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| #acl All:read | #acl DavidGfeller:read,write,delete,revert All:read #format wiki |
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| == Peer-reviewed journals == | = Peer-reviewed journals = |
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| === 2008 === '''Synchronization and Spectral Coarse Graining in Oscillator Networks'''[[BR]] Gfeller D, De Los Rios P; '''Phys. Rev. Lett.''' (in press) |
== 2009 == '''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''' 7(10), e1000218 (2009) [[attachment:YeastSH3.pdf|PDF]] '''How to visually interpret biological data using networks''', <<BR>> Merico D*, Gfeller D*, Bader GD; '''Nature Biotechnology''' 27, 921-924 (2009) [[attachment:Primer.pdf|PDF]] <<BR>> Network Data: [[http://www.baderlab.org/NetworkPrimerNBT|http://www.baderlab.org/NetworkPrimerNBT]]. |
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| === 2007 === | == 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) | == 2007 == |
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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) |
'''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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| '''Complex Network Analysis of Free-energy Landscapes'''[[BR]] Gfeller D, De Los Rios P, Caflisch A, Rao F; '''PNAS''' 104, 1817-1822 (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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| === 2005 === | '''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) |
== 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, posters and Seminar == Poster, Protein Modules and Networks in Health and Disease, Seefeld (2009)<<BR>> Poster, ISMB (2008)<<BR>> Seminar at Mc Gill, Peter Swain, Montreal, Canada, 2007<<BR>> Seminar at University of Toronto, Gary Bader, Canada, 2007<<BR>> Talk at Biowire 2007, Cambridge, UK<<BR>> Talk at International School of Complexity, Biological Networks, 2006, Erice, Italy<<BR>> Talk at International Workshop on Structure and Function of complex networks, 2006, Torino, Italy<<BR>> Seminar at Boston University, Daniel Segre, 2006<<BR>> Seminar at Max Planck Institute, Leipzig, 2006<<BR>> Seminar at University of Zurich, Amedeo Caflisch, Switzerland, 2005<<BR>> * equal contribution |
Peer-reviewed journals
2009
Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins
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 7(10), e1000218 (2009) PDF
How to visually interpret biological data using networks,
Merico D*, Gfeller D*, Bader GD; Nature Biotechnology 27, 921-924 (2009) PDF
Network Data: http://www.baderlab.org/NetworkPrimerNBT.
2008
Synchronization and Spectral Coarse Graining in Oscillator Networks
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, posters and Seminar
Poster, Protein Modules and Networks in Health and Disease, Seefeld (2009)
Poster, ISMB (2008)
Seminar at Mc Gill, Peter Swain, Montreal, Canada, 2007
Seminar at University of Toronto, Gary Bader, Canada, 2007
Talk at Biowire 2007, Cambridge, UK
Talk at International School of Complexity, Biological Networks, 2006, Erice, Italy
Talk at International Workshop on Structure and Function of complex networks, 2006, Torino, Italy
Seminar at Boston University, Daniel Segre, 2006
Seminar at Max Planck Institute, Leipzig, 2006
Seminar at University of Zurich, Amedeo Caflisch, Switzerland, 2005
* equal contribution