Cory Funk, PhD

Senior Research Scientist

PhD, Cell & Developmental Biology, University of Illinois Urbana-Champaign, 2010

Network modeling; Transcription Regulatory Networks (TRNs); Alzheimer’s Disease

2323737 2RQKSFR5 funk 1 apa 50 date desc year 1 1 8709 https://hood.isbscience.org/wp-content/plugins/zotpress/

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Baumgartner, A., Robinson, M., Golde, T., Jaydev, S., Huang, S., Hadlock, J., & Funk, C. (2024). Fokker-Planck diffusion maps of multiple single cell microglial transcriptomes reveals radial differentiation into substates associated with Alzheimer’s pathology. bioRxiv: The Preprint Server for Biology, 2024.06.21.599924. https://doi.org/10.1101/2024.06.21.599924 Cite Download

Ellis, D., Watanabe, K., Wilmanski, T., Lustgarten, M. S., Korat, A. V. A., Glusman, G., Hadlock, J. J., Fiehn, O., Sebastiani, P., Price, N. D., Hood, L., Magis, A. T., Evans, S. J., Pflieger, L., Lovejoy, J. C., Gibbons, S. M., Funk, C. C., Baloni, P., & Rappaport, N. (2024). APOE Genotype and Biological Age Impact Inter-Omic Associations Related to Bioenergetics. bioRxiv. https://doi.org/10.1101/2024.10.17.618322 Cite Download

Readhead, B. P., Mastroeni, D. F., Wang, Q., Sierra, M. A., de Ávila, C., Jimoh, T. O., Haure-Mirande, J.-V., Atanasoff, K. E., Nolz, J., Suazo, C., Barton, N. J., Orszulak, A. R., Chigas, S. M., Tran, K., Mirza, A., Ryon, K., Proszynski, J., Najjar, D., Dudley, J. T., … Reiman, E. M. (2024). Alzheimer’s disease-associated CD83(+) microglia are linked with increased immunoglobulin G4 and human cytomegalovirus in the gut, vagal nerve, and brain. Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association. https://doi.org/10.1002/alz.14401 Cite

Funk, C. C., Darvas, M., Johnston, C., Robinson, M., Schaffer, C., Battaglia, C., Aubert, M., & Wiley, J. C. (2024). Basic Science and Pathogenesis. Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association, 20 Suppl 1, e093497. https://doi.org/10.1002/alz.093497 Cite

Stojakovic, A., Trushin, S., Sheu, A., Khalili, L., Chang, S.-Y., Li, X., Christensen, T., Salisbury, J. L., Geroux, R. E., Gateno, B., Flannery, P. J., Dehankar, M., Funk, C. C., Wilkins, J., Stepanova, A., O’Hagan, T., Galkin, A., Nesbitt, J., Zhu, X., … Trushina, E. (2024). Author Correction: Partial inhibition of mitochondrial complex I ameliorates Alzheimer’s disease pathology and cognition in APP/PS1 female mice. Communications Biology, 7(1), 234. https://doi.org/10.1038/s42003-024-05810-9 Cite

Wang, Q., Antone, J., Alsop, E., Reiman, R., Funk, C., Bendl, J., Dudley, J. T., Liang, W. S., Karr, T. L., Roussos, P., Bennett, D. A., De Jager, P. L., Serrano, G. E., Beach, T. G., Van Keuren-Jensen, K., Mastroeni, D., Reiman, E. M., & Readhead, B. P. (2024). Single cell transcriptomes and multiscale networks from persons with and without Alzheimer’s disease. Nature Communications, 15(1), 5815. https://doi.org/10.1038/s41467-024-49790-0 Cite

Levites, Y., Dammer, E. B., Ran, Y., Tsering, W., Duong, D., Abreha, M., Gadhavi, J., Lolo, K., Trejo-Lopez, J., Phillips, J., Iturbe, A., Erquizi, A., Moore, B. D., Ryu, D., Natu, A., Dillon, K., Torrellas, J., Moran, C., Ladd, T., … Golde, T. E. (2024). Integrative proteomics identifies a conserved Aβ amyloid responsome, novel plaque proteins, and pathology modifiers in Alzheimer’s disease. Cell Reports. Medicine, 101669. https://doi.org/10.1016/j.xcrm.2024.101669 Cite

