Publications

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

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

Diener, Christian, and Sean M. Gibbons. 2024. “Metagenomic Estimation of Dietary Intake from Human Stool.” BioRxiv: The Preprint Server for Biology, February, 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, March. https://doi.org/10.1007/s11357-024-01107-1. 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

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, April. 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 (February): 102435. https://doi.org/10.1016/j.eclinm.2024.102435. 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

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

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, March, S0016-5085(24)00290-7. https://doi.org/10.1053/j.gastro.2024.03.009. Cite

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

Mirchandani, Cade, Pingting Wang, Jodie Jacobs, Maximilian Genetti, Evan Pepper-Tunick, William T. Sullivan, Russ Corbett-Detig, and Shelbi L. Russell. 2024. “Mixed Wolbachia Infections Resolve Rapidly during in Vitro Evolution.” BioRxiv: The Preprint Server for Biology, March, 2024.03.27.586911. https://doi.org/10.1101/2024.03.27.586911. Cite Download

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

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.” BioRxiv: The Preprint Server for Biology, February, 2024.02.02.578510. https://doi.org/10.1101/2024.02.02.578510. 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.” Science Advances 10 (23): eadj7706. https://doi.org/10.1126/sciadv.adj7706. 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

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

Rios, Kelly T., James P. McGee, Aswathy Sebastian, Robert L. Moritz, Marina Feric, Sabrina Absalon, Kristian E. Swearingen, and Scott E. Lindner. 2024. “Global Release of Translational Repression Across Plasmodium’s Host-to-Vector Transmission Event.” BioRxiv: The Preprint Server for Biology, March, 2024.02.01.577866. https://doi.org/10.1101/2024.02.01.577866. Cite Download

Sarmiento, Katherine Ramos, Alex Carr, Christian Diener, Kenneth J. Locey, and Sean M. Gibbons. 2024. “Island Biogeography Theory Provides a Plausible Explanation for Why Larger Vertebrates and Taller Humans Have More Diverse Gut Microbiomes.” The ISME Journal, wrae114. https://doi.org/10.1093/ismejo/wrae114. Cite

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

Sulaiman, Jordy Evan, Jaron Thompson, Yili Qian, Eugenio I. Vivas, Christian Diener, Sean M. Gibbons, Nasia Safdar, and Ophelia S. Venturelli. 2024. “Elucidating Human Gut Microbiota Interactions That Robustly Inhibit Diverse Clostridioides Difficile Strains across Different Nutrient Landscapes.” BioRxiv: The Preprint Server for Biology, 2024.04.13.589383. https://doi.org/10.1101/2024.04.13.589383. Cite Download

Villalona, Seiichi, Brenda S. Castillo, Carlos Chavez Perez, Alana Ferreira, Isoris Nivar, Juan Cisneros, and Carmen E. Guerra. 2024. “Interventions to Mitigate Financial Toxicity in Adult Patients with Cancer in the United States: A Scoping Review.” Current Oncology (Toronto, Ont.) 31 (2): 918–32. https://doi.org/10.3390/curroncol31020068. Cite Download

Wei, Qi, Philip J. Mease, Michael Chiorean, Lulu Iles-Shih, Wanessa F. Matos, Andrew Baumgartner, Sevda Molani, et al. 2024. “Machine Learning to Understand Risks for Severe COVID-19 Outcomes: A Retrospective Cohort Study of Immune-Mediated Inflammatory Diseases, Immunomodulatory Medications, and Comorbidities in a Large US Health-Care System.” The Lancet Digital Health 6 (5): e309–22. https://doi.org/10.1016/S2589-7500(24)00021-9. Cite Download

Zhang, Nathan H., and Eric W. Deutsch. 2024. “SpectiCal: M/z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions.” Journal of Proteome Research 23 (4): 1519–30. https://doi.org/10.1021/acs.jproteome.3c00882. Cite

Zhang, Yue, Guangrong Qin, Boris Aguilar, Noa Rappaport, James T. Yurkovich, Lance Pflieger, Sui Huang, Leroy Hood, and Ilya Shmulevich. 2024. “A Framework towards Digital Twins for Type 2 Diabetes.” Frontiers in Digital Health 6: 1336050. https://doi.org/10.3389/fdgth.2024.1336050. Cite Download

Zhao, Zihao, Chie Amano, Thomas Reinthaler, Mónica V. Orellana, and Gerhard J. Herndl. 2024. “Substrate Uptake Patterns Shape Niche Separation in Marine Prokaryotic Microbiome.” Science Advances 10 (20): eadn5143. https://doi.org/10.1126/sciadv.adn5143. Cite Download