| 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 | 44529 | 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 | 3621 | 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 | 2570 | 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 | 1315 | 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 | 685 | 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 | 670 | 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 | 386 | 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 | 366 | 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 | 343 | 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 | 297 | 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 | 224 | 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 | 198 | 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 | 172 | 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 | 156 | 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 | 147 | |
| 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 | 145 | 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 | 130 | 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 | 126 | 2019 |
| 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 | 118 | 2020 |
| RCytoscape: tools for exploratory network analysis PT Shannon, M Grimes, B Kutlu, JJ Bot, DJ Galas BMC bioinformatics 14, 1-9, 2013 | 114 | 2013 |