Publications

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

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

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

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

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

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

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

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

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

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

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

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

Tan, Marcia M., Terry Bush, Jennifer C. Lovejoy, Harold Javitz, Alula Jimenez Torres, Ken Wassum, and Bonnie Spring. 2021. “Race Differences in Predictors of Weight Gain among a Community Sample of Smokers Enrolled in a Randomized Controlled Trial of a Multiple Behavior Change Intervention.” Preventive Medicine Reports 21: 101303. https://doi.org/10.1016/j.pmedr.2020.101303. Cite Download

Turkarslan, Serdar, Nejc Stopnisek, Anne W. Thompson, Christina E. Arens, Jacob J. Valenzuela, James Wilson, Kristopher A. Hunt, et al. 2021. “Synergistic Epistasis Enhances the Co-Operativity of Mutualistic Interspecies Interactions.” The ISME Journal. https://doi.org/10.1038/s41396-021-00919-9. Cite Download

Vangay, Pajau, Josephine Burgin, Anjanette Johnston, Kristen L. Beck, Daniel C. Berrios, Kai Blumberg, Shane Canon, et al. 2021. “Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and Follow-On Activities.” MSystems 6 (1). https://doi.org/10.1128/mSystems.01194-20. Cite Download

Wilmanski, Tomasz, Christian Diener, Noa Rappaport, Sushmita Patwardhan, Jack Wiedrick, Jodi Lapidus, John C. Earls, et al. 2021. “Gut Microbiome Pattern Reflects Healthy Ageing and Predicts Survival in Humans.” Nature Metabolism 3 (2): 274–86. https://doi.org/10.1038/s42255-021-00348-0. Cite