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BIOINFORMATICS PUBLICATIONS


Year 2014

Pasquale G.; Maj C.; Clematis A.; Mosca E.; Milanesi L.; Merelli I.; Dagostino D. (2014). A CUDA implementation of the Spatial TAU-leaping in Crowded Compartments (STAUCC) simulator in 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP 2014), Torino, Italia, 12-14 Febbraio 2014

Pasquale G., Mosca E., Merelli I., Milanesi L., Clematis A., D'Agostino D. (2014). A full fine-grained parallelization of the multi-objective evolutionary approach NSGA-II for the CUDA architecture in BITS Annual Meeting 2014, Roma, Italia, 26-28 Febbraio 2014

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

Daniele D'Agostino, Andrea Clematis , Sergio Decherchi , Walter Rocchia , Luciano Milanesi and Ivan Merelli (2014). CUDA accelerated molecular surface generation in Concurrency and computation; John Wiley & Sons Ltd., Chichester (Regno Unito)

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

Di Gennaro, P; Zampolli, J; Presti, I; Cappelletti, M; D'Ursi, P; Orro, A; Mezzelani, A; Milanesi, L (2014).Genome Sequence of Rhodococcus opacus Strain R7, a Biodegrader of Mono- and Polycyclic Aromatic Hydrocarbons. in Genome Announcements
 
Manconi, Andrea; Orro, Alessandro; Manca, Emanuele; Armano, Giuliano; Milanesi, Luciano (2014). GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads in PloS one
 
Viti F, Scaglione S, Orro A, Milanesi L. (2014)Guidelines for managing data and processes in bone and cartilage tissue engineering. in BMC Bioinformatics

D'Agostino D.; Pasquale G.; Clematis A.; Maj C.; Mosca E.; Milanesi L.; Merelli I. (2014)Parallel solutions for voxel-based simulations of reaction-diffusion systems in BioMed Research International

Ronchieri E.; Cesini D.; Dagostino D.; Ciaschini V.; Torre G.D.; Cozzi P.; Salomoni D.; Clematis A.; Milanesi L.; Merelli I. (2014)The WNoDeS cloud virtualization framework: A macromolecular surface analysis application case study in 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP 2014),Torino, Italia, 12-14 Febbraio 2014

Year 2013

Ettore Mosca, Ivan Merelli, Luciano Milanesi, Andrea Clematis, Daniele D'Agostino (2013)A Parallel Implementation of the Stau-DPP Stochastic Simulator for the Modelling of Biological Systems in 2013 21st Euromicro International Conference on Parallel, Distributed, and Network-Based Processing PDP, Belfast, 27th February - 1st March 2013

Bocchio-Chiavetto, Luisella; Maffioletti, Elisabetta; Bettinsoli, Paola; Giovannini, Caterina; Bignotti, Stefano; Tardito, Daniela; Corrada, Dario; Milanesi, Luciano; Gennarelli, Massimo (2013)Blood microRNA changes in depressed patients during antidepressant treatment in European neuropsychopharmacology

Daniele D'Agostino, Andrea Clematis, Alfonso Quarati, Daniele Cesini, Federica Chiappori, Luciano Milanesi, and Ivan Merelli (2013)Cloud Infrastructures for In Silico Drug Discovery: Economic and Practical Aspects in BioMed Research International; Hindawi Publishing Corporation, New York (Stati Uniti d'America)

Vezzoli, Giuseppe; Terranegra, Annalisa; Aloia, Andrea; Arcidiacono, Teresa; Milanesi, Luciano; Mosca, Ettore; Mingione, Alessandra; Spotti, Donatella; Cusi, Daniele; Hou, Jianghui; Hendy, Geoffrey N.; Soldati, Laura (2013)Decreased Transcriptional Activity of Calcium-sensing receptor Gene Promoter 1 Is Associated With Calcium Nephrolithiasis in The Journal of clinical endocrinology and metabolism

Cappelletti, M; Di Gennaro, P; D'Ursi, P; Orro, A; Mezzelani, A; Landini, M; Fedi, S; Frascari, D; Presentato, A; Zannoni, D; Milanesi, L (2013)Genome Sequence of Rhodococcus sp. Strain BCP1, a Biodegrader of Alkanes and Chlorinated Compounds. in genome announcements

Cichero, Elena; D'Ursi, Pasqualina; Moscatelli, Marco; Bruno, Olga; Orro, Alessandro; Rotolo, Chiara; Milanesi, Luciano; Fossa, Paola (2013)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 in Chemical biology & drug design (Print)

Pasqualina D'Ursi, Alessandro Orro a, Giulia Morra b, Marco Moscatelli ac, Gabriele Trombetti a, Luciano Milanesi, Ermanna Rovida  (2013)Molecular dynamics and docking simulation of a natural variant of Activated Protein C with impaired protease activity: implications for integrin-mediated antiseptic function. in Journal of biomolecular structure and dynamics; Taylor and Francis, Abingdon (Regno Unito)

Chiappori, Federica; Merelli, Ivan; Colombo, Giorgio; Milanesi, Luciano; Morra, Giulia (2013)Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations in Biophysical Society 57th annual meeting, Philadelphia, February 2-6, 2013

Longeri M, Ferrari P, Knafelz P, Mezzelani A, Marabotti A, Milanesi L, Pertica G, Polli M, Brambilla PG, Kittleson M, Lyons LA, Porciello F. (2013)Myosin-Binding Protein C DNA Variants in Domestic Cats (A31P, A74T, R820W) and their Association with Hypertrophic Cardiomyopathy in Journal of veterinary internal medicine

Mosca, Ettore; Milanesi, Luciano (2013)Network-based analysis of omics with multi-objective optimization in Molecular bioSystems

[Merelli, Ivan; Lio, Pietro; Milanesi, Luciano (2013)NuChart: An R Package to Study Gene Spatial Neighbourhoods with Multi-Omics Annotations in PloS one

Maj, Carlo; Mosca, Ettore; Merelli, Ivan; Mauri, Giancarlo; Milanesi, Luciano (2013)Sensitvity analysis for studying the relation between biochemical reaction and metabolic phenotypes in Journal of bioinformatics and computational biology

Merelli, Ivan; Calabria, Andrea; Cozzi, Paolo; Viti, Federica; Mosca, Ettore; Milanesi, Luciano (2013)SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS in BMC bioinformatics

Chiappori, Federica; Merelli, Ivan; Milanesi, Luciano; Marabotti, Anna (2013)Static and dynamic interactions between GALK enzyme and known inhibitors: Guidelines to design new drugs for galactosemic patients in European journal of medicinal chemistry

