Publications

Bolouri, Hamid, Mary Young, Joshua Beilke, Rebecca Johnson, Brian Fox, Lu Huang, Cristina Costa Santini, et al. 2020. “Integrative Network Modeling Reveals Mechanisms Underlying T Cell Exhaustion.” Scientific Reports 10 (1): 1915. https://doi.org/10.1038/s41598-020-58600-8. Cite Download

Buchweitz, Lea F., James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, et al. 2020. “Visualizing Metabolic Network Dynamics through Time-Series Metabolomic Data.” BMC Bioinformatics 21 (1): 130. https://doi.org/10.1186/s12859-020-3415-z. Cite Download

Derks, S., L. K. de Klerk, X. Xu, T. Fleitas, K. X. Liu, Y. Liu, F. Dietlein, et al. 2020. “Characterizing Diversity in the Tumor-Immune Microenvironment of Distinct Subclasses of Gastroesophageal Adenocarcinomas.” Annals of Oncology: Official Journal of the European Society for Medical Oncology. https://doi.org/10.1016/j.annonc.2020.04.011. Cite

Diener, Christian, Sean M. Gibbons, and Osbaldo Resendis-Antonio. 2020. “MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota.” MSystems 5 (1). https://doi.org/10.1128/mSystems.00606-19. Cite

Doan, Phuong, Aliyu Musa, Akshaya Murugesan, Vili Sipilä, Nuno R. Candeias, Frank Emmert-Streib, Pekka Ruusuvuori, Kirsi Granberg, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2020. “Glioblastoma Multiforme Stem Cell Cycle Arrest by Alkylaminophenol Through the Modulation of EGFR and CSC Signaling Pathways.” Cells 9 (3). https://doi.org/10.3390/cells9030681. Cite Download

Eng, Jimmy K., and Eric W. Deutsch. 2020. “Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.” Proteomics, February, e1900362. https://doi.org/10.1002/pmic.201900362. Cite

Flynn, Jullien M., Robert Hubley, Clément Goubert, Jeb Rosen, Andrew G. Clark, Cédric Feschotte, and Arian F. Smit. 2020. “RepeatModeler2 for Automated Genomic Discovery of Transposable Element Families.” Proceedings of the National Academy of Sciences of the United States of America, April. https://doi.org/10.1073/pnas.1921046117. Cite Download

Ghai, Vikas, Shannon Fallen, David Baxter, Kelsey Scherler, Taek-Kyun Kim, Yong Zhou, James Meabon, et al. 2020. “Alterations in Plasma MicroRNA and Protein Levels in War Veterans with Chronic Mild Traumatic Brain Injury.” Journal of Neurotrauma, February. https://doi.org/10.1089/neu.2019.6826. Cite

Ghai, Vikas, Shannon Fallen, David Baxter, Kelsey Scherler, Taek-Kyun Kim, Yong Zhou, James S. Meabon, et al. 2020. “Alterations in Plasma MicroRNA and Protein Levels in War Veterans with Chronic Mild Traumatic Brain Injury.” Journal of Neurotrauma, March. https://doi.org/10.1089/neu.2019.6826. Cite

Herrmann, Marietta, Anne Babler, Irina Moshkova, Felix Gremse, Fabian Kiessling, Ulrike Kusebauch, Valentin Nelea, et al. 2020. “Lumenal Calcification and Microvasculopathy in Fetuin-A-Deficient Mice Lead to Multiple Organ Morbidity.” PloS One 15 (2): e0228503. https://doi.org/10.1371/journal.pone.0228503. Cite Download

Jung, Jae Hun, Kohei Taniguchi, Hyeong Min Lee, Min Young Lee, Raju Bandu, Kazumasa Komura, Kil Yeon Lee, Yukihiro Akao, and Kwang Pyo Kim. 2020. “Comparative Lipidomics of 5-Fluorouracil-Sensitive and -Resistant Colorectal Cancer Cells Reveals Altered Sphingomyelin and Ceramide Controlled by Acid Sphingomyelinase (SMPD1).” Scientific Reports 10 (1): 6124. https://doi.org/10.1038/s41598-020-62823-0. Cite Download

Kagan, Jacob, Robert L. Moritz, Richard Mazurchuk, Je Hyuk Lee, Peter Vasili Kharchenko, Orit Rozenblatt-Rosen, Eytan Ruppin, et al. 2020. “National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions.” Journal of Proteome Research, April. https://doi.org/10.1021/acs.jproteome.0c00021. Cite

Kauffman, Stuart A., Dávid Péter Jelenfi, and Gábor Vattay. 2020. “Theory of Chemical Evolution of Molecule Compositions in the Universe, in the Miller-Urey Experiment and the Mass Distribution of Interstellar and Intergalactic Molecules.” Journal of Theoretical Biology 486: 110097. https://doi.org/10.1016/j.jtbi.2019.110097. Cite Download

