Department of Biochemistry and Molecular Biophysics

Displaying 251 - 300 of 314CSV
Marcink, T. C., Kicmal, T., Armbruster, E., Zhang, Z., Zipursky, G., Golub, K. L., Idris, M., Khao, J., Drew-Bear, J., McGill, G., Gallagher, T., Porotto, M., des Georges, A., & Moscona, A. (2022). Intermediates in SARS-CoV-2 spike–mediated cell entry. Science Advances, 8(33). https://doi.org/10.1126/sciadv.abo3153
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Boni, N., Shapiro, L., Honig, B., Wu, Y., & Rubinstein, R. (2022). On the formation of ordered protein assemblies in cell–cell interfaces. Proceedings of the National Academy of Sciences, 119(34). https://doi.org/10.1073/pnas.2206175119
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Rajeswaran, W., Ashkar, S. R., Lee, P. H., Yeomans, L., Shin, Y., Franzblau, S. G., Murakami, K. S., Showalter, H. D., & Garcia, G. A. (2022). Optimization of Benzoxazinorifamycins to Improve Mycobacterium tuberculosis RNA Polymerase Inhibition and Treatment of Tuberculosis. ACS Infectious Diseases, 8(8), 1422–1438. https://doi.org/10.1021/acsinfecdis.1c00636
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Owji, A. P., Wang, J., Kittredge, A., Clark, Z., Zhang, Y., Hendrickson, W. A., & Yang, T. (2022). Structures and gating mechanisms of human bestrophin anion channels. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-31437-7
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Shintaku, J., Pernice, W. M., Eyaid, W., GC, J. B., Brown, Z. P., Juanola-Falgarona, M., Torres-Torronteras, J., Sommerville, E. W., Hellebrekers, D. M. E. I., Blakely, E. L., Donaldson, A., van de Laar, I., Leu, C.-S., Marti, R., Frank, J., Tanji, K., Koolen, D. A., Rodenburg, R. J., Chinnery, P. F., … Hirano, M. (2022). RRM1 variants cause a mitochondrial DNA maintenance disorder via impaired de novo nucleotide synthesis. Journal of Clinical Investigation, 132(13). https://doi.org/10.1172/jci145660
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Feng, S., Rastogi, C., Loker, R., Glassford, W. J., Tomas Rube, H., Bussemaker, H. J., & Mann, R. S. (2022). Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-31501-2
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Feng, S., & Mann, R. S. (2022). SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues. Proceedings of the National Academy of Sciences, 119(25). https://doi.org/10.1073/pnas.2122900119
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Chait, M., Yilmaz, M. M., Shakil, S., Ku, A. W., Dogra, P., Connors, T. J., Szabo, P. A., Gray, J. I., Wells, S. B., Kubota, M., Matsumoto, R., Poon, M. M. L., Snyder, M. E., Baldwin, M. R., Sims, P. A., Saqi, A., Farber, D. L., & Weisberg, S. P. (2022). Immune and epithelial determinants of age-related risk and alveolar injury in fatal COVID-19. JCI Insight, 7(11). https://doi.org/10.1172/jci.insight.157608
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Wang, Q., Anang, S., Iketani, S., Guo, Y., Liu, L., Katsamba, P. S., Shapiro, L., Ho, D. D., & Sodroski, J. G. (2022). Functional properties of the spike glycoprotein of the emerging SARS-CoV-2 variant B.1.1.529. Cell Reports, 39(11), 110924. https://doi.org/10.1016/j.celrep.2022.110924
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Fernández, E. C., Wang, J., Griffin, A., Minns, H., Wei, H.-J., Zhang, X., Szalontay, L., Mundi, P., Wu, C.-C., Gartrell, R., Zacharoulis, S., Califano, A., & Pavisic, J. (2022). DIPG-57. A systems biology approach to defining and targeting master regulator dependencies from bulk and single-Cell RNA-seq in diffuse midline glioma (DMG). Neuro-Oncology, 24(Supplement_1), i31–i32. https://doi.org/10.1093/neuonc/noac079.114
