Zobrazeno 1 - 10
of 1 006
pro vyhledávání: '"Pelizzola, A."'
The aim of this study is to provide a foundation to understand the relationship between non-negative matrix factorization (NMF) and non-negative autoencoders enabling proper interpretation and understanding of autoencoder-based alternatives to NMF. S
Externí odkaz:
http://arxiv.org/abs/2405.07879
Autor:
Pelizzola, Alessandro, Pretti, Marco
Publikováno v:
J. Phys. A: Math. Theor. 55, 454001 (2022)
We study a totally asymmetric simple exclusion process with open boundary conditions and local resetting at the injection node. We investigate the stationary state of the model, using both mean-field approximation and kinetic Monte Carlo simulations,
Externí odkaz:
http://arxiv.org/abs/2402.13698
We study the non-equilibrium steady states in a totally-asymmetric simple-exclusion process with periodic boundary conditions, also incorporating (i) an extra (nearest-neighbour) repulsive interaction and (ii) hopping rates characterized by a smooth
Externí odkaz:
http://arxiv.org/abs/2311.03872
Autor:
Lucia Coscujuela Tarrero, Valeria Famà, Giacomo D’Andrea, Simone Maestri, Anna de Polo, Stefano Biffo, Mattia Furlan, Mattia Pelizzola
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-19 (2024)
Abstract The coordinated action of transcriptional and post-transcriptional machineries shapes gene expression programs at steady state and determines their concerted response to perturbations. We have developed Nanodynamo, an experimental and comput
Externí odkaz:
https://doaj.org/article/584e1fbc11954e8b964d146ef1155dda
The spectrum of mutations in a collection of cancer genomes can be described by a mixture of a few mutational signatures. The mutational signatures can be found using non-negative matrix factorization (NMF). To extract the mutational signatures we ha
Externí odkaz:
http://arxiv.org/abs/2206.03257
Autor:
Georgia Dermentzaki, Mattia Furlan, Iris Tanaka, Tommaso Leonardi, Paola Rinchetti, Patricia M.S. Passos, Alliny Bastos, Yuna M. Ayala, Jacob H. Hanna, Serge Przedborski, Dario Bonanomi, Mattia Pelizzola, Francesco Lotti
Publikováno v:
Cell Reports, Vol 43, Iss 4, Pp 113999- (2024)
Summary: Motor neuron (MN) demise is a hallmark of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Post-transcriptional gene regulation can control RNA’s fate, and defects in RNA processing are critical determinan
Externí odkaz:
https://doaj.org/article/464ceed631b845cfb653dd5c230fb38a
Publikováno v:
BMC Bioinformatics, Vol 24, Iss 1, Pp 1-25 (2023)
Abstract Background The identification of genomic regions affected by selection is one of the most important goals in population genetics. If temporal data are available, allele frequency changes at SNP positions are often used for this purpose. Here
Externí odkaz:
https://doaj.org/article/8706d30c47d443499e6d858569fc1174
Publikováno v:
EPL, 133 (2021) 60003
We investigate the stationary state of Symmetric and Totally Asymmetric Simple Exclusion Processes with local resetting, on a one-dimensional lattice with periodic boundary conditions, using mean-field approximations, which appear to be exact in the
Externí odkaz:
http://arxiv.org/abs/2012.10993
Autor:
Ancona, Marco, Bentivoglio, Alessandro, Caraglio, Michele, Gonnella, Giuseppe, Pelizzola, Alessandro
Publikováno v:
Physical Review E 103, 062415 (2021)
We investigate the possibility of extending the notion of temperature in a stochastic model for the RNA/protein folding driven out of equilibrium. We simulate the dynamics of a small RNA hairpin subject to an external pulling force, which is time-dep
Externí odkaz:
http://arxiv.org/abs/2009.11145
Publikováno v:
EPL, 124 (2018) 50004
We study the dynamics of an asymmetric simple exclusion process with open boundaries and local interactions using a pair approximation which generalizes the 2-node cluster mean field theory and the Markov chain approach to kinetics and shares with th
Externí odkaz:
http://arxiv.org/abs/2001.07456