Publications

2024

Armstrong, Sujit Silas, Daniel G. Chen, Sunil Kumar, James R. Heath, Matthew Feinstein, John R. Greenland, Daniel R. Calabrese, Lewis L. Lanier, Klaus Ley, and Avishai Shemesh. 2024. “CITE-Seq Analysis Reveals Human Cytomegalovirus and Diabetes-Associated Adaptive NK Cell Alterations in Cardiovascular Disease.” BioRxiv, 2024–03. https://www.biorxiv.org/content/10.1101/2024.03.22.581997.abstract. Cite Download
Bartolomucci, Alessandro, Alice E. Kane, Lauren Gaydosh, Maria Razzoli, Brianah M. McCoy, Dan Ehninger, Brian H. Chen, Susan E. Howlett, and Noah Snyder-Mackler. 2024. “Animal Models Relevant for Geroscience: Current Trends and Future Perspectives in Biomarkers, and Measures of Biological Aging.” The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences 79 (9): glae135. https://doi.org/10.1093/gerona/glae135. 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, 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
Bronstein, Becky, Molly Griffiths, Claudia McLaughlin Ludwig, Deb L. Morrison, Heidi Smith, and Barbara Steffens. 2024. “Action and Engagement in Climate Science Learning Pedagogy.” Connected Science Learning, 1–3. https://doi.org/10.1080/24758779.2024.2376483. Cite
Chang, Shu-Ching, Gary L. Grunkemeier, Jason D. Goldman, Mansen Wang, Paul A. McKelvey, Jennifer Hadlock, Qi Wei, and George A. Diaz. 2024. “A Simplified Pneumonia Severity Index (PSI) for Clinical Outcome Prediction in COVID-19.” PloS One 19 (5): e0303899. https://doi.org/10.1371/journal.pone.0303899. Cite Download
Chen, Daniel G., Jingyi Xie, Jongchan Choi, Rachel H. Ng, Rongyu Zhang, Sarah Li, Rick Edmark, et al. 2024. “Integrative Systems Biology Reveals NKG2A-Biased Immune Responses Correlate with Protection in Infectious Disease, Autoimmune Disease, and Cancer.” Cell Reports 43 (3). https://doi.org/10.1016/j.celrep.2024.113872. Cite Download
Cyriaque, Valentine, Rodrigo Ibarra-Chávez, Anna Kuchina, Georg Seelig, Joseph Nesme, and Jonas Stenløkke Madsen. 2024. “Single-Cell RNA Sequencing Reveals Plasmid Constrains Bacterial Population Heterogeneity and Identifies a Non-Conjugating Subpopulation.” Nature Communications 15 (1): 5853. https://doi.org/10.1038/s41467-024-49793-x. Cite
Diener, Christian, and Sean M. Gibbons. 2024. “Metagenomic Estimation of Dietary Intake from Human Stool.” BioRxiv: The Preprint Server for Biology, 2024.02.02.578701. https://doi.org/10.1101/2024.02.02.578701. Cite Download
Don, Janith, Andrew J. Schork, Gwênlyn Glusman, Noa Rappaport, Steve R. Cummings, David Duggan, Anish Raju, et al. 2024. “The Relationship between 11 Different Polygenic Longevity Scores, Parental Lifespan, and Disease Diagnosis in the UK Biobank.” GeroScience. https://doi.org/10.1007/s11357-024-01107-1. Cite Download
Eklund, Jen, Kelsie Fowler, Caroline Kiehle, Lori Henrickson, and Deb L. Morrison. 2024. “Make Climate Learning Happen Exactly Where You Are.” Connected Science Learning 0 (0): 1–7. https://doi.org/10.1080/24758779.2024.2371759. Cite
Faust, Saul N., Richard Haynes, Christine E. Jones, Natalie Staplin, Elizabeth Whittaker, Thomas Jaki, Ed Juszczak, Enti Spata, Mandy Wan, and James R. Heath. 2024. “Immunomodulatory Therapy in Children with Paediatric Inflammatory Multisystem Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS, MIS-C; RECOVERY): A Randomised, Controlled, Open-Label, Platform Trial.” The Lancet Child & Adolescent Health 8 (3): 190–200. https://www.thelancet.com/journals/lanchi/article/PIIS2352-4642(23)00316-4/fulltext. Cite
Flower, Cameron T., Chunmei Liu, Hui-Yu Chuang, Xiaoyang Ye, Hanjun Cheng, James R. Heath, Wei Wei, and Forest M. White. 2024. “Signaling and Transcriptional Dynamics Underlying Early Adaptation to Oncogenic BRAF Inhibition.” BioRxiv, 2024–02. https://www.biorxiv.org/content/10.1101/2024.02.19.581004.abstract. Cite Download
