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2020 – today
- 2023
[j90]Valentina Nale, Alice Chiodi
, Noemi Di Nanni, Ingrid Cifola, Marco Moscatelli, Cinzia Cocola, Matteo Gnocchi, Eleonora Piscitelli, Ada Sula, Ileana Zucchi, Rolland A. Reinbold, Luciano Milanesi, Alessandra Mezzelani, Paride Pelucchi, Ettore Mosca:
scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. BMC Bioinform. 24(1): 445 (2023)- 2022
- [j89]Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek James Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, Jean-Baptiste Poline, Prasun Roy, Stephen C. Strother, Tong Boon Tang, Paul H. E. Tiesinga, Thomas Wachtler, Daniel K. Wójcik, Maryann E. Martone:
A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. Neuroinformatics 20(1): 25-36 (2022) - [j88]Mathew Birdsall Abrams, Jan G. Bjaalie, Samir Das, Gary F. Egan, Satrajit S. Ghosh, Wojtek James Goscinski, Jeffrey S. Grethe, Jeanette Hellgren Kotaleski, Eric Tatt Wei Ho, David N. Kennedy, Linda J. Lanyon, Trygve B. Leergaard, Helen S. Mayberg, Luciano Milanesi, Roman Moucek, Jean-Baptiste Poline, Prasun Roy, Stephen C. Strother, Tong Boon Tang, Paul H. E. Tiesinga, Thomas Wachtler, Daniel K. Wójcik, Maryann E. Martone:
Correction to: A Standards Organization for Open and FAIR Neuroscience: the International Neuroinformatics Coordinating Facility. Neuroinformatics 20(1): 37-38 (2022) - 2021
- [j87]Ettore Mosca, Matteo Bersanelli, Tommaso Matteuzzi, Noemi Di Nanni, Gastone C. Castellani, Luciano Milanesi, Daniel Remondini:
Characterization and comparison of gene-centered human interactomes. Briefings Bioinform. 22(6) (2021) - 2020
- [j86]Noemi Di Nanni, Matteo Gnocchi, Marco Moscatelli, Luciano Milanesi, Ettore Mosca:
Gene relevance based on multiple evidences in complex networks. Bioinform. 36(3): 865-871 (2020) - [j85]Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini:
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites. Bioinform. 36(5): 1622-1624 (2020) - [j84]Simone Pernice, Laura Follia, Gianfranco Balbo, Luciano Milanesi, Giulia Sartini, Niccoló Totis, Pietro Lió, Ivan Merelli, Francesca Cordero, Marco Beccuti:
Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice. Fundam. Informaticae 171(1-4): 367-392 (2020)
2010 – 2019
- 2019
- [j83]Noemi Di Nanni, Marco Moscatelli, Matteo Gnocchi, Luciano Milanesi, Ettore Mosca:
isma: an R package for the integrative analysis of mutations detected by multiple pipelines. BMC Bioinform. 20(1): 107:1-107:9 (2019) - [j82]Paolo Romano, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia, Alfonso Urso:
The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes. BMC Bioinform. 20-S(4): 125:1-125:9 (2019) - 2018
- [j81]Marco Moscatelli, Andrea Manconi, Mauro Pessina, Giovanni Fellegara, Stefano Rampoldi, Luciano Milanesi, Andrea Casasco, Matteo Gnocchi:
An infrastructure for precision medicine through analysis of big data. BMC Bioinform. 19-S(10): 257-267 (2018) - [j80]Stefano Beretta, Mauro Castelli, Luis Muñoz, Leonardo Trujillo, Yuliana Martínez, Ales Popovic, Luciano Milanesi, Ivan Merelli:
A Scalable Genetic Programming Approach to Integrate miRNA-Target Predictions: Comparing Different Parallel Implementations of M3GP. Complex. 2018: 4963139:1-4963139:13 (2018) - 2017
- [j79]Riccardo Panero, Antonio Rinaldi, Domenico Memoli, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Luciano Milanesi, Alessandro Weisz, Giorgio Giurato:
iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data. Bioinform. 33(6): 938-940 (2017) - [j78]Riccardo Panero, Antonio Rinaldi, Domenico Memoli, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, Luciano Milanesi, Alessandro Weisz, Giorgio Giurato:
iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data. Bioinform. 33(24): 4050 (2017) - [j77]Giulio Spinozzi, Andrea Calabria, Stefano Brasca, Stefano Beretta, Ivan Merelli, Luciano Milanesi, Eugenio Montini:
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites. BMC Bioinform. 18(1): 520:1-520:12 (2017) - [j76]Fabio Tordini, Maurizio Drocco, Claudia Misale, Luciano Milanesi, Pietro Liò, Ivan Merelli, Massimo Torquati, Marco Aldinucci:
