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Research Areas

Mining Microbioal Genomes: Publications

Geddes, E. J., Gugger, M., Garcia, A., Garcia Chavez, M., Lee, M. R., Perlmutter, S. J., Bieniossek, C., Guasch, L., & Hergenrother, P. (2023). Porin-independent accumulation in Pseudomonas enables antibiotic discovery. Nature, 624(7990), 145-153. https://doi.org/10.1038/s41586-023-06760-8

Boudreau, M. W., Tonogai, E. J., Schane, C. P., Xi, M. X., Fischer, J. H., Vijayakumar, J., Ji, Y., Tarasow, T. M., Fan, T. M., Hergenrother, P. J., & Dudek, A. Z. (2023). The combination of PAC-1 and entrectinib for the treatment of metastatic uveal melanoma. Melanoma research, 33(6), 514-524. https://doi.org/10.1097/CMR.0000000000000927

Ju, S., Kuzelka, K. P., Guo, R., Krohn-Hansen, B., Wu, J., Nair, S. K., & Yang, Y. (2023). A biocatalytic platform for asymmetric alkylation of α-keto acids by mining and engineering of methyltransferases. Nature communications, 14(1), Article 5704. https://doi.org/10.1038/s41467-023-40980-w

Tran, V. G., Mishra, S., Bhagwat, S. S., Shafaei, S., Shen, Y., Allen, J. L., Crosly, B. A., Tan, S. I., Fatma, Z., Rabinowitz, J. D., Guest, J. S., Singh, V., & Zhao, H. (2023). An end-to-end pipeline for succinic acid production at an industrially relevant scale using Issatchenkia orientalis. Nature communications, 14(1), Article 6152. https://doi.org/10.1038/s41467-023-41616-9

Yue, Q., Meng, J., Qiu, Y., Yin, M., Zhang, L., Zhou, W., An, Z., Liu, Z., Yuan, Q., Sun, W., Li, C., Zhao, H., Molnár, I., Xu, Y., & Shi, S. (2023). A polycistronic system for multiplexed and precalibrated expression of multigene pathways in fungi. Nature communications, 14(1), Article 4267. https://doi.org/10.1038/s41467-023-40027-0

Ungarean, C. N., Galer, P., Zhang, Y., Lee, K. S., Ngai, J. M., Lee, S., Liu, P., & Sarlah, D. (2023). Author Correction: Synthesis of (+)-ribostamycin by catalytic, enantioselective hydroamination of benzene (Nature Synthesis, (2022), 1, 7, (542-547), 10.1038/s44160-022-00080-x). Nature Synthesis, 2(12), 1243. https://doi.org/10.1038/s44160-023-00357-9

Qiu, T., Lee, C. J., Huang, C., Lee, D. K., Rubakhin, S. S., Romanova, E. V., & Sweedler, J. V. (2023). Biodistribution and racemization of gut-absorbed l/d-alanine in germ-free mice. Communications biology, 6(1), Article 851. https://doi.org/10.1038/s42003-023-05209-y

Dutta, S., & Shukla, D. (2023). Distinct activation mechanisms regulate subtype selectivity of Cannabinoid receptors. Communications biology, 6(1), Article 485. https://doi.org/10.1038/s42003-023-04868-1

Ren, H., Dommaraju, S. R., Huang, C., Cui, H., Pan, Y., Nesic, M., Zhu, L., Sarlah, D., Mitchell, D. A., & Zhao, H. (2023). Genome mining unveils a class of ribosomal peptides with two amino termini. Nature communications, 14(1), Article 1624. https://doi.org/10.1038/s41467-023-37287-1

Tan, T. J. C., Mou, Z., Lei, R., Ouyang, W. O., Yuan, M., Song, G., Andrabi, R., Wilson, I. A., Kieffer, C., Dai, X., Matreyek, K. A., & Wu, N. C. (2023). High-throughput identification of prefusion-stabilizing mutations in SARS-CoV-2 spike. Nature communications, 14(1), Article 2003. https://doi.org/10.1038/s41467-023-37786-1

Guo, X., Bai, Z., Zhang, Y., Zhao, H., & Shi, S. (2023). Mining and application of constitutive promoters from Rhodosporidium toruloides. AMB Express, 13(1), Article 17. https://doi.org/10.1186/s13568-023-01522-1

Hellinger, R., Sigurdsson, A., Wu, W., Romanova, E. V., Li, L., Sweedler, J. V., Süssmuth, R. D., & Gruber, C. W. (2023). Peptidomics. Nature Reviews Methods Primers, 3(1), Article 25. https://doi.org/10.1038/s43586-023-00205-2

