Luciano Milanesi

Details der Publikationsliste

Zeitraum

1992 - 2009

Anzahl

87

Co-Autoren

Identification of functionally related genes using data mining and data integration: a breast cancer case study (2009)

Mosca, Ettore, Bertoli, Gloria, Piscitelli, Eleonora, Vilardo, Laura, Reinbold, Rolland A, Zucchi, Ileana, ...

Abstract Background The identification of the organisation and dynamics of molecular pathways is crucial for the understanding of cell function. In order to reconstruct the molecular pathways in...

In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study (2009)

Chiappori, Federica, D'Ursi, Pasqualina, Merelli, Ivan, Milanesi, Luciano, Rovida, Ermanna

Abstract Background The design of mutants in protein functional regions, such as the ligand binding sites, is a powerful approach to recognize the determinants of specific protein activities in...

The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections (2009)

Merelli, Ivan, Caprera, Andrea, Stella, Alessandra, Del Corvo, Marcello, Milanesi, Luciano, Lazzari, Barbara

Abstract Background The NCBI dbEST currently contains more than eight million human Expressed Sequenced Tags (ESTs). This wide collection represents an important source of information for gene...

Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation (2009)

Alfieri, Roberta, Barberis, Matteo, Chiaradonna, Ferdinando, Gaglio, Daniela, Milanesi, Luciano, Vanoni, Marco, ...

Abstract Background The cell cycle is a complex process that allows eukaryotic cells to replicate chromosomal DNA and partition it into two daughter cells. A relevant regulatory step is in the G 0 /G...

Trends in modeling Biomedical Complex Systems (2009)

Milanesi, Luciano, Romano, Paolo, Castellani, Gastone, Remondini, Daniel, Liò, Petro

Abstract In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments,...

Ontology-oriented retrieval of putative microRNAs in Vitis viniferavia GrapeMiRNA: a web database of de novopredicted grape microRNAs (2009)

Lazzari, Barbara, Caprera, Andrea, Cestaro, Alessandro, Merelli, Ivan, Del Corvo, Marcello, Fontana, Paolo, ...

Abstract Background Two complete genome sequences are available for Vitis vinifera Pinot noir. Based on the sequence and gene predictions produced by the IASMA, we performed an in silico detection of...

The GENIUS Grid Portal and robot certificates: a new tool for e-Science (2009)

Barbera, Roberto, Donvito, Giacinto, Falzone, Alberto, La Rocca, Giuseppe, Milanesi, Luciano, Maggi, Giorgio, ...

Abstract Background Grid technology is the computing model which allows users to share a wide pletora of distributed computational resources regardless of their geographical location. Up to now, the...

Experimenting Grid Protocols to Improve Privacy Preservation in Efficient Distributed Image Processing (2009)

Antonella Galizia, Federica Viti, Ivan Merelli, Luciano Milanesi, Andrea Clematis, C. Bischof, ...

to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that...

the Reconstruction of Molecular Surfaces (2008)

Ivan Merelli, Andrea Clematis, Luciano Milanesi, Ro Orro, C. Bischof, M. Bücker, ...

to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that...

Reconstructing networks of pathways via significance analysis of their intersections (2008)

Francesconi, Mirko, Remondini, Daniel, Neretti, Nicola, Sedivy, John M, Cooper, Leon N, Verondini, Ettore, ...

Abstract Background Significance analysis at single gene level may suffer from the limited number of samples and experimental noise that can severely limit the power of the chosen statistical test....

Ontology-based, Tissue MicroArray oriented, image centered tissue bank (2008)

Viti, Federica, Merelli, Ivan, Caprera, Andrea, Lazzari, Barbara, Stella, Alessandra, Milanesi, Luciano

Abstract Background Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many...

Bioinformatics Workflow using ASSIST on GRID (2008)

Ivan Merelli, Giulia Morra, Luciano Milanesi, Istituto Tecnologie, Biomediche Consiglio, Nazionale Ricerche

Workflows are very common in bioinformatics because they allow the elaboration of data by delegating the resources management to the information streaming. By the composition of different analysis...

of (2008)

Ezio Bartocci, Diletta Cacciagrano, Nicola Cannata, Flavio Corradini, Emanuela Merelli, Luciano Milanesi, ...

multilayer architecture to support bioinformaticians

Version VI of the ESTree db: an improved tool for peach transcriptome analysis (2008)

Lazzari, Barbara, Caprera, Andrea, Vecchietti, Alberto, Merelli, Ivan, Barale, Francesca, Milanesi, Luciano, ...

Abstract Background The ESTree database (db) is a collection of Prunus persica and Prunus dulcis EST sequences that in its current version encompasses 75,404 sequences from 3 almond and 19 peach...

