Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices. - Victor B. Strelets; Ilya N. Shindyalov; Nikolay A. Kolchanov; Luciano Milanesi (Comput. Appl. Biosci., 1992)

SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. - Alexander E. Kel; Mikhail P. Ponomarenko; E. A. Likhachev; Yuri L. Orlov; I. V. Ischenko; Luciano Milanesi; Nikolay A. Kolchanov (Comput. Appl. Biosci., 1993)

Data bank homology search algorithm with linear computation complexity. - Victor B. Strelets; Andrey A. Ptitsyn; Luciano Milanesi; Hwa A. Lim (Comput. Appl. Biosci., 1994)

Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences. - Alexander E. Kel; Yury V. Kondrakhin; Ph. A. Kolpakov; O. V. Kel; Aida G. Romashchenko; Edgar Wingender; Luciano Milanesi; Nikolay A. Kolchanov (ISMB, 1995)

Eukaryotic promoter recognition by binding sites for transcription factors. - Yury V. Kondrakhin; Alexander E. Kel; Nikolay A. Kolchanov; Aida G. Romashchenko; Luciano Milanesi (Comput. Appl. Biosci., 1995)

Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes. - Yury V. Kondrakhin; Fedor A. Kolpakov; Alexander E. Kel; Nikolay A. Kolchanov; Luciano Milanesi (German Conference on Bioinformatics, 1996)

Hamming-Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes. - Luciano Milanesi; Marco Muselli; P. Arrigo (Comput. Appl. Biosci., 1996)

Gene structure prediction using information on homologous protein sequence. - Igor B. Rogozin; Luciano Milanesi; Nikolay A. Kolchanov (Comput. Appl. Biosci., 1996)

Fragment assembly system for DNA sequencing projects. - Luciano Milanesi; M. Marsilli; Giancarlo Mauri; C. Rolfi; L. Uboldi (Mathematical Support for Molecular Biology, 1998)

GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome. - Nikolay A. Kolchanov; Mikhail P. Ponomarenko; Alexander E. Kel; Yury V. Kondrakhin; Anatoly S. Frolov; Fedor A. Kolpakov; T. N. Goryachkovskaya; O. V. Kel; Elena A. Ananko; Elena V. Ignatieva; Olga A. Podkolodnaya; Vladimir N. Babenko; et al. (ISMB, 1998)

Molecular Probe Data Base (MPDB). - Maria Giuseppina Campi; Paolo Romano 001; Luciano Milanesi; Domenico Marra; Maria Assunta Manniello; Beatrice Iannotta; Gabriella Rondanina; Elena Grasso; Tiziana Ruzzon; Leonardo Santi (Nucleic Acids Res., 1998)

Integrated databases and computer systems for studying eukaryotic gene expression. - Nikolay A. Kolchanov; Mikhail P. Ponomarenko; Anatoly S. Frolov; Elena A. Ananko; Fedor A. Kolpakov; Elena V. Ignatieva; Olga A. Podkolodnaya; T. N. Goryachkovskaya; Irina L. Stepanenko; Tatyana I. Merkulova; V. V. Babenko; Y. V. Ponomarenko; et al. (Bioinform., 1999)

GeneBuilder: interactive in silico prediction of gene structure. - Luciano Milanesi; D. D'Angelo; Igor B. Rogozin (Bioinform., 1999)

Prediction and Phylogenetic Analysis of Mammalian Short Interspersed Elements (SINEs). - Igor B. Rogozin; V. I. Mayorov; M. V. Lavrentieva; Luciano Milanesi; L. R. Adkison (Briefings Bioinform., 2000)

Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. - Igor B. Rogozin; Alexey V. Kochetov; Fyodor A. Kondrashov; Eugene V. Koonin; Luciano Milanesi (Bioinform., 2001)

ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. - Vadim P. Valuev; Dmitry A. Afonnikov; Mikhail P. Ponomarenko; Luciano Milanesi; Nikolay A. Kolchanov (Nucleic Acids Res., 2002)

Computational analysis of mutation spectra. - Igor B. Rogozin; Vladimir N. Babenko; Luciano Milanesi; Youri I. Pavlov (Briefings Bioinform., 2003)

