| 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 | 17396 | 2003 |
| 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, 2010 | 2101 | 2010 |
| Orchestrating high-throughput genomic analysis with Bioconductor W Huber, VJ Carey, R Gentleman, S Anders, M Carlson, BS Carvalho, ... Nature methods 12 (2), 115, 2015 | 1561 | 2015 |
| 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 | 1058 | 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 (5), R36, 2006 | 531 | 2006 |
| 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 | 348 | 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 | 300 | 2007 |
| 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 | 245 | 2003 |
| 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 | 202 | 2018 |
| 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), 2007 | 198 | 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), 176, 2006 | 188 | 2006 |
| Ramage d, Amin N, Schwikowski B and Ideker T: cytoscape: A software environment for integrated models of biomolecular interaction networks P Shannon, A Markiel, O Ozier, NS Baliga, JT Wang Genome res 13, 2498-2504, 2003 | 182 | 2003 |
| Coordinate regulation of energy transduction modules in Halobacterium sp. analyzed by a global systems approach NS Baliga, M Pan, YA Goo, CY Eugene, DR Goodlett, K Dimitrov, ... Proceedings of the National Academy of Sciences 99 (23), 14913-14918, 2002 | 166 | 2002 |
| 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 | 151 | 2014 |
| Derivation of genetic interaction networks from quantitative phenotype data BL Drees, V Thorsson, GW Carter, AW Rives, MZ Raymond, ... Genome biology 6 (4), R38, 2005 | 131 | 2005 |
| 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 | 128 | 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, CY Eugene, P Shannon, ... Cancer research 65 (8), 3081-3091, 2005 | 127 | 2005 |
| System-based proteomic analysis of the interferon response in human liver cells W Yan, H Lee, CY Eugene, D Reiss, P Shannon, BK Kwieciszewski, ... Genome biology 5 (8), R54, 2004 | 94 | 2004 |
| RCytoscape: tools for exploratory network analysis PT Shannon, M Grimes, B Kutlu, JJ Bot, DJ Galas BMC bioinformatics 14 (1), 217, 2013 | 81 | 2013 |
| Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1 R Bonneau, NS Baliga, EW Deutsch, P Shannon, L Hood Genome biology 5 (8), R52, 2004 | 68 | 2004 |
