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Illinois IGB

Research Areas

Anticancer Discovery from Pets to People: Publications

Winter, J., Luu, A., Gapinske, M., Manandhar, S., Shirguppe, S., Woods, W. S., ... Perez-Pinera, P. (2019). Author Correction: Targeted exon skipping with AAV-mediated split adenine base editors (Cell Discovery, (2019), 5, 1, (41), 10.1038/s41421-019-0109-7). Cell Discovery, 5(1), [56].

Janin, M., Ortiz-Barahona, V., de Moura, M. C., Martínez-Cardús, A., Llinàs-Arias, P., Soler, M., ... Esteller, M. (2019). Epigenetic loss of RNA-methyltransferase NSUN5 in glioma targets ribosomes to drive a stress adaptive translational program. Acta Neuropathologica, 138(6), 1053-1074.

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].

Winter, J., Luu, A., Gapinske, M., Manandhar, S., Shirguppe, S., Woods, W. S., ... Perez-Pinera, P. (2019). Targeted exon skipping with AAV-mediated split adenine base editors. Cell Discovery, 5(1), [41].

Parker, E. N., Drown, B. S., Geddes, E. J., Lee, H. Y., Ismail, N., Lau, G. W., & Hergenrother, P. J. (2019). Implementation of permeation rules leads to a FabI inhibitor with activity against Gram-negative pathogens. Nature Microbiology.

Boudreau, M. W., Peh, J., & Hergenrother, P. J. (2019). Procaspase-3 Overexpression in Cancer: A Paradoxical Observation with Therapeutic Potential. ACS chemical biology, 14(11), 2335-2348.

Winter, J., & Perez-Pinera, P. (2019). Directed Evolution of CRISPR-Cas9 Base Editors. Trends in Biotechnology, 37(11), 1151-1153.

Roberts, R. D., Lizardo, M. M., Reed, D. R., Hingorani, P., Glover, J., Allen-Rhoades, W., ... Crompton, B. D. (2019). Provocative questions in osteosarcoma basic and translational biology: A report from the Children's Oncology Group. Cancer, 125(20), 3514-3525.

Brown, A., Winter, J., Gapinske, M., Tague, N., Woods, W. S., & Perez-Pinera, P. (2019). Multiplexed and tunable transcriptional activation by promoter insertion using nuclease-assisted vector integration. Nucleic acids research, 47(12), e67.

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.

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.

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].

Denisov, I. G., Schuler, M. A., & Sligar, S. (2019). Nanodiscs as a New Tool to Examine Lipid–Protein Interactions. In Methods in Molecular Biology (pp. 645-671). (Methods in Molecular Biology; Vol. 2003). Humana Press Inc..

Zhang, Y., Manjunath, M., Kim, Y., Heintz, J., & Song, J. (2019). Sequenceng: An interactive knowledge base of sequencing techniques. Bioinformatics, 35(8), 1438-1440.

Finnegan, A., Cho, R. J., Luu, A., Harirchian, P., Lee, J., Cheng, J. B., & Song, J. S. (2019). Single-cell transcriptomics reveals spatial and temporal turnover of keratinocyte differentiation regulators. Frontiers in Genetics, 10(JUL), [775].

Sharma, P., Harris, D. T., Stone, J. D., & Kranz, D. M. (2019). T-cell receptors engineered de novo for peptide specificity can mediate optimal t-cell activity without self cross-reactivity. Cancer Immunology Research, 7(12), 2025-2035.

Sharma, P., & Kranz, D. M. (2019). T cell receptors for gene transfer in adoptive T cell therapy. Critical Reviews in Immunology, 39(2), 105-122.

Zhang, Y., Manjunath, M., Yan, J., Baur, B. A., Zhang, S., Roy, S., & Song, J. (2019). The cancer-associated genetic variant rs3903072 modulates immune cells in the tumor microenvironment. Frontiers in Genetics, 10(JUL), [754].

Richter, M. F., & Hergenrother, P. J. (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.

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.

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.

Dowling, M., Samuelson, J., 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].

1.2. 2018

Overgaard, N. H., Fan, T. M., Schachtschneider, K. M., Principe, D. R., Schook, L. B., & Jungersen, G. (2018). Of Mice, Dogs, Pigs, and Men: Choosing the Appropriate Model for Immuno-Oncology Research. ILAR Journal, 59(3), 247-262.

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. J. (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. S. (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.

Gurumurthy, C. B., & Perez-Pinera, P. (2018). Technological advances in integrating multi-kilobase DNA sequences into genomes. Current Opinion in Biomedical Engineering, 7, 16-23.

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. S. (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. S. (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.

Manjunath, M., Zhang, Y., Kim, Y., Yeo, S. H., Sobh, O., Russell, N., ... Song, J. S. (2018). ClusterEnG: An interactive educational web resource for clustering and visualizing high-dimensional data. PeerJ Computer Science, 2018(5), [e155].

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. J., ... 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.