Using Parallel Isosurface Extraction in Superficial Molecular Modeling. - Ivan Merelli; Luciano Milanesi; Daniele D'Agostino; Andrea Clematis; Marco Vanneschi; Marco Danelutto (DFMA, 2005)

High performance workflow implementation for protein surface characterization using grid technology. - Ivan Merelli; Giulia Morra; Daniele D'Agostino; Andrea Clematis; Luciano Milanesi (BMC Bioinform., 2005)

Grid-Enabled High Throughput Virtual Screening. - Nicolas Jacq; Vincent Breton; Hsin-Yen Chen; Li-Yung Ho; Martin Hofmann 009; Hurng-Chun Lee; Yannick Legré; Simon C. Lin; Astrid Maaß; Emmanuel Medernach; Ivan Merelli; Luciano Milanesi; et al. (GCCB, 2006)

High Performance GRID Based Implementation for Genomics and Protein Analysis. - Luciano Milanesi; Ivan Merelli (HealthGrid, 2006)

Large Scale In Silico Screening on Grid Infrastructures - Nicolas Jacq; Vincent Breton; Hsin-Yen Chen; Li-Yung Ho; Martin Hofmann 009; Hurng-Chun Lee; Yannick Legré; Simon C. Lin; Astrid Maaß; Emmanuel Medernach; Ivan Merelli; Luciano Milanesi; et al. (CoRR, 2006)

High performance cDNA sequence analysis using grid technology. - Gabriele Antonio Trombetti; Ivan Merelli; Luciano Milanesi (J. Parallel Distributed Comput., 2006)

Parameter Estimation for Cell Cycle Ordinary Differential Equation (ODE) Models using a Grid Approach. - Roberta Alfieri; Ettore Mosca; Ivan Merelli; Luciano Milanesi (HealthGrid, 2007)

BGBlast: A BLAST Grid Implementation with Database Self-Updating and Adaptive Replication. - Gabriele Antonio Trombetti; Ivan Merelli; Alessandro Orro; Luciano Milanesi (HealthGrid, 2007)

Tissue MicroArray: a Distributed Grid Approach for Image Analysis. - Federica Viti; Ivan Merelli; Antonella Galizia; Daniele D'Agostino; Andrea Clematis; Luciano Milanesi (HealthGrid, 2007)

A Parallel Workflow for the Reconstruction of Molecular Surfaces. - Daniele D'Agostino; Ivan Merelli; Andrea Clematis; Luciano Milanesi; Alessandro Orro (PARCO, 2007)

Experimenting Grid Protocols to Improve Privacy Preservation in Efficient Distributed Image Processing. - Antonella Galizia; Federica Viti; Daniele D'Agostino; Ivan Merelli; Luciano Milanesi; Andrea Clematis (PARCO, 2007)

GoSh: a web-based database for goat and sheep EST sequences. - Andrea Caprera; Barbara Lazzari; Alessandra Stella; Ivan Merelli; Alexandre R. Caetano; Paola Mariani (Bioinform., 2007)

A data integration approach for cell cycle analysis oriented to model simulation in systems biology. - Roberta Alfieri; Ivan Merelli; Ettore Mosca; Luciano Milanesi (BMC Syst. Biol., 2007)

Images Based System for Surface Matching in Macromolecular Screening. - Ivan Merelli; Paolo Cozzi; Daniele D'Agostino; Andrea Clematis; Luciano Milanesi (BIBM, 2008)

TMAinspect, an EGEE Framework for Tissue MicroArray Image Handling. - Antonella Galizia; Federica Viti; Alessandro Orro; Daniele D'Agostino; Ivan Merelli; Luciano Milanesi; Andrea Clematis (CCGRID, 2008)

A Visualization ToolKit Based Application for Representing Macromolecular Surfaces. - Paolo Cozzi; Ivan Merelli; Luciano Milanesi (CIBB, 2008)

