Publications

2019

Agnew, Heather D., Matthew B. Coppock, Matthew N. Idso, Bert T. Lai, JingXin Liang, Amy M. McCarthy-Torrens, Carmen M. Warren, and James R. Heath. 2019. “Protein-Catalyzed Capture Agents.” Chemical Reviews. https://doi.org/10.1021/acs.chemrev.8b00660. Cite
Ahalt, Stanley C., Christopher G. Chute, Karamarie Fecho, Gustavo Glusman, Jennifer Hadlock, Casey Overby Taylor, Emily R. Pfaff, et al. 2019. “Clinical Data: Sources and Types, Regulatory Constraints, Applications.” Clinical and Translational Science. https://doi.org/10.1111/cts.12638. Cite Download
Aruoma, Okezie I., Sharon Hausman-Cohen, Jessica Pizano, Michael A. Schmidt, Deanna M. Minich, Yael Joffe, Sebastian Brandhorst, Simon J. Evans, and David M. Brady. 2019. “Personalized Nutrition: Translating the Science of NutriGenomics Into Practice: Proceedings From the 2018 American College of Nutrition Meeting.” Journal of the American College of Nutrition 38 (4): 287–301. https://doi.org/10.1080/07315724.2019.1582980. Cite Download
Azam, Md Facihul, Aliyu Musa, Matthias Dehmer, Olli P. Yli-Harja, and Frank Emmert-Streib. 2019. “Global Genetics Research in Prostate Cancer: A Text Mining and Computational Network Theory Approach.” Frontiers in Genetics 10: 70. https://doi.org/10.3389/fgene.2019.00070. Cite Download
Baloni, Priyanka, Vineet Sangar, James T. Yurkovich, Max Robinson, Scott Taylor, Christine M. Karbowski, Hisham K. Hamadeh, Yudong D. He, and Nathan D. Price. 2019. “Genome-Scale Metabolic Model of the Rat Liver Predicts Effects of Diet Restriction.” Scientific Reports 9 (1): 9807. https://doi.org/10.1038/s41598-019-46245-1. Cite
Baloni, Priyanka, Cory C. Funk, Jingwen Yan, James T. Yurkovich, Alexandra Kueider-Paisley, Kwangsik Nho, Almut Heinken, et al. 2019. “Identifying Differences in Bile Acid Pathways for Cholesterol Clearance in Alzheimer’s Disease Using Metabolic Networks of Human Brain Regions.” BioRxiv, 782987. https://doi.org/10.1101/782987. Cite Download
Bedognetti, Davide, Michele Ceccarelli, Lorenzo Galluzzi, Rongze Lu, Karolina Palucka, Josue Samayoa, Stefani Spranger, et al. 2019. “Correction to: Toward a Comprehensive View of Cancer Immune Responsiveness: A Synopsis from the SITC Workshop.” Journal for Immunotherapy of Cancer 7 (1): 167. https://doi.org/10.1186/s40425-019-0640-y. Cite Download
Binz, Pierre-Alain, Jim Shofstahl, Juan Antonio Vizcaíno, Harald Barsnes, Robert J. Chalkley, Gerben Menschaert, Emanuele Alpi, et al. 2019. “Proteomics Standards Initiative Extended FASTA Format.” Journal of Proteome Research 18 (6): 2686–92. https://doi.org/10.1021/acs.jproteome.9b00064. Cite
Bolyen, Evan, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, et al. 2019. “Author Correction: Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2.” Nature Biotechnology 37 (9): 1091. https://doi.org/10.1038/s41587-019-0252-6. Cite
Carr, Alex, Christian Diener, Nitin S. Baliga, and Sean M. Gibbons. 2019. “Use and Abuse of Correlation Analyses in Microbial Ecology.” The ISME Journal, 1. https://doi.org/10.1038/s41396-019-0459-z. Cite
Chen, Guo, Dongkyoo Park, Andrew T. Magis, Madhusmita Behera, Suresh S. Ramalingam, Taofeek K. Owonikoko, Gabriel L. Sica, et al. 2019. “Mcl-1 Interacts with Akt to Promote Lung Cancer Progression.” Cancer Research. https://doi.org/10.1158/0008-5472.CAN-19-0950. Cite
Cuvitoglu, Ali, Joseph X. Zhou, Sui Huang, and Zerrin Isik. 2019. “Predicting Drug Synergy for Precision Medicine Using Network Biology and Machine Learning.” Journal of Bioinformatics and Computational Biology 17 (2): 1950012. https://doi.org/10.1142/S0219720019500124. Cite
