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For: Hamada M, Wijaya E, Frith MC, Asai K. Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection. ACTA ACUST UNITED AC 2011;27:3085-92. [PMID: 21976422 DOI: 10.1093/bioinformatics/btr537] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Number Cited by Other Article(s)
1
Mayer JU, Hilligan KL, Chandler JS, Eccles DA, Old SI, Domingues RG, Yang J, Webb GR, Munoz-Erazo L, Hyde EJ, Wakelin KA, Tang SC, Chappell SC, von Daake S, Brombacher F, Mackay CR, Sher A, Tussiwand R, Connor LM, Gallego-Ortega D, Jankovic D, Le Gros G, Hepworth MR, Lamiable O, Ronchese F. Homeostatic IL-13 in healthy skin directs dendritic cell differentiation to promote TH2 and inhibit TH17 cell polarization. Nat Immunol 2021;22:1538-1550. [PMID: 34795444 DOI: 10.1038/s41590-021-01067-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/05/2021] [Indexed: 01/27/2023]
2
Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF, Paten B, Durbin R. Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol 2018;36:875-879. [PMID: 30125266 PMCID: PMC6126949 DOI: 10.1038/nbt.4227] [Citation(s) in RCA: 353] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/23/2018] [Indexed: 12/30/2022]
3
Zhou Z, Lundstrøm I, Tran-Dien A, Duchêne S, Alikhan NF, Sergeant MJ, Langridge G, Fotakis AK, Nair S, Stenøien HK, Hamre SS, Casjens S, Christophersen A, Quince C, Thomson NR, Weill FX, Ho SYW, Gilbert MTP, Achtman M. Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia. Curr Biol 2018;28:2420-2428.e10. [PMID: 30033331 PMCID: PMC6089836 DOI: 10.1016/j.cub.2018.05.058] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/09/2018] [Accepted: 05/18/2018] [Indexed: 02/04/2023]
4
Hamada M, Ono Y, Asai K, Frith MC. Training alignment parameters for arbitrary sequencers with LAST-TRAIN. Bioinformatics 2017;33:926-928. [PMID: 28039163 PMCID: PMC5351549 DOI: 10.1093/bioinformatics/btw742] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 11/18/2016] [Indexed: 01/05/2023]  Open
5
Kerpedjiev P, Frellsen J, Lindgreen S, Krogh A. Adaptable probabilistic mapping of short reads using position specific scoring matrices. BMC Bioinformatics 2014;15:100. [PMID: 24717095 PMCID: PMC4021105 DOI: 10.1186/1471-2105-15-100] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 03/28/2014] [Indexed: 11/10/2022]  Open
6
Torri F, Dinov ID, Zamanyan A, Hobel S, Genco A, Petrosyan P, Clark AP, Liu Z, Eggert P, Pierce J, Knowles JA, Ames J, Kesselman C, Toga AW, Potkin SG, Vawter MP, Macciardi F. Next generation sequence analysis and computational genomics using graphical pipeline workflows. Genes (Basel) 2014;3:545-75. [PMID: 23139896 PMCID: PMC3490498 DOI: 10.3390/genes3030545] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
7
Sandoval-Espinola WJ, Makwana ST, Chinn MS, Thon MR, Azcárate-Peril MA, Bruno-Bárcena JM. Comparative phenotypic analysis and genome sequence of Clostridium beijerinckii SA-1, an offspring of NCIMB 8052. MICROBIOLOGY (READING, ENGLAND) 2013;159:2558-2570. [PMID: 24068240 PMCID: PMC7336276 DOI: 10.1099/mic.0.069534-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 09/24/2013] [Indexed: 01/07/2023]
8
Abel HJ, Duncavage EJ. Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet 2013;206:432-40. [PMID: 24405614 DOI: 10.1016/j.cancergen.2013.11.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 11/06/2013] [Accepted: 11/15/2013] [Indexed: 10/26/2022]
9
Hamada M. Fighting against uncertainty: an essential issue in bioinformatics. Brief Bioinform 2013;15:748-67. [PMID: 23803300 DOI: 10.1093/bib/bbt038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
10
Mahmud MP, Wiedenhoeft J, Schliep A. Indel-tolerant read mapping with trinucleotide frequencies using cache-oblivious kd-trees. Bioinformatics 2013;28:i325-i332. [PMID: 22962448 PMCID: PMC3436807 DOI: 10.1093/bioinformatics/bts380] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
11
Menzel P, Frellsen J, Plass M, Rasmussen SH, Krogh A. On the accuracy of short read mapping. Methods Mol Biol 2013;1038:39-59. [PMID: 23872968 DOI: 10.1007/978-1-62703-514-9_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
12
Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. BMC Bioinformatics 2012;13:303. [PMID: 23151247 PMCID: PMC3534400 DOI: 10.1186/1471-2105-13-303] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 11/01/2012] [Indexed: 11/25/2022]  Open
13
Frith MC, Mori R, Asai K. A mostly traditional approach improves alignment of bisulfite-converted DNA. Nucleic Acids Res 2012;40:e100. [PMID: 22457070 PMCID: PMC3401460 DOI: 10.1093/nar/gks275] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]  Open
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