logomakr_7qacx3

Publications

  1. Chi, F, Griffiths, JI, Nath, A, Bild, AH. Paradoxical cancer cell proliferation after FGFR inhibition through decreased p21 signaling in FGFR1-amplified breast cancer cells. Breast Cancer Res. 2024;26 (1):54. doi: 10.1186/s13058-024-01808-7. PubMed PMID:38553760 PubMed Central PMC10979625.
  2. Farmaki, E, Nath, A, Emond, R, Karimi, KL, Grolmusz, VK, Cosgrove, PA et al.. ONC201/TIC10 enhances durability of mTOR inhibitor everolimus in metastatic ER+ breast cancer. Elife. 2023;12 :. doi: 10.7554/eLife.85898. PubMed PMID:37772709 PubMed Central PMC10541180.
  3. Liu, X, Griffiths, JI, Bishara, I, Liu, J, Bild, AH, Chang, JT et al.. Phylogenetic inference from single-cell RNA-seq data. Sci Rep. 2023;13 (1):12854. doi: 10.1038/s41598-023-39995-6. PubMed PMID:37553438 PubMed Central PMC10409753.
  4. Emond, R, Griffiths, JI, Grolmusz, VK, Nath, A, Chen, J, Medina, EF et al.. Cell facilitation promotes growth and survival under drug pressure in breast cancer. Nat Commun. 2023;14 (1):3851. doi: 10.1038/s41467-023-39242-6. PubMed PMID:37386030 PubMed Central PMC10310817.
  5. Burdett, NL, Willis, MO, Alsop, K, Hunt, AL, Pandey, A, Hamilton, PT et al.. Multiomic analysis of homologous recombination-deficient end-stage high-grade serous ovarian cancer. Nat Genet. 2023;55 (3):437-450. doi: 10.1038/s41588-023-01320-2. PubMed PMID:36849657 .
  6. Bishara, I, Chen, J, Griffiths, JI, Bild, AH, Nath, A. A machine learning framework for scRNA-seq UMI threshold optimization and accurate classification of cell types. Front Genet. 2022;13 :982019. doi: 10.3389/fgene.2022.982019. PubMed PMID:36506328 PubMed Central PMC9732024.
  7. Zhang, IY, Liu, S, Zhang, L, Liang, R, Fang, Q, Zhao, J et al.. RAGE ablation attenuates glioma progression and enhances tumor immune responses by suppressing galectin-3 expression. Neuro Oncol. 2023;25 (5):886-898. doi: 10.1093/neuonc/noac250. PubMed PMID:36394567 PubMed Central PMC10158202.
  8. Nath, A, Cosgrove, PA, Chang, JT, Bild, AH. Predicting clinical response to everolimus in ER+ breast cancers using machine-learning. Front Mol Biosci. 2022;9 :981962. doi: 10.3389/fmolb.2022.981962. PubMed PMID:36304922 PubMed Central PMC9592823.
  9. Nath, A, Cohen, AL, Bild, AH. ENDORSE: a prognostic model for endocrine therapy in estrogen-receptor-positive breast cancers. Mol Syst Biol. 2022;18 (6):e10558. doi: 10.15252/msb.202110558. PubMed PMID:35671075 PubMed Central PMC9172932.
  10. Liu, S, Song, Y, Zhang, IY, Zhang, L, Gao, H, Su, Y et al.. RAGE Inhibitors as Alternatives to Dexamethasone for Managing Cerebral Edema Following Brain Tumor Surgery. Neurotherapeutics. 2022;19 (2):635-648. doi: 10.1007/s13311-022-01207-w. PubMed PMID:35226341 PubMed Central PMC9226224.
  11. Mori, H, Saeki, K, Chang, G, Wang, J, Wu, X, Hsu, PY et al.. Influence of Estrogen Treatment on ESR1+ and ESR1- Cells in ER+ Breast Cancer: Insights from Single-Cell Analysis of Patient-Derived Xenograft Models. Cancers (Basel). 2021;13 (24):. doi: 10.3390/cancers13246375. PubMed PMID:34944995 PubMed Central PMC8699443.
