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signaling pathways
Tuncbag N, Braunstein A, Pagnani A, Huang S-, Chayes J, Borgs C, et al. Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. In: Chor B, editor. Research in Computational Molecular Biology. Vol 7262. Springer Berlin Heidelberg; 2012. p. 287-301. (Lecture Notes in Computer Science; vol 7262).
Prize-collecting Steiner forest
Tuncbag N, Braunstein A, Pagnani A, Huang S-, Chayes J, Borgs C, et al. Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. In: Chor B, editor. Research in Computational Molecular Biology. Vol 7262. Springer Berlin Heidelberg; 2012. p. 287-301. (Lecture Notes in Computer Science; vol 7262).
others
Benatti F, Floreanini R, Realpe J. Cooper Pair Boxes Weakly Coupled to External Environments. J. Phys. A: Math. Theor.. 2008;41.
optimization
Bailly-Bechet M, Bradde S, Braunstein A, Flaxman A, Foini L, Zecchina R. Clustering with shallow trees. JSTAT. 2009:17pp. Abstract
Chavas J, Furtlehner C, Mézard M, Zecchina R. Survey-propagation decimation through distributed local computations. J. Stat. Mech.. 2005:P11016.
multiple network reconstruction
Tuncbag N, Braunstein A, Pagnani A, Huang S-, Chayes J, Borgs C, et al. Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. In: Chor B, editor. Research in Computational Molecular Biology. Vol 7262. Springer Berlin Heidelberg; 2012. p. 287-301. (Lecture Notes in Computer Science; vol 7262).
biocomp
Bailly-Bechet M, Borgs C, Braunstein A, Chayes J, Dagkessamanskaia A, François JM, et al. Finding undetected protein associations in cell signaling by belief propagation. Proceedings of the National Academy of Sciences. 2010;108(2):882-7. Abstract  Download: PNAS-2011-Bailly-Bechet-882-7.pdf (324.11 KB)
Bailly-Bechet M, Bradde S, Braunstein A, Flaxman A, Foini L, Zecchina R. Clustering with shallow trees. JSTAT. 2009:17pp. Abstract
Benatti F, Floreanini R, Realpe J. Cooper Pair Boxes Weakly Coupled to External Environments. J. Phys. A: Math. Theor.. 2008;41.
Chavas J, Furtlehner C, Mézard M, Zecchina R. Survey-propagation decimation through distributed local computations. J. Stat. Mech.. 2005:P11016.