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Mining for anti-infectious Molecules from Genomes

To view the full list of publications across IGB's research portfolio, please visit our Illinois Experts page

2023

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

Mazo, N., Rahman, I. R., Navo, C. D., Peregrina, J. M., Busto, J. H., van der Donk, W. A., & Jiménez-Osés, G. (2023). Synthesis of Fluorescent Lanthipeptide Cytolysin S Analogues by Late-Stage Sulfamidate Ring Opening. Organic Letters, 25(9), 1431-1435. https://doi.org/10.1021/acs.orglett.3c00122

Chan, M. C., Chan, K. K., Procko, E., & Shukla, D. (2023). Machine Learning Guided Design of High-Affinity ACE2 Decoys for SARS-CoV-2 Neutralization. Journal of Physical Chemistry B, 127(9), 1995-2001. https://doi.org/10.1021/acs.jpcb.3c00469

Padron, G. C., Shuppara, A. M., Sharma, A., Koch, M. D., Palalay, J. J. S., Radin, J. N., Kehl-Fie, T. E., Imlay, J. A., & Sanfilippo, J. E. (2023). Shear rate sensitizes bacterial pathogens to H2O2 stress. Proceedings of the National Academy of Sciences of the United States of America, 120(11), Article e2216774120. https://doi.org/10.1073/pnas.2216774120

Zhao, M., Shin, G. Y., Stice, S., Bown, J. L., Coutinho, T., Metcalf, W. W., Gitaitis, R., Kvitko, B., & Dutta, B. (2023). A Novel Biosynthetic Gene Cluster Across the Pantoea Species Complex Is Important for Pathogenicity in Onion. Molecular Plant-Microbe Interactions, 36(3), 176-188. https://doi.org/10.1094/MPMI-08-22-0165-R

Yin, Q., Luo, W., Mallajosyula, V., Bo, Y., Guo, J., Xie, J., Sun, M., Verma, R., Li, C., Constantz, C. M., Wagar, L. E., Li, J., Sola, E., Gupta, N., Wang, C., Kask, O., Chen, X., Yuan, X., Wu, N. C., ... Davis, M. M. (2023). A TLR7-nanoparticle adjuvant promotes a broad immune response against heterologous strains of influenza and SARS-CoV-2. Nature Materials, 22(3), 380-390. https://doi.org/10.1038/s41563-022-01464-2

Hu, M., Dinh, H. V., Shen, Y., Suthers, P. F., Foster, C. J., Call, C. M., Ye, X., Pratas, J., Fatma, Z., Zhao, H., Rabinowitz, J. D., & Maranas, C. D. (2023). Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale. Metabolic Engineering, 76, 1-17. https://doi.org/10.1016/j.ymben.2023.01.001

Eberwine, J., Kim, J., Anafi, R. C., Brem, S., Bucan, M., Fisher, S. A., Grady, M. S., Herr, A. E., Issadore, D., Jeong, H., Kim, H. B., Lee, D., Rubakhin, S., Sul, J. Y., Sweedler, J. V., Wolf, J. A., Zaret, K. S., & Zou, J. (2023). Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput. Nature Methods, 20(3), 331-335. https://doi.org/10.1038/s41592-023-01788-0

Solórzano, P. K. P., Bastille, T. S., Radin, J. N., & Kehl-Fie, T. E. (2023). A Manganese-independent Aldolase Enables Staphylococcus aureus To Resist Host-imposed Metal Starvation. mBio, 14(1), e0322322. https://doi.org/10.1128/mbio.03223-22

Zhou, S., Fatma, Z., Xue, P., Mishra, S., Cao, M., Zhao, H., & Sweedler, J. V. (2023). Mass Spectrometry-Based High-Throughput Quantification of Bioproducts in Liquid Culture. Analytical Chemistry, 95(8), 4067-4076. https://doi.org/10.1021/acs.analchem.2c04845

Hergenrother, P. J., Shapiro, D. J., & Boudreau, M. W. (2023). Activators Of The Unfolded Protein Response. (U.S. Patent No. 11584718).