Zhang, M., Ehmann, M. E., Matukumalli, S., Boob, A. G., Gilbert, D. M., & Zhao, H. (2023). SHIELD: a platform for high-throughput screening of barrier-type DNA elements in human cells. Nature communications, 14(1), Article 5616. https://doi.org/10.1038/s41467-023-41468-3

Liu, Q., & Stadtmueller, B. M. (2023). SIgA structures bound to Streptococcus pyogenes M4 and human CD89 provide insights into host-pathogen interactions. Nature communications, 14(1), Article 6726. https://doi.org/10.1038/s41467-023-42469-y

Lyu, M., Malyutin, A. G., & Stadtmueller, B. M. (2023). The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function. Nature communications, 14(1), Article 7583. https://doi.org/10.1038/s41467-023-43240-z

Zhang, M., Zhu, Z., Xun, G., & Zhao, H. (2023). To cut or not to cut: Next-generation genome editors for precision genome engineering. Current Opinion in Biomedical Engineering, 28, Article 100489. https://doi.org/10.1016/j.cobme.2023.100489

Maji, A., Soutar, C. P., Zhang, J., Lewandowska, A., Uno, B. E., Yan, S., Shelke, Y., Murhade, G., Nimerovsky, E., Borcik, C. G., Arango, A. S., Lange, J. D., Marin-Toledo, J. P., Lyu, Y., Bailey, K. L., Roady, P. J., Holler, J. T., Khandelwal, A., SantaMaria, A. M., ... Burke, M. D. (2023). Tuning sterol extraction kinetics yields a renal-sparing polyene antifungal. Nature, 623(7989), 1079-1085. https://doi.org/10.1038/s41586-023-06710-4

Yu, Z., Moshood, Y., Wozniak, M. K., Patel, S., Terpstra, K., Llano, D. A., Dobrucki, L. W., & Mirica, L. M. (2023). Amphiphilic Molecules Exhibiting Zwitterionic Excited-State Intramolecular Proton Transfer and Near-Infrared Emission for the Detection of Amyloid β Aggregates in Alzheimer's Disease**. Chemistry - A European Journal, 29(64), Article e202302408. https://doi.org/10.1002/chem.202302408

Wu, YF., Toba, E. A. D. L., Dvoretskiy, S., Jung, R., Kim, N., Daniels, L., Romanova, E. V., Drnevich, J., Sweedler, J. V., & Boppart, M. D. (2023). Development of a cell‐free strategy to recover aged skeletal muscle after disuse. The Journal of Physiology, 601(22), 5011-5031. https://doi.org/10.1113/JP282867

Lei, R., Kim, W., Lv, H., Mou, Z., Scherm, M. J., Schmitz, A. J., Turner, J. S., Tan, T. J. C., Wang, Y., Ouyang, W. O., Liang, W., Rivera-Cardona, J., Teo, C., Graham, C. S., Brooke, C. B., Presti, R. M., Mok, C. K. P., Krammer, F., Dai, X., ... Wu, N. C. (2023). Leveraging vaccination-induced protective antibodies to define conserved epitopes on influenza N2 neuraminidase. Immunity, 56(11), 2621-2634.e6. https://doi.org/10.1016/j.immuni.2023.10.005

Nguyen, V., Xue, P., Li, Y., Zhao, H., & Lu, T. (2023). Controlling circuitry underlies the growth optimization of Saccharomyces cerevisiae. Metabolic Engineering, 80, 173-183. https://doi.org/10.1016/j.ymben.2023.09.013

Lei, R., Hernandez Garcia, A., Tan, T. J. C., Teo, Q. W., Wang, Y., Zhang, X., Luo, S., Nair, S. K., Peng, J., & Wu, N. C. (2023). Erratum: Mutational fitness landscape of human influenza H3N2 neuraminidase (Cell Reports (2023) 42(1), (S2211124722018526), (10.1016/j.celrep.2022.111951)). Cell Reports, 42(10), Article 113356. https://doi.org/10.1016/j.celrep.2023.113356

Yuan, M., Feng, Z., Lv, H., So, N., Shen, I. R., Tan, T. J. C., Teo, Q. W., Ouyang, W. O., Talmage, L., Wilson, I. A., & Wu, N. C. (2023). Widespread impact of immunoglobulin V-gene allelic polymorphisms on antibody reactivity. Cell Reports, 42(10), Article 113194. https://doi.org/10.1016/j.celrep.2023.113194

