• 9154 Citations
  • 48 Scopus h-Index
1971 …2020

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Open Access
123 Scopus citations

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

Su, Z., Łabaj, P. P., Li, S., Thierry-Mieg, J., Thierry-Mieg, D., Shi, W., Wang, C., Schroth, G. P., Setterquist, R. A., Thompson, J. F., Jones, W. D., Xiao, W., Xu, W., Jensen, R. V., Kelly, R., Xu, J., Conesa, A., Furlanello, C., Gao, H., Hong, H. & 142 others, Jafari, N., Letovsky, S., Liao, Y., Lu, F., Oakeley, E. J., Peng, Z., Praul, C. A., Santoyo-Lopez, J., Scherer, A., Shi, T., Smyth, G. K., Staedtler, F., Sykacek, P., Tan, X. X., Thompson, E. A., Vandesompele, J., Wang, M. D., Wang, J., Wolfinger, R. D., Zavadil, J., Auerbach, S. S., Bao, W., Binder, H., Blomquist, T., Brilliant, M. H., Bushel, P. R., Cai, W., Catalano, J. G., Chang, C. W., Chen, T., Chen, G., Chen, R., Chierici, M., Chu, T. M., Clevert, D. A., Deng, Y., Derti, A., Devanarayan, V., Dong, Z., Dopazo, J., Du, T., Fang, H., Fang, Y., Fasold, M., Fernandez, A., Fischer, M., Furió-Tari, P., Fuscoe, J. C., Caimet, F., Gaj, S., Gandara, J., Gao, H., Ge, W., Gondo, Y., Gong, B., Gong, M., Gong, Z., Green, B., Guo, C., Guo, L., Guo, L. W., Hadfield, J., Hellemans, J., Hochreiter, S., Jia, M., Jian, M., Johnson, C. D., Kay, S., Kleinjans, J., Lababidi, S., Levy, S., Li, Q. Z., Li, L., Li, L., Li, P., Li, Y., Li, H., Li, J., Li, S., Lin, S. M., López, F. J., Lu, X., Luo, H., Ma, X., Meehan, J., Megherbi, D. B., Mei, N., Mu, B., Ning, B., Pandey, A., Pérez-Florido, J., Perkins, R. G., Peters, R., Phan, J. H., Pirooznia, M., Qian, F., Qing, T., Rainbow, L., Rocca-Serra, P., Sambourg, L., Sansone, S. A., Schwartz, S., Shah, R., Shen, J., Smith, T. M., Stegle, O., Stralis-Pavese, N., Stupka, E., Suzuki, Y., Szkotnicki, L. T., Tinning, M., Tu, B., Van Delft, J., Vela-Boza, A., Venturini, E., Walker, S. J., Wan, L., Wang, W., Wang, J., Wang, J., Wieben, E. D., Willey, J. C., Wu, P. Y., Xuan, J., Yang, Y., Ye, Z., Yin, Y., Yu, Y., Yuan, Y. C., Zhang, J., Zhang, K. K., Zhang, W., Zhang, W., Zhang, Y., Zhao, C., Zheng, Y., Zhou, Y., Zumbo, P., Tong, W., Kreil, D. P., Mason, C. E. & Shi, L., Sep 1 2014, In : Nature biotechnology. 32, 9, p. 903-914 12 p.

Research output: Contribution to journalArticle

434 Scopus citations

Akt interacts directly with Smad3 to regulate the sensitivity to TGF-β-induced apoptosis

Conery, A. R., Cao, Y., Thompson, E. A., Townsend, C. M., Ko, T. C. & Luo, K., Apr 1 2004, In : Nature Cell Biology. 6, 4, p. 366-372 7 p.

Research output: Contribution to journalArticle

290 Scopus citations

An integrated model of the transcriptome of HER2-positive breast cancer

Kalari, K. R., Necela, B. M., Tang, X., Thompson, K. J., Lau, M., Eckel-Passow, J. E., Kachergus, J. M., Keith Anderson, S., Sun, Z., Baheti, S., Carr, J. M., Baker, T. R., Barman, P., Radisky, D. C., Joseph, R. W., McLaughlin, S. A., Chai, H. S., Camille, S., Rossell, D., Asmann, Y. W. & 2 others, Aubrey Thompson, E. & Perez, E. A., Nov 2013, In : PloS one. 8, 11, e79298.

