Alfredo Pulvirenti

Alfredo Pulvirenti

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Alfredo Pulvirenti

Alfredo Pulvirenti

Publications by authors named "Alfredo Pulvirenti"

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72Publications

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A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data.

Brief Bioinform 2019 Nov 18. Epub 2019 Nov 18.

Oncology, Nerviano Medical Sciences, Nerviano, Milan, Italy.

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http://dx.doi.org/10.1093/bib/bbz110DOI Listing
November 2019

Risk of Death Associated With Intravitreal Anti-Vascular Endothelial Growth Factor Therapy: A Systematic Review and Meta-analysis.

JAMA Ophthalmol 2019 Nov 21. Epub 2019 Nov 21.

Department of Neurosciences, Psychology, Drug Research and Child Health, University of Firenze and Azienda Ospedaliero Universitaria Careggi, Florence, Italy.

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http://dx.doi.org/10.1001/jamaophthalmol.2019.4636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6902107PMC
November 2019

TACITuS: transcriptomic data collector, integrator, and selector on big data platform.

BMC Bioinformatics 2019 Nov 22;20(Suppl 9):366. Epub 2019 Nov 22.

Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, Catania, 95125, Italy.

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http://dx.doi.org/10.1186/s12859-019-2912-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6873396PMC
November 2019

Computational Methods to Investigate the Impact of miRNAs on Pathways.

Methods Mol Biol 2019 ;1970:183-209

Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.

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http://dx.doi.org/10.1007/978-1-4939-9207-2_11DOI Listing
September 2019

Network-Based Drug Repositioning: Approaches, Resources, and Research Directions.

Methods Mol Biol 2019 ;1903:97-113

Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.

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http://dx.doi.org/10.1007/978-1-4939-8955-3_6DOI Listing
June 2019

Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics.

Interdiscip Sci 2019 Mar 21;11(1):21-32. Epub 2019 Feb 21.

Department of Computer Science, University of Verona, Verona, Italy.

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http://dx.doi.org/10.1007/s12539-019-00323-0DOI Listing
March 2019

A Subset of Patients With Autism Spectrum Disorders Show a Distinctive Metabolic Profile by Dried Blood Spot Analyses.

Front Psychiatry 2018 7;9:636. Epub 2018 Dec 7.

Child Neurology and Psychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.

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http://dx.doi.org/10.3389/fpsyt.2018.00636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6292950PMC
December 2018

INBIA: a boosting methodology for proteomic network inference.

BMC Bioinformatics 2018 07 9;19(Suppl 7):188. Epub 2018 Jul 9.

Department of Computer Science, University of Verona, Strada le Grazie 15, Verona, 37134, Italy.

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http://dx.doi.org/10.1186/s12859-018-2183-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069689PMC
July 2018

Electrocardiographic Evaluation in Patients With Spinal Muscular Atrophy: A Case-Control Study.

J Child Neurol 2018 06 24;33(7):487-492. Epub 2018 Apr 24.

4 Unit of Rare Diseases of the Nervous System in Childhood, Policlinico-Vittorio-Emanuele University Hospital, University of Catania, Italy.

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http://dx.doi.org/10.1177/0883073818767170DOI Listing
June 2018

Reply To: Neutrophil to Lymphocyte Ratio As a Risk Stratification Tool for Older Adults with Pneumonia.

J Am Geriatr Soc 2018 02 20;66(2):418-420. Epub 2017 Nov 20.

Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.

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http://dx.doi.org/10.1111/jgs.15210DOI Listing
February 2018

Current Knowledge and Computational Techniques for Grapevine Meta-Omics Analysis.

Front Plant Sci 2017 9;8:2241. Epub 2018 Jan 9.

Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.

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http://dx.doi.org/10.3389/fpls.2017.02241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5767322PMC
January 2018

Recommendation Techniques for Drug-Target Interaction Prediction and Drug Repositioning.

Methods Mol Biol 2016 ;1415:441-62

Department of Mathematics and Computer Science, University of Catania, Città Universitaria, viale Andrea Doria 6, 95125, Catania, Italy.

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http://link.springer.com/10.1007/978-1-4939-3572-7_23
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http://dx.doi.org/10.1007/978-1-4939-3572-7_23DOI Listing
December 2017

Re-challenge Studies in Non-celiac Gluten Sensitivity: A Systematic Review and Meta-Analysis.

Front Physiol 2017 5;8:621. Epub 2017 Sep 5.

Department of Pediatrics, Università Politecnica delle MarcheAncona, Italy.

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http://dx.doi.org/10.3389/fphys.2017.00621DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5591881PMC
September 2017

Neutrophil-To-Lymphocyte Ratio: An Emerging Marker Predicting Prognosis in Elderly Adults with Community-Acquired Pneumonia.