Paquette, A., Ahuna, K., Hwang, Y. M., Pearl, J., Liao, H., Shannon, P., Kadam, L., Lapehn, S., Bucher, M., Roper, R., Funk, C., MacDonald, J., Bammler, T., Baloni, P., Brockway, H., Mason, W. A., Bush, N., Lewinn, K. Z., Karr, C. J., … Price, N. D. (2024). A genome scale transcriptional regulatory model of the human placenta. Science Advances, 10(26), eadf3411. https://doi.org/10.1126/sciadv.adf3411 Cite

Baumgartner, A., Huang, S., Hadlock, J., & Funk, C. (2024). Dimensional reduction of gradient-like stochastic systems with multiplicative noise via Fokker-Planck diffusion maps (No. arXiv:2401.03095). arXiv. https://doi.org/10.48550/arXiv.2401.03095 Cite Download

Baumgartner, A., Robinson, M., Huang, S., Hadlock, J., & Funk, C. (2023). Integration of multiple single cell microglial datasets reveals radial differentiation into long‐lived substates associated with Alzheimer’s pathology. Alzheimer’s & Dementia, 19. https://doi.org/10.1002/alz.080693 Cite

Rappaport, N., Ellis, D., Watanabe, K., Wilmanski, T., Hood, L., Price, N., Funk, C., & Baloni, P. (2023). BIOLOGICAL AGING AND APOE STATUS REWIRE INTER-OMIC ASSOCIATIONS RELATED TO BIOENERGETICS IN HUMANS. Innovation in Aging, 7(Suppl 1), 631–632. https://doi.org/10.1093/geroni/igad104.2058 Cite Download

Girdhar, K., Bendl, J., Baumgartner, A., Therrien, K., Venkatesh, S., Mathur, D., Dong, P., Rahman, S., Kleopoulos, S. P., Misir, R., Reach, S. M., Auluck, P. K., Marenco, S., Lewis, D. A., Haroutunian, V., Funk, C., Voloudakis, G., Hoffman, G. E., Fullard, J. F., & Roussos, P. (2023). The neuronal chromatin landscape in adult schizophrenia brains is linked to early fetal development. Research Square, rs.3.rs-3393581. https://doi.org/10.21203/rs.3.rs-3393581/v1 Cite Download

Mikheeva, S. A., Funk, C. C., Horner, P. J., Rostomily, R. C., & Mikheev, A. M. (2023). Novel TCF4:TCF12 heterodimer inhibits glioblastoma growth. Molecular Oncology. https://doi.org/10.1002/1878-0261.13496 Cite

Molani, S., Hernandez, P. V., Roper, R. T., Duvvuri, V. R., Baumgartner, A. M., Goldman, J. D., Ertekin-Taner, N., Funk, C. C., Price, N. D., Rappaport, N., & Hadlock, J. J. (2022). Risk factors for severe COVID-19 differ by age for hospitalized adults. Scientific Reports, 12(1), 6568. https://doi.org/10.1038/s41598-022-10344-3 Cite Download Download

Baloni, P., Arnold, M., Buitrago, L., Nho, K., Moreno, H., Huynh, K., Brauner, B., Louie, G., Kueider-Paisley, A., Suhre, K., Saykin, A. J., Ekroos, K., Meikle, P. J., Hood, L., Price, N. D., Alzheimer’s Disease Metabolomics Consortium, Doraiswamy, P. M., Funk, C. C., Hernández, A. I., … Kaddurah-Daouk, R. (2022). Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer’s disease. Communications Biology, 5(1), 1074. https://doi.org/10.1038/s42003-022-04011-6 Cite Download

Sebastiani, P., Song, Z., Ellis, D., Tian, Q., Schwaiger-Haber, M., Stancliffe, E., Lustgarten, M. S., Funk, C. C., Baloni, P., Yao, C.-H., Joshi, S., Marron, M. M., Gurinovich, A., Li, M., Leshchyk, A., Xiang, Q., Andersen, S. L., Feitosa, M. F., Ukraintseva, S., … Perls, T. T. (2022). A metabolomic signature of the APOE2 allele. GeroScience. https://doi.org/10.1007/s11357-022-00646-9 Cite Download