Saad, H., Majer, T., Bhattarai, K., Lampe, S., Nguyen, D. T., Kramer, M., Straetener, J., Brötz-Oesterhelt, H., Mitchell, D. A., & Gross, H. (2023). Bioinformatics-guided discovery of biaryl-linked lasso peptides. Chemical Science, 14(45), 13176-13183. https://doi.org/10.1039/D3SC02380J

Zhang, M., Singh, N., Ehmann, M. E., Zheng, L., & Zhao, H. (2023). Incorporation of noncanonical base Z yields modified mRNA with minimal immunogenicity and improved translational capacity in mammalian cells. iScience, 26(10), Article 107739. https://doi.org/10.1016/j.isci.2023.107739

Asserghine, A., Baby, A., Putnam, S. T., Qian, P., Gao, E., Zhao, H., & Rodríguez-López, J. (2023). In situ detection of reactive oxygen species spontaneously generated on lead acid battery anodes: a pathway for degradation and self-discharge at open circuit. Chemical Science, 14(43), 12292-12298. https://doi.org/10.1039/D3SC04736A

Price, S. L., Thibault, D., Garrison, T. M., Brady, A., Guo, H., Kehl-Fie, T. E., Garneau-Tsodikova, S., Perry, R. D., van Opijnen, T., & Lawrenz, M. B. (2023). Droplet Tn-Seq identifies the primary secretion mechanism for yersiniabactin in Yersinia pestis. EMBO Reports, 24(10), Article e57369. https://doi.org/10.15252/embr.202357369

De La Toba, E. A., Anapindi, K. D. B., & Sweedler, J. V. (2023). Assessment and Comparison of Database Search Engines for Peptidomic Applications. Journal of Proteome Research, 22(10), 3123-3134. https://doi.org/10.1021/acs.jproteome.2c00307

Zheng, Y., Xu, X., Fu, X., Zhou, X., Dou, C., Yu, Y., Yan, W., Yang, J., Xiao, M., van der Donk, W. A., Zhu, X., & Cheng, W. (2023). Structures of the holoenzyme TglHI required for 3-thiaglutamate biosynthesis. Structure, 31(10), 1220-1232.e5. https://doi.org/10.1016/j.str.2023.08.004

LaPorte, A. J., Feldner, J. E., Spies, J. C., Maher, T. J., & Burke, M. D. (2023). MIDA- and TIDA-Boronates Stabilize α-Radicals Through B−N Hyperconjugation. Angewandte Chemie - International Edition, 62(40), Article e202309566. https://doi.org/10.1002/anie.202309566

Ghorbani, A., Ngunjiri, J. M., Rendon, G., Brooke, C. B., Kenney, S. P., & Lee, C-W. (2023). Diversity and Complexity of Internally Deleted Viral Genomes in Influenza A Virus Subpopulations with Enhanced Interferon-Inducing Phenotypes. Viruses, 15(10), Article 2107. https://doi.org/10.3390/v15102107

Yuan, Y., Shi, C., & Zhao, H. (2023). Machine Learning-Enabled Genome Mining and Bioactivity Prediction of Natural Products. ACS synthetic biology, 12(9), 2650-2662. https://doi.org/10.1021/acssynbio.3c00234

Ghosh, S., Yang, R., Duraki, D., Zhu, J., Kim, J. E., Jabeen, M., Mao, C., Dai, X., Livezey, M. R., Boudreau, M. W., Park, B. H., Nelson, E. R., Hergenrother, P. J., & Shapiro, D. J. (2023). Plasma Membrane Channel TRPM4 Mediates Immunogenic Therapy–Induced Necrosis. Cancer Research, 83(18), 3115-3130. https://doi.org/10.1158/0008-5472.CAN-23-0157

Long, C. C., Antevska, A., Mast, D. H., Okyem, S., Sweedler, J. V., & Do, T. D. (2023). Nonenzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers. Journal of the American Society for Mass Spectrometry, 34(9), 1898-1907. https://doi.org/10.1021/jasms.3c00092

Wang, C. K., Huang, Y. H., Shabbir, F., Pham, H. T., Lawrence, N., Benfield, A. H., van der Donk, W., Henriques, S. T., Turner, M. S., & Craik, D. J. (2023). The circular bacteriocin enterocin NKR-5-3B has an improved stability profile over nisin. Peptides, 167, Article 171049. https://doi.org/10.1016/j.peptides.2023.171049