Das, Saumya, Extracellular RNA Communication Consortium, K. Mark Ansel, Markus Bitzer, Xandra O. Breakefield, Alain Charest, David J. Galas, et al. 2019. “The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research.” Cell 177 (2): 231–42. https://doi.org/10.1016/j.cell.2019.03.023. Cite
Dean, Kelsey R., Rasha Hammamieh, Synthia H. Mellon, Duna Abu-Amara, Janine D. Flory, Guia Guffanti, Kai Wang, et al. 2019. “Multi-Omic Biomarker Identification and Validation for Diagnosing Warzone-Related Post-Traumatic Stress Disorder.” Molecular Psychiatry, 1–13. https://doi.org/10.1038/s41380-019-0496-z. Cite Download
Dean, Kelsey R., Rasha Hammamieh, Synthia H. Mellon, Duna Abu-Amara, Janine D. Flory, Guia Guffanti, Kai Wang, et al. 2019. “Multi-Omic Biomarker Identification and Validation for Diagnosing Warzone-Related Post-Traumatic Stress Disorder.” Molecular Psychiatry. https://doi.org/10.1038/s41380-019-0496-z. Cite
Deutsch, Eric W., Lydie Lane, Christopher M. Overall, Nuno Bandeira, Mark S. Baker, Charles Pineau, Robert L. Moritz, et al. 2019. “Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 3.0.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.9b00542. Cite Download
Deutsch, Eric W., Nuno Bandeira, Vagisha Sharma, Yasset Perez-Riverol, Jeremy J. Carver, Deepti J. Kundu, David García-Seisdedos, et al. 2019. “The ProteomeXchange Consortium in 2020: Enabling ‘big Data’ Approaches in Proteomics.” Nucleic Acids Research. https://doi.org/10.1093/nar/gkz984. Cite Download
Diener, Christian, Sean M. Gibbons, and Osbaldo Resendis-Antonio. 2019. “MICOM: Metagenome-Scale Modeling to Infer Metabolic Interactions in the Gut Microbiota.” BioRxiv, 361907. https://doi.org/10.1101/361907. Cite Download
Doan, Phuong, Aliyu Musa, Nuno R. Candeias, Frank Emmert-Streib, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2019. “Alkylaminophenol Induces G1/S Phase Cell Cycle Arrest in Glioblastoma Cells Through P53 and Cyclin-Dependent Kinase Signaling Pathway.” Frontiers in Pharmacology 10: 330. https://doi.org/10.3389/fphar.2019.00330. Cite Download
Earls, John C., Noa Rappaport, Laura Heath, Tomasz Wilmanski, Andrew T. Magis, Nicholas J. Schork, Gilbert S. Omenn, Jennifer Lovejoy, Leroy Hood, and Nathan D. Price. 2019. “Multi-Omic Biological Age Estimation and Its Correlation With Wellness and Disease Phenotypes: A Longitudinal Study of 3,558 Individuals.” The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences 74 (Supplement_1): S52–60. https://doi.org/10.1093/gerona/glz220. Cite
Fecho, Karamarie, Stanley C. Ahalt, Saravanan Arunachalam, James Champion, Christopher G. Chute, Sarah Davis, Kenneth Gersing, et al. 2019. “Sex, Obesity, Diabetes, and Exposure to Particulate Matter among Patients with Severe Asthma: Scientific Insights from a Comparative Analysis of Open Clinical Data Sources during a Five-Day Hackathon.” Journal of Biomedical Informatics 100: 103325. https://doi.org/10.1016/j.jbi.2019.103325. Cite
Gao, Galen F., Joel S. Parker, Sheila M. Reynolds, Tiago C. Silva, Liang-Bo Wang, Wanding Zhou, Rehan Akbani, et al. 2019. “Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data.” Cell Systems 9 (1): 24-34.e10. https://doi.org/10.1016/j.cels.2019.06.006. Cite
Gartung, Allison, Jun Yang, Vikas P. Sukhatme, Diane R. Bielenberg, Djanira Fernandes, Jaimie Chang, Birgitta A. Schmidt, et al. 2019. “Suppression of Chemotherapy-Induced Cytokine/Lipid Mediator Surge and Ovarian Cancer by a Dual COX-2/SEH Inhibitor.” Proceedings of the National Academy of Sciences, 201803999. https://doi.org/10.1073/pnas.1803999116. Cite
Ghai, Vikas, Taek-Kyun Kim, Alton Etheridge, Trine Nielsen, Torben Hansen, Oluf Pedersen, David Galas, and Kai Wang. 2019. “Extracellular Vesicle Encapsulated MicroRNAs in Patients with Type 2 Diabetes Are Affected by Metformin Treatment.” Journal of Clinical Medicine 8 (5). https://doi.org/10.3390/jcm8050617. Cite
