic sites in patient-derived xenograft (PDX) models of triple-negative breast cancer. Breast Cancer Res 18(1):13, 2016. e-Pub 2016. PMID: 26818199.
115. Chekouo T, Stingo FC, Guindani M, Do KA. A Bayesian predictive model for imaging genetics with application to schizophrenia. Annals of Applied Statistics 10(3):1547-1571, 2016. e-Pub 2016.
116. McAuliffe PF, Evans KW, Akcakanat A, Chen K, Zheng X, Zhao H, Eterovic AK, Sangai T, Holder AM, Sharma C, Chen H, Do KA, Tarco E, Gagea M, Naff KA, Sahin A, Multani AS, Black DM, Mittendorf EA, Bedrosian I, Mills GB, Gonzalez-Angulo AM, Meric-Bernstam F. Correction: Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes. PLoS One 11(3):e0151121, 2016. e-Pub 2016. PMID: 26953790.
117. Ha MJ, Baladandayuthapani V, Do KA. DINGO: Differential Network Analysis in Genomics. Bioinformatics 31(21):3413-3420, 2015. e-Pub 2015. PMID: 26148744.
118. Wang Y, Hobbs BP, Hu J, Ng CS, Do KA. Predictive classification of correlated targets with application to detection of metastatic cancer using functional CT imaging. Biometrics 71(3):792-802, 2015. e-Pub 2015. PMID: 25851056.
119. Holder AM, Akcakanat A, Adkins F, Evans K, Chen H, Wei C, Milton DR, Li Y, Do KA, Janku F, Meric-Bernstam F. Epithelial to mesenchymal transition is associated with rapamycin resistance. Oncotarget 6(23):19500-13, 2015. e-Pub 2015. PMID: 25944619.
120. Salameh A, Lee AK, Cardó-Vila M, Nunes DN, Efstathiou E, Staquicini FI, Dobroff AS, Marchiò S, Navone NM, Hosoya H, Lauer RC, Wen S, Salmeron CC, Hoang A, Newsham I, Lima LA, Carraro DM, Oliviero S, Kolonin MG, Sidman RL, Do KA, Troncoso P, Logothetis CJ, Brentani RR, Calin GA, Cavenee WK, Dias-Neto E, Pasqualini R, Arap W. PRUNE2 is a human prostate cancer suppressor regulated by the intronic long noncoding RNA PCA3. Proc Natl Acad Sci U S A 112(27):8403-8, 2015. e-Pub 2015. PMID: 26080435.
121. Pasqualini R, Millikan RE, Christianson DR, Cardó-Vila M, Driessen WH, Giordano RJ, Hajitou A, Hoang AG, Wen S, Barnhart KF, Baze WB, Marcott VD, Hawke DH, Do KA, Navone NM, Efstathiou E, Troncoso P, Lobb RR, Logothetis CJ, Arap W. Targeting the interleukin-11 receptor α in metastatic prostate cancer: A first-in-man study. Cancer 121(14):2411-21, 2015. e-Pub 2015. PMID: 25832466.
122. Chekouo T, Stingo FC, Doecke JD, Do KA. Incorporating microRNA regulatory network and pathways: a Bayesian graphical approach to the selection of miRNAs and genes with censored outcomes. Biometrics 71(2):428-38, 2015. e-Pub 2015. PMID: 25639276.
123. Dasari A, Phan A, Gupta S, Rashid A, Yeung SC, Hess K, Chen H, Tarco E, Chen H, Wei C, Anh-Do K, Halperin D, Meric-Bernstam F, Yao J. Phase I study of the anti-IGF1R antibody cixutumumab with everolimus and octreotide in advanced well-differentiated neuroendocrine tumors. Endocr Relat Cancer 22(3):431-41, 2015. e-Pub 2015. PMID: 25900182.
124. Gonzalez-Angulo AM, Krop I, Akcakanat A, Chen H, Liu S, Li Y, Culotta KS, Tarco E, Piha-Paul S, Moulder-Thompson S, Velez-Bravo V, Sahin AA, Doyle LA, Do KA, Winer EP, Mills GB, Kurzrock R, Meric-Bernstam F. SU2C Phase Ib Study of Paclitaxel and MK-2206 in Advanced Solid Tumors and Metastatic Breast Cancer. J Natl Cancer Inst 107(3), 2015. e-Pub 2015. PMID: 25688104.
125. Mintz PJ, Rietz AC, Cardó-Vila M, Ozawa MG, Dondossola E, Do KA, Kim J, Troncoso P, Logothetis CJ, Sidman RL, Pasqualini R, Arap W. Discovery and horizontal follow-up of an autoantibody signature in human prostate cancer. Proc Natl Acad Sci U S A 112(8):2515-20, 2015. e-Pub 2015. PMID: 25675522.
126. McAuliffe PF, Evans KW, Akcakanat A, Chen K, Zheng X, Zhao H, Eterovic AK, Sangai T, Holder AM, Sharma C, Chen H, Do KA, Tarco E, Gagea M, Naff KA, Sahin A, Multani AS, Black DM, Mittendorf EA, Bedrosian I, Mills GB, Gonzalez-Angulo AM, Meric-Bernstam F. Ability to Generate Patient-Derived Breast Cancer Xenografts Is Enhanced in Chemoresistant Disease and Predicts Poor Patient Outcomes. PLoS One 10(9):e0136851, 2015. e-Pub 2015. PMID: 26325287.
127. Ha MJ, Baladandayuthapani V, Do KA. Prognostic gene signature identification using causal structure learning: applications in kidney cancer. Cancer Inform 14(Suppl 1):23-35, 2015. e-Pub 2015. PMID: 25861215.
128. Rembach A, Stingo FC, Peterson C, Vannucci M, Do KA, Wilson WJ, Macaulay SL, Ryan TM, Martins RN, Ames D, Masters CL, Doecke JD, Group AR. Bayesian graphical network analyses reveal complex biological interactions specific to Alzheimer's disease. J Alzheimers Dis 44(3):917-25, 2015. e-Pub 2015. PMID: 25613103.
129. Tam CS, O'Brien S, Plunkett W, Wierda W, Ferrajoli A, Wang X, Do KA, Cortes J, Khouri I, Kantarjian H, Lerner S, Keating MJ. Life After FCR: Outcomes of patients with chronic lymphocytic leukemia who progress after frontline treatment with Fludarabine, Cyclophosphamide and Rituximab. Blood 124(20):3059-64, 2014. e-Pub 2014. PMID: 25281606.
130. Hassan B, Akcakanat A, Sangai T, Evans KW, Adkins F, Eterovic AK, Zhao H, Chen K, Chen H, Do KA, Xie SM, Holder AM, Naing A, Mills GB, Meric-Bernstam F. Catalytic mTOR inhibitors can overcome intrinsic and acquired resistance to allosteric mTOR inhibitors. Oncotarget 5(18):8544-57, 2014. e-Pub 2014. PMID: 25261369.
131. Pande M, Bondy ML, Do KA, Sahin AA, Ying J, Mills GB, Thompson PA, Brewster AM. Association between germline single nucleotide polymorphisms in the PI3K-AKT-mTOR pathway, obesity, and breast cancer disease-free survival. Breast Cancer Res Treat 147(2):381-7, 2014. e-Pub 2014. PMID: 25108739.
132. Zhang L, Baladandayuthapani V, Mallick BK, Manyam GC, Thompson PA, Bondy ML, Do KA. Bayesian hierarchical structured variable selection methods with application to MIP studies in breast cancer. J R Stat Soc Ser C Appl Stat 63(4):595-620, 2014. e-Pub 2014. PMID: 25705056.
133. Meric-Bernstam F, Akcakanat A, Chen H, Sahin A, Tarco E, Carkaci S, Adrada BE, Singh G, Do KA, Garces ZM, Mittendorf E, Babiera G, Bedrosian I, Hwang R, Krishnamurthy S, Symmans WF, Gonzalez-Angulo AM, Mills GB. Influence of Biospecimen Variables on Proteomic Biomarkers in Breast Cancer. Clin Cancer Res 20(14):3870-83, 2014. e-Pub 2014. PMID: 24895461.
134. Blanco E, Sangai T, Wu S, Hsiao A, Ruiz-Esparza GU, Gonzalez-Delgado CA, Cara FE, Granados-Principal S, Evans KW, Akcakanat A, Wang Y, Do KA, Meric-Bernstam F, Ferrari M. Colocalized delivery of rapamycin and paclitaxel to tumors enhances synergistic targeting of the PI3K/Akt/mTOR pathway. Mol Ther 22(7):1310-9, 2014. e-Pub 2014. PMID: 24569835.