Yu, T., Boob, A. G., Singh, N., Su, Y., & Zhao, H. (2023). In vitro continuous protein evolution empowered by machine learning and automation. Cell Systems, 14(8), 633-644. https://doi.org/10.1016/j.cels.2023.04.006

Li, N., Bullock, D., Butts-Wilmsmeyer, C., Gentry, L., Goodwin, G., Han, J., Kleczweski, N., Martín, N. F., Paulausky, P., Pistorius, P., Seiter, N., Schroeder, N., & Margenot, A. J. (2023). Distinct soil health indicators are associated with variation in maize yield and tile drain nitrate losses. Soil Science Society of America Journal, 87(6), 1332-1347. Advance online publication. https://doi.org/10.1002/saj2.20586

Rappazzo, C. G., Fernandez-Quintero, M. L., Mayer, A., Wu, N. C., Greiff, V., & Guthmiller, J. J. (2023). Defining and studying B cell receptor and TCR interactions. Journal of Immunology, 211(3), 311-322. https://doi.org/10.4049/jimmunol.2300136

Zhang, Z., Feng, J., Yang, C., Cui, H., Harrison, W., Zhong, D., Wang, B., & Zhao, H. (2023). Photoenzymatic enantioselective intermolecular radical hydroamination. Nature Catalysis, 6(8), 687-694. https://doi.org/10.1038/s41929-023-00994-5

Oberg, N., Zallot, R., & Gerlt, J. A. (2023). EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools. Journal of Molecular Biology, 435(14), Article 168018. https://doi.org/10.1016/j.jmb.2023.168018

Blin, K., Shaw, S., Augustijn, H. E., Reitz, Z. L., Biermann, F., Alanjary, M., Fetter, A., Terlouw, B. R., Metcalf, W. W., Helfrich, E. J. N., van Wezel, G. P., Medema, M. H., & Weber, T. (2023). antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic acids research, 51(W1), W46-W50. Article gkad344. https://doi.org/10.1093/nar/gkad344

Choe, K., Jindra, M. A., Hubbard, S. C., Pfleger, B. F., & Sweedler, J. V. (2023). MALDI-MS screening of microbial colonies with isomer resolution to select fatty acid desaturase variants. Analytical Biochemistry, 672, Article 115169. https://doi.org/10.1016/j.ab.2023.115169

Fatma, Z., Tan, S. I., Boob, A. G., & Zhao, H. (2023). A landing pad system for multicopy gene integration in Issatchenkia orientalis. Metabolic Engineering, 78, 200-208. https://doi.org/10.1016/j.ymben.2023.06.010

Peh, G., Gunawan, G. A., Tay, T., Tiong, E., Tan, L. L., Jiang, S., Goh, Y. L., Ye, S., Wong, J., Brown, C. J., Zhao, H., Ang, E. L., Wong, F. T., & Lim, Y. H. (2023). Further Characterization of Fungal Halogenase RadH and Its Homologs. Biomolecules, 13(7), Article 1081. https://doi.org/10.3390/biom13071081

Rivera-Cardona, J., & Brooke, C. B. (2023). How influenza shuts down host transcription. Nature Microbiology, 8(7), 1195-1196. https://doi.org/10.1038/s41564-023-01416-9

Akbari, M. S., Keogh, R. A., Radin, J. N., Sanchez-Rosario, Y., Johnson, M. D. L., Horswill, A. R., Kehl-Fie, T. E., Burcham, L. R., & Doran, K. S. (2023). The impact of nutritional immunity on Group B streptococcal pathogenesis during wound infection. mBio, 14(4). https://doi.org/10.1128/mbio.00304-23

Precord, T. W., Ramesh, S., Dommaraju, S. R., Harris, L. A., Kille, B. L., & Mitchell, D. A. (2023). Catalytic Site Proximity Profiling for Functional Unification of Sequence-Diverse Radical S-Adenosylmethionine Enzymes. ACS Bio and Med Chem Au, 3(3), 240-251. https://doi.org/10.1021/acsbiomedchemau.2c00085

Chadwick, G. L., Joiner, A. M. N., Ramesh, S., Mitchell, D. A., & Nayak, D. D. (2023). McrD binds asymmetrically to methyl-coenzyme M reductase improving active-site accessibility during assembly. Proceedings of the National Academy of Sciences of the United States of America, 120(25), Article e2302815120. https://doi.org/10.1073/pnas.2302815120

