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For: Bushmanova E, Antipov D, Lapidus A, Suvorov V, Prjibelski AD. rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. Bioinformatics 2016;32:2210-2. [PMID: 27153654 DOI: 10.1093/bioinformatics/btw218] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 04/18/2016] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
51
Bliznina A, Masunaga A, Mansfield MJ, Tan Y, Liu AW, West C, Rustagi T, Chien HC, Kumar S, Pichon J, Plessy C, Luscombe NM. Telomere-to-telomere assembly of the genome of an individual Oikopleura dioica from Okinawa using Nanopore-based sequencing. BMC Genomics 2021;22:222. [PMID: 33781200 PMCID: PMC8008620 DOI: 10.1186/s12864-021-07512-6] [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: 09/21/2020] [Accepted: 03/05/2021] [Indexed: 11/10/2022]  Open
52
Behera S, Voshall A, Moriyama EN. Plant Transcriptome Assembly: Review and Benchmarking. Bioinformatics 2021. [DOI: 10.36255/exonpublications.bioinformatics.2021.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
53
Galise TR, Esposito S, D'Agostino N. Guidelines for Setting Up a mRNA Sequencing Experiment and Best Practices for Bioinformatic Data Analysis. Methods Mol Biol 2021;2264:137-162. [PMID: 33263908 DOI: 10.1007/978-1-0716-1201-9_10] [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: 06/12/2023]
54
Sharma P, Sharma BS, Verma RJ. A Guide to RNAseq Data Analysis Using Bioinformatics Approaches. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
55
Mora-Márquez F, Vázquez-Poletti JL, Chano V, Collada C, Soto Á, de Heredia UL. Hardware Performance Evaluation of De novo Transcriptome Assembly Software in Amazon Elastic Compute Cloud. Curr Bioinform 2020. [DOI: 10.2174/1574893615666191219095817] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
56
Alejo-Jacuinde G, González-Morales SI, Oropeza-Aburto A, Simpson J, Herrera-Estrella L. Comparative transcriptome analysis suggests convergent evolution of desiccation tolerance in Selaginella species. BMC PLANT BIOLOGY 2020;20:468. [PMID: 33046015 PMCID: PMC7549206 DOI: 10.1186/s12870-020-02638-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 09/04/2020] [Indexed: 05/04/2023]
57
Puglia GD, Prjibelski AD, Vitale D, Bushmanova E, Schmid KJ, Raccuia SA. Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.). BMC Genomics 2020;21:317. [PMID: 32819282 PMCID: PMC7441626 DOI: 10.1186/s12864-020-6670-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/13/2020] [Indexed: 12/11/2022]  Open
58
Nip KM, Chiu R, Yang C, Chu J, Mohamadi H, Warren RL, Birol I. RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes. Genome Res 2020;30:1191-1200. [PMID: 32817073 PMCID: PMC7462077 DOI: 10.1101/gr.260174.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 07/23/2020] [Indexed: 12/27/2022]
59
Miller CH, Campbell P, Sheehan MJ. Distinct evolutionary trajectories of V1R clades across mouse species. BMC Evol Biol 2020;20:99. [PMID: 32770934 PMCID: PMC7414754 DOI: 10.1186/s12862-020-01662-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 07/21/2020] [Indexed: 11/10/2022]  Open
60
Prjibelski AD, Puglia GD, Antipov D, Bushmanova E, Giordano D, Mikheenko A, Vitale D, Lapidus A. Extending rnaSPAdes functionality for hybrid transcriptome assembly. BMC Bioinformatics 2020;21:302. [PMID: 32703149 PMCID: PMC7379828 DOI: 10.1186/s12859-020-03614-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 06/18/2020] [Indexed: 11/29/2022]  Open
61
Mikheenko A, Bzikadze AV, Gurevich A, Miga KH, Pevzner PA. TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. Bioinformatics 2020;36:i75-i83. [PMID: 32657355 PMCID: PMC7355294 DOI: 10.1093/bioinformatics/btaa440] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
62
Chen LY, Morales-Briones DF, Passow CN, Yang Y. Performance of gene expression analyses using de novo assembled transcripts in polyploid species. Bioinformatics 2020;35:4314-4320. [PMID: 31400193 DOI: 10.1093/bioinformatics/btz620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 07/12/2019] [Accepted: 08/09/2019] [Indexed: 12/24/2022]  Open
63
Malovichko YV, Shtark OY, Vasileva EN, Nizhnikov AA, Antonets KS. Transcriptomic Insights into Mechanisms of Early Seed Maturation in the Garden Pea (Pisum sativum L.). Cells 2020;9:E779. [PMID: 32210065 PMCID: PMC7140803 DOI: 10.3390/cells9030779] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 02/07/2023]  Open
64
Bushmanova E, Antipov D, Lapidus A, Prjibelski AD. rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data. Gigascience 2020;8:5559527. [PMID: 31494669 PMCID: PMC6736328 DOI: 10.1093/gigascience/giz100] [Citation(s) in RCA: 407] [Impact Index Per Article: 81.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 04/20/2019] [Accepted: 08/01/2019] [Indexed: 12/18/2022]  Open
65
MicroRNAs regulate innate immunity against uropathogenic and commensal-like Escherichia coli infections in the surrogate insect model Galleria mellonella. Sci Rep 2020;10:2570. [PMID: 32054914 PMCID: PMC7018962 DOI: 10.1038/s41598-020-59407-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 01/15/2020] [Indexed: 12/23/2022]  Open
66