  12. Pishas, KI, Cowley, KJ, Pandey, A, Hoang, T, Beach, JA, Luu, J et al.. Phenotypic Consequences of SLC25A40-ABCB1 Fusions beyond Drug Resistance in High-Grade Serous Ovarian Cancer. Cancers (Basel). 2021;13 (22):. doi: 10.3390/cancers13225644. PubMed PMID:34830797 PubMed Central PMC8616176.
  13. Griffiths, JI, Chen, J, Cosgrove, PA, O'Dea, A, Sharma, P, Ma, C et al.. Serial single-cell genomics reveals convergent subclonal evolution of resistance as early-stage breast cancer patients progress on endocrine plus CDK4/6 therapy. Nat Cancer. 2021;2 (6):658-671. doi: 10.1038/s43018-021-00215-7. PubMed PMID:34712959 PubMed Central PMC8547038.
  14. Huang, X, Qiao, Y, Brady, SW, Factor, RE, Downs-Kelly, E, Farrell, A et al.. Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies. Genome Med. 2021;13 (1):170. doi: 10.1186/s13073-021-00989-6. PubMed PMID:34711268 PubMed Central PMC8555066.
  15. Piccolo, SR, Ence, ZE, Anderson, EC, Chang, JT, Bild, AH. Simplifying the development of portable, scalable, and reproducible workflows. Elife. 2021;10 :. doi: 10.7554/eLife.71069. PubMed PMID:34643507 PubMed Central PMC8514239.
  16. McQuerry, JA, Chen, J, Chang, JT, Bild, AH. Tepoxalin increases chemotherapy efficacy in drug-resistant breast cancer cells overexpressing the multidrug transporter gene ABCB1. Transl Oncol. 2021;14 (10):101181. doi: 10.1016/j.tranon.2021.101181. PubMed PMID:34298440 PubMed Central PMC8322466.
  17. Nath, A, Cosgrove, PA, Mirsafian, H, Christie, EL, Pflieger, L, Copeland, B et al.. Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer. Nat Commun. 2021;12 (1):3039. doi: 10.1038/s41467-021-23171-3. PubMed PMID:34031395 PubMed Central PMC8144406.
  18. Roosan, MR, Mambetsariev, I, Pharaon, R, Fricke, J, Husain, H, Reckamp, KL et al.. Usefulness of Circulating Tumor DNA in Identifying Somatic Mutations and Tracking Tumor Evolution in Patients With Non-small Cell Lung Cancer. Chest. 2021;160 (3):1095-1107. doi: 10.1016/j.chest.2021.04.016. PubMed PMID:33878340 PubMed Central PMC8449001.
  19. Liu, X, Gosline, SJC, Pflieger, LT, Wallet, P, Iyer, A, Guinney, J et al.. Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data. Brief Bioinform. 2021;22 (5):. doi: 10.1093/bib/bbab039. PubMed PMID:33681983 PubMed Central PMC8536868.
  20. Nath, A, Bild, AH. Leveraging Single-Cell Approaches in Cancer Precision Medicine. Trends Cancer. 2021;7 (4):359-372. doi: 10.1016/j.trecan.2021.01.007. PubMed PMID:33563578 PubMed Central PMC7969443.
  21. El-Chaar, NN, Smith, TE, Shrestha, G, Piccolo, SR, Harper, MK, Van Wagoner, RM et al.. Topsentinol L Trisulfate, a Marine Natural Product That Targets Basal-like and Claudin-Low Breast Cancers. Mar Drugs. 2021;19 (1):. doi: 10.3390/md19010041. PubMed PMID:33477536 PubMed Central PMC7831112.
  22. Reckamp, KL, McQuerry, JA, Mambetsariev, I, Pharaon, R, Yost, SE, Fricke, J et al.. Co-stimulatory and co-inhibitory immune markers in solid tumors with MET alterations. Future Sci OA. 2020;7 (2):FSO662. doi: 10.2144/fsoa-2020-0159. PubMed PMID:33437521 PubMed Central PMC7787173.
