Publications

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2025

Alipour, Ehsan, Samuel Gratzl, Ahmad Algohary, Hao Lin, Manoj Bapat, Duy Do, Charlotte Baker, et al. 2025. “Multimodal Deep Learning Model to Estimate CT-Based Body Composition Measures Using Chest Radiographs and Clinical Data.” medRxiv. https://doi.org/10.1101/2025.01.16.25320684. Cite Download
Baumgartner, Andrew, Max Robinson, Nilufer Ertekin-Taner, Todd E. Golde, Suman Jaydev, Sui Huang, Jennifer Hadlock, and Cory Funk. 2025. “Fokker-Planck Diffusion Maps of Microglial Transcriptomes Reveal Radial Differentiation into Substates Associated with Alzheimer’s Pathology.” Communications Biology 8 (1): 279. https://doi.org/10.1038/s42003-025-07594-y. Cite
Contreras-Moreira, Bruno, Eshan Sharma, Shradha Saraf, Guy Naamati, Parul Gupta, Justin Elser, Dmytro Chebotarov, et al. 2025. “A Pan-Gene Catalogue of Asian Cultivated Rice.” bioRxiv. https://doi.org/10.1101/2025.02.17.638606. Cite Download
Dacon, Cherrelle, Re’em Moskovitz, Kristian Swearingen, Lais Da Silva Pereira, Yevel Flores-Garcia, Maya Aleshnick, Sachie Kanatani, et al. 2025. “Protective Antibodies Target Cryptic Epitope Unmasked by Cleavage of Malaria Sporozoite Protein.” Science (New York, N.Y.) 387 (6729): eadr0510. https://doi.org/10.1126/science.adr0510. Cite
Diener, Christian, Hannah D. Holscher, Klara Filek, Karen D. Corbin, Christine Moissl-Eichinger, and Sean M. Gibbons. 2025. “Metagenomic Estimation of Dietary Intake from Human Stool.” Nature Metabolism. https://doi.org/10.1038/s42255-025-01220-1. Cite Download
Ellrott, Kyle, Christopher K. Wong, Christina Yau, Mauro A. A. Castro, Jordan A. Lee, Brian J. Karlberg, Jasleen K. Grewal, et al. 2025. “Classification of Non-TCGA Cancer Samples to TCGA Molecular Subtypes Using Compact Feature Sets.” Cancer Cell. https://doi.org/10.1016/j.ccell.2024.12.002. Cite
Godsil, Marshall, Nathaniel L. Ritz, Siddarth Venkatesh, and Alexander J. Meeske. 2025. “Gut Phages and Their Interactions with Bacterial and Mammalian Hosts.” Journal of Bacteriology, e0042824. https://doi.org/10.1128/jb.00428-24. Cite
Gupta, Anika, Norma Morella, Dmitry Sutormin, Naisi Li, Karl Gaisser, Alexander Robertson, Yaroslav Ispolatov, Georg Seelig, Neelendu Dey, and Anna Kuchina. 2025. “Combinatorial Phenotypic Landscape Enables Bacterial Resistance to Phage Infection.” bioRxiv. https://doi.org/10.1101/2025.01.13.632860. Cite Download
Gupta, Vishal K., Vijaya V. Vaishnavi, Mario L. Arrieta-Ortiz, Abhirami P.s., Jyothsna K.m., Sharumathi Jeyasankar, Varun Raghunathan, Nitin S. Baliga, and Rachit Agarwal. 2025. “3D Hydrogel Culture System Recapitulates Key Tuberculosis Phenotypes and Demonstrates Pyrazinamide Efficacy.” Advanced Healthcare Materials n/a (n/a): 2304299. https://doi.org/10.1002/adhm.202304299. Cite
Gupta, Anika, Norma Morella, Dmitry Sutormin, Naisi Li, Karl Gaisser, Alexander Robertson, Yaroslav Ispolatov, Georg Seelig, Neelendu Dey, and Anna Kuchina. 2025. “Combinatorial Phenotypic Landscape Enables Bacterial Resistance to Phage Infection.” BioRxiv: The Preprint Server for Biology, 2025.01.13.632860. https://doi.org/10.1101/2025.01.13.632860. Cite Download
