Publications by authors named "Silvio Bicciato"

100Publications

Computational Analysis of Hi-C Data.

Methods Mol Biol 2021 ;2157:103-125

Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.

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http://dx.doi.org/10.1007/978-1-0716-0664-3_7DOI Listing
January 2021

Aptamers against mouse and human tumor-infiltrating myeloid cells as reagents for targeted chemotherapy.

Sci Transl Med 2020 Jun;12(548)

Department of Microbiology and Immunology, Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA.

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http://dx.doi.org/10.1126/scitranslmed.aav9760DOI Listing
June 2020

Computational methods for the integrative analysis of single-cell data.

Brief Bioinform 2020 May 4. Epub 2020 May 4.

Industrial Bioengineering at the University of Modena and Reggio Emilia. His research activity is the development and application of computational approaches for the analysis of multi -omics data.

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http://dx.doi.org/10.1093/bib/bbaa042DOI Listing
May 2020

GATA Factor-Mediated Gene Regulation in Human Erythropoiesis.

iScience 2020 Apr 30;23(4):101018. Epub 2020 Mar 30.

Laboratory of Chromatin and Gene Regulation during Development, Imagine Institute, INSERM UMR, 1163 Paris, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2020.101018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7155206PMC
April 2020

Computational Methods for the Integrative Analysis of Genomics and Pharmacological Data.

Front Oncol 2020 27;10:185. Epub 2020 Feb 27.

Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.

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http://dx.doi.org/10.3389/fonc.2020.00185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7056894PMC
February 2020

APTANI2: update of aptamer selection through sequence-structure analysis.

Bioinformatics 2020 04;36(7):2266-2268

Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btz897DOI Listing
April 2020

Integration of Bioinformatic Predictions and Experimental Data to Identify circRNA-miRNA Associations.

Genes (Basel) 2019 08 24;10(9). Epub 2019 Aug 24.

Center for Genome Research, Department of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi, 287, 41100 Modena, Italy.

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http://dx.doi.org/10.3390/genes10090642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769881PMC
August 2019

Isoprenylcysteine carboxy methyltransferase (ICMT) is associated with tumor aggressiveness and its expression is controlled by the p53 tumor suppressor.

J Biol Chem 2019 03 17;294(13):5060-5073. Epub 2019 Jan 17.

From the Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Rosario 2000, Argentina, the Instituto de Genética Experimental, Facultad de Ciencias Médicas,

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http://dx.doi.org/10.1074/jbc.RA118.006037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6442035PMC
March 2019

Enzymatic Inactivation of Oxysterols in Breast Tumor Cells Constraints Metastasis Formation by Reprogramming the Metastatic Lung Microenvironment.

Front Immunol 2018 2;9:2251. Epub 2018 Oct 2.

Immuno-Biotherapy of Melanoma and Solid Tumors Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, Italy.

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http://dx.doi.org/10.3389/fimmu.2018.02251DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6176086PMC
September 2019

GDA, a web-based tool for Genomics and Drugs integrated analysis.

Nucleic Acids Res 2018 07;46(W1):W148-W156

Dept. of Life Sciences, University of Modena and Reggio Emilia, Via G. Campi, 287, 41125 Modena, Italy.

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http://dx.doi.org/10.1093/nar/gky434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031047PMC
July 2018

Chromosome positioning in interphase nuclei of hematopoietic stem cell and myeloid precursor.

Hematol Rep 2018 Mar 3;10(1):7515. Epub 2018 Apr 3.

Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.

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http://dx.doi.org/10.4081/hr.2018.7515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5907646PMC
March 2018

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles.

BMC Genomics 2018 Apr 27;19(1):302. Epub 2018 Apr 27.

Polaris Research Centre, Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy.

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http://dx.doi.org/10.1186/s12864-018-4679-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5923024PMC
April 2018

A gene expression signature of Retinoblastoma loss-of-function predicts resistance to neoadjuvant chemotherapy in ER-positive/HER2-positive breast cancer patients.

Breast Cancer Res Treat 2018 Jul 22;170(2):329-341. Epub 2018 Mar 22.

Sandro Pitigliani Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, via Suor Niccolina Infermiera 20, 59100, Prato, Italy.

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http://dx.doi.org/10.1007/s10549-018-4766-2DOI Listing
July 2018

Computational methods for analyzing genome-wide chromosome conformation capture data.

Curr Opin Biotechnol 2018 12 15;54:98-105. Epub 2018 Mar 15.

Department of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2018.01.023DOI Listing
December 2018

Comparison of computational methods for Hi-C data analysis.

Nat Methods 2017 Jul 12;14(7):679-685. Epub 2017 Jun 12.

Dept. of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy.

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http://www.nature.com/doifinder/10.1038/nmeth.4325
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http://dx.doi.org/10.1038/nmeth.4325DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5493985PMC
July 2017

MCM7 and its hosted miR-25, 93 and 106b cluster elicit YAP/TAZ oncogenic activity in lung cancer.

