This page shows the publications appeared in journals, collections, conference proceedings,
and books whose authors are currently affiliated with the Institute. The publications
are grouped by research topic.
 GENOMICS AND PROTEIN STRUCTURES
JOURNALS
- 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
- Derelitto C, Daniele Santoni: TRANSPARENT: a Python tool for designing transcription factor regulatory networks, Soft Computing, Accepted for publication, 2023
- 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
- Mascolo E, Liguori F, Stufera Mecarelli L, Amoroso N, Merigliano C, Amadio S, Cinzia Volonté, Contestabile R, Tramonti A, Vernì F: Functional inactivation of Drosophila GCK orthologs causes genomic instability and oxidative stress in a fly model of MODY-2, International Journal of Molecular Sciences, 22(2):918, https://www.mdpi.com/1422-0067/22/2/918, 2021
- 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
- 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
- Celli F, Cumbo F, Weitschek E.: Classification of Large DNA Methylation Datasets for Identifying Cancer Drivers, Big Data Research, https://www.sciencedirect.com/science/article/pii/S2214579617302708, 2018
- Cumbo F, Vergni D, Daniele Santoni: Investigating transcription factor synergism in humans, Dna Research, 25(1): 103-112, 2018
- Fiscon G, Weitschek E., Cialini A, Giovanni Felici, Bertolazzi P., De Salvo S, Bramanti A, Bramanti P, De Cola M C: Combining EEG signal processing with supervised methods for Alzheimer's patients classification, BMC Medical Informatics and Decision Making, https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-018-0613-y, 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
- Conte F, Fiscon G, Chiara M, Colombo T, Farina L., Paci P.: Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer, Plos One 12, 2017
- Cumbo F, Fiscon G, Ceri S., Masseroli M, Weitschek E.: TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas, BMC Bioinformatics, 2017
- Fragale A, Romagnoli G., Licursi V, Buoncervello M, Del Vecchio G, Giuliani C, Parlato S, Leone C, De Angelis M, Canini I, Toschi E, Belardelli F, Negri R, Capone I, Presutti C, Gabriele L.: Antitumor effects of epidrug/IFNalpha combination driven by modulated gene signatures in both colorectal cancer and dendritic cells, Cancer Immunology Research, 2017
- Guadagno N A, Moriconi C, Licursi V, D'Acunto E, Nisi P S, Carucci N, De Jaco A, Cacci E, Negri R, Lupo G, Miranda E: Neuroserpin polymers cause oxidative stress in a neuronal model of the dementia FENIB, Neurobiology of Disease, 2017
- Arbib C., Giovanni Felici, Servilio M, Paolo Ventura: Optimum Solution of the Closest String Problem via Rank Distance, Lecture Notes in Computer Science 9849, 297-307, 2016
- Cestarelli V, Fiscon G, Giovanni Felici, Bertolazzi P., Weitschek E.: CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules, Bioinformatics 32 (5), 697-704, 2016
- Dal Santo S, Palliotti A, Zenoni S, Tornielli GB, Fasoli M, Paci P., Tombesi S, Frioni T, Silvestroni O, Bellincontro A, d'Onofrio C, Matarese F, Gatti M, Poni S, Pezzotti M: Distinct transcriptome responses to water limitation in isohydric and anisohydric grapevine cultivars, BMC Genomics, 2016
- Fiscon G, Weitschek E., Ciccozzi M., Bertolazzi P., Giovanni Felici: A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification, BMC Bioinformatics, 2016
- Krell J, Stebbing J, Carissimi C, Dabrowska A, de Giorgio A, Frampton A.E., Harding V, Fulci V, Macino G., Colombo T, Castellano L: TP53 regulates miRNA association with AGO2 to remodel the miRNA-mRNA interaction network, Genome Research, 2016
- 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, Paci P., 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
- 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
- Bertolazzi P., Giovanni Felici, Festa P., Fiscon G, Weitschek E.: Integer Programming models for Feature Selection: new extensions and a randomized solution algorithm, European Journal of Operational Research, 2015
- Bertolazzi P., Giovanni Felici, Fiscon G, Weitschek E.: Classifying DNA barcode multi-locus sequences with feature vectors and supervised approaches, Genome 58(5), 2015
- Bevilacqua V, Gioia U, Di Carlo V, Tortorelli AF, Colombo T, Bozzoni I, Laneve P, Caffarelli E: Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells, RNA Biology, 2015
- Cestarelli V, Fiscon G, Giovanni Felici, Bertolazzi P., Weitschek E.: CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules, Bioinformatics, 2015
- Tavolaro S, Colombo T, Chiaretti S, Peragine N, Fulci V, Ricciardi MR, Messina M, Bonina S, Brugnoletti F, Marinelli M, Di Maio V, Mauro FR, Del Giudice I, Macino G, Foa' R ., Guarini A: Increased chronic lymphocytic leukemia proliferation upon IgM stimulation is sustained by the upregulation of miR-132 and miR-212, Genome, 2015
