• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (5071419)   Today's Articles (77)
For:  [Subscribe] [Scholar Register]
Number Cited by Other Article(s)
1
Tang F, Gao Y, Li K, Tang D, Hao Y, Lv M, Wu H, Cheng H, Fei J, Jin Z, Wang C, Xu Y, Wei Z, Zhou P, Zhang Z, He X, Cao Y. Novel deleterious splicing variant in HFM1 causes gametogenesis defect and recurrent implantation failure: concerning the risk of chromosomal abnormalities in embryos. J Assist Reprod Genet 2023;40:1689-1702. [PMID: 36864181 PMCID: PMC10352197 DOI: 10.1007/s10815-023-02761-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/21/2023] [Indexed: 03/04/2023]  Open
2
Luo W, Zheng YM, Hao Y, Zhang Y, Zhou P, Wei Z, Cao Y, Chen D. Mitochondrial DNA quantification correlates with the developmental potential of human euploid blastocysts but not with that of mosaic blastocysts. BMC Pregnancy Childbirth 2023;23:447. [PMID: 37322435 DOI: 10.1186/s12884-023-05760-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]  Open
3
Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023;25:100316. [PMID: 36507974 DOI: 10.1016/j.gim.2022.09.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022]  Open
4
Ou, Ni MengZhangDingZouZhengZhang, Li H, Huang Y. Improved pregnancy outcomes from mosaic embryos with lower mtDNA content: a single-center retrospective study. Eur J Obstet Gynecol Reprod Biol 2022;275:110-114. [DOI: 10.1016/j.ejogrb.2022.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 06/08/2022] [Accepted: 06/23/2022] [Indexed: 11/04/2022]
5
Warmuth VM, Weissensteiner MH, Wolf J. Ineffective silencing of transposable elements on an avian W Chromosome. Genome Res 2022;32:671-681. [PMID: 35149543 PMCID: PMC8997356 DOI: 10.1101/gr.275465.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 02/08/2022] [Indexed: 11/24/2022]
6
Sinha R, Pal RK, De RK. GenSeg and MR-GenSeg: A Novel Segmentation Algorithm and its Parallel MapReduce Based Approach for Identifying Genomic Regions With Copy Number Variations. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:443-454. [PMID: 32750860 DOI: 10.1109/tcbb.2020.3000661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
7
Rinaldi AO, Korsfeldt A, Ward S, Burla D, Dreher A, Gautschi M, Stolpe B, Tan G, Bersuch E, Melin D, Askary Lord N, Grant S, Svedenhag P, Tsekova K, Schmid‐Grendelmeier P, Möhrenschlager M, Renner ED, Akdis CA. Electrical impedance spectroscopy for the characterization of skin barrier in atopic dermatitis. Allergy 2021;76:3066-3079. [PMID: 33830511 DOI: 10.1111/all.14842] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/05/2021] [Accepted: 03/23/2021] [Indexed: 12/22/2022]
8
Jugas R, Sedlar K, Vitek M, Nykrynova M, Barton V, Bezdicek M, Lengerova M, Skutkova H. CNproScan: Hybrid CNV detection for bacterial genomes. Genomics 2021;113:3103-3111. [PMID: 34224809 DOI: 10.1016/j.ygeno.2021.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 06/13/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
9
Boujemaa M, Hamdi Y, Mejri N, Romdhane L, Ghedira K, Bouaziz H, El Benna H, Labidi S, Dallali H, Jaidane O, Ben Nasr S, Haddaoui A, Rahal K, Abdelhak S, Boussen H, Boubaker MS. Germline copy number variations in BRCA1/2 negative families: Role in the molecular etiology of hereditary breast cancer in Tunisia. PLoS One 2021;16:e0245362. [PMID: 33503040 PMCID: PMC7840007 DOI: 10.1371/journal.pone.0245362] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 12/28/2020] [Indexed: 12/24/2022]  Open
10
Zhou T, Sengupta S, Müller P, Ji Y. RNDClone: Tumor subclone reconstruction based on integrating DNA and RNA sequence data. Ann Appl Stat 2020. [DOI: 10.1214/20-aoas1368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
11
Jang H, Lee H. Multiresolution correction of GC bias and application to identification of copy number alterations. Bioinformatics 2020;35:3890-3897. [PMID: 30865265 DOI: 10.1093/bioinformatics/btz174] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 03/03/2019] [Accepted: 03/12/2019] [Indexed: 01/03/2023]  Open
12
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
13
Yang H, Zhu D. Combinatorial Detection Algorithm for Copy Number Variations Using High-throughput Sequencing Reads. INT J PATTERN RECOGN 2019. [DOI: 10.1142/s0218001419500228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
14
Luo F. A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing data. BMC Bioinformatics 2019;20:692. [PMID: 31874603 PMCID: PMC6929333 DOI: 10.1186/s12859-019-3266-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
