Publications

  • 2025
  • 2024
  • 2023
  • 2022
  • 2021
  • 2020
  • 2019
  • 2018
  • 2017
  • 2016
  • 2015
  • 2014
  • 2013
  • 2012
  • 2011
  • 2010
  • 2009
  • 2008
  • 2007
  • 2006
  • 2005
  • 2004
  • 2003
  • 2002
  • 2001
  • 2000

Loading…

2025

Alcindor, Thierry, James Tankel, Pierre-Olivier Fiset, Sanjima Pal, Touhid Opu, Michael Strasser, Mehrnoush Dehghani, et al. 2025. “Phase 2 Trial of Perioperative Chemo-Immunotherapy for Gastro-Esophageal Adenocarcinoma: The Role of M2 Macrophage Landscape in Predicting Response.” Cell Reports. Medicine 6 (4): 102045. https://doi.org/10.1016/j.xcrm.2025.102045. Cite
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
Arias-Gaguancela, Omar, Carmen Palii, Mehar Un Nissa, Marjorie Brand, and Jeff Ranish. 2025. “QuickProt: A Bioinformatics and Visualization Tool for DIA and PRM Mass Spectrometry-Based Proteomics Datasets.” BioRxiv: The Preprint Server for Biology, 2025.03.24.645047. https://doi.org/10.1101/2025.03.24.645047. Cite
Armstrong, Sujit Silas, Daniel G. Chen, Sunil Kumar, James R. Heath, Matthew J. Feinstein, John R. Greenland, Daniel R. Calabrese, Lewis L. Lanier, Klaus Ley, and Avishai Shemesh. 2025. “CITE-Seq Analysis Reveals a Differential Natural Killer Cell SPON2 Expression in Cardiovascular Disease Patients Impacted by Human-Cytomegalovirus Serostatus and Diabetes.” International Journal of Molecular Sciences 26 (3): 1369. https://doi.org/10.3390/ijms26031369. Cite Download
Baliga, Nitin, Kathryn Stankiewicz, Jacob Valenzuela, Serdar Turkarslan, Wei-Ju Wu, Kelly Gomez-Campo, Nicolas Locatelli, et al. 2025. “Alternative Splicing in a Coral during Heat Stress Acclimation and Recovery.” Research Square. https://doi.org/10.21203/rs.3.rs-6025431/v1. 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
Carr, Alex V., Anne E. Otwell, Kristopher A. Hunt, Yan Chen, James Wilson, José P. Faria, Filipe Liu, et al. 2025. “Emergence and Disruption of Cooperativity in a Denitrifying Microbial Community.” The ISME Journal 19 (1): wraf093. https://doi.org/10.1093/ismejo/wraf093. Cite
Cavon, Jacob, Melissa Basso, Kathrin Cohen Kadosh, and Sean M Gibbons. 2025. “The Human Gut Microbiome and Sleep across Adulthood: Associations and Therapeutic Potential.” Letters in Applied Microbiology, ovaf043. https://doi.org/10.1093/lambio/ovaf043. Cite Download
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
Bruijn, Ino de, Milen Nikolov, Clarisse Lau, Ashley Clayton, David L. Gibbs, Elvira Mitraka, Dar’ya Pozhidayeva, et al. 2025. “Sharing Data from the Human Tumor Atlas Network through Standards, Infrastructure and Community Engagement.” Nature Methods 22 (4): 664–71. https://doi.org/10.1038/s41592-025-02643-0. Cite
Deutsch, Eric W., Luis Mendoza, and Robert L. Moritz. 2025. “Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.5c00092. 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
Dirvin, Brooke, Heeju Noh, Lorenzo Tomassoni, Danting Cao, Yizhuo Zhou, Xiangyi Ke, Jun Qian, et al. 2025. “Identification and Targeting of Regulators of SARS-CoV-2-Host Interactions in the Airway Epithelium.” Science Advances 11 (20): eadu2079. https://doi.org/10.1126/sciadv.adu2079. Cite
