SMILE

Stochastic Models for the Inference of Life Evolution

Luca Ferretti

Postdoctoral fellow

Luca works in statistical analysis and modeling in population genetics, population genomics, complex systems. He was a postdoc in the SMILE group from 2012 to 2014. He now has a permanent position at the Pirbright Institute.

Visit Luca Ferretti's webpage.

Publications

Freund, F., Kerdoncuff, E., Matuszewski, S., Lapierre, M., Hildebrandt, M., Jensen, J. D., Ferretti, L., Lambert, A., Sackton, T. B., Achaz, G. (2022)
Interpreting the pervasive observation of u-shaped site frequency spectra
bioRxiv
Ferretti, L., Schmiegelt, B., Weinreich, D., Yamauchi, A., Kobayashi, Y., Tajima, F., Achaz, G. (2016)
Measuring epistasis in fitness landscapes: the correlation of fitness effects of mutations
Journal of theoretical biology 396 132-143
Brouillet, S., Annoni, H., Ferretti, L., Achaz, G. (2015)
Magellan: a tool to explore small fitness landscapes
Ledda, A., Achaz, G., Wiehe, T., Ferretti, L. (2015)
Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests
arXiv preprint arXiv:1510.06748
Ferretti, L., Cortelezzi, M., Mamino, M. (2014)
Duality between preferential attachment and hyperbolic networks
EPL (Europhysics Letters) 105
Ferretti, L., Mamino, M., Bianconi, G. (2014)
Condensation and topological phase transitions in a dynamical network model with rewiring of the links
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 89
Lechner, S., Ferretti, L., Schöning, C., Kinuthia, W., Willemsen, D., Hasselmann, M. (2014)
Nucleotide variability at its limit? insights into the number and evolutionary dynamics of the sex-determining specificities of the honey bee apis mellifera
Molecular Biology and Evolution 31 272-287
Esteve-Codina, A., Paudel, Y., Ferretti, L., Raineri, E., Megens, H., Silió, L., Rodríguez, M. C., Groenen, M. A. M., Ramos-Onsins, S. E., Pérez-Enciso, M. (2013)
Dissecting structural and nucleotide genome-wide variation in inbred iberian pigs
BMC genomics 14
Ferretti, L., Disanto, F., Wiehe, T. (2013)
The effect of single recombination events on coalescent tree height and shape
PloS One 8
Ferretti, L., Ramos-Onsins, S. E., Pérez-Enciso, M. (2013)
Population genomics from pool sequencing
Molecular Ecology 22 5561-5576
Segura, J., Ferretti, L., Ramos-Onsins, S., Capilla, L., Farré, M., Reis, F., Oliver-Bonet, M., Fernández-Bellón, H., Garcia, F., Garcia-Caldés, M., Robinson, T. J., Ruiz-Herrera, A. (2013)
Evolution of recombination in eutherian mammals: insights into mechanisms that affect recombination rates and crossover interference
Proceedings. Biological Sciences / The Royal Society 280
Ferretti, L., Cortelezzi, M., Yang, B., Marmorini, G., Bianconi, G. (2012)
Features and heterogeneities in growing network models
Physical Review E 85
Ferretti, L., Raineri, E., Ramos-Onsins, S. (2012)
Neutrality tests for sequences with missing data
Genetics 191 1397-1401
Halu, A., Ferretti, L., Vezzani, A., Bianconi, G. (2012)
Phase diagram of the bose-hubbard model on complex networks
EPL (Europhysics Letters) 99
Pirino, D., Rigosa, J., Ledda, A., Ferretti, L. (2012)
Detecting correlations among functional-sequence motifs
Physical Review E 85
Raineri, E., Ferretti, L., Esteve-Codina, A., Nevado, B., Heath, S., Pérez-Enciso, M. (2012)
Snp calling by sequencing pooled samples
BMC bioinformatics 13
Amaral, A. J., Ferretti, L., Megens, H., Crooijmans, R. P. M. A., Nie, H., Ramos-Onsins, S. E., Perez-Enciso, M., Schook, L. B., Groenen, M. A. M. (2011)
Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled dna
PloS One 6
Esteve-Codina, A., Kofler, R., Himmelbauer, H., Ferretti, L., Vivancos, A. P., Groenen, M. A. M., Folch, J. M., Rodríguez, M. C., Pérez-Enciso, M. (2011)
Partial short-read sequencing of a highly inbred iberian pig and genomics inference thereof
Heredity 107 256-264
Ferretti, L., Cortelezzi, M. (2011)
Preferential attachment in growing spatial networks
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 84
Ferretti, L., Perez-Enciso, M., Ramos-Onsins, S. (2010)
Optimal neutrality tests based on the frequency spectrum
Genetics 186 353-365
Pérez-Enciso, M., Ferretti, L. (2010)
Massive parallel sequencing in animal genetics: wherefroms and wheretos
Animal Genetics 41 561-569
Bianconi, G., Ferretti, L., Franz, S. (2009)
Non-neutral theory of biodiversity
EPL (Europhysics Letters) 87
Calibbi, L., Ferretti, L., Romanino, A., Ziegler, R. (2009)
Consequences of a unified, anarchical model of fermion masses and mixings
Journal of High Energy Physics 3
Calibbi, L., Ferretti, L., Romanino, A., Ziegler, R. (2009)
Gauge coupling unification, the gut scale, and magic fields
Physics Letters B 672 152-157
Ferretti, L., Gudnason, S., Konishi, K. (2008)
Non-abelian vortices and monopoles in so(n) theories
789
Ferretti, L., Bianconi, G. (2008)
Dynamics of condensation in growing complex networks
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 78