NuChart-II: The road to a fast and scalable tool for Hi-C data analysis. Int. J. High Perform. Comput. Appl. 31(3): 196-211 (2017) - [c46]Stefano Beretta, Lucia Morganti, Elena Corni, Andrea Ferraro, Daniele Cesini, Daniele D'Agostino, Luciano Milanesi, Ivan Merelli:
Low-Power Architectures for miRNA-Target Genome Wide Analysis. PDP 2017: 309-312 - [i2]Carlo Maj, Elena Milanesi, Massimo Gennarelli, Luciano Milanesi, Ivan Merelli:
Epistasis analysis reveals associations between gene variants and bipolar disorder. PeerJ Prepr. 5: e3242 (2017) - 2016
- [j75]Gastone C. Castellani, Giulia Menichetti, Paolo Garagnani, Maria Giulia Bacalini, Chiara Pirazzini, Claudio Franceschi, Sebastiano Collino, Claudia Sala, Daniel Remondini, Enrico Giampieri, Ettore Mosca, Matteo Bersanelli, Silvia Vitali, Ìtalo Faria do Valle, Pietro Liò, Luciano Milanesi:
Systems medicine of inflammaging. Briefings Bioinform. 17(3): 527-540 (2016) - [j74]Yoli Shavit, Ivan Merelli, Luciano Milanesi, Pietro Liò:
How computer science can help in understanding the 3D genome architecture. Briefings Bioinform. 17(5): 733-744 (2016) - [j73]Luciano Milanesi, Alessandro Guffanti, Giancarlo Mauri, Marco Masseroli:
BITS 2015: the annual meeting of the Italian Society of Bioinformatics. BMC Bioinform. 17(S-12): 1-4 (2016) - [j72]Andrea Manconi, Marco Moscatelli, Giuliano Armano, Matteo Gnocchi, Alessandro Orro, Luciano Milanesi:
Removing duplicate reads using graphics processing units. BMC Bioinform. 17(S-12): 59-71 (2016) - [j71]Matteo Bersanelli, Ettore Mosca, Daniel Remondini, Enrico Giampieri, Claudia Sala, Gastone C. Castellani, Luciano Milanesi:
Methods for the integration of multi-omics data: mathematical aspects. BMC Bioinform. 17(S-2): 15 (2016) - [j70]Claudia Sala, Silvia Vitali, Enrico Giampieri, Ìtalo Faria do Valle, Daniel Remondini, Paolo Garagnani, Matteo Bersanelli, Ettore Mosca, Luciano Milanesi, Gastone C. Castellani:
Stochastic neutral modelling of the Gut Microbiota's relative species abundance from next generation sequencing data. BMC Bioinform. 17(S-2): 16 (2016) - [j69]Federica Chiappori, Luca Mattiazzi, Luciano Milanesi, Ivan Merelli:
A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study. BMC Bioinform. 17(S-4): 57 (2016) - [j68]Emanuele Manca, Andrea Manconi, Alessandro Orro, Giuliano Armano, Luciano Milanesi:
CUDA-quicksort: an improved GPU-based implementation of quicksort. Concurr. Comput. Pract. Exp. 28(1): 21-43 (2016) - [c45]Marco Moscatelli, Andrea Manconi, Matteo Gnocchi, Luciano Milanesi:
A Infrastructure for Disease Prevention and Precision Medicine. KDWeb 2016 - [c44]Stefano Beretta, Mauro Castelli, Yuliana Martínez, Luis Muñoz, Sara Silva, Leonardo Trujillo, Luciano Milanesi, Ivan Merelli:
A Machine Learning Approach for the Integration of miRNA-Target Predictions. PDP 2016: 528-534 - [c43]Elisabetta Ronchieri, Daniele D'Agostino, Luciano Milanesi, Ivan Merelli:
MicroRNA-Target Interaction: A Parallel Approach for Computing Pairing Energy. PDP 2016: 535-540 - 2015
- [c42]Fabio Tordini, Ivan Merelli, Pietro Liò, Luciano Milanesi, Marco Aldinucci:
NuchaRt: Embedding High-Level Parallel Computing in R for Augmented Hi-C Data Analysis. CIBB 2015: 259-272 - [c41]Fabio Tordini, Maurizio Drocco, Claudia Misale, Luciano Milanesi, Pietro Liò, Ivan Merelli, Marco Aldinucci:
Parallel Exploration of the Nuclear Chromosome Conformation with NuChart-II. PDP 2015: 725-732 - 2014
- [j67]Andrea Manconi, Alessandro Orro, Emanuele Manca, Giuliano Armano, Luciano Milanesi:
A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units. BMC Bioinform. 15(S-1): S10 (2014) - [j66]Federica Viti, Silvia Scaglione, Alessandro Orro, Luciano Milanesi:
Guidelines for managing data and processes in bone and cartilage tissue engineering. BMC Bioinform. 15(S-1): S14 (2014) - [j65]Daniele D'Agostino, Andrea Clematis, Sergio Decherchi, Walter Rocchia, Luciano Milanesi, Ivan Merelli:
CUDA accelerated molecular surface generation. Concurr. Comput. Pract. Exp. 26(10): 1819-1831 (2014) - [c40]Fabio Tordini, Maurizio Drocco, Ivan Merelli, Luciano Milanesi, Pietro Liò, Marco Aldinucci:
