Luciano Milanesi

141 papers A 2B 2C 13Misc 2Journal 93Unranked 27
YearRankTypeTitle / Venue / Authors
2025 J jnl
Implementation of a Digital Maturity Framework for Biobanking.
J. Biomed. Informatics
Federica Rossi, Davide Fragnito, Antonella Cruoglio, Ramona Palombo, Alice Massacci, Alessandro Sulis, Vittorio Meloni, Sara Casati, Antonella Mirabile, Andrea Manconi, Luciano Milanesi, Gennaro Ciliberto, Monica Forni, Valentina Adami, Massimiliano Borsani, Claudia Miele, Marialuisa Lavitrano, Matteo Pallocca
2023 J jnl
scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis.
BMC Bioinform.
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, Alessandra Mezzelani, Paride Pelucchi, Ettore Mosca
2022 J jnl
A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility.
Neuroinformatics
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, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, Jean-Baptiste Poline, Prasun Roy, Stephen C. Strother, Tong Boon Tang, Paul H. E. Tiesinga, Thomas Wachtler, Daniel K. Wójcik, Maryann E. Martone
2022 J jnl
Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility.
Neuroinformatics
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, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, Jean-Baptiste Poline, Prasun Roy, Stephen C. Strother, Tong Boon Tang, Paul H. E. Tiesinga, Thomas Wachtler, Daniel K. Wójcik, Maryann E. Martone
2021 J jnl
Characterization and comparison of gene-centered human interactomes.
Briefings Bioinform.
Ettore Mosca, Matteo Bersanelli, Tommaso Matteuzzi, Noemi Di Nanni, Gastone C. Castellani, Luciano Milanesi, Daniel Remondini
2020 J jnl
Gene relevance based on multiple evidences in complex networks.
Bioinform.
Noemi Di Nanni, Matteo Gnocchi, Marco Moscatelli, Luciano Milanesi, Ettore Mosca
2020 J jnl
Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice.
Fundam. Informaticae
Simone Pernice, Laura Follia, Gianfranco Balbo, Luciano Milanesi, Giulia Sartini, Niccoló Totis, Pietro Lió, Ivan Merelli, Francesca Cordero, Marco Beccuti
2020 J jnl
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites.
Bioinform.
Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini
2019 J jnl
The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes.
BMC Bioinform.
Paolo Romano, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia, Alfonso Urso
2019 J jnl
isma: an R package for the integrative analysis of mutations detected by multiple pipelines.
BMC Bioinform.
Noemi Di Nanni, Marco Moscatelli, Matteo Gnocchi, Luciano Milanesi, Ettore Mosca
2018 J jnl
A Scalable Genetic Programming Approach to Integrate miRNA-Target Predictions: Comparing Different Parallel Implementations of M3GP.
Complex.
Stefano Beretta, Mauro Castelli, Luis Muñoz, Leonardo Trujillo, Yuliana Martínez, Ales Popovic, Luciano Milanesi, Ivan Merelli
2018 J jnl
An infrastructure for precision medicine through analysis of big data.
BMC Bioinform.
Marco Moscatelli, Andrea Manconi, Mauro Pessina, Giovanni Fellegara, Stefano Rampoldi, Luciano Milanesi, Andrea Casasco, Matteo Gnocchi
2017 J jnl
Epistasis analysis reveals associations between gene variants and bipolar disorder.
PeerJ Prepr.
Carlo Maj, Elena Milanesi, Massimo Gennarelli, Luciano Milanesi, Ivan Merelli
2017 C conf
Low-Power Architectures for miRNA-Target Genome Wide Analysis.
PDP
Stefano Beretta, Lucia Morganti, Elena Corni, Andrea Ferraro, Daniele Cesini, Daniele D'Agostino, Luciano Milanesi, Ivan Merelli
2017 J jnl
NuChart-II: The road to a fast and scalable tool for Hi-C data analysis.
Int. J. High Perform. Comput. Appl.
Fabio Tordini, Maurizio Drocco, Claudia Misale, Luciano Milanesi, Pietro Liò, Ivan Merelli, Massimo Torquati, Marco Aldinucci
2017 J jnl
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.
BMC Bioinform.