Carcinogenesis 2017 01 17;38(1):64-75. Epub 2016 Oct 17.

Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, via G. Campi 287, 41100 Modena, Italy.

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http://dx.doi.org/10.1093/carcin/bgw110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276925PMC
January 2017

Induction of Expandable Tissue-Specific Stem/Progenitor Cells through Transient Expression of YAP/TAZ.

Cell Stem Cell 2016 12 15;19(6):725-737. Epub 2016 Sep 15.

Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.08.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5145813PMC
December 2016

A comparative transcriptomic analysis of astrocytes differentiation from human neural progenitor cells.

Eur J Neurosci 2016 11 25;44(10):2858-2870. Epub 2016 Sep 25.

Department of Psychiatry and Behavioral Sciences, Center for Therapeutic Innovation, University of Miami Miller School of Medicine, 1501 NW 10th Ave, BRB 508, Miami, FL, 33136, USA.

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http://dx.doi.org/10.1111/ejn.13382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5118072PMC
November 2016

Dynamic Transcriptional and Epigenetic Regulation of Human Epidermal Keratinocyte Differentiation.

Stem Cell Reports 2016 Apr 31;6(4):618-632. Epub 2016 Mar 31.

Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; Genethon, 1bis rue de l'Internationale, 91002 Evry, France. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2016.03.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834057PMC
April 2016

YAP enhances the pro-proliferative transcriptional activity of mutant p53 proteins.

EMBO Rep 2016 Feb 21;17(2):188-201. Epub 2015 Dec 21.

Translational Oncogenomic Unit, Molecular Medicine Area Regina Elena National Cancer Institute, Rome, Italy

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http://dx.doi.org/10.15252/embr.201540488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5290815PMC
February 2016

Human liver-resident CD56(bright)/CD16(neg) NK cells are retained within hepatic sinusoids via the engagement of CCR5 and CXCR6 pathways.

J Autoimmun 2016 Jan 30;66:40-50. Epub 2015 Aug 30.

Unit of Clinical and Experimental Immunology, Humanitas Clinical and Research Center, 20089 Rozzano, Italy; Department of Medical Biotechnologies and Translational Medicine, University of Milan, 20089 Rozzano, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.jaut.2015.08.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4718768PMC
January 2016

Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth.

Nat Cell Biol 2015 Sep 10;17(9):1218-27. Epub 2015 Aug 10.

Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3 35126 Padua, Italy.

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http://dx.doi.org/10.1038/ncb3216DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186417PMC
September 2015

Prospective Biomarker Analysis of the Randomized CHER-LOB Study Evaluating the Dual Anti-HER2 Treatment With Trastuzumab and Lapatinib Plus Chemotherapy as Neoadjuvant Therapy for HER2-Positive Breast Cancer.

Oncologist 2015 Sep 5;20(9):1001-10. Epub 2015 Aug 5.

Department of Surgery, Oncology and Gastroenterology, University of Padua, Padua, Italy; Division of Medical Oncology 2, Istituto Oncologico Veneto Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Padua, Italy; Division of Oncology, University Hospital, Ferrara, Italy; Division of Pathology, Modena University Hospital, Modena, Italy; Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy; Unità Operativa Multidisciplinare di Patologia Mammaria, Azienda Ospedaliera Istituti Ospitalieri di Cremona, Cremona, Italy; Division of Medical Oncology, Ramazzini Hospital, Carpi, Italy; Department of Medical Oncology, Azienda Ospedaliera ASMN, IRCCS, Reggio Emilia, Italy; Division of Medical Oncology, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori IRCCS, Meldola, Italy; Division of Medical Oncology, University Hospital, Parma, Italy; GlaxoSmithKline, Collegeville, Pennsylvania, USA

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http://dx.doi.org/10.1634/theoncologist.2015-0138DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571802PMC
September 2015

The tissue inhibitor of metalloproteinases 1 increases the clonogenic efficiency of human hematopoietic progenitor cells through CD63/PI3K/Akt signaling.

Exp Hematol 2015 Nov 23;43(11):974-985.e1. Epub 2015 Jul 23.

Department of Experimental, Diagnostic and Specialty Medicine, Institute of Hematology L. and A. Seràgnoli, University of Bologna, Bologna, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.exphem.2015.07.003DOI Listing
November 2015

Notch is a direct negative regulator of the DNA-damage response.

Nat Struct Mol Biol 2015 May 20;22(5):417-24. Epub 2015 Apr 20.

1] Istituto Fondazione Italiana per la Ricerca sul Cancro di Oncologia Molecolare, Milan, Italy. [2] Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy.

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http://dx.doi.org/10.1038/nsmb.3013DOI Listing
May 2015

Mutant p53 reprograms TNF signaling in cancer cells through interaction with the tumor suppressor DAB2IP.