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

From Context-Dependence of Mutations to Molecular Mechanisms of Mutagenesis. - Igor B. Rogozin; B. A. Malyarchuk; Youri I. Pavlov; Luciano Milanesi (Pacific Symposium on Biocomputing, 2005)

A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure. - Giuliano Armano; Gianmaria Mancosu; Luciano Milanesi; Alessandro Orro; Massimiliano Saba; Eloisa Vargiu (BMC Bioinform., 2005)

Modelling the interaction of steroid receptors with endocrine disrupting chemicals. - Pasqualina D'Ursi; Erika Salvi; Paola Fossa; Luciano Milanesi; Ermanna Rovida (BMC Bioinform., 2005)

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. - Manuela Helmer-Citterich; Rita Casadio; Alessandro Guffanti; Giancarlo Mauri; Luciano Milanesi; Graziano Pesole; Giorgio Valle; Cecilia Saccone (BMC Bioinform., 2005)

ESTree db: a Tool for Peach Functional Genomics. - Barbara Lazzari; Andrea Caprera; Alberto Vecchietti; Alessandra Stella; Luciano Milanesi; Carlo Pozzi (BMC Bioinform., 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)

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. - Luciano Milanesi; Mauro Petrillo; Leandra Sepe; Angelo Boccia; Nunzio D'Agostino; Myriam Passamano; Salvatore Di Nardo; Gianluca Tasco; Rita Casadio; Giovanni Paolella (BMC Bioinform., 2005)

Web services and workflow management for biological resources. - Paolo Romano 001; Domenico Marra; Luciano Milanesi (BMC Bioinform., 2005)

Using Secondary Structure Information to Perform Multiple Alignment. - Giuliano Armano; Luciano Milanesi; Alessandro Orro (Trans. Comp. Sys. Biology, 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)

An Agent System for Automatic Workflows Composition in Grid Environments. - Alessandro Orro; Luciano Milanesi (Int. Trans. Syst. Sci. Appl., 2006)

Network integration of data and analysis of oncology interest. - Paolo Romano 001; Guglielmo Bertolini; Flavio De Paoli; M. Fattore; Domenico Marra; Giancarlo Mauri; Emanuela Merelli; Ivan Porro; Silvia Scaglione; Luciano Milanesi (J. Integr. Bioinform., 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)

An Agent Approach for Protein Function Analysis in a Grid Infrastructure. - Alessandro Orro; 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)

Agents in bioinformatics, computational and systems biology. - Emanuela Merelli; Giuliano Armano; Nicola Cannata; Flavio Corradini; Mark d'Inverno; Andreas Doms; Phillip W. Lord; Andrew C. R. Martin; Luciano Milanesi; Steffen Möller; Michael Schroeder 001; Michael Luck (Briefings Bioinform., 2007)

ProCMD: a database and 3D web resource for protein C mutants. - Pasqualina D'Ursi; Francesca Marino; Andrea Caprera; Luciano Milanesi; Elena M. Faioni; Ermanna Rovida (BMC Bioinform., 2007)

ESTuber db: an online database for Tuber borchii EST sequences. - Barbara Lazzari; Andrea Caprera; Cristian Cosentino; Alessandra Stella; Luciano Milanesi; Angelo Viotti (BMC Bioinform., 2007)

SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics - exploring current scientific literature for emerging topics. - Dietrich Rebholz-Schuhmann; Graham Cameron; Dominic Clark; Erik M. van Mulligen; Jean-Louis Coatrieux; Eva del Hoyo-Barbolla; Fernando Martín-Sánchez; Luciano Milanesi; Ivan Porro; Francesco Beltrame; Ioannis G. Tollis; Johan van der Lei (BMC Bioinform., 2007)

Biowep: a workflow enactment portal for bioinformatics applications. - Paolo Romano 001; Ezio Bartocci; Guglielmo Bertolini; Flavio De Paoli; Domenico Marra; Giancarlo Mauri; Emanuela Merelli; Luciano Milanesi (BMC Bioinform., 2007)

Data handling strategies for high throughput pyrosequencers. - Gabriele Antonio Trombetti; Raoul Jean Pierre Bonnal; Ermanno Rizzi; Gianluca De Bellis; Luciano Milanesi (BMC 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)

