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Expanded circulating hematopoietic stem/progenitor cells as novel cell source for the treatment of TCIRG1 osteopetrosis.

Capo V, Penna S, Merelli I, Barcella M, Scala S, Basso-Ricci L, Draghici E, Palagano E, Zonari E, Desantis G, Uva P, Cusano R, Sergi Sergi L, Crisafulli L, Moshous D, Stepensky P, Drabko K, Kaya Z, Unal E, Gezdirici A, Menna G, Serafini M, Aiuti A, Locatelli SL, Carlo-Stella C, Schulz AS, Ficara F, Sobacchi C, Gentner B, Villa A.

Haematologica. 2020 Jan 16. pii: haematol.2019.238261. doi: 10.3324/haematol.2019.238261. [Epub ahead of print]


γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites.

Calabria A, Beretta S, Merelli I, Spinozzi G, Brasca S, Pirola Y, Benedicenti F, Tenderini E, Bonizzoni P, Milanesi L, Montini E.

Bioinformatics. 2020 Mar 1;36(5):1622-1624. doi: 10.1093/bioinformatics/btz747.


Integration of Machine Learning Methods to Dissect Genetically Imputed Transcriptomic Profiles in Alzheimer's Disease.

Maj C, Azevedo T, Giansanti V, Borisov O, Dimitri GM, Spasov S; Alzheimer’s Disease Neuroimaging Initiative, Lió P, Merelli I.

Front Genet. 2019 Sep 3;10:726. doi: 10.3389/fgene.2019.00726. eCollection 2019.


GenHap: a novel computational method based on genetic algorithms for haplotype assembly.

Tangherloni A, Spolaor S, Rundo L, Nobile MS, Cazzaniga P, Mauri G, Liò P, Merelli I, Besozzi D.

BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):172. doi: 10.1186/s12859-019-2691-y.


Precise Gene Editing Preserves Hematopoietic Stem Cell Function following Transient p53-Mediated DNA Damage Response.

Schiroli G, Conti A, Ferrari S, Della Volpe L, Jacob A, Albano L, Beretta S, Calabria A, Vavassori V, Gasparini P, Salataj E, Ndiaye-Lobry D, Brombin C, Chaumeil J, Montini E, Merelli I, Genovese P, Naldini L, Di Micco R.

Cell Stem Cell. 2019 Apr 4;24(4):551-565.e8. doi: 10.1016/j.stem.2019.02.019. Epub 2019 Mar 21.


Advances in distributed computing with modern drug discovery.

Banegas-Luna AJ, Imbernón B, Llanes Castro A, Pérez-Garrido A, Cerón-Carrasco JP, Gesing S, Merelli I, D'Agostino D, Pérez-Sánchez H.

Expert Opin Drug Discov. 2019 Jan;14(1):9-22. doi: 10.1080/17460441.2019.1552936. Epub 2018 Dec 13. Review.


Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: A Logistic Model Tree Solution.

Beretta S, Castelli M, Gonçalves I, Kel I, Giansanti V, Merelli I.

J Comput Biol. 2018 Oct;25(10):1091-1105. doi: 10.1089/cmb.2017.0167. Epub 2018 Jul 27.


ChromStruct 4: A Python Code to Estimate the Chromatin Structure from Hi-C Data.

Caudai C, Salerno E, Zoppe M, Merelli I, Tonazzini A.

IEEE/ACM Trans Comput Biol Bioinform. 2018 May 21. doi: 10.1109/TCBB.2018.2838669. [Epub ahead of print]


VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.

Spinozzi G, Calabria A, Brasca S, Beretta S, Merelli I, Milanesi L, Montini E.

BMC Bioinformatics. 2017 Nov 25;18(1):520. doi: 10.1186/s12859-017-1937-9.


High parathyroid hormone concentration in tenofovir-treated patients are due to inhibition of calcium-sensing receptor activity.