Gibbons, Sean M. 2019. “Defining Microbiome Health through a Host Lens.” MSystems 4 (3). https://doi.org/10.1128/mSystems.00155-19. Cite Download
Gilligan, Molly M., Allison Gartung, Megan L. Sulciner, Paul C. Norris, Vikas P. Sukhatme, Diane R. Bielenberg, Sui Huang, Mark W. Kieran, Charles N. Serhan, and Dipak Panigrahy. 2019. “Aspirin-Triggered Proresolving Mediators Stimulate Resolution in Cancer.” Proceedings of the National Academy of Sciences of the United States of America 116 (13): 6292–97. https://doi.org/10.1073/pnas.1804000116. Cite
Glennon, Elizabeth K. K., Laura S. Austin, Nadia Arang, Heather S. Kain, Fred D. Mast, Kamalakannan Vijayan, John D. Aitchison, Stefan H. I. Kappe, and Alexis Kaushansky. 2019. “Alterations in Phosphorylation of Hepatocyte Ribosomal Protein S6 Control Plasmodium Liver Stage Infection.” Cell Reports 26 (12): 3391-3399.e4. https://doi.org/10.1016/j.celrep.2019.02.085. Cite Download
Goldman, Johanna A. L., Megan J. Schatz, Chris T. Berthiaume, Sacha N. Coesel, Mónica V. Orellana, and E. Virginia Armbrust. 2019. “Fe Limitation Decreases Transcriptional Regulation over the Diel Cycle in the Model Diatom Thalassiosira Pseudonana.” PLoS ONE 14 (9). https://doi.org/10.1371/journal.pone.0222325. Cite Download
Guida, Jennifer L., Tim A. Ahles, Daniel Belsky, Judith Campisi, Harvey Jay Cohen, James DeGregori, Rebecca Fuldner, et al. 2019. “Measuring Aging and Identifying Aging Phenotypes in Cancer Survivors.” Journal of the National Cancer Institute. https://doi.org/10.1093/jnci/djz136. Cite Download
Hada, Arjan, Swetansu K. Hota, Jie Luo, Yuan-Chi Lin, Seyit Kale, Alexey K. Shaytan, Saurabh K. Bhardwaj, et al. 2019. “Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling.” Cell Reports 28 (1): 282-294.e6. https://doi.org/10.1016/j.celrep.2019.05.106. Cite Download
Hagedorn, Rebecca, Alex Pampalone, Lanae Hood, Catherine Yura, Deana Morrow, and Melissa Olfert. 2019. “Development and Evaluation of a Higher Education Food Security Toolkit to Provide Ideas of Initiatives for Student Wellbeing: WISH4Campus (P04-049-19).” Current Developments in Nutrition 3 (Suppl 1). https://doi.org/10.1093/cdn/nzz051.P04-049-19. Cite Download
Hampton, Henry R., and Tatyana Chtanova. 2019. “Lymphatic Migration of Immune Cells.” Frontiers in Immunology 10: 1168. https://doi.org/10.3389/fimmu.2019.01168. Cite Download
Hao, Yang, Daixi Li, Yong Xu, Jian Ouyang, Yongkun Wang, Yuqi Zhang, Baoguo Li, Lu Xie, and Guangrong Qin. 2019. “Investigation of Lipid Metabolism Dysregulation and the Effects on Immune Microenvironments in Pan-Cancer Using Multiple Omics Data.” BMC Bioinformatics 20 (Suppl 7): 195. https://doi.org/10.1186/s12859-019-2734-4. Cite Download
Hartl, Daniela, Patrick May, Wei Gu, Manuel Mayhaus, Sabrina Pichler, Christian Spaniol, Enrico Glaab, et al. 2019. “A Rare Loss-of-Function Variant of ADAM17 Is Associated with Late-Onset Familial Alzheimer Disease.” Molecular Psychiatry. https://doi.org/10.1038/s41380-018-0091-8. Cite Download
Heath, James R. 2019. “Framing Technology Challenges Associated with Improving Cancer Immunotherapies.” Lab on a Chip 19 (20): 3366–67. https://doi.org/10.1039/c9lc90103e. Cite
Hordijk, Wim, Mike Steel, and Stuart A. Kauffman. 2019. “Molecular Diversity Required for the Formation of Autocatalytic Sets.” Life (Basel, Switzerland) 9 (1). https://doi.org/10.3390/life9010023. Cite Download
Hordijk, Wim, Stuart A. Kauffman, and Peter F. Stadler. 2019. “Average Fitness Differences on NK Landscapes.” Theory in Biosciences = Theorie in Den Biowissenschaften. https://doi.org/10.1007/s12064-019-00296-0. Cite
