• 8759 Citations
  • 47 Scopus h-Index
1971 …2019
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Research Output 1971 2019

  • 8759 Citations
  • 47 Scopus h-Index
  • 164 Article
  • 3 Comment/debate
  • 2 Review article
2019

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

Breast Neoplasms
adjuvant P40
B 31
Trastuzumab

Erratum: Protein Kinase Cι and Wnt/β-Catenin Signaling: Alternative Pathways to Kras/Trp53-Driven Lung Adenocarcinoma (Cancer Cell (2019) 36(2) (156–167.e7), (S1535610819303290), (10.1016/j.ccell.2019.07.002))

Yin, N., Liu, Y., Khoor, A., Wang, X., Thompson, E. A., Leitges, M., Justilien, V., Weems, C., Murray, N. R. & Fields, A. P., Dec 9 2019, In : Cancer cell. 36, 6, p. 692-693 2 p.

Research output: Contribution to journalComment/debate

Open Access
Catenins
Confusion
Peer Review
Protein Kinase C
Publications

Incidence of late relapses in patients with HER2-positive breast cancer receiving adjuvant trastuzumab: Combined analysis of NCCTG N9831 (Alliance) and NRG oncology/NSABP B-31

Chumsri, S., Li, Z., Serie, D. J., Mashadi-Hossein, A., Colon-Otero, G., Song, N., Pogue-Geile, K. L., Gavin, P. G., Paik, S., Moreno-Aspitia, A., Perez, E. A. & Aubrey Thompson, E., Jan 1 2019, In : Journal of Clinical Oncology. 37, 35, p. 3425-3435 11 p.

Research output: Contribution to journalArticle

Breast Neoplasms
Recurrence
Incidence
Survival
Lymph Nodes

Integration of Comprehensive Genomic Analysis and Functional Screening of Affected Molecular Pathways to Inform Cancer Therapy

Vasmatzis, G., Liu, M. C., Reganti, S., Feathers, R. W., Smadbeck, J., Johnson, S. H., Schaefer Klein, J. L., Harris, F. R., Yang, L., Kosari, F., Murphy, S. J., Borad, M. J., Thompson, E. A., Cheville, J. C. & Anastasiadis, P. Z., Jan 1 2019, (Accepted/In press) In : Mayo Clinic proceedings.

Research output: Contribution to journalArticle

Open Access
Neoplasms
Mutation
Therapeutics
Precision Medicine
Preclinical Drug Evaluations
3 Citations (Scopus)

Protein Kinase Cι and Wnt/β-Catenin Signaling: Alternative Pathways to Kras/Trp53-Driven Lung Adenocarcinoma

Yin, N., Liu, Y., Khoor, A., Wang, X., Thompson, E. A., Leitges, M., Justilien, V., Weems, C., Murray, N. R. & Fields, A. P., Aug 12 2019, In : Cancer cell. 36, 2, p. 156-167 12 p.

Research output: Contribution to journalArticle

Catenins
Protein Kinase C
Neoplasms
Stem Cells
Wnt Signaling Pathway
2018
5 Citations (Scopus)

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

Chloroquine
Nanoparticles
Pharmaceutical Preparations
Neoplasms
Cellular Microenvironment

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

Chromosomes, Human, Pair 8
Breast Neoplasms
Chromosomes, Human, Pair 17
Transcriptome
Genome
12 Citations (Scopus)

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., 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

Oncolytic Virotherapy
Measles virus
Interferons
Glioblastoma
Heterografts
15 Citations (Scopus)

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

Gene Fusion
Estrogen Receptors
Fusion reactions
Genes
Breast Neoplasms
1 Citation (Scopus)

The phosphorylation status of PIP5K1C at serine 448 can be predictive for invasive ductal carcinoma of the breast

Durand, N., Borges, S., Hall, T., Bastea, L., Döppler, H., Edenfield, B. H., Thompson, E. A., Geiger, X. & Storz, P., Nov 1 2018, In : Oncotarget. 9, 91, p. 36358-36370 13 p.

