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Items: 16

1.

Construction and Analysis of miRNA Regulatory Networks.

Mensi A, Bonnici V, Caligola S, Giugno R.

Methods Mol Biol. 2019;1970:121-167. doi: 10.1007/978-1-4939-9207-2_9.

PMID:
30963492
2.

Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics.

Aparo A, Bonnici V, Micale G, Ferro A, Shasha D, Pulvirenti A, Giugno R.

Interdiscip Sci. 2019 Mar;11(1):21-32. doi: 10.1007/s12539-019-00323-0. Epub 2019 Feb 21.

PMID:
30790228
3.

PanDelos: a dictionary-based method for pan-genome content discovery.

Bonnici V, Giugno R, Manca V.

BMC Bioinformatics. 2018 Nov 30;19(Suppl 15):437. doi: 10.1186/s12859-018-2417-6.

4.

Correction to: cuRnet: an R package for graph traversing on GPU.

Bonnici V, Busato F, Aldegheri S, Akhmedov M, Cascione L, Carmena AA, Bertoni F, Bombieri N, Kwee I, Giugno R.

BMC Bioinformatics. 2018 Nov 27;19(1):456. doi: 10.1186/s12859-018-2484-8.

5.

Arena-Idb: a platform to build human non-coding RNA interaction networks.

Bonnici V, Caro G, Constantino G, Liuni S, D'Elia D, Bombieri N, Licciulli F, Giugno R.

BMC Bioinformatics. 2018 Oct 15;19(Suppl 10):350. doi: 10.1186/s12859-018-2298-8.

6.

cuRnet: an R package for graph traversing on GPU.

Bonnici V, Busato F, Aldegheri S, Akhmedov M, Cascione L, Carmena AA, Bertoni F, Bombieri N, Kwee I, Giugno R.

BMC Bioinformatics. 2018 Oct 15;19(Suppl 10):356. doi: 10.1186/s12859-018-2310-3. Erratum in: BMC Bioinformatics. 2018 Nov 27;19(1):456.

7.

miRandola 2017: a curated knowledge base of non-invasive biomarkers.

Russo F, Di Bella S, Vannini F, Berti G, Scoyni F, Cook HV, Santos A, Nigita G, Bonnici V, Laganà A, Geraci F, Pulvirenti A, Giugno R, De Masi F, Belling K, Jensen LJ, Brunak S, Pellegrini M, Ferro A.

Nucleic Acids Res. 2018 Jan 4;46(D1):D354-D359. doi: 10.1093/nar/gkx854.

8.

Informational laws of genome structures.

Bonnici V, Manca V.

Sci Rep. 2016 Jun 29;6:28840. doi: 10.1038/srep28840.

9.

APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks.

Bonnici V, Busato F, Micale G, Bombieri N, Pulvirenti A, Giugno R.

Bioinformatics. 2016 Jul 15;32(14):2159-66. doi: 10.1093/bioinformatics/btw223. Epub 2016 Apr 29.

PMID:
27153658
10.

On the Variable Ordering in Subgraph Isomorphism Algorithms.

Bonnici V, Giugno R.

IEEE/ACM Trans Comput Biol Bioinform. 2017 Jan-Feb;14(1):193-203. doi: 10.1109/TCBB.2016.2515595. Epub 2016 Jan 7.

PMID:
26761859
11.

NetMatchStar: an enhanced Cytoscape network querying app.

Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A, Giugno R.

Version 2. F1000Res. 2015 Aug 5 [revised 2015 Jan 1];4:479. doi: 10.12688/f1000research.6656.2. eCollection 2015.

12.

DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference.

Alaimo S, Bonnici V, Cancemi D, Ferro A, Giugno R, Pulvirenti A.

BMC Syst Biol. 2015;9 Suppl 3:S4. doi: 10.1186/1752-0509-9-S3-S4. Epub 2015 Jun 1.

13.

Comprehensive reconstruction and visualization of non-coding regulatory networks in human.

Bonnici V, Russo F, Bombieri N, Pulvirenti A, Giugno R.

Front Bioeng Biotechnol. 2014 Dec 10;2:69. doi: 10.3389/fbioe.2014.00069. eCollection 2014.

14.

A knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs.

Russo F, Di Bella S, Bonnici V, Laganà A, Rainaldi G, Pellegrini M, Pulvirenti A, Giugno R, Ferro A.

BMC Genomics. 2014;15 Suppl 3:S4. doi: 10.1186/1471-2164-15-S3-S4. Epub 2014 May 6.

15.

GRAPES: a software for parallel searching on biological graphs targeting multi-core architectures.

Giugno R, Bonnici V, Bombieri N, Pulvirenti A, Ferro A, Shasha D.

PLoS One. 2013 Oct 22;8(10):e76911. doi: 10.1371/journal.pone.0076911. eCollection 2013.

16.

A subgraph isomorphism algorithm and its application to biochemical data.

Bonnici V, Giugno R, Pulvirenti A, Shasha D, Ferro A.

BMC Bioinformatics. 2013;14 Suppl 7:S13. doi: 10.1186/1471-2105-14-S7-S13. Epub 2013 Apr 22.

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