SNPLims: a data management system for genome wide association studies (2008)

Orro, Alessandro, Guffanti, Guia, Salvi, Erika, Macciardi, Fabio, Milanesi, Luciano

Abstract Background Recent progresses in genotyping technologies allow the generation high-density genetic maps using hundreds of thousands of genetic markers for each DNA sample. The availability of...

An Unusal Distribution of 6-nt Sequences Near The Transcription Start Site (2008)

Mitra, Chanchal K., Milanesi, Luciano

A new look at the transcription start is presented in which we can see transcription factors binding to both sides of the TSS as an essential requirement. Naturally the factor binding to the...

The cell cycle DB: a systems biology approach to cell cycle analysis (2008)

Alfieri, Roberta, Merelli, Ivan, Mosca, Ettore, Milanesi, Luciano

The cell cycle database is a biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes. The database, which is...

Mining the Bovine Genome with the "Bovine SNP Retriever" (2008)

Panzitta, Francesca, Caprera, Andrea, Merelli, Ivan, Milanesi, Luciano, Williams, John L., Lazzari, Barbara, ...

Online resources for the bovine genome analysis are provided at the most important Web sites. Nonetheless, retrieval of single-nucleotide polymorphism (SNP)–related information is not always easy...

BioMed Central (2008)

Bmc Bioinformatics, Ro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi, Fabio Macciardi, ...

SNPLims: a data management system for genome wide association studies

Molecular Probe Data Base (MPDB) (2007)

Maria Giuseppina, Paolo Romano, Luciano Milanesi, Domenico Marra, Maria Assunta Manniello, Gabriella Rondanina, ...

In this paper, the current status of the Molecular Probe Data Base (http://www.biotech.ist.unige.it/interlab/ mpdb.html ) is briefly presented together with a short analysis of its activity during...

Data handling strategies for high throughput pyrosequencers (2007)

Trombetti, Gabriele A, Bonnal, Raoul JP, Rizzi, Ermanno, De Bellis, Gianluca, Milanesi, Luciano

Abstract Background New high throughput pyrosequencers such as the 454 Life Sciences GS 20 are capable of massively parallelizing DNA sequencing providing an unprecedented rate of output data as well...

Biowep: a workflow enactment portal for bioinformatics applications (2007)

Romano, Paolo, Bartocci, Ezio, Bertolini, Guglielmo, De Paoli, Flavio, Marra, Domenico, Mauri, Giancarlo, ...

Abstract Background The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and...

SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics – exploring current scientific literature for emerging topics (2007)

Rebholz-Schuhman, Dietrich, Cameron, Graham, Clark, Dominic, Van Mulligen, Erik, Coatrieux, Jean-Louis, Del Hoyo Barbolla, Eva, ...

Abstract Background The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the...

ESTuber db: an online database for Tuber borchiiEST sequences (2007)

Lazzari, Barbara, Caprera, Andrea, Cosentino, Cristian, Stella, Alessandra, Milanesi, Luciano, Viotti, Angelo

Abstract Background The ESTuber database ( http://www.itb.cnr.it/estuber ) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house...

ProCMD: a database and 3D web resource for protein C mutants (2007)

D'Ursi, Pasqualina, Marino, Francesca, Caprera, Andrea, Milanesi, Luciano, Faioni, Elena M, Rovida, Ermanna

Abstract Background Activated Protein C (ProC) is an anticoagulant plasma serine protease which also plays an important role in controlling inflammation and cell proliferation. Several mutations of...

SYMBIOmatics: synergies in Medical Informatics and Bioinformatics--exploring current scientific literature for emerging topics. (2007)

Rebholz-Schuhman, Dietrich, Cameron, Graham, Clark, Dominic, Van Mulligen, Erik, Coatrieux, Jean-Louis, Del Hoyo Barbolla, Eva, ...

BACKGROUND: The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the medical...

Medical informatics and bioinformatics: a bibliometric study. (2007)

Bansard, Jean-Yves, Rebholz-Schuhman, Dietrich, Cameron, Graham, Clark, Dominic, Van Mulligen, Erik, Beltrame, Francesco, ...

This paper reports on an analysis of the bioinformatics and medical informatics literature with the objective to identify upcoming trends that are shared among both research fields to derive benefits...

Medical informatics and bioinformatics: a bibliometric study. (2007)

Bansard, Jean-Yves, Rebholz-Schuhman, Dietrich, Cameron, Graham, Clark, Dominic, Van Mulligen, Erik, Beltrame, Francesco, ...

This paper reports on an analysis of the bioinformatics and medical informatics literature with the objective to identify upcoming trends that are shared among both research fields to derive benefits...

SYMBIOmatics: synergies in Medical Informatics and Bioinformatics--exploring current scientific literature for emerging topics. (2007)

Rebholz-Schuhman, Dietrich, Cameron, Graham, Clark, Dominic, Van Mulligen, Erik, Coatrieux, Jean-Louis, Del Hoyo Barbolla, Eva, ...