NuChart-II: A Graph-Based Approach for Analysis and Interpretation of Hi-C Data. CIBB 2014: 298-311 - [c39]Ivan Merelli, Ettore Mosca, Daniele Cesini, Elisabetta Ronchieri, Luciano Milanesi:
Evaluating mixed HTC/cloud approaches for parameter sweep applications in systems biology. IWBBIO 2014: 551-562 - [c38]Elisabetta Ronchieri, Daniele Cesini, Daniele D'Agostino, Vincenzo Ciaschini, Gianni Dalla Torre, Paolo Cozzi, Davide Salomoni, Andrea Clematis, Luciano Milanesi, Ivan Merelli:
The WNoDeS Cloud Virtualization Framework: A Macromolecular Surface Analysis Application Case Study. PDP 2014: 218-222 - [c37]Giulia Pasquale, Carlo Maj, Andrea Clematis, Ettore Mosca, Luciano Milanesi, Ivan Merelli, Daniele D'Agostino:
A CUDA Implementation of the Spatial TAU-Leaping in Crowded Compartments (STAUCC) Simulator. PDP 2014: 609-616 - 2013
- [j64]Ivan Merelli, Andrea Calabria, Paolo Cozzi, Federica Viti, Ettore Mosca, Luciano Milanesi:
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. BMC Bioinform. 14(S-1): S9 (2013) - [j63]Carlo Maj, Ettore Mosca, Ivan Merelli, Giancarlo Mauri, Luciano Milanesi:
Sensitivity Analysis for Studying the Relation between biochemical reactions and metabolic phenotypes. J. Bioinform. Comput. Biol. 11(1) (2013) - [c36]Mohammad Ali Moni, Pietro Liò, Luciano Milanesi:
Comparing Viral (HIV) and Bacterial (Staphylococcus aureus) Infection of the Bone Tissue. BIOINFORMATICS 2013: 196-201 - [c35]Ettore Mosca, Ivan Merelli, Luciano Milanesi, Andrea Clematis, Daniele D'Agostino:
A Parallel Implementation of the Stau-DPP Stochastic Simulator for the Modelling of Biological Systems. PDP 2013: 427-431 - 2012
- [j62]Andrea Manconi, Eloisa Vargiu, Giuliano Armano, Luciano Milanesi:
Literature Retrieval and Mining in Bioinformatics: State of the Art and Challenges. Adv. Bioinformatics 2012: 573846:1-573846:10 (2012) - [j61]Ivan Merelli, Federica Viti, Luciano Milanesi:
IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis. BMC Bioinform. 13(S-14): S5 (2012) - [j60]Victor Maojo, Martin Fritts, Fernando Martín-Sánchez, Diana de la Iglesia, Raul E. Cachau, Miguel García-Remesal, José Crespo, Joyce A. Mitchell, Alberto Anguita, Nathan A. Baker, José María Barreiro, Sonia E. Benitez, Guillermo de la Calle, Julio C. Facelli, Peter Ghazal, Antoine Geissbühler, Fernando D. González Nilo, Norbert M. Graf, Pierre Grangeat, Isabel Hermosilla, Rada Hussein, Josipa Kern, Sabine Koch, Yannick Legré, Victoria López-Alonso, Guillermo López-Campos, Luciano Milanesi, Vassilis Moustakis, Cristian R. Munteanu, Paula Otero, Alejandro Pazos, David Pérez-Rey, George Potamias, Ferran Sanz, Casimir A. Kulikowski:
Nanoinformatics: developing new computing applications for nanomedicine. Computing 94(6): 521-539 (2012) - [j59]Federica Chiappori, Ivan Merelli, Giorgio Colombo, Luciano Milanesi, Giulia Morra:
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations. PLoS Comput. Biol. 8(12) (2012) - [c34]Daniele D'Agostino, Andrea Clematis, Alessandro Guffanti, Luciano Milanesi, Ivan Merelli:
A CUDA-based Implementation of the SSAKE Genomics Application. PDP 2012: 612-616 - 2011
- [j58]Dario Corrada, Federica Viti, Ivan Merelli, Cristina Battaglia, Luciano Milanesi:
myMIR: a genome-wide microRNA targets identification and annotation tool. Briefings Bioinform. 12(6): 588-600 (2011) - [j57]Roberta Alfieri, Ezio Bartocci, Emanuela Merelli, Luciano Milanesi:
Modeling the cell cycle: From deterministic models to hybrid systems. Biosyst. 105(1): 34-40 (2011) - [j56]Roberto Barbera, Giuseppe Andronico, Giacinto Donvito, Alberto Falzone, J. J. Keijser, Giuseppe La Rocca, Luciano Milanesi, Giorgio Pietro Maggi, Saverio Vicario:
A grid portal with robot certificates for bioinformatics phylogenetic analyses. Concurr. Comput. Pract. Exp. 23(3): 246-255 (2011) - [j55]Federica Viti, Ivan Merelli, Andrea Calabria, Paolo Cozzi, Ettore Mosca, Roberta Alfieri, Luciano Milanesi:
Ontology-based resources for bioinformatics analysis. Int. J. Metadata Semant. Ontologies 6(1): 35-45 (2011) - [j54]Ivan Merelli, Paolo Cozzi, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi:
