Select Publications

    Agyeman, A. S., W. J. Jun, D. A. Proia, C. R. Kim, M. N. Skor, M. Kocherginsky, and S. D. Conzen. "Hsp90 Inhibition Results in Glucocorticoid Receptor Degradation in Association with Increased Sensitivity to Paclitaxel in Triple-Negative Breast Cancer." Horm Cancer 7, no. 2 (Apr 2016): 114-26.

    Bainer, R., C. Frankenberger, D. Rabe, G. An, Y. Gilad, and M. R. Rosner. "Gene Expression in Local Stroma Reflects Breast Tumor States and Predicts Patient Outcome." Sci Rep 6 (Dec 16 2016): 39240.

    Battle, A., Z. Khan, S. H. Wang, A. Mitrano, M. J. Ford, J. K. Pritchard, and Y. Gilad. "Genomic Variation. Impact of Regulatory Variation from Rna to Protein." Science 347, no. 6222 (Feb 6 2015): 664-7.

    Benevolenskaya, E. V., A. B. Islam, H. Ahsan, M. G. Kibriya, F. Jasmine, B. Wolff, U. Al-Alem, et al. "DNA Methylation and Hormone Receptor Status in Breast Cancer." Clin Epigenetics 8 (2016): 17.

    Bourgo, R. J., H. Singhal, and G. L. Greene. "Capture of Associated Targets on Chromatin Links Long-Distance Chromatin Looping to Transcriptional Coordination." Nat Commun 7 (Sep 16 2016): 12893.

    Bunker, J. J., T. M. Flynn, J. C. Koval, D. G. Shaw, M. Meisel, B. D. McDonald, I. E. Ishizuka, et al. "Innate and Adaptive Humoral Responses Coat Distinct Commensal Bacteria with Immunoglobulin A." Immunity 43, no. 3 (Sep 15 2015): 541-53.

    Chapman, C. G., C. J. Mariani, F. Wu, K. Meckel, F. Butun, A. Chuang, J. Madzo, et al. "Tet-Catalyzed 5-Hydroxymethylcytosine Regulates Gene Expression in Differentiating Colonocytes and Colon Cancer." Sci Rep 5 (Dec 03 2015): 17568.

    Chapman, C. G., C. J. Mariani, F. Wu, K. Meckel, F. Butun, A. Chuang, J. Madzo, et al. "Corrigendum: Tet-Catalyzed 5-Hydroxymethylcytosine Regulates Gene Expression in Differentiating Colonocytes and Colon Cancer." Sci Rep 6 (Apr 28 2016): 24963.

    Constantinides, M. G., H. Gudjonson, B. D. McDonald, I. E. Ishizuka, P. A. Verhoef, A. R. Dinner, and A. Bendelac. "Plzf Expression Maps the Early Stages of Ilc1 Lineage Development." Proc Natl Acad Sci U S A 112, no. 16 (Apr 21 2015): 5123-8.

    Couch, F. J., K. B. Kuchenbaecker, K. Michailidou, G. A. Mendoza-Fandino, S. Nord, J. Lilyquist, C. Olswold, et al. "Identification of Four Novel Susceptibility Loci for Oestrogen Receptor Negative Breast Cancer." Nat Commun 7 (Apr 27 2016): 11375.

    Crawley, C. D., S. Kang, G. M. Bernal, J. S. Wahlstrom, D. J. Voce, K. E. Cahill, A. Garofalo, et al. "S-Phase-Dependent P50/Nf-Small Ka, Cyrillicb1 Phosphorylation in Response to Atr and Replication Stress Acts to Maintain Genomic Stability." Cell Cycle 14, no. 4 (2015): 566-76.

    Eckert, M. A., S. Pan, K. M. Hernandez, R. M. Loth, J. Andrade, S. L. Volchenboum, P. Faber, et al. "Genomics of Ovarian Cancer Progression Reveals Diverse Metastatic Trajectories Including Intraepithelial Metastasis to the Fallopian Tube." Cancer Discov 6, no. 12 (Dec 2016): 1342-51.

    Fehringer, G., P. Kraft, P. D. Pharoah, R. A. Eeles, N. Chatterjee, F. R. Schumacher, J. M. Schildkraut, et al. "Cross-Cancer Genome-Wide Analysis of Lung, Ovary, Breast, Prostate, and Colorectal Cancer Reveals Novel Pleiotropic Associations." Cancer Res 76, no. 17 (Sep 1 2016): 5103-14.