  23. Haynes, K, Yau, C, Bild, A, Laughney, A, Morsut, L, Yang, X et al.. How Has the COVID-19 Pandemic Changed How You Will Approach Research and Lab Work in the Future?. Cell Syst. 2020;11 (6):550-554. doi: 10.1016/j.cels.2020.11.011. PubMed PMID:33333028 PubMed Central PMC7833873.
  24. Chi, F, Liu, J, Brady, SW, Cosgrove, PA, Nath, A, McQuerry, JA et al.. A `one-two punch' therapy strategy to target chemoresistance in estrogen receptor positive breast cancer. Transl Oncol. 2021;14 (1):100946. doi: 10.1016/j.tranon.2020.100946. PubMed PMID:33221681 PubMed Central PMC7689336.
  25. Griffiths, JI, Wallet, P, Pflieger, LT, Stenehjem, D, Liu, X, Cosgrove, PA et al.. Circulating immune cell phenotype dynamics reflect the strength of tumor-immune cell interactions in patients during immunotherapy. Proc Natl Acad Sci U S A. 2020;117 (27):16072-16082. doi: 10.1073/pnas.1918937117. PubMed PMID:32571915 PubMed Central PMC7355015.
  26. Grolmusz, VK, Chen, J, Emond, R, Cosgrove, PA, Pflieger, L, Nath, A et al.. Exploiting collateral sensitivity controls growth of mixed culture of sensitive and resistant cells and decreases selection for resistant cells in a cell line model. Cancer Cell Int. 2020;20 :253. doi: 10.1186/s12935-020-01337-1. PubMed PMID:32565737 PubMed Central PMC7301982.
  27. Zhao, D, Mambetsariev, I, Li, H, Chen, C, Fricke, J, Fann, P et al.. Association of molecular characteristics with survival in advanced non-small cell lung cancer patients treated with checkpoint inhibitors. Lung Cancer. 2020;146 :174-181. doi: 10.1016/j.lungcan.2020.05.025. PubMed PMID:32554069 PubMed Central PMC8158847.
  28. Griffiths, JI, Cohen, AL, Jones, V, Salgia, R, Chang, JT, Bild, AH et al.. Opportunities for improving cancer treatment using systems biology. Curr Opin Syst Biol. 2019;17 :41-50. doi: 10.1016/j.coisb.2019.10.018. PubMed PMID:32518857 PubMed Central PMC7282416.
  29. Mambetsariev, I, Wang, Y, Chen, C, Nadaf, S, Pharaon, R, Fricke, J et al.. Precision medicine and actionable alterations in lung cancer: A single institution experience. PLoS One. 2020;15 (2):e0228188. doi: 10.1371/journal.pone.0228188. PubMed PMID:32045431 PubMed Central PMC7012442.
  30. Kalvala, A, Wallet, P, Yang, L, Wang, C, Li, H, Nam, A et al.. Phenotypic Switching of Naïve T Cells to Immune-Suppressive Treg-Like Cells by Mutant KRAS. J Clin Med. 2019;8 (10):. doi: 10.3390/jcm8101726. PubMed PMID:31635338 PubMed Central PMC6832522.
  31. McQuerry, JA, Jenkins, DF, Yost, SE, Zhang, Y, Schmolze, D, Johnson, WE et al.. Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes. BMC Cancer. 2019;19 (1):881. doi: 10.1186/s12885-019-6052-z. PubMed PMID:31488082 PubMed Central PMC6727561.
  32. Ward Rashidi, MR, Mehta, P, Bregenzer, M, Raghavan, S, Fleck, EM, Horst, EN et al.. Engineered 3D Model of Cancer Stem Cell Enrichment and Chemoresistance. Neoplasia. 2019;21 (8):822-836. doi: 10.1016/j.neo.2019.06.005. PubMed PMID:31299607 PubMed Central PMC6624324.
  33. Yoo, JH, Brady, SW, Acosta-Alvarez, L, Rogers, A, Peng, J, Sorensen, LK et al.. The Small GTPase ARF6 Activates PI3K in Melanoma to Induce a Prometastatic State. Cancer Res. 2019;79 (11):2892-2908. doi: 10.1158/0008-5472.CAN-18-3026. PubMed PMID:31048499 PubMed Central PMC7197377.