Thomas, G., Rusman, Q., Morrison, W. R., Magalhães, D. M., Dowell, J. A., Ngumbi, E., Osei-Owusu, J., Kansman, J., Gaffke, A., Pagadala Damodaram, K. J., Kim, S. J., & Tabanca, N. (2023). Deciphering Plant-Insect-Microorganism Signals for Sustainable Crop Production. Biomolecules, 13(6), Article 997. https://doi.org/10.3390/biom13060997

Daulagala, P., Mann, B. R., Leung, K., Lau, E. H. Y., Yung, L., Lei, R., Nizami, S. I. N., Wu, J. T., Chiu, S. S., Daniels, R. S., Wu, N. C., Wentworth, D., Peiris, M., & Yen, H. L. (2023). Imprinted Anti-Hemagglutinin and Anti-Neuraminidase Antibody Responses after Childhood Infections of A(H1N1) and A(H1N1)pdm09 Influenza Viruses. mBio, 14(3). https://doi.org/10.1128/mbio.00084-23

Ranoa, D. R. E., Sharma, P., Schane, C. P., Lewis, A. N., Valdez, E., Marada, V. V. V. R., Hager, M. V., Montgomery, W., Wolf, S. P., Schreiber, K., Schreiber, H., Bailey, K., Fan, T. M., Hergenrother, P. J., Roy, E. J., & Kranz, D. M. (2023). Single CAR-T cell treatment controls disseminated ovarian cancer in a syngeneic mouse model. Journal for ImmunoTherapy of Cancer, 11(5), Article e006509. https://doi.org/10.1136/jitc-2022-006509

Ayikpoe, R. S., Zhu, L., Chen, J. Y., Ting, C. P., & Van Der Donk, W. A. (2023). Macrocyclization and Backbone Rearrangement During RiPP Biosynthesis by a SAM-Dependent Domain-of-Unknown-Function 692. ACS Central Science, 9(5), 1008-1018. https://doi.org/10.1021/acscentsci.3c00160

Jiang, G., Huang, C., Harrison, W., Li, H., Zhou, M., & Zhao, H. (2023). Ene Reductase Enabled Intramolecular β-C−H Functionalization of Substituted Cyclohexanones for Efficient Synthesis of Bridged Bicyclic Nitrogen Scaffolds. Angewandte Chemie - International Edition, 62(22), Article e202302125. https://doi.org/10.1002/anie.202302125

Anmangandla, A., Jana, S., Peng, K., Wallace, S. D., Bagde, S. R., Drown, B. S., Xu, J., Hergenrother, P. J., Fromme, J. C., & Lin, H. (2023). A Fluorescence Polarization Assay for Macrodomains Facilitates the Identification of Potent Inhibitors of the SARS-CoV-2 Macrodomain. ACS chemical biology, 18(5), 1200-1207. https://doi.org/10.1021/acschembio.3c00092

Meng, J., Qiu, Y., Zhang, Y., Zhao, H., & Shi, S. (2023). CMI: CRISPR/Cas9 Based Efficient Multiplexed Integration in Saccharomyces cerevisiae. ACS synthetic biology, 12(5), 1408-1414. https://doi.org/10.1021/acssynbio.2c00591

Xiong, X., Tasan, I., Yang, C., Zhang, M., Hernandez Gonzalez, G. A., Liu, S., Chaturvedi, P., Belmont, A. S & Zhao, H. (2023). Imaging Method Using CRISPR/dCas9 and Engineered gRNA Scaffolds Can Perturb Replication Timing at the HSPA1 Locus. ACS synthetic biology, 12(5), 1424-1436. https://doi.org/10.1021/acssynbio.2c00433

Volk, M. J., Tran, V. G., Tan, S. I., Mishra, S., Fatma, Z., Boob, A., Li, H., Xue, P., Martin, T. A., & Zhao, H. (2023). Metabolic Engineering: Methodologies and Applications. Chemical reviews, 123(9), 5521-5570. https://doi.org/10.1021/acs.chemrev.2c00403

Mi, X., Desormeaux, E. K., Le, T. T., van der Donk, W. A., & Shukla, D. (2023). Sequence controlled secondary structure is important for the site-selectivity of lanthipeptide cyclization. Chemical Science, 14(25), 6904-6914. https://doi.org/10.1039/D2SC06546K

Li, G., Jeon, C. K., Ma, M., Jia, Y., Zheng, Z., Delafield, D. G., Lu, G., Romanova, E. V., Sweedler, J. V., Ruotolo, B. T., & Li, L. (2023). Site-specific chirality-conferred structural compaction differentially mediates the cytotoxicity of Aβ42. Chemical Science, 14(22), 5936-5944. https://doi.org/10.1039/d3sc00678f

