Publications

Akbari, Amir, James T. Yurkovich, Daniel C. Zielinski, and Bernhard O. Palsson. 2021. “The Quantitative Metabolome Is Shaped by Abiotic Constraints.” Nature Communications 12 (1): 3178. https://doi.org/10.1038/s41467-021-23214-9. Cite Download

Arrieta-Ortiz, Mario L., Selva Rupa Christinal Immanuel, Serdar Turkarslan, Wei-Ju Wu, Brintha P. Girinathan, Jay N. Worley, Nicholas DiBenedetto, et al. 2021. “Predictive Regulatory and Metabolic Network Models for Systems Analysis of Clostridioides Difficile.” Cell Host & Microbe, S1931-3128(21)00424-8. https://doi.org/10.1016/j.chom.2021.09.008. Cite

Azer, Karim, Chanchala D. Kaddi, Jeffrey S. Barrett, Jane P. F. Bai, Sean T. McQuade, Nathaniel J. Merrill, Benedetto Piccoli, et al. 2021. “History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications.” Frontiers in Physiology 12: 637999. https://doi.org/10.3389/fphys.2021.637999. Cite Download

Baloni, Priyanka, Wikum Dinalankara, John C. Earls, Theo A. Knijnenburg, Donald Geman, Luigi Marchionni, and Nathan D. Price. 2021. “Identifying Personalized Metabolic Signatures in Breast Cancer.” Metabolites 11 (1): 20. https://doi.org/10.3390/metabo11010020. Cite Download

Baloni, Priyanka, Cory C. Funk, Ben Readhead, and Nathan D. Price. 2021. “Systems Modeling of Metabolic Dysregulation in Neurodegenerative Diseases.” Current Opinion in Pharmacology 60: 59–65. https://doi.org/10.1016/j.coph.2021.06.012. Cite

Bandeira, Nuno, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, and Juan Antonio Vizcaíno. 2021. “Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future.” Molecular & Cellular Proteomics: MCP 20: 100071. https://doi.org/10.1016/j.mcpro.2021.100071. Cite Download

Banerjee, Ushashi, Priyanka Baloni, Amit Singh, and Nagasuma Chandra. 2021. “Immune Subtyping in Latent Tuberculosis.” Frontiers in Immunology 12. https://doi.org/10.3389/fimmu.2021.595746. Cite Download

Bastard, Paul, Adrian Gervais, Tom Le Voyer, Jérémie Rosain, Quentin Philippot, Jérémy Manry, Eleftherios Michailidis, et al. 2021. “Autoantibodies Neutralizing Type I IFNs Are Present in ~4% of Uninfected Individuals over 70 Years Old and Account for ~20% of COVID-19 Deaths.” Science Immunology 6 (62): eabl4340. https://doi.org/10.1126/sciimmunol.abl4340. Cite Download

Bobe, Jason R., Brandon L. Jutras, Elizabeth J. Horn, Monica E. Embers, Allison Bailey, Robert L. Moritz, Ying Zhang, et al. 2021. “Recent Progress in Lyme Disease and Remaining Challenges.” Frontiers in Medicine 8: 666554. https://doi.org/10.3389/fmed.2021.666554. Cite Download

Brand, Marjorie, and Jeffrey A. Ranish. 2021. “Proteomic/Transcriptomic Analysis of Erythropoiesis.” Current Opinion in Hematology 28 (3): 150–57. https://doi.org/10.1097/MOH.0000000000000647. Cite

Cheng, Hanjun, Zhonghan Li, Zhili Guo, Shiqun Shao, Li Mo, Wei Wei, and Min Xue. 2021. “Single-Cell Profiling of D-2-Hydroxyglutarate Using Surface-Immobilized Resazurin Analogs.” Biosensors & Bioelectronics 190: 113368. https://doi.org/10.1016/j.bios.2021.113368. Cite

Cobb, David W., Heather M. Kudyba, Alejandra Villegas, Michael R. Hoopmann, Rodrigo P. Baptista, Baylee Bruton, Michelle Krakowiak, Robert L. Moritz, and Vasant Muralidharan. 2021. “A Redox-Active Crosslinker Reveals an Essential and Inhibitable Oxidative Folding Network in the Endoplasmic Reticulum of Malaria Parasites.” PLoS Pathogens 17 (2): e1009293. https://doi.org/10.1371/journal.ppat.1009293. Cite Download

Corpas, Manuel, Stephan Beck, Gustavo Glusman, and Mahsa Shabani. 2021. “Editorial: Personal Genomes: Accessing, Sharing, and Interpretation.” Frontiers in Genetics 12: 687584. https://doi.org/10.3389/fgene.2021.687584. Cite Download