Gaisser, Karl D., Sophie N. Skloss, Leandra M. Brettner, Luana Paleologu, Charles M. Roco, Alexander B. Rosenberg, Matthew Hirano, R. William DePaolo, Georg Seelig, and Anna Kuchina. 2024. “High-Throughput Single-Cell Transcriptomics of Bacteria Using Combinatorial Barcoding.” Nature Protocols. https://doi.org/10.1038/s41596-024-01007-w. Cite
Griffin, Patrick T., Alice Kane, Alexandre Trapp, Jien Li, Matthew Arnold, Jesse R. Poganik, Ryan J. Conway, et al. 2024. “TIME-Seq Reduces Time and Cost of DNA Methylation Measurement for Epigenetic Clock Construction.” Nature Aging. https://doi.org/10.1038/s43587-023-00555-2. Cite
Hariharan, Ramkumar, Leroy Hood, and Nathan D. Price. 2024. “A Data-Driven Approach to Improve Wellness and Reduce Recurrence in Cancer Survivors.” Frontiers in Oncology 14:1397008. https://doi.org/10.3389/fonc.2024.1397008. Cite Download
Heath, James R. 2024. “Abstract SY41-02: Experimental Methods for High Throughput Discovery and Validation of Tumor Antigens.” Cancer Research 84 (7_Supplement): SY41-02. https://aacrjournals.org/cancerres/article/84/7_Supplement/SY41-02/742137. Cite
Huang, Qiongrong, Zhiyuan Hu, Qiwen Zheng, Xuemei Mao, Wenxi Lv, Fei Wu, Dapeng Fu, et al. 2024. “A Proactive Intervention Study in Metabolic Syndrome High-Risk Populations Using Phenome-Based Actionable P4 Medicine Strategy.” Phenomics (Cham, Switzerland) 4 (2): 91–108. https://doi.org/10.1007/s43657-023-00115-z. Cite
Hunt, Kristopher A., Alex V. Carr, Anne E. Otwell, Jacob J. Valenzuela, Kathleen S. Walker, Emma R. Dixon, Lauren M. Lui, et al. 2024. “Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide.” Environmental Science & Technology. https://doi.org/10.1021/acs.est.3c07972. Cite
Hwang, Yeon Mi, Ryan T. Roper, Samantha N. Piekos, Daniel A. Enquobahrie, Mary F. Hebert, Alison G. Paquette, Priyanka Baloni, Nathan D. Price, Leroy Hood, and Jennifer J. Hadlock. 2024. “Timing of Selective Serotonin Reuptake Inhibitor Use and Risk for Preterm Birth and Related Adverse Events: With a Consideration of the COVID-19 Pandemic Period.” The Journal of Maternal-Fetal & Neonatal Medicine 37 (1): 2313364. https://doi.org/10.1080/14767058.2024.2313364. Cite Download
Hwang, Yeon Mi, Qi Wei, Samantha N. Piekos, Bhargav Vemuri, Sevda Molani, Philip Mease, Leroy Hood, and Jennifer Hadlock. 2024. “Maternal-Fetal Outcomes in Patients with Immune-Mediated Inflammatory Diseases, with Consideration of Comorbidities: A Retrospective Cohort Study in a Large U.S. Healthcare System.” EClinicalMedicine 68:102435. https://doi.org/10.1016/j.eclinm.2024.102435. Cite Download
Johnson-Martínez, Johannes P., Christian Diener, Anne E. Levine, Tomasz Wilmanski, David L. Suskind, Alexandra Ralevski, Jennifer Hadlock, et al. 2024. “Aberrant Bowel Movement Frequencies Coincide with Increased Microbe-Derived Blood Metabolites Associated with Reduced Organ Function.” Cell Reports. Medicine 5 (7): 101646. https://doi.org/10.1016/j.xcrm.2024.101646. Cite
Kane, Alice E., Karthikeyani Chellappa, Michael B. Schultz, Matthew Arnold, Jien Li, Joao Amorim, Christian Diener, et al. 2024. “Long-Term NMN Treatment Increases Lifespan and Healthspan in Mice in a Sex Dependent Manner.” bioRxiv. https://doi.org/10.1101/2024.06.21.599604. Cite Download
Kim, Jungwoo, Rachel H. Ng, JingXin Liang, Dazy Johnson, Young Shik Shin, Arion F. Chatziioannou, Michael E. Phelps, Wei Wei, Raphael D. Levine, and James R. Heath. 2024. “Kinetic Trajectories of Glucose Uptake in Single Cancer Cells Reveal a Drug-Induced Cell-State Change Within Hours of Drug Treatment.” The Journal of Physical Chemistry. B. https://doi.org/10.1021/acs.jpcb.4c03663. Cite
