Luciano Milanesi

Luis Muñoz, Ivan Merelli, Luciano Milanesi, 2016, 2016 24th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP).

Web services and workflow management for biological resources

Luciano Milanesi, Paolo Romano, Domenico Marra, 2005, BMC Bioinformatics.

How computer science can help in understanding the 3D genome architecture

Pietro Liò, Ivan Merelli, Luciano Milanesi, 2016, Briefings Bioinform..

Modelling the interaction of steroid receptors with endocrine disrupting chemicals

Luciano Milanesi, Erika Salvi, Pasqualina D'Ursi, 2005, BMC Bioinformatics.

An infrastructure for precision medicine through analysis of big data

Luciano Milanesi, Andrea Manconi, Marco Moscatelli, 2018, BMC Bioinformatics.

BGBlast: A BLAST Grid Implementation with Database Self-Updating and Adaptive Replication

Ivan Merelli, Alessandro Orro, Luciano Milanesi, 2007, HealthGrid.

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

Alessandro Orro, Luciano Milanesi, Andrea Manconi, 2014, BMC Bioinformatics.

Using Secondary Structure Information to Perform Multiple Alignment

Alessandro Orro, Luciano Milanesi, Giuliano Armano, 2005, Trans. Comp. Sys. Biology.

Ontological Enrichment of the Genes-to-Systems Breast Cancer Database

Ivan Merelli, Luciano Milanesi, Federica Viti, 2009, MTSR.

Trends in modeling Biomedical Complex Systems

Pietro Liò, Luciano Milanesi, Gastone C. Castellani, 2009, BMC Bioinformatics.

Eukaryotic promoter recognition by binding sites for transcription factors

Alexander E. Kel, Luciano Milanesi, Nikolay A. Kolchanov, 1995, Comput. Appl. Biosci..

Tissue MicroArray: a Distributed Grid Approach for Image Analysis

Andrea Clematis, Ivan Merelli, Daniele D'Agostino, 2007, HealthGrid.

NuchaRt: Embedding High-Level Parallel Computing in R for Augmented Hi-C Data Analysis

Pietro Liò, Ivan Merelli, Luciano Milanesi, 2015, CIBB.

A Novel Variant of P Systems for the Modelling and Simulation of Biochemical Systems

Giancarlo Mauri, Paolo Cazzaniga, Luciano Milanesi, 2009, Workshop on Membrane Computing.

Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon

Luciano Milanesi, Igor B. Rogozin, Alexey V. Kochetov, 2001, Bioinform..

A Mathematical Model for the Enhanced Cytoplasmic Transport - How to Get (Faster) to the Nucleus

Luciano Milanesi, Roberto Natalini, Luna Dimitrio, 2011, BIOINFORMATICS.

Ontology-based, Tissue MicroArray oriented, image centered tissue bank

Ivan Merelli, Luciano Milanesi, Federica Viti, 2008, BMC Bioinformatics.

Grid Based Genome Wide Studies on Atrial Flutter

Alessandro Orro, Luciano Milanesi, Davide Di Pasquale, 2010, Journal of Grid Computing.

An Agent Approach to High Level Workflow Management in Functional Genomics

Alessandro Orro, G. Armano, Eloisa Vargiu, 2005 .

Data bank homology search algorithm with linear computation complexity

Hwa A. Lim, Luciano Milanesi, Victor B. Strelets, 1994, Comput. Appl. Biosci..

Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes

Alexander E. Kel, Luciano Milanesi, Nikolay A. Kolchanov, 1996, German Conference on Bioinformatics.

Big Data for disease prevention and precision medicine

Luciano Milanesi, Andrea Manconi, Marco Moscatelli, 2016 .

A Infrastructure for Disease Prevention and Precision Medicine

Luciano Milanesi, Andrea Manconi, Marco Moscatelli, 2016, KDWeb.

