Department of Biochemistry and Molecular Biophysics

Displaying 1 - 50 of 314CSV
Latorraca, N. R., Sabaat, S., Habrian, C. H., Bleier, J., Stanley, C., Kinz-Thompson, C. D., Marqusee, S., & Isacoff, E. Y. (2025). Domain coupling in activation of a family C GPCR. Nature Chemical Biology. https://doi.org/10.1038/s41589-025-01895-3
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Keller, M. R., McKinney, M. G., Sen, A. K., Guagliardo, F. G., Hellwarth, E. B., Islam, K. N., Kaplan, N. A., Gibbons, W. J., Kemmerly, G. E., Meers, C., Wang, X., & Jones, J. A. (2025). Psilocybin biosynthesis enhancement through gene source optimization. Metabolic Engineering, 91, 119–129. https://doi.org/10.1016/j.ymben.2025.04.003
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Rimkute, I., Olia, A. S., Suleiman, M., Woods, K. D., Bylund, T., Morano, N. C., Tully, E. S., Verardi, R., Bao, S., Beddall, M. H., Chaimongkol, N., Donaldson, M. M., Du, R., Dulan, C. N. M., Gorman, J., Henry, A. R., Schramm, C. A., Sosnovtsev, S. V., Stephens, T., … Roederer, M. (2025). A broadly protective human antibody for GI genogroup noroviruses. Nature Microbiology. https://doi.org/10.1038/s41564-025-01952-6
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Shin, Y., Hedglin, M., & Murakami, K. S. (2025). Cryo-EM structure of apo-form human DNA polymerase δ elucidates its minimal DNA synthesis activity without PCNA. Journal of Biological Chemistry, 301(4), 108342. https://doi.org/10.1016/j.jbc.2025.108342
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Qiu, W., Trinh, T. K. H., Catalano, C., Mehta, A., Desai, U. R., Kellogg, G. E., Hendrickson, W. A., & Guo, Y. (2025). Cholesterol-dependent enzyme activity of human TSPO1. Proceedings of the National Academy of Sciences, 122(13). https://doi.org/10.1073/pnas.2323045122
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Tan, L., Xie, X. S., & Lomvardas, S. (2025). Genomic snowflakes: how the uniqueness of DNA folding allows us to smell the chemical universe. Current Opinion in Genetics & Development, 92, 102329. https://doi.org/10.1016/j.gde.2025.102329
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Morano, N. C., Lopez, D. H., Meltzer, H., Sergeeva, A. P., Katsamba, P. S., Rostam, K. D., Gupta, H. P., Becker, J. E., Bornstein, B., Cosmanescu, F., Schuldiner, O., Honig, B., Mann, R. S., & Shapiro, L. (2025). Members of the DIP and Dpr adhesion protein families use cis inhibition to shape neural development in Drosophila. PLOS Biology, 23(3), e3003030. https://doi.org/10.1371/journal.pbio.3003030
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Feng, X., & Frank, J. (2025). A PDMS-based microfluidic chip assembly for time-resolved cryo-EM (TRCEM) sample preparation. Bio-protocol, 15(420). https://doi.org/10.21769/BioProtoc.5193

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Hendrickson, W. A., & Gong, Z. (2025). Structural and evolutionary insights into the functioning of glycoprotein hormones and their receptors. Andrology. Portico. https://doi.org/10.1111/andr.70001
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Goldberg, A. R., Dovas, A., Torres, D., Pereira, B., Viswanathan, A., Das Sharma, S., Mela, A., Merricks, E. M., Megino-Luque, C., McInvale, J. J., Olabarria, M., Shokooh, L. A., Zhao, H. T., Chen, C., Kotidis, C., Calvaresi, P., Banu, M. A., Razavilar, A., Sudhakar, T. D., … Canoll, P. (2025). Glioma-induced alterations in excitatory neurons are reversed by mTOR inhibition. Neuron. https://doi.org/10.1016/j.neuron.2024.12.026
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Mason, R. D., Zhang, B., Morano, N. C., Shen, C.-H., McKee, K., Heimann, A., Du, R., Nazzari, A. F., Hodges, S., Kanai, T., Lin, B. C., Louder, M. K., Doria-Rose, N. A., Zhou, T., Shapiro, L., Roederer, M., Kwong, P. D., & Gorman, J. (2025). Structural development of the HIV-1 apex-directed PGT145-PGDM1400 antibody lineage. Cell Reports, 44(1), 115223. https://doi.org/10.1016/j.celrep.2024.115223
