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List of works by Luciano Milanesi

A Machine Learning Approach for the Integration of miRNA-Target Predictions

scientific article published in February 2016

A data integration approach for cell cycle analysis oriented to model simulation in systems biology

scientific article

A diethylpyrocarbonate-based derivatization method for the LC-MS/MS measurement of plasma arginine and its chemically related metabolites and analogs

scientific article published on 05 February 2019

A fast job scheduling system for a wide range of bioinformatic applications

scientific article published on 01 June 2007

A grid portal with robot certificates for bioinformatics phylogenetic analyses

scholarly article by Roberto Barbera et al published 22 November 2010 in Concurrency and Computation: Practice and Experience

A hybrid genetic-neural system for predicting protein secondary structure

scientific article published in December 2005

A multilevel data integration resource for breast cancer study

scientific article

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

scientific article

A novel polymorphism in SEL1L confers susceptibility to Alzheimer's disease

scientific article

A rare genetic variant of BPIFB4 predisposes to high blood pressure via impairment of nitric oxide signaling.

scientific article

A single amino acid substitution confers B-cell clonogenic activity to the HIV-1 matrix protein p17.

scientific article

A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units

scientific article

Agents in bioinformatics, computational and systems biology

scientific article published on 26 May 2006

An agent-based multilayer architecture for bioinformatics grids

scientific article published on June 2007

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

scientific article published on 30 March 2016

Analysis of donor splice sites in different eukaryotic organisms ⬇️

scientific article published on July 1, 1997

Antarctic marine ciliates under stress: superoxide dismutases from the psychrophilic Euplotes focardii are cold-active yet heat tolerant enzymes

scientific article published in Scientific Reports

Assessment of haptoglobin alleles in autism spectrum disorders

scientific article published on 08 May 2020

Association Analysis of Noncoding Variants in Neuroligins 3 and 4X Genes with Autism Spectrum Disorder in an Italian Cohort

scientific article published on 22 October 2016

Association study on long-living individuals from Southern Italy identifies rs10491334 in the CAMKIV gene that regulates survival proteins.

scientific article published on 25 May 2011

Author Correction: A rare genetic variant of BPIFB4 predisposes to high blood pressure via impairment of nitric oxide signaling

scientific article published on 28 June 2019

BITS 2015: the annual meeting of the Italian Society of Bioinformatics

scientific article published on 8 November 2016

Biowep: a workflow enactment portal for bioinformatics applications

scientific article

Blood microRNA changes in depressed patients during antidepressant treatment.

scientific article published on 25 August 2012

CYCLONET--an integrated database on cell cycle regulation and carcinogenesis

scientific article

Calcium kidney stones are associated with a haplotype of the calcium-sensing receptor gene regulatory region

article

Characterization and fine localization of two new genes in Xq28 using the genomic sequence/EST database screening approach

scientific article published in June 1996

Cloud infrastructures for in silico drug discovery: economic and practical aspects

scientific article published on 10 September 2013

Computational modeling of the metabolic States regulated by the kinase akt

scientific article published on 21 November 2012

Correlation assessment among clinical phenotypes, expression analysis and molecular modeling of 14 novel variations in the human galactose-1-phosphate uridylyltransferase gene ⬇️

scientific article published on April 30, 2012

Decreased transcriptional activity of calcium-sensing receptor gene promoter 1 is associated with calcium nephrolithiasis.

scientific article published on 17 July 2013

Diffusion of information throughout the host interactome reveals gene expression variations in network proximity to target proteins of hepatitis C virus

scientific article

DnaK as Antibiotic Target: Hot Spot Residues Analysis for Differential Inhibition of the Bacterial Protein in Comparison with the Human HSP70

scientific article

Durum wheat genome highlights past domestication signatures and future improvement targets

scientific article published on 08 April 2019

ESTMAP: a system for expressed sequence tags mapping on genomic sequences

scientific article

ESTree db: a tool for peach functional genomics

scientific article published in December 2005

ESTuber db: an online database for Tuber borchii EST sequences

scientific article

Environment, dysbiosis, immunity and sex-specific susceptibility: a translational hypothesis for regressive autism pathogenesis

scientific article

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

scientific article published on 21 July 2016

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

scientific article published in September 2010

FGF2 and EGF Are Required for Self-Renewal and Organoid Formation of Canine Normal and Tumor Breast Stem Cells.