Research output: Contribution to journalArticle

11 Scopus citations

An N-methyl glutamate dehydrogenase from Pseudomonas M.A

Hersh, L. B., Peterson, J. A. & Thompson, A. A., Jul 1971, In : Archives of Biochemistry and Biophysics. 145, 1, p. 115-120 6 p.

Research output: Contribution to journalArticle

11 Scopus citations

A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines

Asmann, Y. W., Hossain, A., Necela, B. M., Middha, S., Kalari, K. R., Sun, Z., Chai, H. S., Williamson, D. W., Radisky, D., Schroth, G. P., Kocher, J. P. A., Perez, E. A. & Thompson, E. A., Aug 2011, In : Nucleic acids research. 39, 15, p. e100

Research output: Contribution to journalArticle

69 Scopus citations

A novel glucocorticoid receptor binding element within the murine c-myc promoter

Ma, T., Copland, J. A., Brasier, A. R. & Thompson, E. A., Jan 1 2000, In : Molecular Endocrinology. 14, 9, p. 1377-1386 10 p.

Research output: Contribution to journalArticle

Open Access
8 Scopus citations
4 Scopus citations

Assessment of tumor heterogeneity, as evidenced by gene expression profiles, pathway activation, and gene copy number, in patients with multifocal invasive lobular breast tumors

Norton, N., Advani, P. P., Serie, D. J., Geiger, X. J., Necela, B. M., Axenfeld, B. C., Kachergus, J. M., Feathers, R. W., Carr, J. M., Crook, J. E., Moreno-Aspitia, A., Anastasiadis, P. Z., Perez, E. A. & Thompson, E. A., Apr 2016, In : PloS one. 11, 4, e0153411.

Research output: Contribution to journalArticle

14 Scopus citations

Association of stromal tumor-infiltrating lymphocytes with recurrence-free survival in the n9831 adjuvant trial in patients with early-stage HER2-positive breast cancer

Perez, E. A., Ballman, K. V., Tenner, K. S., Thompson, E. A., Badve, S. S., Bailey, H. & Baehner, F. L., Jan 1 2016, In : JAMA oncology. 2, 1, p. 56-64 9 p.

Research output: Contribution to journalArticle

105 Scopus citations

Atypical protein kinase Cι expression and aurothiomalate sensitivity in human lung cancer cells

Regala, R. P., Thompson, E. A. & Fields, A. P., Jul 15 2008, In : Cancer research. 68, 14, p. 5888-5895 8 p.

Research output: Contribution to journalArticle

60 Scopus citations

Atypical protein kinase Cτ plays a critical role in human lung cancer cell growth and tumorigenicity

Regala, R. P., Weems, C., Jamieson, L., Copland, J. A., Thompson, E. A. & Fields, A. P., Sep 2 2005, In : Journal of Biological Chemistry. 280, 35, p. 31109-31115 7 p.

Research output: Contribution to journalArticle

154 Scopus citations

Aurothiomalate inhibits transformed growth by targeting the PB1 domain of protein kinase Ci

Erdogan, E., Lamark, T., Stallings-Mann, M., Jamieson, L., Pellechia, M., Aubrey Thompson, E., Johansen, T. & Fields, A. P., Sep 22 2006, In : Journal of Biological Chemistry. 281, 38, p. 28450-28459 10 p.

Research output: Contribution to journalArticle

75 Scopus citations

Bcr-Abl Regulates Protein Kinase Cι (PKCι) Transcription via an Elk1 Site in the PKCι Promoter

Gustafson, W. C., Ray, S., Jamieson, L., Thompson, E. A., Brasier, A. R. & Fields, A. P., Mar 5 2004, In : Journal of Biological Chemistry. 279, 10, p. 9400-9408 9 p.