Networks from Gene Expression Time Series: Characterization of Correlation Patterns. - Daniel Remondini; Nicola Neretti; Claudio Franceschi; Paolo Tieri; John M. Sedivy; Luciano Milanesi; Gastone C. Castellani (Int. J. Bifurc. Chaos, 2007)

CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. - Fedor A. Kolpakov; Vladimir Poroikov; Ruslan N. Sharipov; Yury V. Kondrakhin; Alexey V. Zakharov; Alexey Lagunin; Luciano Milanesi; Alexander E. Kel (Nucleic Acids Res., 2007)

Medical Informatics and Bioinformatics: A Bibliometric Study. - Jean-Yves Bansard; Dietrich Rebholz-Schuhmann; Graham Cameron; Dominic Clark; Erik M. van Mulligen; Francesco Beltrame; Eva del Hoyo-Barbolla; Fernando Martín-Sánchez; Luciano Milanesi; Ioannis G. Tollis; Johan van der Lei; Jean-Louis Coatrieux (IEEE Trans. Inf. Technol. Biomed., 2007)

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

Bayesian Phylogeny on Grid. - Richard Carl Van der Wath; Elizabeth van der Wath; Antonio Carapelli; Francesco Nardi; Francesco Frati; Luciano Milanesi; Pietro Liò (BIRD, 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)

Reconstructing networks of pathways via significance analysis of their intersections. - Mirko Francesconi; Daniel Remondini; Nicola Neretti; John M. Sedivy; Leon N. Cooper; Ettore Verondini; Luciano Milanesi; Gastone C. Castellani (BMC Bioinform., 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)

SNPLims: a data management system for genome wide association studies. - Alessandro Orro; Guia Guffanti; Erika Salvi; Fabio Macciardi; Luciano Milanesi (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)

An Unusal Distribution of 6-nt Sequences Near The Transcription Start Site. - Chanchal K. Mitra; Luciano Milanesi (J. Integr. Bioinform., 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)

On the Performance of Large Scale Bayesian Phylogenetic Analyses with Grid Portals and Robot Certificates. - Roberto Barbera; Giacinto Donvito; Alberto Falzone; Giuseppe La Rocca; Giorgio Pietro Maggi; Saverio Vicario; Luciano Milanesi (IWPLS, 2009)

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)

A Novel Variant of P Systems for the Modelling and Simulation of Biochemical Systems. - Paolo Cazzaniga; Giancarlo Mauri; Luciano Milanesi; Ettore Mosca; Dario Pescini (Workshop on Membrane Computing, 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)

Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. - Roberta Alfieri; Matteo Barberis; Ferdinando Chiaradonna; Daniela Gaglio; Luciano Milanesi; Marco Vanoni; Edda Klipp; Lilia Alberghina (BMC Bioinform., 2009)

The GENIUS Grid Portal and robot certificates: a new tool for e-Science. - Roberto Barbera; Giacinto Donvito; Alberto Falzone; Giuseppe La Rocca; Luciano Milanesi; Giorgio Pietro Maggi; Saverio Vicario (BMC Bioinform., 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)

Trends in modeling Biomedical Complex Systems. - Luciano Milanesi; Paolo Romano 001; Gastone C. Castellani; Daniel Remondini; Pietro Liò (BMC Bioinform., 2009)

Identification of functionally related genes using data mining and data integration: a breast cancer case study. - Ettore Mosca; Gloria Bertoli; Eleonora Piscitelli; Laura Vilardo; Rolland A. Reinbold; Ileana Zucchi; Luciano Milanesi (BMC Bioinform., 2009)

Modelling Spatial Heterogeneity and Macromolecular Crowding with Membrane Systems. - Ettore Mosca; Paolo Cazzaniga; Dario Pescini; Giancarlo Mauri; Luciano Milanesi (Int. Conf. on Membrane Computing, 2010)

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

A Dynamic Parallel Approach to Recognize Tubular Breast Cancer for TMA Image Building. - Antonella Galizia; Federica Viti; Andrea Clematis; Luciano Milanesi (PDP, 2010)

Complex Search, Ranks, and Biological Discovery: A User's Perspective. - Paolo Romano 001; Luciano Milanesi (SeCO Workshop, 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)

