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For: Schatz MC, Delcher AL, Salzberg SL. Assembly of large genomes using second-generation sequencing. Genome Res 2010;20:1165-73. [PMID: 20508146 DOI: 10.1101/gr.101360.109] [Citation(s) in RCA: 278] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Number Cited by Other Article(s)
1
Huang R, Liu Y, Xu J, Lin D, Mao A, Yang L, Zhong G, Wang H, Xu R, Chen Y, Zhou Q. Back-to-Back Comparison of Third-Generation Sequencing and Next-Generation Sequencing in Carrier Screening of Thalassemia. Arch Pathol Lab Med 2024;148:797-804. [PMID: 36630651 DOI: 10.5858/arpa.2022-0168-oa] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2022] [Indexed: 01/13/2023]
2
Thingujam D, Pajerowska-Mukhtar KM, Mukhtar MS. Duckweed: Beyond an Efficient Plant Model System. Biomolecules 2024;14:628. [PMID: 38927032 PMCID: PMC11201744 DOI: 10.3390/biom14060628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]  Open
3
Dayi M. Diversity and evolution of transposable elements in the plant-parasitic nematodes. BMC Genomics 2024;25:511. [PMID: 38783171 PMCID: PMC11118728 DOI: 10.1186/s12864-024-10435-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 05/21/2024] [Indexed: 05/25/2024]  Open
4
Chen Y, Huang JH, Sun Y, Zhang Y, Li Y, Xu X. Haplotype-resolved assembly of diploid and polyploid genomes using quantum computing. CELL REPORTS METHODS 2024;4:100754. [PMID: 38614089 PMCID: PMC11133727 DOI: 10.1016/j.crmeth.2024.100754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/03/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024]
5
Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024;25:471-484. [PMID: 38910493 PMCID: PMC11199093 DOI: 10.1631/jzus.b2300029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
6
Hiralal A, Geelhoed JS, Hidalgo-Martinez S, Smets B, van Dijk JR, Meysman FJR. Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads. Microb Genom 2024;10:001197. [PMID: 38376381 PMCID: PMC10926707 DOI: 10.1099/mgen.0.001197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/23/2024] [Indexed: 02/21/2024]  Open
7
Fernandez LA, Martin-Mayor V, Yllanes D. Phase transition in the computational complexity of the shortest common superstring and genome assembly. Phys Rev E 2024;109:014133. [PMID: 38366408 DOI: 10.1103/physreve.109.014133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 12/11/2023] [Indexed: 02/18/2024]
8
Yu C, Zhao Y, Zhao C, Jin J, Mao K, Wang G. MiniDBG: A Novel and Minimal De Bruijn Graph for Read Mapping. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2024;21:129-142. [PMID: 38060353 DOI: 10.1109/tcbb.2023.3340251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
9
Rattanapan Y, Charong N, Narkpetch S, Chareonsirisuthigul T. Genotyping of the rare Para-Bombay blood group in southern Thailand. Hematol Transfus Cell Ther 2023;45:449-455. [PMID: 36241527 PMCID: PMC10627842 DOI: 10.1016/j.htct.2022.08.004] [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: 04/18/2022] [Revised: 06/15/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]  Open
10
Yang Y, Guo X, Zhang M, Wang H, Mu S, Peng H, Yao Y. A study of application effects of next-generation sequencing based preimplantation genetic testing for aneuploidies in advanced maternal age women. Taiwan J Obstet Gynecol 2023;62:729-734. [PMID: 37679003 DOI: 10.1016/j.tjog.2023.07.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 09/09/2023]  Open
11
Ribeiro M, Maciel C, Cruz P, Darmancier H, Nogueira T, Costa M, Laranjeira J, Morais RMSC, Teixeira P. Exploiting Potential Probiotic Lactic Acid Bacteria Isolated from Chlorella vulgaris Photobioreactors as Promising Vitamin B12 Producers. Foods 2023;12:3277. [PMID: 37685210 PMCID: PMC10486965 DOI: 10.3390/foods12173277] [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: 05/25/2023] [Revised: 08/16/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023]  Open
12