J Am Geriatr Soc 2017 Aug 13;65(8):1796-1801. Epub 2017 Apr 13.

Unit of Internal Medicine, Department of Clinical and Experimental Medicine, School of Emergency Medicine, University of Catania, Cannizzaro Hospital, Catania, Italy.

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http://dx.doi.org/10.1111/jgs.14894DOI Listing
August 2017

Mode of Delivery and Risk of Celiac Disease: Risk of Celiac Disease and Age at Gluten Introduction Cohort Study.

J Pediatr 2017 05 10;184:81-86.e2. Epub 2017 Feb 10.

Departments of Pediatrics, Marche Polytechnic University, Ancona, Italy; Center for Celiac Research, MassGeneral Hospital for Children and the Celiac Program, Harvard Medical School, Boston, MA. Electronic address:

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http://dx.doi.org/10.1016/j.jpeds.2017.01.023DOI Listing
May 2017

Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach.

Noncoding RNA 2017 Apr 19;3(2). Epub 2017 Apr 19.

Bioinformatics Unit, Department of Clinical and Experimental Medicine, University of Catania, c/o Dipartimento di Matematica e Informatica, Viale A. Doria 6, 95125 Catania, Italy.

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http://dx.doi.org/10.3390/ncrna3020020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5831934PMC
April 2017

KAOS: a new automated computational method for the identification of overexpressed genes.

BMC Bioinformatics 2016 Nov 8;17(Suppl 12):340. Epub 2016 Nov 8.

Business Unit Oncology, Nerviano Medical Sciences srl, Nerviano, MI, 20014, Italy.

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http://dx.doi.org/10.1186/s12859-016-1188-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5123341PMC
November 2016

Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification.

Oncotarget 2016 Aug;7(34):54572-54582

Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy.

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http://dx.doi.org/10.18632/oncotarget.9788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5342365PMC
August 2016

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

Bioinformatics 2016 07 29;32(14):2159-66. Epub 2016 Apr 29.

Department of Computer Science, University of Verona, Strada Le Grazie 15 - 37134, Verona Department of Clinical and Experimental Medicine, University of Catania, via Palermo, 636 - 95122, Catania.

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http://dx.doi.org/10.1093/bioinformatics/btw223DOI Listing
July 2016

OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder.

Database (Oxford) 2015 30;2015:bav069. Epub 2015 Jul 30.

Department of Clinical and Experimental Medicine, University of Catania, Viale A. Doria 6, Catania, Italy,

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http://dx.doi.org/10.1093/database/bav069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4519680PMC
March 2016

Geo-Epidemiology of Age-Related Macular Degeneration: New Clues Into the Pathogenesis.

Am J Ophthalmol 2016 Jan 24;161:78-93.e1-2. Epub 2015 Oct 24.

Department of Sciences for Health Promotion and Mother Child Care, University of Palermo, Palermo, Italy.

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http://dx.doi.org/10.1016/j.ajo.2015.09.031DOI Listing
January 2016

NetMatchStar: an enhanced Cytoscape network querying app.

F1000Res 2015 5;4:479. Epub 2015 Aug 5.

Department of Clinical and Experimental Medicine, University of Catania, Catania, 95125, Italy.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4642848PMC
http://dx.doi.org/10.12688/f1000research.6656.2DOI Listing
December 2015

Computational design of artificial RNA molecules for gene regulation.

Methods Mol Biol 2015 ;1269:393-412

Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, OH, USA.

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http://dx.doi.org/10.1007/978-1-4939-2291-8_25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425273PMC
September 2015

New approaches in hepatitis B vaccination for celiac disease.

Immunotherapy 2014 ;6(8):945-52

Department of Medical & Pediatric Science, University of Catania, Catania, Italy.

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http://dx.doi.org/10.2217/imt.14.64DOI Listing
July 2015

Celiac disease from a global perspective.

Best Pract Res Clin Gastroenterol 2015 Jun 14;29(3):365-79. Epub 2015 May 14.

Department of Paediatrics, Marche Polytechnic University, Ancona, Via Corridoni 11, 60123 Ancona, Italy; The Division of Paediatric Gastroenterology and Nutrition, Center for Celiac Research, MassGeneral Hospital for Children, 55 Fruit Street, Boston, MA 02114, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15216918150005
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http://dx.doi.org/10.1016/j.bpg.2015.05.004DOI Listing
June 2015

SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human.

Front Bioeng Biotechnol 2015 8;3:58. Epub 2015 May 8.

Department of Clinical and Molecular Biomedicine, University of Catania , Catania , Italy.

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http://dx.doi.org/10.3389/fbioe.2015.00058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424906PMC
May 2015

Knowledge in the Investigation of A-to-I RNA Editing Signals.

Front Bioeng Biotechnol 2015 24;3:18. Epub 2015 Feb 24.

