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Publications

De Riso V, Raniello R, Maumus F, Rogato A, Bowler C, Falciatore A. Gene silencing in the marine diatom Phaeodactylum tricornutum. Nucleic Acids Res. 37(14), pp.e96 (2009).
Fischer G, Thompson D, Wortman JRusso, Fairhead C. Unraveling the genomic diversity of small eukaryotes. Genome Biol. 10(12), pp.318 (2009).
Koszul R, Fischer G. A prominent role for segmental duplications in modeling eukaryotic genomes. C R Biol. 332(2-3), pp.254-66 (2009).
Payen C, Fischer G, Marck C, Proux C, Sherman DJames, Coppée J-Y, Johnston M, Dujon B, Neuvéglise C. Unusual composition of a yeast chromosome arm is associated with its delayed replication. Genome Res. 19(10), pp.1710-21 (2009).
Ciandrini L, Maffi C, Motta A, Bassetti B, Cosentino Lagomarsino M. Feedback topology and XOR-dynamics in Boolean networks with varying input structure. Phys Rev E Stat Nonlin Soft Matter Phys. 80(2 Pt 2), pp.026122 (2009).
Schug A, Weigt M, Onuchic JN, Hwa T, Szurmant H. High-resolution protein complexes from integrating genomic information with molecular simulation. Proc Natl Acad Sci U S A. 106(52), pp.22124-9 (2009).
Baussand J, Carbone A. A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence. PLoS Comput Biol. 5(9), pp.e1000488 (2009).
Váchová L, Kučerová H, Devaux F, lehlová MÚ, Palková Z. Metabolic diversification of cells during the development of yeast colonies. Environ Microbiol. 11(2), pp.494-504 (2009).
Bailey AG, Lowe CP, Pagonabarraga I, Cosentino Lagomarsino M. Accurate simulation dynamics of microscopic filaments using "caterpillar" Oseen hydrodynamics. Phys Rev E Stat Nonlin Soft Matter Phys. 80(4 Pt 2), pp.046707 (2009).
Cosentino Lagomarsino M, Bassetti B, Castellani G, Remondini D. Functional models for large-scale gene regulation networks: realism and fiction. Mol Biosyst. 5(4), pp.335-44 (2009).
Weigt M, White RA, Szurmant H, Hoch JA, Hwa T. Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A. 106(1), pp.67-72 (2009).
Bernardes JS, Fernandez JH, Vasconcelos ATereza R. Structural descriptor database: a new tool for sequence-based functional site prediction. BMC Bioinformatics. 9, pp.492 (2008).
Costa J, Bernardes JS, Santos V, Zaverucha G Remote Homology Detection Through Discriminative Statistical Relational Learning. in The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases. (2008)
Menezes RA, Amaral C, Batista-Nascimento L, Santos C, Ferreira RBoavida, Devaux F, Eleutherio ECA, Rodrigues-Pousada C. Contribution of Yap1 towards Saccharomyces cerevisiae adaptation to arsenic-mediated oxidative stress. Biochem J. 414(2), pp.301-11 (2008).
Dutta RN, IM Rouzine, Smith SD, Wilke CO, Novella IS. Rapid adaptive amplification of preexisting variation in an RNA virus. J Virol. 82(9), pp.4354-62 (2008).

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