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Ivan Merelli
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2020 – today
- 2023
- [j47]Ivan Merelli, Stefano Beretta, Daniela Cesana, Alessandro Gennari, Fabrizio Benedicenti, Giulio Spinozzi
, Daniele Cesini, Eugenio Montini, Daniele D'Agostino, Andrea Calabria
InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration. Database J. Biol. Databases Curation 2023 (2023) - 2021
- [j46]Daniele D'Agostino, Pietro Liò
Advantages of using graph databases to explore chromatin conformation capture experiments. BMC Bioinform. 22-S(2): 43 (2021) - [j45]Paolo Cazzaniga, Maria Raposo
Selected papers from the 15th and 16th international conference on Computational Intelligence Methods for Bioinformatics and Biostatistics. BMC Bioinform. 22-S(2): 90 (2021) - [j44]Daniele D'Agostino
Hardware and Software Solutions for Energy-Efficient Computing in Scientific Programming. Sci. Program. 2021: 5514284:1-5514284:9 (2021) - [j43]Iacopo Colonnelli
StreamFlow: Cross-Breeding Cloud With HPC. IEEE Trans. Emerg. Top. Comput. 9(4): 1723-1737 (2021) - 2020
- [j42]Andrea Calabria
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites. Bioinform. 36(5): 1622-1624 (2020) - [j41]Ivan Merelli
Latest advances in parallel, distributed, and network-based processing. Concurr. Comput. Pract. Exp. 32(10) (2020) - [j40]Lucia Morganti
On low-power SoCs as storage bricks for Bioinformatics. Concurr. Comput. Pract. Exp. 32(10) (2020) - [j39]Luca Verderame
A secure cloud-edges computing architecture for metagenomics analysis. Future Gener. Comput. Syst. 111: 919-930 (2020) - [j38]Simone Pernice
Integrating Petri Nets and Flux Balance Methods in Computational Biology Models: a Methodological and Computational Practice. Fundam. Informaticae 171(1-4): 367-392 (2020) - [e2]Paolo Cazzaniga
Computational Intelligence Methods for Bioinformatics and Biostatistics - 16th International Meeting, CIBB 2019, Bergamo, Italy, September 4-6, 2019, Revised Selected Papers. Lecture Notes in Computer Science 12313, Springer 2020, ISBN 978-3-030-63060-7 [contents] - [i5]Iacopo Colonnelli, Barbara Cantalupo, Ivan Merelli, Marco Aldinucci:
StreamFlow: cross-breeding cloud with HPC. CoRR abs/2002.01558 (2020)
2010 – 2019
- 2019
- [j37]Andrea Tangherloni
GenHap: a novel computational method based on genetic algorithms for haplotype assembly. BMC Bioinform. 20-S(4): 172:1-172:14 (2019) - [j36]Daniele D'Agostino
Combining Edge and Cloud computing for low-power, cost-effective metagenomics analysis. Future Gener. Comput. Syst. 90: 79-85 (2019) - [j35]Daniele D'Agostino
SoC-based computing infrastructures for scientific applications and commercial services: Performance and economic evaluations. Future Gener. Comput. Syst. 96: 11-22 (2019) - [j34]Ivan Merelli
Exploiting Docker containers over Grid computing for a comprehensive study of chromatin conformation in different cell types. J. Parallel Distributed Comput. 134: 116-127 (2019) - [j33]Claudia Caudai
ChromStruct 4: A Python Code to Estimate the Chromatin Structure from Hi-C Data. IEEE ACM Trans. Comput. Biol. Bioinform. 16(6): 1867-1878 (2019) - [c45]Daniele D'Agostino, Pietro Liò
NeoHiC: A Web Application for the Analysis of Hi-C Data. CIBB 2019: 98-107 - [c44]Valentina Giansanti
Comparing Deep and Machine Learning Approaches in Bioinformatics: A miRNA-Target Prediction Case Study. ICCS (3) 2019: 31-44 - [c43]Valentina Giansanti
Parallel Computing in Deep Learning: Bioinformatics Case Studiesa. PDP 2019: 329-333 - [r2]Ivan Merelli:
Parallel Architectures for Bioinformatics. Encyclopedia of Bioinformatics and Computational Biology (1) 2019: 209-214 - [r1]Ivan Merelli:
Infrastructure for High-Performance Computing: Grids and Grid Computing. Encyclopedia of Bioinformatics and Computational Biology (1) 2019: 230-235 - 2018
- [j32]Stefano Beretta
A Scalable Genetic Programming Approach to Integrate miRNA-Target Predictions: Comparing Different Parallel Implementations of M3GP. Complex. 2018: 4963139:1-4963139:13 (2018) - [j31]Ivan Merelli
Low-power portable devices for metagenomics analysis: Fog computing makes bioinformatics ready for the Internet of Things. Future Gener. Comput. Syst. 88: 467-478 (2018) - [j30]Stefano Beretta, Mauro Castelli
Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: A Logistic Model Tree Solution. J. Comput. Biol. 25(10): 1091-1105 (2018) - [c42]Andrea Tangherloni
High Performance Computing for Haplotyping: Models and Platforms. Euro-Par Workshops 2018: 650-661 - [c41]Claudia Caudai, Monica Zoppè, Emanuele Salerno
Parallelizable Strategy for the Estimation of the 3D Structure of Biological Macromolecules. PDP 2018: 134-137 - [c40]Valentina Giansanti, Daniele D'Agostino
Computing Empirical P-Values for Estimating Gene-Gene Interactions in Genome-Wide Association Studies: A Parallel Computing Approach. PDP 2018: 406-409 - [c39]Lucia Morganti, Daniele Cesini, Elena Corni, Luca Lama
Low-Power Storage Bricks and Bioinformatics on Systems-On-Chip. PDP 2018: 635-638 - [e1]Ivan Merelli, Pietro Liò, Igor V. Kotenko:
26th Euromicro International Conference on Parallel, Distributed and Network-based Processing, PDP 2018, Cambridge, United Kingdom, March 21-23, 2018. IEEE Computer Society 2018, ISBN 978-1-5386-4975-6 [contents] - 2017
- [j29]Giulio Spinozzi
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites. BMC Bioinform. 18(1): 520:1-520:12 (2017) - [j28]Ivan Merelli, Paolo Cozzi
Porting bioinformatics applications from grid to cloud: A macromolecular surface analysis application case study. Int. J. High Perform. Comput. Appl. 31(3): 182-195 (2017) - [j27]Fabio Tordini
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) - [c38]Daniele D'Agostino
Performance and Economic Evaluations in Adopting Low Power Architectures: A Real Case Analysis. GECON 2017: 177-189 - [c37]Stefano Beretta, Carlo Maj, Ivan Merelli:
Rank miRNA: a web tool for identifying polymorphisms altering miRNA target sites. ICCS 2017: 1125-1134 - [c36]Fabio Tordini
Scientific Workflows on Clouds with Heterogeneous and Preemptible Instances. PARCO 2017: 605-614 - [c35]Lucia Morganti, Elena Corni, Andrea Ferraro, Daniele Cesini
Implementing a Space-Aware Stochastic Simulator on Low-Power Architectures: A Systems Biology Case Study. PDP 2017: 303-308 - [c34]Stefano Beretta, Lucia Morganti, Elena Corni, Andrea Ferraro, Daniele Cesini
Low-Power Architectures for miRNA-Target Genome Wide Analysis. PDP 2017: 309-312 - [i4]Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Merelli, Daniele Ramazzotti:
Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks. CoRR abs/1703.03041 (2017) - [i3]Carlo Maj, Elena Milanesi, Massimo Gennarelli, Luciano Milanesi
Epistasis analysis reveals associations between gene variants and bipolar disorder. PeerJ Prepr. 5: e3242 (2017) - [i2]Andrea Tangherloni, Simone Spolaor, Leonardo Rundo, Marco S. Nobile, Ivan Merelli, Paolo Cazzaniga, Daniela Besozzi, Giancarlo Mauri, Pietro Liò:
GenHap: A novel computational method based on genetic algorithms for haplotype assembly. PeerJ Prepr. 5: e3246 (2017) - 2016
- [j26]Yoli Shavit, Ivan Merelli, Luciano Milanesi
How computer science can help in understanding the 3D genome architecture. Briefings Bioinform. 17(5): 733-744 (2016) - [j25]Andrea Bracciali, Marco Aldinucci