Department of Clinical and Experimental Medicine, University of Catania , Catania , Italy.

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http://dx.doi.org/10.3389/fbioe.2015.00018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338823PMC
March 2015

ncPred: ncRNA-Disease Association Prediction through Tripartite Network-Based Inference.

Front Bioeng Biotechnol 2014 12;2:71. Epub 2014 Dec 12.

Department of Clinical and Experimental Medicine, University of Catania , Catania , Italy.

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http://dx.doi.org/10.3389/fbioe.2014.00071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264506PMC
January 2015

Helicobacter pylori infection and atopic diseases: is there a relationship? A systematic review and meta-analysis.

World J Gastroenterol 2014 Dec;20(46):17635-47

Elena Lionetti, Salvatore Leonardi, Angela Lanzafame, Maria Teresa Garozzo, Martina Filippelli, Stefania Tomarchio, Viviana Ferrara, Department of Pediatrics, University of Catania, 95100 Catania, Italy.

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http://dx.doi.org/10.3748/wjg.v20.i46.17635DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4265626PMC
December 2014

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

Front Bioeng Biotechnol 2014 10;2:69. Epub 2014 Dec 10.

Department of Clinical and Experimental Medicine, University of Catania , Catania , Italy.

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http://dx.doi.org/10.3389/fbioe.2014.00069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4261811PMC
December 2014

Introduction of gluten, HLA status, and the risk of celiac disease in children.

N Engl J Med 2014 Oct;371(14):1295-303

From the Departments of Pediatrics (E.L.) and Clinical and Molecular Biomedicine (A.P.), University of Catania, the Department of Pediatrics, San Paolo Hospital (S.C.), and the Department of Developmental Biomedicine, University of Bari (R.F.), Bari, the Department of Immunopathology and Allergology, Udine Hospital, Udine (E.T.), the Department of Pediatrics, Azienda Ospedaliera IRCCS Santa Maria Nuova Hospital, Reggio Emilia (S.A.), the Department of Pediatrics, Sapienza University of Rome, Rome (M.B.), the Department of Pediatrics, University of Turin, Turin (C.B.), the Department of Pediatrics, San Raffaele Hospital (G.B.), and the Department of Pediatrics, Vittore Buzzi Children's Hospital, Milan (G.Z.), the Department of Pediatrics, Bianchi Melacrino Morelli Hospital, Reggio Calabria (A.B.), Pediatric Gastroenterology Unit, Giannina Gaslini Institute, Genoa (E.C.), the Department of Pediatrics, University of Padua, Padua (G.G.), the Department of Pediatrics, Federico II University of Naples, Naples (M.G.L.), Pediatric Gastroenterology and Cystic Fibrosis Unit, University Hospital Gaetano Martino, Messina (S.P.), the Department of Pediatrics, Rovereto Hospital, Rovereto (Trento) (C.P.), the Department of Pediatrics, University of Pisa, Pisa (C.U.), and the Department of Pediatrics, Marche Polytechnic University, Ancona (C.C.) - all in Italy; and the Division of Pediatric Gastroenterology and Nutrition and Center for Celiac Research, MassGeneral Hospital for Children (A.F.), and the Celiac Program, Harvard Medical School (A.F., C.C.) - both in Boston.

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http://dx.doi.org/10.1056/NEJMoa1400697DOI Listing
October 2014

GASOLINE: a Cytoscape app for multiple local alignment of PPI networks.

F1000Res 2014 1;3:140. Epub 2014 Jul 1.

Department of Clinical and Molecular Biomedicine, University of Catania, Catania, 95125, Italy.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4197741PMC
http://dx.doi.org/10.12688/f1000research.4537.2DOI Listing
October 2014

Proteins comparison through probabilistic optimal structure local alignment.

Front Genet 2014 2;5:302. Epub 2014 Sep 2.

Department of Clinical and Molecular Biomedicine, University of Catania Catania, Italy.

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http://dx.doi.org/10.3389/fgene.2014.00302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151033PMC
September 2014

miR-Synth: a computational resource for the design of multi-site multi-target synthetic miRNAs.

Nucleic Acids Res 2014 May 13;42(9):5416-25. Epub 2014 Mar 13.

Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, 43210 USA.

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http://dx.doi.org/10.1093/nar/gku202DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4027198PMC
May 2014

Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics.

BMC Bioinformatics 2013 22;14 Suppl 7:S1. Epub 2013 Apr 22.

Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, I-20133, Italy.

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http://dx.doi.org/10.1186/1471-2105-14-S7-S1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633006PMC
December 2013

A subgraph isomorphism algorithm and its application to biochemical data.

BMC Bioinformatics 2013 22;14 Suppl 7:S13. Epub 2013 Apr 22.

Dept. Computer Science - University of Verona, Verona, 37134, Italy.