    Frankenberger, C., D. Rabe, R. Bainer, D. Sankarasharma, K. Chada, T. Krausz, Y. Gilad, L. Becker, and M. R. Rosner. "Metastasis Suppressors Regulate the Tumor Microenvironment by Blocking Recruitment of Prometastatic Tumor-Associated Macrophages." Cancer Res 75, no. 19 (Oct 1 2015): 4063-73.

    Gomez-Marin, C., J. J. Tena, R. D. Acemel, M. Lopez-Mayorga, S. Naranjo, E. de la Calle-Mustienes, I. Maeso, et al. "Evolutionary Comparison Reveals That Diverging Ctcf Sites Are Signatures of Ancestral Topological Associating Domains Borders." Proc Natl Acad Sci U S A 112, no. 24 (Jun 16 2015): 7542-7.

    Guo, Y., S. Warren Andersen, X. O. Shu, K. Michailidou, M. K. Bolla, Q. Wang, M. Garcia-Closas, et al. "Genetically Predicted Body Mass Index and Breast Cancer Risk: Mendelian Randomization Analyses of Data from 145,000 Women of European Descent." PLoS Med 13, no. 8 (Aug 2016): e1002105.

    Han, D., X. Lu, A. H. Shih, J. Nie, Q. You, M. M. Xu, A. M. Melnick, R. L. Levine, and C. He. "A Highly Sensitive and Robust Method for Genome-Wide 5hmc Profiling of Rare Cell Populations." Mol Cell 63, no. 4 (Aug 18 2016): 711-9.

    Hattori, T., D. Lai, I. S. Dementieva, S. P. Montano, K. Kurosawa, Y. Zheng, L. R. Akin, et al. "Antigen Clasping by Two Antigen-Binding Sites of an Exceptionally Specific Antibody for Histone Methylation." Proc Natl Acad Sci U S A 113, no. 8 (Feb 23 2016): 2092-7.

    Hoi, C. S., W. Xiong, and I. Rebay. "Retinal Axon Guidance Requires Integration of Eya and the Jak/Stat Pathway into Phosphotyrosine-Based Signaling Circuitries in Drosophila." Genetics 203, no. 3 (Jul 2016): 1283-95.

    Hornsby, M., M. Paduch, S. Miersch, A. Saaf, T. Matsuguchi, B. Lee, K. Wypisniak, et al. "A High through-Put Platform for Recombinant Antibodies to Folded Proteins." Mol Cell Proteomics 14, no. 10 (Oct 2015): 2833-47.

    Kariuki, S. N., J. D. Blischak, S. Nakagome, D. B. Witonsky, and A. Di Rienzo. "Patterns of Transcriptional Response to 1,25-Dihydroxyvitamin D3 and Bacterial Lipopolysaccharide in Primary Human Monocytes." G3 (Bethesda) 6, no. 5 (May 03 2016): 1345-55.

    Kariuki, S. N., J. C. Maranville, S. S. Baxter, C. Jeong, S. Nakagome, C. L. Hrusch, D. B. Witonsky, A. I. Sperling, and A. Di Rienzo. "Mapping Variation in Cellular and Transcriptional Response to 1,25-Dihydroxyvitamin D3 in Peripheral Blood Mononuclear Cells." PLoS One 11, no. 7 (2016): e0159779.

    Kregel, S., J. L. Chen, W. Tom, V. Krishnan, J. Kach, H. Brechka, T. B. Fessenden, et al. "Acquired Resistance to the Second-Generation Androgen Receptor Antagonist Enzalutamide in Castration-Resistant Prostate Cancer." Oncotarget 7, no. 18 (May 3 2016): 26259-74.

    Kubic, J. D., E. C. Little, J. W. Lui, T. Iizuka, and D. Lang. "Pax3 and Ets1 Synergistically Activate Met Expression in Melanoma Cells." Oncogene 34, no. 38 (Sep 17 2015): 4964-74.

    Laukka, T., C. J. Mariani, T. Ihantola, J. Z. Cao, J. Hokkanen, W. G. Kaelin, Jr., L. A. Godley, and P. Koivunen. "Fumarate and Succinate Regulate Expression of Hypoxia-Inducible Genes Via Tet Enzymes." J Biol Chem 291, no. 8 (Feb 19 2016): 4256-65.

