Skip to main content

Illinois IGB

Research Areas

Anticancer Discovery from Pets to People: Publications

Alexander, C., Cross, T. W. L., Lee, A. H., Ly, L. K., Vieson, M. D., Ridlon, J. M., Nelson, E. R., & Swanson, K. S. (2021). Development of a novel model of cholecystectomy in subsequently ovariectomized mice and characterization of metabolic and gastrointestinal phenotypes: a pilot study. BMC Gastroenterology, 21(1), [62]. https://doi.org/10.1186/s12876-021-01648-1

Baek, A. E., Krawczynska, N., Das Gupta, A., Dvoretskiy, S. V., You, S., Park, J., Deng, Y-H., Sorrells, J. E., Smith, B. P., Ma, L., Nelson, A. T., McDowell, H. B., Sprenger, A., Henn, M. A., Madak-Erdogan, Z., Kong, H., Boppart, S. A., Boppart, M. D., & Nelson, E. R. (Accepted/In press). The cholesterol metabolite 27-hydroxycholesterol increases the secretion of extracellular vesicles which promote breast cancer progression. Endocrinology, [bqab095]. https://doi.org/10.1210/endocr/bqab095

Hutchinson, S. A., Websdale, A., Cioccoloni, G., Røberg-Larsen, H., Lianto, P., Kim, B., Rose, A., Soteriou, C., Pramanik, A., Wastall, L. M., Williams, B. J., Henn, M. A., Chen, J. J., Ma, L., Moore, J. B., Nelson, E., Hughes, T. A., & Thorne, J. L. (2021). Liver x receptor alpha drives chemoresistance in response to side-chain hydroxycholesterols in triple negative breast cancer. Oncogene, 40(16), 2872-2883. https://doi.org/10.1038/s41388-021-01720-w

Manjunath, M., Yan, J., Youn, Y., Drucker, K. L., Kollmeyer, T. M., McKinney, A. M., Zazubovich, V., Zhang, Y., Costello, J. F., Eckel-Passow, J., Selvin, P. R., Jenkins, R. B., & Song, J. S. (2021). Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors. Neuro-Oncology, 23(4), 638-649. https://doi.org/10.1093/neuonc/noaa248

Luu, A. M., Leistico, J. R., Miller, T., Kim, S., & Song, J. S. (2021). Predicting TCR-Epitope Binding Specificity Using Deep Metric Learning and Multimodal Learning. Genes, 12(4), NA. [572]. https://doi.org/10.3390/genes12040572

Leistico, J. R., Saini, P., Futtner, C. R., Hejna, M., Omura, Y., Soni, P. N., Sandlesh, P., Milad, M., Wei, J. J., Bulun, S., Parker, J. B., Barish, G. D., Song, J. S., & Chakravarti, D. (2021). Epigenomic tensor predicts disease subtypes and reveals constrained tumor evolution. Cell Reports, 34(13), [108927]. https://doi.org/10.1016/j.celrep.2021.108927

Jawad, M. N., Bhattacharjee, A., Lehmann, R., Busza, A., Perez-Pinera, P., & Jensen, K. (2021). Remote Laboratory Exercise to Develop Micropipetting Skills. Journal of Microbiology and Biology Education, 22(1). https://doi.org/10.1128/jmbe.v22i1.2399

Geng, J., Zhang, X., Prabhu, S., Shahoei, S. H., Nelson, E. R., Swanson, K. S., Anastasio, M. A., & Smith, A. M. (2021). 3D microscopy and deep learning reveal the heterogeneity of crown-like structure microenvironments in intact adipose tissue. Science Advances, 7(8), [eabe2480]. https://doi.org/10.1126/sciadv.abe2480

Garcia Chavez, M., Garcia, A., Lee, H. Y., Lau, G. W., Parker, E. N., Komnick, K. E., & Hergenrother, P. J. (2021). Synthesis of Fusidic Acid Derivatives Yields a Potent Antibiotic with an Improved Resistance Profile. ACS Infectious Diseases, 7(2), 493-505. https://doi.org/10.1021/acsinfecdis.0c00869