Mingione A, Maruca K, Chiappori F, Pivari F, Brasacchio C, Quirino T, Merelli I, Soldati L, Bonfanti P, Mora S.

Biomed Pharmacother. 2018 Jan;97:969-974. doi: 10.1016/j.biopha.2017.11.037. Epub 2017 Nov 7.


HIV-1-mediated insertional activation of STAT5B and BACH2 trigger viral reservoir in T regulatory cells.

Cesana D, Santoni de Sio FR, Rudilosso L, Gallina P, Calabria A, Beretta S, Merelli I, Bruzzesi E, Passerini L, Nozza S, Vicenzi E, Poli G, Gregori S, Tambussi G, Montini E.

Nat Commun. 2017 Sep 8;8(1):498. doi: 10.1038/s41467-017-00609-1.


PWHATSHAP: efficient haplotyping for future generation sequencing.

Bracciali A, Aldinucci M, Patterson M, Marschall T, Pisanti N, Merelli I, Torquati M.

BMC Bioinformatics. 2016 Sep 22;17(Suppl 11):342. doi: 10.1186/s12859-016-1170-y.


Editorial: High Performance Computing in Drug Discovery.

Pérez-Sánchez H, Gesing S, Merelli I.

Curr Drug Targets. 2016;17(14):1578-1579. No abstract available.


The Genome Conformation As an Integrator of Multi-Omic Data: The Example of Damage Spreading in Cancer.

Tordini F, Aldinucci M, Milanesi L, Liò P, Merelli I.

Front Genet. 2016 Nov 15;7:194. eCollection 2016.


Association Analysis of Noncoding Variants in Neuroligins 3 and 4X Genes with Autism Spectrum Disorder in an Italian Cohort.

Landini M, Merelli I, Raggi ME, Galluccio N, Ciceri F, Bonfanti A, Camposeo S, Massagli A, Villa L, Salvi E, Cusi D, Molteni M, Milanesi L, Marabotti A, Mezzelani A.

Int J Mol Sci. 2016 Oct 22;17(10). pii: E1765.


SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.

Kel I, Chang Z, Galluccio N, Romeo M, Beretta S, Diomede L, Mezzelani A, Milanesi L, Dieterich C, Merelli I.

Mol Biosyst. 2016 Oct 18;12(11):3447-3458.


An atomistic view of Hsp70 allosteric crosstalk: from the nucleotide to the substrate binding domain and back.

Chiappori F, Merelli I, Milanesi L, Colombo G, Morra G.

Sci Rep. 2016 Mar 30;6:23474. doi: 10.1038/srep23474.


A novel molecular dynamics approach to evaluate the effect of phosphorylation on multimeric protein interface: the αB-Crystallin case study.

Chiappori F, Mattiazzi L, Milanesi L, Merelli I.

BMC Bioinformatics. 2016 Mar 2;17 Suppl 4:57. doi: 10.1186/s12859-016-0909-9.


Portals and Web-Based Resources for Virtual Screening.

Krüger J, Thiel P, Merelli I, Grunzke R, Gesing S.

Curr Drug Targets. 2016;17(14):1649-1660. Review.


HPC Analysis of Multiple Binding Sites Communication and Allosteric Modulations in Drug Design: The HSP Case Study.

Chiappori F, Milanesi L, Merelli I.

Curr Drug Targets. 2016;17(14):1610-1625. Review.


How computer science can help in understanding the 3D genome architecture.

Shavit Y, Merelli I, Milanesi L, Lio' P.

Brief Bioinform. 2016 Sep;17(5):733-44. doi: 10.1093/bib/bbv085. Epub 2015 Oct 3.


DnaK as Antibiotic Target: Hot Spot Residues Analysis for Differential Inhibition of the Bacterial Protein in Comparison with the Human HSP70.

Chiappori F, Fumian M, Milanesi L, Merelli I.

PLoS One. 2015 Apr 23;10(4):e0124563. doi: 10.1371/journal.pone.0124563. eCollection 2015.