Research output: Contribution to journalArticle

Carcinoma, Ductal, Breast
Serine
Phosphorylation
Ductal Carcinoma
Breast Neoplasms
2017
78 Citations (Scopus)

Assessing Tumor-infiltrating Lymphocytes in Solid Tumors: A Practical Review for Pathologists and Proposal for a Standardized Method from the International Immunooncology Biomarkers Working Group: Part 1: Assessing the Host Immune Response, TILs in Invasive Breast Carcinoma and Ductal Carcinoma in Situ, Metastatic Tumor Deposits and Areas for Further Research

Hendry, S., Salgado, R., Gevaert, T., Russell, P. A., John, T., Thapa, B., Christie, M., Van De Vijver, K., Estrada, M. V., Gonzalez-Ericsson, P. I., Sanders, M., Solomon, B., Solinas, C., Van Den Eynden, G. G. G. M., Allory, Y., Preusser, M., Hainfellner, J., Pruneri, G., Vingiani, A., Demaria, S. & 80 others, Symmans, F., Nuciforo, P., Comerma, L., Thompson, E. A., Lakhani, S., Kim, S. R., Schnitt, S., Colpaert, C., Sotiriou, C., Scherer, S. J., Ignatiadis, M., Badve, S., Pierce, R. H., Viale, G., Sirtaine, N., Penault-Llorca, F., Sugie, T., Fineberg, S., Paik, S., Srinivasan, A., Richardson, A., Wang, Y., Chmielik, E., Brock, J., Johnson, D. B., Balko, J., Wienert, S., Bossuyt, V., Michiels, S., Ternes, N., Burchardi, N., Luen, S. J., Savas, P., Klauschen, F., Watson, P. H., Nelson, B. H., Criscitiello, C., O'Toole, S., Larsimont, D., De Wind, R., Curigliano, G., André, F., Lacroix-Triki, M., Van De Vijver, M., Rojo, F., Floris, G., Bedri, S., Sparano, J., Rimm, D., Nielsen, T., Kos, Z., Hewitt, S., Singh, B., Farshid, G., Loibl, S., Allison, K. H., Tung, N., Adams, S., Willard-Gallo, K., Horlings, H. M., Gandhi, L., Moreira, A., Hirsch, F., Dieci, M. V., Urbanowicz, M., Brcic, I., Korski, K., Gaire, F., Koeppen, H., Lo, A., Giltnane, J., Rebelatto, M. C., Steele, K. E., Zha, J., Emancipator, K., Juco, J. W., Denkert, C., Reis-Filho, J., Loi, S. & Fox, S. B., Jan 1 2017, In : Advances in Anatomic Pathology. 24, 5, p. 235-251 17 p.

Research output: Contribution to journalReview article

Tumor-Infiltrating Lymphocytes
Carcinoma, Intraductal, Noninfiltrating
Biomarkers
Breast Neoplasms
Research
89 Citations (Scopus)

Assessing Tumor-Infiltrating Lymphocytes in Solid Tumors: A Practical Review for Pathologists and Proposal for a Standardized Method from the International Immuno-Oncology Biomarkers Working Group: Part 2: TILs in Melanoma, Gastrointestinal Tract Carcinomas, Non-Small Cell Lung Carcinoma and Mesothelioma, Endometrial and Ovarian Carcinomas, Squamous Cell Carcinoma of the Head and Neck, Genitourinary Carcinomas, and Primary Brain Tumors

