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
Bedognetti, Davide, Michele Ceccarelli, Lorenzo Galluzzi, Rongze Lu, Karolina Palucka, Josue Samayoa, Stefani Spranger, et al. 2019. “Toward a Comprehensive View of Cancer Immune Responsiveness: A Synopsis from the SITC Workshop.” Journal for Immunotherapy of Cancer 7 (1): 131. https://doi.org/10.1186/s40425-019-0602-4. 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
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
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
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
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
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 C. Andrews, Katja Bernfur, Christoph H. Borchers, et al. 2019. “The First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.” Analytical Chemistry. https://doi.org/10.1021/acs.analchem.9b00658. 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
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
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
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
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
Palii, Carmen G., Qian Cheng, Mark A. Gillespie, Paul Shannon, Michalina Mazurczyk, Giorgio Napolitani, Nathan D. Price, et al. 2019. “Single-Cell Proteomics Reveal That Quantitative Changes in Co-Expressed Lineage-Specific Transcription Factors Determine Cell Fate.” Cell Stem Cell 24 (5): 812-820.e5. https://doi.org/10.1016/j.stem.2019.02.006. Cite
Panigrahy, Dipak, Allison Gartung, Jun Yang, Haixia Yang, Molly M. Gilligan, Megan L. Sulciner, Swati S. Bhasin, et al. 2019. “Preoperative Stimulation of Resolution and Inflammation Blockade Eradicates Micrometastases.” The Journal of Clinical Investigation 129 (7). https://doi.org/10.1172/JCI127282. Cite Download
Panigrahy, Dipak, Allison Gartung, Jun Yang, Haixia Yang, Molly M. Gilligan, Megan L. Sulciner, Swati S. Bhasin, et al. 2019. “Preoperative Stimulation of Resolution and Inflammation Blockade Eradicates Micrometastases.” The Journal of Clinical Investigation 130. https://doi.org/10.1172/JCI127282. Cite
Pearl, Jocelynn R., Carlo Colantuoni, Dani E. Bergey, Cory C. Funk, Paul Shannon, Bijoya Basu, Alex M. Casella, et al. 2019. “Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders.” Cell Systems 8 (2): 122-135.e7. https://doi.org/10.1016/j.cels.2019.01.002. Cite
Peterson, Eliza Jr, Rebeca Bailo, Alissa C. Rothchild, Mario L. Arrieta-Ortiz, Amardeep Kaur, Min Pan, Dat Mai, et al. 2019. “Path-Seq Identifies an Essential Mycolate Remodeling Program for Mycobacterial Host Adaptation.” Molecular Systems Biology 15 (3): e8584. https://doi.org/10.15252/msb.20188584. Cite Download
Pioner, J. Manuel, Xuan Guan, Jordan M. Klaiman, Alice W. Racca, Lil Pabon, Veronica Muskheli, Jesse Macadangdang, et al. 2019. “Absence of Full-Length Dystrophin Impairs Normal Maturation and Contraction of Cardiomyocytes Derived from Human Induced Pluripotent Stem Cells.” Cardiovascular Research. https://doi.org/10.1093/cvr/cvz109. Cite
Prada, Carlos F., and Jeffrey L. Boore. 2019. “Gene Annotation Errors Are Common in the Mammalian Mitochondrial Genomes Database.” BMC Genomics 20 (1): 73. https://doi.org/10.1186/s12864-019-5447-1. Cite Download
Regier, Mary C., Emily Olszewski, Christoph C. Carter, John D. Aitchison, Alexis Kaushansky, Jennifer Davis, Erwin Berthier, David J. Beebe, and Kelly R. Stevens. 2019. “Spatial Presentation of Biological Molecules to Cells by Localized Diffusive Transfer.” Lab on a Chip 19 (12): 2114–26. https://doi.org/10.1039/c9lc00122k. Cite
Sathe, Santosh, Mónica V. Orellana, Nitin S. Baliga, and Pierre M. Durand. 2019. “Temporal and Metabolic Overlap between Lipid Accumulation and Programmed Cell Death Due to Nitrogen Starvation in the Unicellular Chlorophyte Chlamydomonas Reinhardtii.” Phycological Research 67 (3): 173–83. https://doi.org/10.1111/pre.12368. Cite
Searle, Brian C., and Alfred L. Yergey. 2019. “An Efficient Solution for Resolving ITRAQ and TMT Channel Cross-Talk.” Journal of Mass Spectrometry: JMS. https://doi.org/10.1002/jms.4354. Cite
Shahid, Muhammad, Minhyung Kim, Min Young Lee, Austin Yeon, Sungyong You, Hyung L. Kim, and Jayoung Kim. 2019. “Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism.” Proteomics, e1900038. https://doi.org/10.1002/pmic.201900038. Cite
Shen, Fangzhou, Renliang Sun, Jie Yao, Jian Li, Qian Liu, Nathan D. Price, Chenguang Liu, and Zhuo Wang. 2019. “OptRAM: In-Silico Strain Design via Integrative Regulatory-Metabolic Network Modeling.” PLoS Computational Biology 15 (3): e1006835. https://doi.org/10.1371/journal.pcbi.1006835. Cite Download
Shteynberg, David D., Eric W. Deutsch, David S. Campbell, Michael R. Hoopmann, Ulrike Kusebauch, Dave Lee, Luis Mendoza, et al. 2019. “PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline.” BioRxiv, 679845. https://doi.org/10.1101/679845. Cite Download
Su, Yapeng, Marcus Bintz, Yezi Yang, Lidia Robert, Alphonsus H. C. Ng, Victoria Liu, Antoni Ribas, James R. Heath, and Wei Wei. 2019. “Phenotypic Heterogeneity and Evolution of Melanoma Cells Associated with Targeted Therapy Resistance.” PLoS Computational Biology 15 (6): e1007034. https://doi.org/10.1371/journal.pcbi.1007034. Cite Download