Resell, M., Graarud, E. P., Rabben, H.-L., Sharma, A., Hagen, L., Hoang, L., Skogaker, N. T., Aarvik, A., Svensson, M. K., Amrutkar, M., Verbeke, C. S., Batra, S. K., Qvigstad, G., Wang, T. C., Rustgi, A., Chen, D., & Zhao, C.-M. (2025). Knowledge Discovery in Databases of Proteomics by Systems Modeling in Translational Research on Pancreatic Cancer. Proteomes, 13(2), 20. https://doi.org/10.3390/proteomes13020020

Leung, Y. Y., Lee, W., Kuzma, A. B., Nicaretta, H., Valladares, O., Gangadharan, P., Qu, L., Zhao, Y., Ren, Y., Cheng, P., Kuksa, P. P., Wang, H., White, H., Katanic, Z., Bass, L., Saravanan, N., Greenfest‐Allen, E., Kirsch, M., Cantwell, L., … Wang, L. (2025). Alzheimer’s Disease Sequencing Project release 4 whole genome sequencing dataset. Alzheimer’s & Dementia, 21(5). Portico. https://doi.org/10.1002/alz.70237

Börner, K., Blood, P. D., Silverstein, J. C., Ruffalo, M., Satija, R., Teichmann, S. A., Pryhuber, G. J., Misra, R. S., Purkerson, J. M., Fan, J., Hickey, J. W., Molla, G., Xu, C., Zhang, Y., Weber, G. M., Jain, Y., Qaurooni, D., Kong, Y., … Herr, B. W. (2025). Human BioMolecular Atlas Program (HuBMAP): 3D Human Reference Atlas construction and usage. Nature Methods. https://doi.org/10.1038/s41592-024-02563-5

Matentzoglu, N., Bello, S. M., Stefancsik, R., Alghamdi, S. M., Anagnostopoulos, A. V., Balhoff, J. P., Balk, M. A., Bradford, Y. M., Bridges, Y., Callahan, T. J., Caufield, H., Cuzick, A., Carmody, L. C., Caron, A. R., de Souza, V., Engel, S. R., Fey, P., Fisher, M., Gehrke, S., … Osumi-Sutherland, D. (2025). The Unified Phenotype Ontology : a framework for cross-species integrative phenomics. GENETICS, 229(3). https://doi.org/10.1093/genetics/iyaf027

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

BioEssays 9/2023. (2023). BioEssays, 45(9). Portico. https://doi.org/10.1002/bies.202370082

Meydan, Y., Baldini, F., & Korem, T. (2023). pymgpipe: microbiome metabolic modeling in Python. Journal of Open Source Software, 8(88), 5545. https://doi.org/10.21105/joss.05545

BioEssays 8/2023. (2023). BioEssays, 45(8). Portico. https://doi.org/10.1002/bies.202370072

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

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

BioEssays 7/2023. (2023). BioEssays, 45(7). Portico. https://doi.org/10.1002/bies.202370062

BioEssays 5/2023. (2023). BioEssays, 45(5). Portico. https://doi.org/10.1002/bies.202370042

Griffin, A. T., Vlahos, L. J., Chiuzan, C., & Califano, A. (2023). NaRnEA: An Information Theoretic Framework for Gene Set Analysis. Entropy, 25(3), 542. https://doi.org/10.3390/e25030542

BioEssays 4/2023. (2023). BioEssays, 45(4). Portico. https://doi.org/10.1002/bies.202370032

BioEssays 3/2023. (2023). BioEssays, 45(3). Portico. https://doi.org/10.1002/bies.202370006

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

BioEssays 2/2023. (2023). BioEssays, 45(2). Portico. https://doi.org/10.1002/bies.202370004

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

BioEssays 11/2022. (2022). BioEssays, 44(11). Portico. https://doi.org/10.1002/bies.202270025

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

Laise, P., Bosker, G., Califano, A., & Alvarez, M. J. (2022). A Patient‐to‐Model‐to‐Patient (PMP) Cancer Drug Discovery Protocol for Identifying and Validating Therapeutic Agents Targeting Tumor Regulatory Architecture. Current Protocols, 2(9). Portico. https://doi.org/10.1002/cpz1.544

BioEssays 7/2022. (2022). BioEssays, 44(7). Portico. https://doi.org/10.1002/bies.202270015

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

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

Storm, C. S., Kia, D. A., Almramhi, M. M., Bandres-Ciga, S., Finan, C., Noyce, A. J., Kaiyrzhanov, R., Middlehurst, B., Tan, M., Houlden, H., Morris, H. R., Plun-Favreau, H., Holmans, P., Hardy, J., Trabzuni, D., Quinn, J., Bubb, V., Mok, K. Y., … Wood, N. W. (2021). Finding genetically-supported drug targets for Parkinson’s disease using Mendelian randomization of the druggable genome. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-26280-1

Beebe-Wang, N., Celik, S., Weinberger, E., Sturmfels, P., De Jager, P. L., Mostafavi, S., & Lee, S.-I. (2021). Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer’s disease neuropathologies. Nature Communications, 12(1). https://doi.org/10.1038/s41467-021-25680-7