Articles with public access mandates - Paul ShannonLearn more
Available somewhere: 22
Orchestrating high-throughput genomic analysis with Bioconductor
W Huber, VJ Carey, R Gentleman, S Anders, M Carlson, BS Carvalho, ...
Nature methods 12 (2), 115-121, 2015
Mandates: US National Institutes of Health
Exome sequencing identifies the cause of a mendelian disorder
SB Ng, KJ Buckingham, C Lee, AW Bigham, HK Tabor, KM Dent, CD Huff, ...
Nature genetics 42 (1), 30-35, 2010
Mandates: US National Institutes of Health
Analysis of genetic inheritance in a family quartet by whole-genome sequencing
JC Roach, G Glusman, AFA Smit, CD Huff, R Hubley, PT Shannon, ...
Science 328 (5978), 636-639, 2010
Mandates: US National Institutes of Health
Multiscale analysis of independent Alzheimer’s cohorts finds disruption of molecular, genetic, and clinical networks by human herpesvirus
B Readhead, JV Haure-Mirande, CC Funk, MA Richards, P Shannon, ...
Neuron 99 (1), 64-82. e7, 2018
Mandates: US National Institutes of Health
VariantAnnotation : a Bioconductor package for exploration and annotation of genetic variants
V Obenchain, M Lawrence, V Carey, S Gogarten, P Shannon, M Morgan
Bioinformatics 30 (14), 2076-2078, 2014
Mandates: US National Institutes of Health
PhosphoPep—a phosphoproteome resource for systems biology research in Drosophila Kc167 cells
B Bodenmiller, J Malmstrom, B Gerrits, D Campbell, H Lam, A Schmidt, ...
Molecular systems biology 3 (1), 139, 2007
Mandates: German Research Foundation
Single-cell proteomics reveal that quantitative changes in co-expressed lineage-specific transcription factors determine cell fate
CG Palii, Q Cheng, MA Gillespie, P Shannon, M Mazurczyk, G Napolitani, ...
Cell stem cell 24 (5), 812-820. e5, 2019
Mandates: US National Institutes of Health, UK Medical Research Council, National …
Absolute quantification of transcription factors reveals principles of gene regulation in erythropoiesis
MA Gillespie, CG Palii, D Sanchez-Taltavull, P Shannon, ...
Molecular cell 78 (5), 960-974. e11, 2020
Mandates: US National Institutes of Health, UK Medical Research Council, Wellcome Trust
CyREST: turbocharging Cytoscape access for external tools via a RESTful API
K Ono, T Muetze, G Kolishovski, P Shannon, B Demchak
F1000Research 4, 2015
Mandates: US National Institutes of Health
Reproducible big data science: A case study in continuous FAIRness
R Madduri, K Chard, M D’Arcy, SC Jung, A Rodriguez, D Sulakhe, ...
PloS one 14 (4), e0213013, 2019
Mandates: US Department of Energy, US National Institutes of Health
Genome-scale transcriptional regulatory network models of psychiatric and neurodegenerative disorders
JR Pearl, C Colantuoni, DE Bergey, CC Funk, P Shannon, B Basu, ...
Cell systems 8 (2), 122-135. e7, 2019
Mandates: US National Science Foundation, US National Institutes of Health
Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction
RA Saleem, RS Rogers, AV Ratushny, DJ Dilworth, PT Shannon, ...
Molecular & Cellular Proteomics 9 (9), 2076-2088, 2010
Mandates: US National Institutes of Health, Canadian Institutes of Health Research
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data
H Ramos, P Shannon, R Aebersold
Bioinformatics 24 (18), 2110-2111, 2008
Mandates: US National Institutes of Health
Atlas of transcription factor binding sites from ENCODE DNase hypersensitivity data across 27 tissue types
CC Funk, AM Casella, S Jung, MA Richards, A Rodriguez, P Shannon, ...
Cell reports 32 (7), 2020
Mandates: US Department of Energy, US National Institutes of Health
A comprehensive tyrosine phosphoproteomic analysis reveals novel components of the platelet CLEC-2 signaling cascade
I Izquierdo, MN Barrachina, L Hermida-Nogueira, V Casas, LA Morán, ...
Thrombosis and Haemostasis 120 (02), 262-276, 2020
Mandates: German Research Foundation, European Commission, Government of Spain
Wrangling phosphoproteomic data to elucidate cancer signaling pathways
ML Grimes, WJ Lee, L Van der Maaten, P Shannon
PLoS One 8 (1), e52884, 2013
Mandates: US National Institutes of Health
Differential Plasma Glycoproteome of p19ARF Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform
S Letarte, MY Brusniak, D Campbell, J Eddes, CJ Kemp, H Lau, L Mueller, ...
Clinical proteomics 4, 105-116, 2008
Mandates: Swiss National Science Foundation, US National Institutes of Health
The Protein Information and Property Explorer 2: Gaggle‐like exploration of biological proteomic data within one webpage
H Ramos, P Shannon, MY Brusniak, U Kusebauch, RL Moritz, ...
Proteomics 11 (1), 154-158, 2011
Mandates: US National Institutes of Health
Analysis and visualization of linked molecular and clinical cancer data by using Oncoscape
LG McFerrin, M Zager, J Zhang, G Krenn, R McDermott, D Horse-Grant, ...
Nature genetics 50 (9), 1203-1204, 2018
Mandates: US National Institutes of Health
cyjShiny: A cytoscape. js R Shiny Widget for network visualization and analysis
A Luna, O Shah, C Sander, P Shannon
Plos one 18 (8), e0285339, 2023
Mandates: US National Institutes of Health
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