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For: Salmela L, Rivals E. LoRDEC: accurate and efficient long read error correction. ACTA ACUST UNITED AC 2014;30:3506-14. [PMID: 25165095 PMCID: PMC4253826 DOI: 10.1093/bioinformatics/btu538] [Citation(s) in RCA: 476] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
351
LaPierre N, Egan R, Wang W, Wang Z. De novo Nanopore read quality improvement using deep learning. BMC Bioinformatics 2019;20:552. [PMID: 31694525 PMCID: PMC6833143 DOI: 10.1186/s12859-019-3103-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/20/2019] [Indexed: 11/23/2022]  Open
352
Morisse P, Lecroq T, Lefebvre A. Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph. Bioinformatics 2019;34:4213-4222. [PMID: 29955770 DOI: 10.1093/bioinformatics/bty521] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 06/27/2018] [Indexed: 12/31/2022]  Open
353
Chen S, Qiu G, Yang M. SMRT sequencing of full-length transcriptome of seagrasses Zostera japonica. Sci Rep 2019;9:14537. [PMID: 31601990 PMCID: PMC6787188 DOI: 10.1038/s41598-019-51176-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 09/25/2019] [Indexed: 11/20/2022]  Open
354
Zou J, Mao L, Qiu J, Wang M, Jia L, Wu D, He Z, Chen M, Shen Y, Shen E, Huang Y, Li R, Hu D, Shi L, Wang K, Zhu Q, Ye C, Bancroft I, King GJ, Meng J, Fan L. Genome-wide selection footprints and deleterious variations in young Asian allotetraploid rapeseed. PLANT BIOTECHNOLOGY JOURNAL 2019;17:1998-2010. [PMID: 30947395 PMCID: PMC6737024 DOI: 10.1111/pbi.13115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/16/2019] [Accepted: 03/13/2019] [Indexed: 05/19/2023]
355
Martin SL, Parent JS, Laforest M, Page E, Kreiner JM, James T. Population Genomic Approaches for Weed Science. PLANTS (BASEL, SWITZERLAND) 2019;8:E354. [PMID: 31546893 PMCID: PMC6783936 DOI: 10.3390/plants8090354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
356
He Y, Luo X, Zhou B, Hu T, Meng X, Audano PA, Kronenberg ZN, Eichler EE, Jin J, Guo Y, Yang Y, Qi X, Su B. Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants. Nat Commun 2019;10:4233. [PMID: 31530812 PMCID: PMC6749001 DOI: 10.1038/s41467-019-12174-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022]  Open
357
Gao Y, Xi F, zhang H, Liu X, Wang H, zhao L, Reddy AS, Gu L. Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity. Curr Bioinform 2019. [DOI: 10.2174/1574893614666190204151746] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
358
Wingfield BD, Fourie A, Simpson MC, Bushula-Njah VS, Aylward J, Barnes I, Coetzee MPA, Dreyer LL, Duong TA, Geiser DM, Roets F, Steenkamp ET, van der Nest MA, van Heerden CJ, Wingfield MJ. IMA Genome-F 11: Draft genome sequences of Fusarium xylarioides, Teratosphaeria gauchensis and T. zuluensis and genome annotation for Ceratocystis fimbriata. IMA Fungus 2019;10:13. [PMID: 32355613 PMCID: PMC7184890 DOI: 10.1186/s43008-019-0013-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/01/2019] [Indexed: 01/21/2023]  Open
359
Stroehlein AJ, Korhonen PK, Chong TM, Lim YL, Chan KG, Webster B, Rollinson D, Brindley PJ, Gasser RB, Young ND. High-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing. Gigascience 2019;8:giz108. [PMID: 31494670 PMCID: PMC6736295 DOI: 10.1093/gigascience/giz108] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/25/2019] [Accepted: 08/10/2019] [Indexed: 01/30/2023]  Open
360
Bråte J, Fuss J, Jakobsen KS, Klaveness D. Draft genome assembly and transcriptome sequencing of the golden algae Hydrurus foetidus (Chrysophyceae). F1000Res 2019;8:401. [DOI: 10.12688/f1000research.16734.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/27/2019] [Indexed: 11/20/2022]  Open
361
Zhang J, Guan W, Huang C, Hu Y, Chen Y, Guo J, Zhou C, Chen R, Du B, Zhu L, Huanhan D, He G. Combining next-generation sequencing and single-molecule sequencing to explore brown plant hopper responses to contrasting genotypes of japonica rice. BMC Genomics 2019;20:682. [PMID: 31464583 PMCID: PMC6716848 DOI: 10.1186/s12864-019-6049-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/20/2019] [Indexed: 02/02/2023]  Open
362