Kalyuzhnyy, Anton, Patrick A. Eyers, Claire E. Eyers, Eric W. Deutsch, and Andrew R. Jones. 2025. “Applying a Conservation-Based Approach for Predicting Novel Phosphorylation Sites in Eukaryotes and Evaluating Their Functional Relevance.” bioRxiv. https://doi.org/10.1101/2025.01.09.632054. Cite Download
Mukherjee, Ishita, James H. Park, Anoop P. Patel, and Nitin S. Baliga. 2025. “Transcriptional Mechanisms of Phenotypic Plasticity in Glioblastoma.” Journal of Clinical Oncology 42 (16_suppl): e14027–e14027. https://doi.org/10.1200/JCO.2024.42.16_suppl.e14027. Cite
Qian, Yili, Sarvesh D. Menon, Nick Quinn-Bohmann, Sean M. Gibbons, and Ophelia S. Venturelli. 2025. “A Data-Driven Modeling Framework for Mapping Genotypes to Synthetic Microbial Community Functions.” bioRxiv. https://doi.org/10.1101/2025.01.04.631316. Cite Download
Rios, Kelly T., James P. McGee, Aswathy Sebastian, Sanjaya Aththawala Gedara, Robert L. Moritz, Marina Feric, Sabrina Absalon, Kristian E. Swearingen, and Scott E. Lindner. 2025. “Widespread Release of Translational Repression across Plasmodium’s Host-to-Vector Transmission Event.” PLOS Pathogens 21 (1): e1012823. https://doi.org/10.1371/journal.ppat.1012823. Cite Download
Roach, Jared C., Cory C Funk, Gwênlyn Glusman, David A. Merrill, John F. Hodes, Molly K. Rapozo, Lance Edens, et al. 2025. “Specific Plasma Proteins and Metabolites Convey the Effects of Lifestyle Interventions That Improve Cognition and Function in Alzheimer’s Disease.” Alzheimer’s & Dementia 20 (S7): e091942. https://doi.org/10.1002/alz.091942. Cite Download
Rogina, Blanka, Rozalyn Anderson, Nathan Lebrasseur, Sean Curan, Matthew J. Yousefzadeh, Bhaswati Ghosh, Gustavo Duque, et al. 2025. “Symposia Report of The Annual Biological Sciences Section Meeting of the Gerontological Society of America 2023, Tampa, Florida.” The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences, glaf026. https://doi.org/10.1093/gerona/glaf026. Cite
Shah, Dimpy P., Tanayott Thaweethai, Elizabeth W. Karlson, Hector Bonilla, Benjamin D. Horne, Janet M. Mullington, Juan P. Wisnivesky, et al. 2025. “Sex Differences in Long COVID.” JAMA Network Open 8 (1): e2455430. https://doi.org/10.1001/jamanetworkopen.2024.55430. Cite Download
Spector, Lauren, and Naeha Subramanian. 2025. “Revealing the Dance of NLRP3: Spatiotemporal Patterns in Inflammasome Activation.” Immunometabolism 7 (1): e00053. https://doi.org/10.1097/IN9.0000000000000053. Cite
Stankiewicz, Kathryn H., Jacob J. Valenzuela, Serdar Turkarslan, Wei-Ju Wu, Kelly Gomez-Campo, Nicolas S. Locatelli, Trinity L. Conn, et al. 2025. “Heat-Responsive Dynamic Shifts in Alternative Splicing of the Coral Acropora Cervicornis.” bioRxiv. https://doi.org/10.1101/2025.01.21.634199. Cite Download
Stankiewicz, Kathryn H., Nadège Guiglielmoni, Sheila A. Kitchen, Jean-François Flot, Katie L. Barott, Sarah W. Davies, John R. Finnerty, et al. 2025. “Genomic Comparison of the Temperate Coral Astrangia Poculata with Tropical Corals Yields Insights into Winter Quiescence, Innate Immunity, and Sexual Reproduction.” G3 (Bethesda, Md.), jkaf033. https://doi.org/10.1093/g3journal/jkaf033. Cite Download
