JP Sulzberger Columbia Genome Center

Displaying 1 - 33 of 33CSV
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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Qiao, L., Welch, C. L., Hernan, R., Wynn, J., Krishnan, U. S., Zalieckas, J. M., Buchmiller, T., Khlevner, J., De, A., Farkouh-Karoleski, C., Wagner, A. J., Heydweiller, A., Mueller, A. C., de Klein, A., Warner, B. W., Maj, C., Chung, D., McCulley, D. J., Schindel, D., … Chung, W. K. (2024). Common variants increase risk for congenital diaphragmatic hernia within the context of de novo variants. The American Journal of Human Genetics, 111(11), 2362–2381. https://doi.org/10.1016/j.ajhg.2024.08.024
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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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Utkina-Sosunova, I., Chiorazzi, A., de Planell-Saguer, M., Li, H., Meregalli, C., Pozzi, E., Carozzi, V. A., Canta, A., Monza, L., Alberti, P., Fumagalli, G., Karan, C., Moayedi, Y., Przedborski, S., Cavaletti, G., & Lotti, F. (2024). Molsidomine provides neuroprotection against vincristine-induced peripheral neurotoxicity through soluble guanylyl cyclase activation. Scientific Reports, 14(1). https://doi.org/10.1038/s41598-024-70294-w
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Xu, L., Tan, C., Barr, J., Talaba, N., Verheyden, J., Chin, J. S., Gaboyan, S., Kasaraneni, N., Elgamal, R. M., Gaulton, K. J., Lin, G., Afshar, K., Golts, E., Meier, A., Alexander, L. E. C., Borok, Z., Shen, Y., Chung, W. K., McCulley, D. J., & Sun, X. (2024). Context-dependent roles of mitochondrial LONP1 in orchestrating the balance between airway progenitor versus progeny cells. Cell Stem Cell. https://doi.org/10.1016/j.stem.2024.08.001
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Liu, Z., Mela, A., Argenziano, M. G., Banu, M. A., Furnari, J., Kotidis, C., Sperring, C. P., Humala, N., Mahajan, A., Bruce, J. N., Canoll, P., & Sims, P. A. (2024). Single-cell analysis of 5-aminolevulinic acid intraoperative labeling specificity for glioblastoma. Journal of Neurosurgery, 140(4), 968–978. https://doi.org/10.3171/2023.7.jns23122
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Kim, H. S., Xiao, Y., Chen, X., He, S., Im, J., Willner, M. J., Finlayson, M. O., Xu, C., Zhu, H., Choi, S. J., Mosharov, E. V., Kim, H., Xu, B., & Leong, K. W. (2024). Chronic Opioid Treatment Arrests Neurodevelopment and Alters Synaptic Activity in Human Midbrain Organoids. Advanced Science, 11(21). Portico. https://doi.org/10.1002/advs.202400847
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Hasselluhn, M. C., Decker-Farrell, A. R., Vlahos, L., Thomas, D. H., Curiel-Garcia, A., Maurer, H. C., Wasko, U. N., Tomassoni, L., Sastra, S. A., Palermo, C. F., Dalton, T. C., Ma, A., Li, F., Tolosa, E. J., Hibshoosh, H., Fernandez-Zapico, M. E., Muir, A., Califano, A., & Olive, K. P. (2023). Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression. Cancer Discovery, 14(2), 348–361. https://doi.org/10.1158/2159-8290.cd-23-0240
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Stokes, G., Li, Z., Talaba, N., Genthe, W., Brix, M. B., Pham, B., Wienhold, M. D., Sandok, G., Hernan, R., Wynn, J., Tang, H., Tabima, D. M., Rodgers, A., Hacker, T. A., Chesler, N. C., Zhang, P., Murad, R., Yuan, J. X.-J., Shen, Y., … McCulley, D. J. (2024). Rescuing lung development through embryonic inhibition of histone acetylation. Science Translational Medicine, 16(732). https://doi.org/10.1126/scitranslmed.adc8930
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Zhong, G., Choi, Y. A., & Shen, Y. (2023). VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Communications Biology, 6(1). https://doi.org/10.1038/s42003-023-05155-9
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Hawley, J. E., Obradovic, A. Z., Dallos, M. C., Lim, E. A., Runcie, K., Ager, C. R., McKiernan, J., Anderson, C. B., Decastro, G. J., Weintraub, J., Virk, R., Lowy, I., Hu, J., Chaimowitz, M. G., Guo, X. V., Zhang, Y., Haffner, M. C., Worley, J., Stein, M. N., … Drake, C. G. (2023). Anti-PD-1 immunotherapy with androgen deprivation therapy induces robust immune infiltration in metastatic castration-sensitive prostate cancer. Cancer Cell, 41(11), 1972-1988.e5. https://doi.org/10.1016/j.ccell.2023.10.006
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Hobson, B. D., Stanley, A. T., De Los Santos, M. B., Culbertson, B., Mosharov, E. V., Sims, P. A., & Sulzer, D. (2023). Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain. Brain, Behavior, and Immunity, 111, 277–291. https://doi.org/10.1016/j.bbi.2023.04.008
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Romano, J. D., Li, H., Napolitano, T., Realubit, R., Karan, C., Holford, M., & Tatonetti, N. P. (2023). Discovering Venom-Derived Drug Candidates Using Differential Gene Expression. Toxins, 15(7), 451. https://doi.org/10.3390/toxins15070451
