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

Hwang, Yeon Mi, Samantha N. Piekos, Alison G. Paquette, Qi Wei, Nathan D. Price, Leroy Hood, and Jennifer J. Hadlock. 2024. “Accelerating Adverse Pregnancy Outcomes Research amidst Rising Medication Use: Parallel Retrospective Cohort Analyses for Signal Prioritization.” BMC Medicine 22 (1): 495. https://doi.org/10.1186/s12916-024-03717-0. 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

Kopp, Audrey, Mehar Un Nissa, Roberta Dollinger, Jeff Ranish, and Marjorie Brand. 2024. “3106 – PROTEOMICS AND GENOMICS STUDIES REVEALED A NEW ROLE FOR MLL PARTIAL TANDEM DUPLICATION (PTD) IN MYELODYSPLASTIC SYNDROME (MDS) AND ACUTE MYELOID LEUKEMIA (AML).” Experimental Hematology, SUPP:EXPHEM Abstracts 2024, 137:104428. https://doi.org/10.1016/j.exphem.2024.104428. Cite

Kornilov, Sergey A., Nathan D. Price, Richard Gelinas, Juan Acosta, Mary E. Brunkow, Tiffany Gervasi-Follmar, Ryan C. Winger, et al. 2024. “Multi-Omic Characterization of the Effects of Ocrelizumab in Patients with Relapsing-Remitting Multiple Sclerosis.” Journal of the Neurological Sciences 467:123303. https://doi.org/10.1016/j.jns.2024.123303. Cite

L Rocha, Heber, Boris Aguilar, Michael Getz, Ilya Shmulevich, and Paul Macklin. 2024. “A Multiscale Model of Immune Surveillance in Micrometastases Gives Insights on Cancer Patient Digital Twins.” NPJ Systems Biology and Applications 10 (1): 144. https://doi.org/10.1038/s41540-024-00472-z. 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

Luo, Jie, and Jeff Ranish. 2024. “Isobaric Crosslinking Mass Spectrometry Technology for Studying Conformational and Structural Changes in Proteins and Complexes.” ELife 13. https://doi.org/10.7554/eLife.99809.2. 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

Mo, Chia-Kuei, Jingxian Liu, Siqi Chen, Erik Storrs, Andre Luiz N. Targino da Costa, Andrew Houston, Michael C. Wendl, et al. 2024. “Tumour Evolution and Microenvironment Interactions in 2D and 3D Space.” Nature 634 (8036): 1178–86. https://doi.org/10.1038/s41586-024-08087-4. Cite Download

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