Hendry, S., Salgado, R., Gevaert, T., Russell, P. A., John, T., Thapa, B., Christie, M., Van De Vijver, K., Estrada, M. V., Gonzalez-Ericsson, P. I., Sanders, M., Solomon, B., Solinas, C., Van Den Eynden, G. G. G. M., Allory, Y., Preusser, M., Hainfellner, J., Pruneri, G., Vingiani, A., Demaria, S. & 80 others, Symmans, F., Nuciforo, P., Comerma, L., Thompson, E. A., Lakhani, S., Kim, S. R., Schnitt, S., Colpaert, C., Sotiriou, C., Scherer, S. J., Ignatiadis, M., Badve, S., Pierce, R. H., Viale, G., Sirtaine, N., Penault-Llorca, F., Sugie, T., Fineberg, S., Paik, S., Srinivasan, A., Richardson, A., Wang, Y., Chmielik, E., Brock, J., Johnson, D. B., Balko, J., Wienert, S., Bossuyt, V., Michiels, S., Ternes, N., Burchardi, N., Luen, S. J., Savas, P., Klauschen, F., Watson, P. H., Nelson, B. H., Criscitiello, C., O'Toole, S., Larsimont, D., De Wind, R., Curigliano, G., André, F., Lacroix-Triki, M., Van De Vijver, M., Rojo, F., Floris, G., Bedri, S., Sparano, J., Rimm, D., Nielsen, T., Kos, Z., Hewitt, S., Singh, B., Farshid, G., Loibl, S., Allison, K. H., Tung, N., Adams, S., Willard-Gallo, K., Horlings, H. M., Gandhi, L., Moreira, A., Hirsch, F., Dieci, M. V., Urbanowicz, M., Brcic, I., Korski, K., Gaire, F., Koeppen, H., Lo, A., Giltnane, J., Rebelatto, M. C., Steele, K. E., Zha, J., Emancipator, K., Juco, J. W., Denkert, C., Reis-Filho, J., Loi, S. & Fox, S. B., Jan 1 2017, In : Advances in Anatomic Pathology. 24, 6, p. 311-335 25 p.

Research output: Contribution to journalReview article

Tumor-Infiltrating Lymphocytes
Mesothelioma
Endometrial Neoplasms
Non-Small Cell Lung Carcinoma
Brain Neoplasms
9 Citations (Scopus)

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

RNA-Induced Silencing Complex
Adherens Junctions
Cadherins
Epithelial Cells
Messenger RNA
1 Citation (Scopus)

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. D., Ren, Y., Casler, J. D., Menke, D. M., Oliver, G. R., Joseph, R. W., Copland, J. A. III., Parker, A., Kocher, J-P., Thompson, E. A., Smallridge, R. C. & Asmann, Y., Sep 15 2017, In : Rare Tumors. 9, 2, p. 50-53 4 p., 6834.

Research output: Contribution to journalArticle

Follicular Dendritic Cell Sarcoma
Missense Mutation
Mutation
Gene Fusion
Neoplasms

Corrigendum: Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth

Holst, F., Hoivik, E. A., Gibson, W. J., Taylor-Weiner, A., Schumacher, S. E., Asmann, Y., Grossmann, P., Trovik, J., Necela, B. M., Thompson, E. A., Meyerson, M., Beroukhim, R., Salvesen, H. B. & Cherniack, A. D., Jun 30 2017, In : Scientific Reports. 7, 1 p.

Research output: Contribution to journalComment/debate

Endometrial Neoplasms
Growth Hormone
Hormones
corrigendum
10 Citations (Scopus)

Genome-wide association study of cardiotoxicity in the NCCTG N9831 (Alliance) adjuvant trastuzumab trial

Serie, D. J., Crook, J., Necela, B. M., Dockter, T. J., Wang, X., Asmann, Y., Fairweather, D., Bruno, K. A., Colon-Otero, G., Perez, E. A., Thompson, E. A. & Norton, N., 2017, In : Pharmacogenetics and Genomics. 27, 10, p. 378-385 8 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Single Nucleotide Polymorphism
Stroke Volume
Paclitaxel
Anthracyclines
17 Citations (Scopus)

Intrinsic subtype and therapeutic response among HER2-positive breast tumors from the NCCTG (Alliance) N9831 trial

Perez, E. A., Ballman, K. V., Mashadi-Hossein, A., Tenner, K. S., Kachergus, J. M., Norton, N., Necela, B. M., Carr, J. M., Ferree, S., Perou, C. M., Baehner, F., Cheang, M. C. U. & Thompson, E. A., 2017, In : Journal of the National Cancer Institute. 109, 2

Research output: Contribution to journalArticle

Breast Neoplasms
Neoplasms
Therapeutics
Confidence Intervals
Recurrence
3 Citations (Scopus)

