Computational modeling of the expansion of human cord blood CD133+ hematopoietic stem/progenitor cells with different cytokine combinations. - Francesca Gullo; Mark van der Garde; Giulia Russo; Marzio Pennisi; Santo Motta; Francesco Pappalardo 001; Suzanne Watt (Bioinform., 2015)

A computational model to predict the immune system activation by citrus-derived vaccine adjuvants. - Francesco Pappalardo 001; Epifanio Fichera; Nicoletta Paparone; Alessandro Lombardo; Marzio Pennisi; Giulia Russo; Marco Leotta; Alessandro Pedretti; Francesco De Fiore; Santo Motta (Bioinform., 2016)

Optimization and analisys of vaccination schedules using simulated annealing and agent based models. - Marzio Pennisi; Juan A. Sanchez-Lantaron; Pedro A. Reche; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2017)

Introducing scale factor adjustments on agent-based simulations of the immune system. - Juan A. Sanchez-Lantaron; Pedro A. Reche; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2017)

2DIs: A SBML Compliant Web Platform for the Design and Modeling of Immune System Interactions. - Marzio Pennisi; Giulia Russo; Giuseppe Sgroi; Giuseppe Parasiliti; Francesco Pappalardo 001 (ICIC (2), 2017)

Modeling PI3K/PDK1/Akt and MAPK Signaling Pathways Using Continuous Petri Nets. - Giulia Russo; Marzio Pennisi; Roberta Boscarino; Francesco Pappalardo 001 (ICIC (2), 2017)

Combining agent based-models and virtual screening techniques to predict the best citrus-derived vaccine adjuvants against human papilloma virus. - Marzio Pennisi; Giulia Russo; Silvia Ravalli; Francesco Pappalardo 001 (BMC Bioinform., 2017)

An agent based modeling approach for the analysis of tuberculosis - immune system dynamics. - Francesco Pappalardo 001; Giulia Russo; Marzio Pennisi; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Santo Motta; Epifanio Fichera (BIBM, 2018)

Agent based modeling of relapsing multiple sclerosis: a possible approach to predict treatment outcome. - Francesco Pappalardo 001; Giulia Russo; Marzio Pennisi; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Santo Motta; Davide Maimone; Ferdinando Chiacchio (BIBM, 2018)

Computational modeling approach to suggest possible therapeutic interventions in spinal muscular atrophy. - Giulia Russo; Guanglan Zhang (BIBM, 2018)

GPU Accelerated Analysis of Treg-Teff Cross Regulation in Relapsing-Remitting Multiple Sclerosis. - Marco Beccuti; Paolo Cazzaniga; Marzio Pennisi; Daniela Besozzi; Marco S. Nobile; Simone Pernice; Giulia Russo; Andrea Tangherloni; Francesco Pappalardo 001 (Euro-Par Workshops, 2018)

BIOESOnet: A Tool for the Generation of Personalized Human Metabolic Pathways from 23andMe Exome Data. - Marzio Pennisi; Gabriele Forzano; Giulia Russo; Barbara Tomasello; Marco Favetta; Marcella Renis; Francesco Pappalardo 001 (ICIC (2), 2018)

Combining Parallel Genetic Algorithms and Machine Learning to Improve the Research of Optimal Vaccination Protocols. - Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (PDP, 2018)

Continuous Petri Nets and microRNA Analysis in Melanoma. - Giulia Russo; Marzio Pennisi; Roberta Boscarino; Francesco Pappalardo 001 (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

A MapReduce tool for in-depth analysis of KEGG pathways: identification and visualization of therapeutic target candidates. - Giuseppe Alessandro Parasiliti Palumbo; Pietro Biondi; Giuseppe Sgroi; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2019)

Generation of digital patients for the simulation of tuberculosis with UISS-TB. - Marzio Pennisi; Miguel A. Juárez; Giulia Russo; Marco Viceconti; Francesco Pappalardo 001 (BIBM, 2019)

Exploiting Stochastic Petri Net formalism to capture the Relapsing Remitting Multiple Sclerosis variability under Daclizumab administration. - Simone Pernice; Greta Romano; Giulia Russo; Marco Beccuti; Marzio Pennisi; Francesco Pappalardo 001 (BIBM, 2019)

Evaluation of the efficacy of RUTI and ID93/GLA-SE vaccines in tuberculosis treatment: in silico trial through UISS-TB simulator. - Giulia Russo; Francesco Pappalardo 001; Miguel A. Juárez; Marzio Pennisi; Pere-Joan Cardona; Rhea Coler; Epifanio Fichera; Marco Viceconti (BIBM, 2019)

