Cory Funk, PhD

Senior Research Scientist

Hood-Price Lab

Cory Funk
Molani, Sevda, Patricia V. Hernandez, Ryan T. Roper, Venkata R. Duvvuri, Andrew M. Baumgartner, Jason D. Goldman, Nilüfer Ertekin-Taner, et al. 2022. “Risk Factors for Severe COVID-19 Differ by Age for Hospitalized Adults.” Scientific Reports 12 (1): 6568. Cite Download
Heath, Laura, John C. Earls, Andrew T. Magis, Sergey A. Kornilov, Jennifer C. Lovejoy, Cory C. Funk, Noa Rappaport, et al. 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. Cite Download
Roach, Jared C., John F. Hodes, Cory C. Funk, William R Shankle, David A. Merrill, Leroy Hood, and Jennifer Bramen. 2022. “Dense Data Enables 21th Century Clinical Trials.” Alzheimer’s & Dementia: Translational Research & Clinical Interventions 8 (1): e12297. Cite Download
Ross, Mary Kay, Cyrus Raji, Kristine L. Lokken, Dale E. Bredesen, Jared C. Roach, Cory C. Funk, Nathan Price, Noa Rappaport, Leroy Hood, and James R. Heath. 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, Xue, Mariet Allen, Özkan İş, Joseph S. Reddy, Frederick Q. Tutor-New, Monica Castanedes Casey, Minerva M. Carrasquillo, et al. 2021. “Alzheimer’s Disease and Progressive Supranuclear Palsy Share Similar Transcriptomic Changes in Distinct Brain Regions.” The Journal of Clinical Investigation, e149904. Cite
Baloni, Priyanka, Cory C. Funk, Ben Readhead, and Nathan D. Price. 2021. “Systems Modeling of Metabolic Dysregulation in Neurodegenerative Diseases.” Current Opinion in Pharmacology 60: 59–65. Cite
McFarland, Karen N., Carolina Ceballos, Awilda Rosario, Thomas Ladd, Brenda Moore, Griffin Golde, Xue Wang, et al. 2021. “Microglia Show Differential Transcriptomic Response to Aβ Peptide Aggregates Ex Vivo and in Vivo.” Life Science Alliance 4 (7): e202101108. Cite Download
McEwen, Sarah C., David A. Merrill, Jennifer Bramen, Verna Porter, Stella Panos, Scott Kaiser, John Hodes, et al. 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. Cite Download
Levites, Yona, Cory Funk, Xue Wang, Paramita Chakrabarty, Karen N. McFarland, Baxter Bramblett, Veronica O’Neal, et al. 2021. “Modulating Innate Immune Activation States Impacts the Efficacy of Specific Aβ Immunotherapy.” Molecular Neurodegeneration 16 (1): 32. Cite Download
Wainberg, Michael, Tain Luquez, David M. Koelle, Ben Readhead, Christine Johnston, Martin Darvas, and Cory C. Funk. 2021. “The Viral Hypothesis: How Herpesviruses May Contribute to Alzheimer’s Disease.” Molecular Psychiatry. Cite Download
Stojakovic, Andrea, Sergey Trushin, Anthony Sheu, Layla Khalili, Su-Youne Chang, Xing Li, Trace Christensen, et al. 2021. “Partial Inhibition of Mitochondrial Complex I Ameliorates Alzheimer’s Disease Pathology and Cognition in APP/PS1 Female Mice.” Communications Biology 4 (1): 61. Cite Download
Li, Hong-Dong, Cory C. Funk, Karen McFarland, Eric B. Dammer, Mariet Allen, Minerva M. Carrasquillo, Yona Levites, et al. 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. Cite Download
Baloni, Priyanka, Cory C. Funk, Jingwen Yan, James T. Yurkovich, Alexandra Kueider-Paisley, Kwangsik Nho, Almut Heinken, et al. 2020. “Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer’s Disease.” Cell Reports. Medicine 1 (8): 100138. Cite Download