Research output: Contribution to journalArticle

39 Scopus citations

Biochemical and molecular characterization of the glucocorticoid receptor of lymphosarcoma p1798 variants

Lucas, K. L., Barbour, K. W., Housley, P. R. & Thompson, E. A., Mar 1988, In : Molecular Endocrinology. 2, 3, p. 291-299 9 p.

Research output: Contribution to journalArticle

Open Access
11 Scopus citations

Cadherin complexes recruit mRNAs and RISC to regulate epithelial cell signaling

Kourtidis, A., Necela, B., Lin, W. H., Lu, R., Feathers, R. W., Asmann, Y., Thompson, E. A. & Anastasiadis, P. Z., Oct 1 2017, In : Journal of Cell Biology. 216, 10, p. 3073-3085 13 p.

Research output: Contribution to journalArticle

11 Scopus citations

Cell cycle-mediated regulation of hepatic regeneration

Ehrenfried, J. A., Ko, T. C., Thompson, E. A. & Evers, B. M., Nov 1997, In : Surgery. 122, 5, p. 927-935 9 p.

Research output: Contribution to journalArticle

42 Scopus citations

Cell cycle protein suppression and p21 induction in differentiating Caco-2 cells

Evers, B. M., Ko, T. C., Li, J. & Thompson, E. A., Oct 1 1996, In : American Journal of Physiology - Gastrointestinal and Liver Physiology. 271, 4 34-4, p. G722-G727

Research output: Contribution to journalArticle

65 Scopus citations

Chloroquine and nanoparticle drug delivery: A promising combination

Pelt, J., Busatto, S., Ferrari, M., Thompson, E. A., Mody, K. & Wolfram, J., Jan 1 2018, (Accepted/In press) In : Pharmacology and Therapeutics.

Research output: Contribution to journalArticle

10 Scopus citations

Chromoanasynthesis is a common mechanism that leads to ERBB2 amplifications in a cohort of early stage HER2+ breast cancer samples

Vasmatzis, G., Wang, X., Smadbeck, J., Murphy, S. J., Geiersbach, K. B., Johnson, S. H., Gaitatzes, A. G., Asmann, Y., Kosari, F., Borad, M. J., Serie, D. J., McLaughlin, S. A., Kachergus, J. M., Necela, B. M. & Thompson, E. A., Jul 13 2018, In : BMC Cancer. 18, 1, 738.

Research output: Contribution to journalArticle

Chromosome X genomic and epigenomic aberrations and clinical implications in breast cancer by base resolution profiling

Sun, Z. D., Prodduturi, N., Sun, S. Y., Thompson, E. A. & Kocher, J-P., Oct 1 2015, In : Epigenomics. 7, 7, p. 1099-1110 12 p.

Research output: Contribution to journalArticle

5 Scopus citations

Clinical and molecular features of hürthle cell carcinoma of the thyroid

Chindris, A. M., Casler, J. D., Bernet, V. J., Rivera, M., Thomas, C., Kachergus, J. M., Necela, B. M., Hay, I. D., Westphal, S. A., Grant, C. S., Thompson, G. B., Schlinkert, R. T., Aubrey Thompson, E. & Smallridge, R. C., Jan 1 2015, In : Journal of Clinical Endocrinology and Metabolism. 100, 1, p. 55-62 8 p.

Research output: Contribution to journalArticle

Open Access
49 Scopus citations

Cloning of a novel phosphatidylinositol kinase-related kinase. Characterization of the human SMG-1 RNA surveillance protein

Denning, G., Jamieson, L., Maquat, L. E., Thompson, E. A. & Fields, A. P., Jun 22 2001, In : Journal of Biological Chemistry. 276, 25, p. 22709-22714 6 p.

Research output: Contribution to journalArticle

119 Scopus citations

c-Myc and Cyclin D3 (CcnD3) Genes Are Independent Targets for Glucocorticoid Inhibition of Lymphoid Cell Proliferation

Rhee, K., Bresnahan, W., Hirai, A., Hirai, M., Thompson, E. A., Rhee, K., Hirai, A. & Hirai, M., Sep 15 1995, In : Cancer research. 55, 18, p. 4188-4195 8 p.