Boyko, Y. D., Huck, C. J., Ning, S., Shved, A. S., Yang, C., Chu, T., Tonogai, E. J., Hergenrother, P. J., & Sarlah, D. (2021). Synthetic Studies on Selective, Proapoptotic Isomalabaricane Triterpenoids Aided by Computational Techniques. Journal of the American Chemical Society, 143(4), 2138-2155. https://doi.org/10.1021/jacs.0c12569

Prabhu, S., Deng, H., Cross, T. W. L., Shahoei, S. H., Konopka, C. J., Gonzalez Medina, N., Applegate, C. C., Wallig, M. A., Dobrucki, W., Nelson, E. R., Smith, A. M., & Swanson, K. S. (2021). Nanocarriers targeting adipose macrophages increase glucocorticoid anti-inflammatory potency to ameliorate metabolic dysfunction. Biomaterials Science, 9(2), 506-518. https://doi.org/10.1039/d0bm01142h

Perlmutter, S. J., Geddes, E. J., Drown, B. S., Motika, S. E., Lee, M. R., & Hergenrother, P. J. (2021). Compound Uptake into E. coli Can Be Facilitated by N-Alkyl Guanidiniums and Pyridiniums. ACS Infectious Diseases, 7(1), 162-173. https://doi.org/10.1021/acsinfecdis.0c00715

Polidore, A. L. A., Furiassi, L., Hergenrother, P. J., & Metcalf, W. W. (2021). A phosphonate natural product made by pantoea ananatis is necessary and sufficient for the hallmark lesions of onion center rot. mBio, 12(1), 1-18. [e03402-20]. https://doi.org/10.1128/mBio.03402-20

Basu, A., Bobrovnikov, D. G., Qureshi, Z., Kayikcioglu, T., Ngo, T. T. M., Ranjan, A., Eustermann, S., Cieza, B., Morgan, M. T., Hejna, M., Rube, H. T., Hopfner, K-P., Wolberger, C., Song, J. S., & Ha, T. (2021). Measuring DNA mechanics on the genome scale. Nature, 589(7842), 462-467. https://doi.org/10.1038/s41586-020-03052-3

Finnegan, A. I., Kim, S., Jin, H., Gapinske, M., Woods, W. S., Perez-Pinera, P., & Song, J. S. (2021). Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members. Nucleic acids research, 48(8), 4081-4099. https://doi.org/10.1093/NAR/GKAA161

Muñoz, K. A., & Hergenrother, P. J. (Accepted/In press). Facilitating Compound Entry as a Means to Discover Antibiotics for Gram-Negative Bacteria. Accounts of chemical research. https://doi.org/10.1021/acs.accounts.0c00895

Levitin, H. A., Foss, K. D., Li, Z., Reinhart Dungar, J. M., Hague, D. W., & Fan, T. M. (Accepted/In press). Pharmacokinetics of a cytosine arabinoside subcutaneous protocol in dogs with meningoencephalomyelitis of unknown aetiology. Journal of Veterinary Pharmacology and Therapeutics. https://doi.org/10.1111/jvp.12980

Saba, C. F., Clifford, C., Burgess, K., Phillips, B., Vail, D., Wright, Z., Curran, K., Fan, T., Elmslie, R., Post, G., & Thamm, D. (2020). Rabacfosadine for naïve canine intermediate to large cell lymphoma: Efficacy and adverse event profile across three prospective clinical trials. Veterinary and comparative oncology18(4), 763-769. https://doi.org/10.1111/vco.12605