- Bertolazzi P., Guerra C., Liuzzi G.: Predicting protein-ligand and protein-peptide interfaces, European Physical Journal Plus 129, 132-142, 2014
- Cumbo F, Giovanni Felici, Bertolazzi P.: Selecting relevant nodes and structures in biological networks. BiNAT: a new plugin for Cytoscape, F1000 3, 2014
- Cumbo F, Paci P., Daniele Santoni, Giuliani A, Di Paola L: GIANT: a Cytoscape plugin for modular networks, Plos One, 9(10): e105001, 2014
- Frampton A.E., Castellano L, Colombo T, Giovanetti E., Krell J, Jacob J, Pellegrino L, Roca-Alonso L, Funel N, Gall T.M., de Giorgio A, Pinho FG, Fulci V, Britton DJ, Ahmad R, Habib N.A., Coombes RC, Harding V, Knoesel T, Stebbing J, Jiao LR: MicroRNAs cooperatively inhibit a network of tumor suppressor genes to promote pancreatic tumor growth and progression, Genome, 2014
- Polychronopoulos D, Weitschek E., Dimitrieva S, Bucher P, Giovanni Felici, Almirantis Y: Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers, Genomics 104(2), 79-86, 2014
- Weitschek E., Fiscon G, Giovanni Felici: Supervised DNA Barcodes species classification: analysis, comparisons and results., BMC BioData Mining, http://www.biodatamining.org/content/7/1/4, 2014
- Weitschek E., Daniele Santoni, Fiscon G, De Cola M C, Bertolazzi P., Giovanni Felici: Next generation sequencing reads comparison with an alignment-free distance, BMC Research Notes, 7:869, 2014
- Di Paola L, De Ruvo M, Paci P., Daniele Santoni, Giuliani A: Proteins Contact Networks: an emerging paradigm in chemistry, Chemical Reviews 113(3), 1598-1613, 2013
- Daniele Santoni, Castiglione F, Paci P.: 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., Van Velzen R, Giovanni Felici, Bertolazzi P.: BLOG 2.0: a software system for character-based species classification with DNA Barcode sequences. What it does, how to use it, Molecular Ecology Resources, 2013
- Alberghina L., Gabriella Mavelli, Drovandi G., Palumbo P., Pessina S., Tripodi F., Coccetti P., Vanoni M.: Cell growth and cell cycle in Saccharomyces cerevisiae: Basic regulatory design and protein - protein interaction network, Biotechnology Advances 30, 52-72, 2012
- Arrigo N, Paci P., 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
- Bertolazzi P., Guerra C., Lampariello F., Liuzzi G.: Continuous global optimization for protein structure analysis, Il Nuovo Cimento 35C, 65-70, 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, Paci P., 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, Paci P., 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
- Paci P., Cacace F., Valerio Cusimano, Germani A., Farina L.: Stochastic modeling of expression kinetics identifies messenger half-lives and reveals sequential waves of co-ordinated transcription and decay, PLoS Computational Biology, 2012
- Paci P., 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
- Weitschek E., Lo Presti A., Drovandi G., Giovanni Felici, Ciccozzi M., Ciotti M., Bertolazzi P.: Human polyomaviruses identification by logic mining techniques, BMC Virology Journal 9:58, 2012
- Arisi I., D'Onofrio M., Brandi R, Felsani A, Capsoni S, Drovandi G., Giovanni Felici, Weitschek E., Bertolazzi P., Cattaneo A: Gene Expression Biomarkers in the Brain of a Mouse Model for Alzheimer's Disease: Mining of Microarray Data by Logic Classification and Feature Selection., Journal of Alzheimer's Disease 24, 2011
- Busti S., Gotti L., Balestrieri C., Querin L., Drovandi G., Giovanni Felici, Gabriella Mavelli, Bertolazzi P., Alberghina L., Vanoni M.: Overexpression of Far1, a cyclin-dependent kinase inhibitor, induces a large transcriptional reprogramming in which RNA synthesis senses Far1 in a Sfp1-mediated way, Biotechnology Advances, 2011
- Castiglione F, Daniele Santoni, Rapin N: CTLs' repertoire shaping in the thymus: a Monte Carlo simulation, Autoimmunity, 2011
- Bertolazzi P., Giovanni Felici, Festa P.: Logic Based Methods for SNPs Tagging and Reconstruction, Computers & Operations Research 37, 1419-1426, 2010
- Bertolazzi P., Guerra C., Liuzzi G.: A global optimization algorithm for protein surface alignment, BMC Bioinformatics 11, 488-498, 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
- Bertolazzi P., Giovanni Felici, Weitschek E.: Learning to classify species with barcodes, BMC Bioinformatics, 2009
- 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
- Bertolazzi P., Giovanni Felici, Festa P., Lancia G.: Logic Classification and Feature Selection for Biomedical Data, Computers & Mathematics with Applications 55(5), 889-899, 2008
