Publications

Aguilar, Boris, Kawther Abdilleh, and George K. Acquaah-Mensah. 2023. “Multi-Omics Inference of Differential Breast Cancer-Related Transcriptional Regulatory Network Gene Hubs between Young Black and White Patients.” Cancer Genetics 270–271: 1–11. https://doi.org/10.1016/j.cancergen.2022.11.001. Cite

Akhade, Ajay Suresh, and Naeha Subramanian. 2023. “Cytoplasmic Sensing in Innate Immunity.” In Encyclopedia of Cell Biology (Second Edition), edited by Ralph A. Bradshaw, Gerald W. Hart, and Philip D. Stahl, 624–43. Oxford: Academic Press. https://doi.org/10.1016/B978-0-12-821618-7.00012-2. Cite

Arrieta-Ortiz, Mario L., Min Pan, Amardeep Kaur, Evan Pepper-Tunick, Vivek Srinivas, Ananya Dash, Selva Rupa Christinal Immanuel, Aaron N. Brooks, Tyson R. Shepherd, and Nitin S. Baliga. 2023. “Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia Coli.” MSystems 8 (1): e0090422. https://doi.org/10.1128/msystems.00904-22. Cite Download

Barak, Oren, Tyler Lovelace, Samantha Piekos, Tianjiao Chu, Zhishen Cao, Elena Sadovsky, Jean-Francois Mouillet, et al. 2023. “Integrated Unbiased Multiomics Defines Disease-Independent Placental Clusters in Common Obstetrical Syndromes.” BMC Medicine 21 (1): 349. https://doi.org/10.1186/s12916-023-03054-8. Cite

Bohmann, Nick, Tomasz Wilmanski, Lisa Levy, Johanna W. Lampe, Thomas Gurry, Noa Rappaport, Christian Diener, and Sean M. Gibbons. 2023. “Microbial Community-Scale Metabolic Modeling Predicts Personalized Short-Chain-Fatty-Acid Production Profiles in the Human Gut.” bioRxiv. https://doi.org/10.1101/2023.02.28.530516. Cite Download

Boniolo, Fabio, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A. Gordon Robertson, Dieter Saur, and Markus List. 2023. “SpongEffects: CeRNA Modules Offer Patient-Specific Insights into the MiRNA Regulatory Landscape.” Bioinformatics (Oxford, England) 39 (5): btad276. https://doi.org/10.1093/bioinformatics/btad276. Cite Download

Bramen, Jennifer E., Prabha Siddarth, Emily S. Popa, Gavin T. Kress, Molly K. Rapozo, John F. Hodes, Aarthi S. Ganapathi, et al. 2023. “Impact of Eating a Carbohydrate-Restricted Diet on Cortical Atrophy in a Cross-Section of Amyloid Positive Patients with Alzheimer’s Disease: A Small Sample Study.” Journal of Alzheimer’s Disease: JAD. https://doi.org/10.3233/JAD-230458. Cite Download

Burns, Adam R., Jack Wiedrick, Alicia Feryn, Michal Maes, Mukul K. Midha, David H. Baxter, Seamus R. Morrone, et al. 2023. “Proteomic Changes Induced by Longevity-Promoting Interventions in Mice.” GeroScience. https://doi.org/10.1007/s11357-023-00917-z. Cite

Carr, Alex, Nitin S. Baliga, Christian Diener, and Sean M. Gibbons. 2023. “Personalized Clostridioides Difficile Engraftment Risk Prediction and Probiotic Therapy Assessment in the Human Gut.” BioRxiv: The Preprint Server for Biology, 2023.04.28.538771. https://doi.org/10.1101/2023.04.28.538771. Cite Download

Cheng, Hanjun, Yin Tang, Zhonghan Li, Zhili Guo, James R. Heath, Min Xue, and Wei Wei. 2023. “Non-Mass Spectrometric Targeted Single-Cell Metabolomics.” Trends in Analytical Chemistry: TRAC 168: 117300. https://doi.org/10.1016/j.trac.2023.117300. Cite

Chour, William, Jongchan Choi, Jingyi Xie, Mary E. Chaffee, Thomas M. Schmitt, Kathryn Finton, Diana C. DeLucia, et al. 2023. “Large Libraries of Single-Chain Trimer Peptide-MHCs Enable Antigen-Specific CD8+ T Cell Discovery and Analysis.” Communications Biology 6 (1): 528. https://doi.org/10.1038/s42003-023-04899-8. Cite Download