Ellis, Dylan, Kengo Watanabe, Tomasz Wilmanski, Michael S. Lustgarten, Andres V. Ardisson Korat, Gwênlyn Glusman, Jennifer Hadlock, et al. 2025. “APOE Genotype and Biological Age Impact Inter-Omic Associations Related to Bioenergetics.” Aging 17 (5): 1105–38. https://doi.org/10.18632/aging.206243. 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
Flower, Cameron T., Chunmei Liu, Hui-Yu Chuang, Xiaoyang Ye, Hanjun Cheng, James R. Heath, Wei Wei, and Forest M. White. 2025. “Signaling and Transcriptional Dynamics Underlying Early Adaptation to Oncogenic BRAF Inhibition.” Cell Systems, 101239. https://doi.org/10.1016/j.cels.2025.101239. Cite
Freidin, Maxim B., and Jared C. Roach. 2025. “Editorial: A Year in Review: Discussions in Human and Medical Genomics.” Frontiers in Genetics 16:1618183. https://doi.org/10.3389/fgene.2025.1618183. Cite
Geng, Linda N., Kristine M. Erlandson, Mady Hornig, Rebecca Letts, Caitlin Selvaggi, Hassan Ashktorab, Ornina Atieh, et al. 2025. “2024 Update of the RECOVER-Adult Long COVID Research Index.” JAMA. https://doi.org/10.1001/jama.2024.24184. Cite
Gilbert, Jack A., Meghan B. Azad, Fredrik Bäckhed, Martin J. Blaser, Mariana Byndloss, Charles Y. Chiu, Hiutung Chu, et al. 2025. “Clinical Translation of Microbiome Research.” Nature Medicine, 1–15. https://doi.org/10.1038/s41591-025-03615-9. Cite
Glen, Amy K., Eric W. Deutsch, and Stephen A. Ramsey. 2025. “PloverDB: A High-Performance Platform for Serving Biomedical Knowledge Graphs as Standards-Compliant Web APIs.” BioRxiv: The Preprint Server for Biology, 2025.03.09.642156. https://doi.org/10.1101/2025.03.09.642156. 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
Gomez-Artiguez, Leticia, Samuel de la Cámara-Fuentes, Zhi Sun, María Luisa Hernáez, Ana Borrajo, Aída Pitarch, Gloria Molero, et al. 2025. “Candida Albicans: A Comprehensive View of the Proteome.” Journal of Proteome Research 24 (4): 1636–48. https://doi.org/10.1021/acs.jproteome.4c01020. Cite Download
Grewal, Jasleen K., A. Gordon Robertson, Kyle Ellrott, Christopher K. Wong, Jordan A. Lee, Christina Yau, Bahar Tercan, et al. 2025. “Protocol for Obtaining Cancer Type and Subtype Predictions Using SubSCOPE.” STAR Protocols 6 (2): 103705. https://doi.org/10.1016/j.xpro.2025.103705. 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
Heath, James R., and RECOVERY Collaborative Group. 2025. “Higher Dose Corticosteroids in Patients Admitted to Hospital with COVID-19 Who Are Hypoxic but Not Requiring Ventilatory Support (RECOVERY): A Randomised, Controlled, Open-Label, Platform Trial.” Lancet (London, England) 401 (10387): 1499–1507. https://doi.org/10.1016/S0140-6736(23)00510-X. Cite Download
Huang, Sui, Ana M. Soto, and Carlos Sonnenschein. 2025. “The End of the Genetic Paradigm of Cancer.” PLOS Biology 23 (3): e3003052. https://doi.org/10.1371/journal.pbio.3003052. Cite Download
Hwang, Yeon-Mi, Jennifer M. Hah, Jennifer E. Bramen, Jennifer J. Hadlock, and Tina Hernandez-Boussard. 2025. “Short-Term Mortality after Opioid Initiation among Opioid-Naïve and Non-Naïve Patients with Dementia: A Retrospective Cohort Study.” BMC Medicine 23 (1): 340. https://doi.org/10.1186/s12916-025-04172-1. 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
