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2025

2323737 2RQKSFR5 2025 1 chicago-author-date 50 creator asc 1 1 319 https://isbscience.org/wp-content/plugins/zotpress/

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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

Byrne, Audrey, Christian Diener, Bryan P. Brown, Brandon S. Maust, Colin Feng, Berenice L. Alinde, Sean M. Gibbons, et al. 2024. “Neonates Exposed to HIV but Uninfected Exhibit an Altered Gut Microbiota and Inflammation Associated with Impaired Breast Milk Antibody Function.” Microbiome 12 (1): 261. https://doi.org/10.1186/s40168-024-01973-z. Cite Download

Camacho, Oscar J. M., Kerry A. Ramsbottom, Ananth Prakash, Zhi Sun, Yasset Perez Riverol, Emily Bowler-Barnett, Maria Martin, et al. 2024. “Phosphorylation in the Plasmodium Falciparum Proteome: A Meta-Analysis of Publicly Available Data Sets.” Journal of Proteome Research 23 (12): 5326–41. https://doi.org/10.1021/acs.jproteome.4c00418. 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

Chen, Xinyi, Yapeng Su, Chloe Dai, Jason D. Goldman, James R. Heath, Si Liu, and Wei Sun. 2024. “Association between COVID-19 Disease Severity and T Cell Receptor Repertoire.” bioRxiv. https://doi.org/10.1101/2024.11.26.625333. 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

Deutsch, Eric W., Leron W. Kok, Jonathan M. Mudge, Jorge Ruiz-Orera, Ivo Fierro-Monti, Zhi Sun, Jennifer G. Abelin, et al. 2024. “High-Quality Peptide Evidence for Annotating Non-Canonical Open Reading Frames as Human Proteins.” BioRxiv: The Preprint Server for Biology, 2024.09.09.612016. https://doi.org/10.1101/2024.09.09.612016. 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

Dirvin, Brooke, Heeju Noh, Lorenzo Tomassoni, Danting Cao, Yizhuo Zhou, Xiangyi Ke, Jun Qian, et al. 2024. “Identification and Targeting of Regulators of SARS-CoV-2-Host Interactions in the Airway Epithelium.” BioRxiv: The Preprint Server for Biology, 2024.10.11.617898. https://doi.org/10.1101/2024.10.11.617898. 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

Firsanov, Denis, Max Zacher, Xiao Tian, Todd L. Sformo, Yang Zhao, Greg Tombline, J. Yuyang Lu, et al. 2024. “DNA Repair and Anti-Cancer Mechanisms in the Long-Lived Bowhead Whale.” BioRxiv: The Preprint Server for Biology, 2023.05.07.539748. https://doi.org/10.1101/2023.05.07.539748. Cite Download

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

Funk, Cory C., Martin Darvas, Christine Johnston, Max Robinson, Caitlyn Schaffer, Christian Battaglia, Martine Aubert, and Jesse C. Wiley. 2024. “Basic Science and Pathogenesis.” Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association 20 Suppl 1:e093497. https://doi.org/10.1002/alz.093497. Cite

Funk, Cory C., Tom Paterson, Jennifer Rohrs, and Timothy J. Hohman. 2024. “Basic Science and Pathogenesis.” Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association 20 Suppl 1:e092897. https://doi.org/10.1002/alz.092897. Cite

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

Geng, Linda N., Kristine M. Erlandson, Mady Hornig, Rebecca Letts, Caitlin Selvaggi, Hassan Ashktorab, Ornina Atieh, et al. 2024. “2024 Update of the RECOVER-Adult Long COVID Research Index.” JAMA. https://doi.org/10.1001/jama.2024.24184. Cite

Geyer, Philipp E., Daniel Hornburg, Maria Pernemalm, Stefanie M. Hauck, Krishnan K. Palaniappan, Vincent Albrecht, Laura F. Dagley, et al. 2024. “The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends.” Journal of Proteome Research 23 (12): 5279–95. https://doi.org/10.1021/acs.jproteome.4c00586. Cite

Goetz, Skye L., Amy K. Glen, and Gwênlyn Glusman. 2024. “MicrobiomeKG: Bridging Microbiome Research and Host Health Through Knowledge Graphs.” BioRxiv: The Preprint Server for Biology, 2024.10.10.617697. https://doi.org/10.1101/2024.10.10.617697. 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

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

He, Fuchu, Ruedi Aebersold, Mark S. Baker, Xiuwu Bian, Xiaochen Bo, Daniel W. Chan, Cheng Chang, et al. 2024. “π-HuB: The Proteomic Navigator of the Human Body.” Nature 636 (8042): 322–31. https://doi.org/10.1038/s41586-024-08280-5. Cite

He, Fuchu, Ruedi Aebersold, Mark S. Baker, Xiuwu Bian, Xiaochen Bo, Daniel W. Chan, Cheng Chang, et al. 2024. “Author Correction: π-HuB: The Proteomic Navigator of the Human Body.” Nature. https://doi.org/10.1038/s41586-024-08555-x. Cite

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

Kader, Tanjina, Jia-Ren Lin, Clemens B. Hug, Shannon Coy, Yu-An Chen, Ino de Bruijn, Natalie Shih, et al. 2024. “Multimodal Spatial Profiling Reveals Immune Suppression and Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma.” Cancer Discovery. https://doi.org/10.1158/2159-8290.CD-24-1366. Cite

Kane, Alice. 2024. “TRANSLATIONAL BIOMARKERS FOR AGING AND FRAILTY: IMPORTANT SEX DIFFERENCES.” Innovation in Aging 8 (Suppl 1): 504. https://doi.org/10.1093/geroni/igae098.1645. Cite Download

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

Klein, Joshua, Henry Lam, Tytus D. Mak, Wout Bittremieux, Yasset Perez-Riverol, Ralf Gabriels, Jim Shofstahl, et al. 2024. “The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: MzSpecLib and MzPAF.” Analytical Chemistry 96 (46): 18491–501. https://doi.org/10.1021/acs.analchem.4c04091. 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

Kumari, Suman, Christopher Lausted, Kelsey Scherler, Alphonsus H. C. Ng, Yue Lu, Inyoul Lee, Leroy Hood, and Kai Wang. 2024. “Approaches and Challenges in Characterizing the Molecular Content of Extracellular Vesicles for Biomarker Discovery.” Biomolecules 14 (12): 1599. https://doi.org/10.3390/biom14121599. Cite Download

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

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