Christmas, Matthew J., Irene M. Kaplow, Diane P. Genereux, Michael X. Dong, Graham M. Hughes, Xue Li, Patrick F. Sullivan, et al. 2023. “Evolutionary Constraint and Innovation across Hundreds of Placental Mammals.” Science (New York, N.Y.) 380 (6643): eabn3943. https://doi.org/10.1126/science.abn3943. Cite Download

Cyriaque, Valentine, Rodrigo Ibarra-Chávez, Anna Kuchina, Georg Seelig, Joseph Nesme, and Jonas Madsen. 2023. “Single-Cell RNA Sequencing Suggests Plasmids Constrain Bacterial Heterogeneity and Conjugation Is Subpopulation Specific.” Preprint. In Review. https://doi.org/10.21203/rs.3.rs-3405585/v1. Cite Download

Deutsch, Eric W, Nuno Bandeira, Yasset Perez-Riverol, Vagisha Sharma, Jeremy J Carver, Luis Mendoza, Deepti J Kundu, et al. 2023. “The ProteomeXchange Consortium at 10 Years: 2023 Update.” Nucleic Acids Research 51 (D1): D1539–48. https://doi.org/10.1093/nar/gkac1040. Cite Download

Deutsch, Eric W., Juan Antonio Vizcaíno, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, et al. 2023. “Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.” Journal of Proteome Research 22 (2): 287–301. https://doi.org/10.1021/acs.jproteome.2c00637. Cite Download

Deutsch, Eric W., Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, and Robert L. Moritz. 2023. “Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.” Journal of Proteome Research 22 (2): 615–24. https://doi.org/10.1021/acs.jproteome.2c00624. Cite

Diener, Christian, and Sean M. Gibbons. 2023. “More Is Different: Metabolic Modeling of Diverse Microbial Communities.” MSystems, e0127022. https://doi.org/10.1128/msystems.01270-22. Cite

Diener, Christian, and Sean M. Gibbons. 2023. “Coarse Graining the Human Gut Microbiome.” Cell Host & Microbe 31 (7): 1076–78. https://doi.org/10.1016/j.chom.2023.06.001. Cite

Doty, Raymond T., Christopher G. Lausted, Adam D. Munday, Zhantao Yang, Xiaowei Yan, Changting Meng, Qiang Tian, and Janis L. Abkowitz. 2023. “The Transcriptomic Landscape of Normal and Ineffective Erythropoiesis at Single-Cell Resolution.” Blood Advances 7 (17): 4848–68. https://doi.org/10.1182/bloodadvances.2023010382. Cite Download

Echlin, Moriah, Boris Aguilar, and Ilya Shmulevich. 2023. “Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model.” Entropy (Basel, Switzerland) 25 (2): 319. https://doi.org/10.3390/e25020319. Cite Download

Fang, Hai, Liye Chen, Leroy Hood, and Qiang Tian. 2023. “Editorial: Translational Phenomics and Its Applications in Immunotherapy.” Frontiers in Immunology 14: 1211704. https://doi.org/10.3389/fimmu.2023.1211704. Cite Download

Fecho, Karamarie, Chris Bizon, Tursynay Issabekova, Sierra Moxon, Anne E. Thessen, Shervin Abdollahi, Sergio E. Baranzini, et al. 2023. “An Approach for Collaborative Development of a Federated Biomedical Knowledge Graph-Based Question-Answering System: Question-of-the-Month Challenges.” Journal of Clinical and Translational Science 7 (1): e214. https://doi.org/10.1017/cts.2023.619. Cite Download

Finton, Kathryn A. K., Peter B. Rupert, Della J. Friend, Ana Dinca, Erica S. Lovelace, Matthew Buerger, Domnita V. Rusnac, et al. 2023. “Effects of HLA Single Chain Trimer Design on Peptide Presentation and Stability.” Frontiers in Immunology 14: 1170462. https://doi.org/10.3389/fimmu.2023.1170462. Cite Download

Flower, Cameron T., Chunmei Liu, James R. Heath, Wei Wei, and Forest M. White. 2023. “Abstract 4876: A Systems Pharmacology Approach to Discover Synergistic Targeted Therapy Combinations.” Cancer Research 83 (7_Supplement): 4876. https://doi.org/10.1158/1538-7445.AM2023-4876. Cite

Foy, Susan, Cliff Wang, Benjamin Yuen, Sara Said, Boi Quach, Jonathan Hoover, Saparya Nayak, et al. 2023. “Abstract 901: Monitoring of Neoantigens and Adoptively Transferred Personalized NeoTCR T Cell Populations in the Tumor and PBMCs of Patients with Solid Tumors.” Cancer Research 83 (7_Supplement): 901. https://doi.org/10.1158/1538-7445.AM2023-901. Cite

