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

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

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

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, 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 0 (0). https://doi.org/10.1016/j.eclinm.2024.102435. Cite Download

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

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: The Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians 37 (1): 2313364. https://doi.org/10.1080/14767058.2024.2313364. 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, April, S1550-4131(24)00091-3. https://doi.org/10.1016/j.cmet.2024.03.012. 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

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

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, April, OF1–13. https://doi.org/10.1158/1078-0432.CCR-23-1674. Cite

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

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

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

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