This page shows all publications that appeared in the IASI annual research reports.
Authors currently affiliated with the Institute are always listed with the full name.
You can browse through them using either the links of the following line or those associated with
author names.
Show all publications of the year
ALL, with author Santoni D, in the category Articles in Journals, Collections and Proceedings
(or show them all): (Items found: 54)
2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2016 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2004
2023 [top]
- Apollonio N., Blankenberg D, Cumbo F, Franciosa P.G., Daniele Santoni: Evaluating homophily in networks via HONTO (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks, Bioinformatics, 39 (1): btac763, 2023
- Apollonio N., Franciosa P.G., Daniele Santoni: Network homophily via tail inequalties, Physical Review E, Accepted for publication, 2023
- Derelitto C, Daniele Santoni: TRANSPARENT: a Python tool for designing transcription factor regulatory networks, Soft Computing, 27: 6261-6266, 2023
- Daniele Santoni: Peptide Hamming Graphs: a network representation of peptides presented through specific HLAs to identify potential epitope clusters, Journal of Immunological Methods, 517: 113474, 2023
- Daniele Santoni, Gosh N, Derelitto C, Saha I: Transcription Factor Driven Gene Regulation in COVID-19 Patients, Viruses, 15(5): 1188, 2023
2022 [top]
- Apollonio N., Franciosa P.G., Daniele Santoni: A novel method for assessing and measuring homophily in networks through second-order statistics, Scientific Report, 12: 9757, 2022
- Daniele Santoni, Giovanni Felici: An immunological glimpse of human virus peptides: distance from self, MHC class I binding, Proteasome Cleveage, TAP Transport and sequence composition entropy, Virus Research, 317: 198814, 2022
- Daniele Santoni, Gosh N, Saha I: An Entropy-based study on Mutational Trajectory of SARS-CoV-2 in India, Infection, Genetics and Evolution 97: 105154, 2022
- Vergni D, Daniele Santoni, Bouba Y, Lemme S, Fabeni L, Carioti L, Bertoli A, Gennari W, Perno CF, Gagliardini R, Ceccherini-Silberstein F, Santoro MM: Evaluation of HIV-1 integrase variability by combining computational and probabilistic approaches, Infection, Genetics and Evolution, 101, 2022
2021 [top]
- Daniele Santoni: The impact of flanking sequence features on DNA CpG methylation, Computational Biology and Chemistry, 92: 107480, 2021
- Daniele Santoni: The impact of codon choice on translation process in Saccharomyces cerevisiae: folding class, protein function and secondary structure, Journal of Theoretical Biology, 526: 110806, 2021
- Daniele Santoni, Pignotti D, Vergni D: A genome-wide study on differential methylation in different cancers using TCGA database, Informatics in Medicine Unlocked, 23: 100542, 2021
2020 [top]
- Daniele Santoni, Vergni D: In the search of potential epitopes for Wuhan seafood market pneumonia virus using high order nullomers, Journal of Immunological Methods, 481-482: 112787, 2020
- Vergni D, Gaudio R, Daniele Santoni: The farther the better: investigating how distance from human self affects the propensity of a peptide to be presented on cell surface by MHC class I molecules, the case of Trypanosoma cruzi., Plos One, 15(12): e0243285, 2020
2019 [top]
2018 [top]
- Cumbo F, Vergni D, Daniele Santoni: Investigating transcription factor synergism in humans, Dna Research, 25(1): 103-112, 2018
- Daniele Santoni: Viral peptides-MHC interaction: binding probability and distance from human peptides, Journal of Immunological Methods, 459: 35-43, 2018