Sun, Yingying, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, et al. 2025. “Strategic Priorities for Transformative Progress in Advancing Biology with Proteomics and Artificial Intelligence.” arXiv. https://doi.org/10.48550/arXiv.2502.15867. Cite Download
Tang, Gechlang, Alex V. Carr, Crystal Perez, Katherine Ramos Sarmiento, Lisa Levy, Johanna W. Lampe, Christian Diener, and Sean M. Gibbons. 2025. “Metagenomic Estimation of Absolute Bacterial Biomass in the Mammalian Gut through Host-Derived Read Normalization.” bioRxiv. https://doi.org/10.1101/2025.01.07.631807. Cite Download
Tzvetkov, Jordan, Claire E. Eyers, Patrick A. Eyers, Kerry A. Ramsbottom, Sally O. Oswald, John A. Harris, Zhi Sun, Eric W. Deutsch, and Andrew R. Jones. 2025. “Searching for Sulfotyrosines (SY) in a HA(PY)STACK.” bioRxiv. https://doi.org/10.1101/2024.10.14.618131. Cite Download
Tzvetkov, Jordan, Claire E. Eyers, Patrick A. Eyers, Kerry A. Ramsbottom, Sally O. Oswald, John A. Harris, Zhi Sun, Eric W. Deutsch, and Andrew R. Jones. 2025. “Searching for Sulfotyrosines (SY) in a HA(PY)STACK.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.4c00907. Cite
Wacholder, Aaron, Eric W. Deutsch, Leron W. Kok, Jip T. van Dinter, Jiwon Lee, James C. Wright, Sebastien Leblanc, et al. 2025. “Detection of Human Unannotated Microproteins by Mass Spectrometry-Based Proteomics: A Community Assessment.” bioRxiv. https://doi.org/10.1101/2025.02.19.639069. Cite Download
Xie, Jingyi, Daniel G. Chen, William Chour, Rachel H. Ng, Rongyu Zhang, Dan Yuan, Jongchan Choi, et al. 2025. “APMAT Analysis Reveals the Association between CD8 T Cell Receptors, Cognate Antigen, and T Cell Phenotype and Persistence.” bioRxiv. https://doi.org/10.1101/2025.01.08.631993. Cite Download
Xie, Jingyi, Daniel G. Chen, William Chour, Rachel H. Ng, Rongyu Zhang, Dan Yuan, Jongchan Choi, et al. 2025. “APMAT Analysis Reveals the Association between CD8 T Cell Receptors, Cognate Antigen, and T Cell Phenotype and Persistence.” Nature Communications 16 (1): 1402. https://doi.org/10.1038/s41467-025-56659-3. Cite
Zaslavsky, Maxim E., Erin Craig, Jackson K. Michuda, Nidhi Sehgal, Nikhil Ram-Mohan, Ji-Yeun Lee, Khoa D. Nguyen, et al. 2025. “Disease Diagnostics Using Machine Learning of B Cell and T Cell Receptor Sequences.” Science (New York, N.Y.) 387 (6736): eadp2407. https://doi.org/10.1126/science.adp2407. Cite
Zhu, Dantong, Judy Z. Wu, Patrick Griffin, Brady A. Samuelson, David A. Sinclair, and Alice E. Kane. 2025. “Metabolomics Biomarkers of Frailty: A Longitudinal Study of Aging Female and Male Mice.” bioRxiv. https://doi.org/10.1101/2025.01.22.634160. Cite Download
Zhu, Dantong, Judy Z. Wu, Patrick Griffin, Brady A. Samuelson, David A. Sinclair, and Alice E. Kane. 2025. “Metabolomics Biomarkers of Frailty: A Longitudinal Study of Aging Female and Male Mice.” BioRxiv: The Preprint Server for Biology, 2025.01.22.634160. https://doi.org/10.1101/2025.01.22.634160. Cite