Integrating multi-omic features exploiting Chromosome Conformation Capture data.

Merelli I, Tordini F, Drocco M, Aldinucci M, Liò P, Milanesi L.

Front Genet. 2015 Feb 11;6:40. doi: 10.3389/fgene.2015.00040. eCollection 2015.


High-performance computing and big data in omics-based medicine.

Merelli I, Pérez-Sánchez H, Gesing S, D'Agostino D.

Biomed Res Int. 2014;2014:825649. doi: 10.1155/2014/825649. Epub 2014 Dec 22. No abstract available.


Managing, analysing, and integrating big data in medical bioinformatics: open problems and future perspectives.

Merelli I, Pérez-Sánchez H, Gesing S, D'Agostino D.

Biomed Res Int. 2014;2014:134023. doi: 10.1155/2014/134023. Epub 2014 Sep 1. Review.


Parallel solutions for voxel-based simulations of reaction-diffusion systems.

D'Agostino D, Pasquale G, Clematis A, Maj C, Mosca E, Milanesi L, Merelli I.

Biomed Res Int. 2014;2014:980501. doi: 10.1155/2014/980501. Epub 2014 Jun 12.


Cloud infrastructures for in silico drug discovery: economic and practical aspects.

D'Agostino D, Clematis A, Quarati A, Cesini D, Chiappori F, Milanesi L, Merelli I.

Biomed Res Int. 2013;2013:138012. doi: 10.1155/2013/138012. Epub 2013 Sep 10.


NuChart: an R package to study gene spatial neighbourhoods with multi-omics annotations.

Merelli I, Liò P, Milanesi L.

PLoS One. 2013 Sep 19;8(9):e75146. doi: 10.1371/journal.pone.0075146. eCollection 2013.


Static and dynamic interactions between GALK enzyme and known inhibitors: guidelines to design new drugs for galactosemic patients.

Chiappori F, Merelli I, Milanesi L, Marabotti A.

Eur J Med Chem. 2013 May;63:423-34. doi: 10.1016/j.ejmech.2013.02.021. Epub 2013 Feb 27.


Sensitivity analysis for studying the relation between biochemical reactions and metabolic phenotypes.

Maj C, Mosca E, Merelli I, Mauri G, Milanesi L.

J Bioinform Comput Biol. 2013 Feb;11(1):1340002. doi: 10.1142/S0219720013400027. Epub 2013 Jan 28.


SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS.

Merelli I, Calabria A, Cozzi P, Viti F, Mosca E, Milanesi L.

BMC Bioinformatics. 2013;14 Suppl 1:S9. doi: 10.1186/1471-2105-14-S1-S9. Epub 2013 Jan 14.


Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations.

Chiappori F, Merelli I, Colombo G, Milanesi L, Morra G.

PLoS Comput Biol. 2012;8(12):e1002844. doi: 10.1371/journal.pcbi.1002844. Epub 2012 Dec 27.


IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis.

Merelli I, Viti F, Milanesi L.

BMC Bioinformatics. 2012;13 Suppl 14:S5. doi: 10.1186/1471-2105-13-S14-S5. Epub 2012 Sep 7.


Structural thermal adaptation of β-tubulins from the Antarctic psychrophilic protozoan Euplotes focardii.

Chiappori F, Pucciarelli S, Merelli I, Ballarini P, Miceli C, Milanesi L.

Proteins. 2012 Apr;80(4):1154-66. doi: 10.1002/prot.24016. Epub 2012 Jan 24.


myMIR: a genome-wide microRNA targets identification and annotation tool.

Corrada D, Viti F, Merelli I, Battaglia C, Milanesi L.

Brief Bioinform. 2011 Nov;12(6):588-600. doi: 10.1093/bib/bbr062. Epub 2011 Oct 22.


Image-based surface matching algorithm oriented to structural biology.

Merelli I, Cozzi P, D'Agostino D, Clematis A, Milanesi L.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Jul-Aug;8(4):1004-16. doi: 10.1109/TCBB.2010.21.