- Sener DD, Daniele Santoni, Giovanni Felici, Ogul H: A Content Based Retrieval Framework for Whole Metagenome Sequencing Samples, Journal of Integrative Bioinformatics, Accepted for Publication, 2018
2016 [top]
- Daniele Santoni, Giovanni Felici, Vergni D: Natural vs. Random Protein Sequences: Discovering Combinatorics Properties on Amino Acid Words, Journal of Theoretical Biology 391, 13-20, 2016
- Daniele Santoni, Paola Paci, Di Paola L, Giuliani A: Are proteins just coiled cords? Local and Global analysis of Contact Maps reveals the backbone-dependent nature of proteins, Current Protein & Peptide Science, 17:26-29, 2016
- Daniele Santoni, Pourabbas E.: Automatic Detection of Words Associations in Texts based on Joint Distribution of Words Occurrence, Computational Intelligence 32(4), 535-560, 2016
- Daniele Santoni, Weitschek E., Giovanni Felici: Optimal discretization and selection of features by association rates of joint dstributions, Rairo-Operations Research 50, 437-449, 2016
- Valeriani F, Biagini T, Giampaoli S, Crognale S, Daniele Santoni, Romano-Spica V: Draft Genome Sequence of Tepidimonas taiwanensis Strain VT154-175, Genome Announcements 4(5): e00942-16., 2016
- Vergni D, Daniele Santoni: Nullomers and high order nullomers in genomic sequences., Plos One 11(12) - e0164540, 2016
2014 [top]
- Paola Bertolazzi, Bock M.E., Guerra C., Paola Paci, Daniele Santoni: On the integration of protein-protein interaction networks with gene expression and 3D structural data: What can be gained?, European Physical Journal Plus, 129(6), 2014
- Cumbo F, Paola Paci, Daniele Santoni, Giuliani A, Di Paola L: GIANT: a Cytoscape plugin for modular networks, Plos One, 9(10): e105001, 2014
- Daniele Santoni, Swiercz A., Zmienko A, Kasprzak M, Blazewicz M, Paola Bertolazzi, Giovanni Felici: An integrated approach (CLuster Analysis Integration Method) to combine expression data and protein-protein interaction networks in agrigenomics: Application on Arabidopsis thaliana, OMICS, 18(2): 156-165, 2014
- Tasdighian S, Di Paola L, De Ruvo M, Paola Paci, Daniele Santoni, Pasquale Palumbo, Mei G, Di Venere A, Giuliani A: Modules identification in protein structures: the topological and geometrical solutions, Journal of Chemical Information and Modeling, 54(1): 159-168, 2014
- Tieri P, Prana V, Colombo T, Daniele Santoni, Castiglione F: Multi-scale Simulation of T Helper Lymphocyte Differentiation, in the Proceedings of 9th Brazilian Symposium on Bioinformatics, BSB 2014, Belo Horizonte, Brazil, October 28-30, 2014., Campos S ed., Lecture Notes in Computer Science, 8826, 2014
- Weitschek E., Daniele Santoni, Fiscon G, De Cola M C, Paola Bertolazzi, Giovanni Felici: Next generation sequencing reads comparison with an alignment-free distance, BMC Research Notes, 7:869, 2014
2013 [top]
- Di Paola L, De Ruvo M, Paola Paci, Daniele Santoni, Giuliani A: Proteins Contact Networks: an emerging paradigm in chemistry, Chemical Reviews 113(3), 1598-1613, 2013
- Daniele Santoni, Castiglione F, Paola Paci: Identifying Correlations between Chromosomal Proximity of Genes and Distance of their Products in Protein-Protein Interaction Networks of Yeast, Plos One, 8(3):e57707, 2013
2012 [top]
- Arrigo N, Paola Paci, Di Paola L, Daniele Santoni, De Ruvo M, Giuliani A, Castiglione F: Characterizing Protein Shape by a Volume Distribution Asymmetry Index, The Open Bioinformatics Journal 6(1), 20-27, 2012
