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| == Peer-reviewed journals == | = Peer-reviewed journals = |
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| === 2009 === '''Interpreting biological data using networks''', <<BR>> Merico D*, Gfeller D*, Bader G; '''Nature Biotechnology''', ''in press''. |
== 2009 == |
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| '''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''. | '''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]] |
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| === 2008 === | '''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]]. == 2008 == |
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| === 2007 === | == 2007 == |
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| === 2005 === | == 2005 == |
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| EPFL Doctoral School Award (2007 EPFL's two best thesis). [[attachment:thesis-Gfeller-2007.pdf|PDF]] | EPFL Doctoral School Award (2007 EPFL best thesis). [[attachment:thesis-Gfeller-2007.pdf|PDF]] |
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| == Conference talks and Seminar == | == Conference talks, posters and Seminar == |
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| Seminar at University of Z\"urich", Switzerland, 2005<<BR>> | 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>> |
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| 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>> |
Seminar at University of Zurich, Amedeo Caflisch, Switzerland, 2005<<BR>> |
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