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Kittle, R. H., & Levo, M. (2025). Exploring the interplay between enhancer–promoter interactions and transcription. Current Opinion in Genetics & Development, 90, 102303. https://doi.org/10.1016/j.gde.2024.102303
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Shin, A. E., Sugiura, K., Kariuki, S. W., Cohen, D. A., Flashner, S. P., Klein-Szanto, A. J., Nishiwaki, N., De, D., Vasan, N., Gabre, J. T., Lengner, C. J., Sims, P. A., & Rustgi, A. K. (2025). LIN28B-mediated PI3K/AKT pathway activation promotes metastasis in colorectal cancer models. Journal of Clinical Investigation. https://doi.org/10.1172/jci186035
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Hong, S. J., Resnick, S. J., Iketani, S., Cha, J. W., Albert, B. A., Fazekas, C. T., Chang, C.-W., Liu, H., Dagan, S., Abagyan, M. R., Fajtová, P., Culbertson, B., Brace, B., Reddem, E. R., Forouhar, F., Glickman, J. F., Balkovec, J. M., Stockwell, B. R., Shapiro, L., … Chavez, A. (2025). A multiplex method for rapidly identifying viral protease inhibitors. Molecular Systems Biology, 21(2), 158–172. https://doi.org/10.1038/s44320-024-00082-1
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Vaysset, H., Meers, C., Cury, J., Bernheim, A., & Sternberg, S. H. (2025). Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons. Nature Microbiology, 10(1), 20–27. https://doi.org/10.1038/s41564-024-01889-2
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Wang, W., Gong, Z., & Hendrickson, W. A. (2025). AlphaFold-guided molecular replacement for solving challenging crystal structures. Acta Crystallographica Section D Structural Biology, 81(1), 4–21. https://doi.org/10.1107/s2059798324011999
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Caron, D. P., Specht, W. L., Chen, D., Wells, S. B., Szabo, P. A., Jensen, I. J., Farber, D. L., & Sims, P. A. (2025). Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues. Cell Reports Methods, 5(1), 100938. https://doi.org/10.1016/j.crmeth.2024.100938
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Yu, L., Yang, Y. X., Gong, Z., Wan, Q., Du, Y., Zhou, Q., Xiao, Y., Zahr, T., Wang, Z., Yu, Z., Yang, K., Geng, J., Fried, S. K., Li, J., Haeusler, R. A., Leong, K. W., Bai, L., Wu, Y., Sun, L., … Qiang, L. (2024). FcRn-dependent IgG accumulation in adipose tissue unmasks obesity pathophysiology. Cell Metabolism. https://doi.org/10.1016/j.cmet.2024.11.001
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Bunne, C., Roohani, Y., Rosen, Y., Gupta, A., Zhang, X., Roed, M., Alexandrov, T., AlQuraishi, M., Brennan, P., Burkhardt, D. B., Califano, A., Cool, J., Dernburg, A. F., Ewing, K., Fox, E. B., Haury, M., Herr, A. E., Horvitz, E., Hsu, P. D., … Quake, S. R. (2024). How to build the virtual cell with artificial intelligence: Priorities and opportunities. Cell, 187(25), 7045–7063. https://doi.org/10.1016/j.cell.2024.11.015
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Blattman, S. B., Jiang, W., McGarrigle, E. R., Liu, M., Oikonomou, P., & Tavazoie, S. (2024). Identification and genetic dissection of convergent persister cell states. Nature, 636(8042), 438–446. https://doi.org/10.1038/s41586-024-08124-2
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Nishiwaki, N., Sugiura, K., Suzuki, K., Li, A. L., Contreras, C. T., Efe, G., Shin, A. E., Sadeghian, D., Zhao, J., Maitra, A., Pitarresi, J. R., Sims, P. A., Chandwani, R., & Rustgi, A. K. (2024). PRRX1 has functional roles in pancreatic acinar to ductal metaplasia and carcinogenesis. Cellular and Molecular Gastroenterology and Hepatology, 101442. https://doi.org/10.1016/j.jcmgh.2024.101442
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Gangwar, S. P., Yelshanskaya, M. V., Aktolun, M., Yen, L. Y., Newton, T. P., Strømgaard, K., Kurnikova, M. G., & Sobolevsky, A. I. (2024). Trapping of spermine, Kukoamine A, and polyamine toxin blockers in GluK2 kainate receptor channels. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-54538-x