- De Cola M C, Giovanni Felici, Daniele Santoni, Weitschek E.: Filtering with alignment free distances for high throughput DNA reads assembly, EMBnet.journal, Vol 18, http://journal.embnet.org/index.php/embnetjournal/article/view/538, 2012
- De Ruvo M, Giuliani A, Paola Paci, Daniele Santoni, Di Paola L: Shedding light on protein-ligand binding by graph theory: the topological nature of allostery, Biophysical Chemistry 165-166, 21-29, 2012
- Di Paola L, Paola Paci, Daniele Santoni, De Ruvo M, Giuliani A: Proteins as sponges: a statistical journey along protein structure organization principles, Journal of Chemical Information and Modeling 52(2), 474-482, 2012
- Paola Paci, Di Paola L, Daniele Santoni, De Ruvo M, Giuliani A: Structural and Functional Analysis of Hemoglobin and Serum Albumin through Protein Long-range Interaction Networks, current proteomics 9(3), 160-166, 2012
- Pedone F, Daniele Santoni: Preferential nucleosome occupancy at high values of DNA helical rise, Dna Research 19(1), 81-90, 2012
- Sferra G, Daniele Santoni, Pizzi E: Plasmodium phylogenetic profile: an assessment of a predictive tool for protein-protein interactions, EMBnet.journal, 18(A), 2012
2011 [top]
- Castiglione F, Daniele Santoni, Rapin N: CTLs' repertoire shaping in the thymus: a Monte Carlo simulation, Autoimmunity, 2011
- Clancy T., Pedicini M, Castiglione F, Daniele Santoni, Nygaard V, Lavelle TJ, Benson M, Hovig E: Immunological network signatures of cancer progression and survival, BMC Med Genomics, 2011
2010 [top]
- Castrignanò T., Orsini M, Paoletti D., Daniele Santoni, Romano-Spica V: Genenv: a database-driven system for bacteria identification on nucleotide sequence determination., Biosim 1, 1-8, 2010
- Pedicini M, Barrenas F, Clancy T., Castiglione F, Hovig E, Kanduri K, Daniele Santoni, Benson M: Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation, PLoS Computational Biology, 6, 2010
2009 [top]
- Bhatt TK, Kapil C, Khan S, Jairajpuri MA, Sharma A., Daniele Santoni, Silvestrini F., Pizzi E, Sharma A.: A genomic glimpse of aminoacyl-tRNA synthetases in malaria parasite Plasmodium falciparum, BMC Genomics, 10, 2009
- Pedone F, Daniele Santoni: Sequence-dependent DNA helical rise and nucleosome stability, BMC Molecular Biology 27, 2009
- Daniele Santoni, Romano-Spica V: Comparative genomic analysis by microbial COGs self-attraction rate, Journal of Theoretical Biology 258, 513-520, 2009
2008 [top]
- Cacchiarelli D, Daniele Santoni, Bozzoni I: MicroRNAs as prime players in a combinatorial view of evolution, RNA Biology 5, 120-122, 2008
- Daniele Santoni, Pedicini M, Castiglione F: Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions, Bioinformatics 24, 1374-1380, 2008
2007 [top]
- Brandi G, Sisti M, Paparini A, Gianfranceschi G, Schiavano GF, De Santi M, Daniele Santoni, Magini V, Romano-Spica V: Swimming pools and fungi: an environmental epidemiology survey in Italian indoor swimming facilities, Int J Environ Health Res 17, 197-206, 2007
- Paparini A, Ripani M, Giordano GD, Daniele Santoni, Pigozzi F, Romano-Spica V: ACTN3 genotyping by real-time PCR in the Italian population and athletes, Med Sci Sports Exerc 39, 810-815, 2007
2006 [top]
2004 [top]
- Pedone F, Mazzei F, Daniele Santoni: Sequence-dependent DNA torsional rigidity: a tetranucleotide code, Biophysical Chemistry 112, 77-88, 2004
- Romano-Spica V, Daniele Santoni, Paparini A, Giammanco GM, Canali A, Orsini M, Castrignanò T.: Bioinformatics and GenEnv database in biological risk management, Ig Sanita Pubbl 60, 401-420, 2004
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