Pucciarelli, Sandra; Chiappori, Federica; Sparvoli, Daniela; Milanesi, Luciano; Miceli, Cristina; Melki, Ronald (2013)Tubulin folding: the special case of a beta-tubulin isotype from the Antarctic psychrophilic ciliate Euplotes focardii in Polar biology (Print)

Year 2012

Daniele D'Agostino; Andrea Clematis; Alessandro Guffanti; Luciano Milanesi; Ivan Merelli (2012)A CUDA-based implementation of the SSAKE Genomics Application in 20th Euromicro Conference on Parallel, Distributed and network-based Processing (Euromicro-PDP'12), Garching, Germany, 15-17 February, 2012

F. Viti, I. Merelli, S. Scaglione, L. Milanesi (2012)Bioinformatics approach for data management about bone cells grown on substitute materials in NETTAB workshop on Integrated Bio-Research

Mosca, Ettore; Alfieri, Roberta; Maj, Carlo; Bevilacqua, Annamaria; Canti, Gianfranco; Milanesi, Luciano (2012)Computational modeling of the metabolic States regulated by the kinase akt. in Frontiers in physiology

Mosca E., Alfieri R., Maj C., Bevilacqua A., Canti G., Milanesi L. (2012)Computational Modelling of the Metabolic States Regulated by the Kinase Akt in Frontiers in physiology

Tang M., Facchiano A., Rachamadugu R., Calderon F., Mao R., Milanesi L., Marabotti A., Lai K. (2012)Correlation Assessment among clinical phenotypes, expression analysis and molecular modeling of 14 novel variations in the human galactose-1-phosphate uridylyltransferase gene in Human mutation

Tang M, Facchiano A, Rachamadugu R, Calderon F, Mao R, Milanesi L, Marabotti A, Lai K (2012)Correlation assessment among clinical phenotypes, expression analysis and molecular modeling of 14 novel variations in the human galactose-1-phosphate uridylyltransferase gene. in Human mutation

A Orro, A Manconi, E Manca, G Armano, L Milanesi (2012)G-SNPM-A GPU-based SNP mapping tool in EMBnet journal

Salzano, Maria; Marabotti, Anna; Milanesi, Luciano; Facchiano, Angelo (2012)Human aryl-hydrocarbon receptor and its interaction with dioxin and physiological ligands investigated by molecular modeling and docking simulations (vol 413, pg 176, 2011) in Biochemical and biophysical research communications

Merelli I, Viti F, Milanesi L (2012)IBDsite: a Galaxy-interacting, integrative database for supporting Inflammatory Bowel Disease high throughput data analysis in BMC bioinformatics

Merelli I , Viti F , Milanesi L. (2012)IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis. in BMC bioinformatics

Manconi, Andrea; Vargiu, Eloisa; Armano, Giuliano; Milanesi, Luciano (2012)Literature retrieval and mining in bioinformatics: state of the art and challenges. in Advances in Bioinformatics

Bugatti A, Giagulli C, Urbinati C, Caccuri F, Chiodelli P, Oreste P, Fiorentini S, Orro A, Milanesi L, D'Ursi P, Caruso A, Rusnati M. (2012)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. in The Journal of biological chemistry

Salzano M, Marabotti A, Milanesi L, Facchiano A (2012)Molecular investigations of the interaction between the ligand-binding domain of the human aryl-hydrocarbon receptor and its endogenous ligands and xenobiotics from dietary sources in Biochemical and biophysical research communications

Maojo, Victor; Fritts, Martin; Martin-Sanchez, Fernando; De la Iglesia, Diana; Cachau, Raul E.; Garcia-Remesal, Miguel; Crespo, Jose; Mitchell, Joyce A.; Anguita, Alberto; Baker, Nathan; Maria Barreiro, Jose; Benitez, Sonia E.; De la Calle, Guillermo; Facelli, Julio C.; Ghazal, Peter; Geissbuhler, Antoine; Gonzalez-Nilo, Fernando; Graf, Norbert; Grangeat, Pierre; Hermosilla, Isabel; Hussein, Rada; Kern, Josipa; Koch, Sabine; Legre, Yannick; Lopez-Alonso, Victoria; Lopez-Campos, Guillermo; Milanesi, Luciano; Moustakis, Vassilis; Munteanu, Cristian; Otero, Paula; Pazos, Alejandro; Perez-Rey, David; Potamias, George; Sanz, Ferran; Kulikowski, Casimir (2012). Nanoinformatics: developing new computing applications for nanomedicine in Computing (Wien)

Viti F., Merelli I, Calabria A., Cozzi P., Mosca E.,Alfieri R., Milanesi L. (2012)Ontology-based resources for bioinformatics analysis. in International journal of metadata, semantics and ontologies

Maj C., Mosca E., Merelli I.,Mauri G., Milanesi L. (2012)Sensitivity analysis for unveiling the relation between biochemical reaction and metabolics phenotypes. in Journal of bioinformatics and computational biology

Facchiano A, Festa P, Marabotti A, Milanesi L, Musacchia F. (2012)Solving biclustering with a GRASP-like metaheuristic: Two case-studies on gene expression analysis. in Lecture notes in computer science

Chiappori, Federica; Pucciarelli, Sandra; Merelli, Ivan; Ballarini, Patrizia; Miceli, Cristina; Milanesi, Luciano (2012)Structural thermal adaptation of beta-tubulins from the Antarctic psychrophilic protozoan Euplotes focardii in Proteins

Mosca, Ettore; Barcella, Matteo; Alfieri, Roberta; Bevilacqua, Annamaria; Canti, Gianfranco; Milanesi, Luciano (2012)Systems biology of the metabolic network regulated by the Akt pathway in Biotechnology advances

Year 2011
  
Barbera, R.; Andronico, G.; Donvito, G.; Falzone, A.; Keijser, J. J.; La Rocca, G.; Milanesi, L.; Maggi, G. P.; Vicario, S. (2011)A grid portal with robot certificates for bioinformatics phylogenetic analyses in IWPLS 2009, e-Science Institute, 15 South College Street, Edinburgh, 14-15 Novembre 2009

Dimitrio, Luna; Natalini, Roberto; Milanesi, Luciano (2011)A Mathematical model for the enhanced cytoplasmic transport. How to Get (Faster) to the Nucleus in BIOINFORMATICS is part of BIOSTEC, the International Joint Conference on Biomedical Engineering Systems and Technologies, Roma, 26-29 Gennaio 2011