Giulio Spinozzi, Andrea Calabria, Stefano Brasca, Stefano Beretta, Ivan Merelli, Luciano Milanesi, Eugenio Montini
2017 J jnl
iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data.
Bioinform.
Riccardo Panero, Antonio Rinaldi, Domenico Memoli, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Luciano Milanesi, Alessandro Weisz, Giorgio Giurato
2017 J jnl
iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data.
Bioinform.
Riccardo Panero, Antonio Rinaldi, Domenico Memoli, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Luciano Milanesi, Alessandro Weisz, Giorgio Giurato
2016 — conf
A Infrastructure for Disease Prevention and Precision Medicine.
KDWeb
Marco Moscatelli, Andrea Manconi, Matteo Gnocchi, Luciano Milanesi
2016 C conf
A Machine Learning Approach for the Integration of miRNA-Target Predictions.
PDP
Stefano Beretta, Mauro Castelli, Yuliana Martínez, Luis Muñoz, Sara Silva, Leonardo Trujillo, Luciano Milanesi, Ivan Merelli
2016 J jnl
A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study.
BMC Bioinform.
Federica Chiappori, Luca Mattiazzi, Luciano Milanesi, Ivan Merelli
2016 J jnl
BITS 2015: the annual meeting of the Italian Society of Bioinformatics.
BMC Bioinform.
Luciano Milanesi, Alessandro Guffanti, Giancarlo Mauri, Marco Masseroli
2016 J jnl
CUDA-quicksort: an improved GPU-based implementation of quicksort.
Concurr. Comput. Pract. Exp.
Emanuele Manca, Andrea Manconi, Alessandro Orro, Giuliano Armano, Luciano Milanesi
2016 J jnl
How computer science can help in understanding the 3D genome architecture.
Briefings Bioinform.
Yoli Shavit, Ivan Merelli, Luciano Milanesi, Pietro Liò
2016 J jnl
Methods for the integration of multi-omics data: mathematical aspects.
BMC Bioinform.
Matteo Bersanelli, Ettore Mosca, Daniel Remondini, Enrico Giampieri, Claudia Sala, Gastone C. Castellani, Luciano Milanesi
2016 C conf
MicroRNA-Target Interaction: A Parallel Approach for Computing Pairing Energy.
PDP
Elisabetta Ronchieri, Daniele D'Agostino, Luciano Milanesi, Ivan Merelli
2016 J jnl
Removing duplicate reads using graphics processing units.
BMC Bioinform.
Andrea Manconi, Marco Moscatelli, Giuliano Armano, Matteo Gnocchi, Alessandro Orro, Luciano Milanesi
2016 J jnl
Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data.
BMC Bioinform.
Claudia Sala, Silvia Vitali, Enrico Giampieri, Ìtalo Faria do Valle, Daniel Remondini, Paolo Garagnani, Matteo Bersanelli, Ettore Mosca, Luciano Milanesi, Gastone C. Castellani
2016 J jnl
Systems medicine of inflammaging.
Briefings Bioinform.
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, Silvia Vitali, Ìtalo Faria do Valle, Pietro Liò, Luciano Milanesi
2015 — conf
NuchaRt: Embedding High-Level Parallel Computing in R for Augmented Hi-C Data Analysis.
CIBB
Fabio Tordini, Ivan Merelli, Pietro Liò, Luciano Milanesi, Marco Aldinucci
2015 C conf
Parallel Exploration of the Nuclear Chromosome Conformation with NuChart-II.
PDP
Fabio Tordini, Maurizio Drocco, Claudia Misale, Luciano Milanesi, Pietro Liò, Ivan Merelli, Marco Aldinucci
2014 C conf
A CUDA Implementation of the Spatial TAU-Leaping in Crowded Compartments (STAUCC) Simulator.
PDP
Giulia Pasquale, Carlo Maj, Andrea Clematis, Ettore Mosca, Luciano Milanesi, Ivan Merelli, Daniele D'Agostino
2014 J jnl
A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units.
BMC Bioinform.
Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi
2014 J jnl
CUDA accelerated molecular surface generation.
Concurr. Comput. Pract. Exp.
Daniele D'Agostino, Andrea Clematis, Sergio Decherchi, Walter Rocchia, Luciano Milanesi, Ivan Merelli
2014 — conf
Evaluating mixed HTC/cloud approaches for parameter sweep applications in systems biology.