Semi-automatic identification of punching areas for tissue microarray building: the tubular breast cancer pilot study.

Viti F, Merelli I, Timmermans M, den Bakker M, Beltrame F, Riegman P, Milanesi L.

BMC Bioinformatics. 2010 Nov 18;11:566. doi: 10.1186/1471-2105-11-566.


Exploring the role of the phospholipid ligand in endothelial protein C receptor: a molecular dynamics study.

Chiappori F, Merelli I, Milanesi L, Rovida E.

Proteins. 2010 Sep;78(12):2679-90. doi: 10.1002/prot.22782.


A multilevel data integration resource for breast cancer study.

Mosca E, Alfieri R, Merelli I, Viti F, Calabria A, Milanesi L.

BMC Syst Biol. 2010 Jun 3;4:76. doi: 10.1186/1752-0509-4-76.


RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes.

Merelli I, Guffanti A, Fabbri M, Cocito A, Furia L, Grazini U, Bonnal RJ, Milanesi L, McBlane F.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W262-7. doi: 10.1093/nar/gkq391. Epub 2010 May 16.


SNPRanker: a tool for identification and scoring of SNPs associated to target genes.

Calabria A, Mosca E, Viti F, Merelli I, Milanesi L.

J Integr Bioinform. 2010 Mar 25;7(3). doi: 10.2390/biecoll-jib-2010-138.


In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study.

Chiappori F, D'Ursi P, Merelli I, Milanesi L, Rovida E.

BMC Bioinformatics. 2009 Oct 15;10 Suppl 12:S3. doi: 10.1186/1471-2105-10-S12-S3.


The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections.

Merelli I, Caprera A, Stella A, Del Corvo M, Milanesi L, Lazzari B.

BMC Bioinformatics. 2009 Oct 15;10 Suppl 12:S2. doi: 10.1186/1471-2105-10-S12-S2.


Ontology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAs.

Lazzari B, Caprera A, Cestaro A, Merelli I, Del Corvo M, Fontana P, Milanesi L, Velasco R, Stella A.

BMC Plant Biol. 2009 Jun 29;9:82. doi: 10.1186/1471-2229-9-82.


Virtual screening pipeline and ligand modelling for H5N1 neuraminidase.

D'Ursi P, Chiappori F, Merelli I, Cozzi P, Rovida E, Milanesi L.

Biochem Biophys Res Commun. 2009 Jun 12;383(4):445-9. doi: 10.1016/j.bbrc.2009.04.030. Epub 2009 Apr 14.


A parallel protein surface reconstruction system.

Merelli I, Orro A, D'Agostino D, Clematis A; Luciano Milanesi.

Int J Bioinform Res Appl. 2008;4(3):221-39.


Mining the bovine genome with the "Bovine SNP Retriever".

Panzitta F, Caprera A, Merelli I, Milanesi L, Williams JL, Lazzari B, Stella A.

J Hered. 2008 Nov-Dec;99(6):696-8. doi: 10.1093/jhered/esn044. Epub 2008 Jun 9.


Ontology-based, Tissue MicroArray oriented, image centered tissue bank.

Viti F, Merelli I, Caprera A, Lazzari B, Stella A, Milanesi L.

BMC Bioinformatics. 2008 Apr 25;9 Suppl 4:S4. doi: 10.1186/1471-2105-9-S4-S4.


Version VI of the ESTree db: an improved tool for peach transcriptome analysis.

Lazzari B, Caprera A, Vecchietti A, Merelli I, Barale F, Milanesi L, Stella A, Pozzi C.

BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S9. doi: 10.1186/1471-2105-9-S2-S9.


The cell cycle DB: a systems biology approach to cell cycle analysis.

Alfieri R, Merelli I, Mosca E, Milanesi L.

Nucleic Acids Res. 2008 Jan;36(Database issue):D641-5. Epub 2007 Dec 26.

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