scientific article published on 15 September 2016

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

scientific article published on 6 April 2010

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

scientific article published on 14 February 2020

Further Insights in the Binding Mode of Selective Inhibitors to Human PDE4D Enzyme Combining Docking and Molecular Dynamics.

scientific article published on 20 June 2016

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

scientific article

GPU-BSM: a GPU-based tool to map bisulfite-treated reads

scientific article

Genome Sequence of Rhodococcus opacus Strain R7, a Biodegrader of Mono- and Polycyclic Aromatic Hydrocarbons

scientific article published on 21 August 2014

Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance

scientific article

Genome-based analysis for the identification of genes involved in o-xylene degradation in Rhodococcus opacus R7

article

Grid Based Genome Wide Studies on Atrial Flutter

Grid methodology for identifying co-regulated genes and transcription factor binding sites

scientific article published in June 2007

Grid-enabled high-throughput in silico screening against influenza A neuraminidase.

scientific article published on December 2006

Guest Editorial: Special Section on Grid, Web Services, Software Agents, and Ontology Applications for Life Sciences

scholarly article by Luciano Milanesi et al published June 2007 in IEEE Transactions on NanoBioscience

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

scientific article

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

scientific article

Heparin and heparan sulfate proteoglycans promote HIV-1 p17 matrix protein oligomerization: computational, biochemical and biological implications

scientific article published on 31 October 2019

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

scientific article published on 23 July 2011

Homology modeling, docking studies and molecular dynamic simulations using graphical processing unit architecture to probe the type-11 phosphodiesterase catalytic site: a computational approach for the rational design of selective inhibitors

scientific article published on 26 August 2013

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

scientific article published on 03 October 2015

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

scientific article published on 17 August 2011

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

scientific article

Identification of a U7snRNA homologue mapping to the human Xq27.1 region, between the DXS1232 and DXS119 loci

scientific article published in March 1997

Image-based surface matching algorithm oriented to structural biology

scientific article published in July 2011

Inhibition of histone methyltransferase DOT1L silences ERα gene and blocks proliferation of antiestrogen-resistant breast cancer cells

article

Integrating multi-omic features exploiting Chromosome Conformation Capture data.

scientific article

LAV-BPIFB4 isoform modulates eNOS signalling through Ca2+/PKC-alpha-dependent mechanism

scientific article

Large-scale profiling of signalling pathways reveals an asthma specific signature in bronchial smooth muscle cells

scientific article published on 05 February 2016

Literature retrieval and mining in bioinformatics: state of the art and challenges

scientific article

Medical informatics and bioinformatics: a bibliometric study.

scientific article

Methods for the integration of multi-omics data: mathematical aspects

scientific article

Mining the bovine genome with the "Bovine SNP Retriever".

scientific article

Modeling the cell cycle: from deterministic models to hybrid systems.

scientific article published on 29 March 2011

Modelling the interaction of steroid receptors with endocrine disrupting chemicals

scientific article published in December 2005

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

scientific article published on December 27, 2012

Molecular dynamics and docking simulation of a natural variant of Activated Protein C with impaired protease activity: implications for integrin-mediated antiseptic function.

scientific article

Molecular interaction studies of HIV-1 matrix protein p17 and heparin: identification of the heparin-binding motif of p17 as a target for the development of multitarget antagonists

scientific article published on 19 November 2012

Molecular remodeling of potassium channels in fibroblasts from centenarians: a marker of longevity?

scientific article published on 19 September 2010

Multi-Level Data Integration and Data Mining in Systems Biology

scholarly article

Multiple alignment through protein secondary-structure information

scientific article published in September 2005

Myosin-binding protein C DNA variants in domestic cats (A31P, A74T, R820W) and their association with hypertrophic cardiomyopathy

scientific article

Nanoinformatics: developing new computing applications for nanomedicine

scientific article (publication date: June 2012)

Network Diffusion-Based Prioritization of Autism Risk Genes Identifies Significantly Connected Gene Modules.