BACKGROUND: The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the medical...

BioMed Central Open Access (2007)

Bmc Bioinformatics, Paolo Romano, Ezio Bartocci, Guglielmo Bertolini, Flavio De Paoli, Domenico Marra, ...

Biowep: a workflow enactment portal for bioinformatics applications

BMC Systems Biology Database (2007)

Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi, Biomed Central

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

Medical informatics and bioinformatics: a bibliometric study. (2007)

Bansard, Jean-Yves, Rebholz-Schuhman, Dietrich, Cameron, Graham, Clark, Dominic, Van Mulligen, Erik, Beltrame, Francesco, ...

This paper reports on an analysis of the bioinformatics and medical informatics literature with the objective to identify upcoming trends that are shared among both research fields to derive benefits...

SYMBIOmatics: synergies in Medical Informatics and Bioinformatics--exploring current scientific literature for emerging topics. (2007)

Rebholz-Schuhman, Dietrich, Cameron, Graham, Clark, Dominic, Van Mulligen, Erik, Coatrieux, Jean-Louis, Del Hoyo Barbolla, Eva, ...

BACKGROUND: The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the medical...

CYCLONET--an integrated database on cell cycle regulation and carcinogenesis (2007)

Kolpakov, Fedor, Poroikov, Vladimir, Sharipov, Ruslan, Kondrakhin, Yury, Zakharov, Alexey, Lagunin, Alexey, ...

Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based...

Agents in bioinformatics, computational and systems biology (2007)

Merelli, Emanuela, Armano, Giuliano, Cannata, Nicola, Corradini, Flavio, D'Inverno, Mark, Doms, Andreas, ...

The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics...

A GRID-based multilayer architecture for bioinformatics (2006)

Ezio Bartocci, Diletta Cacciagrano, Nicola Cannata, Flavio Corradini, Emanuela Merelli, Luciano Milanesi, ...

Abstract. The volume and complexity of biological data and informations available today need a significant computational data and processes analysis. A huge amount of bioinformatics databases and...

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)

Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...

Abstract The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005,...

Modelling the interaction of steroid receptors with endocrine disrupting chemicals (2005)

D'Ursi, Pasqualina, Salvi, Erika, Fossa, Paola, Milanesi, Luciano, Rovida, Ermanna

Abstract Background The organic polychlorinated compounds like dichlorodiphenyltrichloroethane with its metabolites and polychlorinated biphenyls are a class of highly persistent environmental...

ESTree db: a Tool for Peach Functional Genomics (2005)

Lazzari, Barbara, Caprera, Andrea, Vecchietti, Alberto, Stella, Alessandra, Milanesi, Luciano, Pozzi, Carlo

Abstract Background The ESTree db http://www.itb.cnr.it/estree/ represents a collection of Prunus persica expressed sequenced tags (ESTs) and is intended as a resource for peach functional genomics....

High performance workflow implementation for protein surface characterization using grid technology (2005)

Merelli, Ivan, Morra, Giulia, D'Agostino, Daniele, Clematis, Andrea, Milanesi, Luciano

Abstract Background This study concerns the development of a high performance workflow that, using grid technology, correlates different kinds of Bioinformatics data, starting from the base pairs of...

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity (2005)

Milanesi, Luciano, Petrillo, Mauro, Sepe, Leandra, Boccia, Angelo, D'Agostino, Nunzio, Passamano, Myriam, ...

Abstract Background Protein kinases are a well defined family of proteins, characterized by the presence of a common kinase catalytic domain and playing a significant role in many important cellular...

Web services and workflow management for biological resources (2005)

Romano, Paolo, Marra, Domenico, Milanesi, Luciano

Abstract Backgorund The completion of the Human Genome Project has resulted in large quantities of biological data which are proving difficult to manage and integrate effectively. There is a need for...

A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure (2005)

Armano, Giuliano, Mancosu, Gianmaria, Milanesi, Luciano, Orro, Alessandro, Saba, Massimiliano, Vargiu, Eloisa

Abstract Background Due to the strict relation between protein function and structure, the prediction of protein 3D-structure has become one of the most important tasks in bioinformatics and...

ESTree db: a tool for peach functional genomics (2005)

Barbara Lazzari, Luciano Milanesi, Ra Stella, Andrea Caprera, Francesca Bianchi, Carlo Pozzi

A collection of about 8000 Expressed Sequence Tags (EST) sequences has been prepared starting from clones belonging to four cDNA peach libraries. Libraries have been prepared from Prunus persica...

BioMed Central (2005)

Bmc Bioinformatics, Ivan Merelli, Giulia Morra, Andrea Clematis, Luciano Milanesi, Andrea Clematis, ...

Research article High performance workflow implementation for protein surface characterization using grid technology

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society (2005)

Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...

The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....