Wang D, Chen X, Zhang X, Li J, Yi Y, Bian C, Shi Q, Lin H, Li S, Zhang Y, You X. Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes. Mar Drugs 2019;17:E503. [PMID: 31466296 PMCID: PMC6780625 DOI: 10.3390/md17090503] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/20/2019] [Accepted: 08/26/2019] [Indexed: 12/25/2022]  Open
363
Feng S, Xu M, Liu F, Cui C, Zhou B. Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe. BMC PLANT BIOLOGY 2019;19:365. [PMID: 31426739 PMCID: PMC6701088 DOI: 10.1186/s12870-019-1968-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 08/09/2019] [Indexed: 05/11/2023]
364
Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU. Getting the Entire Message: Progress in Isoform Sequencing. Front Genet 2019;10:709. [PMID: 31475029 PMCID: PMC6706457 DOI: 10.3389/fgene.2019.00709] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/04/2019] [Indexed: 01/31/2023]  Open
365
Wang J, Deng Y, Zhou Y, Liu D, Yu H, Zhou Y, Lv J, Ou L, Li X, Ma Y, Dai X, Liu F, Zou X, Ouyang B, Li F. Full-length mRNA sequencing and gene expression profiling reveal broad involvement of natural antisense transcript gene pairs in pepper development and response to stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019;99:763-783. [PMID: 31009127 DOI: 10.1111/tpj.14351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/18/2019] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
366
Kaposi Sarcoma-Associated Herpesvirus Glycoprotein H Is Indispensable for Infection of Epithelial, Endothelial, and Fibroblast Cell Types. J Virol 2019;93:JVI.00630-19. [PMID: 31142670 DOI: 10.1128/jvi.00630-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023]  Open
367
Mukherjee S, Cai Z, Mukherjee A, Longkumer I, Mech M, Vupru K, Khate K, Rajkhowa C, Mitra A, Guldbrandtsen B, Lund MS, Sahana G. Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis). BMC Genomics 2019;20:617. [PMID: 31357931 PMCID: PMC6664528 DOI: 10.1186/s12864-019-5980-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/16/2019] [Indexed: 12/20/2022]  Open
368
Panthee S, Paudel A, Blom J, Hamamoto H, Sekimizu K. Complete Genome Sequence of Weissella hellenica 0916-4-2 and Its Comparative Genomic Analysis. Front Microbiol 2019;10:1619. [PMID: 31396169 PMCID: PMC6667553 DOI: 10.3389/fmicb.2019.01619] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/01/2019] [Indexed: 12/21/2022]  Open
369
Gao Y, Liu B, Wang Y, Xing Y. TideHunter: efficient and sensitive tandem repeat detection from noisy long-reads using seed-and-chain. Bioinformatics 2019;35:i200-i207. [PMID: 31510677 PMCID: PMC6612900 DOI: 10.1093/bioinformatics/btz376] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
370
Borgers K, Ou JY, Zheng PX, Tiels P, Van Hecke A, Plets E, Michielsen G, Festjens N, Callewaert N, Lin YC. Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine. BMC Genomics 2019;20:561. [PMID: 31286858 PMCID: PMC6615170 DOI: 10.1186/s12864-019-5909-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022]  Open
371
Wan Y, Liu X, Zheng D, Wang Y, Chen H, Zhao X, Liang G, Yu D, Gan L. Systematic identification of intergenic long-noncoding RNAs in mouse retinas using full-length isoform sequencing. BMC Genomics 2019;20:559. [PMID: 31286854 PMCID: PMC6615288 DOI: 10.1186/s12864-019-5903-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023]  Open
372
Jiang F, Zhang J, Liu Q, Liu X, Wang H, He J, Kang L. Long-read direct RNA sequencing by 5'-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts. RNA Biol 2019;16:950-959. [PMID: 30982421 PMCID: PMC6546357 DOI: 10.1080/15476286.2019.1602437] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/20/2022]  Open
373
Boldogkői Z, Moldován N, Balázs Z, Snyder M, Tombácz D. Long-Read Sequencing – A Powerful Tool in Viral Transcriptome Research. Trends Microbiol 2019;27:578-592. [DOI: 10.1016/j.tim.2019.01.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/21/2019] [Accepted: 01/30/2019] [Indexed: 12/16/2022]
374
Firtina C, Bar-Joseph Z, Alkan C, Cicek AE. Hercules: a profile HMM-based hybrid error correction algorithm for long reads. Nucleic Acids Res 2019;46:e125. [PMID: 30124947 PMCID: PMC6265270 DOI: 10.1093/nar/gky724] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/07/2018] [Indexed: 01/15/2023]  Open
