Paul Shannon
Paul Shannon
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Cytoscape: a software environment for integrated models of biomolecular interaction networks
P Shannon, A Markiel, O Ozier, NS Baliga, JT Wang, D Ramage, N Amin, ...
Genome research 13 (11), 2498-2504, 2003
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
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
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
The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
R Bonneau, DJ Reiss, P Shannon, M Facciotti, L Hood, NS Baliga, ...
Genome biology 7, 1-16, 2006
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
Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea
NS Baliga, R Bonneau, MT Facciotti, M Pan, G Glusman, EW Deutsch, ...
Genome research 14 (11), 2221-2234, 2004
A predictive model for transcriptional control of physiology in a free living cell
R Bonneau, MT Facciotti, DJ Reiss, AK Schmid, M Pan, A Kaur, ...
Cell 131 (7), 1354-1365, 2007
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
Proteomic analysis of human prostasomes
AG Utleg, EC Yi, T Xie, P Shannon, JT White, DR Goodlett, L Hood, B Lin
The Prostate 56 (2), 150-161, 2003
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
The Gaggle: an open-source software system for integrating bioinformatics software and data sources
PT Shannon, DJ Reiss, R Bonneau, NS Baliga
BMC bioinformatics 7, 1-13, 2006
Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach
NS Baliga, M Pan, YA Goo, EC Yi, DR Goodlett, K Dimitrov, P Shannon, ...
Proceedings of the National Academy of Sciences 99 (23), 14913-14918, 2002
Derivation of genetic interaction networks from quantitative phenotype data
BL Drees, V Thorsson, GW Carter, AW Rives, MZ Raymond, ...
Genome biology 6, 1-10, 2005
A software environment for integrated models of biomolecular interaction networks., 2003, 13
P Shannon, A Markiel, O Ozier, NS Baliga, JT Wang, D Ramage, N Amin, ...
DOI: https://doi. org/10.1101/gr 1239303, 2498-2504, 0
General transcription factor specified global gene regulation in archaea
MT Facciotti, DJ Reiss, M Pan, A Kaur, M Vuthoori, R Bonneau, ...
Proceedings of the National Academy of Sciences 104 (11), 4630-4635, 2007
Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease
B Lin, JT White, W Lu, T Xie, AG Utleg, X Yan, EC Yi, P Shannon, ...
Cancer research 65 (8), 3081-3091, 2005
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
RCytoscape: tools for exploratory network analysis
PT Shannon, M Grimes, B Kutlu, JJ Bot, DJ Galas
BMC bioinformatics 14, 1-9, 2013
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
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