Ma, L., Wang, L., Nelson, A. T., Han, C., He, S., Henn, M. A., Menon, K., Chen, J. J., Baek, A. E., Vardanyan, A., Shahoei, S. H., Park, S., Shapiro, D. J., Nanjappa, S. G., & Nelson, E. R. (2020). 27-Hydroxycholesterol acts on myeloid immune cells to induce T cell dysfunction, promoting breast cancer progression. Cancer Letters493, 266-283. https://doi.org/10.1016/j.canlet.2020.08.020

Eckel-Passow, J. E., Drucker, K. L., Kollmeyer, T. M., Kosel, M. L., Decker, P. A., Molinaro, A. M., Rice, T., Praska, C. E., Clark, L., Caron, A., Abyzov, A., Batzler, A., Song, J. S., Pekmezci, M., Hansen, H. M., McCoy, L. S., Bracci, P. M., Wiemels, J., Wiencke, J. K., ... Jenkins, R. B. (2020). Adult diffuse glioma GWAS by molecular subtype identifies variants in D2HGDH and FAM20C. Neuro-Oncology22(11), 1602-1613. https://doi.org/10.1093/neuonc/noaa117

Prabhu, S., Deng, H., Cross, T-W. L., Shahoei, S. H., Konopka, C. J., Gonzalez Medina, N., Applegate, C. C., Wallig, M. A., Dobrucki, L. W., Nelson, E. R., Smith, A. M., & Swanson, K. S. (2020). Nanocarriers targeting adipose macrophages increase glucocorticoid anti-inflammatory potency to ameliorate metabolic dysfunction. Biomaterials Sciencehttps://doi.org/10.1039/d0bm01142h

Singh, N. K., Alonso, J. A., Harris, D. T., Anderson, S. D., Ma, J., Hellman, L. M., Rosenberg, A. M., Kolawole, E. M., Evavold, B. D., Kranz, D. M., & Baker, B. M. (2020). An engineered T cell receptor variant realizes the limits of functional binding modes. Biochemistry59(43), 4163-4175. https://doi.org/10.1021/acs.biochem.0c00689

Manjunath, M., Yan, J., Youn, Y., Drucker, K. L., Kollmeyer, T. M., McKinney, A. M., Zazubovich, V., Zhang, Y., Costello, J. F., Eckel-Passow, J., Selvin, P. R., Jenkins, R. B., & Song, J. S. (2020). Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors. Neuro-Oncologyhttps://doi.org/10.1093/neuonc/noaa248

Motika, S. E., & Hergenrother, P. J. (2020). Re-engineering natural products to engage new biological targets. Natural Product Reports37(11), 1395-1403. https://doi.org/10.1039/d0np00059k

Liu, Y., Cook, C., Sedgewick, A. J., Zhang, S., Fassett, M. S., Ricardo-Gonzalez, R. R., Harirchian, P., Kashem, S. W., Hanakawa, S., Leistico, J. R., North, J. P., Taylor, M. A., Zhang, W., Man, M. Q., Charruyer, A., Beliakova-Bethell, N., Benz, S. C., Ghadially, R., Mauro, T. M., ... Cheng, J. B. (2020). Single-Cell Profiling Reveals Divergent, Globally Patterned Immune Responses in Murine Skin Inflammation. iScience23(10), [101582]. https://doi.org/10.1016/j.isci.2020.101582

Chan, K. K., Dorosky, D., Sharma, P., Abbasi, S. A., Dye, J. M., Kranz, D. M., Herbert, A. S., & Procko, E. (2020). Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2. Science369(6508), 1261-1265. https://doi.org/10.1101/2020.03.16.994236https://doi.org/10.1126/science.abc0870

Koelwyn, G. J., Newman, A. A. C., Afonso, M. S., van Solingen, C., Corr, E. M., Brown, E. J., Albers, K. B., Yamaguchi, N., Narke, D., Schlegel, M., Sharma, M., Shanley, L. C., Barrett, T. J., Rahman, K., Mezzano, V., Fisher, E. A., Park, D. S., Newman, J. D., Quail, D. F., ... Moore, K. J. (2020). Myocardial infarction accelerates breast cancer via innate immune reprogramming. Nature Medicine26(9), 1452-1458. https://doi.org/10.1038/s41591-020-0964-7

