Daniele Santoni
Daniele Santoni Daniele Santoni

Istituto di Analisi dei Sistemi ed Informatica "Antonio Ruberti"
Via dei Taurini, 19
00185 Roma - Italy

Office n. 503
Tel.: +39 06 4993 7119
Fax: +39 06 4993 7137
Personal web page: http://www.iasi.cnr.it/~dsantoni/

Research groups

Selected publications
  • 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
  • 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
  • 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: The impact of flanking sequence features on DNA CpG methylation, Computational Biology and Chemistry, 92: 107480, 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
  • 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
  • Pedone F, Mazzei F, Daniele Santoni: A STUDY OF THE IMPACT OF DNA HELICAL RISE ON PROTEIN-DNA INTERACTION, Genomics, 111(6): 1620-1628, 2019
  • 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
  • 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
  • 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, Giulia Fiscon, De Cola M C, Paola Bertolazzi, Giovanni Felici: Next generation sequencing reads comparison with an alignment-free distance, BMC Research Notes, 7:869, 2014
  • 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?, IASI-CNR, R. 13-07, 2013
  • 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
  • Weitschek E., Daniele Santoni, De Cola M C, Giovanni Felici: About similarity of DNA reads, IASI-CNR, R. 13-17, 12/2013
  • 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
  • Giuliani A, Di Paola L, Paola Paci, De Ruvo M, Arcangeli C, Daniele Santoni, Celino M: Chapter - Updating and revising "Proteins as Networks: Usefulness of Graph Theory in Protein Science", Advances in Protein and Peptide Science, 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
  • 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
  • Castiglione F, Daniele Santoni, Pedicini M: Implementing agent's rules with gene regulatory networks in mesoscopic-level models of cellular interactions, in "A practical guide to bioinformatics analysis", iConcept Press, Annerley, Australia, 2010
  • 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
  • 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
  • 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
  • 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
  • Paparini A, Daniele Santoni, Romano-Spica V: Bioinformatics and microbial biodiversity: analysis of vibrios by the GenEnv system, J Prev Med Hyg 47, 100-104, 2006
  • Daniele Santoni, Romano-Spica V: A gzip-based algorithm to identify bacterial families by 16S rRNA, Letters in Applied Microbiology 42, 312-314, 2006
  • 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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