Kretsch, A. M., Gadgil, M. G., Dicaprio, A. J., Barrett, S. E., Kille, B. L., Si, Y., Zhu, L., & Mitchell, D. A. (2023). Peptidase Activation by a Leader Peptide-Bound RiPP Recognition Element. Biochemistry, 62(4), 956-967. https://doi.org/10.1021/acs.biochem.2c00700

Lee, H., Wu, C., Desormeaux, E. K., Sarksian, R., & van der Donk, W. A. (2023). Improved production of class I lanthipeptides in Escherichia coli. Chemical Science, 14(10), 2537-2546. https://doi.org/10.1039/d2sc06597e

Wu, T. C., Aguilar-Granda, A., Hotta, K., Yazdani, S. A., Pollice, R., Vestfrid, J., Hao, H., Lavigne, C., Seifrid, M., Angello, N., Bencheikh, F., Hein, J. E., Burke, M., Adachi, C., & Aspuru-Guzik, A. (2023). A Materials Acceleration Platform for Organic Laser Discovery. Advanced Materials, 35(6), Article 2207070. https://doi.org/10.1002/adma.202207070

Sweedler, J. (2023). Welcome to 2023. Analytical Chemistry, 95(5), 2589. https://doi.org/10.1021/acs.analchem.3c00132

Xie, Y. R., Chari, V. K., Castro, D. C., Grant, R., Rubakhin, S. S., & Sweedler, J. V. (2023). Data-Driven and Machine Learning-Based Framework for Image-Guided Single-Cell Mass Spectrometry. Journal of Proteome Research, 22(2), 491-500. https://doi.org/10.1021/acs.jproteome.2c00714

Luo, Y., Lv, H., Zhao, S., Sun, Y., Liu, C., Chen, C., Liang, W., Kwok, K. O., Teo, Q. W., So, R. TY., Lin, Y., Deng, Y., Li, B., Dai, Z., Zhu, J., Zhang, D., Fernando, J., Wu, N. C., Tun, H. M., ... Mu, X. (2023). Age-related seroprevalence trajectories of seasonal coronaviruses in children including neonates in Guangzhou, China. International Journal of Infectious Diseases, 127, 26-32. https://doi.org/10.1016/j.ijid.2022.11.044

Yu, T., Boob, A. G., Volk, M. J., Liu, X., Cui, H., & Zhao, H. (2023). Machine learning-enabled retrobiosynthesis of molecules. Nature Catalysis, 6(2), 137-151. https://doi.org/10.1038/s41929-022-00909-w

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. Journal of virology, 97(2). https://doi.org/10.1128/jvi.00089-23

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). Mutational fitness landscape of human influenza H3N2 neuraminidase. Cell Reports, 42(1), Article 111951. https://doi.org/10.1016/j.celrep.2022.111951

Huang, C., Cui, H., Ren, H., & Zhao, H. (2023). Investigation of the Biosynthetic Mechanism of Bipentaromycin Featuring an Unprecedented Cyclic Head-to-Tail Dimeric Scaffold. JACS Au, 3(1), 195-203. https://doi.org/10.1021/jacsau.2c00594

Cheong, C. B., Peh, G. R., Wei, Y., Rehka, T., Ang, E. L., Zhao, H., Zhang, C., & Lim, Y. H. (2023). A Spirobicyclo[3.1.0]Terpene from the Investigation of Sesquiterpene Synthases from Lactarius deliciosus. ACS chemical biology, 18(1), 134-140. https://doi.org/10.1021/acschembio.2c00760

Daniels, P. N., & van der Donk, W. A. (2023). Substrate Specificity of the Flavoenzyme BhaC1 That Converts a C-Terminal Trp to a Hydroxyquinone. Biochemistry, 62(2), 378–387. https://doi.org/10.1021/acs.biochem.2c00206

Ongpipattanakul, C., Liu, S., Luo, Y., Nair, S. K., & Van der donk, W. A. (2023). The mechanism of thia-Michael addition catalyzed by LanC enzymes. Proceedings of the National Academy of Sciences, 120(3), Article e2217523120. https://doi.org/10.1073/pnas.2217523120

Jia, J., Parmar, D., Ellis, J. F., Cao, T., Cutri, A. R., Shrout, J. D., Sweedler, J. V., & Bohn, P. W. (2023). Effect of Micro-Patterned Mucin on Quinolone and Rhamnolipid Profiles of Mucoid Pseudomonas aeruginosa under Antibiotic Stress. ACS Infectious Diseases, 9(1), 150-161. https://doi.org/10.1021/acsinfecdis.2c00519