135. Gonzalez-Angulo AM, Akcakanat A, Liu S, Green MC, Murray JL, Chen H, Palla SL, Koenig KB, Brewster AM, Valero V, Ibrahim NK, Moulder-Thompson S, Litton JK, Tarco E, Moore J, Flores P, Crawford D, Dryden MJ, Symmans WF, Sahin A, Giordano SH, Pusztai L, Do KA, Mills GB, Hortobagyi GN, Meric-Bernstam F. Open-label randomized clinical trial of standard neoadjuvant chemotherapy with paclitaxel followed by FEC versus the combination of paclitaxel and everolimus followed by FEC in women with triple receptor-negative breast cancer . Ann Oncol 25(6):1122-7, 2014. e-Pub 2014. PMID: 24669015.
136. Doecke JD, Chekouo T, Stingo FC, K-A AD. miRNA target gene identification: sourcing miRNA-target gene relationships for the analyses of TCGA Illumina miSeq and RNA-Seq Hiseq platform data. International Journal of Human Genetics 14(1):17-22, 2014. e-Pub 2014.
137. Chavez-Macgregor M, Liu S, De Melo-Gagliato D, Chen H, Do KA, Pusztai L, Fraser Symmans W, Nair L, Hortobagyi GN, Mills GB, Meric-Bernstam F, Gonzalez-Angulo AM. Differences in gene and protein expression and the effects of race/ethnicity on breast cancer subtypes. Cancer Epidemiol Biomarkers Prev 23(2):316-23, 2014. e-Pub 2014. PMID: 24296856.
138. Liu Y, Zhou R, Baumbusch LO, Tsavachidis S, Brewster AM, Do KA, Sahin A, Hortobagyi GN, Taube JH, Mani SA, Aarøe J, Wärnberg F, Børresen-Dale AL, Mills GB, Thompson PA, Bondy ML. Genomic copy number imbalances associated with bone and non-bone metastasis of early-stage breast cancer. Breast Cancer Res Treat 143(1):189-201, 2014. e-Pub 2014. PMID: 24305980.
139. Gorlov IP, Yang JY, Byun J, Logothetis C, Gorlova OY, Do KA, Amos C. How to get the most from microarray data: advice from reverse genomics. BMC Genomics 15:223, 2014. e-Pub 2014. PMID: 24656147.
140. Shirazi F, Farmakiotis D, Yan Y, Albert N, Do KA, Kim-Anh D, Kontoyiannis DP. Diet modification and Metformin have a beneficial cial effect in a model of obesity and mucormycosis. PLoS One 9(9):e108635, 2014. e-Pub 2014. PMID: 25268492.
141. Sohn J, Do KA, Liu S, Chen H, Mills GB, Hortobagyi GN, Meric-Bernstam F, Gonzalez-Angulo AM. Functional proteomics characterization of residual triple-negative breast cancer after standard neoadjuvant chemotherapy. Ann Oncol 24(10):2522-6, 2013. e-Pub 2013. PMID: 23925999.
142. León-Novelo LG, Müller P, Arap W, Sun J, Pasqualini R, Do KA. Bayesian decision theoretic multiple comparison procedures: an application to phage display data. Biom J 55(3):478-89, 2013. e-Pub 2013. PMID: 23281047.
143. Murray JL, Thompson P, Yoo SY, Do KA, Pande M, Zhou R, Liu Y, Sahin AA, Bondy ML, Brewster AM. Prognostic Value of Single Nucleotide Polymorphisms of Candidate Genes Associated with Inflammation in Early Stage Breast Cancer. Breast Cancer Res Treat 138(3):917-24, 2013. e-Pub 2013. PMID: 23529385.
144. Gonzalez-Angulo AM, Liu S, Chen H, Chavez-Macgregor M, Sahin A, Hortobagyi GN, Mills GB, Do KA, Meric-Bernstam F. Functional Proteomics Characterization of Residual Breast Cancer After Neoadjuvant Systemic Chemotherapy. Ann Oncol 24(4):909-16, 2013. e-Pub 2013. PMID: 23139263.
145. Pande M, Thompson PA, Do KA, Sahin AA, Amos CI, Frazier ML, Bondy ML, Brewster AM. Genetic variants in the vitamin D pathway and breast cancer disease-free survival. Carcinogenesis 34(3):587-94, 2013. e-Pub 2013. PMID: 23180655.
146. León-Novelo LG, Müller P, Arap W, Kolonin M, Sun J, Pasqualini R, Do KA. Semiparametric Bayesian Inference for Phage Display Data. Biometrics 69(1):174-83, 2013. e-Pub 2013. PMID: 23339534.
147. Wang W, Baladandayuthapani V, Morris JS, Broom BM, Manyam G, Do KA. iBAG: integrative Bayesian analysis of high-dimensional multi-platform genomics data. Bioinformatics 29(2):149-59, 2013. e-Pub 2013. PMID: 23142963.
148. Gonzalez-Angulo AM, Chen H, Karuturi MS, Chavez-MacGregor M, Tsavachidis S, Meric-Bernstam F, Do KA, Hortobagyi GN, Thompson PA, Mills GB, Bondy ML, Blumenschein GR. Frequency of mesenchymal-epithelial transition factor gene (MET) and the catalytic subunit of phosphoinositide-3-kinase (PIK3CA) copy number elevation and correlation with outcome in patients with early stage breast cancer. Cancer 119(1):7-15, 2013. e-Pub 2013. PMID: 22736407.
149. Holder AM, Gonzalez-Angulo AM, Chen H, Akcakanat A, Do KA, Fraser Symmans W, Pusztai L, Hortobagyi GN, Mills GB, Meric-Bernstam F. High stearoyl-CoA desaturase 1 expression is associated with shorter survival in breast cancer patients. Breast Cancer Res Treat 137(1):319-27, 2013. e-Pub 2013. PMID: 23208590.
150. Wang W, Baladandayuthapani V, Holmes CC, Do KA. Integrative network-based Bayesian analysis of diverse genomics data. BMC Bioinformatics 14 Suppl 13:S8, 2013. e-Pub 2013. PMID: 24267288.
151. Bayraktar S, Thompson PA, Yoo SY, Do KA, Sahin AA, Arun BK, Bondy ML, Brewster AM. The Relationship Between Eight GWAS-Identified Single Nucleotide Polymorphisms and Primary Breast Cancer Outcomes. Oncologist 18(5):493-500, 2013. e-Pub 2013. PMID: 23635555.
152. Sangai T, Akcakanat A, Chen H, Tarco E, Wu Y, Do KA, Miller TW, Arteaga CL, Mills GB, Gonzalez-Angulo AM, Meric-Bernstam F. Biomarkers of response to Akt inhibitor MK-2206 in breast cancer. Clin Cancer Res 18(20):5816-28, 2012. e-Pub 2012. PMID: 22932669.
153. Meric-Bernstam F, Akcakanat A, Chen H, Do KA, Sangai T, Adkins F, Gonzalez-Angulo AM, Rashid A, Crosby K, Dong M, Phan AT, Wolff RA, Gupta S, Mills GB, Yao J. PIK3CA/PTEN mutations and Akt activation as markers of sensitivity to allosteric mTOR inhibitors. Clin Cancer Res 18(6):1777-89, 2012. e-Pub 2012. PMID: 22422409.
154. Raghav KP, Hernandez-Aya LF, Lei X, Chavez-Macgregor M, Meric-Bernstam F, Buchholz TA, Sahin A, Do KA, Hortobagyi GN, Gonzalez-Angulo AM. Impact of low estrogen/progesterone receptor expression on survival outcomes in breast cancers previously classified as triple negative breast cancers. Cancer 118(6):1498-506, 2012. e-Pub 2012. PMID: 21837669.
155. Gonzalez-Angulo AM, Iwamoto T, Liu S, Chen H, Do KA, Hortobagyi GN, Mills GB, Meric-Bernstam F, Symmans WF, Pusztai L. Gene expression, molecular class changes and pathway analysis after neoadjuvant systemic therapy for breast cancer. Clin Cancer Res 18(4):1109-19, 2012. e-Pub 2012. PMID: 22235097.
156. Meric-Bernstam F, Chen H, Akcakanat A, Do KA, Lluch A, Hennessy BT, Hortobagyi GN, Mills GB, Gonzalez-Angulo A. Aberrations in translational regulation are associated with poor prognosis in hormone receptor-positive breast cancer. Breast Cancer Res 14(5):R138, 2012. e-Pub 2012. PMID: 23102376.
157. Broom BM, Do KA, Subramanian D. Model averaging strategies for structure learning in Bayesian networks with limited data. BMC Bioinformatics 13 Suppl 13:S10, 2012. e-Pub 2012. PMID: 23320818.
