Department of Biochemistry and Molecular Biophysics
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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Li, B. I., Alvarez, M. J., Zhao, H., Chirathivat, N., Califano, A., & Shen, M. M. (2025). The regulatory architecture of the primed pluripotent cell state. Nature Communications, 16(1). https://doi.org/10.1038/s41467-025-57894-4
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Columbia Affiliation
Department of Systems Biology; Vagelos College of Physicians and Surgeons; Department of Biochemistry and Molecular Biophysics; Department of Biomedical Informatics; Department of Medicine; Division of Hematology/Oncology; Herbert Irving Comprehensive Cancer Center; Department of Genetics and Development
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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Maniatis, T. (2025). Safeguarding the future of biomedical science in the United States. Cell, 188(6), 1457–1459. https://doi.org/10.1016/j.cell.2025.02.024
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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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Olsen, T. R., Talla, P., Sagatelian, R. K., Furnari, J., Bruce, J. N., Canoll, P., Zha, S., & Sims, P. A. (2025). Scalable co-sequencing of RNA and DNA from individual nuclei. Nature Methods. https://doi.org/10.1038/s41592-024-02579-x
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Department of Systems Biology; Vagelos College of Physicians and Surgeons; Department of Neurosurgery; Department of Pediatrics; Division of Pediatric Hematology, Oncology, and Stem Cell Transplantation; Department of Pathology and Cell Biology; Department of Microbiology and Immunology; Institute for Cancer Genetics; Department of Biochemistry and Molecular Biophysics; JP Sulzberger Columbia Genome Center
Morano, N. C., Guo, Y., Becker, J. E., Li, Z., Yu, J., Ho, D. D., Shapiro, L., & Kwong, P. D. (2025). Structure of a zoonotic H5N1 hemagglutinin reveals a receptor-binding site occupied by an auto-glycan. Structure. https://doi.org/10.1016/j.str.2025.01.001
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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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Columbia Affiliation
Vagelos College of Physicians and Surgeons; Department of Pathology and Cell Biology; Department of Neuroscience; Herbert Irving Comprehensive Cancer Center; Department of Neurosurgery; Department of Neurology; Division of Epilepsy and Sleep Disorders; Department of Systems Biology; Department of Biochemistry and Molecular Biophysics; Zuckerman Mind, Brain, and Behavior Institute; JP Sulzberger Columbia Genome Center; Irving Institute for Cancer Dynamics; Department of Radiology
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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Columbia Affiliation
Vagelos College of Physicians and Surgeons; Department of Medicine; Division of Infectious Diseases; Aaron Diamond AIDS Research Center; Herbert Irving Comprehensive Cancer Center; Department of Pathology and Cell Biology; Department of Biochemistry and Molecular Biophysics; Zuckerman Mind, Brain, and Behavior Institute; Department of Microbiology and Immunology
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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Ke, X., van Soldt, B., Vlahos, L., Zhou, Y., Qian, J., George, J., Capdevila, C., Glass, I., Yan, K., Califano, A., & Cardoso, W. V. (2024). Morphogenesis and regeneration share a conserved core transition cell state program that controls lung epithelial cell fate. Developmental Cell. https://doi.org/10.1016/j.devcel.2024.11.017
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Columbia Affiliation
Vagelos College of Physicians and Surgeons; Department of Molecular Pharmacology and Therapeutics; Department of Medicine; Division of Digestive and Liver Diseases; Department of Genetics and Development; Department of Systems Biology; Department of Biochemistry and Molecular Biophysics; Department of Biomedical Informatics; Division of Hematology/Oncology; Center for Human Development; Division of Pulmonary, Allergy, and Critical Care Medicine
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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Maniatis, T. (2024). From bacterial operons to gene therapy: 50 years of the journal Cell. Cell, 187(23), 6417–6420. https://doi.org/10.1016/j.cell.2024.10.037
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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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Columbia Affiliation
Department of Neurology; Department of Systems Biology; Vagelos College of Physicians and Surgeons; Department of Biochemistry and Molecular Biophysics; Taub Institute for Research on Alzheimer’s Disease and the Aging Brain; Department of Pathology and Cell Biology; Center for Translational and Computational Neuroimmunology
Gallitto, M., Zhang, X., De Los Santos, G., Wei, H.-J., Fernández, E. C., Duan, S., Sedor, G., Yoh, N., Kokossis, D., Angel, J. C., Wang, Y.-F., White, E., Kinslow, C. J., Berg, X., Tomassoni, L., Zandkarimi, F., Chio, I. I. C., Canoll, P., Bruce, J. N., … Wu, C.-C. (2024). Targeted delivery of napabucasin with radiotherapy improves outcomes in diffuse midline glioma. Neuro-Oncology. https://doi.org/10.1093/neuonc/noae215
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Columbia Affiliation
Institute for Cancer Genetics; Vagelos College of Physicians and Surgeons; Department of Radiation Oncology; Department of Neurosurgery; Department of Systems Biology; Department of Genetics and Development; Department of Pathology and Cell Biology; Department of Pediatrics; Division of Pediatric Hematology, Oncology, and Stem Cell Transplantation; Department of Biochemistry and Molecular Biophysics; Department of Biomedical Informatics; Department of Medicine; Division of Hematology/Oncology; Herbert Irving Comprehensive Cancer Center; Department of Molecular Pharmacology and Therapeutics; Department of Neurology
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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Columbia Affiliation
Vagelos College of Physicians and Surgeons; Department of Medicine; Division of Nephrology; Department of Pathology and Cell Biology; Aaron Diamond AIDS Research Center; O’Brien Center for Benign Urology; Department of Biochemistry and Molecular Biophysics; Department of Pediatrics; Zuckerman Mind, Brain, and Behavior Institute
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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Columbia Affiliation
Vagelos College of Physicians and Surgeons; Department of Pathology and Cell Biology; Department of Medicine; Division of Infectious Diseases; Aaron Diamond AIDS Research Center; Zuckerman Mind, Brain, and Behavior Institute; Department of Biochemistry and Molecular Biophysics; Department of Microbiology and Immunology
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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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Columbia Affiliation
Vagelos College of Physicians and Surgeons; Department of Pathology and Cell Biology; Department of Neurosurgery; Department of Neuroscience; Department of Systems Biology; Department of Biochemistry and Molecular Biophysics; Department of Medicine; JP Sulzberger Columbia Genome Center; Herbert Irving Comprehensive Cancer Center
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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Ramadan, Y. H., & Hobert, O. (2024). Visualization of gene expression in Pristionchus pacificus with smFISH and in situ HCR. microPublication Biology. https://doi.org/10.17912/MICROPUB.BIOLOGY.001274
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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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