Matsuoka, W., Kawahara, K. P., Ito, H., Sarlah, D., & Itami, K. (2023). π-Extended Rubrenes via Dearomative Annulative π-Extension Reaction. Journal of the American Chemical Society, 145(1), 658-666. https://doi.org/10.1021/jacs.2c11338

Singh, R., Bhagwat, S. S., Viswanathan, M. B., Cortés‐Peña, Y. R., Eilts, K. K., Mcdonough, G., Cao, M., Guest, J. S., Zhao, H., & Singh, V. (2023). Adsorptive separation and recovery of triacetic acid lactone from fermentation broth. Biofuels, Bioproducts and Biorefining, 17(1), 109-120. https://doi.org/10.1002/bbb.2427

Shelton, K. E., & Mitchell, D. A. (2023). Bioinformatic prediction and experimental validation of RiPP recognition elements. In A. K. Shukla (Ed.), Integrated Methods in Protein Biochemistry: Part B (pp. 191-233). (Methods in Enzymology; Vol. 679). Academic Press Inc.. https://doi.org/10.1016/bs.mie.2022.08.050

Mishra, S., Wang, Z., Volk, M. J., & Zhao, H. (2023). Design and application of a kinetic model of lipid metabolism in Saccharomyces cerevisiae. Metabolic Engineering, 75, 12-18. https://doi.org/10.1016/j.ymben.2022.11.003

Farjo, M., & Brooke, C. B. (2023). Low Viral Diversity Limits the Effectiveness of Sequence-Based Transmission Inference for SARS-CoV-2. mSphere, 8(1). https://doi.org/10.1128/msphere.00544-22

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. mBio, 14(1). https://doi.org/10.1128/mbio.00188-23

Zheng, Y., & Nair, S. K. (2023). YcaO-mediated ATP-dependent peptidase activity in ribosomal peptide biosynthesis. Nature chemical biology, 19(1), 111-119. https://doi.org/10.1038/s41589-022-01141-0

Lim, J., Zhou, S., Baek, J., Kim, A. Y., Valera, E., Sweedler, J., & Bashir, R. (in press). A Blood Drying Process for DNA Amplification. Small. https://doi.org/10.1002/smll.202307959

Wang, J., Su, X., Jiang, L., Boudreau, M. W., Chatkewitz, L. E., Kilgore, J. A., Zahid, K. R., Williams, N. S., Chen, Y., Liu, S., Hergenrother, P. J., & Huang, X. (2023). Augmented Concentration of Isopentyl-Deoxynyboquinone in Tumors Selectively Kills NAD(P)H Quinone Oxidoreductase 1-Positive Cancer Cells through Programmed Necrotic and Apoptotic Mechanisms. Cancers, 15(24). https://doi.org/10.3390/cancers15245844

Wu, C., Lower, B. A., Moreira, R., Dorantes, D., Le, T., Giurgiu, C., Shi, Y., & van der Donk, W. A. (2023). Investigation into the mechanism of action of the antimicrobial peptide epilancin 15X. Frontiers in Microbiology, 14, Article 1247222. https://doi.org/10.3389/fmicb.2023.1247222

Tan, Y., De La Toba, E., Rubakhin, S. S., Labriola, L. T., Canfield, C., Pan, D., & Sweedler, J. V. (in press). NanoLC-timsTOF-Assisted Analysis of Glycated Albumin in Diabetes-Affected Plasma and Tears. Journal of the American Society for Mass Spectrometry. https://doi.org/10.1021/jasms.3c00331

Holdhoff, M., Nicholas, M. K., Peterson, R. A., Maraka, S., Liu, L. C., Fischer, J. H., Wefel, J. S., Fan, T. M., Vannorsdall, T., Russell, M., Iacoboni, M., Tarasow, T. M., Hergenrother, P. J., Dudek, A. Z., & Danciu, O. C. (2023). Phase I dose escalation study of procaspase-activating compound-1 (PAC-1) in combination with temozolomide in patients with recurrent high-grade astrocytomas. Neuro-Oncology Advances, 5(1), Article vdad087. https://doi.org/10.1093/noajnl/vdad087