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Powers, A. S., Khan, A., Paggi, J. M., Latorraca, N. R., Souza, S., Di Salvo, J., Lu, J., Soisson, S. M., Johnston, J. M., Weinglass, A. B., & Dror, R. O. (2024). A non-canonical mechanism of GPCR activation. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-54103-6
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Davis-Porada, J., George, A. B., Lam, N., Caron, D. P., Gray, J. I., Huang, J., Hwu, J., Wells, S. B., Matsumoto, R., Kubota, M., Lee, Y., Morrison-Colvin, R., Jensen, I. J., Ural, B. B., Shaabani, N., Weiskopf, D., Grifoni, A., Sette, A., Szabo, P. A., … Farber, D. L. (2024). Maintenance and functional regulation of immune memory to COVID-19 vaccines in tissues. Immunity, 57(12), 2895-2913.e8. https://doi.org/10.1016/j.immuni.2024.10.003
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Cerutti, G., Arias, R., Bahna, F., Mannepalli, S., Katsamba, P. S., Ahlsen, G., Kloss, B., Bruni, R., Tomlinson, A., & Shapiro, L. (2024). Structures and pH-dependent dimerization of the sevenless receptor tyrosine kinase. Molecular Cell, 84(23), 4677-4690.e6. https://doi.org/10.1016/j.molcel.2024.10.017
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Zarco, N., Dovas, A., de Araujo Farias, V., Nagaiah, N. K. H., Haddock, A., Sims, P. A., Hambardzumyan, D., Meyer, C. T., Canoll, P., Rosenfeld, S. S., & Kenchappa, R. S. (2024). Resistance to spindle inhibitors in glioblastoma depends on STAT3 and therapy induced senescence. IScience, 27(12), 111311. https://doi.org/10.1016/j.isci.2024.111311
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Wang, H., Cheng, C., Dal Santo, J. L., Shen, C.-H., Bylund, T., Henry, A. R., Howe, C. A., Hwang, J., Morano, N. C., Morris, D. J., Pletnev, S., Roark, R. S., Zhou, T., Hansen, B. T., Hoyt, F. H., Johnston, T. S., Wang, S., Zhang, B., Ambrozak, D. R., … Kwong, P. D. (2024). Potent and broad HIV-1 neutralization in fusion peptide-primed SHIV-infected macaques. Cell. https://doi.org/10.1016/j.cell.2024.10.003
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Thiam, L. G., McHugh, K., Ba, A., Li, R., Guo, Y., Pouye, M. N., Cisse, A., Pipini, D., Diallo, F., Sene, S. D., Patel, S. D., Thiam, A., Sadio, B. D., Mbengue, A., Vigan-Womas, I., Sheng, Z., Shapiro, L., Draper, S. J., & Bei, A. K. (2024). Vaccine-induced human monoclonal antibodies to PfRH5 show broadly neutralizing activity against P. falciparum clinical isolates. Npj Vaccines, 9(1). https://doi.org/10.1038/s41541-024-00986-x
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Tuddenham, J. F., Taga, M., Haage, V., Marshe, V. S., Roostaei, T., White, C., Lee, A. J., Fujita, M., Khairallah, A., Zhang, Y., Green, G., Hyman, B., Frosch, M., Hopp, S., Beach, T. G., Serrano, G. E., Corboy, J., Habib, N., Klein, H.-U., … De Jager, P. L. (2024). A cross-disease resource of living human microglia identifies disease-enriched subsets and tool compounds recapitulating microglial states. Nature Neuroscience, 27(12), 2521–2537. https://doi.org/10.1038/s41593-024-01764-7
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Stearns, K., Lampe, G., Hanan, R., Marcink, T., Niewiesk, S., Sternberg, S. H., Greninger, A. L., Porotto, M., & Moscona, A. (2024). Human parainfluenza virus 3 field strains undergo extracellular fusion protein cleavage to activate entry. MBio, 15(11). https://doi.org/10.1128/mbio.02327-24
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Shin, J. H., Cuevas, L. M., Roy, R., Bonilla, S. L., Al-Hashimi, H., Greenleaf, W. J., & Herschlag, D. (2024). Exploring the energetic and conformational properties of the sequence space connecting naturally occurring RNA tetraloop receptor motifs. RNA, 30(12), 1646–1659. https://doi.org/10.1261/rna.080039.124
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Liao, J., Sergeeva, A. P., Harder, E. D., Wang, L., Sampson, J. M., Honig, B., & Friesner, R. A. (2024). A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein–Ligand Binding. Journal of Chemical Theory and Computation, 20(19), 8609–8623. https://doi.org/10.1021/acs.jctc.4c00954