NanoString-based breast cancer risk prediction for women with sclerosing adenosis

Winham, S. J., Mehner, C., Heinzen, E. P., Broderick, B. T., Stallings-Mann, M., Nassar, A., Vierkant, R. A., Hoskin, T. L., Frank, R. D., Wang, C., Denison, L. A., Vachon, C. M., Frost, M. H., Hartmann, L. C., Thompson, E. A., Sherman, M. E., Visscher, D. W., Degnim, A. C. & Radisky, D. C., Aug 10 2017, (Accepted/In press) In : Breast Cancer Research and Treatment. p. 1-10 10 p.

Research output: Contribution to journalArticle

Breast Diseases
ROC Curve
Breast Neoplasms
Area Under Curve
Biopsy

The antineoplastic drug, trastuzumab, dysregulates metabolism in iPSC-derived cardiomyocytes

Necela, B. M., Axenfeld, B. C., Serie, D. J., Kachergus, J. M., Perez, E. A., Thompson, E. A. & Norton, N., Jan 18 2017, In : Clinical and Translational Medicine. 6, 1, 5.

Research output: Contribution to journalArticle

Cardiac Myocytes
Antineoplastic Agents
Gene Expression
Glucose
Gene Ontology
2016
12 Citations (Scopus)

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., Moreno Aspitia, A., Anastasiadis, P. Z., Perez, E. A. & Thompson, E. A., Apr 1 2016, In : PLoS One. 11, 4, e0153411.

Research output: Contribution to journalArticle

Lobular Carcinoma
gene dosage
Gene Dosage
Transcriptome
Gene expression
93 Citations (Scopus)

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

Tumor-Infiltrating Lymphocytes
Breast Neoplasms
Recurrence
Survival
Drug Therapy

Erratum: Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth (Scientific Reports (2016) 6 (25521) DOI: 10.1038/srep25521)

Holst, F., Hoivik, E. A., Gibson, W. J., Taylor-Weiner, A., Schumacher, S. E., Asmann, Y., Grossmann, P., Trovik, J., Necela, B. M., Thompson, E. A., Meyerson, M., Beroukhim, R., Salvesen, H. B. & Cherniack, A. D., Jun 24 2016, In : Scientific Reports. 6, 27960.

Research output: Contribution to journalComment/debate

7 Citations (Scopus)

Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth

Holst, F., Hoivik, E. A., Gibson, W. J., Taylor-Weiner, A., Schumacher, S. E., Asmann, Y., Grossmann, P., Trovik, J., Necela, B. M., Thompson, E. A., Meyerson, M., Beroukhim, R., Salvesen, H. B. & Cherniack, A. D., May 10 2016, In : Scientific Reports. 6, 25521.

Research output: Contribution to journalArticle

Endometrial Neoplasms
Growth Hormone
Estrogen Receptor alpha
Hormones
Breast Neoplasms
2 Citations (Scopus)

Validation of Gene Expression Signatures to Identify Low-risk Clear-cell Renal Cell Carcinoma Patients at Higher Risk for Disease-related Death

Parasramka, M., Serie, D. J., Asmann, Y., Eckel-Passow, J. E., Castle, E. P., Stanton, M. L., Leibovich, B. C., Thompson, R. H., Thompson, E. A., Parker, A., Ho, T. H. & Joseph, R. W., Dec 15 2016, In : European Urology Focus. 2, 6, p. 608-615 8 p.

Research output: Contribution to journalArticle

Transcriptome
Renal Cell Carcinoma
Genes
Paraffin
Formaldehyde
2015
4 Citations (Scopus)

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

X Chromosome
Epigenomics
Breast Neoplasms
DNA Methylation
Cell Line
46 Citations (Scopus)

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., Thompson, E. A. & 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

Thyroid Neoplasms
Cells
Iodine
Recurrence
Neoplasms
4 Citations (Scopus)

Correction: 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., Moreno Aspitia, A., 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., Apr 30 2015, In : PLoS One. 10, 4, e0127133.