158. Wierda WG, O'Brien S, Wang X, Faderl S, Ferrajoli A, Do KA, Garcia-Manero G, Cortes J, Thomas D, Koller CA, Burger JA, Lerner S, Schlette E, Abruzzo L, Kantarjian HM, Keating MJ. Multivariable model for time to first treatment in patients with chronic lymphocytic leukemia. J Clin Oncol 29(31):4088-95, 2011. e-Pub 2011. PMID: 21969505.
159. Staquicini FI, Cardo-Vila M, Kolonin MG, Trepel M, Edwards JK, Nunes DN, Sergeeva A, Efstathiou E, Sun J, Almeida NF, Tu SM, Botz GH, Wallace MJ, O'Connell DJ, Krajewski S, Gershenwald JE, Molldrem JJ, Flamm AL, Koivunen E, Pentz RD, Dias-Neto E, Setubal JC, Cahill DJ, Troncoso P, Do KA, Logothetis CJ, Sidman RL, Pasqualini R, Arap W. Vascular ligand-receptor mapping by direct combinatorial selection in cancer patients. Proc Natl Acad Sci U S A 108(46):18637-42, 2011. e-Pub 2011. PMID: 22049339.
160. Barnhart KF, Christianson DR, Hanley PW, Driessen WH, Bernacky BJ, Baze WB, Wen S, Tian M, Ma J, Kolonin MG, Saha PK, Do KA, Hulvat JF, Gelovani JG, Chan L, Arap W, Pasqualini R. A peptidomimetic targeting white fat causes weight loss and improved insulin resistance in obese monkeys. Sci Transl Med 3(108):108ra112, 2011. e-Pub 2011. PMID: 22072637.
161. Brewster AM, Thompson P, Sahin AA, Do K, Edgerton M, Murray JL, Tsavachidis S, Zhou R, Liu Y, Zhang L, Mills G, Bondy M. Copy number imbalances between screen and symptom-detected breast cancers and impact on disease-free survival. Cancer Prev Res (Phila) 4(10):1609-16, 2011. e-Pub 2011. PMID: 21795423.
162. Heymach JV, Shackleford TJ, Tran HT, Yoo SY, Do KA, Wergin M, Saintigny P, Vollmer RT, Polascik TJ, Snyder DC, Ruffin MT, Yan S, Dewhirst M, Kunnumakkara AB, Aggarwal BB, Demark-Wahnefried W. Effect of low-fat diet on plasma levels of NF-{kappa}B-regulated inflammatory cytokines and angiogenic factors in men with prostate cancer. Cancer Prev Res (Phila) 4(10):1590-8, 2011. e-Pub 2011. PMID: 21764858.
163. Hernandez-Aya LF, Chavez-Macgregor M, Lei X, Meric-Bernstam F, Buchholz TA, Hsu L, Sahin AA, Do KA, Valero V, Hortobagyi GN, Gonzalez-Angulo AM. Nodal status and clinical outcomes in a large cohort of patients with triple-negative breast cancer. J Clin Oncol 29(19):2628-34, 2011. e-Pub 2011. PMID: 21606433.
164. Yang Y, Hobbs BP, Do KA. An Efficient Nonparametric Estimate for Spatially Correlated Functional Data (Accepted). Statistics in Biosciences 11(1):162-183, 2011. e-Pub 2011.
165. Gonzalez-Angulo AM, Timms KM, Liu S, Chen H, Litton JK, Potter J, Lanchbury JS, Stemke-Hale K, Hennessy BT, Arun BK, Hortobagyi GN, Do KA, Mills GB, Meric-Bernstam F. Incidence and outcome of BRCA mutations in unselected patients with triple receptor-negative breast cancer. Clin Cancer Res 17(5):1082-9, 2011. e-Pub 2011. PMID: 21233401.
166. Bonato V, Baladandayuthapani V, Broom BM, Sulman EP, Aldape KD, Do KA. Bayesian ensemble methods for survival prediction in gene expression data. Bioinformatics 27(3):359-67, 2011. e-Pub 2011. PMID: 21148161.
167. Thompson PA, Brewster AM, K-A D, Baladandayuthapani V, Broom BM, Edgerton ME, Hahn KM, Murray JL, Sahin A, Tsavachidis S, Wang Y, Zhang L, Hortobagyi GN, Mills GB, Bondy ML. Selective genomic copy number imbalances and probability of recurrence in early-stage breast cancer. PLoS One 6(8):e23543, 2011. e-Pub 2011. PMID: 21858162.
168. Luyimbazi D, Akcakanat A, McAuliffe PF, Zhang L, Singh G, Gonzalez-Angulo AM, Chen H, Do KA, Zheng Y, Hung MC, Mills GB, Meric-Bernstam F. Rapamycin regulates stearoyl CoA desaturase 1 expression in breast cancer. Mol Cancer Ther 9(10):2770-84, 2010. e-Pub 2010. PMID: 20876744.
169. Yi M, Hunt KK, Arun BK, Bedrosian I, Barrera AG, Do KA, Kuerer HM, Babiera GV, Mittendorf EA, Ready K, Litton J, Meric-Bernstam F. Factors affecting the decision of breast cancer patients to undergo contralateral prophylactic mastectomy. Cancer Prev Res (Phila) 3(8):1026-34, 2010. e-Pub 2010. PMID: 20647335.
170. Efstathiou E, Abrahams NA, Tibbs RF, Wang X, Pettaway CA, Pisters LL, Mathew PF, Do KA, Logothetis CJ, Troncoso P. Morphologic characterization of preoperatively treated prostate cancer: toward a post-therapy histologic classification. Eur Urol 57(6):1030-8, 2010. e-Pub 2010. PMID: 19853370.
171. Zhang S, Mueller P, Do KA. A Bayesian Semiparametric Survival Model with Longitudinal Markers. Biometrics 66(2):435-43, 2010. e-Pub 2010. PMID: 19508243.
172. Broom BM, Sulman EP, Do KA, Edgerton ME, Aldape KD. Bagged Gene Shaving for the Robust CLustering of High Throughput Data. Int J Bioinform Res Appl 6(4):326-43, 2010. e-Pub 2010. PMID: 20940121.
173. Lin YX, Baladandayuthapani V, Bonato V, Do KA. Estimating shared copy number aberrations for array CGH data: the linear-median method. Cancer Inform 9:229-49, 2010. e-Pub 2010. PMID: 21082039.
174. Ravoori M, Czaplinska AJ, Sikes C, Han L, Johnson EM, Qiao W, Ng C, Cody DD, Murphy WA, Do KA, Navone NM, Kundra V. Quantification of mineralized bone response to prostate cancer by noninvasive in vivo microCT and non-destructive ex vivo microCT and DXA in a mouse model. PLoS One 5(3):e9854, 2010. e-Pub 2010. PMID: 20360964.
175. Montero AJ, Diaz-Montero CM, Millikan RE, Liu J, Do KA, Hodges S, Jonasch E, McIntyre BW, Hwu P, Tannir N. Cytokines and angiogenic factors in patients with metastatic renal cell carcinoma treated with interferon-alpha: association of pretreatment serum levels with survival. Ann Oncol 20(10):1682-7, 2009. e-Pub 2009. PMID: 19541791.
176. Mandelin J, Lin EC, Hu DD, Knowles SK, Do KA, Wang X, Sage EH, Smith JW, Arap W, Pasqualini R. Extracellular and intracellular mechanisms that mediate the metastatic activity of exogenous osteopontin. Cancer 115(8):1753-64, 2009. e-Pub 2009. PMID: 19224553.
177. Wierda WG, O'Brien S, Wang X, Faderl S, Ferrajoli A, Do KA, Garcia-Manero G, Cortes J, Thomas D, Koller C, Burger J, Lerner S, Kantarjian H, Keating M. Characteristics associated with important clinical end points in patients with chronic lymphocytic leukemia at initial treatment. J Clin Oncol 27(10):1637-43. e-Pub 2009. PMID: 19224852.
178. Tsavachidou D, McDonnell TJ, Wen S, Wang X, Vakar-Lopez F, Pisters LL, Pettaway CA, Wood CG, Do KA, Thall PF, Stephens C, Efstathiou E, Taylor R, Menter DG, Troncoso P, Lippman SM, Logothetis CJ, Kim J. Selenium and vitamin E: cell type- and intervention-specific tissue effects in prostate cancer. J Natl Cancer Inst 101(5):306-20. e-Pub 2009. PMID: 19244175.
179. Liu Y, Scheurer ME, El-Zein R, Cao Y, Do KA, Gilbert M, Aldape KD, Wei Q, Etzel C, Bondy ML. Association and interactions between DNA repair gene polymorphisms and adult glioma. Cancer Epidemiol Biomarkers Prev 18(1):204-14, 2009. e-Pub 2009. PMID: 19124499.