Liu, C. J., Schaettler, M., Blaha, D. T., Bowman-Kirigin, J. A., Kobayashi, D. K., Livingstone, A. J., Bender, D., Miller, C. A., Kranz, D. M., Johanns, T. M., & Dunn, G. P. (2020). Treatment of an aggressive orthotopic murine glioblastoma model with combination checkpoint blockade and a multivalent neoantigen vaccine. Neuro-Oncology22(9), 1276-1288. https://doi.org/10.1093/neuonc/noaa050

Manjunath, M., Zhang, Y., Zhang, S., Roy, S., Perez-Pinera, P., & Song, J. S. (2020). ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants. Frontiers in Genetics11, [730]. https://doi.org/10.3389/fgene.2020.00730

Zhang, S., Leistico, J. R., Cook, C., Liu, Y., Cho, R. J., Cheng, J. B., & Song, J. S. (2020). Riemannian geometry and statistical modeling correct for batch effects and control false discoveries in single-cell surface protein count data. Physical Review E102(1), [012409]. https://doi.org/10.1103/PhysRevE.102.012409

Sharma, P., Marada, V. V. V. R., Cai, Q., Kizerwetter, M., He, Y., Wolf, S. P., Schreiber, K., Clausen, H., Schreiber, H., & Kranz, D. M. (2020). Structure-guided engineering of the affinity and specificity of CARs against Tn-glycopeptides. Proceedings of the National Academy of Sciences117(26), 15148-15159. [201920662]. https://doi.org/10.1073/pnas.1920662117

Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Brooke, C. B., Burke, M. D., Fan, T. M., & Hergenrother, P. J. (2020). Saliva-based molecular testing for SARS-CoV-2 that bypasses RNA extraction. Unknown Journalhttps://doi.org/10.1101/2020.06.18.159434

Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Brooke, C. B., Burke, M., Fan, T. M., & Hergenrother, P. (2020). Saliva-Based Molecular Testing for SARS-CoV-2 that Bypasses RNA Extraction. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.06.18.159434

Motika, S. E., Ulrich, R. J., Geddes, E. J., Lee, H. Y., Lau, G. W., & Hergenrother, P. J. (2020). Gram-Negative Antibiotic Active through Inhibition of an Essential Riboswitch. Journal of the American Chemical Society142(24), 10856-10862. https://doi.org/10.1021/jacs.0c04427

Laws, M. J., Ziegler, Y., Shahoei, S. H., Dey, P., Kim, S. H., Yasuda, M., Park, B. H., Nettles, K. W., Katzenellenbogen, J. A., Nelson, E. R., & Katzenellenbogen, B. S. (2020). Suppression of breast cancer metastasis and extension of survival by a new antiestrogen in a preclinical model driven by mutant estrogen receptors. Breast Cancer Research and Treatment181(2), 297-307. https://doi.org/10.1007/s10549-020-05629-y

Finnegan, A. I., Kim, S., Jin, H., Gapinske, M., Woods, W. S., Perez-Pinera, P., & Song, J. S. (2020). Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members. Nucleic acids research48(8), 4081-4099. https://doi.org/10.1093/nar/gkaa161

Maxwell, E. A., Phillips, H., Clark-Price, S. C., Vieson, M. D., Selmic, L. E., Schaeffer, D. J., & Fan, T. M. (2020). Pharmacokinetics of platinum and safety evaluation of carboplatin-impregnated calcium sulfate hemihydrate beads after implantation in healthy cats. Veterinary Surgery49(4), 748-757. https://doi.org/10.1111/vsu.13372

Tang, B., Guo, Z. S., Bartlett, D. L., Yan, D. Z., Schane, C. P., Thomas, D. L., Liu, J., McFadden, G., Shisler, J. L., Roy, E. J., & Roy, E. J. (2020). Synergistic Combination of Oncolytic Virotherapy and Immunotherapy for Glioma. Clinical Cancer Research26(9), 2216-2230. https://doi.org/10.1158/1078-0432.CCR-18-3626