IWBBIO
Ivan Merelli, Ettore Mosca, Daniele Cesini, Elisabetta Ronchieri, Luciano Milanesi
2014 J jnl
Guidelines for managing data and processes in bone and cartilage tissue engineering.
BMC Bioinform.
Federica Viti, Silvia Scaglione, Alessandro Orro, Luciano Milanesi
2014 — conf
NuChart-II: A Graph-Based Approach for Analysis and Interpretation of Hi-C Data.
CIBB
Fabio Tordini, Maurizio Drocco, Ivan Merelli, Luciano Milanesi, Pietro Liò, Marco Aldinucci
2014 C conf
The WNoDeS Cloud Virtualization Framework: A Macromolecular Surface Analysis Application Case Study.
PDP
Elisabetta Ronchieri, Daniele Cesini, Daniele D'Agostino, Vincenzo Ciaschini, Gianni Dalla Torre, Paolo Cozzi, Davide Salomoni, Andrea Clematis, Luciano Milanesi, Ivan Merelli
2013 C conf
A Parallel Implementation of the Stau-DPP Stochastic Simulator for the Modelling of Biological Systems.
PDP
Ettore Mosca, Ivan Merelli, Luciano Milanesi, Andrea Clematis, Daniele D'Agostino
2013 — conf
Comparing Viral (HIV) and Bacterial (Staphylococcus aureus) Infection of the Bone Tissue.
BIOINFORMATICS
Mohammad Ali Moni, Pietro Liò, Luciano Milanesi
2013 J jnl
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS.
BMC Bioinform.
Ivan Merelli, Andrea Calabria, Paolo Cozzi, Federica Viti, Ettore Mosca, Luciano Milanesi
2013 J jnl
Sensitivity Analysis for Studying the Relation between biochemical reactions and metabolic phenotypes.
J. Bioinform. Comput. Biol.
Carlo Maj, Ettore Mosca, Ivan Merelli, Giancarlo Mauri, Luciano Milanesi
2012 C conf
A CUDA-based Implementation of the SSAKE Genomics Application.
PDP
Daniele D'Agostino, Andrea Clematis, Alessandro Guffanti, Luciano Milanesi, Ivan Merelli
2012 J jnl
IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis.
BMC Bioinform.
Ivan Merelli, Federica Viti, Luciano Milanesi
2012 J jnl
Literature Retrieval and Mining in Bioinformatics: State of the Art and Challenges.
Adv. Bioinformatics
Andrea Manconi, Eloisa Vargiu, Giuliano Armano, Luciano Milanesi
2012 J jnl
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations.
PLoS Comput. Biol.
Federica Chiappori, Ivan Merelli, Giorgio Colombo, Luciano Milanesi, Giulia Morra
2012 J jnl
Nanoinformatics: developing new computing applications for nanomedicine.
Computing
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, Guillermo de la Calle, Julio C. Facelli, Peter Ghazal, Antoine Geissbühler, Fernando D. González Nilo, Norbert M. Graf, Pierre Grangeat, Isabel Hermosilla, Rada Hussein, Josipa Kern, Sabine Koch, Yannick Legré, Victoria López-Alonso, Guillermo López-Campos, Luciano Milanesi, Vassilis Moustakis, Cristian R. Munteanu, Paula Otero, Alejandro Pazos, David Pérez-Rey, George Potamias, Ferran Sanz, Casimir A. Kulikowski
2011 — conf
A Mathematical Model for the Enhanced Cytoplasmic Transport - How to Get (Faster) to the Nucleus.
BIOINFORMATICS
Luna Dimitrio, Roberto Natalini, Luciano Milanesi
2011 J jnl
A grid portal with robot certificates for bioinformatics phylogenetic analyses.
Concurr. Comput. Pract. Exp.
Roberto Barbera, Giuseppe Andronico, Giacinto Donvito, Alberto Falzone, J. J. Keijser, Giuseppe La Rocca, Luciano Milanesi, Giorgio Pietro Maggi, Saverio Vicario
2011 B conf
Grid Computing for Sensitivity Analysis of Stochastic Biological Models.