scientific article published on 25 September 2017

Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules

scientific article

Network-Based Integrative Analysis of Genomics, Epigenomics and Transcriptomics in Autism Spectrum Disorders

scientific article published on 09 July 2019

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

scientific article published on 14 October 2013

New insights into selective PDE4D inhibitors: 3-(Cyclopentyloxy)-4-methoxybenzaldehyde O-(2-(2,6-dimethylmorpholino)-2-oxoethyl) oxime (GEBR-7b) structural development and promising activities to restore memory impairment

scientific article published on 13 August 2016

NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

scientific article

Ochratoxin A as possible factor trigging autism and its male prevalence via epigenetic mechanism.

scientific article published on 17 January 2015

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

article

Ontology-based resources for bioinformatics analysis

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

scientific article

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

scientific article published on 29 June 2009

Osteogenic Differentiation of MSC through Calcium Signaling Activation: Transcriptomics and Functional Analysis

scientific article

Parallel solutions for voxel-based simulations of reaction-diffusion systems

scientific article

Phenotype microarray analysis may unravel genetic determinants of the stress response by Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7.

scientific article published on 6 July 2016

Population Stratification Analysis in Genome-Wide Association Studies

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

scientific article

Protein-coding regions prediction combining similarity searches and conservative evolutionary properties of protein-coding sequences

scientific article published on January 1999

Quantitative radionuclide angiocardiography using gold-195m

scientific article published on 01 May 1984

RNA-Generated and Gene-Edited Induced Pluripotent Stem Cells for Disease Modeling and Therapy

scientific article published on 15 September 2016

Reconstructing networks of pathways via significance analysis of their intersections

scientific article

Removing duplicate reads using graphics processing units

scientific article

Representation and modeling of protein surface determinants

scientific article published in December 2005

SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites.

scientific article published on December 1993

SNPLims: a data management system for genome wide association studies

scientific article

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

scientific article published on January 14, 2013

SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans

scientific article

SYMBIOmatics: synergies in Medical Informatics and Bioinformatics--exploring current scientific literature for emerging topics

scientific article

Segmenting the Human Genome into Isochores

scientific article

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

scientific article

Sensitivity analysis for studying the relation between biochemical reactions and metabolic phenotypes ⬇️

scientific article published on January 28, 2013

Sequence and gene content in 35 kb genomic clone mapping in the human Xq27.1 region.

scientific article

Serum BPIFB4 levels classify health status in long-living individuals.

scientific article published on 15 December 2015

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

scientific article published on 13 July 2016

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

scientific article published on 8 January 2018

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

scientific article published on February 27, 2013

Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data.

scientific article

Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment

scientific article published on 03 April 2006

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

Study on the Association among Mycotoxins and other Variables in Children with Autism.

scientific article

Systems biology of the metabolic network regulated by the Akt pathway

scientific article published on 12 August 2011

Systems medicine of inflammaging.

scientific article published on 24 August 2015

The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes

scientific article published on 18 April 2019

The GENIUS Grid Portal and robot certificates: a new tool for e-Science

scientific article

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

scientific article

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

scientific article published on 26 December 2007

The exon-intron organization of the human X-linked gene (FLN1) encoding actin-binding protein 280.

scientific article published in May 1994

The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading.

scientific article published on 6 October 2017

The role of extracellular matrix in mouse and human corneal neovascularization

scientific article published on 03 October 2019

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

scientific article published in June 1998

Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes

scientific article

Tubulin folding: the special case of a beta-tubulin isotype from the Antarctic psychrophilic ciliate Euplotes focardii

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

scientific article published on 25 November 2017

Version VI of the ESTree db: an improved tool for peach transcriptome analysis

scientific article

Virtual screening pipeline and ligand modelling for H5N1 neuraminidase.

scientific article published on 14 April 2009

Web services and workflow management for biological resources

scientific article published in December 2005

[Cyclotrons in medicine. A survey of commercial models and their biomedical applications]

scientific article published on 01 May 1986

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

scientific article

isma: an R package for the integrative analysis of mutations detected by multiple pipelines

scientific article published on 28 February 2019

myMIR: a genome-wide microRNA targets identification and annotation tool

article

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