Research output: Contribution to journalArticle

50 Citations (Scopus)

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

Microcomputers
Cadherins
MicroRNAs
Adherens Junctions
Growth
22 Citations (Scopus)

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

Protein Kinase Inhibitors
Estrogen Receptors
Breast Neoplasms
Ductal Carcinoma
Hormones
42 Citations (Scopus)

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. 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

Folic Acid
folic acid
Tumors
receptors
neoplasms

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

Folic Acid
folic acid
Tumors
receptors
neoplasms
119 Citations (Scopus)

Genomic analysis reveals that immune function genes are strongly linked to clinical outcome in the North Central Cancer Treatment Group N9831 adjuvant trastuzumab trial

Perez, E. A., Thompson, E. A., Ballman, K. V., Anderson, S. K., Asmann, Y., Kalari, K. R., Eckel-Passow, J. E., Dueck, A., Tenner, K. S., Jen, J., Fan, J. B., Geiger, X. J., McCullough, A. E., Chen, B., Jenkins, R. B., Sledge, G. W., Winer, E. P., Gralow, J. R. & Reinholz, M. M., Mar 1 2015, In : Journal of Clinical Oncology. 33, 7, p. 701-708 8 p.

Research output: Contribution to journalArticle

Genes
Neoplasms
Recurrence
Survival
Politics
14 Citations (Scopus)

MEN1 mutations in Hürthle cell (oncocytic) thyroid carcinoma

Kasaian, K., Chindris, A. M., Wiseman, S. M., Mungall, K. L., Zeng, T., Tse, K., Schein, J. E., Rivera, M., Necela, B. M., Kachergus, J. M., Casler, J. D., Mungall, A. J., Moore, R. A., Marra, M. A., Copland, J. A. III., Thompson, E. A., Smallridge, R. C. & Jones, S. J. M., Apr 1 2015, In : Journal of Clinical Endocrinology and Metabolism. 100, 4, p. E611-E615

Research output: Contribution to journalArticle

Multiple Endocrine Neoplasia Type 1
Thyroid Neoplasms
Genes
Tumors
Mutation

Non-mutational (epigenomic) structural variation in the transcriptome of cancer cells

Thompson, E. A., 2015, In : Oncotarget. 6, 6, p. 3473-3474 2 p.

Research output: Contribution to journalArticle

Microfilament Proteins
Transcriptome
Epigenomics
Non-Small Cell Lung Carcinoma
Lung Neoplasms
1 Citation (Scopus)

Reply to P.G. Gavin et al

Perez, E. A., Thompson, E. A. & Ballman, K. V., Nov 1 2015, In : Journal of Clinical Oncology. 33, 31, p. 3672 1 p.

Research output: Contribution to journalArticle

Antineoplastic Combined Chemotherapy Protocols
ErbB-2 Receptor
Molecular Targeted Therapy
Antibodies, Monoclonal, Humanized
Tumor Biomarkers
762 Citations (Scopus)

The evaluation of tumor-infiltrating lymphocytes (TILS) in breast cancer: Recommendations by an International TILS Working Group 2014

Salgado, R., Denkert, C., Demaria, S., Sirtaine, N., Klauschen, F., Pruneri, G., Wienert, S., Van den Eynden, G., Baehner, F. L., Penault-Llorca, F., Perez, E. A., Thompson, E. A., Symmans, W. F., Richardson, A. L., Brock, J., Criscitiello, C., Bailey, H., Ignatiadis, M., Floris, G., Sparano, J. & 12 others, Kos, Z., Nielsen, T., Rimm, D. L., Allison, K. H., Reis-Filho, J. S., Loibl, S., Sotiriou, C., Viale, G., Badve, S., Adams, S., Willard-Gallo, K. & Loi, S., Feb 1 2015, In : Annals of Oncology. 26, 2, p. 259-271 13 p., mdu450.

