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Carl R. Woese Institute for Genomic Biology

Where Science Meets Society

Research Areas

Thirawatananond, P., McPherson, R. L., Malhi, J., Nathan, S., Lambrecht, M. J., Brichacek, M., ... Gabelli, S. B. (2019). Structural analyses of NudT16–ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins. Scientific Reports, 9(1), [5940].

Hejna, M., Moon, W. M., Cheng, J., Kawakami, A., Fisher, D. E., & Song, J. (2019). Local genomic features predict the distinct and overlapping binding patterns of the bHLH-Zip family oncoproteins MITF and MYC-MAX. Pigment Cell and Melanoma Research, 32(4), 500-509.

Llabani, E., Hicklin, R. W., Lee, H. Y., Motika, S. E., Crawford, L. A., Weerapana, E., & Hergenrother, P. (2019). Diverse compounds from pleuromutilin lead to a thioredoxin inhibitor and inducer of ferroptosis. Nature Chemistry, 11(6), 521-532.

Aye, Y., & Hergenrother, P. (2019). Editorial overview: From the iceman to modern medicine. Current Opinion in Chemical Biology, 50, A1-A2.

Parks, C. A., Henning, K. R., Pavelko, K. D., Hansen, M. J., Van Keulen, V. P., Reed, B. K., ... Pease, L. R. (2019). Breaking tolerance with engineered class I antigen-presenting molecules. Proceedings of the National Academy of Sciences of the United States of America, 116(8), 3136-3145.

Bingham, T. W., Hernandez, L. W., Olson, D. G., Svec, R. L., Hergenrother, P., & Sarlah, D. (2019). Enantioselective Synthesis of Isocarbostyril Alkaloids and Analogs Using Catalytic Dearomative Functionalization of Benzene. Journal of the American Chemical Society, 141(1), 657-670.

Watson, M. K., Mitchell, M. A., Stern, A. W., Labelle, A. L., Joslyn, S., Fan, T. M., ... Marshall, K. (2019). EVALUATING THE CLINICAL AND PHYSIOLOGICAL EFFECTS OF LONG-TERM ULTRAVIOLET B RADIATION ON RABBITS (ORYCTOLAGUS CUNICULUS). Journal of Exotic Pet Medicine, 28, 43-55.

Roy, J., Dibaeinia, P., Fan, T. M., Sinha, S., & Das, A. (2019). Global analysis of osteosarcoma lipidomes reveal altered lipid profiles in metastatic versus nonmetastatic cells. Journal of Lipid Research, 60(2), 375-387.

Blaha, D. T., Anderson, S. D., Yoakum, D. M., Hager, M. V., Zha, Y., Gajewski, T. F., & Kranz, D. M. (2019). High-throughput stability screening of neoantigen/HLA complexes improves immunogenicity predictions. Cancer immunology research, 7(1), 50-61.

Schlein, L. J., Fadl-Alla, B., Pondenis, H. C., Lezmi, S., Eberhart, C. G., LeBlanc, A. K., ... Fan, T. M. (2019). Immunohistochemical characterization of procaspase-3 overexpression as a druggable target with PAC-1, a procaspase-3 activator, in canine and human brain cancers. Frontiers in Oncology, 9(FEB), [96].

Dowling, M., Samuelson, J. P., Fadl-Alla, B., Pondenis, H. C., Byrum, M., Barger, A. M., & Fan, T. M. (2019). Overexpression of prostate specific membrane antigen by canine hemangiosarcoma cells provides opportunity for the molecular detection of disease burdens within hemorrhagic body cavity effusions. PLoS One, 14(1), [e0210297].

Richter, M. F., & Hergenrother, P. (2019). The challenge of converting gram-positive-only compounds into broad-spectrum antibiotics. Annals of the New York Academy of Sciences, 1435(1), 18-38.