Enabling Parallel TMA Image Analysis in a Grid Environment. - Antonella Galizia; Daniele D'Agostino; Andrea Clematis; Federica Viti; Alessandro Orro; Ivan Merelli; Luciano Milanesi (CISIS, 2008)

A Grid Service based Parallel Molecular Surface Reconstruction System. - Daniele D'Agostino; Andrea Clematis; Ivan Merelli; Luciano Milanesi; Matteo Coloberti (PDP, 2008)

Version VI of the ESTree db: an improved tool for peach transcriptome analysis. - Barbara Lazzari; Andrea Caprera; Alberto Vecchietti; Ivan Merelli; Francesca Barale; Luciano Milanesi; Alessandra Stella; Carlo Pozzi (BMC Bioinform., 2008)

Ontology-based, Tissue MicroArray oriented, image centered tissue bank. - Federica Viti; Ivan Merelli; Andrea Caprera; Barbara Lazzari; Alessandra Stella; Luciano Milanesi (BMC Bioinform., 2008)

A parallel protein surface reconstruction system. - Ivan Merelli; Alessandro Orro; Daniele D'Agostino; Andrea Clematis; Luciano Milanesi (Int. J. Bioinform. Res. Appl., 2008)

The cell cycle DB: a systems biology approach to cell cycle analysis. - Roberta Alfieri; Ivan Merelli; Ettore Mosca; Luciano Milanesi (Nucleic Acids Res., 2008)

Sys-Bio Gateway: a Framework of Bioinformatics Database Resources Oriented to Systems Biology. - Luciano Milanesi; Roberta Alfieri; Ettore Mosca; Federica Viti; Pasqualina D'Ursi; Ivan Merelli (IWPLS, 2009)

Ontological Enrichment of the Genes-to-Systems Breast Cancer Database. - Federica Viti; Ettore Mosca; Ivan Merelli; Andrea Calabria; Roberta Alfieri; Luciano Milanesi (MTSR, 2009)

Parallel Decomposition of 3D Surfaces in Images of Local Descriptors for Molecular Screening. - Daniele D'Agostino; Andrea Clematis; Ivan Merelli; Paolo Cozzi; Luciano Milanesi (PDP, 2009)

In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study. - Federica Chiappori; Pasqualina D'Ursi; Ivan Merelli; Luciano Milanesi; Ermanna Rovida (BMC Bioinform., 2009)

The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections. - Ivan Merelli; Andrea Caprera; Alessandra Stella; Marcello Del Corvo; Luciano Milanesi; Barbara Lazzari (BMC Bioinform., 2009)

A Parallel Algorithm for Molecular Surface Matching Through Image Representation. - Daniele D'Agostino; Andrea Clematis; Ivan Merelli; Paolo Cozzi; Luciano Milanesi (PDP, 2010)

Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study. - Federica Viti; Ivan Merelli; Mieke Timmermans; Michael den Bakker; Francesco Beltrame; Peter Riegman; Luciano Milanesi (BMC Bioinform., 2010)

A multilevel data integration resource for breast cancer study. - Ettore Mosca; Roberta Alfieri; Ivan Merelli; Federica Viti; Andrea Calabria; Luciano Milanesi (BMC Syst. Biol., 2010)

SNPRanker: a tool for identification and scoring of SNPs associated to target genes. - Andrea Calabria; Ettore Mosca; Federica Viti; Ivan Merelli; Luciano Milanesi (J. Integr. Bioinform., 2010)

RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes. - Ivan Merelli; Alessandro Guffanti; Marco Fabbri; Andrea Cocito; Laura Furia; Ursula Grazini; Raoul Jean Pierre Bonnal; Luciano Milanesi; Fraser McBlane (Nucleic Acids Res., 2010)

Grid Computing for Sensitivity Analysis of Stochastic Biological Models. - Ivan Merelli; Dario Pescini; Ettore Mosca; Paolo Cazzaniga; Carlo Maj; Giancarlo Mauri; Luciano Milanesi (PaCT, 2011)

