Analysis of Gene Interaction Networks

Displaying 1 - 45 of 45CSV
Stear, B. J., Mohseni Ahooyi, T., Simmons, J. A., Kollar, C., Hartman, L., Beigel, K., Lahiri, A., Vasisht, S., Callahan, T. J., Nemarich, C. M., Silverstein, J. C., & Taylor, D. M. (2024). Petagraph: A large-scale unifying knowledge graph framework for integrating biomolecular and biomedical data. Scientific Data, 11(1). https://doi.org/10.1038/s41597-024-04070-w
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Cieza, B., Yang, Z., Reyes‐Dumeyer, D., Lee, A. J., Dugger, B. N., Jin, L., Murray, M. E., Dickson, D. W., Pericak‐Vance, M. A., Vance, J. M., Foroud, T. M., Mayeux, R., & Tosto, G. (2024). Polytranscriptomic risk score for Alzheimer Disease in a large diverse multi‐center brain bank study. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.092971
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Gunasekaran, T. I., Reyes‐Dumeyer, D., Corvelo, A., Clarke, W. E., Evani, U. S., Byrska‐Bishop, M. S., Basile, A. O., Runnels, A., Musunuri, R. O., Narzisi, G., Faber, K. M., Goate, A. M., Boeve, B. F., Cruchaga, C., Pericak‐Vance, M. A., Haines, J. L., Rosenberg, R. N., Tsuang, D. W., Mejia, D. R., … Vardarajan, B. N. (2024). Beyond GWAS: Investigating Structural Variants and Their Segregation in Familial Alzheimer’s Disease. Alzheimer’s & Dementia, 20(S2). Portico. https://doi.org/10.1002/alz.092677
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Lee, A. J., Cui, Z., Song, Z., Reyes‐Dumeyer, D., De Jager, P. L., Bennett, D. A., Schneider, J. A., Menon, V., Wang, Y., Lantigua, R. A., Medrano, M., Mejia, D. R., Jiménez‐Velázquez, I. Z., Kukull, W. A., Biber, S. A., Brickman, A. M., Tosto, G., Kizil, C., Farrer, L. A., … Mayeux, R. (2024). Multi‐ancestry Genome‐wide Gene‐Vascular Risk Factors Interaction Analyses in Alzheimer’s Disease. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.093041
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Yang, H., Kivisäkk, P., Viera, A. M. R., Maa, C., Kirn, D., Bellier, J., Liu, L., Selkoe, D. J., Schneider, J. A., Bennett, D. A., Jager, P. L. D., Johnson, K. A., Sperling, R. A., Arnold, S. E., & Chhatwal, J. P. (2024). The relationship between amyloid‐β, plasma/brain GFAP, and neocortical tau: a Mendelian randomization study. Alzheimer’s & Dementia, 20(S2). Portico. https://doi.org/10.1002/alz.091415
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Kumar, A., Ray, N. R., Cuccaro, M. L., Beecham, G., Huey, E. D., & Reitz, C. (2024). Genetic correlation analysis identifies genetic loci shared between Alzheimer’s disease and primary psychiatric disorders. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.093421
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Gomez, N., Jean‐Francois, M., Hamilton‐Nelson, K. L., Slifer, S. H., Kunkle, B. W., Cuccaro, M. L., Martin, E. R., Haines, J. L., Reitz, C., Pericak‐Vance, M. A., Vardarajan, B. N., & Beecham, G. (2024). Linkage analyses identifiy novel loci for Alzheimer’s disease in non‐Hispanic white families. Alzheimer’s & Dementia, 20(S1). Portico. https://doi.org/10.1002/alz.092913
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Gunasekaran, T. I., Lee, A. J., Lao, P. J., Gutierrez, J., Manly, J. J., Gu, Y., Brickman, A. M., Honig, L. S., Vardarajan, B. N., & Mayeux, R. (2024). Understanding Biomarker Discordance: MRI and PET Phenotypes Shed Light on Alzheimer’s Pathology. Alzheimer’s & Dementia, 20(S8). Portico. https://doi.org/10.1002/alz.095708
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Damuka, N., Gollepalli, K. K., Krizan, I., Bhoopal, B., Miller, M., Deep, O., Bashetti, N., Kumar, J. S., Orr, M. E., Macauley, S. L., Whitlow, C. T., Mintz, A., Lockhart, S. N., Craft, S., & Sai, K. K. S. (2024). Exploring Microtubule Dynamics in Alzheimer’s Disease: Longitudinal Assessment Using [11C]MPC‐6827 PET Imaging in APP/PS1 and PS301S Mouse Models. Alzheimer’s & Dementia, 20(S9). Portico. https://doi.org/10.1002/alz.093929
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Reddy, J. S., Heath, L., Linden, A. V., Allen, M., Lopes, K. de P., Seifar, F., Wang, E., Ma, Y., Poehlman, W. L., Quicksall, Z. S., Runnels, A., Wang, Y., Duong, D. M., Yin, L., Xu, K., Modeste, E. S., Shantaraman, A., Dammer, E. B., Ping, L., … Ertekin‐Taner, N. (2024). Bridging the gap: Multi‐omics profiling of brain tissue in Alzheimer’s disease and older controls in multi‐ethnic populations. Alzheimer’s & Dementia. Portico. https://doi.org/10.1002/alz.14208