Malovini, Alberto; Illario, Maddalena; Iaccarino, Guido; Villa, Francesco; Ferrario, Anna; Roncarati, Roberta; Anselmi, Chiara Viviani; Novelli, Valeria; Cipolletta, Ersilia; Leggiero, Eleonora; Orro, Alessandro; Rusciano, Maria Rosaria; Milanesi, Luciano; Maione, Angela Serena; Condorelli, Gianluigi; Bellazzi, Riccardo; Puca, Annibale A. (2011) Association Study on Long-Living Individuals from Southern Italy Identifies rs10491334 in the CAMKIV Gene That Regulates Survival Proteins in Rejuvenation research

Musacchia F, Marabotti A, Facchiano A, Milanesi L, Festa P (2011)Biclustering of gene expression data based on GRASP-like algorithms in BITS2011 - VIII Annual Meeting of the Bioinformatics Italian Society, Pisa, Italy, 20-22 June 2011

Romano, Paolo; Milanesi, Luciano (2011)Complex Search, Ranks, and Biological Discovery: A User's Perspective in SeCO Workshop 2010, Como

Merelli, Ivan; Pescini, Dario; Mosca, Ettore; Cazzaniga, Paolo; Maj, Carlo; Mauri, Giancarlo; Milanesi, Luciano (2011)Grid Computing for Sensitivity Analysis of Stochastic Biological Models in Lecture notes in computer science

Cichero E, Ligresti A, Allarà M, di Marzo V, Lazzati Z, D'Ursi P, Marabotti A, Milanesi L, Spallarossa A, Ranise A, Fossa P. (2011)Homology modeling in tandem with 3D-QSAR analyses: a computational approach to depict the agonist binding site of the human CB2 receptor in European journal of medicinal chemistry

Salzano M, Marabotti A, Milanesi L, Facchiano A. (2011)Human aryl-hydrocarbon receptor and its interaction with dioxin and physiological ligands investigated by molecular modelling and docking simulations. in Biochemical and biophysical research communications

Merelli I., Cozzi P., D'Agostino D., Clematis A., Milanesi L. (2011)Image Based Surface Matching Algorithm Oriented to Structural Biology in IEEE/ACM transactions on computational biology and bioinformatics (Print)

Salzano M, Marabotti A, Milanesi L, Facchiano A (2011)Investigating the physiological role of human aryl hydrocarbon receptor in BITS2011 VIII Annual Meeting of the Bioinformatics Italian Society

Mosca, Ettore; Milanesi, Luciano (2011)Modeling Biochemical Pathways Springer Science and Business Media, New York (Stati Uniti d'America) in Mathematical Approaches to Polymer Sequence Analysis and Related Problems, 2011

Alfieri, R.; Bartocci, Ezio; Merelli, E.; Milanesi, Luciano (2011)Modeling the cell cycle: From deterministic models to hybrid systems in Biosystems (Amst. Print)

Corrada D., Viti F., Merelli I., Battaglia C., Milanesi L. (2011)myMIR: a genome-wide microRNA targets identification and annotation tool in Briefings in bioinformatics

Salvi, Erika; Orro, Alessandro; Guffanti, Guia; Lupoli, Sara; Torri, Federica; Barlassina, Cristina; Potkin, Steven; Cusi, Daniele; Macciardi, Fabio; Milanesi, Luciano (2011)Population Stratification Analysis in Genome-Wide Association Studies

Ruiz-Ruiz S, Navarro B, Gisel A, Peña L, Navarro L, Moreno P, Di Serio F, Flores RCitrus tristeza virus infection induces the accumulation of viral small RNAs (21- 24-nt) mapping preferentially at the 3'-terminal region of the genomic RNA and affects the host small RNA profile. Plant Mol Biol. 2011 Feb 15

Consiglio A, Grillo G, Licciulli F, Ceci LR, Liuni S, Losito N, Volpicella M, Gallerani R, De Leo F. PlantPIs–an interactive web resource on plant protease inhibitors. Curr Protein Pept Sci. 2011 Aug 1;12(5):448-54

Martelli PL, D'Antonio M, Bonizzoni P, Castrignanò T, D'Erchia AM, D'Onorio De Meo P, Fariselli P, Finelli M, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Rizzi R, Rossi I, Valletti A, Zauli A, Zambelli F, Casadio R, Pesole G. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Res. 2011 Jan;39(Database issue):D80-5. Epub 2010 Nov 4

A. Tulipano, C. Marangi, L. Angelini, G. Donvito, G. Cuscela, G. Maggi and A. Gisel GRID distribution supports clustering validation of large mixed microarray data. EMBnet.journal, vol 17, No 1.

Kurelac I, Lang M, Zuntini R, Calabrese C, Simone D, Vicario S, Santamaria M, Attimonelli M, Romeo G, Gasparre G. Searching for a needle in the haystack: Comparing six methods to evaluate heteroplasmy in difficult sequence context. Biotechnol Adv. 2011 Jun 13. [Epub ahead of print]

Castellana S, Vicario S, Saccone C. Evolutionary patterns of the mitochondrial genome in Metazoa: exploring the role of mutation and selection in mitochondrial protein coding genes. Genome Biol Evol. 2011 May 6. [Epub ahead of print]

Battagliero S, Puglia G, Vicario S, Rubino F, Scioscia G, Leo P. An Efficient Algorithm for Approximating Geodesic Distances in Tree Space. IEEE/ACM Trans Comput Biol Bioinform. 8(5):1196-1207, Nov 24. [Epub ahead of print]

Powell JR, Dion K, Papaceit M, Aguadé M, Vicario S, Garrick RC. Nonrecombining genes in a recombination environment: the Drosophila "dot" chromosome. Mol Biol Evol. 2011 Jan;28(1):825-33.
 

Year 2010

Federica Chiappori, Ivan Merelli, Luciano Milanesi, Ermanna Rovida Exploring the role of the phospholipid ligand in endothelial protein C receptor: A molecular dynamics study Proteins. , vol78(12), pp. 2679-90, DOI: 10.1002/prot.22782, 2010
 
Chiappori F, Pucciarelli S, Miceli C, Milanesi L. Structural thermal adaptation of ßtubulins from Euplotes focardii, an Antarctic psychrophilic protozoon. TAGp conference, LAPTH, AnnecyleVieux, France, 2010
 
Anna Marabotti and Angelo Facchiano Critical Assessment of Side Chain Conformation Prediction in Modelling of Single Point Amino Acid MutationAdv Exp Med Biol. 2010;680:283-9, 2010

 
Andrea Scirè, Anna Marabotti, Maria Staiano, Luisa Iozzino, Matthew S. Luchansky, Bryan S. Der, Jonathan D. Dattelbaum, Fabio Tanfani and Sabato D'AuriaAmino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stabilityMolecular BioSystems 6, 687-698 DOI: 10.1039/B922092E, 2010