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Yang, H. H., Brezovec, B. E., Serratosa Capdevila, L., Vanderbeck, Q. X., Adachi, A., Mann, R. S., & Wilson, R. I. (2024). Fine-grained descending control of steering in walking Drosophila. Cell, 187(22), 6290-6308.e27. https://doi.org/10.1016/j.cell.2024.08.033
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Beenken, A., Shen, T., Jin, G., Ghotra, A., Xu, K., Nesanir, K., Sturley, R. E., Vijayakumar, S., Kahn, A., Levitman, A., Stauber, J., Chavez, E. Y., Robbins-Juarez, S. Y., Hao, L., Field, T. B., Erdjument-Bromage, H., Neubert, T. A., Shapiro, L., Qiu, A., & Barasch, J. (2024). Spns1 is an iron transporter essential for megalin-dependent endocytosis. American Journal of Physiology-Renal Physiology. https://doi.org/10.1152/ajprenal.00172.2024
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Salunkhe, S., Daley, J. M., Kaur, H., Tomimatsu, N., Xue, C., Raina, V. B., Jasper, A. M., Rogers, C. M., Li, W., Zhou, S., Mojidra, R., Kwon, Y., Fang, Q., Ji, J.-H., Badamchi Shabestari, A., Fitzgerald, O., Dinh, H., Mukherjee, B., Habib, A. A., … Sung, P. (2024). Promotion of DNA end resection by BRCA1–BARD1 in homologous recombination. Nature, 634(8033), 482–491. https://doi.org/10.1038/s41586-024-07910-2
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Wang, Q., Mellis, I. A., Ho, J., Bowen, A., Kowalski-Dobson, T., Valdez, R., Katsamba, P. S., Wu, M., Lee, C., Shapiro, L., Gordon, A., Guo, Y., Ho, D. D., & Liu, L. (2024). Recurrent SARS-CoV-2 spike mutations confer growth advantages to select JN.1 sublineages. Emerging Microbes & Infections, 13(1). https://doi.org/10.1080/22221751.2024.2402880
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Jeon, Y., Lu, Y., Ferrari, M. M., Channagiri, T., Xu, P., Meers, C., Zhang, Y., Balachander, S., Park, V. S., Marsili, S., Pursell, Z. F., Jonoska, N., & Storici, F. (2024). RNA-mediated double-strand break repair by end-joining mechanisms. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-51457-9
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Quintana-Feliciano, R., Kottur, J., Ni, M., Ghosh, R., Salas-Estrada, L., Ahlsen, G., Rechkoblit, O., Shapiro, L., Filizola, M., Fang, G., & Aggarwal, A. K. (2024). Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-52130-x
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Banu, M. A., Dovas, A., Argenziano, M. G., Zhao, W., Sperring, C. P., Cuervo Grajal, H., Liu, Z., Higgins, D. M., Amini, M., Pereira, B., Ye, L. F., Mahajan, A., Humala, N., Furnari, J. L., Upadhyayula, P. S., Zandkarimi, F., Nguyen, T. T., Teasley, D., Wu, P. B., … Canoll, P. (2024). A cell state-specific metabolic vulnerability to GPX4-dependent ferroptosis in glioblastoma. The EMBO Journal. https://doi.org/10.1038/s44318-024-00176-4
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Li, A. L., Sugiura, K., Nishiwaki, N., Suzuki, K., Sadeghian, D., Zhao, J., Maitra, A., Falvo, D., Chandwani, R., Pitarresi, J. R., Sims, P. A., & Rustgi, A. K. (2024). FRA1 controls acinar cell plasticity during murine Kras-induced pancreatic acinar to ductal metaplasia. Developmental Cell. https://doi.org/10.1016/j.devcel.2024.07.021
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Sampson, J. M., Cannon, D. A., Duan, J., Epstein, J. C. K., Sergeeva, A. P., Katsamba, P. S., Mannepalli, S. M., Bahna, F. A., Adihou, H., Guéret, S. M., Gopalakrishnan, R., Geschwindner, S., Rees, D. G., Sigurdardottir, A., Wilkinson, T., Dodd, R. B., De Maria, L., Mobarec, J. C., Shapiro, L., … Wang, L. (2024). Robust Prediction of Relative Binding Energies for Protein–Protein Complex Mutations Using Free Energy Perturbation Calculations. Journal of Molecular Biology, 436(16), 168640. https://doi.org/10.1016/j.jmb.2024.168640
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Tang, S., Conte, V., Zhang, D. J., Žedaveinytė, R., Lampe, G. D., Wiegand, T., Tang, L. C., Wang, M., Walker, M. W. G., George, J. T., Berchowitz, L. E., Jovanovic, M., & Sternberg, S. H. (2024). De novo gene synthesis by an antiviral reverse transcriptase. Science, 386(6717). https://doi.org/10.1126/science.adq0876
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