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Mundi, P. S., Dela Cruz, F. S., Grunn, A., Diolaiti, D., Mauguen, A., Rainey, A. R., Guillan, K., Siddiquee, A., You, D., Realubit, R., Karan, C., Ortiz, M. V., Douglass, E. F., Accordino, M., Mistretta, S., Brogan, F., Bruce, J. N., Caescu, C. I., Carvajal, R. D., … Califano, A. (2023). A Transcriptome-Based Precision Oncology Platform for Patient–Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies. Cancer Discovery, 13(6), 1386–1407. https://doi.org/10.1158/2159-8290.cd-22-1020
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Obradovic, A., Ager, C., Turunen, M., Nirschl, T., Khosravi-Maharlooei, M., Iuga, A., Jackson, C. M., Yegnasubramanian, S., Tomassoni, L., Fernandez, E. C., McCann, P., Rogava, M., DeMarzo, A. M., Kochel, C. M., Allaf, M., Bivalacqua, T., Lim, M., Realubit, R., Karan, C., … Califano, A. (2023). Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators. Cancer Cell, 41(5), 933-949.e11. https://doi.org/10.1016/j.ccell.2023.04.003
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Verbitsky, M., Krishnamurthy, S., Krithivasan, P., Hughes, D., Khan, A., Marasà, M., Vena, N., Khosla, P., Zhang, J., Lim, T. Y., Glessner, J. T., Weng, C., Shang, N., Shen, Y., Hripcsak, G., Hakonarson, H., Ionita-Laza, I., Levy, B., Kenny, E. E., … Gharavi, A. G. (2022). Genomic Disorders in CKD across the Lifespan. Journal of the American Society of Nephrology, 34(4), 607–618. https://doi.org/10.1681/asn.2022060725
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Vasciaveo, A., Arriaga, J. M., de Almeida, F. N., Zou, M., Douglass, E. F., Picech, F., Shibata, M., Rodriguez-Calero, A., de Brot, S., Mitrofanova, A., Chua, C. W., Karan, C., Realubit, R., Pampou, S., Kim, J. Y., Afari, S. N., Mukhammadov, T., Zanella, L., Corey, E., … Abate-Shen, C. (2022). OncoLoop: A Network-Based Precision Cancer Medicine Framework. Cancer Discovery, 13(2), 386–409. https://doi.org/10.1158/2159-8290.cd-22-0342
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Fan, X., Pan, H., Tian, A., Chung, W. K., & Shen, Y. (2022). SHINE: protein language model-based pathogenicity prediction for short inframe insertion and deletion variants. Briefings in Bioinformatics, 24(1). https://doi.org/10.1093/bib/bbac584
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Liu, H., Iketani, S., Zask, A., Khanizeman, N., Bednarova, E., Forouhar, F., Fowler, B., Hong, S. J., Mohri, H., Nair, M. S., Huang, Y., Tay, N. E. S., Lee, S., Karan, C., Resnick, S. J., Quinn, C., Li, W., Shion, H., Xia, X., … Stockwell, B. R. (2022). Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19. Nature Communications, 13(1). https://doi.org/10.1038/s41467-022-29413-2
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Tan, R., & Shen, Y. (2022). Accuratein silicoconfirmation of rare copy number variant calls from exome sequencing data using transfer learning. Nucleic Acids Research, 50(21), e123–e123. https://doi.org/10.1093/nar/gkac788
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Zhang, H., Xu, M. S., Fan, X., Chung, W. K., & Shen, Y. (2022). Predicting functional effect of missense variants using graph attention neural networks. Nature Machine Intelligence, 4(11), 1017–1028. https://doi.org/10.1038/s42256-022-00561-w
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Zhong, G., & Shen, Y. (2022). Statistical models of the genetic etiology of congenital heart disease. Current Opinion in Genetics & Development, 76, 101967. https://doi.org/10.1016/j.gde.2022.101967
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Lipman, A. R., Fan, X., Shen, Y., & Chung, W. K. (2022). Clinical and genetic characterization of CACNA1A‐related disease. Clinical Genetics, 102(4), 288–295. Portico. https://doi.org/10.1111/cge.14180
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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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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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Schubert, R., Geoffroy, E., Gregga, I., Mulford, A. J., Aguet, F., Ardlie, K., Gerszten, R., Clish, C., Van Den Berg, D., Taylor, K. D., Durda, P., Johnson, W. C., Cornell, E., Guo, X., Liu, Y., Tracy, R., Conomos, M., Blackwell, T., Papanicolaou, G., … Wheeler, H. E. (2022). Protein prediction for trait mapping in diverse populations. PLOS ONE, 17(2), e0264341. https://doi.org/10.1371/journal.pone.0264341
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Qi, H., Zhang, H., Zhao, Y., Chen, C., Long, J. J., Chung, W. K., Guan, Y., & Shen, Y. (2021). MVP predicts the pathogenicity of missense variants by deep learning. Nature Communications, 12(1). https://doi.org/10.1038/s41467-020-20847-0
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Zhao, W., Dovas, A., Spinazzi, E. F., Levitin, H. M., Banu, M. A., Upadhyayula, P., Sudhakar, T., Marie, T., Otten, M. L., Sisti, M. B., Bruce, J. N., Canoll, P., & Sims, P. A. (2021). Deconvolution of cell type-specific drug responses in human tumor tissue with single-cell RNA-seq. Genome Medicine, 13(1). https://doi.org/10.1186/s13073-021-00894-y
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