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Items: 1 to 20 of 35

1.

UNIPred-Web: a web tool for the integration and visualization of biomolecular networks for protein function prediction.

Perlasca P, Frasca M, Ba CT, Notaro M, Petrini A, Casiraghi E, Grossi G, Gliozzo J, Valentini G, Mesiti M.

BMC Bioinformatics. 2019 Aug 14;20(1):422. doi: 10.1186/s12859-019-2959-2.

2.

A GPU-based algorithm for fast node label learning in large and unbalanced biomolecular networks.

Frasca M, Grossi G, Gliozzo J, Mesiti M, Notaro M, Perlasca P, Petrini A, Valentini G.

BMC Bioinformatics. 2018 Oct 15;19(Suppl 10):353. doi: 10.1186/s12859-018-2301-4.

3.

Prediction of Human Phenotype Ontology terms by means of hierarchical ensemble methods.

Notaro M, Schubach M, Robinson PN, Valentini G.

BMC Bioinformatics. 2017 Oct 12;18(1):449. doi: 10.1186/s12859-017-1854-y.

4.

Imbalance-Aware Machine Learning for Predicting Rare and Common Disease-Associated Non-Coding Variants.

Schubach M, Re M, Robinson PN, Valentini G.

Sci Rep. 2017 Jun 7;7(1):2959. doi: 10.1038/s41598-017-03011-5.

5.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

6.

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

Smedley D, Schubach M, Jacobsen JOB, Köhler S, Zemojtel T, Spielmann M, Jäger M, Hochheiser H, Washington NL, McMurry JA, Haendel MA, Mungall CJ, Lewis SE, Groza T, Valentini G, Robinson PN.

Am J Hum Genet. 2016 Sep 1;99(3):595-606. doi: 10.1016/j.ajhg.2016.07.005. Epub 2016 Aug 25.

7.

Application of microwave irradiation for the removal of polychlorinated biphenyls from siloxane transformer and hydrocarbon engine oils.

Antonetti C, Licursi D, Raspolli Galletti AM, Martinelli M, Tellini F, Valentini G, Gambineri F.

Chemosphere. 2016 Sep;159:72-79. doi: 10.1016/j.chemosphere.2016.05.066. Epub 2016 Jun 6.

PMID:
27281539
8.

RANKS: a flexible tool for node label ranking and classification in biological networks.

Valentini G, Armano G, Frasca M, Lin J, Mesiti M, Re M.

Bioinformatics. 2016 Sep 15;32(18):2872-4. doi: 10.1093/bioinformatics/btw235. Epub 2016 Jun 2.

9.

UNIPred: Unbalance-Aware Network Integration and Prediction of Protein Functions.

Frasca M, Bertoni A, Valentini G.

J Comput Biol. 2015 Dec;22(12):1057-74. doi: 10.1089/cmb.2014.0110. Epub 2015 Sep 24.

PMID:
26402488
10.

Think globally and solve locally: secondary memory-based network learning for automated multi-species function prediction.

Mesiti M, Re M, Valentini G.

Gigascience. 2014 Apr 23;3:5. doi: 10.1186/2047-217X-3-5. eCollection 2014.

11.

A novel approach to the problem of non-uniqueness of the solution in hierarchical clustering.

Cattinelli I, Valentini G, Paulesu E, Borghese NA.

IEEE Trans Neural Netw Learn Syst. 2013 Jul;24(7):1166-73. doi: 10.1109/TNNLS.2013.2247058.

PMID:
24808531
12.

An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods.

Valentini G, Paccanaro A, Caniza H, Romero AE, Re M.

Artif Intell Med. 2014 Jun;61(2):63-78. doi: 10.1016/j.artmed.2014.03.003. Epub 2014 Mar 20.

13.

GOssTo: a stand-alone application and a web tool for calculating semantic similarities on the Gene Ontology.

Caniza H, Romero AE, Heron S, Yang H, Devoto A, Frasca M, Mesiti M, Valentini G, Paccanaro A.

Bioinformatics. 2014 Aug 1;30(15):2235-6. doi: 10.1093/bioinformatics/btu144. Epub 2014 Mar 22.

14.

Network-based drug ranking and repositioning with respect to DrugBank therapeutic categories.

Re M, Valentini G.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Nov-Dec;10(6):1359-71. doi: 10.1109/TCBB.2013.62.

15.

Hierarchical ensemble methods for protein function prediction.

Valentini G.

ISRN Bioinform. 2014 May 4;2014:901419. doi: 10.1155/2014/901419. eCollection 2014. Review.

16.

A neural network algorithm for semi-supervised node label learning from unbalanced data.

Frasca M, Bertoni A, Re M, Valentini G.

Neural Netw. 2013 Jul;43:84-98. doi: 10.1016/j.neunet.2013.01.021. Epub 2013 Feb 6.

17.

Regeneration-associated WNT signaling is activated in long-term reconstituting AC133bright acute myeloid leukemia cells.

Beghini A, Corlazzoli F, Del Giacco L, Re M, Lazzaroni F, Brioschi M, Valentini G, Ferrazzi F, Ghilardi A, Righi M, Turrini M, Mignardi M, Cesana C, Bronte V, Nilsson M, Morra E, Cairoli R.

Neoplasia. 2012 Dec;14(12):1236-48.

18.

A fast ranking algorithm for predicting gene functions in biomolecular networks.

Re M, Mesiti M, Valentini G.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1812-8. doi: 10.1109/TCBB.2012.114.

19.

Cancer module genes ranking using kernelized score functions.

Re M, Valentini G.

BMC Bioinformatics. 2012;13 Suppl 14:S3. doi: 10.1186/1471-2105-13-S14-S3. Epub 2012 Sep 7.

20.

A mathematical model for the validation of gene selection methods.

Muselli M, Bertoni A, Frasca M, Beghini A, Ruffino F, Valentini G.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1385-92. doi: 10.1109/TCBB.2010.83.

PMID:
21778526

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