Image-Based Surface Matching Algorithm Oriented to Structural Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 8(4): 1004-1016 (2011) - [c33]Luna Dimitrio, Roberto Natalini, Luciano Milanesi:
A Mathematical Model for the Enhanced Cytoplasmic Transport - How to Get (Faster) to the Nucleus. BIOINFORMATICS 2011: 39-46 - [c32]Angelo M. Facchiano, Paola Festa, Anna Marabotti, Luciano Milanesi, Francesco Musacchia:
Solving Biclustering with a GRASP-Like Metaheuristic: Two Case-Studies on Gene Expression Analysis. CIBB 2011: 253-267 - [c31]Ivan Merelli, Dario Pescini, Ettore Mosca, Paolo Cazzaniga, Carlo Maj, Giancarlo Mauri, Luciano Milanesi:
Grid Computing for Sensitivity Analysis of Stochastic Biological Models. PaCT 2011: 62-73 - [c30]Daniele D'Agostino, Ivan Merelli, René L. Warren, Alessandro Guffanti, Luciano Milanesi, Andrea Clematis:
Parallelization of the SSAKE Genomics Application. PDP 2011: 326-330 - [p2]Ettore Mosca, Luciano Milanesi:
Modeling Biochemical Pathways. Mathematical Approaches to Polymer Sequence Analysis and Related Problems 2011: 111-126 - [p1]Erika Salvi, Alessandro Orro, Guia Guffanti, Sara Lupoli, Federica Torri, Cristina Barlassina, Steven G. Potkin, Daniele Cusi, Fabio Macciardi, Luciano Milanesi:
Population Stratification Analysis in Genome-Wide Association Studies. Mathematical Approaches to Polymer Sequence Analysis and Related Problems 2011: 177-196 - 2010
- [j53]Federica Viti, Ivan Merelli, Mieke Timmermans, Michael den Bakker, Francesco Beltrame, Peter Riegman, Luciano Milanesi:
Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study. BMC Bioinform. 11: 566 (2010) - [j52]Ettore Mosca, Roberta Alfieri, Ivan Merelli, Federica Viti, Andrea Calabria, Luciano Milanesi:
A multilevel data integration resource for breast cancer study. BMC Syst. Biol. 4: 76 (2010) - [j51]Andrea Calabria, Davide Di Pasquale, Matteo Gnocchi, Paolo Alessandro Cozzi, Alessandro Orro, Gabriele Antonio Trombetti, Luciano Milanesi:
Grid Based Genome Wide Studies on Atrial Flutter. J. Grid Comput. 8(4): 511-527 (2010) - [j50]Ettore Mosca, Cinzia Cocola, Davood Sabour, Paride Pelucchi, Giovanni Bertalot, Orazio Palumbo, Massimo Carella, Martin Götte, Hans R. Schöler, Rolland A. Reinbold, Ileana Zucchi, Luciano Milanesi:
Overlapping Genes May Control Reprogramming of Mouse Somatic Cells into Induced Pluripotent Stem Cells (iPSCs) and Breast Cancer Stem Cells. Silico Biol. 10(5-6): 207-221 (2010) - [j49]Andrea Calabria, Ettore Mosca, Federica Viti, Ivan Merelli, Luciano Milanesi:
SNPRanker: a tool for identification and scoring of SNPs associated to target genes. J. Integr. Bioinform. 7(3) (2010) - [j48]Ivan Merelli, Alessandro Guffanti, Marco Fabbri, Andrea Cocito, Laura Furia, Ursula Grazini, Raoul Jean Pierre Bonnal, Luciano Milanesi, Fraser McBlane:
RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes. Nucleic Acids Res. 38(Web-Server-Issue): 262-267 (2010) - [c29]Ettore Mosca, Paolo Cazzaniga, Dario Pescini, Giancarlo Mauri, Luciano Milanesi:
Modelling Spatial Heterogeneity and Macromolecular Crowding with Membrane Systems. Int. Conf. on Membrane Computing 2010: 285-304 - [c28]Daniele D'Agostino, Andrea Clematis, Ivan Merelli, Paolo Cozzi, Luciano Milanesi:
A Parallel Algorithm for Molecular Surface Matching Through Image Representation. PDP 2010: 387-394 - [c27]Antonella Galizia, Federica Viti, Andrea Clematis, Luciano Milanesi:
A Dynamic Parallel Approach to Recognize Tubular Breast Cancer for TMA Image Building. PDP 2010: 403-410 - [c26]Paolo Romano, Luciano Milanesi:
Complex Search, Ranks, and Biological Discovery: A User's Perspective. SeCO Workshop 2010: 226-235
2000 – 2009
- 2009
- [j47]Luciano Milanesi, Paolo Romano, Gastone C. Castellani, Daniel Remondini, Pietro Liò:
Trends in modeling Biomedical Complex Systems. BMC Bioinform. 10(S-12): 0 (2009) - [j46]Ivan Merelli, Andrea Caprera, Alessandra Stella, Marcello Del Corvo, Luciano Milanesi, Barbara Lazzari:
The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections. BMC Bioinform. 10(S-12): 2 (2009) - [j45]Federica Chiappori, Pasqualina D'Ursi, Ivan Merelli, Luciano Milanesi, Ermanna Rovida:
In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study. BMC Bioinform. 10(S-12): 3 (2009) - [j44]Ettore Mosca, Gloria Bertoli, Eleonora Piscitelli, Laura Vilardo, Rolland A. Reinbold, Ileana Zucchi, Luciano Milanesi:
Identification of functionally related genes using data mining and data integration: a breast cancer case study. BMC Bioinform. 10(S-12): 8 (2009) - [j43]Roberta Alfieri, Matteo Barberis, Ferdinando Chiaradonna, Daniela Gaglio, Luciano Milanesi, Marco Vanoni, Edda Klipp, Lilia Alberghina:
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. BMC Bioinform. 10(S-12): 16 (2009) - [j42]Roberto Barbera, Giacinto Donvito, Alberto Falzone, Giuseppe La Rocca, Luciano Milanesi, Giorgio Pietro Maggi, Saverio Vicario:
The GENIUS Grid Portal and robot certificates: a new tool for e-Science. BMC Bioinform. 10(S-6) (2009) - [c25]Roberto Barbera, Giacinto Donvito, Alberto Falzone, Giuseppe La Rocca, Giorgio Pietro Maggi, Saverio Vicario, Luciano Milanesi:
On the Performance of Large Scale Bayesian Phylogenetic Analyses with Grid Portals and Robot Certificates. IWPLS 2009 - [c24]Luciano Milanesi, Roberta Alfieri, Ettore Mosca, Federica Viti, Pasqualina D'Ursi, Ivan Merelli:
Sys-Bio Gateway: a Framework of Bioinformatics Database Resources Oriented to Systems Biology. IWPLS 2009 - [c23]Paolo Cazzaniga, Giancarlo Mauri, Luciano Milanesi, Ettore Mosca, Dario Pescini:
A Novel Variant of P Systems for the Modelling and Simulation of Biochemical Systems. Workshop on Membrane Computing 2009: 210-226 - [c22]Federica Viti, Ettore Mosca, Ivan Merelli, Andrea Calabria, Roberta Alfieri, Luciano Milanesi:
Ontological Enrichment of the Genes-to-Systems Breast Cancer Database. MTSR 2009: 171-182 - [c21]Daniele D'Agostino, Andrea Clematis, Ivan Merelli, Paolo Cozzi, Luciano Milanesi:
Parallel Decomposition of 3D Surfaces in Images of Local Descriptors for Molecular Screening. PDP 2009: 261-267 - 2008
- [j41]Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, Luciano Milanesi, Alessandra Stella, Carlo Pozzi:
Version VI of the ESTree db: an improved tool for peach transcriptome analysis. BMC Bioinform. 9(S-2) (2008) - [j40]Alessandro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi, Luciano Milanesi:
SNPLims: a data management system for genome wide association studies. BMC Bioinform. 9(S-2) (2008) - [j39]Mirko Francesconi, Daniel Remondini, Nicola Neretti, John M. Sedivy, Leon N. Cooper, Ettore Verondini, Luciano Milanesi, Gastone C. Castellani:
Reconstructing networks of pathways via significance analysis of their intersections. BMC Bioinform. 9(S-4) (2008) - [j38]Federica Viti, Ivan Merelli, Andrea Caprera, Barbara Lazzari, Alessandra Stella, Luciano Milanesi:
Ontology-based, Tissue MicroArray oriented, image centered tissue bank. BMC Bioinform. 9(S-4) (2008) - [j37]Ivan Merelli, Alessandro Orro, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi:
A parallel protein surface reconstruction system. Int. J. Bioinform. Res. Appl. 4(3): 221-239 (2008) - [j36]Chanchal K. Mitra, Luciano Milanesi:
An Unusal Distribution of 6-nt Sequences Near The Transcription Start Site. J. Integr. Bioinform. 5(2) (2008) - [j35]Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi:
The cell cycle DB: a systems biology approach to cell cycle analysis. Nucleic Acids Res. 36(Database-Issue): 641-645 (2008) - [c20]Ivan Merelli, Paolo Cozzi, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi:
Images Based System for Surface Matching in Macromolecular Screening. BIBM 2008: 397-401 - [c19]Richard Carl Van der Wath, Elizabeth van der Wath, Antonio Carapelli, Francesco Nardi, Francesco Frati, Luciano Milanesi, Pietro Liò:
Bayesian Phylogeny on Grid. BIRD 2008: 404-416 - [c18]Antonella Galizia, Federica Viti, Alessandro Orro, Daniele D'Agostino, Ivan Merelli, Luciano Milanesi, Andrea Clematis:
TMAinspect, an EGEE Framework for Tissue MicroArray Image Handling. CCGRID 2008: 741-746 - [c17]Paolo Cozzi, Ivan Merelli, Luciano Milanesi:
A Visualization ToolKit Based Application for Representing Macromolecular Surfaces. CIBB 2008: 284-292 - [c16]Antonella Galizia, Daniele D'Agostino, Andrea Clematis, Federica Viti, Alessandro Orro, Ivan Merelli, Luciano Milanesi:
Enabling Parallel TMA Image Analysis in a Grid Environment. CISIS 2008: 394-399 - [c15]Daniele D'Agostino, Andrea Clematis, Ivan Merelli, Luciano Milanesi, Matteo Coloberti:
A Grid Service based Parallel Molecular Surface Reconstruction System. PDP 2008: 455-462 - 2007
- [j34]Emanuela Merelli, Giuliano Armano, Nicola Cannata, Flavio Corradini, Mark d'Inverno, Andreas Doms, Phillip W. Lord, Andrew C. R. Martin, Luciano Milanesi, Steffen Möller, Michael Schroeder, Michael Luck:
Agents in bioinformatics, computational and systems biology. Briefings Bioinform. 8(1): 45-59 (2007) - [j33]Pasqualina D'Ursi, Francesca Marino, Andrea Caprera, Luciano Milanesi, Elena M. Faioni, Ermanna Rovida:
ProCMD: a database and 3D web resource for protein C mutants. BMC Bioinform. 8(S-1) (2007) - [j32]Barbara Lazzari, Andrea Caprera, Cristian Cosentino, Alessandra Stella, Luciano Milanesi, Angelo Viotti:
ESTuber db: an online database for Tuber borchii EST sequences. BMC Bioinform. 8(S-1) (2007) - [j31]Dietrich Rebholz-Schuhmann, Graham Cameron, Dominic Clark, Erik M. van Mulligen, Jean-Louis Coatrieux, Eva del Hoyo-Barbolla, Fernando Martín-Sánchez, Luciano Milanesi, Ivan Porro, Francesco Beltrame, Ioannis G. Tollis, Johan van der Lei:
SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics - exploring current scientific literature for emerging topics. BMC Bioinform. 8(S-1) (2007) - [j30]Paolo Romano, Ezio Bartocci, Guglielmo Bertolini, Flavio De Paoli, Domenico Marra, Giancarlo Mauri, Emanuela Merelli, Luciano Milanesi:
Biowep: a workflow enactment portal for bioinformatics applications. BMC Bioinform. 8(S-1) (2007) - [j29]Gabriele Antonio Trombetti, Raoul Jean Pierre Bonnal, Ermanno Rizzi, Gianluca De Bellis, Luciano Milanesi:
Data handling strategies for high throughput pyrosequencers. BMC Bioinform. 8(S-1) (2007) - [j28]Roberta Alfieri, Ivan Merelli, Ettore Mosca, Luciano Milanesi:
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. BMC Syst. Biol. 1: 35 (2007) - [j27]Daniel Remondini, Nicola Neretti, Claudio Franceschi, Paolo Tieri, John M. Sedivy, Luciano Milanesi, Gastone C. Castellani:
Networks from Gene Expression Time Series: Characterization of Correlation Patterns. Int. J. Bifurc. Chaos 17(7): 2477-2483 (2007) - [j26]Fedor A. Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury V. Kondrakhin, Alexey V. Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel:
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. Nucleic Acids Res. 35(Database-Issue): 550-556 (2007) - [j25]Jean-Yves Bansard, Dietrich Rebholz-Schuhmann, Graham Cameron, Dominic Clark, Erik M. van Mulligen, Francesco Beltrame, Eva del Hoyo-Barbolla, Fernando Martín-Sánchez, Luciano Milanesi, Ioannis G. Tollis, Johan van der Lei, Jean-Louis Coatrieux:
Medical Informatics and Bioinformatics: A Bibliometric Study. IEEE Trans. Inf. Technol. Biomed. 11(3): 237-243 (2007) - [c14]Gabriele Antonio Trombetti, Ivan Merelli, Alessandro Orro, Luciano Milanesi:
BGBlast: A BLAST Grid Implementation with Database Self-Updating and Adaptive Replication. HealthGrid 2007: 23-30 - [c13]Roberta Alfieri, Ettore Mosca, Ivan Merelli, Luciano Milanesi:
Parameter Estimation for Cell Cycle Ordinary Differential Equation (ODE) Models using a Grid Approach. HealthGrid 2007: 93-102 - [c12]Federica Viti, Ivan Merelli, Antonella Galizia, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi:
Tissue MicroArray: a Distributed Grid Approach for Image Analysis. HealthGrid 2007: 291-298 - [c11]Alessandro Orro, Luciano Milanesi:
An Agent Approach for Protein Function Analysis in a Grid Infrastructure. HealthGrid 2007: 314-321 - [c10]Antonella Galizia, Federica Viti, Daniele D'Agostino, Ivan Merelli, Luciano Milanesi, Andrea Clematis:
Experimenting Grid Protocols to Improve Privacy Preservation in Efficient Distributed Image Processing. PARCO 2007: 139-146 - [c9]Daniele D'Agostino, Ivan Merelli, Andrea Clematis, Luciano Milanesi, Alessandro Orro:
A Parallel Workflow for the Reconstruction of Molecular Surfaces. PARCO 2007: 147-154 - 2006
- [j24]Alessandro Orro, Luciano Milanesi:
An Agent System for Automatic Workflows Composition in Grid Environments. Int. Trans. Syst. Sci. Appl. 1(1): 59-66 (2006) - [j23]Paolo Romano, Guglielmo Bertolini, Flavio De Paoli, M. Fattore, Domenico Marra, Giancarlo Mauri, Emanuela Merelli, Ivan Porro, Silvia Scaglione, Luciano Milanesi:
Network integration of data and analysis of oncology interest. J. Integr. Bioinform. 3(1) (2006) - [j22]Gabriele Antonio Trombetti, Ivan Merelli, Luciano Milanesi:
High performance cDNA sequence analysis using grid technology. J. Parallel Distributed Comput. 66(12): 1482-1488 (2006) - [c8]Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Hurng-Chun Lee, Yannick Legré, Simon C. Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli, Luciano Milanesi, Giulio Rastelli, Matthieu Reichstadt, Jean Salzemann, Horst Schwichtenberg, Mahendrakar Sridhar, Vinod Kasam, Ying-Ta Wu, Marc Zimmermann:
Grid-Enabled High Throughput Virtual Screening. GCCB 2006: 45-59 - [c7]Luciano Milanesi, Ivan Merelli:
High Performance GRID Based Implementation for Genomics and Protein Analysis. HealthGrid 2006: 374-380 - [i1]Nicolas Jacq, Vincent Breton, Hsin-Yen Chen, Li-Yung Ho, Martin Hofmann, Hurng-Chun Lee, Yannick Legré, Simon C. Lin, Astrid Maaß, Emmanuel Medernach, Ivan Merelli, Luciano Milanesi, Giulio Rastelli, Matthieu Reichstadt, Jean Salzemann, Horst Schwichtenberg, Mahendrakar Sridhar, Vinod Kasam, Ying-Ta Wu, Marc Zimmermann:
Large Scale In Silico Screening on Grid Infrastructures. CoRR abs/cs/0611084 (2006) - 2005
- [j21]Giuliano Armano, Gianmaria Mancosu, Luciano Milanesi, Alessandro Orro, Massimiliano Saba, Eloisa Vargiu:
A Hybrid Genetic-Neural System for Predicting Protein Secondary Structure. BMC Bioinform. 6(S-4) (2005) - [j20]Pasqualina D'Ursi, Erika Salvi, Paola Fossa, Luciano Milanesi, Ermanna Rovida:
Modelling the interaction of steroid receptors with endocrine disrupting chemicals. BMC Bioinform. 6(S-4) (2005) - [j19]Manuela Helmer-Citterich, Rita Casadio, Alessandro Guffanti, Giancarlo Mauri, Luciano Milanesi, Graziano Pesole, Giorgio Valle, Cecilia Saccone:
Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. BMC Bioinform. 6(S-4) (2005) - [j18]Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Alessandra Stella, Luciano Milanesi, Carlo Pozzi:
ESTree db: a Tool for Peach Functional Genomics. BMC Bioinform. 6(S-4) (2005) - [j17]Ivan Merelli, Giulia Morra, Daniele D'Agostino, Andrea Clematis, Luciano Milanesi:
High performance workflow implementation for protein surface characterization using grid technology. BMC Bioinform. 6(S-4) (2005) - [j16]Luciano Milanesi, Mauro Petrillo, Leandra Sepe, Angelo Boccia, Nunzio D'Agostino, Myriam Passamano, Salvatore Di Nardo, Gianluca Tasco, Rita Casadio, Giovanni Paolella:
Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity. BMC Bioinform. 6(S-4) (2005) - [j15]Paolo Romano, Domenico Marra, Luciano Milanesi:
Web services and workflow management for biological resources. BMC Bioinform. 6(S-4) (2005) - [j14]Giuliano Armano, Luciano Milanesi, Alessandro Orro:
Using Secondary Structure Information to Perform Multiple Alignment. Trans. Comp. Sys. Biology 3: 78-88 (2005) - [c6]Ivan Merelli, Luciano Milanesi, Daniele D'Agostino, Andrea Clematis, Marco Vanneschi, Marco Danelutto:
Using Parallel Isosurface Extraction in Superficial Molecular Modeling. DFMA 2005: 288-294 - [c5]Igor B. Rogozin, B. A. Malyarchuk, Youri I. Pavlov, Luciano Milanesi:
From Context-Dependence of Mutations to Molecular Mechanisms of Mutagenesis. Pacific Symposium on Biocomputing 2005 - 2003
- [j13]Igor B. Rogozin, Vladimir N. Babenko, Luciano Milanesi, Youri I. Pavlov:
Computational analysis of mutation spectra. Briefings Bioinform. 4(3): 210-227 (2003) - 2002
- [j12]Vadim P. Valuev, Dmitry A. Afonnikov, Mikhail P. Ponomarenko, Luciano Milanesi, Nikolay A. Kolchanov:
ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro. Nucleic Acids Res. 30(1): 200-202 (2002) - 2001
- [j11]Igor B. Rogozin, Alexey V. Kochetov, Fyodor A. Kondrashov, Eugene V. Koonin, Luciano Milanesi:
Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. Bioinform. 17(10): 890-900 (2001) - 2000