Murie, Carl, Serdar Turkarslan, Anoop P. Patel, David G. Coffey, Pamela S. Becker, and Nitin S. Baliga. 2025. “Individualized Dynamic Risk Assessment and Treatment Selection for Multiple Myeloma.” British Journal of Cancer, 1–15. https://doi.org/10.1038/s41416-025-02987-6. Cite
Nolan, Sean, Marissa Vignali, Mark Klinger, Jennifer N. Dines, Ian M. Kaplan, Emily Svejnoha, Tracy Craft, et al. 2025. “A Large-Scale Database of T-Cell Receptor Beta Sequences and Binding Associations from Natural and Synthetic Exposure to SARS-CoV-2.” Frontiers in Immunology 16:1488851. https://doi.org/10.3389/fimmu.2025.1488851. Cite Download
Paterson, Tom, Jennifer Rohrs, Timothy J. Hohman, Mark Mapstone, Peter J. Meikle, Rima Kaddurah-Daouk, Allan I. Levey, et al. 2025. “Multiomic Evidence for a Unified Model of Alzheimer’s Disease Etiology Linking Microglial Flux Capacity and Astrocyte-Neuron Metabolic Breakdown.” BioRxiv, 2024.07.23.604835. https://doi.org/10.1101/2024.07.23.604835. Cite Download
Pearl, Jocelynn R., Amol C. Shetty, Jeffrey P. Cantle, Dani E. Bergey, Robert M. Bragg, Sydney R. Coffey, Holly B. Kordasiewicz, et al. 2025. “Altered Huntingtin-Chromatin Interactions Predict Transcriptional and Epigenetic Changes in Huntington’s Disease Mouse Models.” Disease Models & Mechanisms, dmm.052282. https://doi.org/10.1242/dmm.052282. 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
Qualls, Anita E., Tasha Tsao, Irene Lui, Shion A. Lim, Yapeng Su, Ernie Chen, Dylan Duchen, et al. 2025. “High Affinity CD16 Polymorphism Associated with Reduced Risk of Severe COVID-19.” JCI Insight, e191314. https://doi.org/10.1172/jci.insight.191314. Cite
Quinn-Bohmann, Nick, Alex V. Carr, Christian Diener, and Sean M. Gibbons. 2025. “Moving from Genome-Scale to Community-Scale Metabolic Models for the Human Gut Microbiome.” Nature Microbiology, 1–12. https://doi.org/10.1038/s41564-025-01972-2. Cite
Riffle, Michael, Alex Zelter, Daniel Jaschob, Michael R. Hoopmann, Danielle A. Faivre, Robert L. Moritz, Trisha N. Davis, Michael J. MacCoss, and Nina Isoherranen. 2025. “Limelight: An Open, Web-Based Tool for Visualizing, Sharing, and Analyzing Mass Spectrometry Data from DDA Pipelines.” Journal of Proteome Research 24 (4): 1895–1906. https://doi.org/10.1021/acs.jproteome.4c00968. Cite
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
Sadée, Christoph, Stefano Testa, Thomas Barba, Katherine Hartmann, Maximilian Schuessler, Alexander Thieme, George M. Church, et al. 2025. “Medical Digital Twins: Enabling Precision Medicine and Medical Artificial Intelligence.” The Lancet. Digital Health, 100864. https://doi.org/10.1016/j.landig.2025.02.004. 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
Snyder, Thomas M., Rachel M. Gittelman, Mark Klinger, Damon H. May, Edward J. Osborne, Ruth Taniguchi, H. Jabran Zahid, et al. 2025. “Magnitude and Dynamics of the T-Cell Response to SARS-CoV-2 Infection at Both Individual and Population Levels.” Frontiers in Immunology 15:1488860. https://doi.org/10.3389/fimmu.2024.1488860. Cite
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