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Cavalleri, E., Cabri, A., Soto-Gomez, M., Bonfitto, S., Perlasca, P., Gliozzo, J., Callahan, T. J., Reese, J., Robinson, P. N., Casiraghi, E., Valentini, G., & Mesiti, M. (2024). An ontology-based knowledge graph for representing interactions involving RNA molecules. Scientific Data, 11(1). https://doi.org/10.1038/s41597-024-03673-7
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Yang, M., Matan-Lithwick, S., Wang, Y., De Jager, P. L., Bennett, D. A., & Felsky, D. (2023). Multi-omic integration via similarity network fusion to detect molecular subtypes of ageing. Brain Communications, 5(2). https://doi.org/10.1093/braincomms/fcad110
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Rosenberger, G., Li, W., Turunen, M., He, J., Subramaniam, P. S., Pampou, S., Griffin, A. T., Karan, C., Kerwin, P., Murray, D., Honig, B., Liu, Y., & Califano, A. (2024). Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nature Communications, 15(1). https://doi.org/10.1038/s41467-024-47957-3
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Callahan, T. J., Tripodi, I. J., Stefanski, A. L., Cappelletti, L., Taneja, S. B., Wyrwa, J. M., Casiraghi, E., Matentzoglu, N. A., Reese, J., Silverstein, J. C., Hoyt, C. T., Boyce, R. D., Malec, S. A., Unni, D. R., Joachimiak, M. P., Robinson, P. N., Mungall, C. J., Cavalleri, E., Fontana, T., … Hunter, L. E. (2024). An open source knowledge graph ecosystem for the life sciences. Scientific Data, 11(1). https://doi.org/10.1038/s41597-024-03171-w
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Hudgins, A. D., Zhou, S., Arey, R. N., Rosenfeld, M. G., Murphy, C. T., & Suh, Y. (2024). A systems biology-based identification and in vivo functional screening of Alzheimer’s disease risk genes reveal modulators of memory function. Neuron, 112(13), 2112-2129.e4. https://doi.org/10.1016/j.neuron.2024.04.009
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Khan, Z., Malinsky, D., Cohen, A., Pei, S., Berhane, K., Picard, M., Belsky, D., & Wei, Y. (2023). UNDERSTANDING THE DYNAMICS OF INTRINSIC HEALTH USING AGE-DEPENDENT QUANTILE GRAPHICAL MODELS. Innovation in Aging, 7(Supplement_1), 35–36. https://doi.org/10.1093/geroni/igad104.0118
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Lopes, K. de P., Vialle, R. A., Green, G. S., Fujita, M., Wang, Y., Gaiteri, C., Menon, V., De Jager, P. L., Habib, N., Tasaki, S., & Bennett, D. A. A. (2023). Chasing the cell type‐specific molecular networks involved in Alzheimer’s Disease. Alzheimer’s & Dementia, 19(S12). Portico. https://doi.org/10.1002/alz.073444
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Is, O., Wang, X., Reddy, J. S., Patel, T., Min, Y., Quicksall, Z., Heckman, M. G., Gao, J., Bergman, J., Da Mesquita, S. G. (Sandro D. M. F., Kizil, C., Bhattarai, P., Cosacak, M. I., Lee, A. J., Vardarajan, B. N., Mayeux, R., Koga, S., Kanekiyo, T., White, L. J., … Ertekin‐Taner, N. (2023). Gliovascular molecular alterations in Alzheimer’s disease: a cross‐tissue, cross‐species study. Alzheimer’s & Dementia, 19(S13). Portico. https://doi.org/10.1002/alz.073806
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Qiao, M. N., Reyes‐Dumeyer, D., Medrano, M., Lantigua, R. A., Mayeux, R., & Vardarajan, B. N. (2023). Protective variants in Alzheimer’s Disease from healthy elderly APOE‐ε4 participants. Alzheimer’s & Dementia, 19(S12). Portico. https://doi.org/10.1002/alz.080360
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Clifton, M., Seto, M., Buckley, R. F., Gifford, K. A., Jefferson, A. L., De Jager, P. L., Bennett, D. A. A., Barnes, L. L., Wang, Y., Schneider, J. A., Hohman, T. J., & Dumitrescu, L. C. (2023). Sex‐specific associations of gene expression in brain with Alzheimer’s disease pathology and cognitive performance. Alzheimer’s & Dementia, 19(S12). Portico. https://doi.org/10.1002/alz.079096
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Park, D. K., Chen, M., Kim, S., Joo, Y. Y., Loving, R. K., Kim, H. S., Cha, J., Yoo, S., & Kim, J. H. (2023). Overestimated prediction using polygenic prediction derived from summary statistics. BMC Genomic Data, 24(1). https://doi.org/10.1186/s12863-023-01151-4