Parallelization of the SSAKE Genomics Application. - Daniele D'Agostino; Ivan Merelli; René L. Warren; Alessandro Guffanti; Luciano Milanesi; Andrea Clematis (PDP, 2011)

myMIR: a genome-wide microRNA targets identification and annotation tool. - Dario Corrada; Federica Viti; Ivan Merelli; Cristina Battaglia; Luciano Milanesi (Briefings Bioinform., 2011)

Ontology-based resources for bioinformatics analysis. - Federica Viti; Ivan Merelli; Andrea Calabria; Paolo Cozzi; Ettore Mosca; Roberta Alfieri; Luciano Milanesi (Int. J. Metadata Semant. Ontologies, 2011)

Image-Based Surface Matching Algorithm Oriented to Structural Biology. - Ivan Merelli; Paolo Cozzi; Daniele D'Agostino; Andrea Clematis; Luciano Milanesi (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

A CUDA-based Implementation of the SSAKE Genomics Application. - Daniele D'Agostino; Andrea Clematis; Alessandro Guffanti; Luciano Milanesi; Ivan Merelli (PDP, 2012)

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis. - Ivan Merelli; Federica Viti; Luciano Milanesi (BMC Bioinform., 2012)

Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations. - Federica Chiappori; Ivan Merelli; Giorgio Colombo 001; Luciano Milanesi; Giulia Morra (PLoS Comput. Biol., 2012)

A Parallel Implementation of the Stau-DPP Stochastic Simulator for the Modelling of Biological Systems. - Ettore Mosca; Ivan Merelli; Luciano Milanesi; Andrea Clematis; Daniele D'Agostino (PDP, 2013)

SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. - Ivan Merelli; Andrea Calabria; Paolo Cozzi; Federica Viti; Ettore Mosca; Luciano Milanesi (BMC Bioinform., 2013)

Sensitivity Analysis for Studying the Relation between biochemical reactions and metabolic phenotypes. - Carlo Maj; Ettore Mosca; Ivan Merelli; Giancarlo Mauri; Luciano Milanesi (J. Bioinform. Comput. Biol., 2013)

A Fine-Grained CUDA Implementation of the Multi-objective Evolutionary Approach NSGA-II: Potential Impact for Computational and Systems Biology Applications. - Daniele D'Agostino; Giulia Pasquale; Ivan Merelli (CIBB, 2014)

NuChart-II: A Graph-Based Approach for Analysis and Interpretation of Hi-C Data. - Fabio Tordini; Maurizio Drocco; Ivan Merelli; Luciano Milanesi; Pietro Liò; Marco Aldinucci (CIBB, 2014)

Evaluating mixed HTC/cloud approaches for parameter sweep applications in systems biology. - Ivan Merelli; Ettore Mosca; Daniele Cesini; Elisabetta Ronchieri; Luciano Milanesi (IWBBIO, 2014)

The role of High Performance Computing in Bioinformatics. - Horacio Emilio Pérez Sánchez; José M. Cecilia; Ivan Merelli (IWBBIO, 2014)

A CUDA Implementation of the Spatial TAU-Leaping in Crowded Compartments (STAUCC) Simulator. - Giulia Pasquale; Carlo Maj; Andrea Clematis; Ettore Mosca; Luciano Milanesi; Ivan Merelli; Daniele D'Agostino (PDP, 2014)

The WNoDeS Cloud Virtualization Framework: A Macromolecular Surface Analysis Application Case Study. - Elisabetta Ronchieri; Daniele Cesini; Daniele D'Agostino; Vincenzo Ciaschini; Gianni Dalla Torre; Paolo Cozzi; Davide Salomoni; Andrea Clematis; Luciano Milanesi; Ivan Merelli (PDP, 2014)

