2013

Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation
Swaney, Danielle L., Beltrao Pedro, Starita Lea, Guo Ailan, Rush John, Fields Stanley, Krogan Nevan J., and Villén Judit
Nature Methods. (2013), doi: 10.1038/nmeth.2519

2012

Comparative Interaction Networks: Bridging Genotype to Phenotype
Beltrao, P., Ryan C., and Krogan N. J.
Evolutionary Systems Biology. (2012), p.139–156
Hierarchical Modularity and the Evolution of Genetic Interactomes across Species
Ryan, C. J., Roguev A., Patrick K., Xu J., Jahari H., Tong Z., Beltrao P., Shales M., Qu H., Collins S. R., et al.
Molecular Cell. Volume 46, Number 5, (2012), p.691–704
Systematic Functional Prioritization of Protein Posttranslational Modifications
Beltrao, P., Albanèse V., Kenner L. R., Swaney D. L., Burlingame A., Villén J., Lim W. A., Fraser J. S., Frydman J., and Krogan N. J.
Cell. Volume 150, Number 2, (2012), p.413–425

2011

Phenotypic landscape of a bacterial cell
Nichols, R. J., SEN S., Choo Y. J., Beltrao P., Zietek M., Chaba R., Lee S., Kazmierczak K. M., Lee K. J., Wong A., et al.
Cell. Volume 144, Number 1, (2011), p.143–156
Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress
Charles, G. M., Chen C., Shih S. C., Collins S. R., Beltrao P., Zhang X., Sharma T., Tan S., Burlingame A. L., Krogan N. J., et al.
Proceedings of the National Academy of Sciences. Volume 108, Number 26, (2011), p.10620–10625

2010

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers
Lefebvre, C., Rajbhandari P., Alvarez M. J., Bandaru P., Lim W. K., Sato M., Wang K., Sumazin P., Kustagi M., Bisikirska B. C., et al.
Molecular systems biology. Volume 6, Number 1, (2010),
Cross-species chemogenomic profiling reveals evolutionarily conserved drug mode of action
Kapitzky, L., Beltrao P., Berens T. J., Gassner N., Zhou C., Wüster A., Wu J., Babu M. M., Elledge S. J., Toczyski D., et al.
Molecular Systems Biology. Volume 6, Number 1, (2010),
Quantitative genetic interactions reveal biological modularity
Beltrao, P., Cagney G., and Krogan N. J.
Cell. Volume 141, Number 5, (2010), p.739–745 doi:

2009

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species
Beltrao, P., Trinidad J. C., Fiedler D., Roguev A., Lim W. A., Shokat K. M., Burlingame A. L., and Krogan N. J.
PLoS Biology. Volume 7, Number 6, (2009), p.e1000134
Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions.
Fernandez-Ballester, G., Beltrao P., Gonzalez J. M., Song Y. H., Wilmanns M., Valencia A., Serrano L., and others
Journal of molecular biology. Volume 388, Number 4, (2009), p.902
ADAN: a database for prediction of protein–protein interaction of modular domains mediated by linear motifs
Encinar, JA, Fernandez-Ballester G., Sánchez I. E., Hurtado-Gomez E., Stricher F., Beltrao P., and Serrano L.
Bioinformatics. Volume 25, Number 18, (2009), p.2418–2424
Microblogging the ISMB: a new approach to conference reporting
Saunders, N., Beltrão P., Jensen L., Jurczak D., Krause R., Kuhn M., and Wu S.
PLoS computational biology. Volume 5, Number 1, (2009), p.e1000263

2008

Analyzing protein interaction networks using structural information
Kiel, C., Beltrao P., and Serrano L.
Annu. Rev. Biochem.. Volume 77, (2008), p.415–441
Evolvability and hierarchy in rewired bacterial gene networks
Isalan, M., Lemerle C., Michalodimitrakis K., Horn C., Beltrao P., Raineri E., Garriga-Canut M., and Serrano L.
Nature. Volume 452, Number 7189, (2008), p.840–845
Genome-wide prediction of SH2 domain targets using structural information and the FoldX algorithm
Sánchez, I. E., Beltrao P., Stricher F., Schymkowitz J., Ferkinghoff-Borg J., Rousseau F., and Serrano L.
PLoS computational biology. Volume 4, Number 4, (2008), p.e1000052

2007

Specificity and evolvability in eukaryotic protein interaction networks
Beltrao, P., and Serrano L.
PLoS computational biology. Volume 3, Number 2, (2007), p.e25
Structures in systems biology
Beltrao, P., Kiel C., and Serrano L.
Current opinion in structural biology. Volume 17, Number 3, (2007), p.378–384
A genome-wide Ras-effector interaction network
Kiel, C., Foglierini M., Kuemmerer N., Beltrao P., and Serrano L.
Journal of molecular biology. Volume 370, Number 5, (2007), p.1020–1032

2005

Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions
Beltrao, P., and Serrano L.
PLoS Computational Biology. Volume 1, Number 3, (2005), p.e26

2004

SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks
Ander, M., Beltrao P., Di Ventura B., Ferkinghoff-Borg J., Foglierini M., Kaplan A., Lemerle C., Tomas-Oliveira I., Serrano L., and others
Syst. Biol. Volume 1, Number 1, (2004), p.129–138

2003

Comparative evolutionary genomics unveils the molecular mechanism of reassignment of the CTG codon in Candida spp.
Massey, S. E., Moura G., Beltrão P., Almeida R., Garey J. R., Tuite M. F., and Santos M. A. S.
Genome research. Volume 13, Number 4, (2003), p.544–557