Gene expression and pathway bioinformatics analysis detect a potential predictive value of MAP3K8 in thyroid cancer progression. - Valentina Di Salvatore; Fiorenza Gianì; Giulia Russo; Marzio Pennisi; Pasqualino Malandrino; Francesco Frasca; Francesco Pappalardo 001 (BIBM, 2019)

In Silico Evaluation of Daclizumab and Vitamin D Effects in Multiple Sclerosis Using Agent Based Models. - Marzio Pennisi; Giulia Russo; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Francesco Pappalardo 001 (CIBB, 2019)

A MapReduce Based Tool for the Analysis and Discovery of Novel Therapeutic Targets. - Giuseppe Parasiliti; Marzio Pennisi; Pietro Biondi; Giuseppe Sgroi; Giulia Russo; Christian Napoli 001; Francesco Pappalardo 001 (PDP, 2019)

In silico clinical trials: concepts and early adoptions. - Francesco Pappalardo 001; Giulia Russo; Flora Musuamba Tshinanu; Marco Viceconti (Briefings Bioinform., 2019)

Computational modeling reveals MAP3K8 as mediator of resistance to vemurafenib in thyroid cancer stem cells. - Fiorenza Gianì; Giulia Russo; Marzio Pennisi; Laura Sciacca; Francesco Frasca; Francesco Pappalardo 001 (Bioinform., 2019)

EpiMethEx: a tool for large-scale integrated analysis in methylation hotspots linked to genetic regulation. - Saverio Candido; Giuseppe Alessandro Parasiliti Palumbo; Marzio Pennisi; Giulia Russo; Giuseppe Sgroi; Valentina Di Salvatore; Massimo Libra; Francesco Pappalardo 001 (BMC Bioinform., 2019)

Predicting the artificial immunity induced by RUTI® vaccine against tuberculosis using universal immune system simulator (UISS). - Marzio Pennisi; Giulia Russo; Giuseppe Sgroi; Angela Bonaccorso; Giuseppe Alessandro Parasiliti Palumbo; Epifanio Fichera; Dipendra Kumar Mitra; Kenneth B. Walker; Pere-Joan Cardona; Merce Amat; Marco Viceconti; Francesco Pappalardo 001 (BMC Bioinform., 2019)

POSITION PAPER: Credibility of In Silico Trial Technologies: A Theoretical Framing. - Marco Viceconti; Miguel A. Juárez; Cristina Curreli; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (CoRR, 2019)

Computational Immunogenetics. - Marta Gomez-Perosanz; Giulia Russo; Jose Luis Sanchez-Trincado Lopez; Marzio Pennisi; Pedro A. Reche; Adrian J. Shepherd; Francesco Pappalardo 001 (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Toward computational modelling on immune system function. - Francesco Pappalardo 001; Marzio Pennisi; Pedro A. Reche; Giulia Russo (BMC Bioinform., 2019)

Verify: a toolbox for deterministic verification of computational models. - Giuseppe Alessandro Parasiliti Palumbo; Giulia Russo; Giuseppe Sgroi; Marco Viceconti; Marzio Pennisi; Cristina Curreli; Francesco Pappalardo 001 (BIBM, 2020)

Modeling, simulation and prediction of protein structures for the design of oncolytic viruses. - Valentina Di Salvatore; Daniela Formica; Giulia Russo; Viviana Giannino; Francesco Pappalardo 001 (BIBM, 2020)

Evaluation of the predictive capability of PETAL tool: a retrospective study on potential tyrosine kinases drug resistance targets. - Giuseppe Sgroi; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001; Giuseppe Alessandro Parasiliti Palumbo (BIBM, 2020)

Generation of digital patients for the simulation of tuberculosis with UISS-TB. - Miguel A. Juárez; Marzio Pennisi; Giulia Russo; Dimitrios Kiagias; Cristina Curreli; Marco Viceconti; Francesco Pappalardo 001 (BMC Bioinform., 2020)

Toward computational modelling on immune system function. - Francesco Pappalardo 001; Giulia Russo; Pedro A. Reche (BMC Bioinform., 2020)

In silico trial to test COVID-19 candidate vaccines: a case study with UISS platform. - Giulia Russo; Marzio Pennisi; Epifanio Fichera; Santo Motta; Giuseppina Raciti; Marco Viceconti; Francesco Pappalardo 001 (BMC Bioinform., 2020)

Moving forward through the in silico modeling of tuberculosis: a further step with UISS-TB. - Giulia Russo; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Marzio Pennisi; Miguel A. Juárez; Pere-Joan Cardona; Santo Motta; Kenneth B. Walker; Epifanio Fichera; Marco Viceconti; Francesco Pappalardo 001 (BMC Bioinform., 2020)