180. Kim J, Jonasch E, Alexander A, Short JD, Cai S, Wen S, Tsavachidou D, Tamboli P, Czerniak BA, Do KA, Wu KJ, Marlow LA, Wood CG, Copland JA, Walker CL. Cytoplasmic sequestration of p27 via AKT phosphorylation in renal cell carcinoma. Clin Cancer Res 15(1):81-90, 2009. e-Pub 2009. PMID: 19118035.
181. Gregorio SP, Sallet PC, Do KA, Lin E, Gattaz WF, Dias-Neto E. Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: preliminary evidence. Psychiatry Res 165(1-2):1-9, 2009. e-Pub 2009. PMID: 19054571.
182. Millikan RE, Wen S, Pagliaro LC, Brown MA, Moomey B, Do KA, Logothetis CJ. Phase III Trial of Androgen Ablation With or Without Three Cycles of Systemic Chemotherapy for Advanced Prostate Cancer. J Clin Oncol 26(36):5936-42, 2008. e-Pub 2008. PMID: 19029421.
183. Tam CS, O'Brien S, Wierda W, Kantarjian H, Wen S, Do KA, Thomas DA, Cortes J, Lerner S, Keating MJ. Long-term results of the fludarabine, cyclophosphamide, and rituximab regimen as initial therapy of chronic lymphocytic leukemia. Blood 112(4):975-80, 2008. e-Pub 2008. PMID: 18411418.
184. Lin SH, Lee YC, Choueiri MB, Wen S, Mathew P, Ye X, Do KA, Navone NM, Kim J, Tu SM, Yu-Lee LY, Logothetis CJ. Soluble ErbB3 levels in bone marrow and plasma of men with prostate cancer. Clin Cancer Res 14(12):3729-36, 2008. e-Pub 2008. PMID: 18559590.
185. Kuwai T, Nakamura T, Sasaki T, Kitadai Y, Kim JS, Langley RR, Fan D, Wang X, Do KA, Kim SJ, Fidler IJ. Targeting the EGFR, VEGFR, and PDGFR on colon cancer cells and stromal cells is required for therapy. Clin Exp Metastasis 25(4):477-89, 2008. e-Pub 2008. PMID: 18324358.
186. McDonnell TJ, Chari NS, Cho-Vega JH, Troncoso P, Wang X, Bueso-Ramos CE, Coombes K, Brisbay S, Lopez R, Prendergast G, Logothetis C, Do KA. Biomarker expression patterns that correlate with high grade features in treatment naive, organ-confined prostate cancer. BMC Med Genomics 1:1, 2008. e-Pub 2008. PMID: 18237448.
187. Cho-Vega JH, Tsavachidis S, Do KA, Nakagawa J, Medeiros LJ, McDonnell TJ. Dicarbonyl/L-xylulose reductase: a potential biomarker identified by laser-capture microdissection-micro serial analysis of gene expression of human prostate adenocarcinoma. Cancer Epidemiol Biomarkers Prev 16(12):2615-22, 2007. e-Pub 2007. PMID: 18086765.
188. Mao S, Daliani DD, Wang X, Thall PF, Do KA, Perez CA, Brown MA, Bouchillon K, Carter CM, Logothetis CJ, Kim J. Employing the treatment-free interval of intermittent androgen ablation to screen candidate prostate cancer therapies. Prostate 67(15):1677-85, 2007. e-Pub 2007. PMID: 17879948.
189. Spiess PE, Pettaway CA, Vakar-Lopez F, Kassouf W, Wang X, Busby JE, Do KA, Davuluri R, Tannir NM. Treatment outcomes of small cell carcinoma of the prostate: a single-center study. Cancer 110(8):1729-37, 2007. e-Pub 2007. PMID: 17786954.
190. Tsimberidou AM, Wen S, O'Brien S, McLaughlin P, Wierda WG, Ferrajoli A, Faderl S, Manning J, Lerner S, Mai CV, Rodriguez AM, Hess M, Do KA, Freireich EJ, Kantarjian HM, Medeiros LJ, Keating MJ. Assessment of chronic lymphocytic leukemia and small lymphocytic lymphoma by absolute lymphocyte counts in 2,126 patients: 20 years of experience at the University of Texas M.D. Anderson Cancer Center. J Clin Oncol 25(29):4648-56, 2007. e-Pub 2007. PMID: 17925562.
191. Brewster AM, Do KA, Thompson PA, Hahn KM, Sahin AA, Cao Y, Stewart MM, Murray JL, Hortobagyi GN, Bondy ML. Relationship between epidemiologic risk factors and breast cancer recurrence. J Clin Oncol 25(28):4438-44. e-Pub 2007. PMID: 17785707.
192. Wierda WG, O'Brien S, Wang X, Faderl S, Ferrajoli A, Do KA, Cortes J, Thomas D, Garcia-Manero G, Koller C, Beran M, Giles F, Ravandi F, Lerner S, Kantarjian H, Keating M. Prognostic nomogram and index for overall survival in previously untreated patients with chronic lymphocytic leukemia. Blood 109(11):4679-85, 2007. e-Pub 2007. PMID: 17299097.
193. Ji Y, Yin G, K-W T, Kolonin MG, Sun J, Arap W, Pasqualini R, K-A D. Bayesian mixture models for complex high dimensional count data in phage display experiments. Journal of the Royal Statistical Society: Series C (Applied Statistics) 56(2):139-52, 2007. e-Pub 2007.
194. Albitar M, Johnson M, Do KA, Day A, Jilani I, Pierce S, Estey E, Kantarjian H, Keating M, Verstovsek S, O'Brien S, Giles FJ. Levels of soluble HLA-I and beta2M in patients with acute myeloid leukemia and advanced myelodysplastic syndrome: association with clinical behavior and outcome of induction therapy. Leukemia 21(3):480-8, 2007. e-Pub 2007. PMID: 17215857.
195. Albitar M, Vose JM, Johnson MM, Do KA, Day A, Jilani I, Kantarjian H, Keating M, O'Brien SM, Verstovsek S, Armitage JO, Giles FJ. Clinical relevance of soluble HLA-I and beta2-microglobulin levels in non-Hodgkin's lymphoma and Hodgkin's disease. Leuk Res 31(2):139-45, 2007. e-Pub 2007. PMID: 16545870.
196. Efstathiou E, Troncoso P, Wen S, Do KA, Pettaway CA, Pisters LL, McDonnell TJ, Logothetis CJ. Initial modulation of the tumor microenvironment accounts for thalidomide activity in prostate cancer. Clin Cancer Res 13(4):1224-31, 2007. e-Pub 2007. PMID: 17317833.
197. Kundra V, Ng CS, Ma J, Bankson JA, Price RE, Cody DD, Do KA, Han L, Navone NM. In vivo imaging of prostate cancer involving bone in a mouse model. Prostate 67(1):50-60, 2007. e-Pub 2007. PMID: 17031813.
198. K-A D, McLachlan GJ, Bean R, Wen S. Gene shaving versus mixture models for the clustering of microarray gene expression data. Cancer Informatics 2:25-43, 2007. e-Pub 2007.
199. Busby JE, Kim SJ, Yazici S, Nakamura T, Kim JS, He J, Maya M, Wang X, Do KA, Fan D, Fidler IJ. Therapy of multidrug resistant human prostate tumors in the prostate of nude mice by simultaneous targeting of the epidermal growth factor receptor and vascular endothelial growth factor receptor on tumor-associated endothelial cells. Prostate 66(16):1788-98, 2006. e-Pub 2006. PMID: 17013882.
200. Wu X, Gu J, Dong Q, Huang M, Do KA, Hong WK, Spitz MR. Joint effect of mutagen sensitivity and insulin-like growth factors in predicting the risk of developing secondary primary tumors and tumor recurrence in patients with head and neck cancer. Clin Cancer Res 12(23):7194-201, 2006. e-Pub 2006. PMID: 17145846.
201. Tannir N, Jonasch E, Pagliaro LC, Mathew P, Siefker-Radtke A, Rhines L, Lin P, Tibbs R, Do KA, Lin SH, Tu SM. Pilot trial of bone-targeted therapy with zoledronate, thalidomide, and interferon-gamma for metastatic renal cell carcinoma. Cancer 107(3):497-505, 2006. e-Pub 2006. PMID: 16795067.
202. Esmaeli B, Amin S, Valero V, Adinin R, Arbuckle R, Banay R, Do KA, Rivera E. Prospective study of incidence and severity of epiphora and canalicular stenosis in patients with metastatic breast cancer receiving docetaxel. J Clin Oncol 24(22):3619-22, 2006. e-Pub 2006. PMID: 16877729.
203. Soliman AS, Wang X, Stanley JD, El-Ghawalby N, Bondy ML, Ezzat F, Soultan A, Abdel-Wahab M, Fathy O, Ebidi G, Abdel-Karim N, Do KA, Levin B, Hamilton SR, Abbruzzese JL. Geographical clustering of pancreatic cancers in the Northeast Nile Delta region of Egypt. Arch Environ Contam Toxicol 51(1):142-8, 2006. e-Pub 2006. PMID: 16453066.