15
Lee J, Chen J. A penalized regression approach for DNA copy number study using the sequencing data. Stat Appl Genet Mol Biol 2019;18:sagmb-2018-0001. [PMID: 31145697 DOI: 10.1515/sagmb-2018-0001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
16
Wang X, Lebarbier E, Aubert J, Robin S. Variational Inference for Coupled Hidden Markov Models Applied to the Joint Detection of Copy Number Variations. Int J Biostat 2019;15:/j/ijb.ahead-of-print/ijb-2018-0023/ijb-2018-0023.xml. [PMID: 30779702 DOI: 10.1515/ijb-2018-0023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 11/21/2018] [Indexed: 02/04/2023]
17
Zhou T, Müller P, Sengupta S, Ji Y. PairClone: a Bayesian subclone caller based on mutation pairs. J R Stat Soc Ser C Appl Stat 2018. [DOI: 10.1111/rssc.12328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
18
Magi A, Giusti B, Tattini L. Characterization of MinION nanopore data for resequencing analyses. Brief Bioinform 2018;18:940-953. [PMID: 27559152 DOI: 10.1093/bib/bbw077] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Indexed: 02/04/2023]  Open
19
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]
20
Resistome of carbapenem- and colistin-resistant Klebsiella pneumoniae clinical isolates. PLoS One 2018;13:e0198526. [PMID: 29883490 PMCID: PMC5993281 DOI: 10.1371/journal.pone.0198526] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/21/2018] [Indexed: 12/21/2022]  Open
21
Wang W, Mao B, Wei X, Yin D, Li H, Mao L, Guo X, Sun Y, Yang Y. Application of an improved targeted next generation sequencing method to diagnose non‑syndromic mental retardation in one step: A case report. Mol Med Rep 2018;18:981-986. [PMID: 29845227 DOI: 10.3892/mmr.2018.9031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/01/2018] [Indexed: 11/06/2022]  Open
22
Nishio S, Moteki H, Usami S. Simple and efficient germline copy number variant visualization method for the Ion AmpliSeq™ custom panel. Mol Genet Genomic Med 2018;6:678-686. [PMID: 29633566 PMCID: PMC6081219 DOI: 10.1002/mgg3.399] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022]  Open
23
DNase-capture reveals differential transcription factor binding modalities. PLoS One 2017;12:e0187046. [PMID: 29284001 PMCID: PMC5746236 DOI: 10.1371/journal.pone.0187046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 10/12/2017] [Indexed: 11/19/2022]  Open
24
Detecting differential copy number variation between groups of samples. Genome Res 2017;28:256-265. [PMID: 29229672 PMCID: PMC5793789 DOI: 10.1101/gr.206938.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 11/27/2017] [Indexed: 01/20/2023]
25
do Nascimento F, Guimaraes KS. Copy Number Variations Detection: Unravelling the Problem in Tangible Aspects. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;14:1237-1250. [PMID: 27295681 DOI: 10.1109/tcbb.2016.2576441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
26
Tan R, Wang J, Wu X, Juan L, Zheng L, Ma R, Zhan Q, Wang T, Jin S, Jiang Q, Wang Y. ERDS-exome: a Hybrid Approach for Copy Number Variant Detection from Whole-exome Sequencing Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2017;17:796-803. [PMID: 28981421 DOI: 10.1109/tcbb.2017.2758779] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
27
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
28
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
29
Chan CH, Octavia S, Sintchenko V, Lan R. SnpFilt: A pipeline for reference-free assembly-based identification of SNPs in bacterial genomes. Comput Biol Chem 2016;65:178-184. [DOI: 10.1016/j.compbiolchem.2016.09.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 09/07/2016] [Indexed: 10/21/2022]
30
Manconi A, Moscatelli M, Armano G, Gnocchi M, Orro A, Milanesi L. Removing duplicate reads using graphics processing units. BMC Bioinformatics 2016;17:346. [PMID: 28185553 PMCID: PMC5123249 DOI: 10.1186/s12859-016-1192-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
31
Zhang C, Cai H, Huang J, Song Y. nbCNV: a multi-constrained optimization model for discovering copy number variants in single-cell sequencing data. BMC Bioinformatics 2016;17:384. [PMID: 27639558 PMCID: PMC5027123 DOI: 10.1186/s12859-016-1239-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 09/04/2016] [Indexed: 02/02/2023]  Open
32
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
33
Samarakoon PS, Sorte HS, Stray-Pedersen A, Rødningen OK, Rognes T, Lyle R. cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data. BMC Genomics 2016;17:51. [PMID: 26764020 PMCID: PMC4712464 DOI: 10.1186/s12864-016-2374-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/06/2016] [Indexed: 12/30/2022]  Open