Castro, D. C., Smith, K. W., Norsworthy, M. D., Rubakhin, S. S., Weisbrod, C. R., Hendrickson, C. L., & Sweedler, J. V. (2023). Single-Cell and Subcellular Analysis Using Ultrahigh Resolution 21 T MALDI FTICR Mass Spectrometry. Analytical Chemistry, 95(17), 6980-6988. https://doi.org/10.1021/acs.analchem.3c00393

Sendra, K. M., Barwinska-Sendra, A., Mackenzie, E. S., Baslé, A., Kehl-Fie, T. E., & Waldron, K. J. (2023). An ancient metalloenzyme evolves through metal preference modulation. Nature Ecology and Evolution, 7(5), 732-744. https://doi.org/10.1038/s41559-023-02012-0

Bown, L., Hirota, R., Goettge, M. N., Cui, J., Krist, D. T., Zhu, L., Giurgiu, C., van der Donk, W. A., Ju, K. S., & Metcalf, W. W. (2023). A Novel Pathway for Biosynthesis of the Herbicidal Phosphonate Natural Product Phosphonothrixin Is Widespread in Actinobacteria. Journal of bacteriology, 205(5). https://doi.org/10.1128/jb.00485-22

Jindra, M. A., Choe, K., Chowdhury, R., Kong, R., Ghaffari, S., Sweedler, J. V., & Pfleger, B. F. (2023). Evaluation of strategies to narrow the product chain-length distribution of microbially synthesized free fatty acids. Metabolic Engineering, 77, 21-31. https://doi.org/10.1016/j.ymben.2023.02.012

Farjo, M., & Brooke, C. B. (2023). When influenza viruses don’t play well with others. Nature, 616(7958), 668-669. https://doi.org/10.1038/d41586-023-00983-5

Serrano, R., Boyko, Y. D., Hernandez, L. W., Lotuzas, A., & Sarlah, D. (2023). Total Syntheses of Scabrolide A and Yonarolide. Journal of the American Chemical Society, 145(16), 8805-8809. https://doi.org/10.1021/jacs.3c02317

Lee, D. K., Rubakhin, S. S., & Sweedler, J. V. (2023). Chemical Decrosslinking-Based Peptide Characterization of Formaldehyde-Fixed Rat Pancreas Using Fluorescence-Guided Single-Cell Mass Spectrometry. Analytical Chemistry, 95(16), 6732-6739. https://doi.org/10.1021/acs.analchem.3c00612

Goodrum, F., Lowen, A. C., Lakdawala, S., Alwine, J., Casadevall, A., Imperiale, M. J., Atwood, W., Avgousti, D., Baines, J., Banfield, B., Banks, L., Bhaduri-McIntosh, S., Bhattacharya, D., Blanco-Melo, D., Bloom, D., Boon, A., Boulant, S., Brandt, C., Broadbent, A., ... Yurochko, A. (2023). Virology under the Microscope-a Call for Rational Discourse. mSphere, 8(2), e0003423. https://doi.org/10.1128/msphere.00034-23

Hwang, H. S., Lo, C., Murphy, M., Grudda, T., Gallagher, N., Luo, C. H., Robinson, M. L., Mirza, A., Conte, M., Conte, A., Zhou, R., Vergara, C., Brooke, C. B., Pekosz, A., Mostafa, H. H., Manabe, Y. C., Thio, C. L., & Balagopal, A. (2023). Characterizing SARS-CoV-2 Transcription of Subgenomic and Genomic RNAs During Early Human Infection Using Multiplexed Droplet Digital Polymerase Chain Reaction. The Journal of infectious diseases, 227(8), 981-992. Article jiac472. https://doi.org/10.1093/infdis/jiac472

Park, R., Ongpipattanakul, C., Nair, S. K., Bowers, A. A., & Kuhlman, B. (2023). Designer installation of a substrate recruitment domain to tailor enzyme specificity. Nature chemical biology, 19(4), 460-467. https://doi.org/10.1038/s41589-022-01206-0

Yu, T., Cui, H., Li, J. C., Luo, Y., Jiang, G., & Zhao, H. (2023). Enzyme function prediction using contrastive learning. Science, 379(6639), 1358-1363. https://doi.org/10.1126/science.adf2465

Putt, K. S., Tarasow, T., Sandhorst, J. S., Hergenrother, P. J., Fako, V. E., & Peterson, Q. P. (2023). Compounds And Methods For The Treatment Of Cancer. (U.S. Patent No. 11612598).