de Souza LM, de Oliveira ID, Sales FCS, da Costa AC, Campos KR, Abbud A, Guerra JM, Dos Santos Cirqueira Borges C, Takahashi CPFJ, de Araújo LJT. Technical comparison of MinIon and Illumina technologies for genotyping Chikungunya virus in clinical samples. J Genet Eng Biotechnol 2023;21:88. [PMID: 37642827 PMCID: PMC10465416 DOI: 10.1186/s43141-023-00536-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 07/27/2023] [Indexed: 08/31/2023]
13
Liu P, Ewald J, Pang Z, Legrand E, Jeon YS, Sangiovanni J, Hacariz O, Zhou G, Head JA, Basu N, Xia J. ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species. Nat Commun 2023;14:2995. [PMID: 37225696 DOI: 10.1038/s41467-023-38785-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/16/2023] [Indexed: 05/26/2023]  Open
14
Wang Y, Cai X, Hu S, Qin S, Wang Z, Cao Y, Hou C, Yang J, Zhou W. Comparative genomic analysis provides insight into the phylogeny and potential mechanisms of adaptive evolution of Sphingobacterium sp. CZ-2. Gene 2023;855:147118. [PMID: 36521669 DOI: 10.1016/j.gene.2022.147118] [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: 07/13/2022] [Revised: 11/21/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
15
Zhou QM, Jiang F, Xu J, Lin D, Huang RL, Zhou JY, Qu YX, Li DZ. High accuracy of single-molecule real-time sequencing in detecting a rare α-globin fusion gene in carrier screening population. Ann Hum Genet 2023;87:9-17. [PMID: 36317495 DOI: 10.1111/ahg.12486] [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: 01/13/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
16
Anwar N, Jiang Y, Ma W, Yao Y, Li J, Ababaikeli G, Li G, Ma T. Culturable bacteria diversity in stem liquid and resina from Populus euphratica and screening of plant growth-promoting bacteria. BMC Microbiol 2022;22:322. [PMID: 36581840 PMCID: PMC9798617 DOI: 10.1186/s12866-022-02731-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022]  Open
17
Tounsi WA, Lenis VP, Tammi SM, Sainio S, Haimila K, Avent ND, Madgett TE. Rh Blood Group D Antigen Genotyping Using a Portable Nanopore-based Sequencing Device: Proof of Principle. Clin Chem 2022;68:1196-1201. [PMID: 35652461 DOI: 10.1093/clinchem/hvac075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/13/2022] [Indexed: 11/12/2022]
18
Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022;14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022]  Open
19
Yu C, Mao K, Zhao Y, Chang C, Wang G. StLiter: A Novel Algorithm to Iteratively Build the Compacted de Bruijn Graph From Many Complete Genomes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:2471-2483. [PMID: 33630738 DOI: 10.1109/tcbb.2021.3062068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
20
Goussarov G, Mysara M, Vandamme P, Van Houdt R. Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data. Microbiologyopen 2022;11:e1298. [PMID: 35765182 PMCID: PMC9179125 DOI: 10.1002/mbo3.1298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022]  Open
21
Jiang F, Mao AP, Liu YY, Liu FZ, Li YL, Li J, Zhou JY, Tang XW, Ju AP, Li FT, Wan JH, Zuo LD, Li DZ. Detection of rare thalassemia mutations using long-read single-molecule real-time sequencing. Gene 2022;825:146438. [PMID: 35306112 DOI: 10.1016/j.gene.2022.146438] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/07/2022] [Accepted: 03/14/2022] [Indexed: 11/30/2022]
22
Xian S, Zhong H, Yi B, Liu X, Shen G, Li M, Zhang Z, Luo Q, Li S, Zhou M, Xu F, Chen A. Identification of pellicle formation related microorganisms in traditional Sichuan paocai through metagenomic sequence and the effects of Baijiu/Salt on pellicle and volatile components. Food Res Int 2022;159:111130. [DOI: 10.1016/j.foodres.2022.111130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/14/2022]
23
Li M, Sun C, Xu N, Bian P, Tian X, Wang X, Wang Y, Jia X, Heller R, Wang M, Wang F, Dai X, Luo R, Guo Y, Wang X, Yang P, Hu D, Liu Z, Fu W, Zhang S, Li X, Wen C, Lan F, Siddiki AZ, Suwannapoom C, Zhao X, Nie Q, Hu X, Jiang Y, Yang N. De novo assembly of 20 chicken genomes reveals the undetectable phenomenon for thousands of core genes on micro-chromosomes and sub-telomeric regions. Mol Biol Evol 2022;39:6553873. [PMID: 35325213 PMCID: PMC9021737 DOI: 10.1093/molbev/msac066] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
24
