
Atlas of Transcription Factor Binding Sites from ENCODE DNase Hypersensitivity Data across 27 Tissue Types
- Matthew A Richards
- Paul Shannon
- August 20, 2020
- kedalionlabs.com
- Cory C Funk, Alex M Casella, Segun Jung, …, Ravi Madduri, Nathan D Price, Seth A Ament
- Cell Rep, 10.1016/j.celrep.2020.108029
Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis
- Paul Shannon
- Theodore J Perkins
- April 25, 2020
- kedalionlabs.com
- Mark A Gillespie, Carmen G Palii, Daniel Sanchez-Taltavull, …, Theodore J Perkins, Jeffrey A Ranish, Marjorie Brand
- Mol Cell, 10.1016/j.molcel.2020.03.031
Integrative network modeling reveals mechanisms underlying T cell exhaustion
- Hamid Bolouri
- Paul Shannon
- February 7, 2020
- kedalionlabs.com
- Hamid Bolouri, Mary Young, Joshua Beilke, …, Matthew Trotter, Douglas Bassett, Alexander Ratushny
- Sci Rep, 10.1038/s41598-020-58600-8
Reproducible big data science: A case study in continuous FAIRness
- Matthew A Richards
- Paul Shannon
- April 12, 2019
- kedalionlabs.com
- Ravi Madduri, Kyle Chard, Mike D’Arcy, …, Nathan Price, Carl Kesselman, Ian Foster
- PLoS One, 10.1371/journal.pone.0213013
Single-Cell Proteomics Reveal that Quantitative Changes in Co-expressed Lineage-Specific Transcription Factors Determine Cell Fate
- Paul Shannon
- March 19, 2019
- kedalionlabs.com
- Carmen G Palii, Qian Cheng, Mark A Gillespie, …, Edward Morrissey, Douglas R Higgs, Marjorie Brand
- Cell Stem Cell, 10.1016/j.stem.2019.02.006
Genome-Scale Transcriptional Regulatory Network Models of Psychiatric and Neurodegenerative Disorders
- Paul Shannon
- February 18, 2019
- kedalionlabs.com
- Jocelynn R Pearl, Carlo Colantuoni, Dani E Bergey, …, Leroy Hood, Nathan D Price, Seth A Ament
- Cell Syst, 10.1016/j.cels.2019.01.002
Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape
- Paul Shannon
- August 31, 2018
- kedalionlabs.com
- Lisa G McFerrin, Michael Zager, Jianan Zhang, …, Paul Shannon, Hamid Bolouri, Eric C Holland
- Nat Genet, 10.1038/s41588-018-0208-7
CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API
- Paul Shannon
- December 18, 2015
- kedalionlabs.com
- Keiichiro Ono, Tanja Muetze, Georgi Kolishovski, Paul Shannon, Barry Demchak
- F1000Res, 10.12688/f1000research.6767.1
Orchestrating high-throughput genomic analysis with Bioconductor
- Paul Shannon
- January 31, 2015
- kedalionlabs.com
- Wolfgang Huber, Vincent J Carey, Robert Gentleman, …, Dan Tenenbaum, Levi Waldron, Martin Morgan
- Nat Methods, 10.1038/nmeth.3252