34
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
35
CNV-CH: A Convex Hull Based Segmentation Approach to Detect Copy Number Variations (CNV) Using Next-Generation Sequencing Data. PLoS One 2015;10:e0135895. [PMID: 26291322 PMCID: PMC4546278 DOI: 10.1371/journal.pone.0135895] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 07/28/2015] [Indexed: 11/19/2022]  Open
36
Liu Y, Wei X, Kong X, Guo X, Sun Y, Man J, Du L, Zhu H, Qu Z, Tian P, Mao B, Yang Y. Targeted Next-Generation Sequencing for Clinical Diagnosis of 561 Mendelian Diseases. PLoS One 2015;10:e0133636. [PMID: 26274329 PMCID: PMC4537117 DOI: 10.1371/journal.pone.0133636] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/30/2015] [Indexed: 12/04/2022]  Open
37
Ji T, Chen J. Modeling the next generation sequencing read count data for DNA copy number variant study. Stat Appl Genet Mol Biol 2015;14:361-74. [PMID: 26140731 DOI: 10.1515/sagmb-2014-0054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
38
Yiğiter A, Chen J, An L, Danacioğlu N. An online copy number variant detection method for short sequencing reads. J Appl Stat 2015. [DOI: 10.1080/02664763.2014.1001330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
39
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
40
Manconi A, Manca E, Moscatelli M, Gnocchi M, Orro A, Armano G, Milanesi L. G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods. Front Bioeng Biotechnol 2015;3:28. [PMID: 25806367 PMCID: PMC4354384 DOI: 10.3389/fbioe.2015.00028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/19/2015] [Indexed: 11/23/2022]  Open
41
Kuilman T, Velds A, Kemper K, Ranzani M, Bombardelli L, Hoogstraat M, Nevedomskaya E, Xu G, de Ruiter J, Lolkema MP, Ylstra B, Jonkers J, Rottenberg S, Wessels LF, Adams DJ, Peeper DS, Krijgsman O. CopywriteR: DNA copy number detection from off-target sequence data. Genome Biol 2015;16:49. [PMID: 25887352 PMCID: PMC4396974 DOI: 10.1186/s13059-015-0617-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 02/20/2015] [Indexed: 12/13/2022]  Open
42
Brynildsrud O, Snipen LG, Bohlin J. CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data. Bioinformatics 2015;31:1708-15. [DOI: 10.1093/bioinformatics/btv070] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 01/28/2015] [Indexed: 01/22/2023]  Open
43
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
44
Huang S, Holt J, Kao CY, McMillan L, Wang W. A novel multi-alignment pipeline for high-throughput sequencing data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014;2014:bau057. [PMID: 24948510 PMCID: PMC4062837 DOI: 10.1093/database/bau057] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
45
Mosen-Ansorena D, Telleria N, Veganzones S, De la Orden V, Maestro ML, Aransay AM. seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing. BMC Genomics 2014;15:178. [PMID: 24597965 PMCID: PMC4022175 DOI: 10.1186/1471-2164-15-178] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 02/26/2014] [Indexed: 11/25/2022]  Open
46
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
47
Duitama J, Quintero JC, Cruz DF, Quintero C, Hubmann G, Foulquié-Moreno MR, Verstrepen KJ, Thevelein JM, Tohme J. An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments. Nucleic Acids Res 2014;42:e44. [PMID: 24413664 PMCID: PMC3973327 DOI: 10.1093/nar/gkt1381] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
48
Nakachi I, Rice JL, Coldren CD, Edwards MG, Stearman RS, Glidewell SC, Varella-Garcia M, Franklin WA, Keith RL, Lewis MT, Gao B, Merrick DT, Miller YE, Geraci MW. Application of SNP microarrays to the genome-wide analysis of chromosomal instability in premalignant airway lesions. Cancer Prev Res (Phila) 2013;7:255-65. [PMID: 24346345 DOI: 10.1158/1940-6207.capr-12-0485] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
49
Zhang L, Zhang L. Use of autocorrelation scanning in DNA copy number analysis. Bioinformatics 2013;29:2678-82. [PMID: 24045776 DOI: 10.1093/bioinformatics/btt479] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
50
Zhao M, Wang Q, Wang Q, Jia P, Zhao Z. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics 2013;14 Suppl 11:S1. [PMID: 24564169 PMCID: PMC3846878 DOI: 10.1186/1471-2105-14-s11-s1] [Citation(s) in RCA: 350] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
PrevPage 1 of 2 12Next
© 2004-2025 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA