Stojakovic, Andrea, Sergey Trushin, Anthony Sheu, Layla Khalili, Su-Youne Chang, Xing Li, Trace Christensen, et al. 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

Baumgartner, Andrew, Max Robinson, Todd Golde, Suman Jaydev, Sui Huang, Jennifer Hadlock, and Cory Funk. 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

Wang, Qi, Jerry Antone, Eric Alsop, Rebecca Reiman, Cory Funk, Jaroslav Bendl, Joel T. Dudley, et al. 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, Yona, Eric B. Dammer, Yong Ran, Wangchen Tsering, Duc Duong, Measho Abreha, Joshna Gadhavi, et al. 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, Alison, Kylia Ahuna, Yeon Mi Hwang, Jocelynn Pearl, Hanna Liao, Paul Shannon, Leena Kadam, et al. 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, Andrew, Sui Huang, Jennifer Hadlock, and Cory Funk. 2024. “Dimensional Reduction of Gradient-like Stochastic Systems with Multiplicative Noise via Fokker-Planck Diffusion Maps.” arXiv. https://doi.org/10.48550/arXiv.2401.03095. Cite Download

Baumgartner, Andrew, Max Robinson, Sui Huang, Jennifer Hadlock, and Cory Funk. 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, Noa, Dylan Ellis, Kengo Watanabe, Tomasz Wilmanski, Leroy Hood, Nathan Price, Cory Funk, and Priyanka Baloni. 2023. “BIOLOGICAL AGING AND APOE STATUS REWIRE INTER-OMIC ASSOCIATIONS RELATED TO BIOENERGETICS IN HUMANS.” Innovation in Aging 7 (Suppl 1): 631–32. https://doi.org/10.1093/geroni/igad104.2058. Cite Download

Girdhar, Kiran, Jaroslav Bendl, Andrew Baumgartner, Karen Therrien, Sanan Venkatesh, Deepika Mathur, Pengfei Dong, et al. 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, Svetlana A., Cory C. Funk, Philip J. Horner, Robert C. Rostomily, and Andrei M. Mikheev. 2023. “Novel TCF4:TCF12 Heterodimer Inhibits Glioblastoma Growth.” Molecular Oncology. https://doi.org/10.1002/1878-0261.13496. Cite

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. https://doi.org/10.1038/s41598-022-10344-3. Cite Download Download

Baloni, Priyanka, Matthias Arnold, Luna Buitrago, Kwangsik Nho, Herman Moreno, Kevin Huynh, Barbara Brauner, et al. 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, Paola, Zeyuan Song, Dylan Ellis, Qu Tian, Michaela Schwaiger-Haber, Ethan Stancliffe, Michael S. Lustgarten, et al. 2022. “A Metabolomic Signature of the APOE2 Allele.” GeroScience. https://doi.org/10.1007/s11357-022-00646-9. Cite Download

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: A Retrospective Study of Hospitalized Adults.” Preprint. Public and Global Health. https://doi.org/10.1101/2022.02.02.22270287. Cite Download

Baloni, Priyanka, Kwangsik Nho, Matthias Arnold, Gregory Louie, Alexandra Kueider-Paisley, Andrew J. Saykin, Kim Ekroos, et al. 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, Kristen R., Karen N. McFarland, Jennifer Phillips, Mariet Allen, Christian B. Lessard, Lillian Zobel, Elsa Gonzalez De La Cruz, et al. 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, Jared C., Junko Hara, Deborah Fridman, Jennifer C. Lovejoy, Kathleen Jade, Laura Heim, Rachel Romansik, et al. 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, Jared C., Lance Edens, Daria R. Markewych, Molly K. Rapozo, Junko Hara, Gustavo Glusman, Cory Funk, et al. 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, 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. https://doi.org/10.1038/s41598-022-09825-2. 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. https://doi.org/10.1002/trc2.12297. 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. https://doi.org/10.1172/JCI149904. 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. https://doi.org/10.1016/j.coph.2021.06.012. 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. https://doi.org/10.26508/lsa.202101108. 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. https://doi.org/10.1002/trc2.12191. 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. https://doi.org/10.1186/s13024-021-00453-4. 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. https://doi.org/10.1038/s41380-021-01138-6. 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. https://doi.org/10.1038/s42003-020-01584-y. 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. https://doi.org/10.1002/alz.12254. 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. https://doi.org/10.1016/j.xcrm.2020.100138. 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. https://doi.org/10.1016/j.celrep.2020.107908. 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. https://doi.org/10.1016/j.celrep.2020.108029. 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. https://doi.org/10.1186/s12864-020-6541-0. 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. https://doi.org/10.1101/782987. 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. https://doi.org/10.1016/j.cels.2019.01.002. 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. https://doi.org/10.1371/journal.pone.0213013. 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. https://doi.org/10.1084/jem.20180484. 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. https://doi.org/10.1007/s00401-018-1900-5. 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. https://doi.org/10.1002/1878-0261.12320. 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. https://doi.org/10.1016/j.neuron.2018.05.023. 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. https://doi.org/10.1038/ng.3916. 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. https://doi.org/10.1016/j.cels.2017.03.004. 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. https://doi.org/10.1016/j.jalz.2017.09.012. 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. https://doi.org/10.1371/journal.pone.0172884. 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. https://doi.org/10.1038/sdata.2016.89. 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. https://doi.org/10.1016/j.immuni.2015.11.001. 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. https://doi.org/10.1016/j.tcb.2015.04.005. 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. https://doi.org/10.1016/j.neuron.2014.11.020. Cite