Wan, Ying-Wooi, Rami Al-Ouran, Carl G. Mangleburg, Thanneer M. Perumal, Tom V. Lee, Katherine Allison, Vivek Swarup, et al. 2020. “Meta-Analysis of the Alzheimer’s Disease Human Brain Transcriptome and Functional Dissection in Mouse Models.” Cell Reports 32 (2): 107908. Cite Download
Baloni, Priyanka, Cory C. Funk, Jingwen Yan, James T. Yurkovich, Alexandra Kueider-Paisley, Kwangsik Nho, Almut Heinken, et al. 2020. “Metabolic Network Analysis Reveals Altered Bile Acid Synthesis and Metabolism in Alzheimer’s Disease.” Cell Reports Medicine 1 (8). Cite Download
Funk, Cory C., Alex M. Casella, Segun Jung, Matthew A. Richards, Alex Rodriguez, Paul Shannon, Rory Donovan-Maiye, et al. 2020. “Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types.” Cell Reports 32 (7): 108029. Cite Download
Li, Hong-Dong, Cory C. Funk, and Nathan D. Price. 2020. “IREAD: A Tool for Intron Retention Detection from RNA-Seq Data.” BMC Genomics 21 (1): 128. Cite Download
Baloni, Priyanka, Cory C. Funk, Jingwen Yan, James T. Yurkovich, Alexandra Kueider-Paisley, Kwangsik Nho, Almut Heinken, et al. 2019. “Identifying Differences in Bile Acid Pathways for Cholesterol Clearance in Alzheimer’s Disease Using Metabolic Networks of Human Brain Regions.” BioRxiv, 782987. Cite Download
Pearl, Jocelynn R., Carlo Colantuoni, Dani E. Bergey, Cory C. Funk, Paul Shannon, Bijoya Basu, Alex M. Casella, et al. 2019. “Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders.” Cell Systems 8 (2): 122-135.e7. Cite
Madduri, Ravi, Kyle Chard, Mike D’Arcy, Segun C. Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric Deutsch, et al. 2019. “Reproducible Big Data Science: A Case Study in Continuous FAIRness.” PloS One 14 (4): e0213013. Cite Download
Chakrabarty, Paramita, Andrew Li, Thomas B. Ladd, Michael R. Strickland, Emily J. Koller, Jeremy D. Burgess, Cory C. Funk, et al. 2018. “TLR5 Decoy Receptor as a Novel Anti-Amyloid Therapeutic for Alzheimer’s Disease.” The Journal of Experimental Medicine 215 (9): 2247–64. Cite
Allen, Mariet, Xue Wang, Daniel J. Serie, Samantha L. Strickland, Jeremy D. Burgess, Shunsuke Koga, Curtis S. Younkin, et al. 2018. “Divergent Brain Gene Expression Patterns Associate with Distinct Cell-Specific Tau Neuropathology Traits in Progressive Supranuclear Palsy.” Acta Neuropathologica 136 (5): 709–27. Cite Download
Mikheev, Andrei M., Svetlana A. Mikheeva, Liza J. Severs, Cory C. Funk, Lei Huang, José L. McFaline-Figueroa, Jeanette Schwensen, et al. 2018. “Targeting TWIST1 through Loss of Function Inhibits Tumorigenicity of Human Glioblastoma.” Molecular Oncology 12 (7): 1188–1202. Cite
Readhead, Ben, Jean-Vianney Haure-Mirande, Cory C. Funk, Matthew A. Richards, Paul Shannon, Vahram Haroutunian, Mary Sano, et al. 2018. “Multiscale Analysis of Independent Alzheimer’s Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus.” Neuron. Cite
Sims, Rebecca, Sven J. van der Lee, Adam C. Naj, Céline Bellenguez, Nandini Badarinarayan, Johanna Jakobsdottir, Brian W. Kunkle, et al. 2017. “Rare Coding Variants in PLCG2, ABI3, and TREM2 Implicate Microglial-Mediated Innate Immunity in Alzheimer’s Disease.” Nature Genetics. Cite
Ghosh, Dhimankrishna, Cory C. Funk, Juan Caballero, Nameeta Shah, Katherine Rouleau, John C. Earls, Liliana Soroceanu, et al. 2017. “A Cell-Surface Membrane Protein Signature for Glioblastoma.” Cell Systems 4 (5): 516-529.e7. Cite