Research output: Contribution to journalArticle

66 Scopus citations

Comparison of GLUT1, GLUT3, and GLUT4 mRNA and the subcellular distribution of their proteins in normal human muscle

Stuart, C. A., Wen, G., Gustafson, W. C. & Thompson, E. A., Jan 1 2000, In : Metabolism: Clinical and Experimental. 49, 12, p. 1604-1609 6 p.

Research output: Contribution to journalArticle

13 Scopus citations

Comprehensive genomic profiling of a rare thyroid follicular dendritic cell sarcoma

Davila, J. I., Starr, J. S., Attia, S., Wang, C., Knudson, R. A., Necela, B. M., Sarangi, V., Sun, Z., Ren, Y., Casler, J. D., Menke, D. M., Oliver, G. R., Joseph, R. W., Copland, J. A., Parker, A. S., Kocher, J. P. A., Thompson, E. A., Smallridge, R. C. & Asmann, Y. W., Sep 15 2017, In : Rare Tumors. 9, 2, p. 50-53 4 p., 6834.

Research output: Contribution to journalArticle

1 Scopus citations

Constitutive Interferon Pathway Activation in Tumors as an Efficacy Determinant Following Oncolytic Virotherapy

Kurokawa, C., Iankov, I. D., Anderson, S. K., Aderca, I., Leontovich, A. A., Maurer, M. J., Oberg, A. L., Schroeder, M. A., Giannini, C., Greiner, S. M., Becker, M. A., Thompson, E. A., Haluska, P. R. J., Jentoft, M. E., Parney, I. F., Weroha, S. J., Jen, J., Sarkaria, J. N. & Galanis, E., Oct 1 2018, In : Journal of the National Cancer Institute. 110, 10, p. 1123-1132 10 p.

Research output: Contribution to journalArticle

19 Scopus citations

Copurification of RNA polymerase I and the glucocorticoid-regulated transcription factor IC

Mahajan, P. B. & Aubrey Thompson, E., Oct 1992, In : Protein Expression and Purification. 3, 5, p. 410-416 7 p.

Research output: Contribution to journalArticle

9 Scopus citations

Cyclin D3 is essential for intestinal epithelial cell proliferation

Ko, T. C., Pan, F., Sheng, H., Brown, D. B., Thompson, E. A. & Beauchamp, R. D., Jul 1 2002, In : World Journal of Surgery. 26, 7, p. 812-818 7 p.

Research output: Contribution to journalArticle

7 Scopus citations

Cyclin E/Cdk2 activity is controlled by different mechanisms in the G0 and G1 phases of the cell cycle

Bresnahan, W. A., Boldogh, I., Ma, T., Albrecht, T. & Aubrey Thompson, E., Nov 7 1996, In : Cell Growth and Differentiation. 7, 10, p. 1283-1290 8 p.

Research output: Contribution to journalArticle

51 Scopus citations

Cyclosporin A inhibits rDNA transcription in lymphosarcoma P1798 cells

Mahajan, P. B. & Thompson, E. A., Dec 1 1987, In : Journal of Biological Chemistry. 262, 33, p. 16150-16156 7 p.

Research output: Contribution to journalArticle

29 Scopus citations
4 Scopus citations

Deep sequence analysis of non-small cell lung cancer: Integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations

Kalari, K. R., Rossell, D., Necela, B. M., Asmann, Y. W., Nair, A., Baheti, S., Kachergus, J. M., Younkin, C. S., Baker, T., Carr, J. M., Tang, X., Walsh, M. P., Chai, H. S., Sun, Z., Hart, S. N., Leontovich, A. A., Hossain, A., Kocher, J. P., Perez, E. A., Reisman, D. N. & 2 others, Fields, A. P. & Thompson, E. A., 2012, In : Frontiers in Oncology. 2, FEB, 00012.

Research output: Contribution to journalArticle

32 Scopus citations

Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer

Asmann, Y. W., Necela, B. M., Kalari, K. R., Hossain, A., Baker, T. R., Carr, J. M., Davis, C., Getz, J. E., Hostetter, G., Li, X., McLaughlin, S. A., Radisky, D. C., Schroth, G. P., Cunliffe, H. E., Perez, E. A. & Thompson, E. A., Apr 15 2012, In : Cancer research. 72, 8, p. 1921-1928 8 p.

