Department of Systems Biology

Displaying 401 - 444 of 444CSV
Rashkovan, M., Albero, R., Gianni, F., Perez-Duran, P., Miller, H. I., Mackey, A. L., Paietta, E. M., Tallman, M. S., Rowe, J. M., Litzow, M. R., Wiernik, P. H., Luger, S., Sulis, M. L., Soni, R. K., & Ferrando, A. A. (2022). Intracellular Cholesterol Pools Regulate Oncogenic Signaling and Epigenetic Circuitries in Early T-cell Precursor Acute Lymphoblastic Leukemia. Cancer Discovery, 12(3), 856–871. https://doi.org/10.1158/2159-8290.cd-21-0551
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Liu, L., Iketani, S., Guo, Y., Chan, J. F.-W., Wang, M., Liu, L., Luo, Y., Chu, H., Huang, Y., Nair, M. S., Yu, J., Chik, K. K.-H., Yuen, T. T.-T., Yoon, C., To, K. K.-W., Chen, H., Yin, M. T., Sobieszczyk, M. E., Huang, Y., … Ho, D. D. (2021). Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2. Nature, 602(7898), 676–681. https://doi.org/10.1038/s41586-021-04388-0
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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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Lopez-Bujanda, Z. A., Haffner, M. C., Chaimowitz, M. G., Chowdhury, N., Venturini, N. J., Patel, R. A., Obradovic, A., Hansen, C. S., Jacków, J., Maynard, J. P., Sfanos, K. S., Abate-Shen, C., Bieberich, C. J., Hurley, P. J., Selby, M. J., Korman, A. J., Christiano, A. M., De Marzo, A. M., & Drake, C. G. (2021). Castration-mediated IL-8 promotes myeloid infiltration and prostate cancer progression. Nature Cancer, 2(8), 803–818. https://doi.org/10.1038/s43018-021-00227-3
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Arrieta, V. A., Chen, A. X., Kane, J. R., Kang, S. J., Kassab, C., Dmello, C., Zhao, J., Burdett, K. B., Upadhyayula, P. S., Lee-Chang, C., Shilati, J., Jaishankar, D., Chen, L., Gould, A., Zhang, D., Yuan, J., Zhao, W., Ling, X., Burks, J. K., … Sonabend, A. M. (2021). ERK1/2 phosphorylation predicts survival following anti-PD-1 immunotherapy in recurrent glioblastoma. Nature Cancer, 2(12), 1372–1386. https://doi.org/10.1038/s43018-021-00260-2
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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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Ware, S. M., Bhatnagar, S., Dexheimer, P. J., Wilkinson, J. D., Sridhar, A., Fan, X., Shen, Y., Tariq, M., Schubert, J. A., Colan, S. D., Shi, L., Canter, C. E., Hsu, D. T., Bansal, N., Webber, S. A., Everitt, M. D., Kantor, P. F., Rossano, J. W., Pahl, E., … Lipshultz, S. E. (2022). The genetic architecture of pediatric cardiomyopathy. The American Journal of Human Genetics, 109(2), 282–298. https://doi.org/10.1016/j.ajhg.2021.12.006
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Freedberg, D. E., Richardson, M., Nattakom, M., Cheung, J., Lynch, E., Zachariah, P., & Wang, H. H. (2022). Are There Bad ICU Rooms? Temporal Relationship between Patient and ICU Room Microbiome, and Influence on Vancomycin-Resistant Enterococcus Colonization. MSphere, 7(1). https://doi.org/10.1128/msphere.01007-21
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Lombardo, K. A., Obradovic, A., Singh, A. K., Liu, J. L., Joice, G., Kates, M., Bishai, W., McConkey, D., Chaux, A., Eich, M., Rezaei, M. K., Netto, G. J., Drake, C. G., Tran, P., Matoso, A., & Bivalacqua, T. J. (2021). BCG invokes superior STING‐mediated innate immune response over radiotherapy in a carcinogen murine model of urothelial cancer. The Journal of Pathology, 256(2), 223–234. Portico. https://doi.org/10.1002/path.5830
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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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Shi, C., Dawulieti, J., Shi, F., Yang, C., Qin, Q., Shi, T., Wang, L., Hu, H., Sun, M., Ren, L., Chen, F., Zhao, Y., Liu, F., Li, M., Mu, L., Liu, D., Shao, D., Leong, K. W., & She, J. (2022). A nanoparticulate dual scavenger for targeted therapy of inflammatory bowel disease. Science Advances, 8(4). https://doi.org/10.1126/sciadv.abj2372