Molani, S., Hernandez, P. V., Roper, R. T., Duvvuri, V. R., Baumgartner, A. M., Goldman, J. D., Ertekin-Taner, N., Funk, C. C., Price, N. D., Rappaport, N., & Hadlock, J. J. (2022). Risk factors for severe COVID-19 differ by age: a retrospective study of hospitalized adults [Preprint]. Public and Global Health. https://doi.org/10.1101/2022.02.02.22270287 Cite Download

Baloni, P., Nho, K., Arnold, M., Louie, G., Kueider-Paisley, A., Saykin, A. J., Ekroos, K., Funk, C., Hood, L., Price, N. D., Baillie, R., Kastenmüller, G., Han, X., & Kaddurah-Daouk, R. F. (2022). Investigating the importance of acylcarnitines in Alzheimer’s disease. Alzheimer’s & Dementia, 17(S3), e056647. https://doi.org/10.1002/alz.056647 Cite Download

Ibanez, K. R., McFarland, K. N., Phillips, J., Allen, M., Lessard, C. B., Zobel, L., De La Cruz, E. G., Shah, S., Vo, Q., Wang, X., Quicksall, Z., Ryu, D., Funk, C., Ertekin-Taner, N., Prokop, S., Golde, T. E., & Chakrabarty, P. (2022). Deletion of Abi3/Gngt2 influences age-progressive amyloid β and tau pathologies in distinctive ways. Alzheimer’s Research & Therapy, 14(1), 104. https://doi.org/10.1186/s13195-022-01044-1 Cite Download

Roach, J. C., Hara, J., Fridman, D., Lovejoy, J. C., Jade, K., Heim, L., Romansik, R., Swietlikowski, A., Phillips, S., Rapozo, M. K., Shay, M. A., Fischer, D., Funk, C., Dill, L., Brant-Zawadzki, M., Hood, L., & Shankle, W. R. (2022). The Coaching for Cognition in Alzheimer’s (COCOA) trial: Study design. Alzheimer’s & Dementia (New York, N. Y.), 8(1), e12318. https://doi.org/10.1002/trc2.12318 Cite Download

Roach, J. C., Edens, L., Markewych, D. R., Rapozo, M. K., Hara, J., Glusman, G., Funk, C., Bramen, J., Baloni, P., Shankle, W. R., & Hood, L. (2022). A multimodal intervention for Alzheimer’s disease results in multifaceted systemic effects reflected in blood and ameliorates functional and cognitive outcomes. medRxiv. https://doi.org/10.1101/2022.09.27.22280385 Cite Download

Heath, L., Earls, J. C., Magis, A. T., Kornilov, S. A., Lovejoy, J. C., Funk, C. C., Rappaport, N., Logsdon, B. A., Mangravite, L. M., Kunkle, B. W., Martin, E. R., Naj, A. C., Ertekin-Taner, N., Golde, T. E., Hood, L., Price, N. D., & Alzheimer’s Disease Genetics Consortium. (2022). Manifestations of Alzheimer’s disease genetic risk in the blood are evident in a multiomic analysis in healthy adults aged 18 to 90. Scientific Reports, 12(1), 6117. https://doi.org/10.1038/s41598-022-09825-2 Cite Download

Roach, J. C., Hodes, J. F., Funk, C. C., Shankle, W. R., Merrill, D. A., Hood, L., & Bramen, J. (2022). Dense data enables 21th century clinical trials. Alzheimer’s & Dementia: Translational Research & Clinical Interventions, 8(1), e12297. https://doi.org/10.1002/trc2.12297 Cite Download

Ross, M. K., Raji, C., Lokken, K. L., Bredesen, D. E., Roach, J. C., Funk, C. C., Price, N., Rappaport, N., Hood, L., & Heath, J. R. (2021). Case Study: A Precision Medicine Approach to Multifactorial Dementia and Alzheimer’s Disease. Journal of Alzheimer’s Disease & Parkinsonism, 11(Suppl 5), 018. Cite

Wang, X., Allen, M., İş, Ö., Reddy, J. S., Tutor-New, F. Q., Castanedes Casey, M., Carrasquillo, M. M., Oatman, S. R., Min, Y., Asmann, Y. W., Funk, C., Nguyen, T., Ho, C. C., Malphrus, K. G., Seyfried, N. T., Levey, A. I., Younkin, S. G., Murray, M. E., Dickson, D. W., … Ertekin-Taner, N. (2021). Alzheimer’s disease and progressive supranuclear palsy share similar transcriptomic changes in distinct brain regions. The Journal of Clinical Investigation, e149904. https://doi.org/10.1172/JCI149904 Cite