Crouser, Elliott D., Mark W. Julian, Sabahattin Bicer, Vikas Ghai, Taek-Kyun Kim, Lisa A. Maier, May Gillespie, Nabeel Y. Hamzeh, and Kai Wang. 2021. “Circulating Exosomal MicroRNA Expression Patterns Distinguish Cardiac Sarcoidosis from Myocardial Ischemia.” PloS One 16 (1): e0246083. https://doi.org/10.1371/journal.pone.0246083. Cite Download

D, Park, Anisuzzaman Asm, Magis At, Chen G, Xie M, Zhang G, Behera M, et al. 2021. “Discovery of Small Molecule Bak Activator for Lung Cancer Therapy.” Theranostics 11 (17). https://doi.org/10.7150/thno.60349. Cite Download

D’Agnillo, Felice, K.A. Walters, Yongli Xiao, Zong-Mei Sheng, Kelsey Scherler, Jaekeun Park, Sebastian Gygli, et al. 2021. “Lung Epithelial and Endothelial Damage, Loss of Tissue Repair, Inhibition of Fibrinolysis, and Cellular Senescence in Fatal COVID-19.” Science Translational Medicine 13 (620): eabj7790. https://doi.org/10.1126/scitranslmed.abj7790. Cite Download

Dai, Chengzhen L., Sergey A. Kornilov, Ryan T. Roper, Hannah Cohen-Cline, Kathleen Jade, Brett Smith, James R. Heath, et al. 2021. “Characteristics and Factors Associated with COVID-19 Infection, Hospitalization, and Mortality Across Race and Ethnicity.” Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America. https://doi.org/10.1093/cid/ciab154. Cite Download

Dai, Chengxin, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M. Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, et al. 2021. “A Proteomics Sample Metadata Representation for Multiomics Integration and Big Data Analysis.” Nature Communications 12 (1): 5854. https://doi.org/10.1038/s41467-021-26111-3. Cite

Day, JA, CM Ludwig, and NS Baliga. 2021. “Cultivating Environmental Sustainable Food through a Community Ambassador Program.” Clearing: Journal of Community-Based Environmental Literacy Education Winter Edition: 12–16. Cite

Day, Jessica A., Christian Diener, Anne E. Otwell, Kourtney E. Tams, Brad Bebout, Angela M. Detweiler, Michael D. Lee, et al. 2021. “Lettuce (Lactuca Sativa) Productivity Influenced by Microbial Inocula under Nitrogen-Limited Conditions in Aquaponics.” PloS One 16 (2): e0247534. https://doi.org/10.1371/journal.pone.0247534. Cite Download

Deutsch, Eric W., Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, et al. 2021. “Universal Spectrum Identifier for Mass Spectra.” Nature Methods 18 (7): 768–70. https://doi.org/10.1038/s41592-021-01184-6. Cite Download

Deutsch, Eric W., Gilbert S. Omenn, Zhi Sun, Michal Maes, Maria Pernemalm, Krishnan K. Palaniappan, Natasha Letunica, et al. 2021. “Advances and Utility of the Human Plasma Proteome.” Journal of Proteome Research 20 (12): 5241–63. https://doi.org/10.1021/acs.jproteome.1c00657. Cite

Diaz, George A, Alyssa B Christensen, Tobias Pusch, Delaney Goulet, Shu-Ching Chang, Gary L Grunkemeier, Paul A McKelvey, et al. 2021. “Remdesivir and Mortality in Patients With Coronavirus Disease 2019.” Clinical Infectious Diseases, ciab698. https://doi.org/10.1093/cid/ciab698. Cite Download

Diener, Christian, Anna C. H. Hoge, Sean M. Kearney, Ulrike Kusebauch, Sushmita Patwardhan, Robert L. Moritz, Susan E. Erdman, and Sean M. Gibbons. 2021. “Non-Responder Phenotype Reveals Apparent Microbiome-Wide Antibiotic Tolerance in the Murine Gut.” Communications Biology 4 (1): 316. https://doi.org/10.1038/s42003-021-01841-8. Cite Download

Doan, Phuong, Phung Nguyen, Akshaya Murugesan, Kumar Subramanian, Saravanan Konda Mani, Vignesh Kalimuthu, Bobin George Abraham, et al. 2021. “Targeting Orphan G Protein-Coupled Receptor 17 with T0 Ligand Impairs Glioblastoma Growth.” Cancers 13 (15): 3773. https://doi.org/10.3390/cancers13153773. Cite Download

Doan, Phuong, Phung Nguyen, Akshaya Murugesan, Nuno R. Candeias, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2021. “Alkylaminophenol and GPR17 Agonist for Glioblastoma Therapy: A Combinational Approach for Enhanced Cell Death Activity.” Cells 10 (8): 1975. https://doi.org/10.3390/cells10081975. Cite Download