- Bertolazzi P., Godi A., Labbè M., Tininini L.: Solving haplotyping inference parsimony problem using a new basic polynomial formulation, Computers & Mathematics with Applications 55(5), 900-911, 2008
- Cacchiarelli D, Daniele Santoni, Bozzoni I: MicroRNAs as prime players in a combinatorial view of evolution, RNA Biology 5, 120-122, 2008
- Michel C.J., Pirillo G., Pirillo M.A.: A relation between trinucleotide comma-free codes and trinucleotide circular codes, Theoretical Computer Science 401, 17-26, 2008
- Tininini L., Bertolazzi P., Godi A., Lancia G.: CollHaps: A Heuristic Approach to Haplotype Inference by Parsimony, IEEE/ACM Transaction on Computational Biology and Bioinformatics, 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
COLLECTIONS
- Cappelli E, Weitschek E.: Extending the Genomic Data Model and the Genometric Query Language with Domain Taxonomies, in the Proceedings of International Conference on Web Engineering, Lecture Notes in Computer Science, 10360, 2017
- Cumbo F, Weitschek E., Bertolazzi P., Giovanni Felici: IRIS-TCGA: an information retrieval and integration system for genomic data of cancer, in the Proceedings of Computational Intelligence Methods for Bioinformatics and Biostatistics, Lecture Notes in Computer Science, 10477, 2017
- Weitschek E., Cumbo F, Cappelli E, Giovanni Felici: Genomic data integration: A case study on next generation sequencing of cancer, DEXA - Database and Expert Systems Applications, 2016
- Weitschek E., Fiscon G, Bertolazzi P., Giovanni Felici: GELA: a software tool for the analysis of gene expression data., DEXA Workshops, 2015
- Weitschek E., Fiscon G, Cestarelli V, Cestarelli V, Bertolazzi P., Giovanni Felici: LAF Barcoding: classifying DNA Barcode multi-locus sequences with feature vectors and supervised approaches, Rovetta S., Angelini C., Bongcam-Rudloff E., Decarli A., Rancoita P.M.V. eds., 12th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, 2015
- Weitschek E., Fiscon G, Fustaino V, Giovanni Felici, Bertolazzi P.: Clustering and Classification Techniques for Gene Expression Profiles Pattern Analysis, in: Pattern Recognition in Computational Molecular Biology: Techniques and Approaches, Elloumi M, Zomaya AY eds., Wiley Series in Bioinformatics, Wiley, 2015
- Fustaino V, Giovanni Felici, Ruberti G.: Integrated analysis of DNA copy number and gene expression data in Lung cancer models of resistance to targeted therapy, IV EURO WG Conference on Operational Research in Computational Biology, Bioinformatics and Medicine, 2014
- Weitschek E., Cunial F, Giovanni Felici: Classifying bacterial genomes with compact logic formulas on k-mer frequencies, Tjoa A.M., Wagner R.R., Morvan F eds., DEXA - Database and Expert Systems Applications, 2014
- Weitschek E., Fiscon G, Giovanni Felici, Bertolazzi P.: GELA: Gene Expression Logic Analyzer, Nettab2014 Workshop, From structural bioinformatics to integrative systems biology. Book of Abstract, 2014
- Weitschek E., Giovanni Felici, Bertolazzi P.: MALA: A Microarray clustering and classification software, Wagner R.R., Tjoa A.M., Hameurlain A eds., DEXA - Database and Expert Systems Applications, 2012
- Bertolazzi P., Giovanni Felici, Lancia G.: Application of Feature Selection and Classification to Computational Molecular Biology, in: Biological data Mining, Chen J.K., Lonardi S. eds., 257-294, 2010
- Giovanni Felici, Bertolazzi P., Guarracino M., Chinchuluun A, Pardalos P. M.: Logic formulas based knowledge discovery and its application to the classification of biological data, in the Proceedings of Biomat 2008: International Symposium On Mathematical And Computational Biology, Mondaini R.P. ed., 2009
BOOKS
- Giuliani A, Di Paola L, Paci P., 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
- Bertolazzi P., Blazewicz J., Turkay M. eds.: Special Issue on Operations Research Models for Computational Biology, Bioinformatics and Medicine, Journal of Mathematical Models and Algorithms, 9, Springer, 2010
SELECTED REPORTS
- Weitschek E., Fiscon G, Fustaino V, Giovanni Felici, Bertolazzi P.: Analysis of microarray and RNA-sequencing gene expression profiles through clustering and classification techniques, IASI-CNR, R. 14-11, 12/2014
- Fiscon G, Weitschek E., Bertolazzi P., De Cola M C, De Salvo S, Bramanti P, Giovanni Felici: EEG signals analysis to detect Alzheimer's disease patients, IASI-CNR, R. 14-10, 12/2014
- Fiscon G, Paci P., Colombo T, Iannello G: Structural Analysis of Long Non-coding RNAs, IASI-CNR, R. 13-21, 12/2013
- Weitschek E., Arisi I., Giovanni Felici, Bertolazzi P.: Knowledge extraction in clinical data, IASI-CNR, R. 13-20, 12/2013
- Weitschek E., Cunial F, Giovanni Felici: Discovering genome-wide k-mer compositional rules using logic formulas, IASI-CNR, R. 13-19, 12/2013
