Department of Systems Biology

Displaying 201 - 250 of 444CSV
Trauernicht, M., Rastogi, C., Manzo, S. G., Bussemaker, H. J., & van Steensel, B. (2023). Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements. Nucleic Acids Research, 51(18), 9690–9702. https://doi.org/10.1093/nar/gkad718
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Vincent, R. L., Gurbatri, C. R., Li, F., Vardoshvili, A., Coker, C., Im, J., Ballister, E. R., Rouanne, M., Savage, T., de los Santos-Alexis, K., Redenti, A., Brockmann, L., Komaranchath, M., Arpaia, N., & Danino, T. (2023). Probiotic-guided CAR-T cells for solid tumor targeting. Science, 382(6667), 211–218. https://doi.org/10.1126/science.add7034
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Hahn, J., Ding, S., Im, J., Harimoto, T., Leong, K. W., & Danino, T. (2023). Bacterial therapies at the interface of synthetic biology and nanomedicine. Nature Reviews Bioengineering, 2(2), 120–135. https://doi.org/10.1038/s44222-023-00119-4
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Wei, A. Z., Chen, L. N., Orloff, M., Ariyan, C. E., Asgari, M., Barker, C. A., Buchbinder, E., Chandra, S., Couts, K., Frumovitz, M. M., Futreal, A., Gershenwald, J. E., Hanna, E. Y., Izar, B., LeBlanc, A. K., Leitao, M. M., Lipson, E. J., Liu, D., McCarter, M., … Carvajal, R. D. (2023). Proceedings from the Melanoma Research Foundation Mucosal Melanoma Meeting (December 16, 2022, New York, USA). Pigment Cell & Melanoma Research, 36(6), 542–556. Portico. https://doi.org/10.1111/pcmr.13139
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Pavlick, A. C., Ariyan, C. E., Buchbinder, E. I., Davar, D., Gibney, G. T., Hamid, O., Hieken, T. J., Izar, B., Johnson, D. B., Kulkarni, R. P., Luke, J. J., Mitchell, T. C., Mooradian, M. J., Rubin, K. M., Salama, A. K., Shirai, K., Taube, J. M., Tawbi, H. A., Tolley, J. K., … Sullivan, R. J. (2023). Society for Immunotherapy of Cancer (SITC) clinical practice guideline on immunotherapy for the treatment of melanoma, version 3.0. Journal for ImmunoTherapy of Cancer, 11(10), e006947. https://doi.org/10.1136/jitc-2023-006947
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Huang, Y., Sheth, R. U., Zhao, S., Cohen, L. A., Dabaghi, K., Moody, T., Sun, Y., Ricaurte, D., Richardson, M., Velez-Cortes, F., Blazejewski, T., Kaufman, A., Ronda, C., & Wang, H. H. (2023). High-throughput microbial culturomics using automation and machine learning. Nature Biotechnology, 41(10), 1424–1433. https://doi.org/10.1038/s41587-023-01674-2
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Singh, J., Sah, B., Shen, Y., & Liu, L. (2023). Histone methyltransferase inhibitor UNC0642 promotes breast cancer cell death by upregulating TXNIP-dependent oxidative stress. Chemico-Biological Interactions, 385, 110720. https://doi.org/10.1016/j.cbi.2023.110720
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Johnson, M., Bell, A., Lauing, K. L., Ladomersky, E., Zhai, L., Penco-Campillo, M., Shah, Y., Mauer, E., Xiu, J., Nicolaides, T., Drumm, M., McCortney, K., Elemento, O., Kim, M., Bommi, P., Low, J. T., Memon, R., Wu, J., Zhao, J., … Wainwright, D. A. (2023). Advanced Age in Humans and Mouse Models of Glioblastoma Show Decreased Survival from Extratumoral Influence. Clinical Cancer Research, 29(23), 4973–4989. https://doi.org/10.1158/1078-0432.ccr-23-0834
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Colvin, A., Youssef, S., Noh, H., Wright, J., Jumonville, G., LaRow Brown, K., Tatonetti, N. P., Milner, J. D., Weng, C., Bordone, L. A., & Petukhova, L. (2024). Inborn Errors of Immunity Contribute to the Burden of Skin Disease and Create Opportunities for Improving the Practice of Dermatology. Journal of Investigative Dermatology, 144(2), 307-315.e1. https://doi.org/10.1016/j.jid.2023.08.018
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Nagendra, K., Izzet, A., Judd, N. B., Zakine, R., Friedman, L., Harrison, O. J., Pontani, L.-L., Shapiro, L., Honig, B., & Brujic, J. (2023). Push-pull mechanics of E-cadherin ectodomains in biomimetic adhesions. Biophysical Journal, 122(17), 3506–3515. https://doi.org/10.1016/j.bpj.2023.07.026
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Schreidah, C. M., Reynolds, G. B., Fahmy, L. M., Carvajal, R. D., Vermeer, M. H., Whittaker, S., Pe’er, I., & Geskin, L. J. (2023). Scoping review of genetic databases for rare dermatologic diseases: Opportunity for artificial intelligence and machine learning. JAAD International, 12, 24–31. https://doi.org/10.1016/j.jdin.2023.02.017
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Stegemann, J. P., Wagner, W. R., Göbel, U., Perets, E., Leong, K. W., Leach, J. K., & Gilbert, J. (2023). The Year 2022 in biomaterials research: A perspective from the editors of six leading journals. Journal of Biomedical Materials Research Part A, 111(9), 1298–1308. Portico. https://doi.org/10.1002/jbm.a.37529
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Ager, C. R., Zhang, M., Chaimowitz, M., Bansal, S., Tagore, S., Obradovic, A., Jugler, C., Rogava, M., Melms, J. C., McCann, P., Spina, C., Drake, C. G., Dallos, M. C., & Izar, B. (2023). KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with tumor progression and immunotherapy response. Journal for ImmunoTherapy of Cancer, 11(9), e006782. https://doi.org/10.1136/jitc-2023-006782
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De Martino, M., Daviaud, C., Minns, H. E., Lazarian, A., Wacker, A., Costa, A. P., Attarwala, N., Chen, Q., Choi, S.-W., Rabadàn, R., McIntire, L. B. J., Gartrell, R. D., Kelly, J. M., Laiakis, E. C., & Vanpouille-Box, C. (2023). Radiation therapy promotes unsaturated fatty acids to maintain survival of glioblastoma. Cancer Letters, 570, 216329. https://doi.org/10.1016/j.canlet.2023.216329
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Lao, Y.-H., Ji, R., Zhou, J. K., Snow, K. J., Kwon, N., Saville, E., He, S., Chauhan, S., Chi, C.-W., Datta, M. S., Zhang, H., Quek, C. H., Cai, S. S., Li, M., Gaitan, Y., Bechtel, L., Wu, S.-Y., Lutz, C. M., Tomer, R., … Leong, K. W. (2023). Focused ultrasound–mediated brain genome editing. Proceedings of the National Academy of Sciences, 120(34). https://doi.org/10.1073/pnas.2302910120
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Brown, B. C., Wang, C., Kasela, S., Aguet, F., Nachun, D. C., Taylor, K. D., Tracy, R. P., Durda, P., Liu, Y., Johnson, W. C., Van Den Berg, D., Gupta, N., Gabriel, S., Smith, J. D., Gerzsten, R., Clish, C., Wong, Q., Papanicolau, G., Blackwell, T. W., … Lappalainen, T. (2023). Multiset correlation and factor analysis enables exploration of multi-omics data. Cell Genomics, 3(8), 100359. https://doi.org/10.1016/j.xgen.2023.100359
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Connors, T. J., Matsumoto, R., Verma, S., Szabo, P. A., Guyer, R., Gray, J., Wang, Z., Thapa, P., Dogra, P., Poon, M. M. L., Rybkina, K., Bradley, M. C., Idzikowski, E., McNichols, J., Kubota, M., Pethe, K., Shen, Y., Atkinson, M. A., Brusko, M., … Farber, D. L. (2023). Site-specific development and progressive maturation of human tissue-resident memory T cells over infancy and childhood. Immunity, 56(8), 1894-1909.e5. https://doi.org/10.1016/j.immuni.2023.06.008