PaCT
Ivan Merelli, Dario Pescini, Ettore Mosca, Paolo Cazzaniga, Carlo Maj, Giancarlo Mauri, Luciano Milanesi
2011 J jnl
Image-Based Surface Matching Algorithm Oriented to Structural Biology.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ivan Merelli, Paolo Cozzi, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi
2011 — ch.
Modeling Biochemical Pathways.
Mathematical Approaches to Polymer Sequence Analysis and Related Problems
Ettore Mosca, Luciano Milanesi
2011 J jnl
Modeling the cell cycle: From deterministic models to hybrid systems.
Biosyst.
Roberta Alfieri, Ezio Bartocci, Emanuela Merelli, Luciano Milanesi
2011 J jnl
Ontology-based resources for bioinformatics analysis.
Int. J. Metadata Semant. Ontologies
Federica Viti, Ivan Merelli, Andrea Calabria, Paolo Cozzi, Ettore Mosca, Roberta Alfieri, Luciano Milanesi
2011 C conf
Parallelization of the SSAKE Genomics Application.
PDP
Daniele D'Agostino, Ivan Merelli, René L. Warren, Alessandro Guffanti, Luciano Milanesi, Andrea Clematis
2011 — ch.
Population Stratification Analysis in Genome-Wide Association Studies.
Mathematical Approaches to Polymer Sequence Analysis and Related Problems
Erika Salvi, Alessandro Orro, Guia Guffanti, Sara Lupoli, Federica Torri, Cristina Barlassina, Steven G. Potkin, Daniele Cusi, Fabio Macciardi, Luciano Milanesi
2011 — conf
Solving Biclustering with a GRASP-Like Metaheuristic: Two Case-Studies on Gene Expression Analysis.
CIBB
Angelo M. Facchiano, Paola Festa, Anna Marabotti, Luciano Milanesi, Francesco Musacchia
2011 J jnl
myMIR: a genome-wide microRNA targets identification and annotation tool.
Briefings Bioinform.
Dario Corrada, Federica Viti, Ivan Merelli, Cristina Battaglia, Luciano Milanesi
2010 C conf
A Dynamic Parallel Approach to Recognize Tubular Breast Cancer for TMA Image Building.
PDP
Antonella Galizia, Federica Viti, Andrea Clematis, Luciano Milanesi
2010 C conf
A Parallel Algorithm for Molecular Surface Matching Through Image Representation.
PDP
Daniele D'Agostino, Andrea Clematis, Ivan Merelli, Paolo Cozzi, Luciano Milanesi
2010 J jnl
A multilevel data integration resource for breast cancer study.
BMC Syst. Biol.
Ettore Mosca, Roberta Alfieri, Ivan Merelli, Federica Viti, Andrea Calabria, Luciano Milanesi
2010 — conf
Complex Search, Ranks, and Biological Discovery: A User's Perspective.
SeCO Workshop
Paolo Romano, Luciano Milanesi
2010 J jnl
Grid Based Genome Wide Studies on Atrial Flutter.
J. Grid Comput.
Andrea Calabria, Davide Di Pasquale, Matteo Gnocchi, Paolo Alessandro Cozzi, Alessandro Orro, Gabriele Antonio Trombetti, Luciano Milanesi
2010 — conf
Modelling Spatial Heterogeneity and Macromolecular Crowding with Membrane Systems.
Int. Conf. on Membrane Computing
Ettore Mosca, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri, Luciano Milanesi
2010 J jnl
Overlapping Genes May Control Reprogramming of Mouse Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) and Breast Cancer Stem Cells.
Silico Biol.
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
2010 J jnl
RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes.
Nucleic Acids Res.
Ivan Merelli, Alessandro Guffanti, Marco Fabbri, Andrea Cocito, Laura Furia, Ursula Grazini, Raoul Jean Pierre Bonnal, Luciano Milanesi, Fraser McBlane
2010 J jnl
SNPRanker: a tool for identification and scoring of SNPs associated to target genes.
J. Integr. Bioinform.
Andrea Calabria, Ettore Mosca, Federica Viti, Ivan Merelli, Luciano Milanesi
2010 J jnl
Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study.
BMC Bioinform.