Research output: Contribution to journalArticle

Tumor-Infiltrating Lymphocytes
Breast Neoplasms
Biomarkers
Clinical Trials
Research
11 Citations (Scopus)

The relationship between quantitative human epidermal growth factor receptor 2 gene expression by the 21-gene reverse transcriptase polymerase chain reaction assay and adjuvant trastuzumab benefit in Alliance N9831

Perez, E. A., Baehner, F. L., Butler, S. M., Thompson, E. A., Dueck, A., Jamshidian, F., Cherbavaz, D., Yoshizawa, C., Shak, S., Kaufman, P. A., Davidson, N. E., Gralow, J., Asmann, Y. & Ballman, K. V., Oct 1 2015, In : Breast Cancer Research. 17, 1, 133.

Research output: Contribution to journalArticle

erbB-1 Genes
Reverse Transcriptase Polymerase Chain Reaction
Gene Expression
Genes
Fluorescence In Situ Hybridization
2014
398 Citations (Scopus)

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

RNA Sequence Analysis
RNA
Quality Control
Quality control
Polymerase Chain Reaction
1 Citation (Scopus)

Correction: Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues (PLoS ONE)

Kolbert, C. P., Feddersen, R. M., Rakhshan, F., Grill, D. E., Simon, G., Middha, S., Jang, J. S., Simon, V., Schultz, D. A., Zschunke, M., Lingle, W., Carr, J. M., Thompson, E. A., Oberg, A. L., Eckloff, B. W., Wieben, E. D., Li, P., Yang, P. & Jen, J., Jan 8 2014, In : PLoS One. 9, 1

Research output: Contribution to journalArticle

MicroRNAs
RNA
Tissue
98 Citations (Scopus)

MAP-RSeq: Mayo Analysis Pipeline for RNA sequencing

Kalari, K. R., Nair, A. A., Bhavsar, J. D., O'Brien, D. R., Davila, J. I., Bockol, M. A., Nie, J., Tang, X., Baheti, S., Doughty, J. B., Middha, S., Sicotte, H., Thompson, E. A., Asmann, Y. & Kocher, J-P., Jun 27 2014, In : BMC Bioinformatics. 15, 1, 224.

Research output: Contribution to journalArticle

RNA Sequence Analysis
Workflow
RNA
Sequencing
Work Flow
29 Citations (Scopus)

RNA sequencing identifies multiple fusion transcripts, differentially expressed genes, and reduced expression of immune function genes in BRAF (V600E) mutant vs BRAF wild-type papillary thyroid carcinoma

Smallridge, R. C., Chindris, A. M., Asmann, Y., Casler, J. D., Serie, D. J., Reddi, H. V., Cradic, K. W., Rivera, M., Grebe, S. K., Necela, B. M., Eberhardt, N. L., Carr, J. M., McIver, B., Copland, J. A. III. & Thompson, E. A., Feb 2014, In : Journal of Clinical Endocrinology and Metabolism. 99, 2

Research output: Contribution to journalArticle

RNA Sequence Analysis
Tumors
Fusion reactions
Genes
RNA
13 Citations (Scopus)

RVboost: RNA-seq variants prioritization using a boosting method

Wang, C., Davila, J. I., Baheti, S., Bhagwate, A. V., Wang, X., Kocher, J-P., Slager, S. L., Feldman, A. L., Novak, A. J., Cerhan, J. R., Thompson, E. A. & Asmann, Y., 2014, In : Bioinformatics. 30, 23, p. 3414-3416 3 p.

Research output: Contribution to journalArticle

Prioritization
Boosting
RNA
Sequencing
Preparation
20 Citations (Scopus)

The eSNV-detect: A computational system to identify expressed single nucleotide variants from transcriptome sequencing data

Tang, X., Baheti, S., Shameer, K., Thompson, K. J., Wills, Q., Niu, N., Holcomb, I. N., Boutet, S. C., Ramakrishnan, R., Kachergus, J. M., Kocher, J-P., Weinshilboum, R. M., Wang, L. M., Thompson, E. A. & Kalari, K. R., Dec 16 2014, In : Nucleic Acids Research. 42, 22, e172.