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Zheng, C., Wei, Y., Zhang, Q., Sun, M., Wang, Y., Hou, J., Zhang, P., Lv, X., Su, D., Jiang, Y., Gumin, J., Sahni, N., Hu, B., Wang, W., Chen, X., McGrail, D. J., Zhang, C., Huang, S., Xu, H., … Chen, Y. (2023). Multiomics analyses reveal DARS1-AS1 /YBX1–controlled posttranscriptional circuits promoting glioblastoma tumorigenesis/radioresistance. Science Advances, 9(31). https://doi.org/10.1126/sciadv.adf3984
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Jiang, Z., Wu, F., Laise, P., Takayuki, T., Na, F., Kim, W., Kobayashi, H., Chang, W., Takahashi, R., Valenti, G., Sunagawa, M., White, R. A., Macchini, M., Renz, B. W., Middelhoff, M., Hayakawa, Y., Dubeykovskaya, Z. A., Tan, X., Chu, T. H., … Wang, T. C. (2023). Tff2 defines transit-amplifying pancreatic acinar progenitors that lack regenerative potential and are protective against Kras-driven carcinogenesis. Cell Stem Cell, 30(8), 1091-1109.e7. https://doi.org/10.1016/j.stem.2023.07.002
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Shao, Z., Lee, B. J., Zhang, H., Lin, X., Li, C., Jiang, W., Chirathivat, N., Gershik, S., Shen, M. M., Baer, R., & Zha, S. (2023). Inactive PARP1 causes embryonic lethality and genome instability in a dominant-negative manner. Proceedings of the National Academy of Sciences, 120(31). https://doi.org/10.1073/pnas.2301972120
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Zhang, Y., Zhang, W., Zhao, J., Ito, T., Jin, J., Aparicio, A. O., Zhou, J., Guichard, V., Fang, Y., Que, J., Urban, J. F., Hanna, J. H., Ghosh, S., Wu, X., Ding, L., Basu, U., & Huang, Y. (2023). m6A RNA modification regulates innate lymphoid cell responses in a lineage-specific manner. Nature Immunology, 24(8), 1256–1264. https://doi.org/10.1038/s41590-023-01548-4
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Sergeeva, A. P., Katsamba, P. S., Liao, J., Sampson, J. M., Bahna, F., Mannepalli, S., Morano, N. C., Shapiro, L., Friesner, R. A., & Honig, B. (2023). Free Energy Perturbation Calculations of Mutation Effects on SARS-CoV-2 RBD::ACE2 Binding Affinity. Journal of Molecular Biology, 435(15), 168187. https://doi.org/10.1016/j.jmb.2023.168187
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Matsumoto, R., Gray, J., Rybkina, K., Oppenheimer, H., Levy, L., Friedman, L. M., Khamaisi, M., Meng, W., Rosenfeld, A. M., Guyer, R. S., Bradley, M. C., Chen, D., Atkinson, M. A., Brusko, T. M., Brusko, M., Connors, T. J., Luning Prak, E. T., Hershberg, U., Sims, P. A., … Farber, D. L. (2023). Induction of bronchus-associated lymphoid tissue is an early life adaptation for promoting human B cell immunity. Nature Immunology, 24(8), 1370–1381. https://doi.org/10.1038/s41590-023-01557-3
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Li, J., Hubisz, M. J., Earlie, E. M., Duran, M. A., Hong, C., Varela, A. A., Lettera, E., Deyell, M., Tavora, B., Havel, J. J., Phyu, S. M., Amin, A. D., Budre, K., Kamiya, E., Cavallo, J.-A., Garris, C., Powell, S., Reis-Filho, J. S., Wen, H., … Bakhoum, S. F. (2023). Non-cell-autonomous cancer progression from chromosomal instability. Nature, 620(7976), 1080–1088. https://doi.org/10.1038/s41586-023-06464-z
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Sugiura, K., Masuike, Y., Suzuki, K., Shin, A. E., Sakai, N., Matsubara, H., Otsuka, M., Sims, P. A., Lengner, C. J., & Rustgi, A. K. (2023). LIN28B promotes cell invasion and colorectal cancer metastasis via CLDN1 and NOTCH3. JCI Insight, 8(14). https://doi.org/10.1172/jci.insight.167310
