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

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

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

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 and Bioelectronics, 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

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

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

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

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

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

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

Giurgea, Luca T., Jae-Keun Park, Kathie-Anne 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

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

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

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

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

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

Lee, Ming-Jen, Jen-Chieh Lee, Jung-Hsien Hsieh, May-Yao Lin, I.-An Shih, Huey-Ling You, and Kai Wang. 2021. “Cordycepin Inhibits the Proliferation of Malignant Peripheral Nerve Sheath Tumor Cells through the P53/Sp1/Tubulin Pathway.” American Journal of Cancer Research 11 (4): 1247–66. Cite

Lehman, Niles E., and Stuart A. Kauffman. 2021. “Constraint Closure Drove Major Transitions in the Origins of Life.” Entropy (Basel, Switzerland) 23 (1). https://doi.org/10.3390/e23010105. Cite Download

Levites, Yona, Cory Funk, Xue Wang, Paramita Chakrabarty, Karen N. McFarland, Baxter Bramblett, Veronica O’Neal, et al. 2021. “Modulating Innate Immune Activation States Impacts the Efficacy of Specific Aβ Immunotherapy.” Molecular Neurodegeneration 16 (1): 32. https://doi.org/10.1186/s13024-021-00453-4. Cite Download

Li, Hong-Dong, Cory C. Funk, Karen McFarland, Eric B. Dammer, Mariet Allen, Minerva M. Carrasquillo, Yona Levites, et al. 2021. “Integrative Functional Genomic Analysis of Intron Retention in Human and Mouse Brain with Alzheimer’s Disease.” Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association. https://doi.org/10.1002/alz.12254. Cite Download

Lo, Yuan-Hung, Kevin S. Kolahi, Yuhong Du, Chiung-Ying Chang, Andrey Krokhotin, Ajay Nair, Walter D. Sobba, et al. 2021. “A CRISPR/Cas9-Engineered ARID1A-Deficient Human Gastric Cancer Organoid Model Reveals Essential and Non-Essential Modes of Oncogenic Transformation.” Cancer Discovery. https://doi.org/10.1158/2159-8290.CD-20-1109. Cite Download

Lui, Lauren M., Erica L.-W. Majumder, Heidi J. Smith, Hans K. Carlson, Frederick von Netzer, Matthew W. Fields, David A. Stahl, et al. 2021. “Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.” Frontiers in Microbiology 12: 642422. https://doi.org/10.3389/fmicb.2021.642422. Cite Download

Manjang, Kalifa, Shailesh Tripathi, Olli Yli-Harja, Matthias Dehmer, Galina Glazko, and Frank Emmert-Streib. 2021. “Prognostic Gene Expression Signatures of Breast Cancer Are Lacking a Sensible Biological Meaning.” Scientific Reports 11 (1): 156. https://doi.org/10.1038/s41598-020-79375-y. Cite Download

Mao, Yafei, Claudia R. Catacchio, LaDeana W. Hillier, David Porubsky, Ruiyang Li, Arvis Sulovari, Jason D. Fernandes, et al. 2021. “A High-Quality Bonobo Genome Refines the Analysis of Hominid Evolution.” Nature 594 (7861): 77–81. https://doi.org/10.1038/s41586-021-03519-x. Cite Download

McElroy, Kyle E., Stefan Müller, Dunja Lamatsch, Laura Bankers, Peter D. Fields, Joseph R. Jalinsky, Joel Sharbrough, Jeffrey L. Boore, John M. Logsdon, and Maurine Neiman. 2021. “Asexuality Associated with Marked Genomic Expansion of Tandemly Repeated RRNA and Histone Genes.” Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msab121. Cite Download

Montenegro Benavides, Nathaly Andrea, Alejandro Alvarez B, Mario L. Arrieta-Ortiz, Luis Miguel Rodriguez-R, David Botero, Javier Felipe Tabima, Luisa Castiblanco, Cesar Trujillo, Silvia Restrepo, and Adriana Bernal. 2021. “The Type VI Secretion System of Xanthomonas Phaseoli Pv. Manihotis Is Involved in Virulence and in Vitro Motility.” BMC Microbiology 21 (1): 14. https://doi.org/10.1186/s12866-020-02066-1. Cite Download

Neal, Maxwell L., Ling Wei, Eliza Peterson, Mario L. Arrieta-Ortiz, Samuel A. Danziger, Nitin S. Baliga, Alexis Kaushansky, and John D. Aitchison. 2021. “A Systems-Level Gene Regulatory Network Model for Plasmodium Falciparum.” Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa1245. Cite Download

