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 oncology, 18(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 Letters, 493, 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-Oncology, 22(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 Science. https://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. Biochemistry, 59(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-Oncology. https://doi.org/10.1093/neuonc/noaa248
Motika, S. E., & Hergenrother, P. J. (2020). Re-engineering natural products to engage new biological targets. Natural Product Reports, 37(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. iScience, 23(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. Science, 369(6508), 1261-1265. https://doi.org/10.1101/2020.03.16.994236, https://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 Medicine, 26(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-Oncology, 22(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 Genetics, 11, [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 E, 102(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 Sciences, 117(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 Journal. https://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 Society, 142(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 Treatment, 181(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 research, 48(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 Surgery, 49(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 Research, 26(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 Journal. https://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 Endocrinology, 289, [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 Oncology, 10, [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 Edition, 59(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 Journal. https://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 Therapy, 28(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 Diseases. https://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 biology, 18(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