Grid Based Genome Wide Studies on Atrial Flutter. - Andrea Calabria; Davide Di Pasquale; Matteo Gnocchi; Paolo Alessandro Cozzi; Alessandro Orro; Gabriele Antonio Trombetti; Luciano Milanesi (J. Grid Comput., 2010)

Overlapping Genes May Control Reprogramming of Mouse Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) and Breast Cancer Stem Cells. - Ettore Mosca; Cinzia Cocola; Davood Sabour; Paride Pelucchi; Giovanni Bertalot; Orazio Palumbo; Massimo Carella; Martin Götte; Hans R. Schöler; Rolland A. Reinbold; Ileana Zucchi; Luciano Milanesi (Silico 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)

Modeling Biochemical Pathways. - Ettore Mosca; Luciano Milanesi (Mathematical Approaches to Polymer Sequence Analysis and Related Problems, 2011)

Population Stratification Analysis in Genome-Wide Association Studies. - Erika Salvi; Alessandro Orro; Guia Guffanti; Sara Lupoli; Federica Torri; Cristina Barlassina; Steven G. Potkin; Daniele Cusi; Fabio Macciardi; Luciano Milanesi (Mathematical Approaches to Polymer Sequence Analysis and Related Problems, 2011)

A Mathematical Model for the Enhanced Cytoplasmic Transport - How to Get (Faster) to the Nucleus. - Luna Dimitrio; Roberto Natalini; Luciano Milanesi (BIOINFORMATICS, 2011)

Solving Biclustering with a GRASP-Like Metaheuristic: Two Case-Studies on Gene Expression Analysis. - Angelo M. Facchiano; Paola Festa; Anna Marabotti; Luciano Milanesi; Francesco Musacchia (CIBB, 2011)

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)

Modeling the cell cycle: From deterministic models to hybrid systems. - Roberta Alfieri; Ezio Bartocci; Emanuela Merelli; Luciano Milanesi (Biosyst., 2011)

A grid portal with robot certificates for bioinformatics phylogenetic analyses. - Roberto Barbera; Giuseppe Andronico; Giacinto Donvito; Alberto Falzone; J. J. Keijser; Giuseppe La Rocca; Luciano Milanesi; Giorgio Pietro Maggi; Saverio Vicario (Concurr. Comput. Pract. Exp., 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)

Literature Retrieval and Mining in Bioinformatics: State of the Art and Challenges. - Andrea Manconi; Eloisa Vargiu; Giuliano Armano; Luciano Milanesi (Adv. Bioinformatics, 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)

Nanoinformatics: developing new computing applications for nanomedicine. - Victor Maojo; Martin Fritts; Fernando Martín-Sánchez; Diana de la Iglesia; Raul E. Cachau; Miguel García-Remesal; José Crespo; Joyce A. Mitchell; Alberto Anguita; Nathan A. Baker; José María Barreiro; Sonia E. Benitez; et al. (Computing, 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)

Comparing Viral (HIV) and Bacterial (Staphylococcus aureus) Infection of the Bone Tissue. - Mohammad Ali Moni; Pietro Liò; Luciano Milanesi (BIOINFORMATICS, 2013)

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)

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)

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)

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units. - Andrea Manconi; Alessandro Orro; Emanuele Manca; Giuliano Armano; Luciano Milanesi (BMC Bioinform., 2014)

Guidelines for managing data and processes in bone and cartilage tissue engineering. - Federica Viti; Silvia Scaglione; Alessandro Orro; Luciano Milanesi (BMC Bioinform., 2014)

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

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)

A Infrastructure for Disease Prevention and Precision Medicine. - Marco Moscatelli; Andrea Manconi; Matteo Gnocchi; Luciano Milanesi (KDWeb, 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)

Systems medicine of inflammaging. - Gastone C. Castellani; Giulia Menichetti; Paolo Garagnani; Maria Giulia Bacalini; Chiara Pirazzini; Claudio Franceschi; Sebastiano Collino; Claudia Sala; Daniel Remondini; Enrico Giampieri; Ettore Mosca; Matteo Bersanelli; et al. (Briefings Bioinform., 2016)

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

Methods for the integration of multi-omics data: mathematical aspects. - Matteo Bersanelli; Ettore Mosca; Daniel Remondini; Enrico Giampieri; Claudia Sala; Gastone C. Castellani; Luciano Milanesi (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)