Ettore Mosca, Roberta Alfieri, Ivan Merelli, Federica Viti, Andrea Calabria and Luciano MilanesiA multilevel data integration resource for breast cancer studyBMC Systems Biology 4:76, 2010
 
E. Mosca, M. Barcella, R. Alfieri, A. Bevilacqua, L. MilanesiA Systems Biology Approach for the Identification of Glycolysis Key Regulators in Cancer Cells14th International Biotechnology Symposium and Exhibition, 2010

M. Gnocchi, D. Ronzoni and L. MilanesiBiobanking semantic Multilanguage concepts management web system. 5th WP5 team meeting, Klagenfurt, Austria, February 2010

Ettore Mosca, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri, Luciano MilanesiModelling spatial heterogeneity and macromolecular crowding with membrane systemsMembrane computing - Lecture Notes in Computer Science, 2010

Ettore Mosca and Luciano MilanesiModeling Biochemical PathwaysMathematical approaches to polymer sequence analysis and related problems (ISBN: 978-1-4419-6799-2), 2010

A. Facchiano, A. MarabottiAnalysis of galactosemia-linked mutations of GALT enzyme using a computational biology approachProtein Engineering, Design & Selection vol. 23 no. 2 pp. 103-113, doi:10.1093/protein/gzp076, 2010

Paolo Cozzi, Federica Viti, Ivan Merelli and Luciano MilanesiExploitation of a 3D-oriented ontology for choosing the representative proteins in protein surfaces comparisonFOCUSk3D 2010, Sophia Antipolis, 2010

Erika Salvi, Alessandro Orro, Guia Guffanti, Sara Lupoli, Federica Torri, Cristina Barlassina, Steven Potkin, Daniele Cusi, Fabio Macciardi, Luciano MilanesiPopulation Stratification Analysis in Genome-Wide Association StudiesMathematical Approaches to Polymer Sequence Analysis and Related Problems (ISBN: 978-1-4419-6799-2), 2010

Andrea Calabria, Ettore Mosca, Federica Viti, Ivan Merelli, Luciano MilanesiSNPRanker: a tool for identification and scoring of SNPs associated to target genesJournal of Integrative Bioinformatics, 7(3):138, doi:10.2390/biecoll-jib-2010-138, 2010
 
Dario Corrada, Cristina Battaglia, Luciano MilanesiGenome-wide microRNA target gene identification and annotation using multiple prediction algorithms. BITS2010

 
Giuseppe Vezzoli, Annalisa Terranegra, Teresa Arcidiacono, Giovanni Gambaro, Luciano Milanesi, Ettore Mosca, Laura Soldati and On behalf of GENIAL network (Genetics and Environment in Nephrolithiasis Italian Alliance)Calcium kidney stones are associated with a haplotype of the calcium-sensing receptor gene regulatory region Nephrol Dial Transplant (2010) 25: 2245-2252, doi: 10.1093/ndt/gfp760
 
Anna Marabotti, Angelo FacchianoThe misure of terms in scientific literatureBioinformatics, Vol. 26 no. 19 2010, page 2498 doi:10.1093/bioinformatics/btq438
 
Federica Viti, Ivan Merelli, Andrea Calabria, Paolo Cozzi, Ettore Mosca, Roberta Alfieri, Luciano MilanesiOntology-based resources for bioinformatics AnalysisIJMSO, 2010
 
Ivan Merelli, Alessandro Guffanti, Marco Fabbri, Andrea Cocito, Laura Furia, Ursula Grazini, Raoul J. Bonnal, Luciano Milanesi, Fraser McBlaneRSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomesNucleic Acids Research, 1-6, doi:10.1093/nar/gkq391, 2010
 
Federica Torri, Anna Akelai, Sara Lupoli, Manuela Sironi, Daniela Amann-Zalcenstein, Matteo Fumagalli, Chiara Dal Fiume, Edna Ben-Asher, Kyra Kanyas, Rachele Cagliani, Paolo Cozzi, Gabriele Trombetti, Luisa Strik Lievers, Erika Salvi, Alessandro Orro, Jacques S. Beckmann, Doron Lancet, Yoav Kohn, Luciano Milanesi, Richard B. Ebstein, Bernard Lerer, Fabio MacciardiFine mapping of AHI1 as a schizophrenia susceptibility gene: from association to evolutionary evidenceThe FASEB Journal 2010; 24(8):3066-82. doi: 10.1096/fj.09-152611.

Matteo Gnocchi, Alessandro Orro, Davide Di Pasquale, Luciano MilanesiA web portal for management of biological data and applicationsISBN 978-88-95892-03-0 - INTERNATIONAL WORKSHOP ON SCIENCE GATEWAYS (IWSG 2010), 20-22 SEPTEMBER 2010, 54-59
 
Andrea Calabria, Davide Di Pasquale, Matteo Gnocchi, Paolo Alessandro Cozzi, Alessandro Orro, Gabriele Antonio Trombetti, Luciano MilanesiGrid Based Genome Wide Studies on Atrial FlutterJ Grid Computing (DOI: 10.1007/s10723-010-9163-y), July 2010
 
Alessandro Orro, Matteo Gnocchi, Andrea Calabria, Davide Di Pasquale, Luciano MilanesiGenetic Linkage Analysis on the Desktop Grid InfrastructureThird AlmereGrid Desktop Experience Workshop, Almere, 2010
 
Antonella Galizia, Federica Viti, Luciano Milanesi, Andrea ClematisA dynamic parallel approach to recognize tubular breast cancer for TMA image building18th Euromicro Conference on Parallel, Distributed and Network-based Processing (PDP2010), February 2010, Pisa, Italy, 2010
 
Paolo Cozzi, Ivan Merelli, Daniele D'Agostino, Luciano MilanesiA parallel implementation of Genetic Algorithms for parameters estimation of Molecular Surfaces similarity analysisBITS 2010

Moscatelli M., Bolzacchini E., D'Ursi P., Ferrero L., Gnocchi M., Lazzati Z., Orro A., Perrone M.G., Milanesi L. Bioinformatics infrastructure for the analysis of the relationships between particulate matter and human health VII Annual Meeting of the Bioinformatics Italian Society (BITS), April 14-16 2010 - Bari, Italy
 
Paolo Cazzaniga, Giancarlo Mauri, Luciano Milanesi, Ettore Mosca, Dario PesciniA Novel Variant of P Systems for the Modelling and Simulation of Biochemical SystemsLecture Notes in Computer Science, Volume 5957/2010, 210-226, DOI: 10.1007/978-3-642-11467-0_16 , 2010
 

