Publications

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

Bolyen, Evan, Jai Ram Rideout, Matthew R. Dillon, Nicholas A. Bokulich, Christian C. Abnet, Gabriel A. Al-Ghalith, Harriet Alexander, et al. 2019. “Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2.” Nature Biotechnology 37 (8): 852–57. https://doi.org/10.1038/s41587-019-0209-9. Cite Download

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

Carr, Alex, Christian Diener, Nitin S. Baliga, and Sean M. Gibbons. 2019. “Use and Abuse of Correlation Analyses in Microbial Ecology.” The ISME Journal. https://doi.org/10.1038/s41396-019-0459-z. 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

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

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

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

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

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

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

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

Liu, Xindong, Yun Wang, Huiping Lu, Jing Li, Xiaowei Yan, Minglu Xiao, Jing Hao, et al. 2019. “Genome-Wide Analysis Identifies NR4A1 as a Key Mediator of T Cell Dysfunction.” Nature 567 (7749): 525–29. https://doi.org/10.1038/s41586-019-0979-8. Cite

Lu, Yue, Byung-Kuk Yoo, Alphonsus H. C. Ng, Jungwoo Kim, Sinchul Yeom, Jau Tang, Milo M. Lin, Ahmed H. Zewail, and James R. Heath. 2019. “4D Electron Microscopy of T Cell Activation.” Proceedings of the National Academy of Sciences, 201914078. https://doi.org/10.1073/pnas.1914078116. Cite

Luo, Jie, Jacob Bassett, and Jeff Ranish. 2019. “Identification of Cross-Linked Peptides Using Isotopomeric Cross-Linkers.” Journal of the American Society for Mass Spectrometry. https://doi.org/10.1007/s13361-019-02253-z. Cite

Madduri, Ravi, Kyle Chard, Mike D’Arcy, Segun C. Jung, Alexis Rodriguez, Dinanath Sulakhe, Eric Deutsch, et al. 2019. “Reproducible Big Data Science: A Case Study in Continuous FAIRness.” PloS One 14 (4): e0213013. https://doi.org/10.1371/journal.pone.0213013. Cite Download

Memoli, Matthew J., Alison Han, Kathie-Anne Walters, Lindsay Czajkowski, Susan Reed, Rani Athota, Luz Angela Rosas, et al. 2019. “Influenza A Reinfection in Sequential Human Challenge: Implications for Protective Immunity and ‘Universal’ Vaccine Development.” Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America. https://doi.org/10.1093/cid/ciz281. Cite

Möller, Katrin, Sara Sigurbjornsdottir, Asgeir O. Arnthorsson, Vivian Pogenberg, Ramile Dilshat, Valerie Fock, Solveig H. Brynjolfsdottir, et al. 2019. “MITF Has a Central Role in Regulating Starvation-Induced Autophagy in Melanoma.” Scientific Reports 9 (1): 1055. https://doi.org/10.1038/s41598-018-37522-6. Cite

Musa, Aliyu, Shailesh Tripathi, Matthias Dehmer, Olli Yli-Harja, Stuart A. Kauffman, and Frank Emmert-Streib. 2019. “Systems Pharmacogenomic Landscape of Drug Similarities from LINCS Data: Drug Association Networks.” Scientific Reports 9 (1): 7849. https://doi.org/10.1038/s41598-019-44291-3. Cite Download

Ng, Alphonsus H. C., Songming Peng, Alexander M. Xu, Won Jun Noh, Katherine Guo, Michael T. Bethune, William Chour, et al. 2019. “MATE-Seq: Microfluidic Antigen-TCR Engagement Sequencing.” Lab on a Chip 19 (18): 3011–21. https://doi.org/10.1039/C9LC00538B. Cite Download

Ngô, Huân M., Ying Zhou, Hernan Lorenzi, Kai Wang, Taek-Kyun Kim, Yong Zhou, Kamal El Bissati, et al. 2019. “Publisher Correction: Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer.” Scientific Reports 9 (1): 8110. https://doi.org/10.1038/s41598-019-44545-0. Cite Download