204. Tsimberidou AM, Catovsky D, Schlette E, O'Brien S, Wierda WG, Kantarjian H, Garcia-Manero G, Wen S, Do KA, Lerner S, Keating MJ. Outcomes in patients with splenic marginal zone lymphoma and marginal zone lymphoma treated with rituximab with or without chemotherapy or chemotherapy alone. Cancer 107(1):125-35, 2006. e-Pub 2006. PMID: 16700034.
205. Spiess PE, Lee AK, Leibovici D, Wang X, Do KA, Pisters LL. Presalvage prostate-specific antigen (PSA) and PSA doubling time as predictors of biochemical failure of salvage cryotherapy in patients with locally recurrent prostate cancer after radiotherapy. Cancer 107(2):275-80, 2006. e-Pub 2006. PMID: 16770783.
206. Kim SJ, Uehara H, Yazici S, Busby JE, Nakamura T, He J, Maya M, Logothetis C, Mathew P, Wang X, Do KA, Fan D, Fidler IJ. Targeting platelet-derived growth factor receptor on endothelial cells of multidrug-resistant prostate cancer. J Natl Cancer Inst 98(11):783-93, 2006. e-Pub 2006. PMID: 16757703.
207. Tsimberidou AM, O'Brien S, Khouri I, Giles FJ, Kantarjian HM, Champlin R, Wen S, Do KA, Smith SC, Lerner S, Freireich EJ, Keating MJ. Clinical outcomes and prognostic factors in patients with Richter's syndrome treated with chemotherapy or chemoimmunotherapy with or without stem-cell transplantation. J Clin Oncol 24(15):2343-51, 2006. e-Pub 2006. PMID: 16710033.
208. Kolonin MG, Sun J, Do KA, Vidal CI, Ji Y, Baggerly KA, Pasqualini R, Arap W. Synchronous selection of homing peptides for multiple tissues by in vivo phage display. FASEB J 20(7):979-81, 2006. e-Pub 2006. PMID: 16581960.
209. Rosser CJ, Kamat AM, Wang X, Do KA, Naya Y, Hoover DC, Troncoso P, Sanches-Ortiz RF, Pisters LL. Biochemical disease-free survival in men younger than 60 years with prostate cancer treated with radical prostatectomy. Urology 67(4):769-73, 2006. e-Pub 2006. PMID: 16584762.
210. Spiess PE, Kassouf W, Brown G, Highshaw R, Wang X, Do KA, Kamat AM, Czerniak B, Dinney CP, Grossman HB. Immediate versus staged urethrectomy in patients at high risk of urethral recurrence: is there a benefit to either approach?. Urology 67(3):466-71, 2006. e-Pub 2006. PMID: 16527559.
211. Wierda W, O'Brien S, Faderl S, Ferrajoli A, Wang X, Do KA, Garcia-Manero G, Thomas D, Cortes J, Ravandi-Kashani F, Giles F, Lerner S, Kantarjian H, Keating M. A retrospective comparison of three sequential groups of patients with Recurrent/Refractory chronic lymphocytic leukemia treated with fludarabine-based regimens. Cancer 106(2):337-45, 2006. e-Pub 2006. PMID: 16353201.
212. Kolonin MG, Bover L, Sun J, Zurita AJ, Do KA, Lahdenranta J, Cardo-Vila M, Giordano RJ, Jaalouk DE, Ozawa MG, Moya CA, Souza GR, Staquicini FI, Kunyiasu A, Scudiero DA, Holbeck SL, Sausville EA, Arap W, Pasqualini R. Ligand-directed surface profiling of human cancer cells with combinatorial peptide libraries. Cancer Res 66(1):34-40, 2006. e-Pub 2006. PMID: 16397212.
213. Wang J, K-A D, Wen S, Tsavachidis S, McDonnell TJ, Logothetis C, Coombes KR. Merging microarray data, robust feature selection, and predicting prognosis in prostate cancer. Cancer Informatics 2:87-97, 2006. e-Pub 2006.
214. Faderl S, Do KA, Johnson MM, Keating M, O'Brien S, Jilani I, Ferrajoli A, Ravandi-Kashani F, Aguilar C, Dey A, Thomas DA, Giles FJ, Kantarjian HM, Albitar M. Angiogenic factors may have a different prognostic role in adult acute lymphoblastic leukemia. Blood 106(13):4303-7, 2005. e-Pub 2005. PMID: 16123221.
215. Strom SS, Wang X, Pettaway CA, Logothetis CJ, Yamamura Y, Do KA, Babaian RJ, Troncoso P. Obesity, weight gain, and risk of biochemical failure among prostate cancer patients following prostatectomy. Clin Cancer Res 11(19 Pt 1):6889-94, 2005. e-Pub 2005. PMID: 16203779.
216. Rosser CJ, Kamat AM, Wang X, Do KA, Sanchez-Ortiz RF, Kuban DA, Lee AK, Cheung R, Chichakli R, Pisters LL. Is patient age a factor in the occurrence of prostate-specific antigen bounce phenomenon after external beam radiotherapy for prostate cancer?. Urology 66(2):327-31, 2005. e-Pub 2005. PMID: 16040084.
217. Wierda W, O'Brien S, Wen S, Faderl S, Garcia-Manero G, Thomas D, Do KA, Cortes J, Koller C, Beran M, Ferrajoli A, Giles F, Lerner S, Albitar M, Kantarjian H, Keating M. Chemoimmunotherapy with fludarabine, cyclophosphamide, and rituximab for relapsed and refractory chronic lymphocytic leukemia. J Clin Oncol 23(18):4070-8, 2005. e-Pub 2005. PMID: 15767647.
218. Cho-Vega JH, Troncoso P, Do KA, Rago C, Wang X, Tsavachidis S, Medeiros LJ, Spurgers K, Logothetis C, McDonnell TJ. Combined laser capture microdissection and serial analysis of gene expression from human tissue samples. Mod Pathol 18(4):577-84, 2005. e-Pub 2005. PMID: 15529182.
219. Do K-A Mueller P, Tang F. A Bayesian mixture model for differential gene expression. Journal of the Royal Statistical Society, Series C-Applied Statistics 54(3):1-18, 2005. e-Pub 2005.
220. Leibovici D, Kamat AM, Do KA, Pettaway CA, Ng CS, Evans RB, Rodriguez-Bigas M, Skibber J, Wang X, Pisters LL. Transrectal ultrasound versus magnetic resonance imaging for detection of rectal wall invasion by prostate cancer. Prostate 62(1):101-4, 2005. e-Pub 2005. PMID: 15389800.
221. Do KA, Johnson MM, Lee JJ, Wu XF, Dong Q, Hong WK, Khuri FR, Spitz MR. Longitudinal study of smoking patterns in relation to the development of smoking-related secondary primary tumors in patients with upper aerodigestive tract malignancies. Cancer 101(12):2837-42, 2004. e-Pub 2004. PMID: 15536619.
222. Assikis VJ, Do KA, Wen S, Wang X, Cho-Vega JH, Brisbay S, Lopez R, Logothetis CJ, Troncoso P, Papandreou CN, McDonnell TJ. Clinical and biomarker correlates of androgen-independent, locally aggressive prostate cancer with limited metastatic potential. Clin Cancer Res 10(20):6770-8, 2004. e-Pub 2004. PMID: 15501953.
223. Albitar M, Do KA, Johnson MM, Giles FJ, Jilani I, O'Brien S, Cortes J, Thomas D, Rassenti LZ, Kipps TJ, Kantarjian HM, Keating M. Free circulating soluble CD52 as a tumor marker in chronic lymphocytic leukemia and its implication in therapy with anti-CD52 antibodies. Cancer 101(5):999-1008, 2004. e-Pub 2004. PMID: 15329909.
224. Wu X, Zhao H, Do KA, Johnson MM, Dong Q, Hong WK, Spitz MR. Serum levels of insulin growth factor (IGF-I) and IGF-binding protein predict risk of second primary tumors in patients with head and neck cancer. Clin Cancer Res 10(12 Pt 1):3988-95, 2004. e-Pub 2004. PMID: 15217929.
225. Giles FJ, Vose JM, Do KA, Johnson MM, Manshouri T, Bociek G, Bierman PJ, O'Brien SM, Kantarjian HM, Armitage JO, Albitar M. Clinical relevance of circulating angiogenic factors in patients with non-Hodgkin's lymphoma or Hodgkin's lymphoma. Leuk Res 28(6):595-604, 2004. e-Pub 2004. PMID: 15120936.