Zelda Lazzati, Pasqualina D'Ursi, Alessandro Orro, Enzo Bolzacchini, Luciano MilanesiNuclear receptors database for predictive toxicity of EDCISB2010 - 14th International Biotechnology Symposium and Exhibition, Rimini, Italy, 2010
 
Z. Lzzati, P. D'Ursi, A. Orro, E. Bolzacchini, L. Ferrero, G. Sangiorgi, M.G. Perrone, M. Gnocchi, L. MilanesiAnalisi in silico dei meccanismi d'azione (MOA) correlati all'esposizione da particolato atmosferico: esame critico del caso del bisfenolo APM2010 - 4° convegno nazionale sul particolato atmosferico, Venezia, Italy

Pantaleo V, Saldarelli P, Miozzi L, Giampetruzzi A, Gisel A, Moxon S, Dalmay T, Bisztray G, Burgyan J. Deep sequencing analysis of viral short RNAs from an infected Pinot Noir grapevine. Virology. 2010 Dec 5;408(1):49-56. Epub 2010 Sep 26.

Di Serio F, Martínez de Alba AE, Navarro B, Gisel A, Flores R. RNA-dependent RNA polymerase 6 delays accumulation and precludes meristem invasion of a viroid that replicates in the nucleus. J Virol. 2010 Mar;84(5):2477-89. Epub 2009 Dec 16.

M. Ceci, C. Loglisci, E. Salvemini, D. D'Elia, D. MalerbaMining Spatial Association Rules for Composite Motif Discovery, (Book Chapter) (2010): 87-119. Mathematical Approaches to Polymer Sequence Analysis and Related Problems by Renato Bruni Editor. [Springer book page]

Grillo G, Turi A, Licciulli F, Mignone F, Liuni S, Banfi S, Gennarino VA, Horner DS, Pavesi G, Picardi E, Pesole G. UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAsNucleic Acids Res. 2010 Jan;38(Database issue):D75-80. Epub 2009 Oct 30

Horner DS, Pavesi G, Castrignanò T, De Meo PD, Liuni S, Sammeth M, Picardi E, Pesole G. Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing. Brief Bioinform. 2010 Mar;11(2):181-97. Epub 2009 Oct 27. Review.

Year 2009

Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F, Burgyán J. Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One. 2009 Nov 5;4(11):e7686.

Di Serio F, Gisel A, Navarro B, Delgado S, Martínez de Alba AE, Donvito G, Flores R. Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis. PLoS One. 2009 Oct 21;4(10):e7539.

Turi A, Loglisci C, Salvemini E, Grillo G, Malerba D, D'Elia D. Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining. BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S25.

D'Elia D, Gisel A, Eriksson NE, Kossida S, Mattila K, Klucar L, Bongcam-Rudloff E. The 20th anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community. BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S1.

M. Mirto, I. Epicoco, S. Fiore, M. Cafaro, A. Negro, D. Tartarini, D. Lezzi, O. Marra, A. Turi, A. Ferramosca, V. Zara, G. Aloisio, G. Donvito, L. Carota, G. Cuscela, G. P. Maggi, G. La Rocca, M. Mazzucato, S. My, G. Selvaggi, G. Scioscia, P. Leo, L. Di Pace, G. Pappada‘, V. Quinto, M. Berardi, F. Falciano, A. Emerson, E. Rossi, G. Lavorgna, A. Vanni, Lisa Bartoli, P. Di Lena, P. Fariselli, R. Fronza, L. Margara, L. Montanucci, P. L. Martelli, I. Rossi, M. Vassura, R. Casadio, T. Castrignan√ö, D. D‘Elia, G. Grillo, F. Licciulli, S. Liuni, A. Gisel, M. Santamaria, S. Vicario, C. Saccone, A. Anselmo, D. Horner, F. Mignone, G. Pavesi, E. Picardi, V. Piccolo, M. Re, F. Zambelli, G. Pesole. The LIBI Grid Platform for Bioinformatics (Handbook chapter) (2009)Handbook of Research on Computational Grid Technologies for Life Sciences, Biomedicine and Healthcare, IGI Global.

E. Bongcam-Rudloff, D. D'Elia, A. Gisel, S. Kossida, K. Mattila, L. KlucarProceedings from European Molecular Biology Network (EMBnet) Conference 2008: 20th Anniversary Celebration. Leading applications and technologies in bioinformatics. BMC Bioinformatics volume 10, Suppl 6 (2009).

Santamaria M, Vicario S, Pappadà G, Scioscia G, Scazzocchio C, Saccone C. Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria. BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S15.

Barbera R, Donvito G, Falzone A, La Rocca G, Milanesi L, Maggi GP, Vicario S. The GENIUS Grid Portal and robot certificates: a new tool for e-Science. BMC Bioinformatics. Jun 16;10 Suppl 6:S21.

Federica Chiappori, Pasqualina D'Ursi, Ivan Merelli, Luciano Milanesi, Ermanna RovidaIn silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case studyBMC Bioinformatics 2009, 10(Suppl 12):S3 doi: 10.1186/1471-2105-10-S12-S3
 
Pasqualina D'Ursi, Federica Chiappori, Ivan Merelli, Paolo Cozzi, Ermanna Rovida, Luciano MilanesiVirtual screening pipeline and ligand modelling for H5N1 neuraminidaseBiochemical and Biophysical Research Communications 383 (2009) pp. 445-449
 
Vincenzo Aurilia, Jean-Francois Rioux-Dube, Anna Marabotti, Michel Pezolet, Sabato D'AuriaStructure and Dynamics of Cold-Adapted Enzymes as Investigated by FT-IR Spectroscopy and MD. The Case of an Esterase from Pseudoalteromonas haloplanktisJ. Phys. Chem. B 2009, 113, 7753-7761
 
Dario Corrada, Pasqualina D'ursi, Sara Botti, Aldo Luperini, Luciano Milanesi, Ermanna Rovida3D-structure prediction of the modular protein Sialoadhesin using a multi-step modelling strategyBITS 2009

Roberta Alfieri, Matteo Barberis, Ferdinando Chiaradonna, Daniela Gaglio, Luciano Milanesi, Marco Vanoni, Edda Klipp, Lilia AlberghinaTowards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulationBMC Bioinformatics 2009, 10(Suppl 12):S16 doi: 10.1186/1471-2105-10-S12-S16
 
Roberta Alfieri, Luciano MilanesiMulti-Level Data Integration and Data Mining in Systems BiologyHandbook of Research on Systems Biology Applications in Medicine (ISBN 978-1-60566-076-9), 2009
 
Carlo MAJ, Roberta ALFIERI, Ettore MOSCA, Luciano MILANESITowards an integrative model for the calcium role in the neurodegenerative diseasesSBHSymposium 2009
 
Steven G. Potkin, Guia Guffanti, Anita Lakatos, Jessica A. Turner, Frithjof Kruggel, James H. Fallon, Andrew J. Saykin, Alessandro Orro, Sara Lupoli, Erika Salvi, Michael Weiner, Fabio MacciardiAlzheimer's Disease Neuroimaging Initiative Hippocampal Atrophy as a Quantitative Trait in a Genome-Wide Association Study Identifying Novel Susceptibility Genes for Alzheimer's DiseasePLoS One. 2009; 4(8): e6501. doi: 10.1371/journal.pone.0006501. 
 