PWHATSHAP: efficient haplotyping for future generation sequencing. BMC Bioinform. 17(S-11): 342 (2016) - [j24]Federica Chiappori
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) - [c33]Stefano Beretta, Mauro Castelli
Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks. IJCCI (ECTA) 2016: 217-224 - [c32]Stefano Beretta, Mauro Castelli
A Machine Learning Approach for the Integration of miRNA-Target Predictions. PDP 2016: 528-534 - [c31]Elisabetta Ronchieri
MicroRNA-Target Interaction: A Parallel Approach for Computing Pairing Energy. PDP 2016: 535-540 - 2015
- [c30]Giacomo Paschina, Luca Roverelli, Daniele D'Agostino
Clustering Protein Structures with Hadoop. CIBB 2015: 141-153 - [c29]Fabio Tordini, Ivan Merelli, Pietro Liò
NuchaRt: Embedding High-Level Parallel Computing in R for Augmented Hi-C Data Analysis. CIBB 2015: 259-272 - [c28]Fabio Tordini
Parallel Exploration of the Nuclear Chromosome Conformation with NuChart-II. PDP 2015: 725-732 - 2014
- [j23]Ivan Merelli
Latest advances in distributed, parallel, and graphic processing unit accelerated approaches to computational biology. Concurr. Comput. Pract. Exp. 26(10): 1699-1704 (2014) - [j22]Daniele D'Agostino
CUDA accelerated molecular surface generation. Concurr. Comput. Pract. Exp. 26(10): 1819-1831 (2014) - [c27]Daniele D'Agostino
A Fine-Grained CUDA Implementation of the Multi-objective Evolutionary Approach NSGA-II: Potential Impact for Computational and Systems Biology Applications. CIBB 2014: 273-284 - [c26]Fabio Tordini
NuChart-II: A Graph-Based Approach for Analysis and Interpretation of Hi-C Data. CIBB 2014: 298-311 - [c25]Horacio Emilio Pérez Sánchez, José M. Cecilia, Ivan Merelli:
The role of High Performance Computing in Bioinformatics. IWBBIO 2014: 494-506 - [c24]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 - [c23]Elisabetta Ronchieri
The WNoDeS Cloud Virtualization Framework: A Macromolecular Surface Analysis Application Case Study. PDP 2014: 218-222 - [c22]Giulia Pasquale
A CUDA Implementation of the Spatial TAU-Leaping in Crowded Compartments (STAUCC) Simulator. PDP 2014: 609-616 - 2013
- [j21]Ivan Merelli
SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS. BMC Bioinform. 14(S-1): S9 (2013) - [j20]Carlo Maj
Sensitivity Analysis for Studying the Relation between biochemical reactions and metabolic phenotypes. J. Bioinform. Comput. Biol. 11(1) (2013) - [c21]Ettore Mosca
A Parallel Implementation of the Stau-DPP Stochastic Simulator for the Modelling of Biological Systems. PDP 2013: 427-431 - 2012
- [j19]Ivan Merelli
IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis. BMC Bioinform. 13(S-14): S5 (2012) - [j18]Federica Chiappori
Molecular Mechanism of Allosteric Communication in Hsp70 Revealed by Molecular Dynamics Simulations. PLoS Comput. Biol. 8(12) (2012) - [c20]Daniele D'Agostino
A CUDA-based Implementation of the SSAKE Genomics Application. PDP 2012: 612-616 - 2011
- [j17]Dario Corrada, Federica Viti
myMIR: a genome-wide microRNA targets identification and annotation tool. Briefings Bioinform. 12(6): 588-600 (2011) - [j16]Federica Viti
Ontology-based resources for bioinformatics analysis. Int. J. Metadata Semant. Ontologies 6(1): 35-45 (2011) - [j15]Ivan Merelli
Image-Based Surface Matching Algorithm Oriented to Structural Biology. IEEE ACM Trans. Comput. Biol. Bioinform. 8(4): 1004-1016 (2011) - [c19]Ivan Merelli
Grid Computing for Sensitivity Analysis of Stochastic Biological Models. PaCT 2011: 62-73 - [c18]Daniele D'Agostino
Parallelization of the SSAKE Genomics Application. PDP 2011: 326-330 - 2010
- [j14]Federica Viti
Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study. BMC Bioinform. 11: 566 (2010) - [j13]Ettore Mosca