In Silico Trial to test COVID-19 candidate vaccines: a case study with UISS platform. - Giulia Russo; Marzio Pennisi; Marco Viceconti; Francesco Pappalardo 001 (CoRR, 2020)

Credibility of In Silico Trial Technologies - A Theoretical Framing. - Marco Viceconti; Miguel A. Juárez; Cristina Curreli; Marzio Pennisi; Giulia Russo; Francesco Pappalardo 001 (IEEE J. Biomed. Health Informatics, 2020)

Uncertainty quantification and sensitivity analysis for in silico trial platform: a preliminary application on UISS-MS. - Giuseppe Alessandro Parasiliti Palumbo; Avisa Maleki; Serena Anna Italia; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2021)

A multi-step and multi-scale bioinformatic approach to investigate potential source of cross-reactive immunity against SARS-CoV-2 UK variant. - Valentina Di Salvatore; Avisa Maleki; Giulia Russo; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Francesco Pappalardo 001 (BIBM, 2021)

PEAK: A Clever Python Tool for Exploratory, Regression, and Classification Data. A Case Study for COVID-19. - Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Valentina Di Salvatore; Giulia Russo; Francesco Pappalardo 001 (BIOMESIP, 2021)

PETAL: a Python tool for deep analysis of biological pathways. - Giuseppe Sgroi; Giulia Russo; Francesco Pappalardo 001 (Bioinform., 2021)

In silico design of recombinant multi-epitope vaccine against influenza A virus. - Avisa Maleki; Giulia Russo; Giuseppe Alessandro Parasiliti Palumbo; Francesco Pappalardo 001 (BMC Bioinform., 2021)

Model verification tools: a computational framework for verification assessment of mechanistic agent-based models. - Giulia Russo; Giuseppe Alessandro Parasiliti Palumbo; Marzio Pennisi; Francesco Pappalardo 001 (BMC Bioinform., 2021)

Evaluation of word embedding models to extract and predict surgical data in breast cancer. - Giuseppe Sgroi; Giulia Russo; Anna Maglia; Giuseppe Catanuto; Peter Barry; Andreas Karakatsanis; Nicola Rocco; Francesco Pappalardo 001 (BMC Bioinform., 2021)

Possible Contexts of Use for In Silico Trials Methodologies: A Consensus-Based Review. - Marco Viceconti; Luca Emili; Payman Afshari; Eulalie Courcelles; Cristina Curreli; Nele Famaey; Liesbet Geris; Marc Horner; Maria Cristina Jori; Alexander Kulesza; Axel Loewe; Michael Neidlin; et al. (IEEE J. Biomed. Health Informatics, 2021)

Genetic algorithm application for the prediction of potential SARS-CoV-2 new variant of concern. - Avisa Maleki; Alvaro Ras-Carmona; Valentina Di Salvatore; Giulia Russo; Elena Crispino; Francesco Pappalardo 001 (BIBM, 2022)

Cutaneous Leishmaniasis: discovering new effective therapies using the Universal Immune System Simulator. - Nandu Chandran Nair; Elena Crispino; Avisa Maleki; Valentina Di Salvatore; Giulia Russo; Maria Adelaida Gomez; Francesco Pappalardo 001 (BIBM, 2022)

UISS-GPU: Accelerated In-Silico Tuberculosis Vaccine Trials Using FLAME GPU. - Paul Richmond; Matthew Leach; Peter Heywood; Francesco Pappalardo 001; Giulia Russo; Marzio Pennisi (BIBM, 2022)

A multi-step and multi-scale bioinformatic protocol to investigate potential SARS-CoV-2 vaccine targets. - Giulia Russo; Valentina Di Salvatore; Giuseppe Sgroi; Giuseppe Alessandro Parasiliti Palumbo; Pedro A. Reche; Francesco Pappalardo 001 (Briefings Bioinform., 2022)

In silico clinical trials for relapsing-remitting multiple sclerosis with MS TreatSim. - Fianne L. P. Sips; Francesco Pappalardo 001; Giulia Russo; Roberta Bursi (BMC Medical Informatics Decis. Mak., 2022)

Toward A Regulatory Pathway for the Use of in Silico Trials in the CE Marking of Medical Devices. - Francesco Pappalardo 001; John Wilkinson; Francois Busquet; Antoine Bril; Mark Palmer; Kenneth B. Walker; Cristina Curreli; Giulia Russo; Thierry Marchal; Elena Toschi; Rossana Alessandrello; Vincenzo Costignola; et al. (IEEE J. Biomed. Health Informatics, 2022)

Modeling and Simulation of anakinra effects on severe COVID19 Patients. - William Cavallaro; Marzio Pennisi; Evdoxia Kyriazopoulou; Giulia Russo; Maria Cristina Jori; Evangelos J. Giamarellos-Bourboulis; Francesco Pappalardo 001 (BIBM, 2023)