Dady, E. R., Kleczewski, N. M., Ugarte, C. M., & Ngumbi, E. (in press). Plant Variety, Mycorrhization, and Herbivory Influence Induced Volatile Emissions and Plant Growth Characteristics in Tomato. Journal of Chemical Ecology. https://doi.org/10.1007/s10886-023-01455-w

Castro, D. C., Chan-Andersen, P., Romanova, E. V., & Sweedler, J. V. (in press). Probe-based mass spectrometry approaches for single-cell and single-organelle measurements. Mass Spectrometry Reviews. https://doi.org/10.1002/mas.21841

Farrell, A., Phan, T., Brooke, C. B., Koelle, K., & Ke, R. (2023). Semi-infectious particles contribute substantially to influenza virus within-host dynamics when infection is dominated by spatial structure. Virus Evolution, 9(1), Article vead020. https://doi.org/10.1093/ve/vead020

Lindley, S. E., Lu, Y., & Shukla, D. (in press). The Experimentalist’s Guide to Machine Learning for Small Molecule Design. ACS Applied Bio Materials. https://doi.org/10.1021/acsabm.3c00054

Choe, K., & Sweedler, J. V. (2023). Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies. Bio-protocol, 13(21), Article e4862. https://doi.org/10.21769/BioProtoc.4862

 

2022

Milenkovic, O., Hernandez, A. G., Zhao, H., & Tabatabaei, S. (2022). Nick-based Data Storage In Native Nucleic Acids. (U.S. Patent No. 11538554).

Cabrera, A., Edelstein, H. I., Glykofrydis, F., Love, K. S., Palacios, S., Tycko, J., Zhang, M., Lensch, S., Shields, C. E., Livingston, M., Weiss, R., Zhao, H., Haynes, K. A., Morsut, L., Chen, Y. Y., Khalil, A. S., Wong, W. W., Collins, J. J., Rosser, S. J., ... Deans, T. L. (2022). The sound of silence: Transgene silencing in mammalian cell engineering. Cell Systems, 13(12), 950-973. https://doi.org/10.1016/j.cels.2022.11.005

Liu, Y., Wei, Y., Teh, T. M., Liu, D., Zhou, Y., Zhao, S., Ang, E. L., Zhao, H., & Zhang, Y. (2022). Identification and Characterization of the Biosynthetic Pathway of the Sulfonolipid Capnine. Biochemistry, 61(24), 2861-2869. https://doi.org/10.1021/acs.biochem.2c00102

Burke, M. D., Fan, T. M., Hergenrother, P. J., Brooke, C. B., Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., & Wang, L. (2022). Saliva-based Molecular Testing For SARS-CoV-2. (U.S. Patent No. 11530457).

Huck, C. J., Boyko, Y. D., & Sarlah, D. (2022). Erratum: Correction: Dearomative logic in natural product total synthesis (Natural product reports (2022)). Natural Product Reports, 39(12), 2336-2337. https://doi.org/10.1039/d2np90039d

Sarksian, R., Zhu, L., & Van der donk, W. A. (2022). syn-Elimination of glutamylated threonine in lanthipeptide biosynthesis. Chemical Communications, 59(9), 1165-1168. https://doi.org/10.1039/D2CC06345J

Shi, W., Bell, S., Iyer, H., Brenden, C. K., Zhang, Y., Kim, S., Park, I., Bashir, R., Sweedler, J., & Vlasov, Y. (2022). Integrated silicon microfluidic chip for picoliter-scale analyte segmentation and microscale printing for mass spectrometry imaging. Lab on a chip, 23(1), 72-80. https://doi.org/10.1039/d2lc00688j

Burke, M. D., & Grillo, A. S. (2022). Restoring Physiology In Iron-deficient Organisms Using Small Molecules. (U.S. Patent No. 11517540).