CUDA accelerated molecular surface generation. - Daniele D'Agostino; Andrea Clematis; Sergio Decherchi; Walter Rocchia; Luciano Milanesi; Ivan Merelli (Concurr. Comput. Pract. Exp., 2014)

Latest advances in distributed, parallel, and graphic processing unit accelerated approaches to computational biology. - Ivan Merelli; Horacio Emilio Pérez Sánchez; Sandra Gesing; Daniele D'Agostino (Concurr. Comput. Pract. Exp., 2014)

Clustering Protein Structures with Hadoop. - Giacomo Paschina; Luca Roverelli; Daniele D'Agostino; Federica Chiappori; Ivan Merelli (CIBB, 2015)

NuchaRt: Embedding High-Level Parallel Computing in R for Augmented Hi-C Data Analysis. - Fabio Tordini; Ivan Merelli; Pietro Liò; Luciano Milanesi; Marco Aldinucci (CIBB, 2015)

Parallel Exploration of the Nuclear Chromosome Conformation with NuChart-II. - Fabio Tordini; Maurizio Drocco; Claudia Misale; Luciano Milanesi; Pietro Liò; Ivan Merelli; Marco Aldinucci (PDP, 2015)

Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks. - Stefano Beretta 001; Mauro Castelli; Ivo Gonçalves; Ivan Merelli; Daniele Ramazzotti (IJCCI (ECTA), 2016)

A Machine Learning Approach for the Integration of miRNA-Target Predictions. - Stefano Beretta 001; Mauro Castelli; Yuliana Martínez; Luis Muñoz; Sara Silva; Leonardo Trujillo; Luciano Milanesi; Ivan Merelli (PDP, 2016)

MicroRNA-Target Interaction: A Parallel Approach for Computing Pairing Energy. - Elisabetta Ronchieri; Daniele D'Agostino; Luciano Milanesi; Ivan Merelli (PDP, 2016)

How computer science can help in understanding the 3D genome architecture. - Yoli Shavit; Ivan Merelli; Luciano Milanesi; Pietro Liò (Briefings Bioinform., 2016)

PWHATSHAP: efficient haplotyping for future generation sequencing. - Andrea Bracciali; Marco Aldinucci; Murray Patterson; Tobias Marschall; Nadia Pisanti; Ivan Merelli; Massimo Torquati (BMC Bioinform., 2016)

A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study. - Federica Chiappori; Luca Mattiazzi; Luciano Milanesi; Ivan Merelli (BMC Bioinform., 2016)

Performance and Economic Evaluations in Adopting Low Power Architectures: A Real Case Analysis. - Daniele D'Agostino; Daniele Cesini; Elena Corni; Andrea Ferraro; Lucia Morganti; Alfonso Quarati; Ivan Merelli (GECON, 2017)

Rank miRNA: a web tool for identifying polymorphisms altering miRNA target sites. - Stefano Beretta 001; Carlo Maj; Ivan Merelli (ICCS, 2017)

Scientific Workflows on Clouds with Heterogeneous and Preemptible Instances. - Fabio Tordini; Marco Aldinucci; Paolo Viviani 001; Ivan Merelli; Pietro Liò (PARCO, 2017)

Low-Power Architectures for miRNA-Target Genome Wide Analysis. - Stefano Beretta 001; Lucia Morganti; Elena Corni; Andrea Ferraro; Daniele Cesini; Daniele D'Agostino; Luciano Milanesi; Ivan Merelli (PDP, 2017)

Implementing a Space-Aware Stochastic Simulator on Low-Power Architectures: A Systems Biology Case Study. - Lucia Morganti; Elena Corni; Andrea Ferraro; Daniele Cesini; Daniele D'Agostino; Ivan Merelli (PDP, 2017)

VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites. - Giulio Spinozzi; Andrea Calabria; Stefano Brasca; Stefano Beretta 001; Ivan Merelli; Luciano Milanesi; Eugenio Montini (BMC Bioinform., 2017)