Smirnov DN, Shekhovtsov SV, Shipova AA, Gazizova GR, Shagimardanova EI, Bulakhova NA, Meshcheryakova EN, Poluboyarova TV, Khrameeva EE, Peltek SE, Berman DI. De novo assembly and analysis of the transcriptome of the Siberian wood frog Rana amurensis. Vavilovskii Zhurnal Genet Selektsii 2022;26:109-116. [PMID: 35342853 PMCID: PMC8894097 DOI: 10.18699/vjgb-22-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022]  Open
25
Regueira-Iglesias A, Vázquez-González L, Balsa-Castro C, Blanco-Pintos T, Martín-Biedma B, Arce VM, Carreira MJ, Tomás I. In-Silico Detection of Oral Prokaryotic Species With Highly Similar 16S rRNA Sequence Segments Using Different Primer Pairs. Front Cell Infect Microbiol 2022;11:770668. [PMID: 35223533 PMCID: PMC8863748 DOI: 10.3389/fcimb.2021.770668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022]  Open
26
Hurgobin B. Annotation of Protein-Coding Genes in Plant Genomes. Methods Mol Biol 2022;2443:309-326. [PMID: 35037214 DOI: 10.1007/978-1-0716-2067-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
27
OUP accepted manuscript. Clin Chem 2022;68:927-939. [DOI: 10.1093/clinchem/hvac046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/11/2022] [Indexed: 11/13/2022]
28
Wolf E, Gaquerel E, Scharmann M, Yant L, Koch MA. Evolutionary footprints of a cold relic in a rapidly warming world. eLife 2021;10:e71572. [PMID: 34930524 PMCID: PMC8741218 DOI: 10.7554/elife.71572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022]  Open
29
Comparative genomics of Leishmania isolates from Brazil confirms the presence of Leishmania major in the Americas. Int J Parasitol 2021;51:1047-1057. [PMID: 34329650 DOI: 10.1016/j.ijpara.2021.05.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 05/06/2021] [Accepted: 05/24/2021] [Indexed: 11/22/2022]
30
Fritz A, Bremges A, Deng ZL, Lesker TR, Götting J, Ganzenmueller T, Sczyrba A, Dilthey A, Klawonn F, McHardy AC. Haploflow: strain-resolved de novo assembly of viral genomes. Genome Biol 2021;22:212. [PMID: 34281604 PMCID: PMC8287296 DOI: 10.1186/s13059-021-02426-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 06/29/2021] [Indexed: 01/03/2023]  Open
31
Zhao L, Wang H, Li P, Sun K, Guan DL, Xu SQ. Genome Size Estimation and Full-Length Transcriptome of Sphingonotus tsinlingensis: Genetic Background of a Drought-Adapted Grasshopper. Front Genet 2021;12:678625. [PMID: 34322153 PMCID: PMC8313316 DOI: 10.3389/fgene.2021.678625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/14/2021] [Indexed: 11/25/2022]  Open
32
Dida F, Yi G. Empirical evaluation of methods for de novo genome assembly. PeerJ Comput Sci 2021;7:e636. [PMID: 34307867 PMCID: PMC8279138 DOI: 10.7717/peerj-cs.636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/19/2021] [Indexed: 06/12/2023]
33
Li XY, Tan ZJ. Advances in research technology of regulation of intestinal microecology by traditional Chinese medicine. Shijie Huaren Xiaohua Zazhi 2021;29:479-487. [DOI: 10.11569/wcjd.v29.i9.479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
34
Gómez-Muñoz C, García-Ortega LF, Montalvo-Arredondo J, Pérez-Ortega E, Damas-Buenrostro LC, Riego-Ruiz L. Long insert clone experimental evidence for assembly improvement and chimeric chromosomes detection in an allopentaploid beer yeast. G3-GENES GENOMES GENETICS 2021;11:6188626. [PMID: 33768233 PMCID: PMC8495930 DOI: 10.1093/g3journal/jkab088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/12/2021] [Indexed: 11/18/2022]
35
Biological computation and computational biology: survey, challenges, and discussion. Artif Intell Rev 2021. [DOI: 10.1007/s10462-020-09951-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
36
Fritz A, Bremges A, Deng ZL, Lesker TR, Götting J, Ganzenmüller T, Sczyrba A, Dilthey A, Klawonn F, McHardy A. Haploflow: Strain-resolved de novo assembly of viral genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.25.428049. [PMID: 33532769 PMCID: PMC7852260 DOI: 10.1101/2021.01.25.428049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
37
Xavier MJ, Salas-Huetos A, Oud MS, Aston KI, Veltman JA. Disease gene discovery in male infertility: past, present and future. Hum Genet 2021;140:7-19. [PMID: 32638125 PMCID: PMC7864819 DOI: 10.1007/s00439-020-02202-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022]
