Paul Shannon

Senior Software Engineer

Paul Shannon spent his twenties as a carpenter, eventually returning to college to prepare for a second career as a scientific programmer. He subsequently worked in a variety of disciplines: atmospheric chemistry, psychoacoustics, mechanical engineering, radio astronomy, then realized his long-held aspiration to work in biology and medicine by joining the ISB in 2001. He recently spent 4 years at the Fred Hutch in the Bioconductor and the Solid Tumor Translational Research projects, and is delighted to now be back at the ISB.

BA Mathematics, University of Virginia

Bioinformatics, Interactive Data Visualization

Baliga, N. S., M. Pan, Y. A. Goo, E. C. Yi, D. R. Goodlett, K. Dimitrov, P. Shannon, R. Aebersold, W. V. Ng, and L. Hood. 2002. “Coordinate Regulation of Energy Transduction Modules in Halobacterium Sp. Analyzed by a Global Systems Approach.” Proc Natl Acad Sci U S A 99 (23): 14913–18. Cite
Utleg, A. G., E. C. Yi, T. Xie, P. Shannon, J. T. White, D. R. Goodlett, L. Hood, and B. Lin. 2003. “Proteomic Analysis of Human Prostasomes.” Prostate 56 (2): 150–61. Cite
Shannon, P., A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. “Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks.” Genome Res 13 (11): 2498–2504. Cite
Bonneau, R., N. S. Baliga, E. W. Deutsch, P. Shannon, and L. Hood. 2004. “Comprehensive de Novo Structure Prediction in a Systems-Biology Context for the Archaea Halobacterium Sp. NRC-1.” Genome Biol 5 (8): R52. Cite
Yan, W., H. Lee, E. C. Yi, D. Reiss, P. Shannon, B. K. Kwieciszewski, C. Coito, et al. 2004. “System-Based Proteomic Analysis of the Interferon Response in Human Liver Cells.” Genome Biol 5 (8): R54. Cite
Baliga, N. S., R. Bonneau, M. T. Facciotti, M. Pan, G. Glusman, E. W. Deutsch, P. Shannon, et al. 2004. “Genome Sequence of Haloarcula Marismortui: A Halophilic Archaeon from the Dead Sea.” Genome Res 14 (11): 2221–34. Cite
Drees, B. L., V. Thorsson, G. W. Carter, A. W. Rives, M. Z. Raymond, I. Avila-Campillo, P. Shannon, and T. Galitski. 2005. “Derivation of Genetic Interaction Networks from Quantitative Phenotype Data.” Genome Biol 6 (4): R38. Cite
Lin, B., J. T. White, W. Lu, T. Xie, A. G. Utleg, X. Yan, E. C. Yi, et al. 2005. “Evidence for the Presence of Disease-Perturbed Networks in Prostate Cancer Cells by Genomic and Proteomic Analyses: A Systems Approach to Disease.” Cancer Res 65 (8): 3081–91. Cite
Shannon, P., D. J. Reiss, R. Bonneau, and N. S. Baliga. 2006. “The Gaggle: An Open-Source Software System for Integrating Bioinformatics Software and Data Sources.” BMC Bioinformatics 7: 176. Cite
Bonneau, R., D. J. Reiss, P. Shannon, M. Facciotti, L. Hood, N. S. Baliga, and V. Thorsson. 2006. “The Inferelator: An Algorithm for Learning Parsimonious Regulatory Networks from Systems-Biology Data Sets de Novo.” Genome Biol 7 (5): R36. Cite
Bodenmiller, B., J. Malmstrom, B. Gerrits, D. Campbell, H. Lam, A. Schmidt, O. Rinner, et al. 2007. “PhosphoPep–a Phosphoproteome Resource for Systems Biology Research in Drosophila Kc167 Cells.” Mol Syst Biol 3: 139. Cite
Facciotti, M. T., D. J. Reiss, M. Pan, A. Kaur, M. Vuthoori, R. Bonneau, P. Shannon, et al. 2007. “General Transcription Factor Specified Global Gene Regulation in Archaea.” Proc Natl Acad Sci U S A 104 (11): 4630–35. Cite