Zhang, S., Leistico, J. R., Cook, C., Liu, Y., Cho, R. J., Cheng, J. B., & Song, J. S. (2020). Riemannian geometry and statistical modeling correct for batch effects and control false discoveries in single-cell surface protein count data from CITE-seq. Unknown Journalhttps://doi.org/10.1101/2020.04.28.067306

Allan, E. R. O., Dores, C. B., Nelson, E. R., & Habibi, H. R. (2020). Acute exposure to physiological doses of triiodothyronine does not induce gonadal caspase 3 activity in goldfish in vitro. General and Comparative Endocrinology289, [113382]. https://doi.org/10.1016/j.ygcen.2019.113382

Fan, T. M., Roberts, R. D., & Lizardo, M. M. (2020). Understanding and Modeling Metastasis Biology to Improve Therapeutic Strategies for Combating Osteosarcoma Progression. Frontiers in Oncology10, [13]. https://doi.org/10.3389/fonc.2020.00013

Svec, R. L., & Hergenrother, P. J. (2020). Imidazotetrazines as Weighable Diazomethane Surrogates for Esterifications and Cyclopropanations. Angewandte Chemie - International Edition59(5), 1857-1862. https://doi.org/10.1002/anie.201911896

Finnegan, A. I., Kim, S., Jin, H., Gapinske, M., Woods, W. S., Perez-Pinera, P., & Song, J. S. (2020). Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members. Unknown Journalhttps://doi.org/10.1101/2020.01.26.919936

Lim, C. K. W., Gapinske, M., Brooks, A. K., Woods, W. S., Powell, J. E., Zeballos C., M. A., Winter, J., Perez-Pinera, P., & Gaj, T. (Accepted/In press). Treatment of a Mouse Model of ALS by In Vivo Base Editing. Molecular Therapy28(4), 1177-1189. https://doi.org/10.1016/j.ymthe.2020.01.005

Perlmutter, S. J., Geddes, E. J., Drown, B. S., Motika, S. E., Lee, M. R., & Hergenrother, P. J. (Accepted/In press). Compound Uptake into E. coli Can Be Facilitated by N-Alkyl Guanidiniums and Pyridiniums. ACS Infectious Diseaseshttps://doi.org/10.1021/acsinfecdis.0c00715

Blatti, C., Emad, A., Berry, M. J., Gatzke, L., Epstein, M., Lanier, D., Rizal, P., Ge, J., Liao, X., Sobh, O., Lambert, M., Post, C. S., Xiao, J., Groves, P., Epstein, A. T., Chen, X., Srinivasan, S., Lehnert, E., Kalari, K. R., ... Sinha, S. (2020). Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform. PLoS biology18(1), [e3000583]. https://doi.org/10.1371/journal.pbio.3000583

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]. https://doi.org/10.1038/s41421-019-0125-7

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. https://doi.org/10.1007/s00401-019-02062-4

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]. https://doi.org/10.1038/s41598-019-39491-w

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]. https://doi.org/10.1038/s41421-019-0109-7

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. https://doi.org/10.1038/s41564-019-0604-5

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. https://doi.org/10.1021/acschembio.9b00338

Winter, J., & Perez-Pinera, P. (2019). Directed Evolution of CRISPR-Cas9 Base Editors. Trends in Biotechnology, 37(11), 1151-1153. https://doi.org/10.1016/j.tibtech.2019.09.005

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. https://doi.org/10.1002/cncr.32351

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. https://doi.org/10.1093/nar/gkz210

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. https://doi.org/10.1111/pcmr.12762

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. https://doi.org/10.1038/s41557-019-0261-6

Aye, Y., & Hergenrother, P. (2019). Editorial overview: From the iceman to modern medicine. Current Opinion in Chemical Biology, 50, A1-A2. https://doi.org/10.1016/j.cbpa.2019.04.021