Ettore Mosca, Gloria Bertoli, Eleonora Piscitelli, Laura Vilardo, Rolland A Reinbold, Ileana Zucchi, Luciano MilanesiIdentification of functionally related genes using data mining and data integration: a breast cancer case studyBMC Bioinformatics, 10(Suppl 12):S8 doi: 10.1186/1471-2105-10-S12-S8, 2009
 
Paolo Monciardini, Linda Cavaletti, Anna Ranghetti, Peter Schumann, Manfred Rohde, Ruggiero Bamonte, Margherita Sosio, Alessandra Mezzelani, Stefano DonadioNovel members of the family Micromonosporaceae, Rugosimonospora acidiphila gen. nov., sp. nov. And Rugosimonospora africana sp. nov. International Journal of Systematic and Evolutionary Microbiology (2009), 59, 2752-2758, DOI 10.1099/ijs.0.010231-0
 
Ivan Merelli, Andrea Caprera, Alessandra Stella, Marcello Del Corvo, Luciano Milanesi, Barbara LazzariThe Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collectionsBMC Bioinformatics 2009, 10(Suppl 12):S2 doi: 10.1186/1471-2105-10-S12-S2

Andrea Calabria, Davide Di Pasquale, Alessandro Orro, Gabriele Trombetti, Matteo Gnocchi, Luciano MilanesiGenetic linkage analysis challenges on a distributed grid environmentVOGiS Herald, vol. 13, issue 1, pp 96-101, 2009
 
L. Milanesi, A. Calabria, D. Di Pasquale, M. Gnocchi, A. Orro, G. TrombettiA HPC and Grid enabling framework for genetic linkage analysis of SNPsIl Nuovo Cimento, vol. 32 C, issue 2, pp 249-252, Ottobre 2009

P. Cozzi, I. Merelli, L. MilanesiA Visualization ToolKit based application for representing macromolecular surfacesLecture Notes in Computer Science 2009 Jun 23, Volume 5488/2009, 284-292, doi: 10.1007/978-3-642-02504-4_26,

M. Gnocchi and L. MilanesiGenomics and biomedical data management systemBITS 2009 Genova, Italy, 18-20 March 2009

E. Mosca, I. Merelli, R. Alfieri and L. MilanesiA distributed approach for parameter estimation in Systems Biology modelsIl Nuovo Cimento C, vol. 032, Issue 02, p.165-168 DOI 10.1393/ncc/i2009-10400-2, 2009
 
Ettore Mosca, Paolo Cazzaniga, Ivan Merelli, Dario Pescini, Giancarlo Mauri, Luciano MilanesiStochastic simulations on a grid framework for parameter sweep applications in biological modelsProceedings of the 2009 International Workshop on High Performance Computational Systems Biology (CoSBi, Trento, Italy), Pages: 33-42, ISBN:978-0-7695-3809-9, 2009
 
Ivan Merelli, Alessandro Orro, Daniele D'Agostino, Andrea Clematis, Luciano MilanesiA parallel protein surface reconstruction systemInt. J. Bioinformatics Research and Applications, Vol. 4, No. 3, 221-239, 2009

Zelda Lazzati, Pasqualina D'Ursi, Ermanna Rovida, Andrea Gambaro, Roberta Zangrando, Federica Chiappori, Luciano Milanesi, Enzo BolzacchiniA docking procedure for the identification of potential Bisphenol A' protein targets and characterization of the major environmental matrix involved in their pathwaysXXIII Congresso Nazionale della Società Chimica Italiana, Sorrento, Italy, 2009

Barbara Lazzari, Andrea Caprera, Alessandro Cestaro, Ivan Merelli, Marcello Del Corvo, Paolo Fontana, Luciano Milanesi, Riccardo Velasco, Alessandra StellaOntology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAsBMC Plant Biology 2009, 9:82 doi:10.1186/1471-2229-9-82, 2009

Year 2008

Nils-Einar Eriksson, Domenica D'Elia, Erik Bongcam-RudloffEMBnet, a brief history and a current pictureEMBnet.news, 2008, 14 (3), 3-6

G. Gadaleta, C.Saccone Chapter Organization and Evolution of Metazoan Mitochondrial Genomesin the book Dual Genome Coordination of Energy Biogenesis – edited by: Graziano Pesole,

David Horner and Marco Sardiello. Castrignanò T, D'Antonio M, Anselmo A, Carrabino D, D'Onorio DM, D'Erchia A, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Riva A, Rizzi R, Bonizzoni P, Pesole G. ASPicDB: A database resource for alternative splicing analysis Bioinformatics. 2008 May 15;24(10):1300-4. Epub 2008 Apr 3.

Meo, P. D'Onorio De; Carrabino, D.; D'Antonio, M.; D'Addabbo, A.; Liuni, S.; Mignone, F.; Pesole, G.; Ancona, N. HT-RLS: High-Throughput Web Tool for Analysis of DNA Microarray Data Using RLS classifiers Cluster Computing and the Grid, 2008. CCGRID'08. 8th IEEE International Symposium on Volume , Issue , 19-22 May 2008 Page(s):747 – 752.

De Grassi A., Lanave C., Saccone C. Genome duplication and gene-family evolution: the case of three OXPHOS gene families. Gene. 2008 Sep 15;421(1-2):1-6. Epub 2008 Jun 23. Review.

Mignone F, Anselmo A, Donvito G, Maggi GP, Grillo G, Pesole G. Genome-wide assessment of coding and non-coding conserved sequence tags in human and mouse genomes. BMC Genomics 2008, 9:277

G.P Maggi , D. D'Elia , A. Gisel, G. Donvito, G. Cuscela, G. La RoccaTutorial on Grid Computing. Satellite event of the EMBnet Conference 2008. EMBnet.news 14(4): 15-16, ISSN: 1023-4144

Anna Marabotti, Thierry Lefevre, Maria Staiano, Roberta Crescenzo, Antonio Varriale, Mosè Rossi, Michel Pèzolet, Sabato D'AuriaMutant bovine odorant-binding protein: Temperature affects the protein stability and dynamics as revealed by infrared spectroscopy and molecular dynamics simulationsProteins. 2008 Aug;72(2):769-78.