Iacobucci, Claudio, Christine Piotrowski, Ruedi Aebersold, Bruno C. Amaral, Philip Andrews, Katja Bernfur, Christoph Borchers, et al. 2019. “First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.” Analytical Chemistry 91 (11): 6953–61. https://doi.org/10.1021/acs.analchem.9b00658. Cite
Ignjatovic, Vera, Philipp E. Geyer, Krishnan K. Palaniappan, Jessica E. Chaaban, Gilbert S. Omenn, Mark S. Baker, Eric W. Deutsch, and Jochen M. Schwenk. 2019. “Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.9b00503. Cite
Javitz, Harold S., Terry M. Bush, Jennifer C. Lovejoy, Alula J. Torres, Tallie Wetzel, Ken P. Wassum, Marcia M. Tan, Nabil Alshurafa, and Bonnie Spring. 2019. “Six Month Abstinence Heterogeneity in the Best Quit Study.” Annals of Behavioral Medicine: A Publication of the Society of Behavioral Medicine. https://doi.org/10.1093/abm/kaz014. Cite
Johnson, Kaitlyn E., Grant Howard, William Mo, Michael K. Strasser, Ernesto A. B. F. Lima, Sui Huang, and Amy Brock. 2019. “Cancer Cell Population Growth Kinetics at Low Densities Deviate from the Exponential Growth Model and Suggest an Allee Effect.” PLoS Biology 17 (8): e3000399. https://doi.org/10.1371/journal.pbio.3000399. Cite Download
Johnson, Richard, Brian C. Searle, Brook L. Nunn, Jason M. Gilmore, Molly Phillips, Chris T. Amemiya, Michelle Heck, and Michael J. MacCoss. 2019. “Assessing Protein Sequence Database Suitability Using de Novo Sequencing.” Molecular & Cellular Proteomics: MCP. https://doi.org/10.1074/mcp.TIR119.001752. Cite
Katrib, Amal, Hyun-Hwan Jeong, Nina L. Fransen, Kristin S. Henzel, and Jeremy A. Miller. 2019. “An Inflammatory Landscape for Preoperative Neurologic Deficits in Glioblastoma.” Frontiers in Genetics 10: 488. https://doi.org/10.3389/fgene.2019.00488. Cite Download
Knijnenburg, Theo A., Joseph G. Vockley, Nyasha Chambwe, David L. Gibbs, Crystal Humphries, Kathi C. Huddleston, Elisabeth Klein, et al. 2019. “Genomic and Molecular Characterization of Preterm Birth.” Proceedings of the National Academy of Sciences of the United States of America 116 (12): 5819–27. https://doi.org/10.1073/pnas.1716314116. Cite Download
Lee, Min Young, Taek-Kyun Kim, Kathie-Anne Walters, and Kai Wang. 2019. “A Biological Function Based Biomarker Panel Optimization Process.” Scientific Reports 9 (1): 7365. https://doi.org/10.1038/s41598-019-43779-2. Cite Download
Lee, Min Young, David Baxter, Kelsey Scherler, Taek-Kyun Kim, Xiaogang Wu, Duna Abu-Amara, Janine Flory, et al. 2019. “Distinct Profiles of Cell-Free MicroRNAs in Plasma of Veterans with Post-Traumatic Stress Disorder.” Journal of Clinical Medicine 8 (7). https://doi.org/10.3390/jcm8070963. Cite Download
Lee, Ming-Jen, Shannon Fallen, Yong Zhou, David Baxter, Kelsey Scherler, Meng-Fai Kuo, and Kai Wang. 2019. “The Impact of Moyamoya Disease and RNF213 Mutations on the Spectrum of Plasma Protein and MicroRNA.” Journal of Clinical Medicine 8 (10). https://doi.org/10.3390/jcm8101648. Cite Download
Li, Ziming, Zhuo Wang, Yin Tang, Xiang Lu, Jie Chen, Yu Dong, Baojun Wu, et al. 2019. “Liquid Biopsy-Based Single-Cell Metabolic Phenotyping of Lung Cancer Patients for Informative Diagnostics.” Nature Communications 10 (1): 3856. https://doi.org/10.1038/s41467-019-11808-3. Cite Download
Li, Jeremiah H., Felix X.-F. Ye, Hong Qian, and Sui Huang. 2019. “Time-Dependent Saddle-Node Bifurcation: Breaking Time and the Point of No Return in a Non-Autonomous Model of Critical Transitions.” Physica D. Nonlinear Phenomena 395: 7–14. https://doi.org/10.1016/j.physd.2019.02.005. Cite Download
Liang, JingXin, David N. Bunck, Anvita Mishra, Sunga Hong, Matthew N. Idso, and James R. Heath. 2019. “Inhibition of Heme Sequestration of Histidine-Rich Protein 2 Using Multiple Epitope-Targeted Peptides.” Journal of Peptide Science: An Official Publication of the European Peptide Society 25 (9): e3203. https://doi.org/10.1002/psc.3203. Cite