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Number Cited by Other Article(s)
1
Magi A, Mattei G, Mingrino A, Caprioli C, Ronchini C, Frigè G, Semeraro R, Bolognini D, Rambaldi A, Candoni A, Colombo E, Mazzarella L, Pelicci PG. High-resolution Nanopore methylome-maps reveal random hyper-methylation at CpG-poor regions as driver of chemoresistance in leukemias. Commun Biol 2023;6:382. [PMID: 37031307 PMCID: PMC10082806 DOI: 10.1038/s42003-023-04756-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/24/2023] [Indexed: 04/10/2023]  Open
2
Qin F, Luo X, Cai G, Xiao F. Shall genomic correlation structure be considered in copy number variants detection? Brief Bioinform 2021;22:6295811. [PMID: 34114005 DOI: 10.1093/bib/bbab215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/16/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022]  Open
3
Statistical Considerations on NGS Data for Inferring Copy Number Variations. Methods Mol Biol 2021;2243:27-58. [PMID: 33606251 DOI: 10.1007/978-1-0716-1103-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
4
Magi A, Bolognini D, Bartalucci N, Mingrino A, Semeraro R, Giovannini L, Bonifacio S, Parrini D, Pelo E, Mannelli F, Guglielmelli P, Maria Vannucchi A. Nano-GLADIATOR: real-time detection of copy number alterations from nanopore sequencing data. Bioinformatics 2020;35:4213-4221. [PMID: 30949684 DOI: 10.1093/bioinformatics/btz241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/05/2019] [Accepted: 04/03/2019] [Indexed: 12/15/2022]  Open
5
D'Aurizio R, Semeraro R, Magi A. Using XCAVATOR and EXCAVATOR2 to Identify CNVs from WGS, WES, and TS Data. CURRENT PROTOCOLS IN HUMAN GENETICS 2018;98:e65. [PMID: 29975818 DOI: 10.1002/cphg.65] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
6
XCAVATOR: accurate detection and genotyping of copy number variants from second and third generation whole-genome sequencing experiments. BMC Genomics 2017;18:747. [PMID: 28934930 PMCID: PMC5609061 DOI: 10.1186/s12864-017-4137-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 09/11/2017] [Indexed: 11/10/2022]  Open
7
SLMSuite: a suite of algorithms for segmenting genomic profiles. BMC Bioinformatics 2017;18:321. [PMID: 28659129 PMCID: PMC5490196 DOI: 10.1186/s12859-017-1734-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 06/20/2017] [Indexed: 11/10/2022]  Open
8
Ji T, Chen J. Statistical models for DNA copy number variation detection using read-depth data from next generation sequencing experiments. AUST NZ J STAT 2016. [DOI: 10.1111/anzs.12175] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
9
Yu Z, Li A, Wang M. CloneCNA: detecting subclonal somatic copy number alterations in heterogeneous tumor samples from whole-exome sequencing data. BMC Bioinformatics 2016;17:310. [PMID: 27538789 PMCID: PMC4990858 DOI: 10.1186/s12859-016-1174-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 08/11/2016] [Indexed: 12/13/2022]  Open
10
D'Aurizio R, Pippucci T, Tattini L, Giusti B, Pellegrini M, Magi A. Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2. Nucleic Acids Res 2016;44:e154. [PMID: 27507884 PMCID: PMC5175347 DOI: 10.1093/nar/gkw695] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 12/26/2022]  Open
11
Orrico A, Marseglia G, Pescucci C, Cortesi A, Piomboni P, Giansanti A, Gerundino F, Ponchietti R. Molecular Dissection Using Array Comparative Genomic Hybridization and Clinical Evaluation of An Infertile Male Carrier of An Unbalanced Y;21 Translocation: A Case Report and Review of The Literature. INTERNATIONAL JOURNAL OF FERTILITY & STERILITY 2015;9:581-5. [PMID: 26985348 PMCID: PMC4793181 DOI: 10.22074/ijfs.2015.4619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 08/09/2014] [Indexed: 11/04/2022]
12
Anjum S, Morganella S, D'Angelo F, Iavarone A, Ceccarelli M. VEGAWES: variational segmentation on whole exome sequencing for copy number detection. BMC Bioinformatics 2015;16:315. [PMID: 26416038 PMCID: PMC4587906 DOI: 10.1186/s12859-015-0748-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 09/16/2015] [Indexed: 11/10/2022]  Open
13
Tattini L, D'Aurizio R, Magi A. Detection of Genomic Structural Variants from Next-Generation Sequencing Data. Front Bioeng Biotechnol 2015;3:92. [PMID: 26161383 PMCID: PMC4479793 DOI: 10.3389/fbioe.2015.00092] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 06/10/2015] [Indexed: 01/16/2023]  Open
14
Magi A, Tattini L, Cifola I, D'Aurizio R, Benelli M, Mangano E, Battaglia C, Bonora E, Kurg A, Seri M, Magini P, Giusti B, Romeo G, Pippucci T, De Bellis G, Abbate R, Gensini GF. EXCAVATOR: detecting copy number variants from whole-exome sequencing data. Genome Biol 2014;14:R120. [PMID: 24172663 PMCID: PMC4053953 DOI: 10.1186/gb-2013-14-10-r120] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 10/30/2013] [Indexed: 12/11/2022]  Open
15
Li X, Chen S, Xie W, Vogel I, Choy KW, Chen F, Christensen R, Zhang C, Ge H, Jiang H, Yu C, Huang F, Wang W, Jiang H, Zhang X. PSCC: sensitive and reliable population-scale copy number variation detection method based on low coverage sequencing. PLoS One 2014;9:e85096. [PMID: 24465483 PMCID: PMC3897425 DOI: 10.1371/journal.pone.0085096] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 11/22/2013] [Indexed: 11/28/2022]  Open
16
Vandeweyer G, Kooy RF. Detection and interpretation of genomic structural variation in health and disease. Expert Rev Mol Diagn 2014;13:61-82. [DOI: 10.1586/erm.12.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
17
Gandolfi A, Benelli M, Magi A, Chiti S. Moment estimation in discrete shifting level model applied to fast array-CGH segmentation. STAT NEERL 2013. [DOI: 10.1111/stan.12005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
18
Marseglia G, Scordo MR, Pescucci C, Nannetti G, Biagini E, Scandurra V, Gerundino F, Magi A, Benelli M, Torricelli F. 372 kb microdeletion in 18q12.3 causing SETBP1 haploinsufficiency associated with mild mental retardation and expressive speech impairment. Eur J Med Genet 2012;55:216-21. [PMID: 22333924 DOI: 10.1016/j.ejmg.2012.01.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 01/12/2012] [Indexed: 10/14/2022]
19
Magi A, Tattini L, Pippucci T, Torricelli F, Benelli M. Read count approach for DNA copy number variants detection. Bioinformatics 2011;28:470-8. [DOI: 10.1093/bioinformatics/btr707] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
20
Magi A, Benelli M, Yoon S, Roviello F, Torricelli F. Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm. Nucleic Acids Res 2011;39:e65. [PMID: 21321017 PMCID: PMC3105418 DOI: 10.1093/nar/gkr068] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
21
Morganella S, Cerulo L, Viglietto G, Ceccarelli M. VEGA: variational segmentation for copy number detection. ACTA ACUST UNITED AC 2010;26:3020-7. [PMID: 20959380 DOI: 10.1093/bioinformatics/btq586] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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