Ayikpoe, R. S., Shi, C., Battiste, A. J., Eslami, S. M., Ramesh, S., Simon, M. A., Bothwell, I. R., Lee, H., Rice, A. J., Ren, H., Tian, Q., Harris, L. A., Sarksian, R., Zhu, L., Frerk, A. M., Precord, T. W., van der Donk, W. A., Mitchell, D. A., & Zhao, H. (2022). A scalable platform to discover antimicrobials of ribosomal origin. Nature communications, 13(1), [6135]. https://doi.org/10.1038/s41467-022-33890-w

Ju, K. S., & Nair, S. K. (2022). Convergent and divergent biosynthetic strategies towards phosphonic acid natural products. Current Opinion in Chemical Biology, 71, [102214]. https://doi.org/10.1016/j.cbpa.2022.102214

Peng, Q., Huang, Z., Sun, K., Liu, Y., Yoon, C. W., Harrison, R. E. S., Schmitt, D. L., Zhu, L., Wu, Y., Tasan, I., Zhao, H., Zhang, J., Zhong, S., Chien, S., & Wang, Y. (2022). Engineering inducible biomolecular assemblies for genome imaging and manipulation in living cells. Nature communications, 13(1), [7933]. https://doi.org/10.1038/s41467-022-35504-x

Schultz, J. C., Mishra, S., Gaither, E., Mejia, A., Dinh, H., Maranas, C., & Zhao, H. (2022). Metabolic engineering of Rhodotorula toruloides IFO0880 improves C16 and C18 fatty alcohol production from synthetic media. Microbial cell factories, 21(1), [26]. https://doi.org/10.1186/s12934-022-01750-3

Ranoa, D. R. E., Holland, R. L., Alnaji, F. G., Green, K. J., Wang, L., Fredrickson, R. L., Wang, T., Wong, G. N., Uelmen, J., Maslov, S., Weiner, Z. J., Tkachenko, A. V., Zhang, H., Liu, Z., Ibrahim, A., Patel, S. J., Paul, J. M., Vance, N. P., Gulick, J. G., ... Burke, M. D. (2022). Mitigation of SARS-CoV-2 transmission at a large public university. Nature communications, 13(1), [3207]. https://doi.org/10.1038/s41467-022-30833-3

Enghiad, B., Xue, P., Singh, N., Boob, A. G., Shi, C., Petrov, V. A., Liu, R., Peri, S. S., Lane, S. T., Gaither, E. D., & Zhao, H. (2022). PlasmidMaker is a versatile, automated, and high throughput end-to-end platform for plasmid construction. Nature communications, 13(1), [2697]. https://doi.org/10.1038/s41467-022-30355-y

Lei, R., Tan, T. J. C., Hernandez Garcia, A., Wang, Y., Diefenbacher, M., Teo, C., Gopan, G., Tavakoli Dargani, Z., Teo, Q. W., Graham, C. S., Brooke, C. B., Nair, S. K., & Wu, N. C. (2022). Prevalence and mechanisms of evolutionary contingency in human influenza H3N2 neuraminidase. Nature communications, 13(1), [6443]. https://doi.org/10.1038/s41467-022-34060-8

Revie, N. M., Iyer, K. R., Maxson, M. E., Zhang, J., Yan, S., Fernandes, C. M., Meyer, K. J., Chen, X., Skulska, I., Fogal, M., Sanchez, H., Hossain, S., Li, S., Yashiroda, Y., Hirano, H., Yoshida, M., Osada, H., Boone, C., Shapiro, R. S., ... Cowen, L. E. (2022). Targeting fungal membrane homeostasis with imidazopyrazoindoles impairs azole resistance and biofilm formation. Nature communications, 13(1), [3634]. https://doi.org/10.1038/s41467-022-31308-1

Li, S., Jira, E. R., Angello, N. H., Li, J., Yu, H., Moore, J. S., Diao, Y., Burke, M. D., & Schroeder, C. M. (2022). Using automated synthesis to understand the role of side chains on molecular charge transport. Nature communications, 13(1), [2102]. https://doi.org/10.1038/s41467-022-29796-2

Tarasow, T., Peh, J., Hergenrother, P. J., & Boudreau, M. W. (2022). Cancer Therapy By Degrading Dual Mek Signaling. (U.S. Patent No. 11510919).