  34. Christie, EL, Pattnaik, S, Beach, J, Copeland, A, Rashoo, N, Fereday, S et al.. Multiple ABCB1 transcriptional fusions in drug resistant high-grade serous ovarian and breast cancer. Nat Commun. 2019;10 (1):1295. doi: 10.1038/s41467-019-09312-9. PubMed PMID:30894541 PubMed Central PMC6426934.
  35. Chefetz, I, Grimley, E, Yang, K, Hong, L, Vinogradova, EV, Suciu, R et al.. A Pan-ALDH1A Inhibitor Induces Necroptosis in Ovarian Cancer Stem-like Cells. Cell Rep. 2019;26 (11):3061-3075.e6. doi: 10.1016/j.celrep.2019.02.032. PubMed PMID:30865894 PubMed Central PMC7061440.
  36. Bild, A, Teo, JL, Kahn, M. Enhanced Kat3A/Catenin transcription: a common mechanism of therapeutic resistance. Cancer Drug Resist. 2019;2 (3):917-932. doi: 10.20517/cdr.2019.32. PubMed PMID:32426696 PubMed Central PMC7234864.
  37. Brady, SW, McQuerry, JA, Qiao, Y, Piccolo, SR, Shrestha, G, Jenkins, DF et al.. Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes. Nat Commun. 2018;9 (1):572. doi: 10.1038/s41467-017-02383-6. PubMed PMID:29402882 PubMed Central PMC5799176.
  38. Brady, SW, McQuerry, JA, Qiao, Y, Piccolo, SR, Shrestha, G, Jenkins, DF et al.. Combating subclonal evolution of resistant cancer phenotypes. Nat Commun. 2017;8 (1):1231. doi: 10.1038/s41467-017-01174-3. PubMed PMID:29093439 PubMed Central PMC5666005.
  39. McQuerry, JA, Chang, JT, Bowtell, DDL, Cohen, A, Bild, AH. Mechanisms and clinical implications of tumor heterogeneity and convergence on recurrent phenotypes. J Mol Med (Berl). 2017;95 (11):1167-1178. doi: 10.1007/s00109-017-1587-4. PubMed PMID:28871446 PubMed Central PMC6296823.
  40. Rahman, M, MacNeil, SM, Jenkins, DF, Shrestha, G, Wyatt, SR, McQuerry, JA et al.. Activity of distinct growth factor receptor network components in breast tumors uncovers two biologically relevant subtypes. Genome Med. 2017;9 (1):40. doi: 10.1186/s13073-017-0429-x. PubMed PMID:28446242 PubMed Central PMC5406893.
  41. Cohen, AL, Neumayer, L, Boucher, K, Factor, RE, Shrestha, G, Wade, M et al.. Window-of-Opportunity Study of Valproic Acid in Breast Cancer Testing a Gene Expression Biomarker. JCO Precis Oncol. 2017;1 :. doi: 10.1200/PO.16.00011. PubMed PMID:32913974 PubMed Central PMC7446454.
  42. Lam, S, Mandrekar, SJ, Gesthalter, Y, Allen Ziegler, KL, Seisler, DK, Midthun, DE et al.. A Randomized Phase IIb Trial of myo-Inositol in Smokers with Bronchial Dysplasia. Cancer Prev Res (Phila). 2016;9 (12):906-914. doi: 10.1158/1940-6207.CAPR-15-0254. PubMed PMID:27658890 PubMed Central PMC5136333.
  43. Shrestha, G, MacNeil, SM, McQuerry, JA, Jenkins, DF, Sharma, S, Bild, AH et al.. The value of genomics in dissecting the RAS-network and in guiding therapeutics for RAS-driven cancers. Semin Cell Dev Biol. 2016;58 :108-17. doi: 10.1016/j.semcdb.2016.06.012. PubMed PMID:27338857 PubMed Central PMC5951171.
  44. Piccolo, SR, Hoffman, LM, Conner, T, Shrestha, G, Cohen, AL, Marks, JR et al.. Integrative analyses reveal signaling pathways underlying familial breast cancer susceptibility. Mol Syst Biol. 2016;12 (3):860. doi: 10.15252/msb.20156506. PubMed PMID:26969729 PubMed Central PMC4812528.