Laubenbacher, Reinhard, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, et al. 2024. “Toward Mechanistic Medical Digital Twins: Some Use Cases in Immunology.” Frontiers in Digital Health 6:1349595. https://doi.org/10.3389/fdgth.2024.1349595. Cite Download
Laubenbacher, Reinhard, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James Glazier, et al. 2024. “Forum on Immune Digital Twins: A Meeting Report.” NPJ Systems Biology and Applications 10 (1): 19. https://doi.org/10.1038/s41540-024-00345-5. Cite Download
Laubenbacher, R., B. Mehrad, I. Shmulevich, and N. Trayanova. 2024. “Digital Twins in Medicine.” Nature Computational Science 4 (3): 184–91. https://doi.org/10.1038/s43588-024-00607-6. Cite Download
Leblebici, Asim, Ceren Sancar, Bahar Tercan, Zerrin Isik, Mehmet Emin Arayici, Ender Berat Ellidokuz, Yasemin Basbinar, and Nuri Yildirim. 2024. “In Silico Approach to Molecular Profiling of the Transition from Ovarian Epithelial Cells to Low-Grade Serous Ovarian Tumors for Targeted Therapeutic Insights.” Current Issues in Molecular Biology 46 (3): 1777–98. https://doi.org/10.3390/cimb46030117. Cite Download
Lee, Su-Hyung, Yoonkyung Won, David Gibbs, Brianna Caldwell, Anna Goldstein, Eunyoung Choi, and James R. Goldenring. 2024. “Amphiregulin Switches Progenitor Cell Fate for Lineage Commitment During Gastric Mucosal Regeneration.” Gastroenterology, S0016-5085(24)00290-7. https://doi.org/10.1053/j.gastro.2024.03.009. 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
Li, Luna Xingyu, Boris Aguilar, John Gennari, and Guangrong Qin. 2024. “Merging Logical Models: An Application in Acute Myeloid Leukemia Modeling.” bioRxiv. https://doi.org/10.1101/2024.09.13.612961. Cite Download
Ludwig, Claudia McLaughlin, Rebecca A. Howsmon, Shelley Stromholt, Jacob J. Valenzuela, Rachel Calder, and Nitin S. Baliga. 2024. “Consequential Insights for Advancing Informal STEM Learning and Outcomes for Students from Historically Marginalized Communities.” Humanities and Social Sciences Communications 11 (1): 351. https://doi.org/10.1057/s41599-024-02797-w. Cite Download
Matuozzo, Daniela, Estelle Talouarn, Astrid Marchal, Peng Zhang, Jeremy Manry, Yoann Seeleuthner, Yu Zhang, et al. 2024. “Correction: Rare Predicted Loss-of-Function Variants of Type I IFN Immunity Genes Are Associated with Life-Threatening COVID-19.” Genome Medicine 16 (1): 6. https://doi.org/10.1186/s13073-023-01278-0. Cite Download
Metz, Torri D., Harrison T. Reeder, Rebecca G. Clifton, Valerie Flaherman, Leyna V. Aragon, Leah Castro Baucom, Carmen J. Beamon, et al. 2024. “Post-Acute Sequelae of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) After Infection During Pregnancy.” Obstetrics and Gynecology. https://doi.org/10.1097/AOG.0000000000005670. Cite
Meyer, Stacy, Kelsie Fowler, Claudia McLaughlin Ludwig, Philip Bell, Isabel Carrera Zamanillo, Barbara Steffens, Lori Henrickson, et al. 2024. “Should Climate Science Be Local? YES‼.” Connected Science Learning 0 (0): 1–10. https://doi.org/10.1080/24758779.2024.2360517. Cite
Mirchandani, Cade, Pingting Wang, Jodie Jacobs, Maximilian Genetti, Evan Pepper-Tunick, William T. Sullivan, Russell Corbett-Detig, and Shelbi L. Russell. 2024. “Mixed Wolbachia Infections Resolve Rapidly during in Vitro Evolution.” PLoS Pathogens 20 (7): e1012149. https://doi.org/10.1371/journal.ppat.1012149. Cite
Mishra, Manish, Judy Wu, Alice E. Kane, and Susan E. Howlett. 2024. “The Intersection of Frailty and Metabolism.” Cell Metabolism, S1550-4131(24)00091-3. https://doi.org/10.1016/j.cmet.2024.03.012. Cite