Grid Computing for Sensitivity Analysis of Stochastic Biological Models

Giancarlo Mauri, Ivan Merelli, Paolo Cazzaniga, 2011, PaCT.

INFN, IT the GENIUS grid portal and the robot certificates to perform phylogenetic analysis on large scale: a success story from the International LIBI project

Luciano Milanesi, Roberto Barbera, Giuseppe La Rocca, 2010 .

Frailness and resilience of gene networks predicted by detection of co-occurring mutations via a stochastic perturbative approach

Luciano Milanesi, Ettore Mosca, Gastone Castellani, 2020, Scientific Reports.

A Dynamic Parallel Approach to Recognize Tubular Breast Cancer for TMA Image Building

Andrea Clematis, Antonella Galizia, Luciano Milanesi, 2010, 2010 18th Euromicro Conference on Parallel, Distributed and Network-based Processing.

A GRID-based multilayer architecture for bioinformatics

Ezio Bartocci, Emanuela Merelli, Luciano Milanesi, 2006 .

Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems

Andrea Clematis, Ivan Merelli, Daniele D'Agostino, 2014, BioMed research international.

Comparing Viral (HIV) and Bacterial (Staphylococcus aureus) Infection of the Bone Tissue

Pietro Liò, Mohammad Ali Moni, Luciano Milanesi, 2013, BIOINFORMATICS.

High performance cDNA sequence analysis using grid technology

Ivan Merelli, Luciano Milanesi, Gabriele Antonio Trombetti, 2006, J. Parallel Distributed Comput..

Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations

Ivan Merelli, Luciano Milanesi, Giorgio Colombo, 2012, PLoS Comput. Biol..

iSmaRT: a toolkit for a comprehensive analysis of small RNA‐Seq data

Luciano Milanesi, Riccardo Panero, Antonio Rinaldi, 2017, Bioinform..

Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study

Ivan Merelli, Luciano Milanesi, Francesco Beltrame, 2010, BMC Bioinformatics.

Bayesian Phylogeny on Grid

Pietro Liò, Luciano Milanesi, Richard Carl Van der Wath, 2008, BIRD.

Modeling the cell cycle: From deterministic models to hybrid systems

Ezio Bartocci, Emanuela Merelli, Luciano Milanesi, 2011, Biosyst..

Guidelines for managing data and processes in bone and cartilage tissue engineering

Alessandro Orro, Luciano Milanesi, Federica Viti, 2014, BMC Bioinformatics.

Fragment assembly system for DNA sequencing projects

Giancarlo Mauri, Luciano Milanesi, M. Marsilli, 1998, Mathematical Support for Molecular Biology.

Parameter Estimation for Cell Cycle Ordinary Differential Equation (ODE) Models using a Grid Approach

Ivan Merelli, Luciano Milanesi, Ettore Mosca, 2007, HealthGrid.

ProCMD: a database and 3D web resource for protein C mutants

Luciano Milanesi, Andrea Caprera, Pasqualina D'Ursi, 2007, BMC Bioinformatics.

Parallel Exploration of the Nuclear Chromosome Conformation with NuChart-II

Pietro Liò, Ivan Merelli, Luciano Milanesi, 2015, 2015 23rd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing.

Molecular Probe Data Base (MPDB)

Luciano Milanesi, Paolo Romano, Domenico Marra, 1998, Nucleic Acids Res..

Cloud Infrastructures for In Silico Drug Discovery: Economic and Practical Aspects

Andrea Clematis, Ivan Merelli, Daniele D'Agostino, 2013, BioMed research international.

G-SNPM - A GPU-based SNP mapping tool

Alessandro Orro, Luciano Milanesi, Andrea Manconi, 2012 .

Epistasis analysis reveals associations between gene variants and bipolar disorder

Ivan Merelli, Luciano Milanesi, Carlo Maj, 2017, PeerJ Prepr..