  45. Piccolo, SR, Andrulis, IL, Cohen, AL, Conner, T, Moos, PJ, Spira, AE et al.. Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility. BMC Med Genomics. 2015;8 :72. doi: 10.1186/s12920-015-0145-6. PubMed PMID:26538066 PubMed Central PMC4634735.
  46. Rahman, M, Jackson, LK, Johnson, WE, Li, DY, Bild, AH, Piccolo, SR et al.. Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results. Bioinformatics. 2015;31 (22):3666-72. doi: 10.1093/bioinformatics/btv377. PubMed PMID:26209429 PubMed Central PMC4804769.
  47. MacNeil, SM, Johnson, WE, Li, DY, Piccolo, SR, Bild, AH. Inferring pathway dysregulation in cancers from multiple types of omic data. Genome Med. 2015;7 (1):61. doi: 10.1186/s13073-015-0189-4. PubMed PMID:26170901 PubMed Central PMC4499940.
  48. Shen, Y, Rahman, M, Piccolo, SR, Gusenleitner, D, El-Chaar, NN, Cheng, L et al.. ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. Bioinformatics. 2015;31 (11):1745-53. doi: 10.1093/bioinformatics/btv031. PubMed PMID:25617415 PubMed Central PMC4443674.
  49. El-Chaar, NN, Piccolo, SR, Boucher, KM, Cohen, AL, Chang, JT, Moos, PJ et al.. Genomic classification of the RAS network identifies a personalized treatment strategy for lung cancer. Mol Oncol. 2014;8 (7):1339-54. doi: 10.1016/j.molonc.2014.05.005. PubMed PMID:24908424 PubMed Central PMC4450766.
  50. Zhang, H, Cohen, AL, Krishnakumar, S, Wapnir, IL, Veeriah, S, Deng, G et al.. Patient-derived xenografts of triple-negative breast cancer reproduce molecular features of patient tumors and respond to mTOR inhibition. Breast Cancer Res. 2014;16 (2):R36. doi: 10.1186/bcr3640. PubMed PMID:24708766 PubMed Central PMC4053092.
  51. Bild, AH, Chang, JT, Johnson, WE, Piccolo, SR. A field guide to genomics research. PLoS Biol. 2014;12 (1):e1001744. doi: 10.1371/journal.pbio.1001744. PubMed PMID:24409093 PubMed Central PMC3883637.
  52. Piccolo, SR, Withers, MR, Francis, OE, Bild, AH, Johnson, WE. Multiplatform single-sample estimates of transcriptional activation. Proc Natl Acad Sci U S A. 2013;110 (44):17778-83. doi: 10.1073/pnas.1305823110. PubMed PMID:24128763 PubMed Central PMC3816418.
  53. Cohen, AL, Piccolo, SR, Cheng, L, Soldi, R, Han, B, Johnson, WE et al.. Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers. BMC Med Genomics. 2013;6 :35. doi: 10.1186/1755-8794-6-35. PubMed PMID:24079712 PubMed Central PMC3850967.
  54. Steiling, K, van den Berge, M, Hijazi, K, Florido, R, Campbell, J, Liu, G et al.. A dynamic bronchial airway gene expression signature of chronic obstructive pulmonary disease and lung function impairment. Am J Respir Crit Care Med. 2013;187 (9):933-42. doi: 10.1164/rccm.201208-1449OC. PubMed PMID:23471465 PubMed Central PMC3707363.
  55. Beane, J, Cheng, L, Soldi, R, Zhang, X, Liu, G, Anderlind, C et al.. SIRT1 pathway dysregulation in the smoke-exposed airway epithelium and lung tumor tissue. Cancer Res. 2012;72 (22):5702-11. doi: 10.1158/0008-5472.CAN-12-1043. PubMed PMID:22986747 PubMed Central PMC4053174.
  56. Piccolo, SR, Sun, Y, Campbell, JD, Lenburg, ME, Bild, AH, Johnson, WE et al.. A single-sample microarray normalization method to facilitate personalized-medicine workflows. Genomics. 2012;100 (6):337-44. doi: 10.1016/j.ygeno.2012.08.003. PubMed PMID:22959562 PubMed Central PMC3508193.