- Weitschek E., Giovanni Felici, Bertolazzi P.: Microarray Logic Analyzer Software, IASI-CNR, R. 13-18, 12/2013
- Weitschek E., Daniele Santoni, De Cola M C, Giovanni Felici: About similarity of DNA reads, IASI-CNR, R. 13-17, 12/2013
- Weitschek E., Polychronopoulos D, Almirantis Y, Giovanni Felici: Conserved non coding elements classification, IASI-CNR, R. 13-15, 12/2013
- Weitschek E., Van Velzen R, Giovanni Felici: Species classification using DNA Barcode sequences: A comparative analysis, IASI-CNR, R. 11-07, 2011
- Bertolazzi P., Giovanni Felici, Weitschek E., Drovandi G., Lo Presti A., Ciccozzi M., Ciotti M.: Human Polyomaviruses genome analysis by logic mining techniques, IASI-CNR, R. 10-23, 12/2010
- Bertolazzi P., Giovanni Felici, Festa P.: Logic Based Methods for SNPs Tagging and Reconstruction, IASI-CNR, R. 667, 7/2007
- Bertolazzi P., Giovanni Felici: Learning to Classify Species with Barcodes, IASI-CNR, R. 665, 7/2007
JOURNALS
- 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
- Derelitto C, Daniele Santoni: TRANSPARENT: a Python tool for designing transcription factor regulatory networks, Soft Computing, Accepted for publication, 2023
- Liguori F, Amadio S, Cinzia Volonté: Fly for ALS: Drosophila modeling on the route to amyotrophic lateral sclerosis modifiers, Cellular and Molecular Life Sciences, 78(17-18):6143-6160, https://link.springer.com/article/10.1007%2Fs00018-021-03905-8, 2021
- Liguori F., Amadio S, Cinzia Volonté: Where and Why Modeling Amyotrophic Lateral Sclerosis, International Journal of Molecular Sciences, 22(8):3977, https://www.mdpi.com/1422-0067/22/8/3977, 2021
- Bersani A., Alessandro Borri, Francesco Carravetta, Gabriella Mavelli, Palumbo P: On a stochastic approach to model the double phosphorylation/dephosphorylation cycle, MATHEMATICS AND MECHANICS OF COMPLEX SYSTEMS, 2020
- Conte F, Fiscon G, Licursi V, Bizzarri D, D'Anto' T, Farina L., Paci P.: A paradigm shift in medicine: A comprehensive review of network-based approaches, BBA - Gene Regulatory Mechanisms, 1863, 2020
- Gaglio D., Bonanomi M., Valtorta S., Bharat R., Ripamonti M., Conte F, Fiscon G., Righi N., Napodano E., Federico Papa, Raccagni I., Parker S.J., Cifola I., Camboni T., Paci P, Colangelo A.M., Vanoni M., Metallo C.M., Moresco R.M., Alberghina L.: Disruption of redox homeostasis for combinatorial drug efficacy in K-Ras tumors as revealed by metabolic connectivity profiling, Cancer & Metabolism, 2020
- Paci P., Fiscon G, Conte F, Licursi V, Morrow J, Hersh C, Cho M, Castaldi P, Glass K, Silverman EK, Farina L.: Integrated transcriptomic correlation network analysis identi fies COPD molecular determinants, Scientific Report, 10, 2020
- Panebianco V, Pecoraro M, Fiscon G, Paci P., Farina L., Catalano C: Prostate Cancer Screening Research Can Benefit from Network Medicine: An Emerging Awareness, npj Systems Biology and Applications, 2020
- Silverman EK, Schmid HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L., Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paci P., Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach J: Molecular Networks in Network Medicine: Development and Applications, WIREs Systems Biology and Medicine, 2020
- Bersani A., Alessandro Borri, Milanesi A, Tomassetti G., Vellucci P.: A study case for the analysis of asymptotic expansions beyond the tQSSA for inhibitory mechanisms in enzyme kinetics, Communications in Applied and Industrial Mathematics vol. 10(1), pp. 162-181, 2019
- Capalbo C, Belardinilli F, Raimondo D, Milanetti E, Malapelle U, Pisapia P, Magri V, Prete A, Pecorari S, Colella M, Coppa A, Bonfiglio C, Nicolussi A, Valentini V, Tessitore A, Cardinali B, Petroni M, Infante P, Santoni M, Filetti M, Colicchia V, Paci P., Mezi S, Longo F, Cortesi E, Marchetti P, Troncone G, Bellavia D, Canettieri G, Giannini G: A Simplified Genomic Profiling Approach Predicts Outcome in Metastatic Colorectal Cancer, Cancers, 11, 2019
- Falcone R, Conte F, Fiscon G, Pecce V, Sponziello M, Durante C, Farina L., Filetti S, Paci P., Verrienti A: BRAF(V600E)-mutant cancers display a variety of networks by SWIM analysis: prediction of vemurafenib clinical response, Endocrine, 64, 2019
- Licursi V, Conte F, Fiscon G, Paci P.: MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis, BMC Bioinformatics, 20, 2019
- Magris G, Di Gaspero G, Marroni F, Zenoni S, Tornielli GB, Celii M, De Paoli E, Pezzotti M, Conte F, Paci P., Morgante M: Genetic, epigenetic and genomic effects on variation of gene expression among grape varieties, The Plant Journal, 99, 2019
- Gabriella Mavelli, Palombo G, Palumbo P: A Stochastic Optimal Regulator for a Class of Nonlinear Systems, Mathematical Problems in Engineering, 2019