Allen, Mariet, Xue Wang, Jeremy D. Burgess, Jens Watzlawik, Daniel J. Serie, Curtis S. Younkin, Thuy Nguyen, et al. 2017. “Conserved Brain Myelination Networks Are Altered in Alzheimer’s and Other Neurodegenerative Diseases.” Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association. Cite
Pollak, Julia, Karan G. Rai, Cory C. Funk, Sonali Arora, Eunjee Lee, Jun Zhu, Nathan D. Price, Patrick J. Paddison, Jan-Marino Ramirez, and Robert C. Rostomily. 2017. “Ion Channel Expression Patterns in Glioblastoma Stem Cells with Functional and Therapeutic Implications for Malignancy.” PloS One 12 (3): e0172884. Cite
Allen, Mariet, Minerva M. Carrasquillo, Cory Funk, Benjamin D. Heavner, Fanggeng Zou, Curtis S. Younkin, Jeremy D. Burgess, et al. 2016. “Human Whole Genome Genotype and Transcriptome Data for Alzheimer’s and Other Neurodegenerative Diseases.” Scientific Data 3: 160089. Cite
Pestal, K., C. C. Funk, J. M. Snyder, N. D. Price, P. M. Treuting, and D. B. Stetson. 2015. “Isoforms of RNA-Editing Enzyme ADAR1 Independently Control Nucleic Acid Sensor MDA5-Driven Autoimmunity and Multi-Organ Development.” Immunity 43 (November): 933–44. Cite
Eddy, James A., Cory C. Funk, and Nathan D. Price. 2015. “Fostering Synergy between Cell Biology and Systems Biology.” Trends in Cell Biology, May. Cite
Chakrabarty, Paramita, Andrew Li, Carolina Ceballos-Diaz, James A. Eddy, Cory C. Funk, Brenda Moore, Nadia DiNunno, et al. 2015. “IL-10 Alters Immunoproteostasis in APP Mice, Increasing Plaque Burden and Worsening Cognitive Behavior.” Neuron 85 (3): 519–33. Cite
Sangar, Vineet, Cory C. Funk, Ulrike Kusebauch, D. Campbell, Robert L. Moritz, and Nathan D. Price. 2014. “Quantitative Proteomic Analysis Reveals Effects of Epidermal Growth Factor Receptor (EGFR) on Invasion-Promoting Proteins Secreted by Glioblastoma Cells.” Molecular & Cellular Proteomics: MCP 13 (10): 2618–31. Cite
Craig, Theodore A., Yuji Zhang, Andrew T. Magis, Cory C. Funk, Nathan D. Price, Stephen C. Ekker, and Rajiv Kumar. 2014. “Detection of 1α,25-Dihydroxyvitamin D-Regulated MiRNAs in Zebrafish by Whole Transcriptome Sequencing.” Zebrafish 11 (3): 207–18. Cite
Wang, Chunjing, Cory C. Funk, James A. Eddy, and Nathan D. Price. 2013. “Transcriptional Analysis of Aggressiveness and Heterogeneity across Grades of Astrocytomas.” PloS One 8 (10). Cite
Sung, Jaeyun, Pan-Jun Kim, Shuyi Ma, Cory C. Funk, Andrew T. Magis, Yuliang Wang, Leroy Hood, Donald Geman, and Nathan D. Price. 2013. “Multi-Study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures.” PLoS Computational Biology 9 (7). Cite
Earls, John C., James A. Eddy, Cory C. Funk, Younhee Ko, Andrew T. Magis, and Nathan D. Price. 2013. “AUREA: An Open-Source Software System for Accurate and User-Friendly Identification of Relative Expression Molecular Signatures.” BMC Bioinformatics 14. Cite
Craig, Theodore A., Yuji Zhang, Melissa S. McNulty, Sumit Middha, Hemamalini Ketha, Ravinder J. Singh, Andrew T. Magis, et al. 2012. “Research Resource: Whole Transcriptome RNA Sequencing Detects Multiple 1alpha,25-Dihydroxyvitamin D(3)-Sensitive Metabolic Pathways in Developing Zebrafish.” Molecular Endocrinology (Baltimore, Md.) 26 (9): 1630–42. Cite
Ma, Shuyi, Cory C. Funk, and Nathan D. Price. 2010. “Systems Approaches to Molecular Cancer Diagnostics.” Discovery Medicine 10 (55): 531–42. Cite

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

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