    Lin, S., R. T. Luo, A. Ptasinska, J. Kerry, S. A. Assi, M. Wunderlich, T. Imamura, et al. "Instructive Role of Mll-Fusion Proteins Revealed by a Model of T(4;11) Pro-B Acute Lymphoblastic Leukemia." Cancer Cell 30, no. 5 (Nov 14 2016): 737-49.

    Liu, F., W. Clark, G. Luo, X. Wang, Y. Fu, J. Wei, X. Wang, et al. "Alkbh1-Mediated Trna Demethylation Regulates Translation." Cell 167, no. 7 (Dec 15 2016): 1897.

    Mandal, M., K. M. Hamel, M. Maienschein-Cline, A. Tanaka, G. Teng, J. H. Tuteja, J. J. Bunker, et al. "Histone Reader Brwd1 Targets and Restricts Recombination to the Igk Locus." Nat Immunol 16, no. 10 (Oct 2015): 1094-103.

    Mansour, N. M., G. M. Bernal, L. Wu, C. D. Crawley, K. E. Cahill, D. J. Voce, I. V. Balyasnikova, et al. "Decoy Receptor Dcr1 Is Induced in a P50/Bcl3-Dependent Manner and Attenuates the Efficacy of Temozolomide." Cancer Res 75, no. 10 (May 15 2015): 2039-48.

    Mao, A. P., M. G. Constantinides, R. Mathew, Z. Zuo, X. Chen, M. T. Weirauch, and A. Bendelac. "Multiple Layers of Transcriptional Regulation by Plzf in Nkt-Cell Development." Proc Natl Acad Sci U S A 113, no. 27 (Jul 5 2016): 7602-7.

    Marcon, E., H. Jain, A. Bhattacharya, H. Guo, S. Phanse, S. Pu, G. Byram, et al. "Assessment of a Method to Characterize Antibody Selectivity and Specificity for Use in Immunoprecipitation." Nat Methods 12, no. 8 (Aug 2015): 725-31.

    McConnell, S. C., K. M. Hernandez, D. J. Wcisel, R. N. Kettleborough, D. L. Stemple, J. A. Yoder, J. Andrade, and J. L. de Jong. "Alternative Haplotypes of Antigen Processing Genes in Zebrafish Diverged Early in Vertebrate Evolution." Proc Natl Acad Sci U S A 113, no. 34 (Aug 23 2016): E5014-23.

    Metcalfe, K., H. T. Lynch, W. D. Foulkes, N. Tung, C. Kim-Sing, O. I. Olopade, A. Eisen, et al. "Effect of Oophorectomy on Survival after Breast Cancer in Brca1 and Brca2 Mutation Carriers." JAMA Oncol 1, no. 3 (Jun 2015): 306-13.

    Michailidou, K., J. Beesley, S. Lindstrom, S. Canisius, J. Dennis, M. J. Lush, M. J. Maranian, et al. "Genome-Wide Association Analysis of More Than 120,000 Individuals Identifies 15 New Susceptibility Loci for Breast Cancer." Nat Genet 47, no. 4 (Apr 2015): 373-80.

    Miersch, S., Z. Li, R. Hanna, M. E. McLaughlin, M. Hornsby, T. Matsuguchi, M. Paduch, et al. "Scalable High Throughput Selection from Phage-Displayed Synthetic Antibody Libraries." J Vis Exp, no. 95 (Jan 17 2015): 51492.

    Moen, E. L., E. Litwin, S. Arnovitz, X. Zhang, W. Zhang, M. E. Dolan, and L. A. Godley. "Characterization of Cpg Sites That Escape Methylation on the Inactive Human X-Chromosome." Epigenetics 10, no. 9 (2015): 810-8.

    Mukherjee, S., M. Ura, R. J. Hoey, and A. A. Kossiakoff. "A New Versatile Immobilization Tag Based on the Ultra High Affinity and Reversibility of the Calmodulin-Calmodulin Binding Peptide Interaction." J Mol Biol 427, no. 16 (Aug 14 2015): 2707-25.

    Oshima, G., M. E. Stack, S. C. Wightman, D. Bryan, E. Poli, L. Xue, K. B. Skowron, et al. "Advanced Animal Model of Colorectal Metastasis in Liver: Imaging Techniques and Properties of Metastatic Clones." J Vis Exp, no. 117 (Nov 30 2016).