Kenerson, Heidi L., Kevin M. Sullivan, Yongwoo D. Seo, Kathryn M. Stadeli, Cigdem Ussakli, Xiaowei Yan, Chris Lausted, et al. 2020. “Tumor Slice Culture as a Biologic Surrogate of Human Cancer.” Annals of Translational Medicine 8 (4): 114. https://doi.org/10.21037/atm.2019.12.88. Cite Download

Kim, Taek-Kyun, Inyoul Lee, Ji-Hoon Cho, Brenda Canine, Andrew Keller, Nathan D. Price, Daehee Hwang, George Carlson, and Leroy Hood. 2020. “Core Transcriptional Regulatory Circuits in Prion Diseases.” Molecular Brain 13 (1): 10. https://doi.org/10.1186/s13041-020-0551-3. Cite Download

Kim, Mun Kyoung, An Tranvo, Ann Marie Hurlburt, Neha Verma, Phuc Phan, Jie Luo, Jeff Ranish, and William E. Stumph. 2020. “Assembly of SNAPc, Bdp1, and TBP on the U6 SnRNA Gene Promoter in Drosophila Melanogaster.” Molecular and Cellular Biology, April. https://doi.org/10.1128/MCB.00641-19. Cite

Lee, Wei-Hao, Kai-Pu Chen, Kai Wang, Hsuan-Cheng Huang, and Hsueh-Fen Juan. 2020. “Characterizing the Cancer-Associated Microbiome with Small RNA Sequencing Data.” Biochemical and Biophysical Research Communications 522 (3): 776–82. https://doi.org/10.1016/j.bbrc.2019.11.166. Cite Download

Li, Hong-Dong, Cory C. Funk, and Nathan D. Price. 2020. “IREAD: A Tool for Intron Retention Detection from RNA-Seq Data.” BMC Genomics 21 (1): 128. https://doi.org/10.1186/s12864-020-6541-0. Cite Download

Lieven, Christian, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, et al. 2020. “Publisher Correction: MEMOTE for Standardized Genome-Scale Metabolic Model Testing.” Nature Biotechnology 38 (4): 504. https://doi.org/10.1038/s41587-020-0477-4. Cite Download

Lieven, Christian, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, et al. 2020. “MEMOTE for Standardized Genome-Scale Metabolic Model Testing.” Nature Biotechnology 38 (3): 272–76. https://doi.org/10.1038/s41587-020-0446-y. Cite Download

McPhillie, Martin, Ying Zhou, Kamal El Bissati, Jitender Dubey, Hernan Lorenzi, Michael Capper, Amanda K. Lukens, et al. 2020. “Author Correction: New Paradigms for Understanding and Step Changes in Treating Active and Chronic, Persistent Apicomplexan Infections.” Scientific Reports 10 (1): 5512. https://doi.org/10.1038/s41598-020-62323-1. Cite Download

Mische, Sheenah M., Nancy C. Fisher, Susan M. Meyn, Katia Sol Church, Rebecca L. Hegstad-Davies, Frances Weis-Garcia, Marie Adams, et al. 2020. “A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups.” Journal of Biomolecular Techniques: JBT. https://doi.org/10.7171/jbt.20-3101-003. Cite

Palanivel, Suresh, Akshaya Murugesan, Olli Yli-Harja, and Meenakshisundaram Kandhavelu. 2020. “Anticancer Activity of THMPP: Downregulation of PI3K/ S6K1 in Breast Cancer Cell Line.” Saudi Pharmaceutical Journal: SPJ: The Official Publication of the Saudi Pharmaceutical Society 28 (4): 495–503. https://doi.org/10.1016/j.jsps.2020.02.015. Cite Download

Paquette, Alison G., Leroy Hood, Nathan D. Price, and Yoel Sadovsky. 2020. “Deep Phenotyping during Pregnancy for Predictive and Preventive Medicine.” Science Translational Medicine 12 (527). https://doi.org/10.1126/scitranslmed.aay1059. Cite

Piening, Brian D., Jennifer Lovejoy, and John C. Earls. 2020. “Ageotypes: Distinct Biomolecular Trajectories in Human Aging.” Trends in Pharmacological Sciences 41 (5): 299–301. https://doi.org/10.1016/j.tips.2020.02.003. Cite

Pino, Lindsay K., Seth C. Just, Michael J. MacCoss, and Brian C. Searle. 2020. “Acquiring and Analyzing Data Independent Acquisition Proteomics Experiments without Spectrum Libraries.” Molecular & Cellular Proteomics: MCP, April. https://doi.org/10.1074/mcp.P119.001913. Cite Download