Dokic, Anja, Eliza Peterson, Mario L. Arrieta-Ortiz, Min Pan, Alessandro Di Maio, Nitin Baliga, and Apoorva Bhatt. 2021. “Mycobacterium Abscessus Biofilms Produce an Extracellular Matrix and Have a Distinct Mycolic Acid Profile.” Cell Surface (Amsterdam, Netherlands) 7: 100051. https://doi.org/10.1016/j.tcsw.2021.100051. Cite Download

Doty, Raymond T., Xiaowei Yan, Changting Meng, Christopher Lausted, Qiang Tian, and Janis L. Abkowitz. 2021. “Single-Cell Analysis of Erythropoiesis in Rpl11 Haploinsufficient Mice Reveals Insight into the Pathogenesis of Diamond Blackfan Anemia.” Experimental Hematology. https://doi.org/10.1016/j.exphem.2021.02.010. Cite

Emmert-Streib, Frank, Kalifa Manjang, Matthias Dehmer, Olli Yli-Harja, and Anssi Auvinen. 2021. “Are There Limits in Explainability of Prognostic Biomarkers? Scrutinizing Biological Utility of Established Signatures.” Cancers 13 (20): 5087. https://doi.org/10.3390/cancers13205087. Cite Download

Fecho, Karamarie, James Balhoff, Chris Bizon, William E. Byrd, Sui Hang, David Koslicki, Stefano E. Rensi, et al. 2021. “Application of MCAT Questions as a Testing Tool and Evaluation Metric for Knowledge Graph-Based Reasoning Systems.” Clinical and Translational Science. https://doi.org/10.1111/cts.13021. Cite Download

Fedorov, Andrey, William J. R. Longabaugh, David Pot, David A. Clunie, Steve Pieper, Hugo J. W. L. Aerts, André Homeyer, et al. 2021. “NCI Imaging Data Commons.” Cancer Research 81 (16): 4188–93. https://doi.org/10.1158/0008-5472.CAN-21-0950. Cite Download

Ghiselli, Fabrizio, André Gomes-Dos-Santos, Coen M. Adema, Manuel Lopes-Lima, Joel Sharbrough, and Jeffrey L. Boore. 2021. “Molluscan Mitochondrial Genomes Break the Rules.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 376 (1825): 20200159. https://doi.org/10.1098/rstb.2020.0159. Cite

Gibbs, David L., Boris Aguilar, Vésteinn Thorsson, Alexander V. Ratushny, and Ilya Shmulevich. 2021. “Patient-Specific Cell Communication Networks Associate With Disease Progression in Cancer.” Frontiers in Genetics 12: 667382. https://doi.org/10.3389/fgene.2021.667382. Cite Download

Girinathan, Brintha P., Nicholas DiBenedetto, Jay N. Worley, Johann Peltier, Mario L. Arrieta-Ortiz, Selva Rupa Christinal Immanuel, Richard Lavin, et al. 2021. “In Vivo Commensal Control of Clostridioides Difficile Virulence.” Cell Host & Microbe, S1931-3128(21)00423-6. https://doi.org/10.1016/j.chom.2021.09.007. Cite

Giurgea, Luca T., Jae-Keun Park, K.A. Walters, Kelsey Scherler, Adriana Cervantes-Medina, Ashley Freeman, Luz Angela Rosas, John C. Kash, Jeffery K. Taubenberger, and Matthew J. Memoli. 2021. “The Effect of Calcium and Magnesium on Activity, Immunogenicity, and Efficacy of a Recombinant N1/N2 Neuraminidase Vaccine.” NPJ Vaccines 6 (1): 48. https://doi.org/10.1038/s41541-021-00310-x. Cite Download

Giurgea, Luca T., Adriana Cervantes-Medina, K.A. Walters, Kelsey Scherler, Alison Han, Lindsay M. Czajkowski, Holly Ann Baus, et al. 2021. “Sex Differences in Influenza: The Challenge Study Experience.” The Journal of Infectious Diseases, jiab422. https://doi.org/10.1093/infdis/jiab422. Cite Download

Gnanavel, Mutharasu, Akshaya Murugesan, Saravanan Konda Mani, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2021. “Identifying the MiRNA Signature Association with Aging-Related Senescence in Glioblastoma.” International Journal of Molecular Sciences 22 (2). https://doi.org/10.3390/ijms22020517. Cite Download

Grasberger, Helmut, Andrew T. Magis, Elisa Sheng, Matthew P. Conomos, Min Zhang, Lea S. Garzotto, Guoqing Hou, et al. 2021. “DUOX2 Variants Associate with Preclinical Disturbances in Microbiota-Immune Homeostasis and Increased Inflammatory Bowel Disease Risk.” The Journal of Clinical Investigation. https://doi.org/10.1172/JCI141676. Cite Download