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http://dx.doi.org/10.1186/1471-2105-14-S7-S13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633016PMC
December 2013

VIRGO: visualization of A-to-I RNA editing sites in genomic sequences.

BMC Bioinformatics 2013 22;14 Suppl 7:S5. Epub 2013 Apr 22.

Department of Mathematics and Computer Science - University of Catania, Catania, Italy.

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http://dx.doi.org/10.1186/1471-2105-14-S7-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3837470PMC
December 2013

Integrated microRNA and mRNA signatures associated with survival in triple negative breast cancer.

PLoS One 2013 6;8(2):e55910. Epub 2013 Feb 6.

Department of Molecular Virology, Immunology and Medical Genetics, Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055910PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566108PMC
August 2013

Drug-target interaction prediction through domain-tuned network-based inference.

Bioinformatics 2013 Aug 29;29(16):2004-8. Epub 2013 May 29.

Department of Mathematics and Computer Science and Department of Clinical and Molecular Biomedicine, University of Catania, Catania, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btt307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722516PMC
August 2013

Elucidating the role of microRNAs in cancer through data mining techniques.

Adv Exp Med Biol 2013 ;774:291-315

Department of Clinical and Molecular Biomedicine, University of Catania, Catania, Italy.

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http://dx.doi.org/10.1007/978-94-007-5590-1_15DOI Listing
June 2013

Extracellular circulating viral microRNAs: current knowledge and perspectives.

Front Genet 2013 24;4:120. Epub 2013 Jun 24.

Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University Columbus, OH, USA.

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http://dx.doi.org/10.3389/fgene.2013.00120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3690336PMC
June 2013

A pilot study on neurological manifestations and antibodies against antigens in children with hematological and other cancers.

Eur J Paediatr Neurol 2013 Jan 11;17(1):97-101. Epub 2012 Aug 11.

National Centre for Rare Diseases, Superior Institute of Health (ISS), Rome, Italy.

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http://dx.doi.org/10.1016/j.ejpn.2012.06.006DOI Listing
January 2013

miR-EdiTar: a database of predicted A-to-I edited miRNA target sites.

Bioinformatics 2012 Dec 7;28(23):3166-8. Epub 2012 Oct 7.

Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3509495PMC
December 2012

Tools and collaborative environments for bioinformatics research.

Brief Bioinform 2011 Nov 7;12(6):549-61. Epub 2011 Oct 7.

Bioinformatics, National Cancer Research Institute (IST), Genoa, Italy.

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http://dx.doi.org/10.1093/bib/bbr055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220874PMC
November 2011

The NETTAB 2009 workshop.

Brief Bioinform 2011 Nov;12(6):547-8

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http://dx.doi.org/10.1093/bib/bbr068DOI Listing
November 2011

Prediction of human targets for viral-encoded microRNAs by thermodynamics and empirical constraints.

J RNAi Gene Silencing 2010 May 24;6(1):379-85. Epub 2010 May 24.

Department of Mathematics and Computer Science, University of Catania, Italy.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902144PMC
May 2010

SIGMA: a set-cover-based inexact graph matching algorithm.

J Bioinform Comput Biol 2010 Apr;8(2):199-218

Dipartimento di Matematica ed Informatica, Università di Catania, V.le A. Doria, 6, Catania, 95125, Italy.

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http://dx.doi.org/10.1142/s021972001000477xDOI Listing
April 2010

SING: subgraph search in non-homogeneous graphs.

BMC Bioinformatics 2010 Feb 19;11:96. Epub 2010 Feb 19.

Dipartimento di Matematica ed Informatica, Università di Catania, Catania, Italy.

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http://dx.doi.org/10.1186/1471-2105-11-96DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2850364PMC
February 2010

GraphFind: enhancing graph searching by low support data mining techniques.

BMC Bioinformatics 2008 Apr 25;9 Suppl 4:S10. Epub 2008 Apr 25.

Dipartimento di Matematica e Informatica, Università di Catania, Catania, 95125, Italy.

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http://dx.doi.org/10.1186/1471-2105-9-S4-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2367637PMC
April 2008

Sequence similarity is more relevant than species specificity in probabilistic backtranslation.

BMC Bioinformatics 2007 Feb 21;8:58. Epub 2007 Feb 21.

Dipartimento di Matematica e Informatica, Università di Catania, Viale A, Doria 6, I-95125 Catania, Italy.

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http://dx.doi.org/10.1186/1471-2105-8-58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810562PMC
February 2007

In vitro and in silico cloning of Xenopus laevis SOD2 cDNA and its phylogenetic analysis.

DNA Cell Biol 2005 Feb;24(2):111-6

Dipartimento di Scienze Biomediche, Sezione di Biologia e Genetica, Università di Catania, Catania, Italy.

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http://dx.doi.org/10.1089/dna.2005.24.111DOI Listing
February 2005