- [j10]Igor B. Rogozin, V. I. Mayorov, M. V. Lavrentieva, Luciano Milanesi, L. R. Adkison:
Prediction and Phylogenetic Analysis of Mammalian Short Interspersed Elements (SINEs). Briefings Bioinform. 1(3): 260-274 (2000)
1990 – 1999
- 1999
- [j9]Luciano Milanesi, D. D'Angelo, Igor B. Rogozin:
GeneBuilder: interactive in silico prediction of gene structure. Bioinform. 15(7): 612-621 (1999) - [j8]Nikolay A. Kolchanov, Mikhail P. Ponomarenko, Anatoly S. Frolov, Elena A. Ananko, Fedor A. Kolpakov, Elena V. Ignatieva, Olga A. Podkolodnaya, T. N. Goryachkovskaya, Irina L. Stepanenko, Tatyana I. Merkulova, V. V. Babenko, Y. V. Ponomarenko, Alexey V. Kochetov, Nikolay L. Podkolodny, Denis G. Vorobiev, Sergey V. Lavryushev, Dmitry A. Grigorovich, Yury V. Kondrakhin, Luciano Milanesi, Edgar Wingender, Victor V. Solovyev, G. Christian Overton:
Integrated databases and computer systems for studying eukaryotic gene expression. Bioinform. 15(7): 669-686 (1999) - 1998
- [j7]Maria Giuseppina Campi, Paolo Romano, Luciano Milanesi, Domenico Marra, Maria Assunta Manniello, Beatrice Iannotta, Gabriella Rondanina, Elena Grasso, Tiziana Ruzzon, Leonardo Santi:
Molecular Probe Data Base (MPDB). Nucleic Acids Res. 26(1): 145-147 (1998) - [c4]Luciano Milanesi, M. Marsilli, Giancarlo Mauri, C. Rolfi, L. Uboldi:
Fragment assembly system for DNA sequencing projects. Mathematical Support for Molecular Biology 1998: 241-258 - [c3]Nikolay A. Kolchanov, Mikhail P. Ponomarenko, Alexander E. Kel, Yury V. Kondrakhin, Anatoly S. Frolov, Fedor A. Kolpakov, T. N. Goryachkovskaya, O. V. Kel, Elena A. Ananko, Elena V. Ignatieva, Olga A. Podkolodnaya, Vladimir N. Babenko, Irina L. Stepanenko, Aida G. Romashchenko, Tatyana I. Merkulova, Denis G. Vorobiev, Sergey V. Lavryushev, Y. V. Ponomarenko, Alexey V. Kochetov, G. B. Kolesov, Victor V. Solovyev, Luciano Milanesi, Nikolay L. Podkolodny, Edgar Wingender, T. Heinemeyer:
GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome. ISMB 1998: 95-104 - 1996
- [j6]Igor B. Rogozin, Luciano Milanesi, Nikolay A. Kolchanov:
Gene structure prediction using information on homologous protein sequence. Comput. Appl. Biosci. 12(3): 161-170 (1996) - [j5]Luciano Milanesi, Marco Muselli, P. Arrigo:
Hamming-Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes. Comput. Appl. Biosci. 12(5): 399-404 (1996) - [c2]Yury V. Kondrakhin, Fedor A. Kolpakov, Alexander E. Kel, Nikolay A. Kolchanov, Luciano Milanesi:
Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes. German Conference on Bioinformatics 1996: 247-250 - 1995
- [j4]Yury V. Kondrakhin, Alexander E. Kel, Nikolay A. Kolchanov, Aida G. Romashchenko, Luciano Milanesi:
Eukaryotic promoter recognition by binding sites for transcription factors. Comput. Appl. Biosci. 11(5): 477-488 (1995) - [c1]Alexander E. Kel, Yury V. Kondrakhin, Ph. A. Kolpakov, O. V. Kel, Aida G. Romashchenko, Edgar Wingender, Luciano Milanesi, Nikolay A. Kolchanov:
Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences. ISMB 1995: 197-205 - 1994
- [j3]Victor B. Strelets, Andrey A. Ptitsyn, Luciano Milanesi, Hwa A. Lim:
Data bank homology search algorithm with linear computation complexity. Comput. Appl. Biosci. 10(3): 319-322 (1994) - 1993
- [j2]Alexander E. Kel, Mikhail P. Ponomarenko, E. A. Likhachev, Yuri L. Orlov, I. V. Ischenko, Luciano Milanesi, Nikolay A. Kolchanov:
SITEVIDEO: a computer system for functional site analysis and recognition. Investigation of the human splice sites. Comput. Appl. Biosci. 9(6): 617-627 (1993) - 1992
- [j1]Victor B. Strelets, Ilya N. Shindyalov, Nikolay A. Kolchanov, Luciano Milanesi:
Fast, statistically based alignment of amino acid sequences on the base of diagonal fragments of DOT-matrices. Comput. Appl. Biosci. 8(6): 529-534 (1992)
Coauthor Index
[j85] [j84] [j80] [j77] [j76] [c46] [i2] [j74] [j69] [c44] [c43] [c42] [c41] [j65] [c40] [c39] [c38] [c37] [j64] [j63] [c35] [j61] [j59] [c34] [j58] [j55] [j54] [c31] [c30] [j53] [j52] [j49] [j48] [c28] [j46] [j45] [c24] [c22] [c21] [j41] [j38] [j37] [j35] [c20] [c18] [c17] [c16] [c15] [j28] [c14] [c13] [c12] [c10] [c9] [j22] [c8] [c7] [i1] [j17] [c6]
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