  57. Poerschke, RL, Franklin, MR, Bild, AH, Moos, PJ. Major differences among chemopreventive organoselenocompounds in the sustained elevation of cytoprotective genes. J Biochem Mol Toxicol. 2012;26 (9):344-53. doi: 10.1002/jbt.21427. PubMed PMID:22807314 PubMed Central PMC4551423.
  58. Cohen, AL, Soldi, R, Zhang, H, Gustafson, AM, Wilcox, R, Welm, BE et al.. A pharmacogenomic method for individualized prediction of drug sensitivity. Mol Syst Biol. 2011;7 :513. doi: 10.1038/msb.2011.47. PubMed PMID:21772261 PubMed Central PMC3159972.
  59. Potti, A, Mukherjee, S, Petersen, R, Dressman, HK, Bild, A, Koontz, J et al.. Retraction: A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med 2006;355:570-80. N Engl J Med. 2011;364 (12):1176. doi: 10.1056/NEJMc1101915. PubMed PMID:21366430 .
  60. Potti, A, Dressman, HK, Bild, A, Riedel, RF, Chan, G, Sayer, R et al.. Retraction: Genomic signatures to guide the use of chemotherapeutics. Nat Med. 2011;17 (1):135. doi: 10.1038/nm0111-135. PubMed PMID:21217686 .
  61. Gustafson, AM, Soldi, R, Anderlind, C, Scholand, MB, Qian, J, Zhang, X et al.. Airway PI3K pathway activation is an early and reversible event in lung cancer development. Sci Transl Med. 2010;2 (26):26ra25. doi: 10.1126/scitranslmed.3000251. PubMed PMID:20375364 PubMed Central PMC3694402.
  62. Tejpar, S, Bertagnolli, M, Bosman, F, Lenz, HJ, Garraway, L, Waldman, F et al.. Prognostic and predictive biomarkers in resected colon cancer: current status and future perspectives for integrating genomics into biomarker discovery. Oncologist. 2010;15 (4):390-404. doi: 10.1634/theoncologist.2009-0233. PubMed PMID:20350999 PubMed Central PMC3227961.
  63. Bild, AH, Parker, JS, Gustafson, AM, Acharya, CR, Hoadley, KA, Anders, C et al.. An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer. Breast Cancer Res. 2009;11 (4):R55. doi: 10.1186/bcr2344. PubMed PMID:19638211 PubMed Central PMC2750116.
  64. Chang, JT, Carvalho, C, Mori, S, Bild, AH, Gatza, ML, Wang, Q et al.. A genomic strategy to elucidate modules of oncogenic pathway signaling networks. Mol Cell. 2009;34 (1):104-14. doi: 10.1016/j.molcel.2009.02.030. PubMed PMID:19362539 PubMed Central PMC2694616.
  65. Mori, S, Rempel, RE, Chang, JT, Yao, G, Lagoo, AS, Potti, A et al.. Utilization of pathway signatures to reveal distinct types of B lymphoma in the Emicro-myc model and human diffuse large B-cell lymphoma. Cancer Res. 2008;68 (20):8525-34. doi: 10.1158/0008-5472.CAN-08-1329. PubMed PMID:18922927 PubMed Central PMC3617051.
  66. Dressman, HK, Berchuck, A, Chan, G, Zhai, J, Bild, A, Sayer, R et al.. An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer. J Clin Oncol. 2007;25 (5):517-25. doi: 10.1200/JCO.2006.06.3743. PubMed PMID:17290060 .
  67. Dressman, HK, Bild, A, Garst, J, Harpole, D Jr, Potti, A. Genomic signatures in non-small-cell lung cancer: targeting the targeted therapies. Curr Oncol Rep. 2006;8 (4):252-7. doi: 10.1007/s11912-006-0029-1. PubMed PMID:17254524 .
  68. Potti, A, Dressman, HK, Bild, A, Riedel, RF, Chan, G, Sayer, R et al.. Genomic signatures to guide the use of chemotherapeutics. Nat Med. 2006;12 (11):1294-300. doi: 10.1038/nm1491. PubMed PMID:17057710 .