226. Pisters LL, Pettaway CA, Troncoso P, McDonnell TJ, Stephens LC, Wood CG, Do KA, Brisbay SM, Wang X, Hossan EA, Evans RB, Soto C, Jacobson MG, Parker K, Merritt JA, Steiner MS, Logothetis CJ. Evidence that transfer of functional p53 protein results in increased apoptosis in prostate cancer. Clin Cancer Res 10(8):2587-93, 2004. e-Pub 2004. PMID: 15102659.
227. Do KA, Aitken JF, Green AC, Martin NG. Analysis of melanoma onset: assessing familial aggregation by using estimating equations and fitting variance components via Bayesian random effects models. Twin Res 7(1):98-113, 2004. e-Pub 2004. PMID: 15053858.
228. Giles FJ, Vose JM, K-A D, Johnson MM, Manshouri T, Bociek G, Bierman PJ, O'Brien SM, Keating MJ, Kantarjian HM, Armitage JO, Albitar M. Circulating CD20 and CD52 in patients with non-Hodgkin's lymphoma or Hodgkin's disease. Br J Haematol 123(5):850-7, 2003. e-Pub 2003. PMID: 14632776.
229. Kuhnert PM, K-A D. Fitting genetic models to twin data with binary and ordered categorical responses: a comparison of structural equation modelling and Bayesian hierarchical models. Behav Genet 33(4):441-54, 2003. e-Pub 2003. PMID: 14574143.
230. Soliman AS, Wang X, DiGiovanni J, Eissa S, Morad M, Vulimiri S, Mahgoub KG, Johnston DA, K-A D, Seifeldin IA, Boffetta P, Bondy ML. Serum organochlorine levels and history of lactation in Egypt. Environ Res 92(2):110-7, 2003. e-Pub 2003. PMID: 12854690.
231. Manshouri T, K-A D, Wang X, Giles FJ, O'Brien SM, Saffer H, Thomas D, Jilani I, Kantarjian HM, Keating MJ, Albitar M. Circulating CD20 is detectable in the plasma of patients with chronic lymphocytic leukemia and is of prognostic significance. Blood 101(7):2507-13, 2003. e-Pub 2003. PMID: 12446458.
232. K-A D, Johnson MM, Doherty DA, Lee JJ, Wu XF, Dong Q, Hong WK, Khuri FR, Fu KK, Spitz MR. Second primary tumors in patients with upper aerodigestive tract cancers: joint effects of smoking and alcohol (United States). Cancer Causes Control 14:131-8, 2003. e-Pub 2003. PMID: 12749718.
233. Wierda WG, Johnson MM, K-A D, Manshouri T, Dey A, O'Brien S, Giles FJ, Kantarjian H, Thomas D, Faderl S, Lerner S, Keating M, Albitar M. Plasma interleukin 8 level predicts for survival in chronic lymphocytic leukemia. Br J Haematol 120(3):452-6, 2003. e-Pub 2003. PMID: 12580959.
234. Mintz PJ, Kim J, K-A D, Wang X, Zinner RG, Cristofanilli M, Arap MA, Hong WK, Troncoso P, Logothetis CJ, Pasqualini R, Arap W. Fingerprinting the circulating repertoire of antibodies from cancer patients. Nat Biotechnol 21(1):57-63, 2003. e-Pub 2003. PMID: 12496764.
235. K-A D. Biostatistical approaches for modeling longitudinal and event time data. Clin Cancer Res 8(8):2473-4, 2002. e-Pub 2002. PMID: 12171871.
236. Pu YS, K-A D, Luo W, Logothetis CJ, Lin SH. Enhanced suppression of prostate tumor growth by combining C-CAM1 gene therapy and angiogenesis inhibitor TNP-470. Anticancer Drugs 13(7):743-9, 2002. e-Pub 2002. PMID: 12187331.
237. Faderl S, Keating MJ, K-A D, Liang SY, Kantarjian HM, O'Brien S, Garcia-Manero G, Manshouri T, Albitar M. Expression profile of 11 proteins and their prognostic significance in patients with chronic lymphocytic leukemia (CLL). Leukemia 16:1045-52, 2002. e-Pub 2002. PMID: 12040436.
238. Wayne JD, Lauwers GY, Ikai I, Doherty DA, Belghiti J, Yamaoka Y, Regimbeau JM, Nagorney DM, K-A D, Ellis LM, Curley SA, Pollock RE, Vauthey JN. Preoperative predictors of survival after resection of small hepatocellular carcinomas. Ann Surg 235(5):722-30, 2002. e-Pub 2002. PMID: 11981219.
239. Fizazi K, Prow DM, K-A D, Wang X, Finn L, Kim J, Daliani D, Papandreou CN, Tu SM, Millikan RE, Pagliaro LC, Logothetis CJ, Amato RJ. Alternating dose-dense chemotherapy in patients with high volume disseminated non-seminomatous germ cell tumours. Br J Cancer 86(10):1555-60, 2002. e-Pub 2002. PMID: 12085204.
240. Vauthey JN, Abdalla EK, Doherty DA, Gertsch P, Fenstermacher MJ, Loyer EM, Lerut J, Materne R, Wang X, Encarnacion A, Herron D, Mathey C, Ferrari G, Charnsangavej C, K-A D, Denys A. Body surface area and body weight predict total liver volume in Western adults. Liver Transpl 8(3):233-40, 2002. e-Pub 2002. PMID: 11910568.
241. Vauthey JN, Lauwers GY, Esnaola NF, K-A D, Belghiti J, Mirza N, Curley SA, Ellis LM, Regimbeau JM, Rashid A, Cleary KR, Nagorney DM. Simplified staging for hepatocellular carcinoma. J Clin Oncol 20(6):1527-36, 2002. e-Pub 2002. PMID: 11896101.
242. Sample D, Wargovich M, Fischer SM, Inamdar N, Schwartz P, Wang X, K-A D, Sinicrope FA. A dose-finding study of aspirin for chemoprevention utilizing rectal mucosal prostaglandin E(2) levels as a biomarker. Cancer Epidemiol Biomarkers Prev 11(3):275-9, 2002. e-Pub 2002. PMID: 11895877.
243. Arap W, Kolonin MG, Trepel M, Lahdenranta J, Cardo-Vila M, Giordano RJ, Mintz PJ, Ardelt PU, Yao VJ, Vidal CI, Chen L, Flamm A, Valtanen H, Weavind LM, Hicks ME, Pollock RE, Botz GH, Bucana CD, Koivunen E, Cahill D, Troncoso P, Baggerly KA, Pentz RD, K-A D, Logothetis CJ, Pasqualini R. Steps toward mapping the human vasculature by phage display. Nat Med 8(2):121-7, 2002. e-Pub 2002. PMID: 11821895.
244. K-A D, McLachlan GJ, Bean R, Wen S. Some recent methods in clustering microarray gene expression data and applications. Computing Science and Statistics 34:28, 2002. e-Pub 2002.
245. Fizazi K, K-A D, Wang X, Finn L, Logothetis CJ, Amato RJ. A 20% dose reduction of the original CISCA/VB regimen allows better tolerance and similar survival rate in disseminated testicular non-seminomatous germ-cell tumors: final results of a phase III randomized trial. Ann Oncol 13(1):125-34, 2002. e-Pub 2002. PMID: 11863094.
246. Moore RJ, Doherty DA, K-A D, Chamberlain RM, Khuri FR. Racial disparity in survival of patients with squamous cell carcinoma of the oral cavity and pharynx. Ethn Health 6(3):165-77, 2001. e-Pub 2001. PMID: 11696928.
247. Ibrahim S, Keating M, K-A D, O'Brien S, Huh YO, Jilani I, Lerner S, Kantarjian HM, Albitar M. CD38 expression as an important prognostic factor in B-cell chronic lymphocytic leukemia. Blood 98(1):181-6, 2001. e-Pub 2001. PMID: 11418478.
248. Bilimoria MM, Lauwers GY, Doherty DA, Nagorney DM, Belghiti J, K-A D, Regimbeau JM, Ellis LM, Curley SA, Ikai I, Yamaoka Y, Vauthey JN. Underlying liver disease, not tumor factors, predicts long-term survival after resection of hepatocellular carcinoma. Arch Surg 136(5):528-35, 2001. e-Pub 2001. PMID: 11343543.
249. Chang DW, Langstein HN, Gupta A, De Monte F, K-A D, Wang X, Robb G. Reconstructive management of cranial base defects after tumor ablation with discussion. Plast Reconstr Surg 107(6):1346-57, 2001. e-Pub 2001. PMID: 11335798.
250. K-A D, Broom BM, Wang X. Importance bootstrap resampling for proportional hazards regression. Communications in Statistics - Theory and Methods 30(10):2173-88, 2001. e-Pub 2001.