Anna Marabotti, Andrea Scire, Maria Staiano, Roberta Crescenzo, Vincenzo Aurilia, Fabio Tanfani, Sabato D'AuriaWild-Type and Mutant Bovine Odorant-Binding Proteins To Probe the Role of the Quaternary Structure Organization in the Protein Thermal StabilityJ Proteome Res. 2008 Dec;7(12):5221-9, 2008
 
Ivan Merelli, Paolo Cozzi, Daniele D'Agostino, Andrea Cleamatis, Luciano MilanesiImages based system for surface matching in macromolecular screeningProceedings of the 2008 IEEE International Conference on Bioinformatics and Biomedicine (ISBN:978-0-7695-3452-7), 2008
 
Paolo Cozzi, Ivan Merelli, Luciano MilanesiA Visualization ToolKit based application for representing macromolecular surfacesCIBB 2008

Alessandro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi, Luciano MilanesiSNPLims: a data management system for genome wide association studiesBMC Bioinformatics 2008, 9(Suppl 2):S13 doi:10.1186/1471-2105-9-S2-S13

Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano MilanesiThe cell cycle DB: a systems biology approach to cell cycle analysisNucleic Acids Research, 2008, Vol. 36, Database issue D641-D645, doi:10.1093/nar/gkm873
 
Federica Viti, Ivan Merelli, Andrea Caprera, Barbara Lazzari, Alessandra Stella, Luciano MilanesiOntology-based, Tissue MicroArray oriented, image centered tissue bankBMC Bioinformatics 2008, 9(Suppl 4):S4 doi:10.1186/1471-2105-9-S4-S4

Andrea Calabria, Davide Di Pasquale, Alessandro Orro, Gabriele Trombetti, Erika Salvi, Fabio Macciardi, Luciano MilanesiGenome wide linkage analysis using SNPs in high Performance distributed environmentsAmerican Society of Human Genetics, 58th Annual ASHG Meeting, Philadelphia Pennsylvania, 2008
 
Antonella Galizia, Federica Viti, Alessandro Orro, Daniele D'Agostino, Ivan Merelli, Luciano Milanesi, Andrea ClematisTMAinspect, an EGEE Framework for Tissue MicroArray image handlingEighth IEEE International Symposium on Cluster Computing and the Grid (CCGRID2008), May 2008, Lyon, France, 2008

Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, Luciano Milanesi, Alessandra Stella and Carlo PozziVersion VI of the ESTree db: an improved tool for peach transcriptome analysisBMC Bioinformatics 2008, 9(Suppl 2):S9 doi:10.1186/1471-2105-9-S2-S9
 
Francesca Panzitta, Andrea Caprera, Ivan Merelli, Luciano Milanesi, John L. Williams, Barbara Lazzari, Alessandra StellaMining the Bovine Genome with the Bovine SNP RetrieverJournal of Heredity 2008:99(6):696-698, doi:10.1093/jhered/esn044, 2008

Year 2007

D. D'EliaThe MitoRes database (2007) EMBnet.news, 2007, 13 (1), 19-22.

Lanave C, Colangelo AM, Saccone C, Alberghina L. Molecular evolution of the neurotrophin family members and their Trk receptors. Gene. 2007 Jun 1;394(1-2):1-12. Epub 2007 Feb 9.

Santamaria, M., Lanave, C., Vicario, S. and C. Saccone- Variability of the mitochondrial genome in mammals at the inter-species/intra-species boundary. Biol Chem. 2007 Sep;388(9):943-6. Review. 

Lioi, L., Galasso, I., Lanave, C., Daminati, M.G., Bollini, R. and F. Sparsoli. Evolutionary analysis of the APA genes in the Phaseolus genus: wild and cultivated bean species as sources of lectin-related resistance factors. Theor Appl Genet. 2007 Nov;115(7):959-70. Epub 2007 Aug 16.

Horner DS, Lefkimmiatis K, Reyes A, Gissi C, Saccone C, Pesole G. Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus. BMC Evol Biol. 2007 Feb 8;7:16.

Sbisà E, Catalano D, Grillo G, Licciulli F, Turi A, Liuni S, Pesole G, De Grassi A, Caratozzolo MF, D'Erchia AM, Navarro B, Tullo A, Saccone C, Gisel A. p53FamTaG : a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data. BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S20.

R.Maglietta, A.Piepoli, D.Catalano, F.Licciulli, M.Carella, S.Liuni, G.Pesole, F.Perri and N.Ancona. Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data. Bioinformatics 2007 Aug 15;23(16):2063-72.

Tulipano A, Donvito G, Licciulli F, Maggi G, Gisel A. Gene analogue finder: a GRID solution for finding functionally analogous gene products. BMC Bioinformatics. 2007 Sep 3;8:329.

Paolo D, Onorio De Meo, Danilo Carrabino, Nico Sanna, Tiziana Castrignanò, Giorgio Grillo, Flavio Licciulli, Sabino Liuni, Matteo Re, Flavio Mignone, Graziano Pesole. A High Performance grid-web service framework for the identification of √´conserved sequence tags. Future Generation Computer Systems 23 (2007) 371-381

Horner DS, Lefkimmiatis K, Reyes A, Gissi C, Saccone C, Pesole G. Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus. BMC Evol Biol. 2007 Feb 8;7:16.

Ermanna Rovida, Giuliana Merati, Pasqualina D'Ursi, Sara Zanardelli, Francesca Marino, Gessica Fontana, Giancarlo Castaman, Elena M. FaioniIdentification and Computationally-Based Structural Interpretation of Naturally Occurring Variants of Human Protein CHuman Mutation 28(4), pp. 345-355, 2007
 
Anna Marabotti, Giovanni Colonna, Angelo FacchianoNew Computational Strategy to Analyze the Interactions of ERa and ERb with Different ERE SequencesJournal of Computational Chemistry Volume 28, Issue 6, 2007

Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano MilanesiA data integration approach for cell cycle analysis oriented to model simulation in systems biologyBMC Systems Biology 2007, 1:35 doi:10.1186/1752-0509-1-35
 
Pasqualina D'Ursi, Francesca Marino, Andrea Caprera, Luciano Milanesi, Elena M Faioni and Ermanna RovidaProCMD: a database and 3D web resource for protein C mutantsBMC Bioinformatics 2007, 8(Suppl 1):S11 doi:10.1186/1471-2105-8-S1-S11