Research output: Contribution to journalArticle

Transcriptome
Nucleotides
RNA
Breast Neoplasms
Exome
167 Citations (Scopus)

The PRKCI and SOX2 Oncogenes Are Coamplified and Cooperate to Activate Hedgehog Signaling in Lung Squamous Cell Carcinoma

Justilien, V., Walsh, M. P., Ali, S. A., Thompson, E. A., Murray, N. R. & Fields, A. P., Feb 10 2014, In : Cancer Cell. 25, 2, p. 139-151 13 p.

Research output: Contribution to journalArticle

Acyltransferases
Oncogenes
Protein Kinase C
Squamous Cell Carcinoma
Lung
2013
11 Citations (Scopus)

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. D., 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. & 2 others, Thompson, E. A. & Perez, E. A., Nov 2013, In : PLoS One. 8, 11, e79298.

Research output: Contribution to journalArticle

Transcriptome
transcriptome
breast neoplasms
Tumors
Breast Neoplasms
32 Citations (Scopus)

Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors

Norton, N., Sun, Z. D., Asmann, Y., Serie, D. J., Necela, B. M., Bhagwate, A., Jen, J., Eckloff, B. W., Kalari, K. R., Thompson, K. J., Carr, J. M., Kachergus, J. M., Geiger, X. J., Perez, E. A. & Thompson, E. A., Nov 22 2013, In : PLoS One. 8, 11, e81925.

Research output: Contribution to journalArticle

Gene expression
breast neoplasms
Tumors
Fusion reactions
Nucleotides
12 Citations (Scopus)

Impact of library preparation on downstream analysis and interpretation of RNA-Seq data: comparison between Illumina PolyA and NuGEN Ovation protocol.

Sun, Z., Asmann, Y., Nair, A., Zhang, Y., Wang, L., Kalari, K. R., Bhagwate, A. V., Baker, T. R., Carr, J. M., Kocher, J-P., Perez, E. A. & Thompson, E. A., 2013, In : PLoS One. 8, 8, e71745.

Research output: Contribution to journalArticle

Libraries
Long Noncoding RNA
RNA
Genes
Untranslated RNA
22 Citations (Scopus)

Inverse association between programmed death ligand 1 and genes in the VEGF pathway in primary clear cell renal cell carcinoma

Joseph, R. W., Parasramka, M., Eckel-Passow, J. E., Serie, D., Wu, K., Jiang, L., Kalari, K. R., Thompson, R. H., Ho, T. H., Castle, E. P., Cheville, J., Kwon, E. D., Thompson, E. A. & Parker, A., Dec 1 2013, In : Cancer immunology research. 1, 6, p. 378-385 8 p.

Research output: Contribution to journalArticle

Renal Cell Carcinoma
Vascular Endothelial Growth Factor A
Ligands
Tumor-Infiltrating Lymphocytes
Immunohistochemistry
72 Citations (Scopus)

Multi-Platform Analysis of MicroRNA Expression Measurements in RNA from Fresh Frozen and FFPE Tissues

Kolbert, C. P., Feddersen, R. M., Rakhshan, F., Grill, D. E., Simon, G., Middha, S., Jang, J. S., Simon, V., Schultz, D. A., Zschunke, M., Lingle, W., Carr, J. M., Thompson, E. A., Oberg, A. L., Eckloff, B. W., Wieben, E. D., Li, P., Yang, P. & Jen, J., Jan 31 2013, In : PLoS One. 8, 1, e52517.

Research output: Contribution to journalArticle

MicroRNAs
microRNA
RNA
Tissue
Biological Phenomena
18 Citations (Scopus)

Overexpression of Evi-1 oncoprotein represses TGF-β signaling in colorectal cancer

Deng, X., Cao, Y., Liu, Y., Li, F., Sambandam, K., Rajaraman, S., Perkins, A. S., Fields, A. P., Hellmich, M. R., Townsend, C. M., Thompson, E. A. & Ko, T. C., Apr 2013, In : Molecular Carcinogenesis. 52, 4, p. 255-264 10 p.

Research output: Contribution to journalArticle

Virus Integration
Oncogene Proteins
Transforming Growth Factors
Colorectal Neoplasms
Colonic Neoplasms