BioMed Central Research article A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure (2005)

Bmc Bioinformatics, Giuliano Armano, Gianmaria Mancosu, Luciano Milanesi, Ro Orro, Massimiliano Saba, ...

<p>Italian Society of Bioinformatics (BITS): Annual Meeting 2005</p> </title> <editor>Rita Casadio, Alessandro Guffanti, Manuela Helmer-Citterich, Giancarlo Mauri, Luciano...

Based on invited talks by (2004)

Emanuela Merelli, Michael Luck, Giuliano Armano, Andrea Doms, Nicola Cannata, Flavio Corradini, ...

The first Technical Forum Group (TFG) on Agents in Bioinformatics (BIOAGENTS) was held on the 2nd of July, 2004, in Rome, Italy. The scope of the TFG was to inspire collaboration between the agent...

Computational analysis of mutation spectra (2003)

Rogozin, Igor B., Babenko, Vladimir N., Milanesi, Luciano, Pavlov, Youri I.

Mutation frequencies vary along a nucleotide sequence, and nucleotide positions with an exceptionally high mutation frequency are called hotspots. Mutation hotspots in DNA often reflect intrinsic...

ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro (2002)

Valuev, Vadim P., Afonnikov, Dmitry A., Ponomarenko, Mikhail P., Milanesi, Luciano, Kolchanov, Nikolay A.

ASPD is a new curated database that incorporates data on full-length proteins, protein domains and peptides that were obtained through in vitro directed evolution processes (mainly by means of phage...

Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a weak' context of the start codon (2001)

Rogozin, Igor B., Kochetov, Alexey V., Kondrashov, Fyodor A., Koonin, Eugene V., Milanesi, Luciano

Motivation: The context of the start codon (typically, AUG) and the features of the 5′ Untranslated Regions (5′ UTRs) are important for understanding translation regulation in eukaryotic mRNAs...

Prediction and phylogenetic analysis of mammalian short interspersed elements (SINEs) (2000)

Rogozin, Igor B., Mayorov, Vladimir I., Lavrentieva, Marina V., Milanesi, Luciano, Adkison, Linda R.

The presence of repetitive elements can create serious problems for sequence analysis, especially in the case of homology searches in nucleotide sequence databases. Repetitive elements should be...

Gene structure prediction using information on homologous protein sequence (1996)

Rogozin, Igor B., Milanesi, Luciano, Kolchanov, Nikolay A.

In this paper a new approach for the prediction of protein coding gene structures is described. The principal scheme of prediction is as follows: first, the exons with the best potential are...

Methylation and sequence analysis around Eagi sites: identification of 28 new CpG islands in XQ24-XQ28 (1992)

Tribioli, Carla, Tamanini, Filippo, Patrosso, Cristina, Milanesi, Luciano, Villa, Anna, Pergolizzi, Rossana, ...

Thirtytwo probes for CpG islands of the distal long arm of the human X chromosome have been Identified. From a genomic library of ONA of the hamster-human cell hybrid X3000.1 digested with the rare...

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

Valuev, Vadim P., Afonnikov, Dmitry A., Ponomarenko, Mikhail P., Milanesi, Luciano, Kolchanov, Nikolay A.

ASPD is a new curated database that incorporates data on full-length proteins, protein domains and peptides that were obtained through in vitro directed evolution processes (mainly by means of phage...

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

Valuev, Vadim P., Afonnikov, Dmitry A., Ponomarenko, Mikhail P., Milanesi, Luciano, Kolchanov, Nikolay A.

ASPD is a new curated database that incorporates data on full-length proteins, protein domains and peptides that were obtained through in vitro directed evolution processes (mainly by means of phage...

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society

Helmer-Citterich, Manuela, Casadio, Rita, Guffanti, Alessandro, Mauri, Giancarlo, Milanesi, Luciano, Pesole, Graziano, ...

The BITS2005 Conference brought together about 200 Italian scientists working in the field of Bioinformatics, students in Biology, Computer Science and Bioinformatics on March 17–19 2005, in Milan....

CYCLONET—an integrated database on cell cycle regulation and carcinogenesis

Kolpakov, Fedor, Poroikov, Vladimir, Sharipov, Ruslan, Kondrakhin, Yury, Zakharov, Alexey, Lagunin, Alexey, ...

Computational modelling of mammalian cell cycle regulation is a challenging task, which requires comprehensive knowledge on many interrelated processes in the cell. We have developed a web-based...

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

Alfieri, Roberta, Merelli, Ivan, Mosca, Ettore, Milanesi, Luciano

The cell cycle database is a biological resource that collects the most relevant information related to genes and proteins involved in human and yeast cell cycle processes. The database, which is...

Trends in modeling Biomedical Complex Systems

Milanesi, Luciano, Romano, Paolo, Castellani, Gastone, Remondini, Daniel, Liò, Petro

In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments,...