Groussin, Mathieu, Mathilde Poyet, Ainara Sistiaga, Sean M. Kearney, Katya Moniz, Mary Noel, Jeff Hooker, et al. 2021. “Elevated Rates of Horizontal Gene Transfer in the Industrialized Human Microbiome.” Cell 184 (8): 2053-2067.e18. https://doi.org/10.1016/j.cell.2021.02.052. Cite Download

Guo, Zhili, Hanjun Cheng, Zhonghan Li, Shiqun Shao, Priyanka Sarkar, Siwen Wang, Rohit Chaudhuri, et al. 2021. “Single-Cell Profiling of Fatty Acid Uptake Using Surface-Immobilized Dendrimers.” Journal of the American Chemical Society 143 (29): 11191–98. https://doi.org/10.1021/jacs.1c05103. Cite

Haak, Victoria M., Sui Huang, and Dipak Panigrahy. 2021. “Debris-Stimulated Tumor Growth: A Pandora’s Box?” Cancer Metastasis Reviews 40 (3): 791–801. https://doi.org/10.1007/s10555-021-09998-8. Cite Download

Haiman, Zachary B., Daniel C. Zielinski, Yuko Koike, James T. Yurkovich, and Bernhard O. Palsson. 2021. “MASSpy: Building, Simulating, and Visualizing Dynamic Biological Models in Python Using Mass Action Kinetics.” PLoS Computational Biology 17 (1): e1008208. https://doi.org/10.1371/journal.pcbi.1008208. Cite Download

Hansell, Dennis A., and Mónica V. Orellana. 2021. “Dissolved Organic Matter in the Global Ocean: A Primer.” Gels (Basel, Switzerland) 7 (3): 128. https://doi.org/10.3390/gels7030128. Cite Download

Hernandez-Boussard, Tina, Paul Macklin, Emily J. Greenspan, Amy L. Gryshuk, Eric Stahlberg, Tanveer Syeda-Mahmood, and Ilya Shmulevich. 2021. “Digital Twins for Predictive Oncology Will Be a Paradigm Shift for Precision Cancer Care.” Nature Medicine. https://doi.org/10.1038/s41591-021-01558-5. Cite

Huang, Sui. 2021. “Reconciling Non-Genetic Plasticity with Somatic Evolution in Cancer.” Trends in Cancer. https://doi.org/10.1016/j.trecan.2020.12.007. Cite

Hwang, Yu Jin, Seung Jae Hyeon, Younghee Kim, Sungsu Lim, Min Young Lee, Jieun Kim, Ashwini M. Londhe, et al. 2021. “Modulation of SETDB1 Activity by APQ Ameliorates Heterochromatin Condensation, Motor Function, and Neuropathology in a Huntington’s Disease Mouse Model.” Journal of Enzyme Inhibition and Medicinal Chemistry 36 (1): 856–68. https://doi.org/10.1080/14756366.2021.1900160. Cite Download

Idso, Matthew N., Bert T. Lai, Heather D. Agnew, and James R. Heath. 2021. “Protein Catalyzed Capture (PCC) Agents for Antigen Targeting.” Methods in Molecular Biology (Clifton, N.J.) 2371: 177–91. https://doi.org/10.1007/978-1-0716-1689-5_10. Cite

Immanuel, Selva Rupa Christinal, Avinash D. Ghanate, Dharmeshkumar S. Parmar, Ritu Yadav, Riya Uthup, Venkateswarlu Panchagnula, and Anu Raghunathan. 2021. “Integrated Genetic and Metabolic Landscapes Predict Vulnerabilities of Temozolomide Resistant Glioblastoma Cells.” NPJ Systems Biology and Applications 7 (1): 2. https://doi.org/10.1038/s41540-020-00161-7. Cite Download

Jensen, Bryan C., Isabelle Q. Phan, Jacquelyn R. McDonald, Aakash Sur, Mark A. Gillespie, Jeffrey A. Ranish, Marilyn Parsons, and Peter J. Myler. 2021. “Chromatin-Associated Protein Complexes Link DNA Base J and Transcription Termination in Leishmania.” MSphere 6 (1). https://doi.org/10.1128/mSphere.01204-20. Cite

Jiang, Yonghou, Fergal Duffy, Jennifer Hadlock, Andrew Raappana, Sheila Styrchak, Ingrid Beck, Fred D. Mast, et al. 2021. “Angiotensin II Receptor I Auto-Antibodies Following SARS-CoV-2 Infection.” PloS One 16 (11): e0259902. https://doi.org/10.1371/journal.pone.0259902. Cite Download