Removing duplicate reads using graphics processing units. - Andrea Manconi; Marco Moscatelli; Giuliano Armano; Matteo Gnocchi; Alessandro Orro; Luciano Milanesi (BMC Bioinform., 2016)

BITS 2015: the annual meeting of the Italian Society of Bioinformatics. - Luciano Milanesi; Alessandro Guffanti; Giancarlo Mauri; Marco Masseroli (BMC Bioinform., 2016)

Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data. - Claudia Sala; Silvia Vitali; Enrico Giampieri; Ìtalo Faria do Valle; Daniel Remondini; Paolo Garagnani; Matteo Bersanelli; Ettore Mosca; Luciano Milanesi; Gastone C. Castellani (BMC Bioinform., 2016)

CUDA-quicksort: an improved GPU-based implementation of quicksort. - Emanuele Manca; Andrea Manconi; Alessandro Orro; Giuliano Armano; Luciano Milanesi (Concurr. Comput. Pract. Exp., 2016)

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)

iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data. - Riccardo Panero; Antonio Rinaldi; Domenico Memoli; Giovanni Nassa; Maria Ravo; Francesca Rizzo 002; Roberta Tarallo; Luciano Milanesi; Alessandro Weisz; Giorgio Giurato (Bioinform., 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)

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)

An infrastructure for precision medicine through analysis of big data. - Marco Moscatelli; Andrea Manconi; Mauro Pessina; Giovanni Fellegara; Stefano Rampoldi; Luciano Milanesi; Andrea Casasco; Matteo Gnocchi (BMC Bioinform., 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)

isma: an R package for the integrative analysis of mutations detected by multiple pipelines. - Noemi Di Nanni; Marco Moscatelli; Matteo Gnocchi; Luciano Milanesi; Ettore Mosca (BMC Bioinform., 2019)

The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes. - Paolo Romano 001; Arnaud Céol; Andreas Dräger; Antonino Fiannaca; Rosalba Giugno; Massimo La Rosa; Luciano Milanesi; Ulrich Pfeffer; Riccardo Rizzo; Soo-Yong Shin; Junfeng Xia; Alfonso Urso (BMC Bioinform., 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)

Gene relevance based on multiple evidences in complex networks. - Noemi Di Nanni; Matteo Gnocchi; Marco Moscatelli; Luciano Milanesi; Ettore Mosca (Bioinform., 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)

Characterization and comparison of gene-centered human interactomes. - Ettore Mosca; Matteo Bersanelli; Tommaso Matteuzzi; Noemi Di Nanni; Gastone C. Castellani; Luciano Milanesi; Daniel Remondini (Briefings Bioinform., 2021)

A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. - Mathew Birdsall Abrams; Jan G. Bjaalie; Samir Das; Gary F. Egan; Satrajit S. Ghosh; Wojtek James Goscinski; Jeffrey S. Grethe; Jeanette Hellgren Kotaleski; Eric Tatt Wei Ho; David N. Kennedy; Linda J. Lanyon; Trygve B. Leergaard; et al. (Neuroinformatics, 2022)

Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. - Mathew Birdsall Abrams; Jan G. Bjaalie; Samir Das; Gary F. Egan; Satrajit S. Ghosh; Wojtek James Goscinski; Jeffrey S. Grethe; Jeanette Hellgren Kotaleski; Eric Tatt Wei Ho; David N. Kennedy; Linda J. Lanyon; Trygve B. Leergaard; et al. (Neuroinformatics, 2022)

scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. - Valentina Nale; Alice Chiodi; Noemi Di Nanni; Ingrid Cifola; Marco Moscatelli; Cinzia Cocola; Matteo Gnocchi; Eleonora Piscitelli; Ada Sula; Ileana Zucchi; Rolland A. Reinbold; Luciano Milanesi; et al. (BMC Bioinform., 2023)

Implementation of a Digital Maturity Framework for Biobanking. - Federica Rossi; Davide Fragnito; Antonella Cruoglio; Ramona Palombo; Alice Massacci; Alessandro Sulis; Vittorio Meloni; Sara Casati; Antonella Mirabile; Andrea Manconi; Luciano Milanesi; Gennaro Ciliberto; et al. (J. Biomed. Informatics, 2025)