Baloni, P., Funk, C. C., Readhead, B., & Price, N. D. (2021). Systems modeling of metabolic dysregulation in neurodegenerative diseases. Current Opinion in Pharmacology, 60, 59–65. https://doi.org/10.1016/j.coph.2021.06.012 Cite

McFarland, K. N., Ceballos, C., Rosario, A., Ladd, T., Moore, B., Golde, G., Wang, X., Allen, M., Ertekin-Taner, N., Funk, C. C., Robinson, M., Baloni, P., Rappaport, N., Chakrabarty, P., & Golde, T. E. (2021). Microglia show differential transcriptomic response to Aβ peptide aggregates ex vivo and in vivo. Life Science Alliance, 4(7), e202101108. https://doi.org/10.26508/lsa.202101108 Cite Download

McEwen, S. C., Merrill, D. A., Bramen, J., Porter, V., Panos, S., Kaiser, S., Hodes, J., Ganapathi, A., Bell, L., Bookheimer, T., Glatt, R., Rapozo, M., Ross, M. K., Price, N. D., Kelly, D., Funk, C. C., Hood, L., & Roach, J. C. (2021). A systems-biology clinical trial of a personalized multimodal lifestyle intervention for early Alzheimer’s disease. Alzheimer’s & Dementia (New York, N. Y.), 7(1), e12191. https://doi.org/10.1002/trc2.12191 Cite Download

Levites, Y., Funk, C., Wang, X., Chakrabarty, P., McFarland, K. N., Bramblett, B., O’Neal, V., Liu, X., Ladd, T., Robinson, M., Allen, M., Carrasquillo, M. M., Dickson, D., Cruz, P., Ryu, D., Li, H.-D., Price, N. D., Ertekin-Taner, Ni., & Golde, T. E. (2021). Modulating innate immune activation states impacts the efficacy of specific Aβ immunotherapy. Molecular Neurodegeneration, 16(1), 32. https://doi.org/10.1186/s13024-021-00453-4 Cite Download

Wainberg, M., Luquez, T., Koelle, D. M., Readhead, B., Johnston, C., Darvas, M., & Funk, C. C. (2021). The viral hypothesis: how herpesviruses may contribute to Alzheimer’s disease. Molecular Psychiatry. https://doi.org/10.1038/s41380-021-01138-6 Cite Download

Stojakovic, A., Trushin, S., Sheu, A., Khalili, L., Chang, S.-Y., Li, X., Christensen, T., Salisbury, J. L., Geroux, R. E., Gateno, B., Flannery, P. J., Dehankar, M., Funk, C. C., Wilkins, J., Stepanova, A., O’Hagan, T., Galkin, A., Nesbitt, J., Zhu, X., … Trushina, E. (2021). Partial inhibition of mitochondrial complex I ameliorates Alzheimer’s disease pathology and cognition in APP/PS1 female mice. Communications Biology, 4(1), 61. https://doi.org/10.1038/s42003-020-01584-y Cite Download

Li, H.-D., Funk, C. C., McFarland, K., Dammer, E. B., Allen, M., Carrasquillo, M. M., Levites, Y., Chakrabarty, P., Burgess, J. D., Wang, X., Dickson, D., Seyfried, N. T., Duong, D. M., Lah, J. J., Younkin, S. G., Levey, A. I., Omenn, G. S., Ertekin-Taner, N., Golde, T. E., & Price, N. D. (2021). Integrative functional genomic analysis of intron retention in human and mouse brain with Alzheimer’s disease. Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association. https://doi.org/10.1002/alz.12254 Cite Download

Baloni, P., Funk, C. C., Yan, J., Yurkovich, J. T., Kueider-Paisley, A., Nho, K., Heinken, A., Jia, W., Mahmoudiandehkordi, S., Louie, G., Saykin, A. J., Arnold, M., Kastenmüller, G., Griffiths, W. J., Thiele, I., Alzheimer’s Disease Metabolomics Consortium, Kaddurah-Daouk, R., & Price, N. D. (2020). Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer’s Disease. Cell Reports. Medicine, 1(8), 100138. https://doi.org/10.1016/j.xcrm.2020.100138 Cite Download

