• 9002 Citations
  • 48 Scopus h-Index
1971 …2020

Research output per year

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Research Output

2020

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., Feb 2020, In : Mayo Clinic proceedings. 95, 2, p. 306-318 13 p.

Research output: Contribution to journalArticle

Open Access

The path to a better biomarker: Application of a risk management framework for the implementation of PD-L1 and TILs as immuno-oncology biomarkers in breast cancer clinical trials and daily practice

International Immuno-Oncology Biomarker Working Group, Jan 1 2020, (Accepted/In press) In : Journal of Pathology.

Research output: Contribution to journalReview article

Open Access
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

Open Access

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

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.e7

Research output: Contribution to journalArticle

3 Scopus citations
2018

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

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

16 Scopus citations

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

20 Scopus citations

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

1 Scopus citations
2017

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

99 Scopus citations

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

109 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

10 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. 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

1 Scopus citations

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

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

12 Scopus citations

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

17 Scopus citations

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., Aubrey Thompson, E., Sherman, M. E., Visscher, D. W., Degnim, A. C. & Radisky, D. C., Nov 1 2017, In : Breast Cancer Research and Treatment. 166, 2, p. 641-650 10 p.

Research output: Contribution to journalArticle

3 Scopus citations

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

2016

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

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

102 Scopus citations

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

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

9 Scopus citations

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

2 Scopus citations
2015

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

4 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

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

4 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

53 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

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

50 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

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. W., Kalari, K. R., Eckel-Passow, J. E., Dueck, A. C., 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

123 Scopus citations

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

15 Scopus citations

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

Aubrey Thompson, E., Jan 1 2015, In : Oncotarget. 6, 6, p. 3473-3474 2 p.

Research output: Contribution to journalEditorial

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

1 Scopus citations

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 journalReview article

821 Scopus citations

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

Research output: Contribution to journalArticle

12 Scopus citations
2014

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

422 Scopus citations

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 journalComment/debate

1 Scopus citations

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, A. E., Asmann, Y. W. & Kocher, J. P. A., Jun 27 2014, In : BMC bioinformatics. 15, 1, 224.

Research output: Contribution to journalArticle

106 Scopus citations

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. W., 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. & Thompson, E. A., Feb 1 2014, In : Journal of Clinical Endocrinology and Metabolism. 99, 2, p. E338-E347

Research output: Contribution to journalArticle

30 Scopus citations

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

15 Scopus citations

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. A., Weinshilboum, R. M., Wang, L., Thompson, E. A. & Kalari, K. R., Dec 16 2014, In : Nucleic acids research. 42, 22, e172.

Research output: Contribution to journalArticle

22 Scopus citations

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

171 Scopus citations
2013

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 1 2013, In : PloS one. 8, 11, e79298.

Research output: Contribution to journalArticle

11 Scopus citations

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

Norton, N., Sun, Z., Asmann, Y. W., 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

35 Scopus citations

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. W., Nair, A., Zhang, Y., Wang, L., Kalari, K. R., Bhagwate, A. V., Baker, T. R., Carr, J. M., Kocher, J. P. A., Perez, E. A. & Thompson, E. A., 2013, In : PloS one. 8, 8, e71745.

Research output: Contribution to journalArticle

Open Access
12 Scopus citations

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

22 Scopus citations

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

73 Scopus citations