38
Cechova M. Probably Correct: Rescuing Repeats with Short and Long Reads. Genes (Basel) 2020;12:48. [PMID: 33396198 PMCID: PMC7823596 DOI: 10.3390/genes12010048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023]  Open
39
Larson MA, Abdalhamid B, Puniya BL, Helikar T, Kelley DW, Iwen PC. Differences in Blood-derived Francisella tularensis Type B Strains from Clinical Cases of Tularemia. Microorganisms 2020;8:microorganisms8101515. [PMID: 33019689 PMCID: PMC7600085 DOI: 10.3390/microorganisms8101515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/26/2020] [Accepted: 09/30/2020] [Indexed: 11/16/2022]  Open
40
Alonge M, Shumate A, Puiu D, Zimin AV, Salzberg SL. Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies. Genetics 2020;216:599-608. [PMID: 32796007 PMCID: PMC7536849 DOI: 10.1534/genetics.120.303501] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/10/2020] [Indexed: 11/18/2022]  Open
41
Zhao H, Chen Y, Shen C, Li L, Li Q, Tan K, Huang H, Hu G. Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient with e14a3 BCR-ABL1 transcript using Nanopore sequencing. J Gene Med 2020;23:e3276. [PMID: 32949441 DOI: 10.1002/jgm.3276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 01/01/2023]  Open
42
Yuan H, Zhang X, Zhao L, Chang H, Yang C, Qiu Z, Huang Y. Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus. Sci Rep 2020;10:14228. [PMID: 32848169 PMCID: PMC7450073 DOI: 10.1038/s41598-020-71178-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 08/06/2020] [Indexed: 11/09/2022]  Open
43
Chen G, Xie X. Exon sequencing mutation detection algorithm based on PCR matching. PLoS One 2020;15:e0236709. [PMID: 32790736 PMCID: PMC7425927 DOI: 10.1371/journal.pone.0236709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 07/13/2020] [Indexed: 01/08/2023]  Open
44
Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum. BMC Genomics 2020;21:470. [PMID: 32640982 PMCID: PMC7346634 DOI: 10.1186/s12864-020-06814-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 06/09/2020] [Indexed: 11/10/2022]  Open
45
Batista FM, Stapleton T, Lowther JA, Fonseca VG, Shaw R, Pond C, Walker DI, van Aerle R, Martinez-Urtaza J. Whole Genome Sequencing of Hepatitis A Virus Using a PCR-Free Single-Molecule Nanopore Sequencing Approach. Front Microbiol 2020;11:874. [PMID: 32523561 PMCID: PMC7261825 DOI: 10.3389/fmicb.2020.00874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/14/2020] [Indexed: 12/18/2022]  Open
46
Park SY, Jeon J, Kim JA, Jeon MJ, Jeong MH, Kim Y, Lee Y, Chung H, Lee YH, Kim S. Draft Genome Sequence of Alternaria alternata JS-1623, a Fungal Endophyte of Abies koreana. MYCOBIOLOGY 2020;48:240-244. [PMID: 37970559 PMCID: PMC10635108 DOI: 10.1080/12298093.2020.1756134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 11/17/2023]
47
Lal Gupta C, Kumar Tiwari R, Cytryn E. Platforms for elucidating antibiotic resistance in single genomes and complex metagenomes. ENVIRONMENT INTERNATIONAL 2020;138:105667. [PMID: 32234679 DOI: 10.1016/j.envint.2020.105667] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/15/2020] [Accepted: 03/16/2020] [Indexed: 05/21/2023]
48
Norrell AE, Jones KL, Saillant EA. Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis. PLoS One 2020;15:e0232402. [PMID: 32348345 PMCID: PMC7190162 DOI: 10.1371/journal.pone.0232402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/15/2020] [Indexed: 11/19/2022]  Open
49
Medvedev P. Modeling biological problems in computer science: a case study in genome assembly. Brief Bioinform 2020;20:1376-1383. [PMID: 29394324 DOI: 10.1093/bib/bby003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 12/07/2017] [Indexed: 11/14/2022]  Open
50
Tang L, Li M, Wu FX, Pan Y, Wang J. MAC: Merging Assemblies by Using Adjacency Algebraic Model and Classification. Front Genet 2020;10:1396. [PMID: 32082361 PMCID: PMC7005248 DOI: 10.3389/fgene.2019.01396] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022]  Open
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