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Barry Demchak, Ph.D. - Publications

Affiliations: 
2013 Computer Science and Engineering University of California, San Diego, La Jolla, CA 
Area:
Computer Science
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27 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

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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