Mol Cell 2014 Dec 13;56(5):617-29. Epub 2014 Nov 13.

Laboratorio Nazionale CIB (LNCIB), AREA Science Park, 34149 Trieste, Italy; Dip. Scienze della Vita, Università degli Studi di Trieste, 34127 Trieste, Italy. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.10.013DOI Listing
December 2014

Human fibrocytic myeloid-derived suppressor cells express IDO and promote tolerance via Treg-cell expansion.

Eur J Immunol 2014 Nov 18;44(11):3307-19. Epub 2014 Oct 18.

Diabetes Research Institute, University of Miami, Miami, FL, USA.

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http://dx.doi.org/10.1002/eji.201444522DOI Listing
November 2014

YAP/TAZ incorporation in the β-catenin destruction complex orchestrates the Wnt response.

Cell 2014 Jul 26;158(1):157-70. Epub 2014 Jun 26.

Department of Molecular Medicine, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674140073
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http://dx.doi.org/10.1016/j.cell.2014.06.013DOI Listing
July 2014

UCbase 2.0: ultraconserved sequences database (2014 update).

Database (Oxford) 2014 19;2014. Epub 2014 Jun 19.

Computer Engineering Department, University of Modena, Via Campi 213/b, 44100, Modena, Department of Statistical Sciences, University of Bologna, Via Belle Arti 41, 40126, Bologna, Italy, Department of Genetics, Environment and Evolution, Genetics Institute, University College London, London, WC1E 6BT, UK and Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Via G. Campi 287, 41100, Modena, Italy

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http://dx.doi.org/10.1093/database/bau062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064129PMC
August 2014

Quantitative phenotypic analysis of multistress response in Zygosaccharomyces rouxii complex.

FEMS Yeast Res 2014 Jun 13;14(4):586-600. Epub 2014 Mar 13.

Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy.

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http://dx.doi.org/10.1111/1567-1364.12146DOI Listing
June 2014

Transcriptomic profiling of the development of the inflammatory response in human monocytes in vitro.

PLoS One 2014 3;9(2):e87680. Epub 2014 Feb 3.

Institute of Biomedical Technologies, National Research Council, Pisa/Segrate, Italy ; Institute of Protein Biochemistry, National Research Council, Naples, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0087680PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912012PMC
December 2014

MafB is a downstream target of the IL-10/STAT3 signaling pathway, involved in the regulation of macrophage de-activation.

Biochim Biophys Acta 2014 May 25;1843(5):955-64. Epub 2014 Jan 25.

Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 287, 41125 Modena, Italy.

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http://dx.doi.org/10.1016/j.bbamcr.2014.01.021DOI Listing
May 2014

Role of TAZ as mediator of Wnt signaling.

Cell 2012 Dec 13;151(7):1443-56. Epub 2012 Dec 13.

Department of Biomedical Sciences, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy.

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http://dx.doi.org/10.1016/j.cell.2012.11.027DOI Listing
December 2012

Hmgb3 is regulated by microRNA-206 during muscle regeneration.

PLoS One 2012 17;7(8):e43464. Epub 2012 Aug 17.

Stem Cell Laboratory, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Centro Dino Ferrari, Milano, Italy.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0043464PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3422271PMC
March 2013

SHARP1 suppresses breast cancer metastasis by promoting degradation of hypoxia-inducible factors.

Nature 2012 Jul;487(7407):380-4

Department of Medical Biotechnologies, University of Padua School of Medicine, Viale Colombo 3, 35131 Padua, Italy.

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http://dx.doi.org/10.1038/nature11207DOI Listing
July 2012

The Hippo transducer TAZ confers cancer stem cell-related traits on breast cancer cells.

Cell 2011 Nov;147(4):759-72

Department of Histology, Microbiology, and Medical Biotechnologies, University of Padua School of Medicine, viale Colombo 3, 35126 Padua, Italy.

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http://dx.doi.org/10.1016/j.cell.2011.09.048DOI Listing
November 2011

The reconstruction of transcriptional networks reveals critical genes with implications for clinical outcome of multiple myeloma.

Clin Cancer Res 2011 Dec 2;17(23):7402-12. Epub 2011 Sep 2.

Department of Medical Sciences, University of Milan and Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Italy.

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http://dx.doi.org/10.1158/1078-0432.CCR-11-0596DOI Listing
December 2011

PREDA: an R-package to identify regional variations in genomic data.

Bioinformatics 2011 Sep 7;27(17):2446-7. Epub 2011 Jul 7.

Department of Biomedical Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btr404DOI Listing
September 2011

Role of YAP/TAZ in mechanotransduction.

Nature 2011 Jun 8;474(7350):179-83. Epub 2011 Jun 8.

Department of Histology, Microbiology and Medical Biotechnologies, University of Padua School of Medicine, viale Colombo 3, 35131 Padua, Italy.

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http://dx.doi.org/10.1038/nature10137DOI Listing
June 2011