A multilevel data integration resource for breast cancer study. BMC Syst. Biol. 4: 76 (2010) - [j12]Andrea Calabria, Ettore Mosca
SNPRanker: a tool for identification and scoring of SNPs associated to target genes. J. Integr. Bioinform. 7(3) (2010) - [j11]Ivan Merelli
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) - [c17]Daniele D'Agostino
A Parallel Algorithm for Molecular Surface Matching Through Image Representation. PDP 2010: 387-394
2000 – 2009
- 2009
- [j10]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) - [j9]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) - [c16]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 - [c15]Federica Viti
Ontological Enrichment of the Genes-to-Systems Breast Cancer Database. MTSR 2009: 171-182 - [c14]Daniele D'Agostino
Parallel Decomposition of 3D Surfaces in Images of Local Descriptors for Molecular Screening. PDP 2009: 261-267 - 2008
- [j8]Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli
Version VI of the ESTree db: an improved tool for peach transcriptome analysis. BMC Bioinform. 9(S-2) (2008) - [j7]Federica Viti
Ontology-based, Tissue MicroArray oriented, image centered tissue bank. BMC Bioinform. 9(S-4) (2008) - [j6]Ivan Merelli
A parallel protein surface reconstruction system. Int. J. Bioinform. Res. Appl. 4(3): 221-239 (2008) - [j5]Roberta Alfieri
The cell cycle DB: a systems biology approach to cell cycle analysis. Nucleic Acids Res. 36(Database-Issue): 641-645 (2008) - [c13]Ivan Merelli
Images Based System for Surface Matching in Macromolecular Screening. BIBM 2008: 397-401 - [c12]Antonella Galizia
TMAinspect, an EGEE Framework for Tissue MicroArray Image Handling. CCGRID 2008: 741-746 - [c11]Paolo Cozzi
A Visualization ToolKit Based Application for Representing Macromolecular Surfaces. CIBB 2008: 284-292 - [c10]Antonella Galizia
Enabling Parallel TMA Image Analysis in a Grid Environment. CISIS 2008: 394-399 - [c9]Daniele D'Agostino
A Grid Service based Parallel Molecular Surface Reconstruction System. PDP 2008: 455-462 - 2007
- [j4]Andrea Caprera, Barbara Lazzari, Alessandra Stella, Ivan Merelli
GoSh: a web-based database for goat and sheep EST sequences. Bioinform. 23(8): 1043-1045 (2007) - [j3]Roberta Alfieri
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. BMC Syst. Biol. 1: 35 (2007) - [c8]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 - [c7]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 - [c6]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 - [c5]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 - [c4]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
- [j2]Gabriele Antonio Trombetti, Ivan Merelli
High performance cDNA sequence analysis using grid technology. J. Parallel Distributed Comput. 66(12): 1482-1488 (2006) - [c3]Nicolas Jacq, Vincent Breton
Grid-Enabled High Throughput Virtual Screening. GCCB 2006: 45-59 - [c2]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
- [j1]Ivan Merelli, Giulia Morra
High performance workflow implementation for protein surface characterization using grid technology. BMC Bioinform. 6(S-4) (2005) - [c1]Ivan Merelli
Using Parallel Isosurface Extraction in Superficial Molecular Modeling. DFMA 2005: 288-294
Coauthor Index
Pietro Liò
aka: Pietro Lió
aka: Pietro Lió
[j42] [j38] [j32] [j29] [j27] [c34] [i3] [j26] [j24] [c32] [c31] [c29] [c28] [j22] [c26] [c24] [c23] [c22] [j21] [j20] [c21] [j19] [j18] [c20] [j17] [j16] [j15] [c19] [c18] [j14] [j13] [j12] [j11] [c17] [j10] [j9] [c16] [c15] [c14] [j8] [j7] [j6] [j5] [c13] [c12] [c11] [c10] [c9] [j3] [c8] [c7] [c6] [c5] [c4] [j2] [c3] [c2] [i1] [j1] [c1]
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