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Tiwari, P. K., Ko, T.-H., Dubey, R., Chouhan, M., Tsai, L.-W., Singh, H. N., Chaubey, K. K., Dayal, D., Chiang, C.-W., & Kumar, S. (2023). CRISPR/Cas9 as a therapeutic tool for triple negative breast cancer: from bench to clinics. Frontiers in Molecular Biosciences, 10. https://doi.org/10.3389/fmolb.2023.1214489
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Kornberg, A., Botella, T., Moon, C. S., Rao, S., Gelbs, J., Cheng, L., Miller, J., Bacarella, A. M., García-Vilas, J. A., Vargas, J., Yu, X., Krupska, I., Bush, E., Garcia-Carrasquillo, R., Lebwohl, B., Krishnareddy, S., Lewis, S., Green, P. H. R., Bhagat, G., … Han, A. (2023). Gluten induces rapid reprogramming of natural memory αβ and γδ intraepithelial T cells to induce cytotoxicity in celiac disease. Science Immunology, 8(85). https://doi.org/10.1126/sciimmunol.adf4312
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Min, J., Zhao, J., Zagelbaum, J., Lee, J., Takahashi, S., Cummings, P., Schooley, A., Dekker, J., Gottesman, M. E., Rabadan, R., & Gautier, J. (2023). Mechanisms of insertions at a DNA double-strand break. Molecular Cell, 83(14), 2434-2448.e7. https://doi.org/10.1016/j.molcel.2023.06.016
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Ho, P., Melms, J. C., Rogava, M., Frangieh, C. J., Poźniak, J., Shah, S. B., Walsh, Z., Kyrysyuk, O., Amin, A. D., Caprio, L., Fullerton, B. T., Soni, R. K., Ager, C. R., Biermann, J., Wang, Y., Khosravi-Maharlooei, M., Zanetti, G., Mu, M., Fatima, H., … Izar, B. (2023). The CD58-CD2 axis is co-regulated with PD-L1 via CMTM6 and shapes anti-tumor immunity. Cancer Cell, 41(7), 1207-1221.e12. https://doi.org/10.1016/j.ccell.2023.05.014
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Viragova, S., Aparicio, L., Palmerini, P., Zhao, J., Valencia Salazar, L. E., Schurer, A., Dhuri, A., Sahoo, D., Moskaluk, C. A., Rabadan, R., & Dalerba, P. (2023). Inverse agonists of retinoic acid receptor/retinoid X receptor signaling as lineage-specific antitumor agents against human adenoid cystic carcinoma. JNCI: Journal of the National Cancer Institute, 115(7), 838–852. https://doi.org/10.1093/jnci/djad062
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Petrey, D., Zhao, H., Trudeau, S. J., Murray, D., & Honig, B. (2023). PrePPI: A Structure Informed Proteome-wide Database of Protein–Protein Interactions. Journal of Molecular Biology, 435(14), 168052. https://doi.org/10.1016/j.jmb.2023.168052
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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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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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FitzPatrick, V. D., Leemans, C., van Arensbergen, J., van Steensel, B., & Bussemaker, H. J. (2023). Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR. Nucleic Acids Research, 51(11), 5499–5511. https://doi.org/10.1093/nar/gkad232
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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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Yang, K., Mitchell, N. M., Banerjee, S., Cheng, Z., Taylor, S., Kostic, A. M., Wong, I., Sajjath, S., Zhang, Y., Stevens, J., Mohan, S., Landry, D. W., Worgall, T. S., Andrews, A. M., & Stojanovic, M. N. (2023). A functional group–guided approach to aptamers for small molecules. Science, 380(6648), 942–948. https://doi.org/10.1126/science.abn9859
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Fernández, E. C., Wang, J., Zhang, X., Wei, H.-J., Minns, H., Griffin, A., Obradovic, A., Vlahos, L., Martins, T., Becker, P., Crawford, J., Gartrell, R., Szalontay, L., Zacharoulis, S., Zhang, Z., Wechsler-Reya, R., Wu, C.-C., Califano, A., & Pavisic, J. (2023). DIPG-49. A SYSTEMS BIOLOGY APPROACH TO DEFINING AND TARGETING CELL STATE-SPECIFIC MASTER REGULATOR DEPENDENCIES IN DIFFUSE MIDLINE GLIOMA. Neuro-Oncology, 25(Supplement_1), i24–i24. https://doi.org/10.1093/neuonc/noad073.096
