Articolo in rivista, 2019, ENG, 10.1109/TCBB.2018.2838669
Caudai C.; Salerno E.; Zoppè M.; Merelli I.; Tonazzini A.
CNR-ISTI, Pisa, Italy; CNR-ISTI, Pisa, Italy; CNR-IFC, Pisa, Italy; CNR-ITB, Milan, Italy; CNR-ISTI, Pisa, Italy
A method and a stand-alone Python(TM) code to estimate the 3D chromatin structure from chromosome conformation capture data are presented. The method is based on a multiresolution, modified-bead-chain chromatin model, evolved through quaternion operators in a Monte Carlo sampling. The solution space to be sampled is generated by a score function with a data-fit part and a constraint part where the available prior knowledge is implicitly coded. The final solution is a set of 3D configurations that are compatible with both the data and the prior knowledge. The iterative code, provided here as additional material, is equipped with a graphical user interface and stores its results in standard-format files for 3D visualization. We describe the mathematical-computational aspects of the method and explain the details of the code. Some experimental results are reported, with a demonstration of their fit to the data.
IEEE/ACM transactions on computational biology and bioinformatics (Online) 16 (6), pp. 1867–1878
Chromosome conformation capture, Chromatin configuration, Bayesian estimation
Caudai Claudia, Zoppe Monica Maria, Merelli Ivan, Salerno Emanuele, Tonazzini Anna
IFC – Istituto di fisiologia clinica, ISTI – Istituto di scienza e tecnologie dell'informazione "Alessandro Faedo", ITB – Istituto di tecnologie biomediche
ID: 387460
Year: 2019
Type: Articolo in rivista
Creation: 2018-05-23 14:16:14.000
Last update: 2021-04-08 00:28:36.000
External links
OAI-PMH: Dublin Core
OAI-PMH: Mods
OAI-PMH: RDF
DOI: 10.1109/TCBB.2018.2838669
URL: https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=8361440
External IDs
CNR OAI-PMH: oai:it.cnr:prodotti:387460
DOI: 10.1109/TCBB.2018.2838669
Scopus: 2-s2.0-85047190075
ISI Web of Science (WOS): 000507924300009