Federica Viti, Ivan Merelli, Mieke Timmermans, Michael den Bakker, Francesco Beltrame, Peter Riegman, Luciano Milanesi
2009 — conf
A Novel Variant of P Systems for the Modelling and Simulation of Biochemical Systems.
Workshop on Membrane Computing
Paolo Cazzaniga, Giancarlo Mauri, Luciano Milanesi, Ettore Mosca, Dario Pescini
2009 J jnl
Identification of functionally related genes using data mining and data integration: a breast cancer case study.
BMC Bioinform.
Ettore Mosca, Gloria Bertoli, Eleonora Piscitelli, Laura Vilardo, Rolland A. Reinbold, Ileana Zucchi, Luciano Milanesi
2009 J jnl
In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study.
BMC Bioinform.
Federica Chiappori, Pasqualina D'Ursi, Ivan Merelli, Luciano Milanesi, Ermanna Rovida
2009 — conf
On the Performance of Large Scale Bayesian Phylogenetic Analyses with Grid Portals and Robot Certificates.
IWPLS
Roberto Barbera, Giacinto Donvito, Alberto Falzone, Giuseppe La Rocca, Giorgio Pietro Maggi, Saverio Vicario, Luciano Milanesi
2009 — conf
Ontological Enrichment of the
MTSR
Federica Viti, Ettore Mosca, Ivan Merelli, Andrea Calabria, Roberta Alfieri, Luciano Milanesi
2009 C conf
Parallel Decomposition of 3D Surfaces in Images of Local Descriptors for Molecular Screening.
PDP
Daniele D'Agostino, Andrea Clematis, Ivan Merelli, Paolo Cozzi, Luciano Milanesi
2009 — conf
Sys-Bio Gateway: a Framework of Bioinformatics Database Resources Oriented to Systems Biology.
IWPLS
Luciano Milanesi, Roberta Alfieri, Ettore Mosca, Federica Viti, Pasqualina D'Ursi, Ivan Merelli
2009 J jnl
The GENIUS Grid Portal and robot certificates: a new tool for e-Science.
BMC Bioinform.
Roberto Barbera, Giacinto Donvito, Alberto Falzone, Giuseppe La Rocca, Luciano Milanesi, Giorgio Pietro Maggi, Saverio Vicario
2009 J jnl
The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections.
BMC Bioinform.
Ivan Merelli, Andrea Caprera, Alessandra Stella, Marcello Del Corvo, Luciano Milanesi, Barbara Lazzari
2009 J jnl
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation.
BMC Bioinform.
Roberta Alfieri, Matteo Barberis, Ferdinando Chiaradonna, Daniela Gaglio, Luciano Milanesi, Marco Vanoni, Edda Klipp, Lilia Alberghina
2009 J jnl
Trends in modeling Biomedical Complex Systems.
BMC Bioinform.
Luciano Milanesi, Paolo Romano, Gastone C. Castellani, Daniel Remondini, Pietro Liò
2008 C conf
A Grid Service based Parallel Molecular Surface Reconstruction System.
PDP
Daniele D'Agostino, Andrea Clematis, Ivan Merelli, Luciano Milanesi, Matteo Coloberti
2008 — conf
A Visualization ToolKit Based Application for Representing Macromolecular Surfaces.
CIBB
Paolo Cozzi, Ivan Merelli, Luciano Milanesi
2008 J jnl
A parallel protein surface reconstruction system.
Int. J. Bioinform. Res. Appl.
Ivan Merelli, Alessandro Orro, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi
2008 J jnl
An Unusal Distribution of 6-nt Sequences Near The Transcription Start Site.
J. Integr. Bioinform.
Chanchal K. Mitra, Luciano Milanesi
2008 — conf
Bayesian Phylogeny on Grid.
BIRD
Richard Carl Van der Wath, Elizabeth van der Wath, Antonio Carapelli, Francesco Nardi, Francesco Frati, Luciano Milanesi, Pietro Liò
2008 Misc conf
Enabling Parallel TMA Image Analysis in a Grid Environment.
CISIS
Antonella Galizia, Daniele D'Agostino, Andrea Clematis, Federica Viti, Alessandro Orro, Ivan Merelli, Luciano Milanesi
2008 — conf
Images Based System for Surface Matching in Macromolecular Screening.