Research output: Contribution to journalArticle

66 Scopus citations

Differential expression, distribution, and function of PPAR-γ in the proximal and distal colon

Su, W., Bush, C. R., Necela, B. M., Calcagno, S. R., Murray, N. R., Fields, A. P. & Thompson, E. A., Aug 20 2007, In : Physiological Genomics. 30, 3, p. 342-353 12 p.

Research output: Contribution to journalArticle

45 Scopus citations

Differential expression of microRNAs in tumors from chronically inflamed or genetic (APCmin/+) models of colon cancer

Necela, B. M., Carr, J. M., Asmann, Y. W. & Thompson, E. A., 2011, In : PloS one. 6, 4, e18501.

Research output: Contribution to journalArticle

49 Scopus citations

Distinct E-cadherin-based complexes regulate cell behaviour through miRNA processing or Src and p120 catenin activity

Kourtidis, A., Ngok, S. P., Pulimeno, P., Feathers, R. W., Carpio, L. R., Baker, T. R., Carr, J. M., Yan, I. K., Borges, S., Perez, E. A., Storz, P., Copland, J. A. III., Patel, T. C., Thompson, E. A., Citi, S. & Anastasiadis, P. Z., Sep 1 2015, In : Nature. 17, 9, p. 1145-1157 13 p.

Research output: Contribution to journalArticle

55 Scopus citations

DNA-dependent RNA polymerase I from hepatomas: Comparison of activity levels and properties

Cavanaugh, A. H. & Thompson, E. A., Jan 1 1981, In : Cancer Biochemistry Biophysics. 5, 2, p. 125-133 9 p.

Research output: Contribution to journalArticle

2 Scopus citations

Durable Complete Response With Immune Checkpoint Inhibitor in Breast Cancer With High Tumor Mutational Burden and APOBEC Signature

Chumsri, S., Sokol, E. S., Soyano-Muller, A. E., Parrondo, R. D., Reynolds, G. A., Nassar, A. & Thompson, E. A., May 1 2020, In : Journal of the National Comprehensive Cancer Network : JNCCN. 18, 5, p. 517-521 5 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Effective targeting of estrogen receptor-negative breast cancers with the protein kinase D inhibitor CRT0066101

Borges, S., Perez, E. A., Thompson, E. A., Radisky, D. C., Geiger, X. J. & Storz, P., Jun 1 2015, In : Molecular cancer therapeutics. 14, 6, p. 1306-1316 11 p.

Research output: Contribution to journalArticle

22 Scopus citations

Effect of dexamethasone on nucleolar casein kinase II activity and phosphorylation of nucleolin in lymphosarcoma P1798 cells

Suzuki, N., Suzuki, T., Uchida, A., Thompson, E. A. & Hosoya, T., May 1992, In : Journal of Steroid Biochemistry and Molecular Biology. 42, 3-4, p. 305-312 8 p.

Research output: Contribution to journalArticle

13 Scopus citations

Effect of verapamil on cell cycle transit and c-myc gene expression in normal and malignant murine cells

Huber, K. R., Schmidt, W. F., Thompson, E. A., Forsthoefel, A. M., Neuberg, R. W. & Ettinger, R. S., May 1989, In : British journal of cancer. 59, 5, p. 714-718 5 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Effects of age and immune landscape on outcome in HER2-positive breast cancer in the NCCTG N9831 (Alliance) and NSABP B-31 (NRG) trials

Chumsri, S., Serie, D. J., Li, Z., Pogue-Geile, K. L., Soyano-Muller, A. E., Mashadi-Hossein, A., Warren, S., Lou, Y., Colon-Otero, G., Knutson, K. L., Perez, E. A., Moreno-Aspitia, A. & Thompson, E. A., Jan 1 2019, In : Clinical Cancer Research. 25, 14, p. 4422-4430 9 p.

