Publications

2021

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
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
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
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
Ga, Diaz, Christensen Ab, Pusch T, Goulet D, Chang Sc, Grunkemeier Gl, McKelvey Pa, et al. 2021. “Remdesivir and Mortality in Patients with COVID-19.” Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. https://doi.org/10.1093/cid/ciab698. 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
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
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
Kailash, Vidur, Luis Mendoza, Robert L. Moritz, and Michael R. Hoopmann. 2021. “SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.0c00928. Cite
Kauffman, Stuart, and Mike Steel. 2021. “The Expected Number of Viable Autocatalytic Sets in Chemical Reaction Systems.” Artificial Life 27 (1): 1–14. https://doi.org/10.1162/artl_a_00333. Cite Download
Kordahi, Melissa C., Ian B. Stanaway, Marion Avril, Denise Chac, Marie-Pierre Blanc, Benjamin Ross, Christian Diener, et al. 2021. “Genomic and Functional Characterization of a Mucosal Symbiont Involved in Early-Stage Colorectal Cancer.” Cell Host & Microbe, S1931-3128(21)00389-9. https://doi.org/10.1016/j.chom.2021.08.013. Cite
Krämer, Benjamin, Rainer Knoll, Lorenzo Bonaguro, Michael ToVinh, Jan Raabe, Rosario Astaburuaga-García, Jonas Schulte-Schrepping, et al. 2021. “Early IFN-α Signatures and Persistent Dysfunction Are Distinguishing Features of NK Cells in Severe COVID-19.” Immunity, S1074-7613(21)00365-4. https://doi.org/10.1016/j.immuni.2021.09.002. Cite Download
Kumar, Ajay, Mukul K. Midha, and Kanury Vs Rao. 2021. “THP1 Proteomics in Response to Mycobacterium Tuberculosis Infection.” Data in Brief 35: 106803. https://doi.org/10.1016/j.dib.2021.106803. Cite
Le, Hien Thi Thu, Akshaya Murugesan, Thiyagarajan Ramesh, Olli Yli-Harja, Saravanan Konda Mani, and Meenakshisundaram Kandhavelu. 2021. “Molecular Interaction of HIC, an Agonist of P2Y1 Receptor, and Its Role in Prostate Cancer Apoptosis.” International Journal of Biological Macromolecules 189: 142–50. https://doi.org/10.1016/j.ijbiomac.2021.08.103. Cite