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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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Palmer, A. C., Izar, B., Hwangbo, H., & Sorger, P. K. (2022). Predictable Clinical Benefits without Evidence of Synergy in Trials of Combination Therapies with Immune-Checkpoint Inhibitors. Clinical Cancer Research, 28(2), 368–377. https://doi.org/10.1158/1078-0432.ccr-21-2275
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Lieu, Y. K., Liu, Z., Ali, A. M., Wei, X., Penson, A., Zhang, J., An, X., Rabadan, R., Raza, A., Manley, J. L., & Mukherjee, S. (2021). SF3B1 mutant-induced missplicing of MAP3K7 causes anemia in myelodysplastic syndromes. Proceedings of the National Academy of Sciences, 119(1). https://doi.org/10.1073/pnas.2111703119
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Flynn, E. D., Tsu, A. L., Kasela, S., Kim-Hellmuth, S., Aguet, F., Ardlie, K. G., Bussemaker, H. J., Mohammadi, P., & Lappalainen, T. (2022). Transcription factor regulation of eQTL activity across individuals and tissues. PLOS Genetics, 18(1), e1009719. https://doi.org/10.1371/journal.pgen.1009719
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Shu, C., Green Snyder, L., Shen, Y., & Chung, W. K. (2021). Imputing cognitive impairment in SPARK, a large autism cohort. Autism Research, 15(1), 156–170. Portico. https://doi.org/10.1002/aur.2622
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Kumar, A., Narayan, R. K., Prasoon, P., Kumari, C., Kaur, G., Kumar, S., Kulandhasamy, M., Sesham, K., Pareek, V., Faiq, M. A., Pandey, S. N., Singh, H. N., Kant, K., Shekhawat, P. S., Raza, K., & Kumar, S. (2022). Mecanismos del COVID-19 en el cuerpo humano: Lo que sabemos hasta ahora. Kompass Neumología, 4(1), 3–20. Portico. https://doi.org/10.1159/000521507
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Cossarizza, A., Chang, H., Radbruch, A., Abrignani, S., Addo, R., Akdis, M., Andrä, I., Andreata, F., Annunziato, F., Arranz, E., Bacher, P., Bari, S., Barnaba, V., Barros‐Martins, J., Baumjohann, D., Beccaria, C. G., Bernardo, D., Boardman, D. A., Borger, J., … Yang, J. (2021). Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition). European Journal of Immunology, 51(12), 2708–3145. Portico. https://doi.org/10.1002/eji.202170126
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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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Bhansali, D., Teng, S. L., Lee, C. S., Schmidt, B. L., Bunnett, N. W., & Leong, K. W. (2021). Nanotechnology for pain management: Current and future therapeutic interventions. Nano Today, 39, 101223. https://doi.org/10.1016/j.nantod.2021.101223
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Brown, B. C., & Knowles, D. A. (2021). Welch-weighted Egger regression reduces false positives due to correlated pleiotropy in Mendelian randomization. The American Journal of Human Genetics, 108(12), 2319–2335. https://doi.org/10.1016/j.ajhg.2021.10.006
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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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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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Zhu, N., Swietlik, E. M., Welch, C. L., Pauciulo, M. W., Hagen, J. J., Zhou, X., Guo, Y., Karten, J., Pandya, D., Tilly, T., Lutz, K. A., Martin, J. M., Treacy, C. M., Rosenzweig, E. B., Krishnan, U., Coleman, A. W., Gonzaga-Jauregui, C., Lawrie, A., Trembath, R. C., … Chung, W. K. (2021). Rare variant analysis of 4241 pulmonary arterial hypertension cases from an international consortium implicates FBLN2, PDGFD, and rare de novo variants in PAH. Genome Medicine, 13(1). https://doi.org/10.1186/s13073-021-00891-1
