| 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 | 14618 | 2003 |
| Integration of biological networks and gene expression data using Cytoscape MS Cline, M Smoot, E Cerami, A Kuchinsky, N Landys, C Workman, ... Nature protocols 2 (10), 2366, 2007 | 1950 | 2007 |
| A network of protein–protein interactions in yeast B Schwikowski, P Uetz, S Fields Nature biotechnology 18 (12), 1257, 2000 | 1502 | 2000 |
| Discovering regulatory and signalling circuits in molecular interaction networks T Ideker, O Ozier, B Schwikowski, AF Siegel Bioinformatics 18 (suppl_1), S233-S240, 2002 | 1188 | 2002 |
| Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis P Nicolas, U Mäder, E Dervyn, T Rochat, A Leduc, N Pigeonneau, ... Science 335 (6072), 1103-1106, 2012 | 556 | 2012 |
| Graph-based methods for analysing networks in cell biology T Aittokallio, B Schwikowski Briefings in bioinformatics 7 (3), 243-255, 2006 | 397 | 2006 |
| ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data N Zhang, R Aebersold, B Schwikowski Proteomics 2 (10), 1406-1412, 2002 | 270 | 2002 |
| Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism JM Buescher, W Liebermeister, M Jules, M Uhr, J Muntel, E Botella, ... Science 335 (6072), 1099-1103, 2012 | 234 | 2012 |
| Algorithms for phylogenetic footprinting M Blanchette, B Schwikowski, M Tompa Journal of computational biology 9 (2), 211-223, 2002 | 230 | 2002 |
| Signal maps for mass spectrometry-based comparative proteomics A Prakash, P Mallick, J Whiteaker, H Zhang, A Paulovich, M Flory, H Lee, ... Molecular & Cellular Proteomics 5 (3), 423-432, 2006 | 130 | 2006 |
| GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring O Garcia, C Saveanu, M Cline, M Fromont-Racine, A Jacquier, ... Bioinformatics 23 (3), 394-396, 2006 | 110 | 2006 |
| Alignment of LC‐MS images, with applications to biomarker discovery and protein identification M Vandenbogaert, S Li‐Thiao‐Té, HM Kaltenbach, R Zhang, T Aittokallio, ... Proteomics 8 (4), 650-672, 2008 | 106 | 2008 |
| Universal DNA tag systems: a combinatorial design scheme A Ben-Dor, R Karp, B Schwikowski, Z Yakhini Journal of computational Biology 7 (3-4), 503-519, 2000 | 102 | 2000 |
| Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli D Duffy, V Rouilly, V Libri, M Hasan, B Beitz, M David, A Urrutia, A Bisiaux, ... Immunity 40 (3), 436-450, 2014 | 95 | 2014 |
| Mining viral protease data to extract cleavage knowledge A Narayanan, X Wu, ZR Yang Bioinformatics 18 (suppl_1), S5-S13, 2002 | 93 | 2002 |
| ProbIDtree: an automated software program capable of identifying multiple peptides from a single collision‐induced dissociation spectrum collected by a tandem mass spectrometer N Zhang, X Li, M Ye, S Pan, B Schwikowski, R Aebersold Proteomics 5 (16), 4096-4106, 2005 | 88 | 2005 |
| On enumerating all minimal solutions of feedback problems B Schwikowski, E Speckenmeyer Discrete Applied Mathematics 117 (1-3), 253-265, 2002 | 86 | 2002 |
| Predicting protein–peptide interactions via a network-based motif sampler DJ Reiss, B Schwikowski Bioinformatics 20 (suppl_1), i274-i282, 2004 | 65 | 2004 |
| Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics A Prakash, B Piening, J Whiteaker, H Zhang, SA Shaffer, D Martin, ... Molecular & cellular proteomics 6 (10), 1741-1748, 2007 | 61 | 2007 |
| An exact algorithm to identify motifs in orthologous sequences from multiple species. M Blanchette, B Schwikowski, M Tompa ISMB, 37-45, 2000 | 61 | 2000 |
Trey IdekerUniversity of California San DiegoVerified email at ucsd.edu