Porting bioinformatics applications from grid to cloud: A macromolecular surface analysis application case study. - Ivan Merelli; Paolo Cozzi; Elisabetta Ronchieri; Daniele Cesini; Daniele D'Agostino (Int. J. High Perform. Comput. Appl., 2017)

NuChart-II: The road to a fast and scalable tool for Hi-C data analysis. - Fabio Tordini; Maurizio Drocco; Claudia Misale; Luciano Milanesi; Pietro Liò; Ivan Merelli; Massimo Torquati; Marco Aldinucci (Int. J. High Perform. Comput. Appl., 2017)

Epistasis analysis reveals associations between gene variants and bipolar disorder. - Carlo Maj; Elena Milanesi; Massimo Gennarelli; Luciano Milanesi; Ivan Merelli (PeerJ Prepr., 2017)

High Performance Computing for Haplotyping: Models and Platforms. - Andrea Tangherloni; Leonardo Rundo; Simone Spolaor; Marco S. Nobile; Ivan Merelli; Daniela Besozzi; Giancarlo Mauri; Paolo Cazzaniga; Pietro Liò (Euro-Par Workshops, 2018)

Parallelizable Strategy for the Estimation of the 3D Structure of Biological Macromolecules. - Claudia Caudai; Monica Zoppè; Emanuele Salerno; Ivan Merelli; Anna Tonazzini (PDP, 2018)

Computing Empirical P-Values for Estimating Gene-Gene Interactions in Genome-Wide Association Studies: A Parallel Computing Approach. - Valentina Giansanti; Daniele D'Agostino; Carlo Maj; Stefano Beretta 001; Ivan Merelli (PDP, 2018)

Low-Power Storage Bricks and Bioinformatics on Systems-On-Chip. - Lucia Morganti; Daniele Cesini; Elena Corni; Luca Lama; Carmelo Pellegrino; Ivan Merelli; Daniele D'Agostino (PDP, 2018)

A Scalable Genetic Programming Approach to Integrate miRNA-Target Predictions: Comparing Different Parallel Implementations of M3GP. - Stefano Beretta 001; Mauro Castelli; Luis Muñoz; Leonardo Trujillo; Yuliana Martínez; Ales Popovic; Luciano Milanesi; Ivan Merelli (Complex., 2018)

Low-power portable devices for metagenomics analysis: Fog computing makes bioinformatics ready for the Internet of Things. - Ivan Merelli; Lucia Morganti; Elena Corni; Carmelo Pellegrino; Daniele Cesini; Luca Roverelli; Gabriele Zereik; Daniele D'Agostino (Future Gener. Comput. Syst., 2018)

Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: A Logistic Model Tree Solution. - Stefano Beretta 001; Mauro Castelli; Ivo Gonçalves; Ivan Kel; Valentina Giansanti; Ivan Merelli (J. Comput. Biol., 2018)

NeoHiC: A Web Application for the Analysis of Hi-C Data. - Daniele D'Agostino; Pietro Liò; Marco Aldinucci; Ivan Merelli (CIBB, 2019)

Comparing Deep and Machine Learning Approaches in Bioinformatics: A miRNA-Target Prediction Case Study. - Valentina Giansanti; Mauro Castelli; Stefano Beretta 001; Ivan Merelli (ICCS (3), 2019)

Parallel Computing in Deep Learning: Bioinformatics Case Studiesa. - Valentina Giansanti; Stefano Beretta 001; Daniele Cesini; Daniele D'Agostino; Ivan Merelli (PDP, 2019)

GenHap: a novel computational method based on genetic algorithms for haplotype assembly. - Andrea Tangherloni; Simone Spolaor; Leonardo Rundo; Marco S. Nobile; Paolo Cazzaniga; Giancarlo Mauri; Pietro Liò; Ivan Merelli; Daniela Besozzi (BMC Bioinform., 2019)