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Riboldi, G. M., Faravelli, I., Kuwajima, T., Delestrée, N., Dermentzaki, G., De Planell-Saguer, M., Rinchetti, P., Hao, L. T., Beattie, C. C., Corti, S., Przedborski, S., Mentis, G. Z., & Lotti, F. (2021). Sumoylation regulates the assembly and activity of the SMN complex. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-25272-5
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Wang, Z., Fan, X., Shen, Y., Pagadala, M. S., Signer, R., Cygan, K. J., Fairbrother, W. G., Carter, H., Chung, W. K., & Huang, K. (2021). Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes. Genome Medicine, 13(1). https://doi.org/10.1186/s13073-021-00964-1
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López de Maturana, E., Rodríguez, J. A., Alonso, L., Lao, O., Molina-Montes, E., Martín-Antoniano, I. A., Gómez-Rubio, P., Lawlor, R., Carrato, A., Hidalgo, M., Iglesias, M., Molero, X., Löhr, M., Michalski, C., Perea, J., O’Rorke, M., Barberà, V. M., … Malats, N. (2021). A multilayered post-GWAS assessment on genetic susceptibility to pancreatic cancer. Genome Medicine, 13(1). https://doi.org/10.1186/s13073-020-00816-4
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Chen, D., Chu, B., Yang, X., Liu, Z., Jin, Y., Kon, N., Rabadan, R., Jiang, X., Stockwell, B. R., & Gu, W. (2021). iPLA2β-mediated lipid detoxification controls p53-driven ferroptosis independent of GPX4. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-23902-6
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Chen, A. X., Gartrell, R. D., Zhao, J., Upadhyayula, P. S., Zhao, W., Yuan, J., Minns, H. E., Dovas, A., Bruce, J. N., Lasorella, A., Iavarone, A., Canoll, P., Sims, P. A., & Rabadan, R. (2021). Single-cell characterization of macrophages in glioblastoma reveals MARCO as a mesenchymal pro-tumor marker. Genome Medicine, 13(1). https://doi.org/10.1186/s13073-021-00906-x
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Koleck, T. A., Topaz, M., Tatonetti, N. P., George, M., Miaskowski, C., Smaldone, A., & Bakken, S. (2021). Characterizing shared and distinct symptom clusters in common chronic conditions through natural language processing of nursing notes. Research in Nursing & Health, 44(6), 906–919. Portico. https://doi.org/10.1002/nur.22190
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Gerson, K. D., Liao, J., McCarthy, C., Burris, H. H., Korem, T., Levy, M., Ravel, J., & Elovitz, M. A. (2021). A non-optimal cervicovaginal microbiota in pregnancy is associated with a distinct metabolomic signature among non-Hispanic Black individuals. Scientific Reports, 11(1). https://doi.org/10.1038/s41598-021-02304-0
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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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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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Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., … Lecellier, C.-H. (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-23143-7
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de Jong, J. O., Llapashtica, C., Genestine, M., Strauss, K., Provenzano, F., Sun, Y., Zhu, H., Cortese, G. P., Brundu, F., Brigatti, K. W., Corneo, B., Migliori, B., Tomer, R., Kushner, S. A., Kellendonk, C., Javitch, J. A., Xu, B., & Markx, S. (2021). Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-24358-4
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Schastnaya, E., Raguz Nakic, Z., Gruber, C. H., Doubleday, P. F., Krishnan, A., Johns, N. I., Park, J., Wang, H. H., & Sauer, U. (2021). Extensive regulation of enzyme activity by phosphorylation in Escherichia coli. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-25988-4
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