Zobrazeno 1 - 10
of 18
pro vyhledávání: '"Anna Paola Muntoni"'
Publikováno v:
Scientific Reports, Vol 13, Iss 1, Pp 1-11 (2023)
Abstract Estimating observables from conditioned dynamics is typically computationally hard. While obtaining independent samples efficiently from unconditioned dynamics is usually feasible, most of them do not satisfy the imposed conditions and must
Externí odkaz:
https://doaj.org/article/3c7cc8ebb24242e0badfe41831a7aa3d
Publikováno v:
BMC Bioinformatics, Vol 22, Iss 1, Pp 1-19 (2021)
Abstract Background Boltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families. They are parametrized in terms of local biases accounting
Externí odkaz:
https://doaj.org/article/79f58c0ef7fa43cbb4914ca48a168964
Publikováno v:
Nature Communications, Vol 8, Iss 1, Pp 1-9 (2017)
Large-scale metabolic models of organisms from microbes to mammals can provide great insight into cellular function, but their analysis remains challenging. Here, the authors provide an approximate analytic method to estimate the feasible solution sp
Externí odkaz:
https://doaj.org/article/a310c3829c1b4c4c9dfde675741de891
Autor:
Anna Paola Muntoni, Andrea De Martino
In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense, optimal strat
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d584ad84a4bf878d4563c911fe2e95da
http://arxiv.org/abs/2210.11167
http://arxiv.org/abs/2210.11167
Autor:
Anna Paola Muntoni, Andrea Pagnani
SummaryDCAlign is a new alignment method able to cope with the conservation and the co-evolution signals that characterize the columns of a multiple sequence alignment of homologous sequences. However, the pre-processing steps required to align a can
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e6922bf6491648d0a551af61f4d3dc4e
https://doi.org/10.1101/2022.05.18.492471
https://doi.org/10.1101/2022.05.18.492471
Autor:
Anna Paola Muntoni, Alfredo Braunstein, Andrea Pagnani, Daniele De Martino, Andrea De Martino
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria, metabolic act
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bbb4427910865bb4da3ad0d262d621ac
http://hdl.handle.net/10261/296486
http://hdl.handle.net/10261/296486
Autor:
Andreas Milias-Argeitis, Daniele de Martino, Matthias Heinemann, Georg Hubmann, Joana Saldida, Alfredo Braunstein, Anna Paola Muntoni, Bastian Niebel, A. Mareike Schmidt
Quantification of cellular metabolic fluxes, for instance with 13C-metabolic flux analysis, is highly important for applied and fundamental metabolic research. A current challenge in 13C-flux analysis is that the available experimental data are usual
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e015715dd6ac13456e118439d20846ea
https://doi.org/10.1101/2020.06.29.177063
https://doi.org/10.1101/2020.06.29.177063
Publikováno v:
Physical Review E
Physical Review E, American Physical Society (APS), 2020, 102 (6), ⟨10.1103/PhysRevE.102.062409⟩
Physical Review E, American Physical Society (APS), 2020, 102 (6), ⟨10.1103/PhysRevE.102.062409⟩
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in such a way to
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::58298565403f800cc15b1a0b49e807b0
http://arxiv.org/abs/2005.08500
http://arxiv.org/abs/2005.08500
Publikováno v:
Phys.Rev.E
Phys.Rev.E, 2021, ⟨10.1103/PhysRevE.104.024407⟩
Phys.Rev.E, 2021, ⟨10.1103/PhysRevE.104.024407⟩
Boltzmann machines (BM) are widely used as generative models. For example, pairwise Potts models (PM), which are instances of the BM class, provide accurate statistical models of families of evolutionarily related protein sequences. Their parameters
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::410b4476843af36cf563fc49facc61e9
We propose a novel approach to the inverse Ising problem which employs the recently introduced Density Consistency approximation (DC) to determine the model parameters (couplings and external fields) maximizing the likelihood of given empirical data.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8a124c8c83ccbb1f054e3dc5599ceee3