251. Vauthey JN, Chaoui A, K-A D, Bilimoria MM, Fenstermacher MJ, Charnsangavej C, Hicks M, Alsfasser G, Lauwers G, Hawkins IF, Caridi J. Standardized measurement of the future liver remnant prior to extended liver resection: methodology and clinical associations. Surgery 127:512-9, 2000. e-Pub 2000. PMID: 10819059.
252. K-A D, Broom BM, Kuhnert P, Duffy DL, Todorov AA, Treloar SA, Martin NG. Genetic analysis of the age at menopause by using estimating equations and Bayesian random effects models. Stat Med 19:1217-35, 2000. e-Pub 2000. PMID: 10797518.
253. K-A D, Green A, Guthrie JR, Dudley EC, Burger HG, Dennerstein L. Longitudinal study of risk factors for coronary heart disease across the menopausal transition. Am J Epidemiol 151:584-93, 2000. e-Pub 2000. PMID: 10733040.
254. Treloar SA, K-A D, Pandeya N. Longitudinal Australian twin data and the age at menopause: Identifying predictors, genetic influences and more. International Journal of Behavioural Medicine 7:84-85, 2000. e-Pub 2000.
255. Kuhnert P, K-A D, McClure R. Visualising multivariate models with focus on MARS in an epidemiological case-control study. Computational Statistics and Data Analysis 34(3):371-386, 2000. e-Pub 2000.
256. S-M T, Kim J, Wang X, et al DK. Analysis of bone marrow supernatants from patients with prostate cancer implicates insulin-like growth factor binding protein 3 in prostate cancer progression. Submitted to Journal of Urology, 2000. e-Pub 2000.
257. Ryan PA, K-A D, Kay BH. Definition of Ross River virus vectors at Maroochy Shire, Australia. J Med Entomol 37:146-52, 2000. e-Pub 2000. PMID: 15218919.
258. Treloar SA, Sadrzadeh S, K-A D, Martin NG, Lambalk CB. Birth weight and age at menopause in Australian female twin pairs: exploration of the fetal origin hypothesis. Hum Reprod 15:55-9, 2000. e-Pub 2000. PMID: 10611188.
259. Bellamy N, Klestov A, Muirden K, Kuhnert P, K-A D, O'Gorman L, Martin N. Perceptual variation in categorizing individuals according to American College of Rheumatology classification criteria for hand, knee, and hip osteoarthritis (OA): observations based on an Australian Twin Registry study of OA. J Rheumatol 26:2654-8, 1999. e-Pub 1999. PMID: 10606378.
260. Bellamy N, Tesar P, Walker D, Klestov A, Muirden K, Kuhnert P, K-A D, O'Gorman L, Martin N. Perceptual variation in grading hand, hip and knee radiographs: observations based on an Australian twin registry study of osteoarthritis. Ann Rheum Dis 58:766-9, 1999. e-Pub 1999. PMID: 10577964.
261. Pratiwi R, Fletcher LM, Pyper WR, K-A D, Crawford DH, Powell LW, Jazwinska EC. Linkage disequilibrium analysis in Australian haemochromatosis patients indicates bipartite association with clinical expression. J Hepatol 31:39-46, 1999. e-Pub 1999. PMID: 10424281.
262. Ryan PA, K-A D, Kay BH. Spatial and temporal analysis of Ross River virus disease patterns at Maroochy Shire, Australia: association between human morbidity and mosquito (Diptera: Culicidae) abundance. J Med Entomol 36:515-21, 1999. e-Pub 1999. PMID: 10467782.
263. Treloar SA, K-A D, O'Connor VM, O'Connor DT, Yeo MA, Martin NG. Predictors of hysterectomy: an Australian study. Am J Obstet Gynecol 180:945-54, 1999. e-Pub 1999. PMID: 10203663.
264. Brandt ER, Hayman WA, Currie B, Carapetis J, Jackson DC, K-A D, Good MF. Functional analysis of IgA antibodies specific for a conserved epitope within the M protein of group A streptococci from Australian Aboriginal endemic communities. Int Immunol 11:569-76, 1999. e-Pub 1999. PMID: 10323210.
265. K-A D, Kirk K. Discriminant analysis of event-related potential curves using smoothed principal components. Biometrics 55:174-81, 1999. e-Pub 1999. PMID: 11318152.
266. Bellamy N, Klestov A, Muirden K, Kuhnert P, K-A D, O'Gorman L, Martin N. Perceptual variation in categorising individual peripheral joints for the presence or absence of osteoarthritis using a standard homunculus: observations based on an Australian Twin Registry Study of osteoarthritis. Inflammopharmacol 71:37-46, 1999. e-Pub 1999.
267. Treloar SA, K-A D, Martin NG. Genetic influences on the age at menopause (Commentary). Lancet 352:1084-85, 1999. e-Pub 1999.
268. K-A D, Treloar SA, Pandeya N, Purdie D, Green AC, Heath AC, Martin NG. Predictive factors of age at menopause in a large Australian twin study. Hum Biol 70:1073-91, 1998. e-Pub 1998. PMID: 9825597.
269. Jass JR, K-A D, Simms LA, Iino H, Wynter C, Pillay SP, Searle J, Radford-Smith G, Young J, Leggett B. Morphology of sporadic colorectal cancer with DNA replication errors. GUT 42:673-9, 1998. e-Pub 1998. PMID: 9659163.
270. Wright K, Wilson PJ, Kerr J, K-A D, Hurst T, Khoo SK, Ward B, Chenevix-Trench G. Frequent loss of heterozygosity and three critical regions on the short arm of chromosome 8 in ovarian adenocarcinomas. Oncogene 3(17):1185-88, 1998. e-Pub 1998.
271. Khan S, K-A D. Diagnostic value of P53 immunohistochemistry in Barrett's esophagus: an endoscopic study. Pathol 30:136-40, 1998. e-Pub 1998.
272. Carlstein E, K-A D, Hall P, Hesterberg T, Künsch H. Matched-block bootstrap for dependent data. Bernouilli 4:305-28, 1998. e-Pub 1998.
273. Brayne C, K-A D, Green L, Green AC. Is health protective behaviour in adolescents related to personality? A study of sun protective behaviour and the Eysenck Personality Questionnaire (junior version) in Queensland. Personality and Individual Differences 25:889-95, 1998. e-Pub 1998.
274. Wood ATA, K-A D, Broom BM. Sequential linearization of empirical likelihood constraints with application to U-statistics. Journal of Computational and Graphical Statistics 5:365-85, 1996. e-Pub 1996.
275. Chen Z, K-A D. Bootstrap method with saddlepoint approximations and importance resampling. Statistica Sinica 4:407-21, 1994. e-Pub 1994.
276. Booth JG, K-A D. Simple and efficient methods for constructing bootstrap confidence intervals. Computational Statistics 8:333-46, 1994. e-Pub 1994.
277. K-A D, Hall P. Distribution estimation using concomitants of order statistics, with application to Monte Carlo stimulation for the bootstrap. Journal of the Royal Statistical Society, Series B 54:1-14, 1992. e-Pub 1992.
278. Chen Z, K-A D. Importance resampling for the smoothed bootstrap. Journal of Statistical Computation and Simulation 42:107-24, 1992. e-Pub 1992.
279. K-A D. A simulation study of balanced and antithetic bootstrap resampling methods. Journal of Statistical Computation and Simulation 40:153-66, 1991. e-Pub 1991.
280. K-A Do, Hall P. Quasi-random resampling for the bootstrap. Statistics and Computing 1:13-22, 1991. e-Pub 1991.
281. K-A D, Hall P. On importance sampling for the bootstrap. Biometrika 78:161-167, 1991. e-Pub 1991.
282. Powell BL, Craig JB, Kute TE, Lyerly ES, Gregory W, K-A D, Contento MM, Capizzi RL. Correlation of the proliferative index of residual leukemia with outcome in patients treated with sequential high dose ara-C and asparaginase. Leukemia 4:316-20, 1990. e-Pub 1990. PMID: 2388477.
283. Weber SF, Peacock JE, K-A D, Cruz JM, Powell BL, Capizzi R. Interaction of granulocytopenia and construction activity as risk factors in nosocomial invasive filamentous fungal disease in patients with hematologic disorders: potential role of high-efficiency particulate air filtrating during construction activity. Infection Control and Hospital Epidemiology 11:235-42, 1990. e-Pub 1990.
284. K-A D, Solomon HS. A simulation study of Sylvester's problem in three dimensions. Journal of Applied Probability 23:509-13, 1986. e-Pub 1986.
285. K-A D, McLachlan GJ. Estimation of mixing proportions: a case study. Applied Statistics 33:134-40, 1984. e-Pub 1984.
286. Zhang X, Irajizad E, Hoffman K, Fahrmann J, Long JP, K-A D, Hanash S, Scheet P, MacDougall C. Addition and depletion of a dry bean prebiotic food source influences the gut microbiome and blood metabolome of obese patients with a history of colorectal neoplasia: the BE GONE trial. Gut.