Predictive Modelling of Allergic Responses to Chemical Sensitizers: Distinguishing Skin and Respiratory Reactions. - Elena Crispino; Emanuela Corsini; Giulia Russo; Andrew Worth; Silvia Casati; Francesco Pappalardo 001 (BIBM, 2023)

Modeling Cutaneous Leishmaniasis: Insights into M1/M2 Macrophage Dynamics Using the Universal Immune System Simulator. - Elena Crispino; Giulia Russo; Maria Adelaida Gomez; Francesco Pappalardo 001; Avisa Maleki; Valentina Di Salvatore (BIBM, 2023)

Universal Immune System Simulator Analysis: The Impact of the Variable Approach Technique® on Enhancing Immune Defense Against infectious diseases. - Giuseppe Cultrera; Agnese Maccarrone; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2023)

Genetic Algorithm-Based Prediction of Emerging SARS-CoV-2 Variants: A Computational Biology Perspective. - Avisa Maleki; Alvaro Ras-Carmona; Elena Crispino; Valentina Di Salvatore; Giulia Russo; Pedro A. Reche; Francesco Pappalardo 001 (BIBM, 2023)

Enhancing Multiple Sclerosis Lesion Segmentation in Multimodal MRI Scans with Diffusion Models. - Alessia Rondinella; Francesco Guarnera; Oliver Giudice; Alessandro Ortis; Giulia Russo; Elena Crispino; Francesco Pappalardo 001; Sebastiano Battiato (BIBM, 2023)

Machine Learning techniques application to predict the quality of life degree in breast cancer patients. - Valentina Di Salvatore; Giuseppe Catanuto; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2023)

Boosting multiple sclerosis lesion segmentation through attention mechanism. - Alessia Rondinella; Elena Crispino; Francesco Guarnera; Oliver Giudice; Alessandro Ortis; Giulia Russo; Clara Di Lorenzo; Davide Maimone; Francesco Pappalardo 001; Sebastiano Battiato (Comput. Biol. Medicine, 2023)

Beyond the state of the art of reverse vaccinology: predicting vaccine efficacy with the universal immune system simulator for influenza. - Giulia Russo; Elena Crispino; Avisa Maleki; Valentina Di Salvatore; Filippo Stanco; Francesco Pappalardo 001 (BMC Bioinform., 2023)

Predicting Skin Sensitizer Potency and Immune Response Using UISS-TOX: A Novel Approach for Assessing Allergenic Potential. - Elena Crispino; Giulia Russo; Elisabetta Arcidiacono; Silvia Casati; Emanuela Corsini; Andrew Worth; Francesco Pappalardo 001 (BIBM, 2024)

Application of PBK models for long-chain PFAS to short-chain PFAS: a proposal for toxicokinetic evaluation and in vitro to in vivo extrapolation. - Martina Iulini; Giulia Russo; Elena Crispino; Emanuela Corsini; Francesco Pappalardo 001; Alicia Paini (BIBM, 2024)

A Head-to-Head Evaluation of a Novel Universal Influenza Vaccine Against Current Formulation: Implications for Future Immunization Strategies. - Valentina Di Salvatore; Elena Crispino; Avisa Maleki; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2024)

Unintended Risks of mRNA COVID-19 Vaccines: A UISS Simulation Study on Immune and Organ Health. - Valentina Di Salvatore; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2024)

Agent-Based Modeling of Cutaneous Lupus Erythematosus: Exploring Keratinocyte-Driven Mechanisms. - Abdul Wahab; Giulia Russo; Francesco Pappalardo 001 (BIBM, 2024)

ICPR 2024 Competition on Multiple Sclerosis Lesion Segmentation - Methods and Results. - Alessia Rondinella; Francesco Guarnera; Elena Crispino; Giulia Russo; Clara Di Lorenzo; Davide Maimone; Francesco Pappalardo 001; Sebastiano Battiato (ICPR (34), 2024)

Breaking the Cycle: Advancements in Universal Influenza Vaccine Design. - Valentina Di Salvatore; Elena Crispino; Giulia Russo; Francesco Pappalardo 001 (MetroXRAINE, 2024)

Pioneering bioinformatics with agent-based modelling: an innovative protocol to accurately forecast skin or respiratory allergic reactions to chemical sensitizers. - Giulia Russo; Elena Crispino; Silvia Casati; Emanuela Corsini; Andrew Worth; Francesco Pappalardo 001 (Briefings Bioinform., 2024)

MSValid Data Collection. - Francesco Pappalardo 001; Giulia Russo; Valentina Di Salvatore; Sebastiano Battiato; Francesco Guarnera; Alessia Rondinella (Zenodo, 2024)