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Middelhoff, M., Valenti, G., Tomassoni, L., Ochiai, Y., Belin, B., Takahashi, R., Malagola, E., Nienhüser, H., Finlayson, M., Hayakawa, Y., Zamechek, L. B., Renz, B. W., Westphalen, C. B., Quante, M., Margolis, K. G., Sims, P. A., Laise, P., Califano, A., Rao, M., … Wang, T. C. (2022). Adult enteric Dclk1-positive glial and neuronal cells reveal distinct responses to acute intestinal injury. American Journal of Physiology-Gastrointestinal and Liver Physiology, 322(6), G583–G597. https://doi.org/10.1152/ajpgi.00244.2021
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Liu, L., Iketani, S., Guo, Y., Reddem, E. R., Casner, R. G., Nair, M. S., Yu, J., Chan, J. F.-W., Wang, M., Cerutti, G., Li, Z., Morano, N. C., Castagna, C. D., Corredor, L., Chu, H., Yuan, S., Poon, V. K.-M., Chan, C. C.-S., Chen, Z., … Ho, D. D. (2022). An antibody class with a common CDRH3 motif broadly neutralizes sarbecoviruses. Science Translational Medicine, 14(646). https://doi.org/10.1126/scitranslmed.abn6859
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Obradovic, A., Graves, D., Korrer, M., Wang, Y., Roy, S., Naveed, A., Xu, Y., Luginbuhl, A., Curry, J., Gibson, M., Idrees, K., Hurley, P., Jiang, P., Liu, X. S., Uppaluri, R., Drake, C. G., Califano, A., & Kim, Y. J. (2022). Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer. Clinical Cancer Research, 28(10), 2094–2109. https://doi.org/10.1158/1078-0432.ccr-21-3570
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Domínguez Conde, C., Xu, C., Jarvis, L. B., Rainbow, D. B., Wells, S. B., Gomes, T., Howlett, S. K., Suchanek, O., Polanski, K., King, H. W., Mamanova, L., Huang, N., Szabo, P. A., Richardson, L., Bolt, L., Fasouli, E. S., Mahbubani, K. T., Prete, M., Tuck, L., … Teichmann, S. A. (2022). Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science, 376(6594). https://doi.org/10.1126/science.abl5197
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Moy, R. H., Nguyen, A., Loo, J. M., Yamaguchi, N., Kajba, C. M., Santhanam, B., Ostendorf, B. N., Wu, Y. G., Tavazoie, S., & Tavazoie, S. F. (2022). Functional genetic screen identifies ITPR3/calcium/RELB axis as a driver of colorectal cancer metastatic liver colonization. Developmental Cell, 57(9), 1146-1159.e7. https://doi.org/10.1016/j.devcel.2022.04.010
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Ronaldson-Bouchard, K., Teles, D., Yeager, K., Tavakol, D. N., Zhao, Y., Chramiec, A., Tagore, S., Summers, M., Stylianos, S., Tamargo, M., Lee, B. M., Halligan, S. P., Abaci, E. H., Guo, Z., Jacków, J., Pappalardo, A., Shih, J., Soni, R. K., Sonar, S., … Vunjak-Novakovic, G. (2022). A multi-organ chip with matured tissue niches linked by vascular flow. Nature Biomedical Engineering, 6(4), 351–371. https://doi.org/10.1038/s41551-022-00882-6
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Bekdash, R., Quejada, J. R., Ueno, S., Kawano, F., Morikawa, K., Klein, A. D., Matsumoto, K., Lee, T. C., Nakanishi, K., Chalan, A., Lee, T. M., Liu, R., Homma, S., Lin, C.-S., Yelshanskaya, M. V., Sobolevsky, A. I., Goda, K., & Yazawa, M. (2021). GEM-IL: A highly responsive fluorescent lactate indicator. Cell Reports Methods, 1(7), 100092. https://doi.org/10.1016/j.crmeth.2021.100092
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Chang, A., Xiang, X., Wang, J., Lee, C., Arakhamia, T., Simjanoska, M., Wang, C., Carlomagno, Y., Zhang, G., Dhingra, S., Thierry, M., Perneel, J., Heeman, B., Forgrave, L. M., DeTure, M., DeMarco, M. L., Cook, C. N., Rademakers, R., Dickson, D. W., … Fitzpatrick, A. W. P. (2022). Homotypic fibrillization of TMEM106B across diverse neurodegenerative diseases. Cell, 185(8), 1346-1355.e15. https://doi.org/10.1016/j.cell.2022.02.026
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Snyder, M. E., Moghbeli, K., Bondonese, A., Craig, A., Popescu, I., Fan, L., Tabib, T., Lafyatis, R., Chen, K., Trejo Bittar, H. E., Lendermon, E., Pilewski, J., Johnson, B., Kilaru, S., Zhang, Y., Sanchez, P. G., Alder, J. K., Sims, P. A., & McDyer, J. F. (2022). Modulation of tissue resident memory T cells by glucocorticoids after acute cellular rejection in lung transplantation. Journal of Experimental Medicine, 219(4). https://doi.org/10.1084/jem.20212059
