Publications

  1. McQuerry JA, Chen J, Chang J, Bild AH. 2020. Tepoxalin increases chemotherapy efficacy in drug-resistant breast cancer cells overexpressing the multidrug transporter gene ABCB1. Transl Oncol. 2021 Oct;14(10):101181. DOI: 1016/j.tranon.2021.101181; Pubmed PMID:34298440; PMCID: PMC8322466.
  2. Liu X, Gosline SJ, Pflieger LT, Wallet P, Iyer A, et al, Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data, Brief Bioinform. 2021 Sep 2;22(5):bbab039. DOI: 1093/bib/bbab039; Pubmed PMID:33681983; Pubmed Central: PMC8536868 (available on 2022-03-03).
  3. Griffiths J.I., Chen J, Cosgrove P.A, et al. Serial single-cell genomics reveals convergent subclonal evolution of resistance as patients with early-stage breast cancer progress on endocrine plus CDK4/6 therapy.  Nat Cancer. 2021 Jun;2(6):658-671. DOI: 1038/s43018-021-00215-7;  Pubmed PMID:34712959; Pubmed Central: PMC8547038.
  4. Nath A , Cosgrove PA, Mirsafian H, Christie E, Pflieger L, et al. Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer. Nat Commun. 2021 May 24;12(1):3039. DOI: 1038/s41467-021-23171-3; Pubmed PMID:34031395; Pubmed Central: PMC8144406.
  5. Nath A and Bild AH. Leveraging Single-Cell Approaches in Cancer Precision Medicine. Trends Cancer. 2021 Apr;7(4):359-372. DOI: 1016/j.trecan.2021.01.007. Pubmed PMID:33563578; Pubmed Central: PMC7969443 (available on 2022-04-01).
  6. Chi F, Liu J, Brady SW, Cosgrove PA, Nath A, et al. A ‘one-two punch’ therapy strategy to target chemoresistance in ER+ breast cancer. Trans Oncol. 2021; 14(1): 100946. DOI: 1016/j.tranon.2020.100946; Pubmed PMID:33221681; Pubmed Central: PMC7689336.
  7. Huang, X., Qiao, Y., Brady, S.W. et al. Novel temporal and spatial patterns of metastatic colonization from breast cancer rapid-autopsy tumor biopsies. Genome Med 13, 170 (2021). DOI: 1186/s13073-021-00989-6; Pubmed PMID:34711268; Pubmed Central: PMC8555066.
  8. Grolmusz V, Chen J, Emond E, Cosgrove P, Pflieger L, et al. Exploiting collateral sensitivity controls growth of mixed culture of sensitive and resistant cells and decreases selection for resistant cells. Cancer cell international 20 (1), 1-13. DOI: 1186/s12935-020-01337-1; Pubmed PMID:32565737 Pubmed Central: PMC7301982.
  9. 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):16072-82. Epub 2020/06/24. DOI: 1073/pnas.1918937117; Pubmed PMID:32571915; Pubmed Central: PMC7355015.
  10. Reckamp KL, McQuerry JA, Mambetsariev I, Pharaon R, Yost SE, et al. o-stimulatory and co-inhibitory immune markers in solid tumors with MET alterations Future Sci OA. 2020 Nov 25;7(2):FSO662. DOI: 2144/fsoa-2020-0159; Pubmed PMID:33437521; Pubmed Central: PMC7787173.
  11. Griffiths JI, Cohen AL, Jones V, Salgia R, Chang JT, Bild AH. Opportunities for improving cancer treatment using systems biology. Curr Opin Syst Biol. 2019 Oct;17:41-50. DOI: 1016/j.coisb.2019.10.018; Pubmed PMID:32518857; Pubmed Central: PMC7282416.
  12. Bild A, Teo JL, Kahn M. Enhanced Kat3A/Catenin transcription: a common mechanism of therapeutic resistance. Cancer Drug Resist 2019;2:917-932. DOI: 20517/cdr.2019.32; Pubmed PMID:32426696 Pubmed Central: PMC7234864.
  13. Kalvala A, Wallet P, Yang L, Wang C, Li H, et al. Phenotypic Switching of Naïve T Cells to Immune-Suppressive Treg-Like Cells by Mutant KRAS. J Clin Med. 2019 Oct 18;8(10). pii: E1726. DOI: 3390/jcm8101726; Pubmed PMID:31635338; Pubmed Central: PMC6832522.
  14. McQuerry JA, Jenkins DF, Yost SE, Zhang Y, Schmolze D, et al. Pathway activity profiling of growth factor receptor network and stemness pathways differentiates metaplastic breast cancer histological subtypes. BMC Cancer. 2019 Sep 5;19(1):881. DOI: 1186/s12885-019-6052-z; Pubmed PMID:31488082; Pubmed Central: PMC6727561.
  15. 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.
  16. 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.
  17. 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. 2017;95 (11):1167-1178. doi: 10.1007/s00109-017-1587-4. PubMed PMID:28871446 PubMed Central PMC6296823.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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:24128763PubMed Central PMC3816418.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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 .
  37. 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 .
  38. 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.
  39. 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.
  40. 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.
  41. 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:19362539PubMed Central PMC2694616.
  42. 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.
  43. 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 .
  44. 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. . PubMed PMID:17254524 .
  45. 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 .
  46. 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 .
  47. 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 .
  48. 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 .
  49. 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 .
  50. 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 .
  51. 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.
  52. 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.
  53. 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 .
  54. 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.
  55. 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 .
  56. 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 .
  57. 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 .
  58. 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.

  Search PubMed