Pagnani, Andrea

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

Morcos, F., Pagnani, A., Lunt, B., Bertolino, A., Marks, D. S., Sander, C., Zecchina, R., Onuchic, J. N., Hwa, T., & Weigt, M. (2011) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 1,434

Protein 3D Structure Computed from Evolutionary Sequence Variation

Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) · PLoS ONE

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 1,144

A critical assessment of Mus musculusgene function prediction using integrated genomic evidence

Peña-Castillo, L., Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. K., et al. (2008) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 248

Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells

Neri, F., Incarnato, D., Krepelova, A., Rapelli, S., Pagnani, A., Zecchina, R., Parlato, C., & Oliviero, S. (2013) · Genome Biology

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 179

Bridging the gaps in systems biology

Cvijovic, M., Almquist, J., Hagmar, J., Hohmann, S., Kaltenbach, H.-M., Klipp, E., Krantz, M., Mendes, P., Nelander, S., Nielsen, J., et al. (2014) · Molecular Genetics and Genomics

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 40

Direct Coupling Analysis and The Attention Mechanism

Caredda, F., & Pagnani, A. (2024) · BMC Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 5

Direct Coupling Analysis and the Attention Mechanism

Caredda, F., & Pagnani, A. (2024) · BMC Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 5

Controllable Protein Design via Autoregressive Direct Coupling Analysis Conditioned on Principal Components

Caredda, F., Gennai, L., De Los Rios, P., & Pagnani, A. (2025) · PLoS Computational Biology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 1