Biowep: a workflow enactment portal for bioinformatics applications

Giancarlo Mauri, Ezio Bartocci, Emanuela Merelli, 2007, BMC Bioinformatics.

High Performance GRID Based Implementation for Genomics and Protein Analysis

Ivan Merelli, Luciano Milanesi, 2006, HealthGrid.

VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites

Ivan Merelli, Luciano Milanesi, Stefano Beretta, 2017, BMC Bioinformatics.

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity

Luciano Milanesi, Rita Casadio, Nunzio D'Agostino, 2005, BMC Bioinformatics.

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis

Ivan Merelli, Luciano Milanesi, Federica Viti, 2012, BMC Bioinformatics.

On the Performance of Large Scale Bayesian Phylogenetic Analyses with Grid Portals and Robot Certificates

Giacinto Donvito, Luciano Milanesi, Roberto Barbera, 2009, IWPLS.

Networks from Gene Expression Time Series: Characterization of Correlation Patterns

Luciano Milanesi, Nicola Neretti, Gastone C. Castellani, 2006, Int. J. Bifurc. Chaos.

Modeling Biochemical Pathways

Luciano Milanesi, Ettore Mosca, L. Milanesi, 2011, Mathematical Approaches to Polymer Sequence Analysis and Related Problems.

The cell cycle DB: a systems biology approach to cell cycle analysis

Ivan Merelli, Luciano Milanesi, Ettore Mosca, 2007, Nucleic Acids Res..

A grid portal with robot certificates for bioinformatics phylogenetic analyses

Giacinto Donvito, Luciano Milanesi, Roberto Barbera, 2011, Concurr. Comput. Pract. Exp..

GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome

T. Heinemeyer, Alexander E. Kel, Edgar Wingender, 1998, ISMB.

Population Stratification Analysis in Genome-Wide Association Studies

Steven G. Potkin, Alessandro Orro, Luciano Milanesi, 2011, Mathematical Approaches to Polymer Sequence Analysis and Related Problems.

Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation

Edda Klipp, Luciano Milanesi, Matteo Barberis, 2009, BMC Bioinformatics.

Overlapping Genes May Control Reprogramming of Mouse Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) and Breast Cancer Stem Cells

Luciano Milanesi, Ettore Mosca, Massimo Carella, 2010, Silico Biol..

In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study

Ivan Merelli, Luciano Milanesi, Federica Chiappori, 2009, BMC Bioinformatics.

G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods

Alessandro Orro, Luciano Milanesi, Andrea Manconi, 2015, Front. Bioeng. Biotechnol..

CUDA‐quicksort: an improved GPU‐based implementation of quicksort

Alessandro Orro, Luciano Milanesi, Andrea Manconi, 2016, Concurr. Comput. Pract. Exp..

Bioinfogrid:. Bioinformatics Simulation and Modeling Based on Grid

Luciano Milanesi, L. Milanesi, 2007 .

A GPU-based high performance computing infrastructure for specialized NGS analyses

Luciano Milanesi, Andrea Manconi, Giuliano Armano, 2016 .

Multi-Level Data Integration and Data Mining in Systems Biology

Luciano Milanesi, Roberta Alfieri, L. Milanesi, 2009 .

Reconstructing networks of pathways via significance analysis of their intersections

Mirko Francesconi, Luciano Milanesi, Nicola Neretti, 2008, BMC Bioinformatics.

SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS

Ivan Merelli, Luciano Milanesi, Federica Viti, 2013, BMC Bioinformatics.

Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences

Alexander E. Kel, Edgar Wingender, Luciano Milanesi, 1995, ISMB.

A Scalable Genetic Programming Approach to Integrate miRNA-Target Predictions: Comparing Different Parallel Implementations of M3GP

Luis Muñoz, Ivan Merelli, Luciano Milanesi, 2018, Complex..

