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| #acl All:read | #acl DavidGfeller:read,write,delete,revert All:read #format wiki |
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| == Peer-reviewd journals == | == Peer-reviewed journals == === 2009 === ''How to visually interpret biological data using networks''', <<BR>> Merico D*, Gfeller D*, Bader G; '''Nature Biotechnology''', ''in press''. '''Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins''' <<BR>> Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Yu H, Winsor B, Vidal M, Davidson AR, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C; '''PLoS Biology''', ''in press''. === 2008 === '''Synchronization and Spectral Coarse Graining in Oscillator Networks'''<<BR>> Gfeller D, De Los Rios P; '''Phys. Rev. Lett.''' 100, 174104 (2008) [[attachment:Sync-Gfeller-PRL-2008.pdf|PDF]] |
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| '''Spectral coarse graining of complex networks'''[[BR]] Gfeller D, De Los Rios P; '''Phys. Rev. Lett.''' 99, 038701 (2007) | '''Spectral Coarse Graining of Complex Networks'''<<BR>> Gfeller D, De Los Rios P; '''Phys. Rev. Lett.''' 99, 038701 (2007) [[attachment:SCG-Gfeller-PRL-2007.pdf|PDF]] |
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| '''Uncovering the topology of configuration space networks'''[[BR]] Gfeller D, Morton de Lachapelle D, De Los Rios P, Caldarelli P, Rao F; '''Phys. Rev. E''' 76, 026113 (2007) |
'''Uncovering the topology of configuration space networks'''<<BR>> Gfeller D, Morton de Lachapelle D, De Los Rios P, Caldarelli P, Rao F; '''Phys. Rev. E''' 76, 026113 (2007) [[attachment:ConfNet-Gfeller-PRE-2007.pdf|PDF]] |
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| '''Complex network analysis of free-energy landscapes'''[[BR]] Gfeller D, De Los Rios P, Caflisch A, Rao F; '''PNAS''' 104, 1817-1822 (2007) |
'''Complex Network Analysis of Free-energy Landscapes'''<<BR>> Gfeller D, De Los Rios P, Caflisch A, Rao F; '''PNAS''' 104, 1817-1822 (2007) [[attachment:Alanine-Gfeller-PNAS-2007.pdf|PDF]] |
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| '''Finding instabilities in the community structure of complex networks'''[[BR]] Gfeller D, Chappelier J-C, De Los Rios P; '''Phys. Rev. E''' 72 056135 (2005) |
'''Finding instabilities in the community structure of complex networks'''<<BR>> Gfeller D, Chappelier J-C, De Los Rios P; '''Phys. Rev. E''' 72 056135 (2005) [[attachment:Instabilities-Gfeller-PRE-2005.pdf|PDF]] == Thesis == '''Simplifying complex networks: form a clustering to a coarse graining strategy''' Gfeller D, PhD Thesis.<<BR>> EPFL Doctoral School Award (2007 EPFL best thesis). [[attachment:thesis-Gfeller-2007.pdf|PDF]] == Conference papers == '''Synonym Dictionary Improvement through Markov Clustering and Clustering Stability'''<<BR>> Gfeller D, Chappelier J-C, De Los Rios P; Proceedings of International Symposium an Applied Stochastic Models and Data Analysis (ASMDA'05) (2005) [[attachment:Ling-Gfeller-ASMDA-2005.pdf|PDF]] == Conference talks and Seminar == Seminar at University of Z\"urich", Switzerland, 2005<<BR>> Seminar at Max Planck Institute, Leipzig, 2006<<BR>> Seminar at Boston University, 2006<<BR>> Talk at International Workshop on Structure and Function of complex networks, 2006, Torino, Italy<<BR>> Talk at International School of Complexity, Biological Networks, 2006, Erice, Italy<<BR>> Talk at Biowire 2007, Cambridge, UK<<BR>> Seminar at University of Toronto, Canada, 2007<<BR>> Seminar at Mc Gill, Montreal, Canada, 2007<<BR>> * equal contribution |
Peer-reviewed journals
2009
How to visually interpret biological data using networks, Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins
Synchronization and Spectral Coarse Graining in Oscillator Networks
Seminar at University of Z\"urich", Switzerland, 2005 * equal contribution
Merico D*, Gfeller D*, Bader G; Nature Biotechnology, in press.
Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Yu H, Winsor B, Vidal M, Davidson AR, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C; PLoS Biology, 2008
Gfeller D, De Los Rios P; Phys. Rev. Lett. 100, 174104 (2008) PDF 2007
Spectral Coarse Graining of Complex Networks
Gfeller D, De Los Rios P; Phys. Rev. Lett. 99, 038701 (2007) PDF Uncovering the topology of configuration space networks
Gfeller D, Morton de Lachapelle D, De Los Rios P, Caldarelli P, Rao F; Phys. Rev. E 76, 026113 (2007) PDF Complex Network Analysis of Free-energy Landscapes
Gfeller D, De Los Rios P, Caflisch A, Rao F; PNAS 104, 1817-1822 (2007) PDF 2005
Finding instabilities in the community structure of complex networks
Gfeller D, Chappelier J-C, De Los Rios P; Phys. Rev. E 72 056135 (2005) PDF Thesis
Simplifying complex networks: form a clustering to a coarse graining strategy Gfeller D, PhD Thesis.
EPFL Doctoral School Award (2007 EPFL best thesis). PDF Conference papers
Synonym Dictionary Improvement through Markov Clustering and Clustering Stability
Gfeller D, Chappelier J-C, De Los Rios P; Proceedings of International Symposium an Applied Stochastic Models and Data Analysis (ASMDA'05) (2005) PDF Conference talks and Seminar
Seminar at Max Planck Institute, Leipzig, 2006
Seminar at Boston University, 2006
Talk at International Workshop on Structure and Function of complex networks, 2006, Torino, Italy
Talk at International School of Complexity, Biological Networks, 2006, Erice, Italy
Talk at Biowire 2007, Cambridge, UK
Seminar at University of Toronto, Canada, 2007
Seminar at Mc Gill, Montreal, Canada, 2007