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Xicota, L., Cheng, R., Barral, S., Honig, L. S., Schupf, N., Gu, Y., Cosentino, S., Zmuda, J. M., Perls, T. T., Christensen, K., Province, M. A., & Lee, J. H. (2023). Examination of Genetic Risk Factors for Alzheimer’s Disease in a Cohort of Familial Longevity: the Long Life Family Study. Alzheimer’s & Dementia, 19(S24). Portico. https://doi.org/10.1002/alz.082363
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Wang, Y., Tsang, S. P., Khan, Z., Malinsky, D., Wei, Y., Cohen, A., Picard, M., & Pei, S. (2023). QUANTIFYING INTRINSIC HEALTH USING STRESS-EVOKED INFORMATION FLOW BETWEEN PHYSIOLOGICAL SYSTEMS. Innovation in Aging, 7(Supplement_1), 35–35. https://doi.org/10.1093/geroni/igad104.0117
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Lee, A. J., Reyes‐Dumeyer, D., De Jager, P. L., Bennett, D. A. A., Schneider, J. A., Menon, V., Wang, Y., Lantigua, R. A., Medrano, M., Mejia, D. R., Jiménez‐Velázquez, I. Z., Kukull, W. A., Brickman, A. M., Manly, J. J., Tosto, G., Kizil, C., Farrer, L. A., Mez, J. B., Chung, J., … Mayeux, R. (2023). Multi‐ethnic genome‐wide, gene‐based study identifies genes that interact with vascular risk factors in Alzheimer’s Disease (AD). Alzheimer’s & Dementia, 19(S12). Portico. https://doi.org/10.1002/alz.079970
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Wagemann, O., Li, Y., Hassenstab, J., Aschenbrenner, A. J., McKay, N. S., Gordon, B. A., Benzinger, T. L. S., Xiong, C., Cruchaga, C., Renton, A. E., Perrin, R. J., Berman, S. B., Chhatwal, J. P., Farlow, M. R., Day, G. S., Ikeuchi, T., Jucker, M., Lopera, F., … Mori, H. (2023). Investigation of sex differences in mutation carriers of the Dominantly Inherited Alzheimer Network. Alzheimer’s & Dementia, 20(1), 47–62. Portico. https://doi.org/10.1002/alz.13460
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Caufield, J. H., Putman, T., Schaper, K., Unni, D. R., Hegde, H., Callahan, T. J., Cappelletti, L., Moxon, S. A. T., Ravanmehr, V., Carbon, S., Chan, L. E., Cortes, K., Shefchek, K. A., Elsarboukh, G., Balhoff, J., Fontana, T., Matentzoglu, N., Bruskiewich, R. M., Thessen, A. E., … Reese, J. T. (2023). KG-Hub—building and exchanging biological knowledge graphs. Bioinformatics, 39(7). https://doi.org/10.1093/bioinformatics/btad418
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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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Chen, F., Wang, X., Jang, S.-K., Quach, B. C., Weissenkampen, J. D., Khunsriraksakul, C., Yang, L., Sauteraud, R., Albert, C. M., Allred, N. D. D., Arnett, D. K., Ashley-Koch, A. E., Barnes, K. C., Barr, R. G., Becker, D. M., Bielak, L. F., Bis, J. C., Blangero, J., Boorgula, M. P., … Liu, D. J. (2023). Multi-ancestry transcriptome-wide association analyses yield insights into tobacco use biology and drug repurposing. Nature Genetics, 55(2), 291–300. https://doi.org/10.1038/s41588-022-01282-x
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Kulminski, A. M., Jain‐Washburn, E., Philipp, I., He, L., Loika, Y., Loiko, E., Bagley, O., Ukraintseva, S., Yashin, A., Arbeev, K., Stallard, E., Feitosa, M. F., Schupf, N., Christensen, K., & Culminskaya, I. (2022). APOE ɛ4 allele and TOMM40‐APOC1 variants jointly contribute to survival to older ages. Aging Cell, 21(12). Portico. https://doi.org/10.1111/acel.13730
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Columbia Affiliation
Liu, C., Ta, C. N., Havrilla, J. M., Nestor, J. G., Spotnitz, M. E., Geneslaw, A. S., Hu, Y., Chung, W. K., Wang, K., & Weng, C. (2022). OARD: Open annotations for rare diseases and their phenotypes based on real-world data. The American Journal of Human Genetics, 109(9), 1591–1604. https://doi.org/10.1016/j.ajhg.2022.08.002
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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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Maurits, M. P., Korsunsky, I., Raychaudhuri, S., Murphy, S. N., Smoller, J. W., Weiss, S. T., Petukhova, L. M., Weng, C., Wei, W.-Q., Huizinga, T. W. J., Reinders, M. J. T., Karlson, E. W., van den Akker, E. B., & Knevel, R. (2022). A framework for employing longitudinally collected multicenter electronic health records to stratify heterogeneous patient populations on disease history. Journal of the American Medical Informatics Association, 29(5), 761–769. https://doi.org/10.1093/jamia/ocac008
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