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Xu, S., Sergeeva, A. P., Katsamba, P. S., Mannepalli, S., Bahna, F., Bimela, J., Zipursky, S. L., Shapiro, L., Honig, B., & Zinn, K. (2022). Affinity requirements for control of synaptic targeting and neuronal cell survival by heterophilic IgSF cell adhesion molecules. Cell Reports, 39(1), 110618. https://doi.org/10.1016/j.celrep.2022.110618
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Martin, J. A., & Palmer, A. G. (2022). Comparisons of Ribonuclease HI Homologs and Mutants Uncover a Multistate Model for Substrate Recognition. Journal of the American Chemical Society, 144(12), 5342–5349. https://doi.org/10.1021/jacs.1c11897
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Zazhytska, M., Kodra, A., Hoagland, D. A., Frere, J., Fullard, J. F., Shayya, H., McArthur, N. G., Moeller, R., Uhl, S., Omer, A. D., Gottesman, M. E., Firestein, S., Gong, Q., Canoll, P. D., Goldman, J. E., Roussos, P., tenOever, B. R., Jonathan B. Overdevest, & Lomvardas, S. (2022). Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia. Cell, 185(6), 1052-1064.e12. https://doi.org/10.1016/j.cell.2022.01.024
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Goodman, K. M., Katsamba, P. S., Rubinstein, R., Ahlsén, G., Bahna, F., Mannepalli, S., Dan, H., Sampogna, R. V., Shapiro, L., & Honig, B. (2022). How clustered protocadherin binding specificity is tuned for neuronal self-/nonself-recognition. ELife, 11. CLOCKSS. https://doi.org/10.7554/elife.72416
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Douglass, E. F., Allaway, R. J., Szalai, B., Wang, W., Tian, T., Fernández-Torras, A., Realubit, R., Karan, C., Zheng, S., Pessia, A., Tanoli, Z., Jafari, M., Wan, F., Li, S., Xiong, Y., Duran-Frigola, M., Bertoni, M., Badia-i-Mompel, P., Mateo, L., … Califano, A. (2022). A community challenge for a pancancer drug mechanism of action inference from perturbational profile data. Cell Reports Medicine, 3(1), 100492. https://doi.org/10.1016/j.xcrm.2021.100492
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Klompe, S. E., Jaber, N., Beh, L. Y., Mohabir, J. T., Bernheim, A., & Sternberg, S. H. (2022). Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons. Molecular Cell, 82(3), 616-628.e5. https://doi.org/10.1016/j.molcel.2021.12.021
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Lassman, A. B., Wen, P. Y., van den Bent, M. J., Plotkin, S. R., Walenkamp, A. M. E., Green, A. L., Li, K., Walker, C. J., Chang, H., Tamir, S., Henegar, L., Shen, Y., Alvarez, M. J., Califano, A., Landesman, Y., Kauffman, M. G., Shacham, S., & Mau-Sørensen, M. (2021). A Phase II Study of the Efficacy and Safety of Oral Selinexor in Recurrent Glioblastoma. Clinical Cancer Research, 28(3), 452–460. https://doi.org/10.1158/1078-0432.ccr-21-2225
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Agrafioti, P., Morin‐Baxter, J., Tanagala, K. K. K., Dubey, S., Sims, P., Lalla, E., & Momen‐Heravi, F. (2022). Decoding the role of macrophages in periodontitis and type 2 diabetes using single‐cell RNA‐sequencing. The FASEB Journal, 36(2). Portico. https://doi.org/10.1096/fj.202101198r
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Swaminathan, B., Youn, S.-W., Naiche, L. A., Du, J., Villa, S. R., Metz, J. B., Feng, H., Zhang, C., Kopan, R., Sims, P. A., & Kitajewski, J. K. (2022). Endothelial Notch signaling directly regulates the small GTPase RND1 to facilitate Notch suppression of endothelial migration. Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-05666-1
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Sheng, Z., Bimela, J. S., Katsamba, P. S., Patel, S. D., Guo, Y., Zhao, H., Guo, Y., Kwong, P. D., & Shapiro, L. (2022). Structural Basis of Antibody Conformation and Stability Modulation by Framework Somatic Hypermutation. Frontiers in Immunology, 12. https://doi.org/10.3389/fimmu.2021.811632