Glen, Amy K., Chunyu Ma, Luis Mendoza, Finn Womack, E. C. Wood, Meghamala Sinha, Liliana Acevedo, et al. 2023. “ARAX: A Graph-Based Modular Reasoning Tool for Translational Biomedicine.” Bioinformatics (Oxford, England) 39 (3): btad082. https://doi.org/10.1093/bioinformatics/btad082. Cite Download

Gorman, Chris, Davide Punzo, Igor Octaviano, Steven Pieper, William J. R. Longabaugh, David A. Clunie, Ron Kikinis, Andrey Y. Fedorov, and Markus D. Herrmann. 2023. “Interoperable Slide Microscopy Viewer and Annotation Tool for Imaging Data Science and Computational Pathology.” Nature Communications 14 (1): 1572. https://doi.org/10.1038/s41467-023-37224-2. Cite Download

Halder, Ankit, Deeptarup Biswas, Aparna Chauhan, Adrita Saha, Shreeman Auromahima, Deeksha Yadav, Mehar Un Nissa, et al. 2023. “A Large-Scale Targeted Proteomics of Serum and Tissue Shows the Utility of Classifying High Grade and Low Grade Meningioma Tumors.” Clinical Proteomics 20 (1): 41. https://doi.org/10.1186/s12014-023-09426-9. Cite Download

Happel, Anna-Ursula, Lerato Rametse, Brandon Perumaul, Christian Diener, Sean M. Gibbons, Donald D. Nyangahu, Kirsten A. Donald, Clive Gray, and Heather B. Jaspan. 2023. “Bifidobacterium Infantis Supplementation versus Placebo in Early Life to Improve Immunity in Infants Exposed to HIV: A Protocol for a Randomized Trial.” BMC Complementary Medicine and Therapies 23 (1): 367. https://doi.org/10.1186/s12906-023-04208-0. Cite Download

Heath, James, Daniel Chen, Jingyi Xie, Jongchan Choi, Rachel Ng, Rongyu Zhang, Sarah Li, et al. 2023. “An NKG2A Biased Immune Response Confers Protection for Infection, Autoimmune Disease, and Cancer.” Preprint. In Review. https://doi.org/10.21203/rs.3.rs-3413673/v1. Cite Download

Heilig, Roland, Ralph Eckenberg, Jean-Louis Petit, Núria Fonknechten, Corinne Da Silva, Laurence Cattolico, Michaël Levy, et al. 2023. “Publisher Correction: The DNA Sequence and Analysis of Human Chromosome 14.” Nature. https://doi.org/10.1038/s41586-023-06403-y. Cite

Hochberg, Jessica T., Aalam Sohal, Priya Handa, Bryan D. Maliken, Take-Kyun Kim, Kai Wang, Eric Gochanour, et al. 2023. “Serum MiRNA Profiles Are Altered in Patients with Primary Sclerosing Cholangitis Receiving High-Dose Ursodeoxycholic Acid.” JHEP Reports: Innovation in Hepatology 5 (6): 100729. https://doi.org/10.1016/j.jhepr.2023.100729. Cite Download

Hood, Leroy, and Scott Penberthy. 2023. “‘We’re Doing It Wrong!’ Phenomics and Hyperscale AI for Health Care.” AI in Precision Oncology, 6–7. https://doi.org/10.1089/aipo.2023.29001.lho. Cite Download

Hoopmann, Michael R., David D. Shteynberg, Alex Zelter, Michael Riffle, Andrew S. Lyon, David A. Agard, Qing Luan, et al. 2023. “Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00670. Cite

Horwitz, Leora I., Tanayott Thaweethai, Shari B. Brosnahan, Mine S. Cicek, Megan L. Fitzgerald, Jason D. Goldman, Rachel Hess, et al. 2023. “Researching COVID to Enhance Recovery (RECOVER) Adult Study Protocol: Rationale, Objectives, and Design.” PloS One 18 (6): e0286297. https://doi.org/10.1371/journal.pone.0286297. Cite Download

Huang, Yu Ling, Lindsay K. Dickerson, Heidi Kenerson, Xiuyun Jiang, Venu Pillarisetty, Qiang Tian, Leroy Hood, Taranjit S. Gujral, and Raymond S. Yeung. 2023. “Organotypic Models for Functional Drug Testing of Human Cancers.” BME Frontiers 4: 0022. https://doi.org/10.34133/bmef.0022. Cite Download

Hughes, Laura D., Ginger Tsueng, Jack DiGiovanna, Thomas D. Horvath, Luke V. Rasmussen, Tor C. Savidge, Thomas Stoeger, et al. 2023. “Addressing Barriers in FAIR Data Practices for Biomedical Data.” Scientific Data 10 (1): 98. https://doi.org/10.1038/s41597-023-01969-8. 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. 2023. “Timing of Selective Serotonin Reuptake Inhibitor Use and Risk for Preterm Birth and Related Adverse Events.” medRxiv. https://doi.org/10.1101/2023.03.03.23286717. Cite Download