287. Irajizad E, Tang T, Kenney A, Jody V, Dennison JB, Murage E, Long JP, Loftus M, Chabot J, Ana B, K-A D, Yu B, Wolpin B, Hanash S. Contribution of the microbiome to a metabolomic signature predictive of risk for pancreatic cancer. Cell Medicine.

Review Articles

1. Irajizad E, Fahrmann JF, Toumazis I, Vykoukal J, Dennison JB, Shen Y, Do KA, Ostrin EJ, Feng Z, Hanash S. Biomarker trajectory for earlier detection of lung cancer. EBioMedicine 108, 2024. e-Pub 2024. PMID: 39353277.
2. San Valentin EMD, Do KA, Yeung SJ, Reyes-Gibby CC. Attempts to Understand Oral Mucositis in Head and Neck Cancer Patients.in IJSM: Molecular Pathology, Diagnostics, and Therapeutics, 2023. Int J Mol Sci 24(23), 2023. e-Pub 2023. PMID: 38069314.
3. Hickey K, K-A D, Green A. Smoking and prostate cancer: a review. Epidemiol Rev 23(1):115-25, 2001. e-Pub 2001. PMID: 11588835.

Professional Educational Materials

1. K-A Do. Softwares Developed: FDA-Proteins, 2004.
2. K-A Do. Softwares Developed: BayesMix, 2003.
3. K-A Do. Softwares Developed: PhageDiff, 2002.
4. K-A Do. Softwares Developed: GeneClust, 2000.
5. K-A Do, K-A Do. Softwares developed by K-A Do’s team can be found at the following link: https://kimanhdomda.github.io/COSMIC/softwares/.

Other Articles

1. Khoshfekr Rudsari H, Khorami-Sarvestani S, Fahrmann JF, Long JP, Hanash S, Do KA, Irajizad E SMAGS-LASSO: A Novel Feature Selection Method for Sensitivity Maximization in Early Cancer Detection. Cancer Epidemiol Biomarkers Prev, 2025. PMID: 40996315.
2. Khoshfekr Rudsari H, Khorami-Sarvestani S, Fahrmann JF, Long JP, Hanash S, Do KA, Irajizad E SMAGS-LASSO: A Novel Feature Selection Method for Sensitivity Maximization in Early Cancer Detection. Cancer Epidemiol Biomarkers Prev, 2025. PMID: 40996315.
3. Do D, Asiaee A, Azinfar L, Li J, Liang H, Irajizad E, Do KA, Long JP AUPRC: a metric for evaluating the performance of in-silico perturbation methods in identifying differentially expressed genes, 2025. PMID: 40889115.
4. Saha S, Zhang L, Do K, B Peterson AC Bayesian compositional regression with flexible microbiome feature aggregation and selection, 2025.
5. Anfossi S, Darbaniyan F, Quinlan J, Calin S, Shimizu M, Chen M, Rausseo P, Winters M, Bogatenkova E, Do K, Martinez I, Li Z, Antal L, Olariu TR, Wistuba I, Calin GA MicroRNAs are enriched at COVID-19 genomic risk regions, and their blood levels correlate with the COVID-19 prognosis of cancer patients infected by SARS-CoV-2, 2024.
6. Ghasemi SM, Gu C, Fahrmann JF, Hanash S, Do K, Long JP, Irajizad E A Novel Sensitivity Maximization at a Given Specificity Method for Binary Classifications. To appear, Cancer Prevention Research, 2024, 2024.
7. Long JP, Yang Y, Shimizu S, Pham T, K-A D Causal models and prediction in cell line perturbation experiments.
8. Gu C, Cai Y, Ghasemi SM, Farhmann JF, Long JP, Katayama H, Wu C, Vykouval J, Dennison JB, Hanash S, K-A D, Irajizad E Graph neural network using Protein-protein-interaction for Enhancing Protein Identification.
9. K-A Do, Broom BM, Wang X Importance bootstrap resampling for proportional hazards regression. Computing Science and Statistics 32:405-409, 2000.
10. K-A Do, Wang X Bayesian mixed effects models using BUGS to quantify genetic variance components for normal quantitative traits and age at onset in nuclear families. Genetic Analysis Workshop 12 2:117-121, 2000.
11. K-A Do A numerical study of the matched-block bootstrap for dependent data. Proceedings of the 27th Symposium on the Interface of Computing Science and Statistics, Pittsburgh, Pennsylvania:425-429, 1994.
12. Do K-A Kokic P Bootstrap confidence interval estimation for model-based surveys. Proceedings of the 24th Symposium on the Interface of Computing Science and Statistics, College Station,Texas:511-515, 1992.
13. Tridgell A, Miller B, K-A Do Alternative pre-processing techniques for discrete Hidden Markov model phoneme recognition. Proceedings of the 1992 International Conference on Speech Recognition, Alberta, Canada, 1992.
14. K-A Do Quasi-random resampling for the bootstrap. Proceedings of the 24th Symposium on the Interface of Computing Science and Statistics, Seattle, Washington:297-300, 1991.
15. K-A Do A sequential combination of truncated and censored sampling with recapture debugging. Statistics Research Section Technical Report DSTR-023-90, ANU, 1990.
16. K-A Do On recapture debugging for estimation of population size and confidence bounds. Statistics Research Section Technical Report CSGTR-012-90, ANU, 1990.
17. Khoshfekr Rudsari H, Tseng B, Zhu H, Song L, Gu C, Roy A, Irajizad E, Butner J, JamesLong, Do AK Digital Twins in Healthcare: A Comprehensive Review and Future Directions. To appear in Frontiers (2025).
18. Saha S, Zhang L, K-A D, Peterson C Bayesian compositional regression with flexible microbiome feature aggregation and selection. Submitted to Biometrics, 2024.
19. Irajizad E, Fahrmann JF, Vykoukal J, Dennison JB, Spencer R, Garrett C, Barón A, Toumazis I, Atkar-Khattra S, Lam S, Long JP, K-A D, Hanash S, Ostrin EJ A Blood-Based Biomarker for Reclassifying Malignancy Risk in Indeterminate Pulmonary Nodules Detected in Lung Cancer Screening. Submitted to Chest.
20. Ghasemi SM, Gu C, Farhmann JF, Hanash S, K-A D, Long JP, Irajizad E A novel sensitivity maximization at a given specificity method for binary classifications. To appear, Cancer Prevention Research, 2024.

Book Chapters

1. Huang X, K-A Do. Commentary on: A novel case-control design to estimate the extent of overdiagnosis of breast cancer due to organised population-based mammography screening. In: Breast Diseases: A Year Book Quarterly, 211-214, 2015.
2. Baladandauthapani V, Wang X, Mallick BK, K-A Do. Bayesian Functional Mixed Models for Survival Responses with Application to Prostate Cancer. In: Applied Statistics in Biomedicine and Clinical Trials Design ICSA Book Series in Statistics. Springer, Cham, 35-59, 2015.
3. Wang W, Baladandayuthapani V, Broom BM, K-A Do. Bayesian graphical models for integrating multi-platform genomics data. Methods for the analysis of copy number data in cancer research. In: Advances in Statistical Bioinformatics: Models and Integrative Inferences for High-Throughput Data. Cambridge University Press, 2013.
4. Broom BM, K-A Do, Bondy M, Thompson P, Coombes K. Methods for the analysis of copy number data in cancer research. In: Advances in Statistical Bioinformatics: Models and Integrative Inferences for High-Throughput Data. Cambridge University Press, 2013.
5. Wang W, Baladandayuthapani V, Broom BM, K-A Do. Bayesian graphical models for multi-platform high-dimensional data. In: Advances in Statistical Bioinformatics: Models and Integrative Inference for High-Throughput Data. Cambridge University Press, 2013.
6. Broom BM, Rinsurongkawong W, Pusztai L, Do KA. Building networks with microarray data. In: Methods Mol Biol, 315-43, 2010.
7. Jeong J, Vannuci M, K-A Do, Broom BM, Kim S, Sha N, Tadesse M, Tan K, Pusztai L. Gene Selection for the identification of biomarkers in high-throughput data. In: Bayesian Modeling in Bioinformatics, 2009.
8. K-A Do, Mueller PM, Bandyopadhya R, Baggerley K. A Bayesian mixture model for protein biomarker discovery. In: Bayesian Modeling in Bioinformatics. Chapman & Hall / CRC Press, 2008.
9. K-A D, Broom BM. Statistical methods for biomarker discovery using mass spectometry. In: Statistical Advances in the Biomedical Sciences: Clinical Trials, Epidemiology, Survival Analysis, and Bioinformatics. Wiley Publishers, 465-486, 2008.
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