Research output: Contribution to journalArticle

1 Scopus citations

Elevated methylation levels, reduced expression levels, and frequent contractions in a clinical cohort of C9orf72 expansion carriers

Jackson, J. L., Finch, N. C. A., Baker, M. C., Kachergus, J. M., Dejesus-Hernandez, M., Pereira, K., Christopher, E., Prudencio, M., Heckman, M. G., Thompson, E. A., Dickson, D. W., Shah, J., Oskarsson, B., Petrucelli, L., Rademakers, R. & Van Blitterswijk, M., Jan 30 2020, In : Molecular neurodegeneration. 15, 1, 7.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Evi1 is a survival factor which conveys resistance to both TGFβ- and taxol-mediated cell death via PI3K/AKT

Liu, Y., Chen, L., Ko, T. C., Fields, A. P. & Thompson, E. A., Jun 15 2006, In : Oncogene. 25, 25, p. 3565-3575 11 p.

Research output: Contribution to journalArticle

75 Scopus citations

Expression of c-Myc in glucocorticoid-treated fibroblastic cells

Frost, G. H., Rhee, K., Ma, T. & Aubrey Thompson, E., Aug 1994, In : Journal of Steroid Biochemistry and Molecular Biology. 50, 3-4, p. 109-119 11 p.

Research output: Contribution to journalArticle

15 Scopus citations

Folate receptor-a (FOLR1) expression and function in triple negative tumors

Necela, B. M., Crazier, J. A., Andorfer, C. A., Lewis-Tuffin, L., Kachergus, J. M., Geiger, X. J., Kalari, K. R., Serie, D. J., Sun, Z., Aspita, A. M., O'Shannessy, D. J., Maltzman, J. D., McCullough, A. E., Pockaj, B. A., Cunliffe, H. E., Ballman, K. V., Thompson, E. A. & Perez, E. A., Mar 27 2015, In : PloS one. 10, 3, e0122209.

Research output: Contribution to journalArticle

52 Scopus citations

Folate receptor-α (FOLR1) expression and function in triple negative tumors

Necela, B. M., Crozier, J. A., Andorfer, C. A., Lewis-Tuffin, L., Kachergus, J. M., Geiger, X. J., Kalari, K. R., Serie, D. J., Sun, Z. D., Aspita, A. M., O'Shannessy, D. J., Maltzman, J. D., McCullough, A. E., Pockaj, B. A., Cunliffe, H. E., Ballman, K. V., Thompson, E. A. & Perez, E. A., Mar 27 2015, In : PLoS One. 10, 3, e0122209.

Research output: Contribution to journalArticle

Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer

Lei, J. T., Shao, J., Zhang, J., Iglesia, M., Chan, D. W., Cao, J., Anurag, M., Singh, P., He, X., Kosaka, Y., Matsunuma, R., Crowder, R., Hoog, J., Phommaly, C., Goncalves, R., Ramalho, S., Peres, R. M. R., Punturi, N., Schmidt, C., Bartram, A. & 23 others, Jou, E., Devarakonda, V., Holloway, K. R., Lai, W. V., Hampton, O., Rogers, A., Tobias, E., Parikh, P. A., Davies, S. R., Li, S., Ma, C. X., Suman, V. J., Hunt, K. K., Watson, M. A., Hoadley, K. A., Thompson, E. A., Chen, X., Kavuri, S. M., Creighton, C. J., Maher, C. A., Perou, C. M., Haricharan, S. & Ellis, M. J., Aug 7 2018, In : Cell reports. 24, 6, p. 1434-1444.e7

Research output: Contribution to journalArticle

21 Scopus citations

Functional genomic analysis reveals cross-talk between peroxisome proliferator-activated receptor γ and calcium signaling in human colorectal cancer cells

Bush, C. R., Havens, J. M., Necela, B. M., Su, W., Chen, L., Yanagisawa, M., Anastasiadis, P. Z., Guerra, R., Luxon, B. A. & Thompson, E. A., Aug 10 2007, In : Journal of Biological Chemistry. 282, 32, p. 23387-23401 15 p.

Research output: Contribution to journalArticle

22 Scopus citations