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Jang, M. Y., Patel, P. N., Pereira, A. C., Willcox, J. A. L., Haghighi, A., Tai, A. C., Ito, K., Morton, S. U., Gorham, J. M., McKean, D. M., DePalma, S. R., Bernstein, D., Brueckner, M., Chung, W. K., Giardini, A., Goldmuntz, E., Kaltman, J. R., Kim, R., Newburger, J. W., … Seidman, J. G. (2023). Contribution of Previously Unrecognized RNA Splice-Altering Variants to Congenital Heart Disease. Circulation: Genomic and Precision Medicine, 16(3), 224–231. https://doi.org/10.1161/circgen.122.003924
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Tshering, L. F., Luo, F., Russ, S., Szenk, M., Rubel, D., Tutuska, K., Rail, J. G., Balázsi, G., Shen, M. M., & Talos, F. (2023). Immune mechanisms shape the clonal landscape during early progression of prostate cancer. Developmental Cell, 58(12), 1071-1086.e8. https://doi.org/10.1016/j.devcel.2023.04.010
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Monfrini, E., Arienti, F., Rinchetti, P., Lotti, F., & Riboldi, G. M. (2023). Brain Calcifications: Genetic, Molecular, and Clinical Aspects. International Journal of Molecular Sciences, 24(10), 8995. https://doi.org/10.3390/ijms24108995
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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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Ravi, A., Hellmann, M. D., Arniella, M. B., Holton, M., Freeman, S. S., Naranbhai, V., Stewart, C., Leshchiner, I., Kim, J., Akiyama, Y., Griffin, A. T., Vokes, N. I., Sakhi, M., Kamesan, V., Rizvi, H., Ricciuti, B., Forde, P. M., Anagnostou, V., Riess, J. W., … Gainor, J. F. (2023). Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nature Genetics, 55(5), 807–819. https://doi.org/10.1038/s41588-023-01355-5
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Shapiro, J. T., Zorea, A., Kav, A. B., Ontiveros, V. J., Mizrahi, I., & Pilosof, S. (2023). Multilayer networks of plasmid genetic similarity reveal potential pathways of gene transmission. The ISME Journal, 17(5), 649–659. https://doi.org/10.1038/s41396-023-01373-5
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Kesner, J. S., Chen, Z., Shi, P., Aparicio, A. O., Murphy, M. R., Guo, Y., Trehan, A., Lipponen, J. E., Recinos, Y., Myeku, N., & Wu, X. (2023). Noncoding translation mitigation. Nature, 617(7960), 395–402. https://doi.org/10.1038/s41586-023-05946-4
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Choe, J. H., Kawase, T., Xu, A., Guzman, A., Obradovic, A. Z., Low-Calle, A. M., Alaghebandan, B., Raghavan, A., Long, K., Hwang, P. M., Schiffman, J. D., Zhu, Y., Zhao, R., Lee, D.-F., Katz, C., & Prives, C. (2023). Li–Fraumeni Syndrome–Associated Dimer-Forming Mutant p53 Promotes Transactivation-Independent Mitochondrial Cell Death. Cancer Discovery, 13(5), 1250–1273. https://doi.org/10.1158/2159-8290.cd-22-0882
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Griffin, E. L., Nees, S. N., Morton, S. U., Wynn, J., Patel, N., Jobanputra, V., Robinson, S., Kochav, S. M., Tao, A., Andrews, C., Cross, N., Geva, J., Lanzilotta, K., Ritter, A., Taillie, E., Thompson, A., Meyer, C., Akers, R., King, E. C., … Chung, W. K. (2023). Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study. Circulation: Genomic and Precision Medicine, 16(2). https://doi.org/10.1161/circgen.122.003791
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