Alessandro Orro, Luciano MilanesiAn Agent Approach for Protein Function Analysis in a Grid InfrastructureStudies in Health Technology and Informatics, Volume 126, 2007: From Genes to Personalized HealthCare: Grid Solutions for the Life Sciences - Proceedings of HealthGrid 2007 (ISBN 978-1-58603-738-3), 2007

Ivan Porro, Livia Torterolo, Luca Corradi, Marco Fato, Adam Papadimitropoulos, Silvia Scaglione, Andrea Schenone, Federica VitiA Grid-based solution for management and analysis of microarrays in distributed experimentsBMC Bioinformatics 2007, 8(Suppl 1):S7 doi:10.1186/1471-2105-8-S1-S7, 2007
 
Federica Viti, Ivan Merelli, Antonella Galizia, Daniele D'agostino, Andrea Clematis And Luciano MilanesiTissue MicroArray: a Distributed Grid Approach for Image AnalysisStud Health Technol Inform. 2007;126:291-8, 2007
 
Gabriele A Trombetti, Raoul JP Bonnal, Ermanno Rizzi, Gianluca De Bellis, Luciano MilanesiData handling strategies for high throughput pyrosequencersBMC Bioinformatics 2007, 8(Suppl 1):S22 doi:10.1186/1471-2105-8-S1-S22, 2007
 
Gabriele A. Trombetti, Ivan Merelli, Alessandro Orro, Luciano MilanesiBGBlast: A BLAST Grid Implementation with Database Self-Updating and Adaptive ReplicationFrom Genes to Personalized HealthCare: Grid Solutions for the Life Sciences, IOS Press, 2007
 
G. Trombetti, I. Merelli, A. Orro, L. MilanesiBioinfoGRIDBlast: a new approach at automatic database management, update and replication for Grid-enabled BLASTEGEE User Forum, Manchester, UK, 2007
 
Ivan Merelli, Giulia Morra, Luciano MilanesiEvaluation of a Grid Based Molecular Dynamics Approach for Polypeptide SimulationsIEEE Transactions On Nanobioscience, Vol. 6, No. 3, 2007
 
Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Vinod Kasam, Hurng-Chun Lee, Yannick Legrè, Simon C. Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli, Luciano Milanesi, Giulio Rastelli, Matthieu Reichstadt, Jean Salzemann, Horst Schwichtenberg, Ying-Ta Wu, Marc Zimmermann Virtual screening on large scale gridsParallel Computing 33 (2007) 289-301
 
Roberta ALFIERI, Ettore MOSCA, Ivan MERELLI, Luciano MILANESIParameter Estimation for Cell Cycle Ordinary Differential Equation (ODE) Models using a Grid ApproachStudies in Health Technology and Informatics, Volume 126, 2007

Andrea Caprera, Barbara Lazzari, Alessandra Stella, Ivan Merelli, Alexandre R. Caetano and Paola MarianiGoSh: a web-based database for goat and sheep EST sequencesBioinformatics Vol. 23 no. 8, pages 1043-1045, doi:10.1093/bioinformatics/btm063, 2007

Year 2006

Rè M, Mignone F, Iacono M, Grillo G, Liuni S, Pesole G. A new strategy to identify novel genes and gene isoforms: Analysis of human chromosomes 15, 21 and 22. Gene. 2006 Jan 3;365:35-40. Epub 2005 Dec 15.

Castrignanò T, De Meo PD, Grillo G, Liuni S, Mignone F, Talamo IG, Pesole G. GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags. Bioinformatics. 2006 Feb 15;22(4):497-9. Epub 2005 Nov 2.

D. D'Elia, A. Turi, F. Licciulli, D. Catalano, C. SacconeThe MitoDrome database and recent developments. EMBnet.news, 2006, 12 (1), 6-11

Catalano D, Licciulli F, Turi A, Grillo G, Saccone C, D'Elia D. MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. BMC Bioinformatics. 2006 Jan 24;7:36.

De Grassi A, Lanave C, Saccone C. Evolution of ATP synthase subunit c and cytochrome c gene families in selected Metazoan classes. Gene. 2006 Apr 26;371(2):224-33. Epub 2006 Feb 7.

Saccone C, Lanave C, De Grassi A. Metazoan OXPHOS gene families: evolutionary forces at the level of mitochondrial and nuclear genomes. Biochim Biophys Acta. 2006 Sep-Oct;1757(9-10):1171-8. Epub 2006 May 4. Review. 

D'Elia D, Catalano D, Licciulli F, Turi A, Tripoli G, Porcelli D, Saccone C, Caggese C. The MitoDrome database annotates and compares the OXPHOS nuclear genes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae. Mitochondrion. 2006 Oct;6(5):252-7. Epub 2006 Jul 21.

Domenico Catalano, Flavio Licciulli, Antonio Turi, Giorgio Grillo, Cecilia Saccone, Domenica D'Elia.  What the MitoRes Database Provides and How to Use It MitoMatters, Volume 5, Issue 1, 2006, Pages 3-5

R. Maglietta, A. D‘Addabbo, A. Piepoli, F. Perri, S. Liuni, G. Pesole and N. AnconaSelection of relevant genes in cancer diagnosis based on their prediction accuracy. Artificial Intelligence in Medicine, Aug. 18

Ancona N., Maglietta R., Piepoli A., D‘Addabbo A., Cotugno R., Savino M., Liuni S., Carella M., Pesole G., and Perri F. On the statistical assessment of classifier using DNA microarray data. BMC Bioinformatics Aug 19; 7-387

R. Maglietta, A. D'Addabbo, A. Piepoli, F. Perri, S. Liuni, G. Pesole and N. AnconaClassification error as a measure of gene relevance in cancer diagnosis. International Joint Conference on Neural Networks, Vancouver, BC, Canada

T. Castrignanò, P. D'Onorio De Meo, G. Grillo, S. Liuni, F. Mignone, I. G. Talamo, and G. Pesole.  GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags. Bioinformatics, Vol 22(4), 497-9.

G.A. Trombetti, I. Merelli, L. MilanesiHigh performance cDNAsequence analysis using grid technologyJ. Parallel Distrib. Comput. 66 (2006) 1482-1488, 2006

Hurng-Chun Lee, Jean Salzemann, Nicolas Jacq, Hsin-Yen Chen, Li-Yung Ho, Ivan Merelli, Luciano Milanesi, Vincent Breton, Simon C. Lin, and Ying-Ta WuGrid-Enabled High-Throughput In Silico Screening Against Influenza A NeuraminidaseIEEE Transactions On Nanobioscience, Vol. 5, No. 4, pp. 288-95, 2006

 


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