Bioinformatics approach for data management about bone cells grown on substitute materials

Ivan Merelli, Luciano Milanesi, Federica Viti, 2012 .

iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data

Luciano Milanesi, Riccardo Panero, Antonio Rinaldi, 2017, Bioinform..

The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections

Ivan Merelli, Luciano Milanesi, Barbara Lazzari, 2009, BMC Bioinformatics.

Oncology over Internet (O2I): information querying, filtering and retrieval by means of standard formats

Emanuela Merelli, Luciano Milanesi, Paolo Romano, 2002 .

A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study

Ivan Merelli, Luciano Milanesi, Federica Chiappori, 2016, BMC Bioinformatics.

A Visualization ToolKit Based Application for Representing Macromolecular Surfaces

Ivan Merelli, Luciano Milanesi, Paolo Cozzi, 2009, CIBB.

A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure

Alessandro Orro, Eloisa Vargiu, Luciano Milanesi, 2005, BMC Bioinformatics.

ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro

Luciano Milanesi, Nikolay A. Kolchanov, Dmitry A. Afonnikov, 2002, Nucleic Acids Res..

Data handling strategies for high throughput pyrosequencers

Luciano Milanesi, Raoul Jean Pierre Bonnal, Gabriele Antonio Trombetti, 2007, BMC Bioinformatics.

γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites

Paola Bonizzoni, Yuri Pirola, Ivan Merelli, 2019, Bioinform..

A distributed approach for parameter estimation in Systems Biology models

Ivan Merelli, Luciano Milanesi, Roberta Alfieri, 2009 .

Hamming-Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes

Luciano Milanesi, P. Arrigo, M. Muselli, 1996, Comput. Appl. Biosci..

ESTuber db: an online database for Tuber borchii EST sequences

Luciano Milanesi, Barbara Lazzari, Alessandra Stella, 2007, BMC Bioinformatics.

HPC Analysis of Multiple Binding Sites Communication and Allosteric Modulations in Drug Design: The HSP Case Study.

Ivan Merelli, Luciano Milanesi, Federica Chiappori, 2016, Current drug targets.

Ontology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAs

Riccardo Velasco, Ivan Merelli, Luciano Milanesi, 2009, BMC Plant Biology.

Static and dynamic interactions between GALK enzyme and known inhibitors: guidelines to design new drugs for galactosemic patients.

Ivan Merelli, Luciano Milanesi, Anna Marabotti, 2013, European journal of medicinal chemistry.

Bioinformatics approach for data management about bone cells grown on substitute materials

Ivan Merelli, Luciano Milanesi, Federica Viti, 2012 .

Molecular Interaction Studies of HIV-1 Matrix Protein p17 and Heparin

Alessandro Orro, Luciano Milanesi, Pasqualina D'Ursi, 2012, The Journal of Biological Chemistry.

Human aryl-hydrocarbon receptor and its interaction with dioxin and physiological ligands investigated by molecular modelling and docking simulations.

Luciano Milanesi, Anna Marabotti, Angelo Facchiano, 2011, Biochemical and biophysical research communications.

Medicine and Biology

Hojjat Adeli, Robert S. H. Istepanian, Luciano Milanesi, 2005 .

Segmenting the Human Genome into Isochores

Luciano Milanesi, Giorgio Bernardi, Paolo Cozzi, 2015, Evolutionary bioinformatics online.

10 – Prediction of Human Gene Structure

Luciano Milanesi, Igor B. Rogozin, L. Milanesi, 1998 .

GenViewer: A computing tool for protein-coding regions prediction in nucleotide sequences

Alexander E. Kel, Luciano Milanesi, Nikolay A. Kolchanov, 1993 .

Analysis of donor splice sites in different eukaryotic organisms

Luciano Milanesi, Igor B. Rogozin, L. Milanesi, 1997, Journal of Molecular Evolution.

A Novel Variant of Tissue P Systems for the Modelling of Biochemical Systems

Giancarlo Mauri, Paolo Cazzaniga, Luciano Milanesi, 2009 .