Danciu, O. C., Holdhoff, M., Peterson, R. A., Fischer, J. H., Liu, L. C., Wang, H., Venepalli, N. K., Chowdhery, R., Nicholas, M. K., Russell, M. J., Fan, T. M., Hergenrother, P. J., Tarasow, T. M., & Dudek, A. Z. (2023). Phase I study of procaspase-activating compound-1 (PAC-1) in the treatment of advanced malignancies. British Journal of Cancer, 128(5), 783-792. https://doi.org/10.1038/s41416-022-02089-7

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Hong, Y., Qin, J., Verderosa, A. D., Hawas, S., Zhang, B., Blaskovich, M. A. T., Cronan, J. E., & Totsika, M. (2022). Loss of β-Ketoacyl Acyl Carrier Protein Synthase III Activity Restores Multidrug-Resistant Escherichia coli Sensitivity to Previously Ineffective Antibiotics. mSphere, 7(3). https://doi.org/10.1128/msphere.00117-22

Melzer, M. E., Sweedler, J. V., & Clark, K. D. (2022). Rapid Determination of RNA Modifications in Consensus Motifs by Nuclease Protection with Ion-Tagged Oligonucleotide Probes and Matrix-Assisted Laser Desorption Ionization Mass Spectrometry. Genes, 13(6), [1008]. https://doi.org/10.3390/genes13061008

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Gu, W., Zheng, Y., Pogorelov, T., Nair, S. K., & Schmidt, E. W. (2022). Control of Nucleophile Chemoselectivity in Cyanobactin YcaO Heterocyclases PatD and TruD. ACS chemical biology, 17(5), 1215–1225. https://doi.org/10.1021/acschembio.2c00147

Boudreau, M. W., & Hergenrother, P. J. (2022). Evolution of 3-(4-hydroxyphenyl)indoline-2-one as a scaffold for potent and selective anticancer activity. RSC Medicinal Chemistry, 13(6), 711-725. https://doi.org/10.1039/d2md00110a

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Diefenbacher, M., Tan, T. J. C., Bauer, D. L. V., Stadtmueller, B. M., Wu, N. C., & Brooke, C. B. (2022). Interactions between Influenza A Virus Nucleoprotein and Gene Segment Untranslated Regions Facilitate Selective Modulation of Viral Gene Expression. Journal of virology, 96(10). https://doi.org/10.1128/jvi.00205-22

Frye, K. A., Sendra, K. M., Waldron, K. J., & Kehl-Fie, T. E. (2022). Old dogs, new tricks: New insights into the iron/manganese superoxide dismutase family. Journal of Inorganic Biochemistry, 230, [111748]. https://doi.org/10.1016/j.jinorgbio.2022.111748

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McLaughlin, M. I., Yu, Y., & Van Der Donk, W. A. (2022). Substrate Recognition by the Peptidyl-(S)-2-mercaptoglycine Synthase TglHI during 3-Thiaglutamate Biosynthesis. ACS chemical biology, 17(4), 930-940. https://doi.org/10.1021/acschembio.2c00087

Sarksian, R., Hegemann, J. D., Simon, M. A., Acedo, J. Z., & Van Der Donk, W. A. (2022). Unexpected Methyllanthionine Stereochemistry in the Morphogenetic Lanthipeptide SapT. Journal of the American Chemical Society, 144(14), 6373-6382. https://doi.org/10.1021/jacs.2c00517

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Xie, Y. R., Castro, D. C., Rubakhin, S. S., Sweedler, J. V., & Lam, F. (2022). Enhancing the Throughput of FT Mass Spectrometry Imaging Using Joint Compressed Sensing and Subspace Modeling. Analytical Chemistry, 94(13), 5335-5343. https://doi.org/10.1021/acs.analchem.1c05279

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Clark, K. D., Rubakhin, S. S., & Sweedler, J. V. (2022). Characterizing RNA Modifications in Single Neurons using Mass Spectrometry. Journal of Visualized Experiments, 2022(182), [e63940]. https://doi.org/10.3791/63940

Cogan, D. P., Bhushan, A., Reyes, R., Zhu, L., Piel, J., & Nair, S. K. (2022). Structure and mechanism for iterative amide N-methylation in the biosynthesis of channel-forming peptide cytotoxins. Proceedings of the National Academy of Sciences of the United States of America, 119(13), [e2116578119]. https://doi.org/10.1073/pnas.2116578119