- Mocavini I, Pippa S, Licursi V, Paci P., Trisciuoglio D, Mannironi C, Presutti C, Negri R: JARID1B expression and its function in DNA damage repair are tightly regulated by miRNAs in breast cancer, Cancer Science, 110, 2019
- Vahabi m, Pulito C, Sacconi A, Donzelli S, D’Andrea M, Manciocco V, Pellini R, Paci P., Sanguineti G, Strigari L, Spriano G, Muti P, Pandolfi PP, Strano S, Safarian S, Ganci F, Blandino G: miR-96-5p targets PTEN expression affecting radio-chemosensitivity of HNSCC cells, Journal of Experimental & Clinical Cancer Research, 38, 2019
- Angelini G., Salinari S., Bertuzzi A., Iaconelli A., Mingrone G.: Metabolic surgery improves insulin resistance through the reduction of gut-secreted heat shock proteins, Communications Biology, 1-69, 2018
- Farina L., Paci P.: A feature-based integrated scoring scheme for cell cycle-regulated genes prioritization, Journal of Theoretical Biology, 459, 2018
- Fiscon G, Conte F, Farina L., Paci P.: Network-based approaches to explore complex biological systems towards network medicine, Genes, 2018
- Fiscon G, Conte F, Licursi V, Sergio Nasi, Paci P.: Computational identification of specific genes for glioblastoma stem-like cells identity, Scientific Report, 8, 2018
- Fiscon G, Conte F, Paci P.: SWIM tool application to expression data of glioblastoma stem-like cell lines, corresponding primary tumors and conventional glioma cell lines, BMC Bioinformatics, 19, 2018
- Vernocchi P, Del Chierico F, Russo A, Majo F, Rossitto M, Valerio M, Casadei L, La Storia A, De Filippis F, Rizzo C, Manetti C, Paci P., Ercolini D, Marini F, Fiscarelli EV, Dallapiccola B, Lucidi V, Miccheli A, Putignani L: Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype, Plos One, 13, 2018
- Bersani A, Alessandro Borri, Milanesi A, Vellucci P.: Tihonov theory and center manifolds for inhibitory mechanisms in enzyme kinetics, Communications in Applied and Industrial Mathematics vol. 8(1), pp. 81-102, 2017
- Bonifaci V.: A revised model of fluid transport optimization in Physarum polycephalum, Journal of Mathematical Biology 74, 567-581, 2017
- Massonnet M., Fasoli M, Tornielli GB, Altieri M, Sandri M, Zuccolotto P, Paci P., Gardiman M, Zenoni S, Pezzotti M: Ripening Transcriptomic Program in Red and White Grapevine Varieties Correlates with Berry Skin Anthocyanin Accumulation, Plant Physiology, 174, 2017
- Paci P., Colombo T, Fiscon G, Gurtner A, Pavesi G, Farina L.: SWIM: a computational tool to unveiling crucial nodes in complex biological networks, Scientific Report, 7, 2017
- Previti E., Salinari S., Bertuzzi A., Capristo E., Bornstein S., Mingrone G.: Glycemic control after metabolic surgery: a granger causality and graph analysis, American Journal of Physiology-Endocrinology and Metabolism, E622-E630, 2017
- Salinari S., Mingrone G., Bertuzzi A., Previti E., Capristo E., Rubino F.: Downregulation of insulin sensitivity after oral glucose administration: evidence for the anti-incretin effect, Diabetes 66(11), 2756-2763, 2017
- Bertuzzi A., Conte F, Mingrone G., Federico Papa, Salinari S., Carmela Sinisgalli: Insulin Signaling in Insulin Resistance States and Cancer: A Modeling Analysis, Plos One, http://dx.doi.org/10.1371/journal.pone.0154415, 2016
- Borri A, Palumbo P., Singh A: The impact of negative feedback in metabolic noise propagation, IET Systems Biology 10, 179-186, 2016
- Alessandro Borri, Francesco Carravetta, Gabriella Mavelli, Palumbo P.: Block-tridiagonal state-space realization of Chemical Master Equations: A tool to compute explicit solutions, Journal of Computational and Applied Mathematics vol. 296, pp. 410–426, 2016
- Alessandro Borri, Palumbo P., Singh A: Impact of negative feedback in metabolic noise propagation, IET Systems Biology 10 (5), 179-186, 2016
- Dal Santo S, Palliotti A, Zenoni S, Tornielli GB, Fasoli M, Paci P., Tombesi S, Frioni T, Silvestroni O, Bellincontro A, d'Onofrio C, Matarese F, Gatti M, Poni S, Pezzotti M: Distinct transcriptome responses to water limitation in isohydric and anisohydric grapevine cultivars, BMC Genomics, 2016
- Krell J, Stebbing J, Carissimi C, Dabrowska A, de Giorgio A, Frampton A.E., Harding V, Fulci V, Macino G., Colombo T, Castellano L: TP53 regulates miRNA association with AGO2 to remodel the miRNA-mRNA interaction network, Genome Research, 2016
- Palumbo P., Vanoni M., Valerio Cusimano, Busti S, Marano M., Manes C., Alberghina L.: Whi5 phosphorylation embedded in the G1/S network dynamically controls critical cell size and cell fate, Nature Communications, 2016
- Puszynski K., Gandolfi A., d'Onofrio A.: The role of stochastic gene switching in determining the pharmacodynamics of certain drugs: basic mechanisms, Journal of Pharmacokinetics and Pharmacodynamics, DOI 10.1007/s10928-016-9480-2, 2016