Specific patterns of PIWI-interacting small noncoding RNA expression in dysplastic liver nodules and hepatocellular carcinoma

Luciano Milanesi, Maria Ravo, Alessandro Weisz, 2016, Oncotarget.

Virtual screening pipeline and ligand modelling for H5N1 neuraminidase.

Ivan Merelli, Luciano Milanesi, Federica Chiappori, 2009, Biochemical and biophysical research communications.

An atomistic view of Hsp70 allosteric crosstalk: from the nucleotide to the substrate binding domain and back

Ivan Merelli, Luciano Milanesi, Giorgio Colombo, 2016, Scientific Reports.

Structural thermal adaptation of β‐tubulins from the Antarctic psychrophilic protozoan Euplotes focardii

Ivan Merelli, Luciano Milanesi, Cristina Miceli, 2012, Proteins.

Computational Modeling of the Metabolic States Regulated by the Kinase Akt

Luciano Milanesi, Ettore Mosca, Carlo Maj, 2012, Front. Physio..

Exploitation of a novel biosensor based on the full-length human F508del-CFTR with computational studies, biochemical and biological assays for the characterization of a new Lumacaftor/Tezacaftor analogue

Paolo Bergese, Alessandro Orro, Luciano Milanesi, 2019 .

The subclass approach for mutational spectrum analysis: application of the SEM algorithm.

Luciano Milanesi, Igor B. Rogozin, L. Milanesi, 1998, Journal of theoretical biology.

NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations

Pietro Liò, Ivan Merelli, Luciano Milanesi, 2013, PloS one.

Exploring the role of the phospholipid ligand in endothelial protein C receptor: A molecular dynamics study

Ivan Merelli, Luciano Milanesi, Federica Chiappori, 2010, Proteins.

Exome sequencing identifies variants in two genes encoding the LIM-proteins NRAP and FHL1 in an Italian patient with BAG3 myofibrillar myopathy

Alessandro Orro, Luciano Milanesi, Cristina Barlassina, 2016, Journal of Muscle Research and Cell Motility.

COMPUTER ANALYSIS AND RECOGNITION OF FUNCTIONAL SITES VIA OLIGONUCLEOTIDE PATTERN DISTRIBUTIONS

Alexander E. Kel, Luciano Milanesi, Nikolay A. Kolchanov, 1993 .

Speeding Up the Identification of Cystic Fibrosis Transmembrane Conductance Regulator-Targeted Drugs: An Approach Based on Bioinformatics Strategies and Surface Plasmon Resonance

Alessandro Orro, Luciano Milanesi, Gabriele Trombetti, 2018, Molecules.

Homology modeling in tandem with 3D-QSAR analyses: a computational approach to depict the agonist binding site of the human CB2 receptor.

Luciano Milanesi, Anna Marabotti, Pasqualina D'Ursi, 2011, European journal of medicinal chemistry.

Network-based analysis of omics with multi-objective optimization.

Luciano Milanesi, Ettore Mosca, L. Milanesi, 2013, Molecular bioSystems.

Bioinformatics of Genome Regulation and Structure II

Luciano Milanesi, Nikolay A. Kolchanov, Ralf Hofestaedt, 2006 .

Sitecon—A Tool for Analysis of DNA Physicochemical and Conformational Properties: E2F/DP Transcription Factor Binding Site Analysis and Recognition

Luciano Milanesi, Nikolay A. Kolchanov, M. A. Pozdnyakov, 2004 .

The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer

Pietro Liò, Ivan Merelli, Luciano Milanesi, 2016, Front. Genet..

Fine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidence

Doron Lancet, Alessandro Orro, Luciano Milanesi, 2010, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Oncology over Internet: integrating data and analysis of oncology interest on the net by means of workflows

Giancarlo Mauri, Emanuela Merelli, Luciano Milanesi, 2005 .