Searle, Brian C., Kristian E. Swearingen, Christopher A. Barnes, Tobias Schmidt, Siegfried Gessulat, Bernhard Küster, and Mathias Wilhelm. 2020. “Generating High Quality Libraries for DIA MS with Empirically Corrected Peptide Predictions.” Nature Communications 11 (1): 1548. https://doi.org/10.1038/s41467-020-15346-1. Cite Download

Sigmarsdóttir, Þóra, Sarah McGarrity, Óttar Rolfsson, James T. Yurkovich, and Ólafur E. Sigurjónsson. 2020. “Current Status and Future Prospects of Genome-Scale Metabolic Modeling to Optimize the Use of Mesenchymal Stem Cells in Regenerative Medicine.” Frontiers in Bioengineering and Biotechnology 8: 239. https://doi.org/10.3389/fbioe.2020.00239. Cite Download

Steel, Mike, Wim Hordijk, and Stuart A. Kauffman. 2020. “Dynamics of a Birth-Death Process Based on Combinatorial Innovation.” Journal of Theoretical Biology 491 (April): 110187. https://doi.org/10.1016/j.jtbi.2020.110187. Cite Download

Su, Yapeng, Melissa E. Ko, Hanjun Cheng, Ronghui Zhu, Min Xue, Jessica Wang, Jihoon W. Lee, et al. 2020. “Multi-Omic Single-Cell Snapshots Reveal Multiple Independent Trajectories to Drug Tolerance in a Melanoma Cell Line.” Nature Communications 11 (1): 2345. https://doi.org/10.1038/s41467-020-15956-9. Cite Download

Theobald, Elli J., Mariah J. Hill, Elisa Tran, Sweta Agrawal, E. Nicole Arroyo, Shawn Behling, Nyasha Chambwe, et al. 2020. “Active Learning Narrows Achievement Gaps for Underrepresented Students in Undergraduate Science, Technology, Engineering, and Math.” Proceedings of the National Academy of Sciences of the United States of America 117 (12): 6476–83. https://doi.org/10.1073/pnas.1916903117. Cite Download

Thorsson, Vésteinn. 2020. “Multiplatform Integrative Analysis of Immunogenomic Data for Biomarker Discovery.” Methods in Molecular Biology (Clifton, N.J.) 2055: 679–98. https://doi.org/10.1007/978-1-4939-9773-2_30. Cite

Vizcaíno, Juan Antonio, Peter Kubiniok, Kevin A. Kovalchik, Qing Ma, Jérôme D. Duquette, Ian Mongrain, Eric W. Deutsch, et al. 2020. “The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases.” Molecular & Cellular Proteomics: MCP 19 (1): 31–49. https://doi.org/10.1074/mcp.R119.001743. Cite

Vos, Rutger A., Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, et al. 2020. “BioHackathon 2015: Semantics of Data for Life Sciences and Reproducible Research.” F1000Research 9: 136. https://doi.org/10.12688/f1000research.18236.1. Cite Download

Wenderski, Wendy, Lu Wang, Andrey Krokhotin, Jessica J. Walsh, Hongjie Li, Hirotaka Shoji, Shereen Ghosh, et al. 2020. “Loss of the Neural-Specific BAF Subunit ACTL6B Relieves Repression of Early Response Genes and Causes Recessive Autism.” Proceedings of the National Academy of Sciences of the United States of America, April. https://doi.org/10.1073/pnas.1908238117. Cite Download

Xavier, Joana C., Wim Hordijk, Stuart Kauffman, Mike Steel, and William F. Martin. 2020. “Autocatalytic Chemical Networks at the Origin of Metabolism.” Proceedings. Biological Sciences 287 (1922): 20192377. https://doi.org/10.1098/rspb.2019.2377. Cite Download

Xavier, Joao B., Vincent B. Young, Joseph Skufca, Fiona Ginty, Traci Testerman, Alexander T. Pearson, Paul Macklin, et al. 2020. “The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View.” Trends in Cancer 6 (3): 192–204. https://doi.org/10.1016/j.trecan.2020.01.004. Cite Download

Yang, Zhen, Matthias Dehmer, Olli Yli-Harja, and Frank Emmert-Streib. 2020. “Combining Deep Learning with Token Selection for Patient Phenotyping from Electronic Health Records.” Scientific Reports 10 (1): 1432. https://doi.org/10.1038/s41598-020-58178-1. Cite Download

Yang, Liu, Xiaowei Yan, Jie Chen, Qiong Zhan, Yingqi Hua, Shili Xu, Yu Dong, et al. 2020. “Resolving an Underrepresented Circulating Tumor Cell Population in Lung Cancer Enabled by Hexokinase 2 Analysis.” BioRxiv, 2020.04.27.064345. https://doi.org/10.1101/2020.04.27.064345. Cite Download