375
Complete Genome Sequence of Citrobacter rodentium Strain DBS100. Microbiol Resour Announc 2019;8:8/24/e00421-19. [PMID: 31196922 PMCID: PMC6588040 DOI: 10.1128/mra.00421-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
376
Chen Z, Lu X, Xuan Y, Tang F, Wang J, Shi D, Fu S, Ren J. Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum. BMC PLANT BIOLOGY 2019;19:240. [PMID: 31170934 PMCID: PMC6555730 DOI: 10.1186/s12870-019-1850-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 05/28/2019] [Indexed: 05/05/2023]
377
Current challenges and solutions of de novo assembly. QUANTITATIVE BIOLOGY 2019. [DOI: 10.1007/s40484-019-0166-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
378
Heydari M, Miclotte G, Van de Peer Y, Fostier J. Illumina error correction near highly repetitive DNA regions improves de novo genome assembly. BMC Bioinformatics 2019;20:298. [PMID: 31159722 PMCID: PMC6545690 DOI: 10.1186/s12859-019-2906-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022]  Open
379
Bi Q, Zhao Y, Du W, Lu Y, Gui L, Zheng Z, Yu H, Cui Y, Liu Z, Cui T, Cui D, Liu X, Li Y, Fan S, Hu X, Fu G, Ding J, Ruan C, Wang L. Pseudomolecule-level assembly of the Chinese oil tree yellowhorn (Xanthoceras sorbifolium) genome. Gigascience 2019;8:giz070. [PMID: 31241154 PMCID: PMC6593361 DOI: 10.1093/gigascience/giz070] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/02/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022]  Open
380
Zhao Y, Zhang Z, Li M, Luo J, Chen F, Gong Y, Li Y, Wei Y, Su Y, Kong L. Transcriptomic profiles of 33 opium poppy samples in different tissues, growth phases, and cultivars. Sci Data 2019;6:66. [PMID: 31110243 PMCID: PMC6527585 DOI: 10.1038/s41597-019-0082-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/12/2019] [Indexed: 11/16/2022]  Open
381
Elbers JP, Rogers MF, Perelman PL, Proskuryakova AA, Serdyukova NA, Johnson WE, Horin P, Corander J, Murphy D, Burger PA. Improving Illumina assemblies with Hi-C and long reads: An example with the North African dromedary. Mol Ecol Resour 2019;19:1015-1026. [PMID: 30972949 PMCID: PMC6618069 DOI: 10.1111/1755-0998.13020] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 12/22/2022]
382
Li S, Cha SW, Heffner K, Hizal DB, Bowen MA, Chaerkady R, Cole RN, Tejwani V, Kaushik P, Henry M, Meleady P, Sharfstein ST, Betenbaugh MJ, Bafna V, Lewis NE. Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements. J Proteome Res 2019;18:2433-2445. [PMID: 31020842 DOI: 10.1021/acs.jproteome.8b00935] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
383
Babarinde IA, Li Y, Hutchins AP. Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts. Comput Struct Biotechnol J 2019;17:628-637. [PMID: 31193391 PMCID: PMC6526290 DOI: 10.1016/j.csbj.2019.04.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 12/17/2022]  Open
384
Diploid Genome Assembly of the Wine Grape Carménère. G3-GENES GENOMES GENETICS 2019;9:1331-1337. [PMID: 30923135 PMCID: PMC6505170 DOI: 10.1534/g3.119.400030] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
385
Peng X, Liu H, Chen P, Tang F, Hu Y, Wang F, Pi Z, Zhao M, Chen N, Chen H, Zhang X, Yan X, Liu M, Fu X, Zhao G, Yao P, Wang L, Dai H, Li X, Xiong W, Xu W, Zheng H, Yu H, Shen S. A Chromosome-Scale Genome Assembly of Paper Mulberry (Broussonetia papyrifera) Provides New Insights into Its Forage and Papermaking Usage. MOLECULAR PLANT 2019;12:661-677. [PMID: 30822525 DOI: 10.1016/j.molp.2019.01.021] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 01/18/2019] [Accepted: 01/20/2019] [Indexed: 05/21/2023]
386
Villamor DEV, Ho T, Al Rwahnih M, Martin RR, Tzanetakis IE. High Throughput Sequencing For Plant Virus Detection and Discovery. PHYTOPATHOLOGY 2019;109:716-725. [PMID: 30801236 DOI: 10.1094/phyto-07-18-0257-rvw] [Citation(s) in RCA: 180] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
387
Wang B, Kumar V, Olson A, Ware D. Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing. Front Genet 2019;10:384. [PMID: 31105749 PMCID: PMC6498185 DOI: 10.3389/fgene.2019.00384] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/09/2019] [Indexed: 12/23/2022]  Open