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Seitz, E., Acosta-Reyes, F., Maji, S., Schwander, P., & Frank, J. (2022). Recovery of Conformational Continuum From Single-Particle Cryo-EM Images: Optimization of ManifoldEM Informed by Ground Truth. IEEE Transactions on Computational Imaging, 8, 462–478. https://doi.org/10.1109/tci.2022.3174801
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Rousová, D., Nivsarkar, V., Altmannova, V., Raina, V. B., Funk, S. K., Liedtke, D., Janning, P., Müller, F., Reichle, H., Vader, G., & Weir, J. R. (2021). Novel mechanistic insights into the role of Mer2 as the keystone of meiotic DNA break formation. ELife, 10. CLOCKSS. https://doi.org/10.7554/elife.72330
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Park, J., Zuo, H., Frangaj, A., Fu, Z., Yen, L. Y., Zhang, Z., Mosyak, L., Slavkovich, V. N., Liu, J., Ray, K. M., Cao, B., Vallese, F., Geng, Y., Chen, S., Grassucci, R., Dandey, V. P., Tan, Y. Z., Eng, E., Lee, Y., … Fan, Q. R. (2021). Symmetric activation and modulation of the human calcium-sensing receptor. Proceedings of the National Academy of Sciences, 118(51). https://doi.org/10.1073/pnas.2115849118
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Son, J., Ding, H., Farb, T. B., Efanov, A. M., Sun, J., Gore, J. L., Syed, S. K., Lei, Z., Wang, Q., Accili, D., & Califano, A. (2021). BACH2 inhibition reverses β cell failure in type 2 diabetes models. Journal of Clinical Investigation, 131(24). https://doi.org/10.1172/jci153876
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Gil, V., Miranda, S., Riisnaes, R., Gurel, B., D’Ambrosio, M., Vasciaveo, A., Crespo, M., Ferreira, A., Brina, D., Troiani, M., Sharp, A., Sheehan, B., Christova, R., Seed, G., Figueiredo, I., Lambros, M., Dolling, D., Rekowski, J., Alajati, A., … de Bono, J. (2021). HER3 Is an Actionable Target in Advanced Prostate Cancer. Cancer Research, 81(24), 6207–6218. https://doi.org/10.1158/0008-5472.can-21-3360
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Fischler-Ruiz, W., Clark, D. G., Joshi, N. R., Devi-Chou, V., Kitch, L., Schnitzer, M., Abbott, L. F., & Axel, R. (2021). Olfactory landmarks and path integration converge to form a cognitive spatial map. Neuron, 109(24), 4036-4049.e5. https://doi.org/10.1016/j.neuron.2021.09.055
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Madan, B., Reddem, E. R., Wang, P., Casner, R. G., Nair, M. S., Huang, Y., Fahad, A. S., de Souza, M. O., Banach, B. B., López Acevedo, S. N., Pan, X., Nimrania, R., Teng, I., Bahna, F., Zhou, T., Zhang, B., Yin, M. T., Ho, D. D., Kwong, P. D., … DeKosky, B. J. (2021). Antibody screening at reduced pH enables preferential selection of potently neutralizing antibodies targeting SARS‐CoV‐2. AIChE Journal, 67(12). Portico. https://doi.org/10.1002/aic.17440
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Poon, M. M. L., Byington, E., Meng, W., Kubota, M., Matsumoto, R., Grifoni, A., Weiskopf, D., Dogra, P., Lam, N., Szabo, P. A., Ural, B. B., Wells, S. B., Rosenfeld, A. M., Brusko, M. A., Brusko, T. M., Connors, T. J., Sette, A., Sims, P. A., Luning Prak, E. T., … Farber, D. L. (2021). Heterogeneity of human anti-viral immunity shaped by virus, tissue, age, and sex. Cell Reports, 37(9), 110071. https://doi.org/10.1016/j.celrep.2021.110071
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Klykov, O., Gangwar, S. P., Yelshanskaya, M. V., Yen, L., & Sobolevsky, A. I. (2021). Structure and desensitization of AMPA receptor complexes with type II TARP γ5 and GSG1L. Molecular Cell, 81(23), 4771-4783.e7. https://doi.org/10.1016/j.molcel.2021.09.030
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Bayin, N. S., Mizrak, D., Stephen, D. N., Lao, Z., Sims, P. A., & Joyner, A. L. (2021). Injury-induced ASCL1 expression orchestrates a transitory cell state required for repair of the neonatal cerebellum. Science Advances, 7(50). https://doi.org/10.1126/sciadv.abj1598
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