Combining Edge and Cloud computing for low-power, cost-effective metagenomics analysis. - Daniele D'Agostino; Lucia Morganti; Elena Corni; Daniele Cesini; Ivan Merelli (Future Gener. Comput. Syst., 2019)

SoC-based computing infrastructures for scientific applications and commercial services: Performance and economic evaluations. - Daniele D'Agostino; Alfonso Quarati; Andrea Clematis; Lucia Morganti; Elena Corni; Valentina Giansanti; Daniele Cesini; Ivan Merelli (Future Gener. Comput. Syst., 2019)

Exploiting Docker containers over Grid computing for a comprehensive study of chromatin conformation in different cell types. - Ivan Merelli; Federico Fornari; Fabio Tordini; Daniele D'Agostino; Marco Aldinucci; Daniele Cesini (J. Parallel Distributed Comput., 2019)

ChromStruct 4: A Python Code to Estimate the Chromatin Structure from Hi-C Data. - Claudia Caudai; Emanuele Salerno; Monica Zoppè; Ivan Merelli; Anna Tonazzini (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Parallel Architectures for Bioinformatics. - Ivan Merelli (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Infrastructure for High-Performance Computing: Grids and Grid Computing. - Ivan Merelli (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites. - Andrea Calabria; Stefano Beretta 001; Ivan Merelli; Giulio Spinozzi; Stefano Brasca; Yuri Pirola; Fabrizio Benedicenti; Erika Tenderini; Paola Bonizzoni; Luciano Milanesi; Eugenio Montini (Bioinform., 2020)

Latest advances in parallel, distributed, and network-based processing. - Ivan Merelli; Pietro Liò; Igor V. Kotenko; Daniele D'Agostino (Concurr. Comput. Pract. Exp., 2020)

On low-power SoCs as storage bricks for Bioinformatics. - Lucia Morganti; Elena Corni; Luca Lama; Carmelo Pellegrino; Francieli Zanon Boito; Ivan Merelli; Daniele D'Agostino; Daniele Cesini (Concurr. Comput. Pract. Exp., 2020)

A secure cloud-edges computing architecture for metagenomics analysis. - Luca Verderame; Ivan Merelli; Lucia Morganti; Elena Corni; Daniele Cesini; Daniele D'Agostino; Alessio Merlo (Future Gener. Comput. Syst., 2020)

Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice. - Simone Pernice; Laura Follia; Gianfranco Balbo; Luciano Milanesi; Giulia Sartini; Niccoló Totis; Pietro Lió; Ivan Merelli; Francesca Cordero; Marco Beccuti (Fundam. Informaticae, 2020)

Selected papers from the 15th and 16th international conference on Computational Intelligence Methods for Bioinformatics and Biostatistics. - Paolo Cazzaniga; Maria Raposo; Daniela Besozzi; Ivan Merelli; Antonino Staiano; Angelo Ciaramella; Riccardo Rizzo; Luca Manzoni (BMC Bioinform., 2021)

Advantages of using graph databases to explore chromatin conformation capture experiments. - Daniele D'Agostino; Pietro Liò; Marco Aldinucci; Ivan Merelli (BMC Bioinform., 2021)

Hardware and Software Solutions for Energy-Efficient Computing in Scientific Programming. - Daniele D'Agostino; Ivan Merelli; Marco Aldinucci; Daniele Cesini (Sci. Program., 2021)

StreamFlow: Cross-Breeding Cloud With HPC. - Iacopo Colonnelli; Barbara Cantalupo; Ivan Merelli; Marco Aldinucci (IEEE Trans. Emerg. Top. Comput., 2021)

InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration. - Ivan Merelli; Stefano Beretta 001; Daniela Cesana; Alessandro Gennari; Fabrizio Benedicenti; Giulio Spinozzi; Daniele Cesini; Eugenio Montini; Daniele D'Agostino; Andrea Calabria (Database J. Biol. Databases Curation, 2023)