388
Unveiling novel targets of paclitaxel resistance by single molecule long-read RNA sequencing in breast cancer. Sci Rep 2019;9:6032. [PMID: 30988345 PMCID: PMC6465246 DOI: 10.1038/s41598-019-42184-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/19/2019] [Indexed: 12/31/2022]  Open
389
Bråte J, Fuss J, Mehrota S, Jakobsen KS, Klaveness D. Draft genome assembly and transcriptome sequencing of the golden algae Hydrurus foetidus (Chrysophyceae). F1000Res 2019;8:401. [PMID: 31632652 PMCID: PMC6784874 DOI: 10.12688/f1000research.16734.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/03/2019] [Indexed: 01/01/2023]  Open
390
Zhang X, Li G, Jiang H, Li L, Ma J, Li H, Chen J. Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system. FISH & SHELLFISH IMMUNOLOGY 2019;87:346-359. [PMID: 30677515 DOI: 10.1016/j.fsi.2019.01.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 06/09/2023]
391
Kuosmanen A, Norri T, Mäkinen V. Evaluating approaches to find exon chains based on long reads. Brief Bioinform 2019;19:404-414. [PMID: 28069635 PMCID: PMC5952954 DOI: 10.1093/bib/bbw137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 11/25/2022]  Open
392
Bao E, Xie F, Song C, Song D. FLAS: fast and high-throughput algorithm for PacBio long-read self-correction. Bioinformatics 2019;35:3953-3960. [DOI: 10.1093/bioinformatics/btz206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 02/18/2019] [Accepted: 03/19/2019] [Indexed: 02/02/2023]  Open
393
Zhao L, Zhang H, Kohnen MV, Prasad KVSK, Gu L, Reddy ASN. Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing. Front Genet 2019;10:253. [PMID: 30949200 PMCID: PMC6438080 DOI: 10.3389/fgene.2019.00253] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/06/2019] [Indexed: 12/18/2022]  Open
394
Minio A, Massonnet M, Figueroa-Balderas R, Vondras AM, Blanco-Ulate B, Cantu D. Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development. G3 (BETHESDA, MD.) 2019;9:755-767. [PMID: 30642874 PMCID: PMC6404599 DOI: 10.1534/g3.118.201008] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/09/2019] [Indexed: 01/13/2023]
395
Nielsen SKD, Koch TL, Hauser F, Garm A, Grimmelikhuijzen CJP. De novo transcriptome assembly of the cubomedusa Tripedalia cystophora, including the analysis of a set of genes involved in peptidergic neurotransmission. BMC Genomics 2019;20:175. [PMID: 30836949 PMCID: PMC6402141 DOI: 10.1186/s12864-019-5514-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 02/07/2019] [Indexed: 11/20/2022]  Open
396
Limasset A, Flot JF, Peterlongo P. Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs. Bioinformatics 2019;36:1374-1381. [DOI: 10.1093/bioinformatics/btz102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 01/07/2019] [Accepted: 02/18/2019] [Indexed: 12/25/2022]  Open
397
Song QA, Catlin NS, Brad Barbazuk W, Li S. Computational analysis of alternative splicing in plant genomes. Gene 2019;685:186-195. [PMID: 30321657 DOI: 10.1016/j.gene.2018.10.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 09/16/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022]
398
Fu S, Wang A, Au KF. A comparative evaluation of hybrid error correction methods for error-prone long reads. Genome Biol 2019;20:26. [PMID: 30717772 PMCID: PMC6362602 DOI: 10.1186/s13059-018-1605-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 12/05/2018] [Indexed: 12/20/2022]  Open
399
Ma J, Wan D, Duan B, Bai X, Bai Q, Chen N, Ma T. Genome sequence and genetic transformation of a widely distributed and cultivated poplar. PLANT BIOTECHNOLOGY JOURNAL 2019;17:451-460. [PMID: 30044051 PMCID: PMC6335071 DOI: 10.1111/pbi.12989] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 05/20/2023]
400
Chebbi MA, Becking T, Moumen B, Giraud I, Gilbert C, Peccoud J, Cordaux R. The Genome ofArmadillidium vulgare(Crustacea, Isopoda) Provides Insights into Sex Chromosome Evolution in the Context of Cytoplasmic Sex Determination. Mol Biol Evol 2019;36:727-741. [DOI: 10.1093/molbev/msz010] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
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