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. https://doi.org/10.1073/pnas.1807465116

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. https://doi.org/10.1021/jacs.8b12123

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. https://doi.org/10.1194/jlr.M088559

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]. https://doi.org/10.3389/fonc.2019.00096

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.. https://doi.org/10.1007/978-1-4939-9512-7_25

Zhang, Y., Manjunath, M., Kim, Y., Heintz, J., & Song, J. (2019). Sequenceng: An interactive knowledge base of sequencing techniques. Bioinformatics, 35(8), 1438-1440. https://doi.org/10.1093/bioinformatics/bty794

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]. https://doi.org/10.3389/fgene.2019.00775

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. https://doi.org/10.1158/2326-6066.CIR-19-0035

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. https://doi.org/10.1615/CritRevImmunol.2019030788

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]. https://doi.org/10.3389/fgene.2019.00754

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. https://doi.org/10.1111/nyas.13598

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. https://doi.org/10.1053/j.jepm.2018.04.016

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. https://doi.org/10.1158/2326-6066.CIR-18-0395

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]. https://doi.org/10.1371/journal.pone.0210297

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. https://doi.org/10.1093/ilar/ily014

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. https://doi.org/10.1016/j.chembiol.2018.11.001

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. https://doi.org/10.1016/j.chembiol.2018.09.008

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. https://doi.org/10.1158/1078-0432.CCR-18-1498

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]. https://doi.org/10.1038/s41467-017-02587-w

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. https://doi.org/10.1021/acschembio.8b00864

Svec, R. L., & Hergenrother, P. (2018). Oxygen Starvation Unmasks a Killer. Cell chemical biology, 25(11), 1313-1314. https://doi.org/10.1016/j.chembiol.2018.10.028

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. https://doi.org/10.1016/j.celrep.2018.09.006

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. https://doi.org/10.1038/s41418-018-0143-2

Gaj, T., & Perez Pinera, P. (2018). The continuously evolving CRISPR barcoding toolbox Jin-Soo Kim. Genome biology, 19(1), [143]. https://doi.org/10.1186/s13059-018-1541-y

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. https://doi.org/10.1021/acs.orglett.8b02562

Jin, H., Finnegan, A. I., & Song, J. S. (2018). A unified computational framework for modeling genome-wide nucleosome landscape. Physical Biology, 15(6), [066011]. https://doi.org/10.1088/1478-3975/aadad2

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. https://doi.org/10.1016/j.ccell.2018.08.003

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. https://doi.org/10.1016/j.cobme.2018.08.004

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. https://doi.org/10.1021/acscentsci.8b00313

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. https://doi.org/10.1016/j.chembiol.2018.05.008

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]. https://doi.org/10.1186/s13059-018-1482-5

Zhao, C., & Song, J. S. (2018). Quantum transport senses community structure in networks. Physical Review E, 98(2), [022301]. https://doi.org/10.1103/PhysRevE.98.022301

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. https://doi.org/10.1021/acs.jmedchem.8b00243

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. https://doi.org/10.1073/pnas.1807278115

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. https://doi.org/10.2460/ajvr.79.6.592

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. https://doi.org/10.1039/c8bm00149a

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. https://doi.org/10.1158/0008-5472.CAN-17-3486

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. https://doi.org/10.1111/vco.12337

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. https://doi.org/10.1038/nchembio.2576

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. https://doi.org/10.1021/acs.biochem.7b01012

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. https://doi.org/10.4049/jimmunol.1700236

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. https://doi.org/10.1111/vsu.12709

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]. https://doi.org/10.7717/peerj-cs.155

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. https://doi.org/10.1117/12.2290462

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. https://doi.org/10.1074/jbc.M117.814152

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.. https://doi.org/10.1007/978-1-4939-7795-6_13

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. https://doi.org/10.18632/oncotarget.10819