Rack, J. G. M., Ariza, A., Drown, B. S., Henfrey, C., Bartlett, E., Shirai, T., ... Ahel, I. (2018). (ADP-ribosyl)hydrolases: Structural Basis for Differential Substrate Recognition and Inhibition. Cell chemical biology, 25(12), 1533-1546.e12.

Drown, B. S., Shirai, T., Rack, J. G. M., Ahel, I., & Hergenrother, P. (2018). Monitoring Poly(ADP-ribosyl)glycohydrolase Activity with a Continuous Fluorescent Substrate. Cell Chemical Biology, 25(12), 1562-1570.e19.

Burton, J. H., Mazcko, C., LeBlanc, A., Covey, J. M., Ji, J., Kinders, R. J., ... Pommier, Y. (2018). NCI comparative oncology program testing of non-camptothecin indenoisoquinoline topoisomerase I inhibitors in naturally occurring canine lymphoma. Clinical Cancer Research, 24(23), 5830-5840.

Cao, J., Perez Pinera, P., Lowenhaupt, K., Wu, M. R., Purcell, O., De La Fuente-Nunez, C., & Lu, T. K. (2018). Versatile and on-demand biologics co-production in yeast. Nature communications, 9(1), [77].

Svec, R. L., Furiassi, L., Skibinski, C. G., Fan, T. M., Riggins, G. J., & Hergenrother, P. (2018). Tunable Stability of Imidazotetrazines Leads to a Potent Compound for Glioblastoma. ACS chemical biology, 13(11), 3206-3216.

Svec, R. L., & Hergenrother, P. (2018). Oxygen Starvation Unmasks a Killer. Cell chemical biology, 25(11), 1313-1314.

Cheng, J. B., Sedgewick, A. J., Finnegan, A. I., Harirchian, P., Lee, J., Kwon, S., ... Cho, R. J. (2018). Transcriptional Programming of Normal and Inflamed Human Epidermis at Single-Cell Resolution. Cell Reports, 25(4), 871-883.

Livezey, M., Huang, R., Hergenrother, P., & Shapiro, D. J. (2018). Strong and sustained activation of the anticipatory unfolded protein response induces necrotic cell death. Cell Death and Differentiation, 25(10), 1796-1807.

Gaj, T., & Perez Pinera, P. (2018). The continuously evolving CRISPR barcoding toolbox Jin-Soo Kim. Genome Biology, 19(1), [143].

Tasker, S. Z., Cowfer, A. E., & Hergenrother, P. (2018). Preparation of Structurally Diverse Compounds from the Natural Product Lycorine. Organic Letters, 20(18), 5894-5898.

Jin, H., Finnegan, A. I., & Song, J. (2018). A unified computational framework for modeling genome-wide nucleosome landscape. Physical Biology, 15(6), [066011].

Mancini, A., Xavier-Magalhães, A., Woods, W. S., Nguyen, K. T., Amen, A. M., Hayes, J. L., ... Costello, J. F. (2018). Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner. Cancer Cell, 34(3), 513-528.e8.

Anorma, C., Hedhli, J., Bearrood, T. E., Pino, N. W., Gardner, S. H., Inaba, H., ... Chan, J. K. F. (2018). Surveillance of Cancer Stem Cell Plasticity Using an Isoform-Selective Fluorescent Probe for Aldehyde Dehydrogenase 1A1. ACS Central Science, 4(8), 1045-1055.

Peh, J., Boudreau, M. W., Smith, H. M., & Hergenrother, P. (2018). Overcoming Resistance to Targeted Anticancer Therapies through Small-Molecule-Mediated MEK Degradation. Cell chemical biology, 25(8), 996-1005.e4.

Gapinske, M., Luu, A., Winter, J., Woods, W. S., Kostan, K. A., Shiva, N., ... Perez Pinera, P. (2018). CRISPR-SKIP: Programmable gene splicing with single base editors. Genome biology, 19(1), [107].