- Daniele Santoni, Paci P., 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
- Arisi I., D'Onofrio M., Brandi R., Cattaneo A., Bertolazzi P., Cumbo F, Giovanni Felici, Guerra C.: Time dynamics of protein complexes in the AD11 transgenic mouse model for Alzheimer's disease like pathology, Bmc Neuroscience, 2015
- Bevilacqua V, Gioia U, Di Carlo V, Tortorelli AF, Colombo T, Bozzoni I, Laneve P, Caffarelli E: Identification of linc-NeD125, a novel long non coding RNA that hosts miR-125b-1 and negatively controls proliferation of human neuroblastoma cells, RNA Biology, 2015
- Colombo T, Farina L., Macino G., Paci P.: PVT1: A rising star among oncogenic long noncoding RNAs, BioMed Research International, http://www.scopus.com/inward/record.url?eid=2-s2.0-84926673517&partnerID=q2rCbXpz, 2015
- Del Chierico F, Vernocchi P, Petrucca A, Paci P., Fuentes S, Pratic G, Capuani G, Masotti A, Reddel S, Russo A, Vallone C, Salvatori G, Buffone E, Signore F, Rigon G, Dotta A, Miccheli A, de Vos WM, Dallapiccola B, Putignani L: Gut microbiota phylogenetic and metabolic tracking during perinatal age, Plos One, 10, 2015
- Fiscon G, Paci P., Colombo T, Iannello G: A new procedure to analyze RNA non-branching structures, Current bioinformatics 10, 2015
- Fiscon G, Paci P., Iannello G: MONSTER v1.1: a tool to extract and search for RNA non-branching structures., BMC Genomics 16, 2015
- Garbuglia A.R., Lionetti R., Lapa D., Taibi C., Visco-Comandini U., Montalbano M., D'Offizi G., Castiglione F., Capobianchi M.R., Paci P.: The clinical significance of HCV core antigen detection during Telaprevir/Peg-Interferon/Ribavirin therapy in patients with HCV 1 genotype infection, Journal of Clinical Virology 69, 68-73, 2015
- Guerra C.: On the interconnection of stable protein complexes: inter-complex hubs and their conservation in Saccharomyces cerevisiae and Homo sapiens networks, International Journal of Bioinformatics Research and Applications 11(6), 483-502, 2015
- Palumbo MC, Farina L., Paci P.: Kinetic effects and modelling of mRNA turnover, Wiley interdisciplinary reviews. RNA 6, 327-336, 2015
- Tavolaro S, Colombo T, Chiaretti S, Peragine N, Fulci V, Ricciardi MR, Messina M, Bonina S, Brugnoletti F, Marinelli M, Di Maio V, Mauro FR, Del Giudice I, Macino G, Foa' R ., Guarini A: Increased chronic lymphocytic leukemia proliferation upon IgM stimulation is sustained by the upregulation of miR-132 and miR-212, Genome, 2015
- Amir A., Apostolico A., Eisenberg E., Landau G.M., Levy A., Lewenstein N.: Detecting approximate periodic patterns, Theoretical Computer Science 525, 60-67, 2014
- Amir A., Apostolico A., Landau G.M., Levy A., Lewenstein M., Porat E.: Range LCP, Journal of Computer and System Sciences 80, 1245-1253, 2014
- Apostolico A., Erdos P.L., Miklos I., Siemons J.: Modulated string searching, Theoretical Computer Science 525, 23-29, 2014
- Bertolazzi P., Bock M.E., Guerra C., Paci P., 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
- Cazzaniga P, Daminani C., Besozzi D, Colombo R., Nobile M.S., Gaglio D., Pescini D., Molinari S., Mauri G., Alberghina L., Vanoni M.: Computational strategies for a system-level understanding of metabolism, Metabolites 4, 1034-1087, 2014
- Cazzaniga P, Nobile M.S., Besozzi D, Bellini M., Mauri G.: Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization, BioMed Research International 2014, 2014
- Cumbo F, Giovanni Felici, Bertolazzi P.: Selecting relevant nodes and structures in biological networks. BiNAT: a new plugin for Cytoscape, F1000 3, 2014
- Cumbo F, Paci P., Daniele Santoni, Giuliani A, Di Paola L: GIANT: a Cytoscape plugin for modular networks, Plos One, 9(10): e105001, 2014
- Frampton A.E., Castellano L, Colombo T, Giovanetti E., Krell J, Jacob J, Pellegrino L, Roca-Alonso L, Funel N, Gall T.M., de Giorgio A, Pinho FG, Fulci V, Britton DJ, Ahmad R, Habib N.A., Coombes RC, Harding V, Knoesel T, Stebbing J, Jiao LR: MicroRNAs cooperatively inhibit a network of tumor suppressor genes to promote pancreatic tumor growth and progression, Genome, 2014
- Nobile M.S., Cazzaniga P, Besozzi D, Mauri G.: GPU-accelerated simulations of mass-action kinetics models with cupSODA, Journal of Supercomputing 69, 17-24, 2014
- Nobile M.S., Cazzaniga P, Besozzi D, Pescini D., Mauri G.: cuTauLeaping: a GPU-powered tau-leaping stochastic simulator for massive parallel analyses of biological systems, Plos One 9, 2014
- Paci P., Colombo T, Farina L.: Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer, BMC Systems Biology, 2014
- Paci P., Colombo T, Farina L.: Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer., BMC Systems Biology, 2014
- Palumbo MC, Zenoni S., Fasoli M., Massonnet M., Farina L., Castiglione F, Pezzotti M., Paci P.: Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development, The Plant Cell, 2014