Nagar, Rupa, Stefano S. Garcia Castillo, Maria Pinzon-Ortiz, Sharon Patray, Alida Coppi, Sachie Kanatani, Robert L. Moritz, Kristian E. Swearingen, Michael A. J. Ferguson, and Photini Sinnis. 2024. “The Major Surface Protein of Malaria Sporozoites Is GPI-Anchored to the Plasma Membrane.” The Journal of Biological Chemistry 300 (8): 107557. https://doi.org/10.1016/j.jbc.2024.107557. Cite
Nelson, Taiji, Carissa Haug, Claudia McLaughlin Ludwig, Isabel Carrera Zamanillo, Luke Matlack, and Kelsie Fowler. 2024. “Grounded in Community: Leveraging Partnerships for K–12 Climate Education.” Connected Science Learning 0 (0): 1–9. https://doi.org/10.1080/24758779.2024.2358221. Cite
Nguyen, Kim Truc, Xilal Y. Rima, Luong T. H. Nguyen, Xinyu Wang, Kwang Joo Kwak, Min Jin Yoon, Hong Li, et al. 2024. “Integrated Antigenic and Nucleic Acid Detection in Single Virions and Extracellular Vesicles with Viral Content.” Advanced Healthcare Materials, e2400622. https://doi.org/10.1002/adhm.202400622. Cite
Omenn, Gilbert S., Lydie Lane, Christopher M. Overall, Cecilia Lindskog, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, et al. 2024. “The 2023 Report on the Proteome from the HUPO Human Proteome Project.” Journal of Proteome Research 23 (2): 532–49. https://doi.org/10.1021/acs.jproteome.3c00591. 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
Park, James H., Parvinder Hothi, Adrian Lopez Garcia de Lomana, Min Pan, Rachel Calder, Serdar Turkarslan, Wei-Ju Wu, et al. 2024. “Gene Regulatory Network Topology Governs Resistance and Treatment Escape in Glioma Stem-like Cells.” Science Advances 10 (23): eadj7706. https://doi.org/10.1126/sciadv.adj7706. Cite Download
Park, James H., Parvinder Hothi, Adrian Lopez Garcia de Lomana, Min Pan, Rachel Calder, Serdar Turkarslan, Wei-Ju Wu, et al. 2024. “Gene Regulatory Network Topology Governs Resistance and Treatment Escape in Glioma Stem-like Cells.” BioRxiv: The Preprint Server for Biology, 2024.02.02.578510. https://doi.org/10.1101/2024.02.02.578510. Cite Download
Qin, Guangrong, Jin Dai, Sylvia Chien, Timothy J. Martins, Brenda Loera, Quy H. Nguyen, Melanie L. Oakes, et al. 2024. “Mutation Patterns Predict Drug Sensitivity in Acute Myeloid Leukemia.” Clinical Cancer Research: An Official Journal of the American Association for Cancer Research 30 (12): 2659–71. https://doi.org/10.1158/1078-0432.CCR-23-1674. Cite Download
Qin, Guangrong, Yue Zhang, Jeffrey W. Tyner, Christopher J. Kemp, and Ilya Shmulevich. 2024. “Knowledge Graphs Facilitate Prediction of Drug Response for Acute Myeloid Leukemia.” IScience 27 (9). https://doi.org/10.1016/j.isci.2024.110755. Cite Download
Quinn-Bohmann, Nick, Tomasz Wilmanski, Katherine Ramos Sarmiento, Lisa Levy, Johanna W. Lampe, Thomas Gurry, Noa Rappaport, et al. 2024. “Microbial Community-Scale Metabolic Modelling Predicts Personalized Short-Chain Fatty Acid Production Profiles in the Human Gut.” Nature Microbiology 9 (7): 1700–1712. https://doi.org/10.1038/s41564-024-01728-4. Cite
Quinn-Bohmann, Nick, Jose A. Freixas-Coutin, Jin Seo, Ruth Simmons, Christian Diener, and Sean M. Gibbons. 2024. “Meta-Analysis of the Human Upper Respiratory Tract Microbiome Reveals Robust Taxonomic Associations with Health and Disease.” BMC Biology 22 (1): 93. https://doi.org/10.1186/s12915-024-01887-0. Cite Download
Ralevski, Alexandra, Nadaa Taiyab, Michael Nossal, Lindsay Mico, Samantha N. Piekos, and Jennifer Hadlock. 2024. “Using Large Language Models to Annotate Complex Cases of Social Determinants of Health in Longitudinal Clinical Records.” medRxiv. https://doi.org/10.1101/2024.04.25.24306380. Cite Download
Ramsbottom, Kerry A., Ananth Prakash, Yasset Perez-Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J. Kundu, Emily Bowler-Barnett, et al. 2024. “Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.” Journal of Proteome Research 23 (7): 2518–31. https://doi.org/10.1021/acs.jproteome.4c00187. Cite Download