Rice, A. J., Pelton, J. M., Kramer, N. J., Catlin, D. S., Nair, S. K., Pogorelov, T. V., Mitchell, D. A., & Bowers, A. A. (2022). Enzymatic Pyridine Aromatization during Thiopeptide Biosynthesis. Journal of the American Chemical Society, 144(46), 21116-21124. https://doi.org/10.1021/jacs.2c07377

Zheng, Y., Ongpipattanakul, C., & Nair, S. K. (2022). Bioconjugate Platform for Iterative Backbone N-Methylation of Peptides. ACS Catalysis, 12(22), 14006-14014. https://doi.org/10.1021/acscatal.2c04681

Ornelas, M. Y., Thomas, A. Y., Johnson Rosas, L. I., Scoville, R. O., & Mehta, A. P. (2022). Synthetic Platforms for Characterizing and Targeting of SARS-CoV-2 Genome Capping Enzymes. ACS synthetic biology, 11(11), 3759-3771. https://doi.org/10.1021/acssynbio.2c00359

Zhao, H. (2022). The Ever-Expanding Boundaries of Synthetic Biology. ACS synthetic biology, 11(11), 3550. https://doi.org/10.1021/acssynbio.2c00582

Hooper, A. R., Oštrek, A., Milian-Lopez, A., & Sarlah, D. (2022). Bioinspired Total Synthesis of Pyritide A2 through Pyridine Ring Synthesis. Angewandte Chemie - International Edition, 61(46), [e202212299]. https://doi.org/10.1002/anie.202212299

Zhao, F., Wei, Y., Wang, X., Zhou, Y., Tong, Y., Ang, E. L., Liu, S., Zhao, H., & Zhang, Y. (2022). Enzymatic Synthesis of the Unnatural Nucleotide 2’-Deoxyisoguanosine 5’-Monophosphate. ChemBioChem, 23(21), [e202200295]. https://doi.org/10.1002/cbic.202200295

Roy, P., Dennis, D. G., Eschbach, M. D., Anand, S. D., Xu, F., Maturano, J., Hellman, J., Sarlah, D., & Das, A. (2022). Metabolites of Cannabigerol Generated by Human Cytochrome P450s Are Bioactive. Biochemistry, 61(21), 2398-2408. https://doi.org/10.1021/acs.biochem.2c00383

Qiao, W., Xu, S., Liu, Z., Fu, X., Zhao, H., & Shi, S. (2022). Challenges and opportunities in C1-based biomanufacturing. Bioresource Technology, 364, [128095]. https://doi.org/10.1016/j.biortech.2022.128095

Dong, H., & Cronan, J. E. (2022). Unsaturated fatty acid synthesis in Enterococcus faecalis requires a specific enoyl-ACP reductase. Molecular Microbiology, 118(5), 541-551. https://doi.org/10.1111/mmi.14981

Angello, N. H., Rathore, V., Beker, W., Wołos, A., Jira, E. R., Roszak, R., Wu, T. C., Schroeder, C. M., Aspuru-Guzik, A., Grzybowski, B. A., & Burke, M. D. (2022). Closed-loop optimization of general reaction conditions for heteroaryl Suzuki-Miyaura coupling. Science, 378(6618), 399-405. https://doi.org/10.1126/science.adc8743

Zhang, Z., & Zhao, H. (2022). Tunnel engineering enables multifaceted improvements in halogenase. Chem Catalysis, 2(10), 2432-2434. https://doi.org/10.1016/j.checat.2022.09.010

Zhang, Y., Li, K., Zhao, Y., Shi, W., Iyer, H., Kim, S., Brenden, C., Sweedler, J. V., & Vlasov, Y. (2022). Attomole-Level Multiplexed Detection of Neurochemicals in Picoliter Droplets by On-Chip Nanoelectrospray Ionization Coupled to Mass Spectrometry. Analytical Chemistry, 94(40), 13804-13809. https://doi.org/10.1021/acs.analchem.2c02323

Muñoz, K. A., & Hergenrother, P. J. (2022). Computational discovery of dynobactin antibiotics. Nature Microbiology, 7(10), 1512-1513. https://doi.org/10.1038/s41564-022-01234-5

Ali, A., Davidson, S., Fraenkel, E., Gilmore, I., Hankemeier, T., Kirwan, J. A., Lane, A. N., Lanekoff, I., Larion, M., McCall, L. I., Murphy, M., Sweedler, J. V., & Zhu, C. (2022). Single cell metabolism: current and future trends. Metabolomics, 18(10), [77]. https://doi.org/10.1007/s11306-022-01934-3

Huck, C. J., Boyko, Y. D., & Sarlah, D. (2022). Dearomative logic in natural product total synthesis. Natural Product Reports, 39(12), 2231-2291. https://doi.org/10.1039/d2np00042c

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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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