Bare, J. C., P. Shannon, A. K. Schmid, and N. S. Baliga. 2007. “The Firegoose: Two-Way Integration of Diverse Data from Different Bioinformatics Web Resources with Desktop Applications.” BMC Bioinformatics 8 (1): 456. Cite
Bonneau, R., M. T. Facciotti, D. J. Reiss, A. K. Schmid, M. Pan, A. Kaur, V. Thorsson, et al. 2007. “A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell.” Cell 131 (7): 1354–65. Cite
Ramos, H., P. Shannon, and R. Aebersold. 2008. “The Protein Information and Property Explorer: An Easy-to-Use, Rich-Client Web Application for the Management and Functional Analysis of Proteomic Data.” Bioinformatics 24 (18): 2110–11. Cite
Letarte, S., M. Y. Brusniak, D. Campbell, J. Eddes, C. J. Kemp, H. Lau, L. Mueller, et al. 2008. “Differential Plasma Glycoproteome of P19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform.” Clin Proteomics 4 (3–4): 105. Cite
Ng, S. B., K. J. Buckingham, C. Lee, A. W. Bigham, H. K. Tabor, K. M. Dent, C. D. Huff, et al. 2010. “Exome Sequencing Identifies the Cause of a Mendelian Disorder.” Nat Genet 42 (1): 30–35. Cite
Roach, J., G. Glusman, A. Smit, C. D. Huff, R. Hubley, P. Shannon, L. Rowen, et al. 2010. “Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing.” Science 328 (5978): 636–39. Cite
Saleem, R. A., R. S. Rogers, A. V. Ratushny, D. J. Dilworth, P. Shannon, D. Shteynberg, Y. Wan, et al. 2010. “Integrated Phosphoproteomics Analysis of a Signaling Network Governing Nutrient Response and Peroxisome Induction.” Mol Cell Proteomics 9 (9): 2076–88. Cite
Ramos, H., P. Shannon, M. Y. Brusniak, U. Kusebauch, R. L. Moritz, and R. Aebersold. 2011. “The Protein Information and Property Explorer 2: Gaggle-like Exploration of Biological Proteomic Data within One Webpage.” Proteomics 11 (1): 154–58. Cite
Sperber, Henrik, Alan Beem, Sandra Shannon, Ross Jones, Pratyusha Banik, Yu Chen, Sherman Ku, Gabriele Varani, Shuyuan Yao, and Hannele Ruohola-Baker. 2014. “MiRNA Sensitivity to Drosha Levels Correlates with Pre-MiRNA Secondary Structure.” RNA (New York, N.Y.) 20 (5): 621–31. https://doi.org/10.1261/rna.043943.113. Cite
Saltz, Joel, Rajarsi Gupta, Le Hou, Tahsin Kurc, Pankaj Singh, Vu Nguyen, Dimitris Samaras, et al. 2018. “Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.” Cell Reports 23 (1): 181-193.e7. https://doi.org/10.1016/j.celrep.2018.03.086. Cite Download
Readhead, Ben, Jean-Vianney Haure-Mirande, Cory C. Funk, Matthew A. Richards, Paul Shannon, Vahram Haroutunian, Mary Sano, et al. 2018. “Multiscale Analysis of Independent Alzheimer’s Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus.” Neuron. https://doi.org/10.1016/j.neuron.2018.05.023. Cite
McFerrin, Lisa G., Michael Zager, Jianan Zhang, Gretchen Krenn, Robert McDermott, Desert Horse-Grant, Emily Silgard, et al. 2018. “Analysis and Visualization of Linked Molecular and Clinical Cancer Data by Using Oncoscape.” Nature Genetics 50 (9): 1203–4. https://doi.org/10.1038/s41588-018-0208-7. 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
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
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