Wan, Y.-W., Al-Ouran, R., Mangleburg, C. G., Perumal, T. M., Lee, T. V., Allison, K., Swarup, V., Funk, C. C., Gaiteri, C., Allen, M., Wang, M., Neuner, S. M., Kaczorowski, C. C., Philip, V. M., Howell, G. R., Martini-Stoica, H., Zheng, H., Mei, H., Zhong, X., … Logsdon, B. A. (2020). Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models. Cell Reports, 32(2), 107908. https://doi.org/10.1016/j.celrep.2020.107908 Cite Download

Funk, C. C., Casella, A. M., Jung, S., Richards, M. A., Rodriguez, A., Shannon, P., Donovan-Maiye, R., Heavner, B., Chard, K., Xiao, Y., Glusman, G., Ertekin-Taner, N., Golde, T. E., Toga, A., Hood, L., Van Horn, J. D., Kesselman, C., Foster, I., Madduri, R., … Ament, S. A. (2020). Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types. Cell Reports, 32(7), 108029. https://doi.org/10.1016/j.celrep.2020.108029 Cite Download

Li, H.-D., Funk, C. C., & Price, N. D. (2020). iREAD: a tool for intron retention detection from RNA-seq data. BMC Genomics, 21(1), 128. https://doi.org/10.1186/s12864-020-6541-0 Cite Download

Baloni, P., Funk, C. C., Yan, J., Yurkovich, J. T., Kueider-Paisley, A., Nho, K., Heinken, A., Jia, W., Mahmoudiandehkordi, S., Louie, G., Saykin, A. J., Arnold, M., Kastenmüller, G., Griffiths, W. J., Thiele, I., Consortium, A.-A., Consortium, T. A. D. M., Kaddurah-Daouk, R., & Price, N. D. (2019). Identifying differences in bile acid pathways for cholesterol clearance in Alzheimer’s disease using metabolic networks of human brain regions. bioRxiv, 782987. https://doi.org/10.1101/782987 Cite Download

Pearl, J. R., Colantuoni, C., Bergey, D. E., Funk, C. C., Shannon, P., Basu, B., Casella, A. M., Oshone, R. T., Hood, L., Price, N. D., & Ament, S. A. (2019). Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders. Cell Systems, 8(2), 122-135.e7. https://doi.org/10.1016/j.cels.2019.01.002 Cite

Madduri, R., Chard, K., D’Arcy, M., Jung, S. C., Rodriguez, A., Sulakhe, D., Deutsch, E., Funk, C., Heavner, B., Richards, M., Shannon, P., Glusman, G., Price, N., Kesselman, C., & Foster, I. (2019). Reproducible big data science: A case study in continuous FAIRness. PloS One, 14(4), e0213013. https://doi.org/10.1371/journal.pone.0213013 Cite Download

Chakrabarty, P., Li, A., Ladd, T. B., Strickland, M. R., Koller, E. J., Burgess, J. D., Funk, C. C., Cruz, P. E., Allen, M., Yaroshenko, M., Wang, X., Younkin, C., Reddy, J., Lohrer, B., Mehrke, L., Moore, B. D., Liu, X., Ceballos-Diaz, C., Rosario, A. M., … Golde, T. E. (2018). TLR5 decoy receptor as a novel anti-amyloid therapeutic for Alzheimer’s disease. The Journal of Experimental Medicine, 215(9), 2247–2264. https://doi.org/10.1084/jem.20180484 Cite

Allen, M., Wang, X., Serie, D. J., Strickland, S. L., Burgess, J. D., Koga, S., Younkin, C. S., Nguyen, T. T., Malphrus, K. G., Lincoln, S. J., Alamprese, M., Zhu, K., Chang, R., Carrasquillo, M. M., Kouri, N., Murray, M. E., Reddy, J. S., Funk, C., Price, N. D., … Ertekin-Taner, N. (2018). Divergent brain gene expression patterns associate with distinct cell-specific tau neuropathology traits in progressive supranuclear palsy. Acta Neuropathologica, 136(5), 709–727. https://doi.org/10.1007/s00401-018-1900-5 Cite Download