Hwang, Yeon-Mi, Samantha Piekos, Tanya Sorensen, Leroy Hood, and Jennifer Hadlock. 2023. “Adoption of a National Prophylactic Anticoagulation Guideline for Hospitalized Pregnant Women with COVID-19: Retrospective Cohort Study.” JMIR Public Health and Surveillance. https://doi.org/10.2196/45586. Cite

Jennison, Charlie, Janna M. Armstrong, Dorender A. Dankwa, Nina Hertoghs, Sudhir Kumar, Biley A. Abatiyow, Myo Naung, et al. 2023. “Plasmodium GPI-Anchored Micronemal Antigen Is Essential for Parasite Transmission through the Mosquito Host.” Molecular Microbiology. https://doi.org/10.1111/mmi.15078. Cite Download

Jo, Taeho, Junpyo Kim, Paula Bice, Kevin Huynh, Tingting Wang, Matthias Arnold, Peter J. Meikle, et al. 2023. “Circular-SWAT for Deep Learning Based Diagnostic Classification of Alzheimer’s Disease: Application to Metabolome Data.” EBioMedicine 97. https://doi.org/10.1016/j.ebiom.2023.104820. Cite Download

Johnson, James P., Christian Diener, Anne E. Levine, Tomasz Wilmanski, David L. Suskind, Alexandra Ralevski, Jennifer Hadlock, et al. 2023. “Generally-Healthy Individuals with Aberrant Bowel Movement Frequencies Show Enrichment for Microbially-Derived Blood Metabolites Associated with Impaired Kidney Function.” bioRxiv. https://doi.org/10.1101/2023.03.04.531100. Cite Download

Kertesz-Farkas, Attila, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K. Eng, William E. Fondrie, Charles Grant, Michael R. Hoopmann, et al. 2023. “The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00615. Cite Download

Kirkpatrick, Joanna, Paul M. Stemmer, Brian C. Searle, Laura E. Herring, LeRoy Martin, Mukul K. Midha, Brett S. Phinney, et al. 2023. “2019 Association of Biomolecular Resource Facilities Multi-Laboratory Data-Independent Acquisition Proteomics Study.” Journal of Biomolecular Techniques: JBT 34 (2): 3fc1f5fe.9b78d780. https://doi.org/10.7171/3fc1f5fe.9b78d780. Cite Download

Kusebauch, Ulrike, Alan P. R. Lorenzetti, David S. Campbell, Min Pan, David Shteynberg, Charu Kapil, Mukul K. Midha, Adrián López García de Lomana, Nitin S. Baliga, and Robert L. Moritz. 2023. “A Comprehensive Spectral Assay Library to Quantify the Halobacterium Salinarum NRC-1 Proteome by DIA/SWATH-MS.” Scientific Data 10 (1): 697. https://doi.org/10.1038/s41597-023-02590-5. Cite Download

Kwasniewski, Miroslaw, Urszula Korotko, Karolina Chwialkowska, Magdalena Niemira, Jerzy Jaroszewicz, Barbara Sobala-Szczygiel, Beata Puzanowska, et al. 2023. “Implementation of the Web-Based Calculator Estimating Odds Ratio of Severe COVID-19 for Unvaccinated Individuals in a Country with High Coronavirus-Related Death Toll.” Allergy 78 (1): 311–14. https://doi.org/10.1111/all.15524. Cite Download

Lee, Su-Hyung, Ela W. Contreras Panta, David Gibbs, Yoonkyung Won, Jimin Min, Changqing Zhang, Joseph T. Roland, et al. 2023. “Apposition of Fibroblasts With Metaplastic Gastric Cells Promotes Dysplastic Transition.” Gastroenterology, S0016-5085(23)00731-X. https://doi.org/10.1053/j.gastro.2023.04.038. Cite

Lim, Joe J., Christian Diener, James Wilson, Jacob J. Valenzuela, Nitin S. Baliga, and Sean M. Gibbons. 2023. “Growth Phase Estimation for Abundant Bacterial Populations Sampled Longitudinally from Human Stool Metagenomes.” Nature Communications 14 (1): 5682. https://doi.org/10.1038/s41467-023-41424-1. Cite Download

Lorenzetti, Alan P. R., Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L G de Lomana, et al. 2023. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” MSystems, e0081622. https://doi.org/10.1128/msystems.00816-22. Cite Download