Beker, W., Roszak, R., Wolos, A., Angello, N. H., Rathore, V., Burke, M. D., & Grzybowski, B. A. (2022). Machine Learning May Sometimes Simply Capture Literature Popularity Trends: A Case Study of Heterocyclic Suzuki-Miyaura Coupling. Journal of the American Chemical Society, 144(11), 4819-4827. https://doi.org/10.1021/jacs.1c12005

Lundahl, M. N., Sarksian, R., Yang, H., Jodts, R. J., Pagnier, A., Smith, D. F., Mosquera, M. A., Van Der Donk, W. A., Hoffman, B. M., Broderick, W. E., & Broderick, J. B. (2022). Mechanism of Radical S-Adenosyl- l -methionine Adenosylation: Radical Intermediates and the Catalytic Competence of the 5′-Deoxyadenosyl Radical. Journal of the American Chemical Society, 144(11), 5087-5098. https://doi.org/10.1021/jacs.1c13706

Wu, YF., Toba, E. A. D. L., Dvoretskiy, S., Jung, R., Kim, N., Daniels, L., Romanova, E. V., Drnevich, J., Sweedler, J. V., & Boppart, M. D. (Accepted/In press). Development of a cell‐free strategy to recover aged skeletal muscle after disuse. The Journal of Physiology. https://doi.org/10.1113/JP282867

Hergenrother, P. J., & Riley, A. (2022). Topoisomerase inhibitors with antibacterial and anticancer activity. (U.S. Patent No. 11274106).

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Zhao, H., & Enghiad, B. (2022). Programmable DNA-guided artificial restriction enzymes. (U.S. Patent No. 11261483).

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Che, C., Xue, R., Li, N., Gupta, P., Wang, X., Zhao, B., Singamaneni, S., Nie, S., & Cunningham, B. T. (2022). Accelerated Digital Biodetection Using Magneto-plasmonic Nanoparticle-Coupled Photonic Resonator Absorption Microscopy. ACS Nano, 16(2), 2345–2354. https://doi.org/10.1021/acsnano.1c08569

Vasan, A. K., Haloi, N., Ulrich, R. J., Metcalf, M. E., Wen, P. C., Metcalf, W. W., Hergenrother, P. J., Shukla, D., & Tajkhorshid, E. (2022). Role of internal loop dynamics in antibiotic permeability of outer membrane porins. Proceedings of the National Academy of Sciences of the United States of America, 119(8), [e2117009119]. https://doi.org/10.1073/pnas.2117009119

Liang, J., Zhang, H., Tan, Y. L., Zhao, H., & Ang, E. L. (2022). Directed Evolution of Replication-Competent Double-Stranded DNA Bacteriophage toward New Host Specificity. ACS synthetic biology, 11(2), 634-643. https://doi.org/10.1021/acssynbio.1c00319

Svec, R. L., Mckee, S. A., Berry, M. R., Kelly, A. M., Fan, T. M., & Hergenrother, P. J. (2022). Novel Imidazotetrazine Evades Known Resistance Mechanisms and Is Effective against Temozolomide-Resistant Brain Cancer in Cell Culture. ACS chemical biology, 17(2), 299–313. https://doi.org/10.1021/acschembio.2c00022

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Dainton, A. N., He, F., Bingham, T. W., Sarlah, D., Detweiler, K. B., Mangian, H. J., & De Godoy, M. R. C. (2022). Nutritional and physico-chemical implications of avocado meal as a novel dietary fiber source in an extruded canine diet. Journal of animal science, 100(2), [skac026]. https://doi.org/10.1093/jas/skac026

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Zhang, Y., Kim, S., Shi, W., Zhao, Y., Park, I., Brenden, C., Iyer, H., Jha, P., Bashir, R., Sweedler, J. V., & Vlasov, Y. (2022). Droplet-assisted electrospray phase separation using an integrated silicon microfluidic platform. Lab on a chip, 22(1), 40-46. https://doi.org/10.1039/d1lc00758k

Daniels, P. N., Lee, H., Splain, R. A., Ting, C. P., Zhu, L., Zhao, X., Moore, B. S., & van der Donk, W. A. (2022). A biosynthetic pathway to aromatic amines that uses glycyl-tRNA as nitrogen donor. Nature Chemistry, 14(1), 71-77. https://doi.org/10.1038/s41557-021-00802-2

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