- Daniele Santoni, Swiercz A., Zmienko A, Kasprzak M, Blazewicz M, Bertolazzi P., 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, Paci P., Daniele Santoni, Palumbo P., 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
- Bertolazzi P., Bock M.E., Guerra C.: On the functional and structural characterization of hubs in protein-protein interaction networks, Biotechnology Advances 31, 274-286, 2013
- Bonifaci V.: Physarum Can Compute Shortest Paths: A Short Proof, Information Processing Letters 113, 4-7, 2013
- Di Paola L, De Ruvo M, Paci P., Daniele Santoni, Giuliani A: Proteins Contact Networks: an emerging paradigm in chemistry, Chemical Reviews 113(3), 1598-1613, 2013
- Daniele Santoni, Castiglione F, Paci P.: 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
- Alberghina L., Gaglio D., Gelfi C., Moresco R.M., Mauri G., Bertolazzi P., Messa C., Gilardi M.C., Chiaradonna F., Vanoni M.: Cancer cell growth and survival as a system-level property sustained by enhanced glycolysis and mitochondrial metabolic remodeling, Frontiers in Physiology, 2012
- Alberghina L., Gabriella Mavelli, Drovandi G., Palumbo P., Pessina S., Tripodi F., Coccetti P., Vanoni M.: Cell growth and cell cycle in Saccharomyces cerevisiae: Basic regulatory design and protein - protein interaction network, Biotechnology Advances 30, 52-72, 2012
- Bonifaci V., Mehlhorn K., Varma G.: Physarum Can Compute Shortest Paths, Journal of Theoretical Biology 309, 121-133, 2012
- Cacace F., Germani A., Palumbo P.: The state observer as a tool for the estimation of gene expression, Journal of Mathematical Analysis and Applications 391, 382-396, 2012
- Paci P., Cacace F., Valerio Cusimano, Germani A., Farina L.: Stochastic modeling of expression kinetics identifies messenger half-lives and reveals sequential waves of co-ordinated transcription and decay, PLoS Computational Biology, 2012
- Paci P., 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
- Sferra G, Daniele Santoni, Pizzi E: Plasmodium phylogenetic profile: an assessment of a predictive tool for protein-protein interactions, EMBnet.journal, 18(A), 2012
- Busti S., Gotti L., Balestrieri C., Querin L., Drovandi G., Giovanni Felici, Gabriella Mavelli, Bertolazzi P., Alberghina L., Vanoni M.: Overexpression of Far1, a cyclin-dependent kinase inhibitor, induces a large transcriptional reprogramming in which RNA synthesis senses Far1 in a Sfp1-mediated way, Biotechnology Advances, 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
- Bertuzzi A., Fasano A., Gandolfi A., Carmela Sinisgalli: Necrotic core in EMT6/Ro tumour spheroids: Is it caused by an ATP deficit?, Journal of Theoretical Biology 262, 142-150, 2010
- Brümmer A., Salazar C., Zinzalla V., Alberghina L., Höfer T.: Mathematical Modelling of DNA Replication Reveals a Trade-off between Coherence of Origin Activation and Robustness against Rereplication, PLoS Computational Biology, 2010
- Farina L., Germani A., Gabriella Mavelli, Palumbo P.: Identification of regulatory network motifs from gene expression data, Journal of Mathematical Modelling and Algortihms 9, 233-245, 2010
- Palumbo P., Gabriella Mavelli, Farina L., Alberghina L.: Networks and circuits in cell regulation, Biochemical and Biophysical Research Communications 396, 881-886, 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
- Salazar C., Höfer T., Brümmer A., Alberghina L.: Timing Control in Regulatory Networks by Multisite Phosphorylation, Trends in Cell Biology 20, 634-641, 2010
- 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
- Bertuzzi A., Fasano A., Gandolfi A., Carmela Sinisgalli: ATP production and necrosis formation in a tumour spheroid model, Mathematical Modelling of Natural Phenomena 2, 30-46, 2007
COLLECTIONS
- Alessandro Borri, Palumbo P., Singh A: Noise propagation in feedback coupling between cell growth and metabolic activity, Proceedings of the 57th IEEE Conference on Decision and Control (CDC 2018), Miami Beach, FL, USA, pp. 2679-2684, 2018
- Guzzi R., Colombo T, Paci P.: Inverse Problems in Systems Biology: A Critical Review, in: Systems Biology, Bizzarri M ed., Methods in Molecular Biology, 1702, Humana Press, New York, NY, 69-94, 2018
- Russo F, Fiscon G, Conte F, Rizzo M, Paci P., Pellegrini M: Interplay between long non-coding RNAs and microRNAs in cancer, in: Computational Cell Biology: Methods and Protocols, von Stechow L, Santos Delgado A eds., Methods in Molecular Biology, 1819, Humana Press, New York, NY, 75-92, 2018
- Tieri P, Farina L., Petti M, Astolfi L, Paci P., Castiglione F.: Network inference and reconstruction in Bioinformatics, in: Encyclopedia of Bioinformatics and Computational Biology, Gribskov M, Ranganathan S, Nakai K, Schnbach C eds., Reference Module in Life Sciences, 2, Elsevier, 805-813, 2018