    Park, S., J. Choi, S. B. Biering, E. Dominici, L. E. Williams, and S. Hwang. "Targeting by Autophagy Proteins (Tag): Targeting of Ifng-Inducible Gtpases to Membranes by the Lc3 Conjugation System of Autophagy." Autophagy 12, no. 7 (Jul 2 2016): 1153-67.

    Pekow, J., K. Meckel, U. Dougherty, F. Butun, R. Mustafi, J. Lim, C. Crofton, et al. "Tumor Suppressors Mir-143 and Mir-145 and Predicted Target Proteins Api5, Erk5, K-Ras, and Irs-1 Are Differentially Expressed in Proximal and Distal Colon." Am J Physiol Gastrointest Liver Physiol 308, no. 3 (Feb 1 2015): G179-87.

    Pelaez, N., A. Gavalda-Miralles, B. Wang, H. T. Navarro, H. Gudjonson, I. Rebay, A. R. Dinner, et al. "Dynamics and Heterogeneity of a Fate Determinant During Transition Towards Cell Differentiation." Elife 4 (Nov 19 2015).

    Pu, J., I. Chronis, D. Ahn, and B. C. Dickinson. "A Panel of Protease-Responsive Rna Polymerases Respond to Biochemical Signals by Production of Defined Rna Outputs in Live Cells." J Am Chem Soc 137, no. 51 (Dec 30 2015): 15996-9.

    Rizk, S. S., J. L. Kouadio, A. Szymborska, E. M. Duguid, S. Mukherjee, J. Zheng, C. V. Clevenger, and A. A. Kossiakoff. "Engineering Synthetic Antibody Binders for Allosteric Inhibition of Prolactin Receptor Signaling." Cell Commun Signal 13 (Jan 15 2015): 1.

    Rolle, C. E., Y. C. Tan, T. Y. Seiwert, S. Vora, R. Kanteti, R. Hasina, G. B. Carey, et al. "Expression and Mutational Analysis of C-Cbl and Its Relationship to the Met Receptor in Head and Neck Squamous Cell Carcinoma." Oncotarget  (May 26 2016).

    Sasaki, M. M., A. D. Skol, E. A. Hungate, R. Bao, L. Huang, S. A. Kahn, J. M. Allan, et al. "Whole-Exome Sequence Analysis Implicates Rare Il17rel Variants in Familial and Sporadic Inflammatory Bowel Disease." Inflamm Bowel Dis 22, no. 1 (Jan 2016): 20-7.

    Seiwert, T. Y., Z. Zuo, M. K. Keck, A. Khattri, C. S. Pedamallu, T. Stricker, C. Brown, et al. "Integrative and Comparative Genomic Analysis of Hpv-Positive and Hpv-Negative Head and Neck Squamous Cell Carcinomas." Clin Cancer Res 21, no. 3 (Feb 1 2015): 632-41.

    Seow, W. J., W. C. Pan, M. L. Kile, L. Tong, A. A. Baccarelli, Q. Quamruzzaman, M. Rahman, et al. "A Distinct and Replicable Variant of the Squamous Cell Carcinoma Gene Inositol Polyphosphate-5-Phosphatase Modifies the Susceptibility of Arsenic-Associated Skin Lesions in Bangladesh." Cancer 121, no. 13 (Jul 1 2015): 2222-9.

    Shi, Y., T. Liu, L. He, U. Dougherty, L. Chen, S. Adhikari, L. Alpert, et al. "Activation of the Renin-Angiotensin System Promotes Colitis Development." Sci Rep 6 (Jun 08 2016): 27552.

    Singhal, H., M. E. Greene, G. Tarulli, A. L. Zarnke, R. J. Bourgo, M. Laine, Y. F. Chang, et al. "Genomic Agonism and Phenotypic Antagonism between Estrogen and Progesterone Receptors in Breast Cancer." Sci Adv 2, no. 6 (Jun 2016): e1501924.

    Skowron, K. B., S. P. Pitroda, J. P. Namm, O. Balogun, M. A. Beckett, M. L. Zenner, O. Fayanju, et al. "Basal Tumor Cell Isolation and Patient-Derived Xenograft Engraftment Identify High-Risk Clinical Bladder Cancers." Sci Rep 6 (Oct 24 2016): 35854.

    Spranger, S., R. Bao, and T. F. Gajewski. "Melanoma-Intrinsic Beta-Catenin Signalling Prevents Anti-Tumour Immunity." Nature 523, no. 7559 (Jul 9 2015): 231-5.

