Year |
Citation |
Score |
2019 |
Gustavsen JA, Pai S, Isserlin R, Demchak B, Pico AR. RCy3: Network biology using Cytoscape from within R. F1000research. 8: 1774. PMID 31819800 DOI: 10.12688/F1000Research.20887.3 |
0.376 |
|
2019 |
Otasek D, Morris JH, Bouças J, Pico AR, Demchak B. Cytoscape Automation: empowering workflow-based network analysis. Genome Biology. 20: 185. PMID 31477170 DOI: 10.1186/S13059-019-1758-4 |
0.365 |
|
2019 |
Yu MK, Ma J, Ono K, Zheng F, Fong SH, Gary A, Chen J, Demchak B, Pratt D, Ideker T. DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. Cell Systems. PMID 30878356 DOI: 10.1016/J.Cels.2019.02.003 |
0.397 |
|
2018 |
Settle B, Otasek D, Morris JH, Demchak B. aMatReader: Importing adjacency matrices via Cytoscape Automation. F1000research. 7: 823. PMID 30026937 DOI: 10.12688/F1000Research.15146.2 |
0.338 |
|
2018 |
Settle B, Otasek D, Morris JH, Demchak B. Copycat Layout: Network layout alignment via Cytoscape Automation. F1000research. 7: 822. PMID 30026936 DOI: 10.12688/F1000Research.15144.2 |
0.341 |
|
2018 |
Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. The Cytoscape Automation app article collection. F1000research. 7: 800. PMID 29983926 DOI: 10.12688/F1000Research.15355.1 |
0.394 |
|
2018 |
Ma J, Yu MK, Fong S, Ono K, Sage E, Demchak B, Sharan R, Ideker T. Using deep learning to model the hierarchical structure and function of a cell. Nature Methods. PMID 29505029 DOI: 10.1038/Nmeth.4627 |
0.303 |
|
2017 |
Pratt D, Chen J, Pillich R, Rynkov V, Gary A, Demchak B, Ideker T. NDEx 2.0: A Clearinghouse for Research on Cancer Pathways. Cancer Research. 77: e58-e61. PMID 29092941 DOI: 10.1158/0008-5472.Can-17-0606 |
0.335 |
|
2017 |
Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Network propagation in the cytoscape cyberinfrastructure. Plos Computational Biology. 13: e1005598. PMID 29023449 DOI: 10.1371/Journal.Pcbi.1005598 |
0.346 |
|
2016 |
Fitts B, Zhang Z, Maher M, Demchak B. dot-app: a Graphviz-Cytoscape conversion plug-in. F1000research. 5: 2543. PMID 27853520 DOI: 10.12688/F1000Research.9751.1 |
0.328 |
|
2016 |
Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, et al. Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature Methods. PMID 26780094 DOI: 10.1038/Nmeth.3732 |
0.379 |
|
2015 |
Ono K, Muetze T, Kolishovski G, Shannon P, Demchak B. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API. F1000research. 4: 478. PMID 26672762 DOI: 10.12688/F1000Research.6767.1 |
0.403 |
|
2015 |
Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobrin R, Braxenthaler M, Kuentzer J, Demchak B, et al. NDEx, the Network Data Exchange. Cell Systems. 1: 302-305. PMID 26594663 DOI: 10.1016/J.Cels.2015.10.001 |
0.358 |
|
2015 |
Summer G, Kelder T, Ono K, Radonjic M, Heymans S, Demchak B. cyNeo4j: connecting Neo4j and Cytoscape. Bioinformatics (Oxford, England). 31: 3868-9. PMID 26272981 DOI: 10.1093/Bioinformatics/Btv460 |
0.338 |
|
2014 |
Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. The Cytoscape app article collection. F1000research. 3: 138. PMID 25580224 DOI: 10.12688/F1000Research.4642.1 |
0.385 |
|
2014 |
Ono K, Demchak B, Ideker T. Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. F1000research. 3: 143. PMID 25520778 DOI: 10.12688/F1000Research.4510.2 |
0.413 |
|
2014 |
Su G, Morris JH, Demchak B, Bader GD. Biological network exploration with cytoscape 3. Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis ... [Et Al.]. 47: 8.13.1-8.13.24. PMID 25199793 DOI: 10.1002/0471250953.Bi0813S47 |
0.372 |
|
2014 |
Demchak B, Hull T, Reich M, Liefeld T, Smoot M, Ideker T, Mesirov JP. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000research. 3: 151. PMID 25165537 DOI: 10.12688/F1000Research.4492.2 |
0.378 |
|
2014 |
Welker D, Demchak B. Porting and using PanGIA for Cytoscape 3: challenges and solutions. F1000research. 3: 150. PMID 25075307 DOI: 10.12688/F1000Research.4546.1 |
0.353 |
|
2014 |
Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. NeXO Web: the NeXO ontology database and visualization platform. Nucleic Acids Research. 42: D1269-74. PMID 24271398 DOI: 10.1093/Nar/Gkt1192 |
0.4 |
|
2012 |
Demchak B, Krüger I. Policy Driven Development: Flexible Policy Insertion for Large Scale Systems. Proceedings. Ieee International Symposium On Policies For Distributed Systems and Networks. 2012: 17-24. PMID 25383258 DOI: 10.1109/POLICY.2012.13 |
0.584 |
|
2012 |
Krüger I, Demchak B, Menarini M. Dynamic Service Composition and Deployment with OpenRichServices Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 7365: 120-146. DOI: 10.1007/978-3-642-30835-2-9 |
0.625 |
|
2008 |
Demchak B, Ermagan V, Farcas C, Farcas E, Krüger IH, Menarini M. Rich services: Addressing challenges of ultra-large-scale software-intensive systems International Conference On Software Engineering - Proceedings of the 2nd International Workshop On Ultra-Large-Scale Software-Intensive Systems, Ulssis'08. 29-32. DOI: 10.1145/1370700.1370709 |
0.634 |
|
2008 |
Demchak B, Ermagan V, Farcas E, Huang TJ, Krüger IH, Menarini M. A rich services approach to CoCoME Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5153: 85-115. DOI: 10.1007/978-3-540-85289-6_5 |
0.644 |
|
2008 |
Demchak B, Krüger IH. Rich feeds for RESCUE Proceedings of Iscram 2008 - 5th International Conference On Information Systems For Crisis Response and Management. 566-575. |
0.34 |
|
2007 |
Demchak B, Farcas C, Farcas E, Krüger IH. The treasure map for Rich Services 2007 Ieee International Conference On Information Reuse and Integration, Ieee Iri-2007. 400-405. DOI: 10.1109/IRI.2007.4296653 |
0.404 |
|
2007 |
Arrott M, Demchak B, Ermagan V, Farcas C, Farcas E, Krüger IH, Menarini M. Rich services: The integration piece of the SOA puzzle Proceedings - 2007 Ieee International Conference On Web Services, Icws 2007. 176-183. DOI: 10.1109/ICWS.2007.155 |
0.641 |
|
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