Tung LH, Shao M, Kingsford C. Quantifying the benefit offered by transcript assembly with Scallop-LR on single-molecule long reads. Genome Biol 2019;20:287. [PMID: 31849338 PMCID: PMC6918626 DOI: 10.1186/s13059-019-1883-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 11/06/2019] [Indexed: 12/19/2022]  Open
67
Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study. High Throughput 2019;8:ht8040020. [PMID: 31801255 PMCID: PMC6970227 DOI: 10.3390/ht8040020] [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] [Received: 10/31/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 12/15/2022]  Open
68
Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris. G3-GENES GENOMES GENETICS 2019;9:3409-3421. [PMID: 31427456 PMCID: PMC6778806 DOI: 10.1534/g3.119.400357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
69
Bendele KG, Guerrero FD, Cameron C, Bodine DM, Miller RJ. Gene expression during the early stages of host perception and attachment in adult female Rhipicephalus microplus ticks. EXPERIMENTAL & APPLIED ACAROLOGY 2019;79:107-124. [PMID: 31552563 DOI: 10.1007/s10493-019-00420-1] [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: 06/19/2019] [Accepted: 09/13/2019] [Indexed: 06/10/2023]
70
Van de Weyer AL, Monteiro F, Furzer OJ, Nishimura MT, Cevik V, Witek K, Jones JDG, Dangl JL, Weigel D, Bemm F. A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. Cell 2019;178:1260-1272.e14. [PMID: 31442410 PMCID: PMC6709784 DOI: 10.1016/j.cell.2019.07.038] [Citation(s) in RCA: 220] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/13/2019] [Accepted: 07/19/2019] [Indexed: 12/18/2022]
71
Ojeda DI, Koenen E, Cervantes S, de la Estrella M, Banguera-Hinestroza E, Janssens SB, Migliore J, Demenou BB, Bruneau A, Forest F, Hardy OJ. Phylogenomic analyses reveal an exceptionally high number of evolutionary shifts in a florally diverse clade of African legumes. Mol Phylogenet Evol 2019;137:156-167. [DOI: 10.1016/j.ympev.2019.05.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 04/26/2019] [Accepted: 05/02/2019] [Indexed: 11/15/2022]
72
Drukewitz SH, von Reumont BM. The Significance of Comparative Genomics in Modern Evolutionary Venomics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00163] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
73
Hölzer M, Marz M. De novo transcriptome assembly: A comprehensive cross-species comparison of short-read RNA-Seq assemblers. Gigascience 2019;8:giz039. [PMID: 31077315 PMCID: PMC6511074 DOI: 10.1093/gigascience/giz039] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/21/2018] [Accepted: 03/09/2019] [Indexed: 12/13/2022]  Open
74
Rivera-García L, Rivera-Vicéns RE, Veglia AJ, Schizas NV. De novo transcriptome assembly of the digitate morphotype of Briareum asbestinum (Octocorallia: Alcyonacea) from the southwest shelf of Puerto Rico. Mar Genomics 2019;47:100676. [PMID: 31005610 DOI: 10.1016/j.margen.2019.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022]
75
The assembled transcriptome of the adult horn fly, Haematobia irritans. Data Brief 2018;19:1933-1940. [PMID: 30229068 PMCID: PMC6141423 DOI: 10.1016/j.dib.2018.06.095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 06/27/2018] [Indexed: 11/20/2022]  Open
76
Khan H, Mohamadi H, Vandervalk BP, Warren RL, Chu J, Birol I. ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole genome sequencing data. Bioinformatics 2018;34:1697-1704. [PMID: 29300846 PMCID: PMC5946899 DOI: 10.1093/bioinformatics/btx839] [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: 01/25/2017] [Accepted: 12/28/2017] [Indexed: 11/13/2022]  Open
77
Mora-Márquez F, Vázquez-Poletti JL, López de Heredia U. NGScloud: RNA-seq analysis of non-model species using cloud computing. Bioinformatics 2018;34:3405-3407. [DOI: 10.1093/bioinformatics/bty363] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 05/02/2018] [Indexed: 01/13/2023]  Open
78
Esteve-Codina A. RNA-Seq Data Analysis, Applications and Challenges. COMPREHENSIVE ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/bs.coac.2018.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
79
Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. THE JOURNAL OF IMMUNOLOGY 2017;199:3369-3380. [PMID: 28978691 DOI: 10.4049/jimmunol.1700485] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/24/2017] [Indexed: 12/16/2022]
80
Challenges and advances for transcriptome assembly in non-model species. PLoS One 2017;12:e0185020. [PMID: 28931057 PMCID: PMC5607178 DOI: 10.1371/journal.pone.0185020] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 09/04/2017] [Indexed: 12/28/2022]  Open
81
Duan J, Sanggaard KW, Schauser L, Lauridsen SE, Enghild JJ, Schierup MH, Wang T. Transcriptome analysis of the response of Burmese python to digestion. Gigascience 2017;6:1-18. [PMID: 28873961 PMCID: PMC5597892 DOI: 10.1093/gigascience/gix057] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/12/2017] [Accepted: 07/06/2017] [Indexed: 12/13/2022]  Open
82
Gravouil K, Ferru-Clément R, Colas S, Helye R, Kadri L, Bourdeau L, Moumen B, Mercier A, Ferreira T. Transcriptomics and Lipidomics of the Environmental Strain Rhodococcus ruber Point out Consumption Pathways and Potential Metabolic Bottlenecks for Polyethylene Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017;51:5172-5181. [PMID: 28345896 DOI: 10.1021/acs.est.7b00846] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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