  69. Bild, AH, Potti, A, Nevins, JR. Linking oncogenic pathways with therapeutic opportunities. Nat Rev Cancer. 2006;6 (9):735-41. doi: 10.1038/nrc1976. PubMed PMID:16915294 .
  70. Potti, A, Mukherjee, S, Petersen, R, Dressman, HK, Bild, A, Koontz, J et al.. A genomic strategy to refine prognosis in early-stage non-small-cell lung cancer. N Engl J Med. 2006;355 (6):570-80. doi: 10.1056/NEJMoa060467. PubMed PMID:16899777 .
  71. Edelman, E, Porrello, A, Guinney, J, Balakumaran, B, Bild, A, Febbo, PG et al.. Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles. Bioinformatics. 2006;22 (14):e108-16. doi: 10.1093/bioinformatics/btl231. PubMed PMID:16873460 .
  72. Dressman, HK, Hans, C, Bild, A, Olson, JA, Rosen, E, Marcom, PK et al.. Gene expression profiles of multiple breast cancer phenotypes and response to neoadjuvant chemotherapy. Clin Cancer Res. 2006;12 (3 Pt 1):819-26. doi: 10.1158/1078-0432.CCR-05-1447. PubMed PMID:16467094 .
  73. Bild, AH, Yao, G, Chang, JT, Wang, Q, Potti, A, Chasse, D et al.. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature. 2006;439 (7074):353-7. doi: 10.1038/nature04296. PubMed PMID:16273092 .
  74. Potti, A, Bild, A, Dressman, HK, Lewis, DA, Nevins, JR, Ortel, TL et al.. Gene-expression patterns predict phenotypes of immune-mediated thrombosis. Blood. 2006;107 (4):1391-6. doi: 10.1182/blood-2005-07-2669. PubMed PMID:16263789 PubMed Central PMC1895419.
  75. Bild, A, Febbo, PG. Application of a priori established gene sets to discover biologically important differential expression in microarray data. Proc Natl Acad Sci U S A. 2005;102 (43):15278-9. doi: 10.1073/pnas.0507477102. PubMed PMID:16230612 PubMed Central PMC1266131.
  76. Delong, M, Yao, G, Wang, Q, Dobra, A, Black, EP, Chang, JT et al.. DIG--a system for gene annotation and functional discovery. Bioinformatics. 2005;21 (13):2957-9. doi: 10.1093/bioinformatics/bti467. PubMed PMID:15870167 .
  77. Pittman, J, Huang, E, Dressman, H, Horng, CF, Cheng, SH, Tsou, MH et al.. Integrated modeling of clinical and gene expression information for personalized prediction of disease outcomes. Proc Natl Acad Sci U S A. 2004;101 (22):8431-6. doi: 10.1073/pnas.0401736101. PubMed PMID:15152076 PubMed Central PMC420411.
  78. Huang, E, Ishida, S, Pittman, J, Dressman, H, Bild, A, Kloos, M et al.. Gene expression phenotypic models that predict the activity of oncogenic pathways. Nat Genet. 2003;34 (2):226-30. doi: 10.1038/ng1167. PubMed PMID:12754511 .
  79. Huang, E, Cheng, SH, Dressman, H, Pittman, J, Tsou, MH, Horng, CF et al.. Gene expression predictors of breast cancer outcomes. Lancet. 2003;361 (9369):1590-6. doi: 10.1016/S0140-6736(03)13308-9. PubMed PMID:12747878 .
  80. Bild, AH, Mendoza, FJ, Gibson, EM, Huang, M, Villanueva, J, Garrington, TP et al.. MEKK1-induced apoptosis requires TRAIL death receptor activation and is inhibited by AKT/PKB through inhibition of MEKK1 cleavage. Oncogene. 2002;21 (43):6649-56. doi: 10.1038/sj.onc.1205819. PubMed PMID:12242663 .
  81. Bild, AH, Turkson, J, Jove, R. Cytoplasmic transport of Stat3 by receptor-mediated endocytosis. EMBO J. 2002;21 (13):3255-63. doi: 10.1093/emboj/cdf351. PubMed PMID:12093727 PubMed Central PMC126099.
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