BIBM
Ivan Merelli, Paolo Cozzi, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi
2008 J jnl
Ontology-based, Tissue MicroArray oriented, image centered tissue bank.
BMC Bioinform.
Federica Viti, Ivan Merelli, Andrea Caprera, Barbara Lazzari, Alessandra Stella, Luciano Milanesi
2008 J jnl
Reconstructing networks of pathways via significance analysis of their intersections.
BMC Bioinform.
Mirko Francesconi, Daniel Remondini, Nicola Neretti, John M. Sedivy, Leon N. Cooper, Ettore Verondini, Luciano Milanesi, Gastone C. Castellani
2008 J jnl
SNPLims: a data management system for genome wide association studies.
BMC Bioinform.
Alessandro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi, Luciano Milanesi
2008 B conf
TMAinspect, an EGEE Framework for Tissue MicroArray Image Handling.
CCGRID
Antonella Galizia, Federica Viti, Alessandro Orro, Daniele D'Agostino, Ivan Merelli, Luciano Milanesi, Andrea Clematis
2008 J jnl
The cell cycle DB: a systems biology approach to cell cycle analysis.
Nucleic Acids Res.
Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi
2008 J jnl
Version VI of the ESTree db: an improved tool for peach transcriptome analysis.
BMC Bioinform.
Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, Luciano Milanesi, Alessandra Stella, Carlo Pozzi
2007 — conf
A Parallel Workflow for the Reconstruction of Molecular Surfaces.
PARCO
Daniele D'Agostino, Ivan Merelli, Andrea Clematis, Luciano Milanesi, Alessandro Orro
2007 J jnl
A data integration approach for cell cycle analysis oriented to model simulation in systems biology.
BMC Syst. Biol.
Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi
2007 J jnl
Agents in bioinformatics, computational and systems biology.
Briefings Bioinform.
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, Michael Luck
2007 — conf
An Agent Approach for Protein Function Analysis in a Grid Infrastructure.
HealthGrid
Alessandro Orro, Luciano Milanesi
2007 — conf
BGBlast: A BLAST Grid Implementation with Database Self-Updating and Adaptive Replication.
HealthGrid
Gabriele Antonio Trombetti, Ivan Merelli, Alessandro Orro, Luciano Milanesi
2007 J jnl
Biowep: a workflow enactment portal for bioinformatics applications.
BMC Bioinform.
Paolo Romano, Ezio Bartocci, Guglielmo Bertolini, Flavio De Paoli, Domenico Marra, Giancarlo Mauri, Emanuela Merelli, Luciano Milanesi
2007 J jnl
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis.
Nucleic Acids Res.
Fedor A. Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury V. Kondrakhin, Alexey V. Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel
2007 J jnl
Data handling strategies for high throughput pyrosequencers.
BMC Bioinform.
Gabriele Antonio Trombetti, Raoul Jean Pierre Bonnal, Ermanno Rizzi, Gianluca De Bellis, Luciano Milanesi
2007 J jnl
ESTuber db: an online database for
BMC Bioinform.
Barbara Lazzari, Andrea Caprera, Cristian Cosentino, Alessandra Stella, Luciano Milanesi, Angelo Viotti
2007 — conf
Experimenting Grid Protocols to Improve Privacy Preservation in Efficient Distributed Image Processing.
PARCO
Antonella Galizia, Federica Viti, Daniele D'Agostino, Ivan Merelli, Luciano Milanesi, Andrea Clematis
2007 J jnl
Medical Informatics and Bioinformatics: A Bibliometric Study.
IEEE Trans. Inf. Technol. Biomed.
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
2007 J jnl
Networks from Gene Expression Time Series: Characterization of Correlation Patterns.
Int. J. Bifurc. Chaos
Daniel Remondini, Nicola Neretti, Claudio Franceschi, Paolo Tieri, John M. Sedivy, Luciano Milanesi, Gastone C. Castellani
2007 — conf
Parameter Estimation for Cell Cycle Ordinary Differential Equation (ODE) Models using a Grid Approach.
HealthGrid
Roberta Alfieri, Ettore Mosca, Ivan Merelli, Luciano Milanesi
2007 J jnl
ProCMD: a database and 3D web resource for protein C mutants.