    Spranger, S., J. J. Luke, R. Bao, Y. Zha, K. M. Hernandez, Y. Li, A. P. Gajewski, J. Andrade, and T. F. Gajewski. "Density of Immunogenic Antigens Does Not Explain the Presence or Absence of the T-Cell-Inflamed Tumor Microenvironment in Melanoma." Proc Natl Acad Sci U S A 113, no. 48 (Nov 29 2016): E7759-E68.

    Stoddart, A., Z. Qian, A. A. Fernald, R. J. Bergerson, J. Wang, T. Karrison, J. Anastasi, et al. "Retroviral Insertional Mutagenesis Identifies the Del(5q) Genes, Cxxc5, Tifab and Etf1, as Well as the Wnt Pathway, as Potential Targets in Del(5q) Myeloid Neoplasms." Haematologica 101, no. 6 (Jun 2016): e232-6.

    Stuwe, T., C. J. Bley, K. Thierbach, S. Petrovic, S. Schilbach, D. J. Mayo, T. Perriches, et al. "Architecture of the Fungal Nuclear Pore Inner Ring Complex." Science 350, no. 6256 (Oct 2 2015): 56-64.

    Teng, G., Y. Maman, W. Resch, M. Kim, A. Yamane, J. Qian, K. R. Kieffer-Kwon, et al. "Rag Represents a Widespread Threat to the Lymphocyte Genome." Cell 162, no. 4 (Aug 13 2015): 751-65.

    Vasanthakumar, A., H. Zullow, J. B. Lepore, K. Thomas, N. Young, J. Anastasi, C. A. Reardon, and L. A. Godley. "Epigenetic Control of Apolipoprotein E Expression Mediates Gender-Specific Hematopoietic Regulation." Stem Cells 33, no. 12 (Dec 2015): 3643-54.

    Wang, X., C. R. Chow, K. Ebine, J. Lee, M. R. Rosner, T. Pan, and H. G. Munshi. "Interaction of Trna with Mek2 in Pancreatic Cancer Cells." Sci Rep 6 (Jun 15 2016): 28260.
    Ward, M. A., J. F. Pierre, R. F. Leal, Y. Huang, B. Shogan, S. R. Dalal, C. R. Weber, et al. "Insights into the Pathogenesis of Ulcerative Colitis from a Murine Model of

    Stasis-Induced Dysbiosis, Colonic Metaplasia, and Genetic Susceptibility." Am J Physiol Gastrointest Liver Physiol 310, no. 11 (Jun 1 2016): G973-88.

    West, D. C., D. Pan, E. Y. Tonsing-Carter, K. M. Hernandez, C. F. Pierce, S. C. Styke, K. R. Bowie, et al. "Gr and Er Coactivation Alters the Expression of Differentiation Genes and Associates with Improved Er+ Breast Cancer Outcome." Mol Cancer Res 14, no. 8 (Aug 2016): 707-19.

    Yang, Y. A., J. C. Zhao, K. W. Fong, J. Kim, S. Li, C. Song, B. Song, et al. "Foxa1 Potentiates Lineage-Specific Enhancer Activation through Modulating Tet1 Expression and Function." Nucleic Acids Res 44, no. 17 (Sep 30 2016): 8153-64.

    Zhang, B., X. O. Shu, R. J. Delahanty, C. Zeng, K. Michailidou, M. K. Bolla, Q. Wang, et al. "Height and Breast Cancer Risk: Evidence from Prospective Studies and Mendelian Randomization." J Natl Cancer Inst 107, no. 11 (Nov 2015).

    Zhang, W., E. R. Gamazon, X. Zhang, A. Konkashbaev, C. Liu, K. L. Szilagyi, M. E. Dolan, and N. J. Cox. "Scan Database: Facilitating Integrative Analyses of Cytosine Modification and Expression Qtl." Database (Oxford) 2015 (2015).

    Zhao, Z., W. Wen, K. Michailidou, M. K. Bolla, Q. Wang, B. Zhang, J. Long, et al. "Association of Genetic Susceptibility Variants for Type 2 Diabetes with Breast Cancer Risk in Women of European Ancestry." Cancer Causes Control 27, no. 5 (May 2016): 679-93.


    Acknowledgement of core facility contributions in publications is appreciated.
    Cancer center members should cite the Cancer Center Support Grant (P30 CA014599) when publishing any work assisted by this core facility.