Zhao, C., & Song, J. (2018). Quantum transport senses community structure in networks. Physical Review E, 98(2), [022301].

Roy, J., Watson, J. E., Hong, I. S., Fan, T. M., & Das, A. (2018). Antitumorigenic Properties of Omega-3 Endocannabinoid Epoxides. Journal of Medicinal Chemistry, 61(13), 5569-5579.

Drown, B. S., & Hergenrother, P. (2018). Going on offense against the gram-negative defense. Proceedings of the National Academy of Sciences of the United States of America, 115(26), 6530-6532.

Phillips, H., Maxwell, E. A., Schaeffer, D. J., & Fan, T. M. (2018). Simulation of spatial diffusion of platinum from carboplatin-impregnated calcium sulfate hemihydrate beads by use of an agarose gelatin tissue phantom. American journal of veterinary research, 79(6), 592-599.

Yin, Q., Tang, L., Cai, K., Yang, X., Yin, L., Zhang, Y., ... Cheng, J. (2018). Albumin as a "trojan Horse" for polymeric nanoconjugate transendothelial transport across tumor vasculatures for improved cancer targeting. Biomaterials Science, 6(5), 1189-1200.

Zhang, Y., Manjunath, M., Zhang, S., Chasman, D., Roy, S., & Song, J. (2018). Integrative genomic analysis predicts causative cis-regulatory mechanisms of the breast cancer–associated genetic variant rs4415084. Cancer Research, 78(7), 1579-1591.

Saba, C. F., Vickery, K. R., Clifford, C. A., Burgess, K. E., Phillips, B., Vail, D. M., ... Thamm, D. H. (2018). Rabacfosadine for relapsed canine B-cell lymphoma: Efficacy and adverse event profiles of 2 different doses. Veterinary and comparative oncology, 16(1), E76-E82.

Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., ... Zhang, B. (2018). How many human proteoforms are there? Nature chemical biology, 14(3), 206-214.

Denisov, I. G., Baylon, J. L., Grinkova, Y. V., Tajkhorshid, E., & Sligar, S. G. (2018). Drug-Drug Interactions between Atorvastatin and Dronedarone Mediated by Monomeric CYP3A4. Biochemistry, 57(5), 805-816.

Harris, D. T., Hager, M. V., Smith, S. N., Cai, Q., Stone, J. D., Kruger, P., ... Kranz, D. M. (2018). Comparison of t cell activities mediated by human TCRs and CARs that use the same recognition domains. Journal of Immunology, 200(3), 1088-1100.

Maxwell, E. A., Phillips, H., Schaeffer, D. J., & Fan, T. M. (2018). In vitro chemosensitivity of feline injection site-associated sarcoma cell lines to carboplatin. Veterinary Surgery, 47(2), 219-226.

Hejna, M., Jorapur, A., Zhang, Y., Song, J., & Judson, R. L. (2018). Quantification of mammalian tumor cell state plasticity with digital holographic cytometry. In Quantitative Phase Imaging IV (Vol. 10503). [1050312] SPIE.

Sharma, P., & Kranz, D. M. (2018). Subtle changes at the variable domain interface of the T-cell receptor can strongly increase affinity. Journal of Biological Chemistry, 293(5), 1820-1834.

Gapinske, M., Tague, N., Winter, J., Underhill, G. H., & Perez Pinera, P. (2018). Targeted gene knock out using nuclease-assisted vector integration: Hemi- and Homozygous deletion of JAG1. In Methods in Molecular Biology (pp. 233-248). (Methods in Molecular Biology; Vol. 1772). Humana Press Inc..

Zheng, X., Andruska, N., Lambrecht, M. J., He, S., Parissenti, A., Hergenrother, P., ... Shapiro, D. J. (2018). Targeting multidrug-resistant ovarian cancer through estrogen receptor a dependent ATP depletion caused by hyperactivation of the unfolded protein response. Oncotarget, 9(19), 14741-14753.