BMC Bioinform.
Pasqualina D'Ursi, Francesca Marino, Andrea Caprera, Luciano Milanesi, Elena M. Faioni, Ermanna Rovida
2007 J jnl
SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics - exploring current scientific literature for emerging topics.
BMC Bioinform.
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
2007 — conf
Tissue MicroArray: a Distributed Grid Approach for Image Analysis.
HealthGrid
Federica Viti, Ivan Merelli, Antonella Galizia, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi
2006 J jnl
An Agent System for Automatic Workflows Composition in Grid Environments.
Int. Trans. Syst. Sci. Appl.
Alessandro Orro, Luciano Milanesi
2006 — conf
Grid-Enabled High Throughput Virtual Screening.
GCCB
Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Hurng-Chun Lee, Yannick Legré, Simon C. Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli, Luciano Milanesi, Giulio Rastelli, Matthieu Reichstadt, Jean Salzemann, Horst Schwichtenberg, Mahendrakar Sridhar, Vinod Kasam, Ying-Ta Wu, Marc Zimmermann
2006 — conf
High Performance GRID Based Implementation for Genomics and Protein Analysis.
HealthGrid
Luciano Milanesi, Ivan Merelli
2006 J jnl
High performance cDNA sequence analysis using grid technology.
J. Parallel Distributed Comput.
Gabriele Antonio Trombetti, Ivan Merelli, Luciano Milanesi
2006 J jnl
Large Scale In Silico Screening on Grid Infrastructures
CoRR
Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Hurng-Chun Lee, Yannick Legré, Simon C. Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli, Luciano Milanesi, Giulio Rastelli, Matthieu Reichstadt, Jean Salzemann, Horst Schwichtenberg, Mahendrakar Sridhar, Vinod Kasam, Ying-Ta Wu, Marc Zimmermann
2006 J jnl
Network integration of data and analysis of oncology interest.
J. Integr. Bioinform.
Paolo Romano, Guglielmo Bertolini, Flavio De Paoli, M. Fattore, Domenico Marra, Giancarlo Mauri, Emanuela Merelli, Ivan Porro, Silvia Scaglione, Luciano Milanesi
2005 J jnl
A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure.
BMC Bioinform.
Giuliano Armano, Gianmaria Mancosu, Luciano Milanesi, Alessandro Orro, Massimiliano Saba, Eloisa Vargiu
2005 J jnl
ESTree db: a Tool for Peach Functional Genomics.
BMC Bioinform.
Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Alessandra Stella, Luciano Milanesi, Carlo Pozzi
2005 Misc conf
From Context-Dependence of Mutations to Molecular Mechanisms of Mutagenesis.
Pacific Symposium on Biocomputing
Igor B. Rogozin, B. A. Malyarchuk, Youri I. Pavlov, Luciano Milanesi
2005 J jnl
High performance workflow implementation for protein surface characterization using grid technology.
BMC Bioinform.
Ivan Merelli, Giulia Morra, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi
2005 J jnl
Modelling the interaction of steroid receptors with endocrine disrupting chemicals.
BMC Bioinform.
Pasqualina D'Ursi, Erika Salvi, Paola Fossa, Luciano Milanesi, Ermanna Rovida
2005 J jnl
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society.
BMC Bioinform.
Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Giorgio Valle, Cecilia Saccone
2005 J jnl
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.
BMC Bioinform.
Luciano Milanesi, Mauro Petrillo, Leandra Sepe, Angelo Boccia, Nunzio D'Agostino, Myriam Passamano, Salvatore Di Nardo, Gianluca Tasco, Rita Casadio, Giovanni Paolella
2005 — conf
Using Parallel Isosurface Extraction in Superficial Molecular Modeling.
DFMA
Ivan Merelli, Luciano Milanesi, Daniele D'Agostino, Andrea Clematis, Marco Vanneschi, Marco Danelutto
2005 J jnl
Using Secondary Structure Information to Perform Multiple Alignment.
Trans. Comp. Sys. Biology
Giuliano Armano, Luciano Milanesi, Alessandro Orro
2005 J jnl
Web services and workflow management for biological resources.
BMC Bioinform.
Paolo Romano, Domenico Marra, Luciano Milanesi
2003 J jnl
Computational analysis of mutation spectra.
