Computational Biology

Publications

C. Caudai, E. Salerno
Complementing Hi-C information for 3D chromatin reconstruction by ChromStruct
Frontiers in Bioinformatics, 3:1287168, 2024, DOI: 10.3389/fbinf.2023.1287168

C. Caudai, A. Galizia, F. Geraci, L. Le Pera, V. Morea, E. Salerno, A. Via, T. Colombo
AI Applications in Functional Genomics
Computational and Structural Biotechnology Journal, Vol. 19, pp. 5762-5790, 2021, DOI: 10.1016/j.csbj.2021.10.009

C. Caudai, M. Zoppè, A. Tonazzini, I. Merelli, E. Salerno
Integration of Multiple Resolution Data in 3D Chromatin Reconstruction Using ChromStruct
Biology, Vol. 10, No. 4, Article n. 338, 2021, DOI: 10.3390/biology10040338

C. Caudai, E. Salerno, M. Zoppè, I. Merelli, A. Tonazzini
ChromStruct 4: A Python Code to Estimate the Chromatin Structure from Hi-C Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 16, No. 6, pp. 1867-1878, November/December 2019, DOI: 10.1109/TCBB.2018.2838669

C. Caudai, E. Salerno, M. Zoppè, A. Tonazzini
Estimation of the Spatial Chromatin Structure Based on a Multiresolution Bead-Chain Model
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 16, No. 2, pp. 550-559, March/April 2019, DOI: 10.1109/TCBB.2018.2791439

C. Caudai, M. Zoppè, E. Salerno, I. Merelli, A. Tonazzini
Parallelizable Strategy for the Estimation of the 3D Structure of Biological Macromolecules
in I. Merelli, P. Liò and I. Kotenko, Eds., Proc. 26th Euromicro International Conference on Parallel, Distributed and Network-based Processing - PDP 2018, Cambridge, UK, March 21-23 2018, pp. 134-137. DOI: 10.1109/PDP2018.2018.00026.

C. Caudai, M. Zoppè, M.  A. Pascali, E. Salerno, A. Tonazzini
Protein Molecular Dynamics using Quaternions and Monte Carlo Methods
Bioinformatiha 5, Quinta Edizione della Giornata Toscana di Bioinformatica e Systems Biology, Firenze, Italy, 28 October 2016.

C. Caudai, E. Salerno, M. Zoppè, A. Tonazzini
A statistical approach to infer 3D chromatin structure
in V. Zazzu et al. (Eds.), Mathematical Models in Biology, Springer International Publishing Switzerland, 2015, pp. 161-171, DOI: 10.1007/978-3-319-23497-7_12

C. Caudai, E. Salerno, M. Zoppè, A. Tonazzini
Inferring 3D chromatin structure using a multiscale approach based on quaternions
BMC Bioinformatics, Vol. 16, 2015, p. 234, DOI: 10.1186/s12859-015-0667-0

C. Caudai, E. Salerno, M. Zoppè, A. Tonazzini
A statistical approach to infer 3D chromatin structure
in BMTL 2014 - Bringing Maths to Life, Napoli, Italy, 27-29 October 2014, p. 42.

C. Caudai, E. Salerno, M. Zoppè, A. Tonazzini
A multiscale model for 3D chromatin structure estimation using quaternions
in Poster Proc., 13th European Conference on Computational Biology - ECCB, Strasbourg, France, 7th-10th September 2014, E66.


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