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Barry Demchak
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Cytoscape automation: empowering workflow-based network analysis
D Otasek, JH Morris, J Bouças, AR Pico, B Demchak
Genome biology 20, 1-15, 2019
10682019
Biological network exploration with Cytoscape 3
G Su, JH Morris, B Demchak, GD Bader
Current protocols in bioinformatics 47 (1), 8.13. 1-8.13. 24, 2014
9432014
Using deep learning to model the hierarchical structure and function of a cell
J Ma, MK Yu, S Fong, K Ono, E Sage, B Demchak, R Sharan, T Ideker
Nature methods 15 (4), 290-298, 2018
3802018
NDEx, the network data exchange
D Pratt, J Chen, D Welker, R Rivas, R Pillich, V Rynkov, K Ono, C Miello, ...
Cell systems 1 (4), 302-305, 2015
2452015
Cytoscape: the network visualization tool for GenomeSpace workflows
B Demchak, T Hull, M Reich, T Liefeld, M Smoot, T Ideker, JP Mesirov
F1000Research 3, 2014
1832014
RCy3: Network biology using Cytoscape from within R
JA Gustavsen, S Pai, R Isserlin, B Demchak, AR Pico
F1000Research 8, 2019
1592019
Validity of PALMS GPS scoring of active and passive travel compared to SenseCam
JA Carlson, MM Jankowska, K Meseck, S Godbole, L Natarajan, F Raab, ...
Medicine and science in sports and exercise 47 (3), 662, 2015
1282015
CyREST: turbocharging Cytoscape access for external tools via a RESTful API
K Ono, T Muetze, G Kolishovski, P Shannon, B Demchak
F1000Research 4, 2015
922015
Network propagation in the cytoscape cyberinfrastructure
DE Carlin, B Demchak, D Pratt, E Sage, T Ideker
PLoS computational biology 13 (10), e1005598, 2017
872017
NDEx 2.0: a clearinghouse for research on cancer pathways
D Pratt, J Chen, R Pillich, V Rynkov, A Gary, B Demchak, T Ideker
Cancer research 77 (21), e58-e61, 2017
662017
Rich Services: The integration piece of the SOA puzzle
M Arrott, B Demchak, V Ermagan, C Farcas, E Farcas, IH Kriiger, ...
IEEE International Conference on Web Services (ICWS 2007), 176-183, 2007
522007
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace
K Qu, S Garamszegi, F Wu, H Thorvaldsdottir, T Liefeld, M Ocana, ...
Nature methods 13 (3), 245-247, 2016
482016
Cytoscape tools for the web age: D3. js and Cytoscape. js exporters
K Ono, B Demchak, T Ideker
F1000Research 3, 2014
442014
The anatomy of successful computational biology software
S Altschul, B Demchak, R Durbin, R Gentleman, M Krzywinski, H Li, ...
Nature biotechnology 31 (10), 894-897, 2013
402013
Active interaction mapping reveals the hierarchical organization of autophagy
MH Kramer, JC Farre, K Mitra, MK Yu, K Ono, B Demchak, K Licon, ...
Molecular cell 65 (4), 761-774. e5, 2017
372017
cyNeo4j: connecting Neo4j and Cytoscape
G Summer, T Kelder, K Ono, M Radonjic, S Heymans, B Demchak
Bioinformatics 31 (23), 3868-3869, 2015
322015
PALMS: a modern coevolution of community and computing using policy driven development
B Demchak, J Kerr, F Raab, K Patrick, IH Kruger
2012 45th Hawaii International Conference on System Sciences, 2735-2744, 2012
322012
Validating GPS data with the PALMS system to detect different active transportation modes
J Kerr, G Norman, S Godbole, F Raab, B Demchak, K Patrick
Medicine and Science in Sports and Exercise 44, 647-647, 2012
282012
Middleware for reliable mobile medical workflow support in disaster settings
SW Brown, WG Griswold, B Demchak, BALA Lenert
AMIA Annual Symposium Proceedings 2006, 309, 2006
282006
A rich services approach to cocome
B Demchak, V Ermagan, E Farcas, T Huang, IH Krüger, M Menarini
The Common Component Modeling Example: Comparing Software Component Models …, 2008
252008
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Articles 1–20