Briefings Bioinform.
Igor B. Rogozin, Vladimir N. Babenko, Luciano Milanesi, Youri I. Pavlov
2002 J jnl
ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro.
Nucleic Acids Res.
Vadim P. Valuev, Dmitry A. Afonnikov, Mikhail P. Ponomarenko, Luciano Milanesi, Nikolay A. Kolchanov
2001 J jnl
Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon.
Bioinform.
Igor B. Rogozin, Alexey V. Kochetov, Fyodor A. Kondrashov, Eugene V. Koonin, Luciano Milanesi
2000 J jnl
Prediction and Phylogenetic Analysis of Mammalian Short Interspersed Elements (SINEs).
Briefings Bioinform.
Igor B. Rogozin, V. I. Mayorov, M. V. Lavrentieva, Luciano Milanesi, L. R. Adkison
1999 J jnl
GeneBuilder: interactive in silico prediction of gene structure.
Bioinform.
Luciano Milanesi, D. D'Angelo, Igor B. Rogozin
1999 J jnl
Integrated databases and computer systems for studying eukaryotic gene expression.
Bioinform.
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, Alexey V. Kochetov, Nikolay L. Podkolodny, Denis G. Vorobiev, Sergey V. Lavryushev, Dmitry A. Grigorovich, Yury V. Kondrakhin, Luciano Milanesi, Edgar Wingender, Victor V. Solovyev, G. Christian Overton
1998 — conf
Fragment assembly system for DNA sequencing projects.
Mathematical Support for Molecular Biology
Luciano Milanesi, M. Marsilli, Giancarlo Mauri, C. Rolfi, L. Uboldi
1998 A conf
GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome.
ISMB
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, Irina L. Stepanenko, Aida G. Romashchenko, Tatyana I. Merkulova, Denis G. Vorobiev, Sergey V. Lavryushev, Y. V. Ponomarenko, Alexey V. Kochetov, G. B. Kolesov, Victor V. Solovyev, Luciano Milanesi, Nikolay L. Podkolodny, Edgar Wingender, T. Heinemeyer
1998 J jnl
Molecular Probe Data Base (MPDB).
Nucleic Acids Res.
Maria Giuseppina Campi, Paolo Romano, Luciano Milanesi, Domenico Marra, Maria Assunta Manniello, Beatrice Iannotta, Gabriella Rondanina, Elena Grasso, Tiziana Ruzzon, Leonardo Santi
1996 — conf
Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes.
German Conference on Bioinformatics
Yury V. Kondrakhin, Fedor A. Kolpakov, Alexander E. Kel, Nikolay A. Kolchanov, Luciano Milanesi
1996 J jnl
Gene structure prediction using information on homologous protein sequence.
Comput. Appl. Biosci.
Igor B. Rogozin, Luciano Milanesi, Nikolay A. Kolchanov
1996 J jnl
Hamming-Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes.
Comput. Appl. Biosci.
Luciano Milanesi, Marco Muselli, P. Arrigo
1995 A conf
Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences.
ISMB
Alexander E. Kel, Yury V. Kondrakhin, Ph. A. Kolpakov, O. V. Kel, Aida G. Romashchenko, Edgar Wingender, Luciano Milanesi, Nikolay A. Kolchanov
1995 J jnl
Eukaryotic promoter recognition by binding sites for transcription factors.
Comput. Appl. Biosci.
Yury V. Kondrakhin, Alexander E. Kel, Nikolay A. Kolchanov, Aida G. Romashchenko, Luciano Milanesi
1994 J jnl
Data bank homology search algorithm with linear computation complexity.
Comput. Appl. Biosci.
Victor B. Strelets, Andrey A. Ptitsyn, Luciano Milanesi, Hwa A. Lim
1993 J jnl
SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites.
Comput. Appl. Biosci.
Alexander E. Kel, Mikhail P. Ponomarenko, E. A. Likhachev, Yuri L. Orlov, I. V. Ischenko, Luciano Milanesi, Nikolay A. Kolchanov
1992 J jnl
Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices.
Comput. Appl. Biosci.
Victor B. Strelets, Ilya N. Shindyalov, Nikolay A. Kolchanov, Luciano Milanesi