- Alessandro Borri, Palumbo P., Singh A: Noise propagation in a class of metabolic networks, Proceedings of the 56th IEEE Conference on Decision and Control (CDC 2017), Melbourne, Australia, pp. 447-452, 2017
- Borri A, Palumbo P., Singh A: Noise reduction for enzymatic reactions: a case study for stochastic product clearance, 55th IEEE Conference on Decision and Control (CDC16), 2016
- Alessandro Borri, Francesco Carravetta, Palumbo P.: Stochastic Differential Equations and Approximate Moments Calculation of the Langevin Equation, Proceedings of the 55th IEEE Conference on Decision and Control (CDC 2016), Las Vegas, USA, pp. 4540-4545, 2016
- Alessandro Borri, Palumbo P., Singh A: Noise reduction for enzymatic reactions: a case study for stochastic product clearance, Proceedings of the 55th IEEE Conference on Decision and Control (CDC 2016), Las Vegas, USA, pp. 5851-5856, 2016
- Alessandro Borri, Palumbo P., Singh A: Metabolic noise reduction for enzymatic reactions: the role of a negative feedback, Proceedings of the 54th IEEE Conference on Decision and Control (CDC 2015), Osaka, Giappone, pp. 2537–2542, 2015
- Amir A., Apostolico A., Hirst T, Landau G.M., Lewenstein N., Rozenberg L.: Algorithms for Jumbled Indexing, Jumbled Border and Jumbled Square on Run-Length Encoded Strings, in the Proceedings of String Processing and Information Retrieval (SPIRE 2014), Lecture Notes in Computer Science, 8799, 2014
- Apostolico A., Guerra C., Pizzi C.: Alignment Free Sequence Similarity with Bounded Hamming Distance, in the Proceedings of 2014 Data Compression Conference, Compression Conference (DCC), 2014
- Nobile M.S., Citrolo A.G., Cazzaniga P, Besozzi D, Mauri G.: A memetic hybrid method for the Molecular Distance Geometry Problem with incomplete information, IEEE Congress on Evolutionary Computation (CEC 2014), 2014
- Becchetti L., Bonifaci V., Dirnberger M., Karrenbauer A., Mehlhorn K.: Physarum Can Compute Shortest Paths: Convergence Proofs and Complexity Bounds, in the Proceedings of the 40th Int. Colloquium on Automata, Languages and Programming, Lecture Notes in Computer Science, 2013
- Alessandro Borri, Francesco Carravetta, Gabriella Mavelli, Palumbo P.: Chemical Master Equations: a mathematical scheme for the multi-site phosphorylation case, Proceedings of the 3rd International Conference on Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2013), Reykjavik, Iceland, pp. 681-688, 2013
- Alessandro Borri, Francesco Carravetta, Gabriella Mavelli, Palumbo P.: Some Results on the structural properties and the solution of the Chemical Master Equation, Proceedings of the 2013 American Control Conference (ACC 2013), Washington, DC, USA, pp. 3777-3782, 2013
- Nobile M.S., Besozzi D, Cazzaniga P, Mauri G., Pescini D.: cupSODA: a CUDA-powered simulator of mass-action kinetics, in the Proceedings of Proceedings of 12th International Conference on Parallel Computing Technologies (PaCT 2013), Malyshkin V. ed., Lecture Notes in Computer Science, 7979, 2013
- Bonifaci V., Mehlhorn K., Varma G.: Physarum Can Compute Shortest Paths, in the Proceedings of the 23rd Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM Proceedings in Applied Mathematics, 2012
- Cacace F., Germani A., Palumbo P.: Observer-based identification of a multi-output feedforward loop from gene expression data, 48th Conference on Decision and Control (CDC2009) held jointly with 2009 28-th Chinese Control Conference, 2009
- Bertuzzi A., Fasano A., Gandolfi A., Carmela Sinisgalli: A mathematical model of ATP production in a multicellular spheroid model with necrotic core, in the Proceedings of SysBioHealth Symposium 2007, Alberghina L., Milanesi L. eds., 2007
BOOKS
- Fiscon G, Conte F, Farina L., Pellegrini M, Russo F, Paci P.: Identification of Disease-miRNA Networks Across Different Cancer Types Using SWIM, Methods in Molecular Biology, 1970, Humana Press, New York, NY, 2019
- Giuliani A, Di Paola L, Paci P., 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
- 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
SELECTED REPORTS
- Alessandro Borri, Francesco Carravetta, Palumbo P.: A Cubification Approach for the Approximate Moments Computation in Stochastic Differential Equations: Application to the Chemical Langevin Equation, IASI-CNR, R. 16-01, 2016
- Bertolazzi P., Bock M.E., Guerra C., Paci P., 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
- Alessandro Borri, Francesco Carravetta, Gabriella Mavelli, Palumbo P.: A study on the structural properties and the solution of the Chemical Master Equation, IASI-CNR, R. 12-10, 10/2012
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