Otwell, Anne E., Alex V. Carr, Erica L. W. Majumder, Maryann K. Ruiz, Regina L. Wilpiszeski, Linh T. Hoang, Bill Webb, et al. 2021. “Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification.” MSystems 6 (1). https://doi.org/10.1128/mSystems.01025-20. Cite Download

Palanivel, Suresh, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2021. “Molecular Interaction Study of Novel Indoline Derivatives with EGFR-Kinase Domain Using Multiple Computational Analysis.” Journal of Biomolecular Structure & Dynamics, 1–10. https://doi.org/10.1080/07391102.2021.1900917. Cite

Reales-Calderón, J. A., Z. Sun, V. Mascaraque, E. Pérez-Navarro, V. Vialás, E. W. Deutsch, R. L. Moritz, C. Gil, J. L. Martínez, and G. Molero. 2021. “A Wide-Ranging Pseudomonas Aeruginosa PeptideAtlas Build: A Useful Proteomic Resource for a Versatile Pathogen.” Journal of Proteomics 239: 104192. https://doi.org/10.1016/j.jprot.2021.104192. Cite Download

Robertson, A. Gordon, Christina Yau, Jian Carrot-Zhang, Jeffrey S. Damrauer, Theo A. Knijnenburg, Nyasha Chambwe, Katherine A. Hoadley, et al. 2021. “Integrative Modeling Identifies Genetic Ancestry-Associated Molecular Correlates in Human Cancer.” STAR Protocols 2 (2): 100483. https://doi.org/10.1016/j.xpro.2021.100483. Cite Download

Sayaman, Rosalyn W., Mohamad Saad, Vésteinn Thorsson, Donglei Hu, Wouter Hendrickx, Jessica Roelands, Eduard Porta-Pardo, et al. 2021. “Germline Genetic Contribution to the Immune Landscape of Cancer.” Immunity 54 (2): 367-386.e8. https://doi.org/10.1016/j.immuni.2021.01.011. Cite Download

Schmidt, Tobias, Patroklos Samaras, Viktoria Dorfer, Christian Panse, Tobias Kockmann, Leon Bichmann, Bart van Puyvelde, et al. 2021. “Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.1c00096. Cite Download

Siegel, Carole E., Eugene M. Laska, Ziqiang Lin, Mu Xu, Duna Abu-Amara, Michelle K. Jeffers, Meng Qian, et al. 2021. “Utilization of Machine Learning for Identifying Symptom Severity Military-Related PTSD Subtypes and Their Biological Correlates.” Translational Psychiatry 11 (1): 227. https://doi.org/10.1038/s41398-021-01324-8. Cite Download

Steel, Ryan W. J., Vladimir Vigdorovich, Nicholas Dambrauskas, Brandon K. Wilder, Silvia A. Arredondo, Debashree Goswami, Sudhir Kumar, et al. 2021. “Platelet Derived Growth Factor Receptor β (PDGFRβ) Is a Host Receptor for the Human Malaria Parasite Adhesin TRAP.” Scientific Reports 11 (1): 11328. https://doi.org/10.1038/s41598-021-90722-5. Cite Download

Stojakovic, Andrea, Sergey Trushin, Anthony Sheu, Layla Khalili, Su-Youne Chang, Xing Li, Trace Christensen, et al. 2021. “Partial Inhibition of Mitochondrial Complex I Ameliorates Alzheimer’s Disease Pathology and Cognition in APP/PS1 Female Mice.” Communications Biology 4 (1): 61. https://doi.org/10.1038/s42003-020-01584-y. Cite Download

Storer, Jessica, Robert Hubley, Jeb Rosen, Travis J. Wheeler, and Arian F. Smit. 2021. “The Dfam Community Resource of Transposable Element Families, Sequence Models, and Genome Annotations.” Mobile DNA 12 (1): 2. https://doi.org/10.1186/s13100-020-00230-y. Cite Download

Su, Yapeng, Dan Yuan, Daniel G. Chen, Kai Wang, Jongchan Choi, Chengzhen L. Dai, Sunga Hong, et al. 2021. “Heterogeneous Immunological Recovery Trajectories Revealed in Post-Acute COVID-19.” MedRxiv, 2021.03.19.21254004. https://doi.org/10.1101/2021.03.19.21254004. Cite Download