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For: Ren X, Liu T, Dong J, Sun L, Yang J, Zhu Y, Jin Q. Evaluating de Bruijn graph assemblers on 454 transcriptomic data. PLoS One 2012;7:e51188. [PMID: 23236450 PMCID: PMC3517413 DOI: 10.1371/journal.pone.0051188] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 10/31/2012] [Indexed: 12/29/2022]  Open
Number Cited by Other Article(s)
1
Fallon TR, Čalounová T, Mokrejš M, Weng JK, Pluskal T. transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation. BMC Bioinformatics 2023;24:133. [PMID: 37016291 PMCID: PMC10074830 DOI: 10.1186/s12859-023-05254-8] [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: 03/21/2022] [Accepted: 03/24/2023] [Indexed: 04/06/2023]  Open
2
Gibney D, Thankachan SV, Aluru S. On the Hardness of Sequence Alignment on De Bruijn Graphs. J Comput Biol 2022;29:1377-1396. [DOI: 10.1089/cmb.2022.0411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]  Open
3
Steffen K, Laborde Q, Gunasekera S, Payne CD, Rosengren KJ, Riesgo A, Göransson U, Cárdenas P. Barrettides: A Peptide Family Specifically Produced by the Deep-Sea Sponge Geodia barretti. JOURNAL OF NATURAL PRODUCTS 2021;84:3138-3146. [PMID: 34874154 PMCID: PMC8713285 DOI: 10.1021/acs.jnatprod.1c00938] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Indexed: 05/16/2023]
4
Luo Y, Liao X, Wu FX, Wang J. Computational Approaches for Transcriptome Assembly Based on Sequencing Technologies. Curr Bioinform 2020. [DOI: 10.2174/1574893614666190410155603] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
5
Bibi N, Niaz H, Hupp T, Kamal MA, Rashid S. Screening and Identification of PLK1-Polo Box Binding Peptides by High-Throughput Sequencing of Phage-Selected Libraries. Protein Pept Lett 2019;26:620-633. [PMID: 30887917 DOI: 10.2174/0929866526666190318101054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 01/08/2023]
6
Persinoti GF, Martinez DA, Li W, Döğen A, Billmyre RB, Averette A, Goldberg JM, Shea T, Young S, Zeng Q, Oliver BG, Barton R, Metin B, Hilmioğlu-Polat S, Ilkit M, Gräser Y, Martinez-Rossi NM, White TC, Heitman J, Cuomo CA. Whole-Genome Analysis Illustrates Global Clonal Population Structure of the Ubiquitous Dermatophyte Pathogen Trichophyton rubrum. Genetics 2018;208:1657-1669. [PMID: 29467168 PMCID: PMC5887155 DOI: 10.1534/genetics.117.300573] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 02/07/2018] [Indexed: 11/18/2022]  Open
7
Enriching Genomic Resources and Marker Development from Transcript Sequences of Jatropha curcas for Microgravity Studies. Int J Genomics 2017;2017:8614160. [PMID: 28154822 PMCID: PMC5244023 DOI: 10.1155/2017/8614160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/28/2016] [Indexed: 01/22/2023]  Open
8
Kang SW, Patnaik BB, Hwang HJ, Park SY, Chung JM, Song DK, Patnaik HH, Lee JB, Kim C, Kim S, Park HS, Han YS, Lee JS, Lee YS. Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers. Mol Genet Genomics 2016;291:1999-2014. [PMID: 27507702 DOI: 10.1007/s00438-016-1233-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/25/2016] [Indexed: 02/03/2023]
9
De novo assembly of transcriptome from next-generation sequencing data. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0069-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
10
Serra AA, Couée I, Heijnen D, Michon-Coudouel S, Sulmon C, Gouesbet G. Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress. FRONTIERS IN PLANT SCIENCE 2015;6:1124. [PMID: 26734031 PMCID: PMC4681785 DOI: 10.3389/fpls.2015.01124] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 11/27/2015] [Indexed: 05/26/2023]
11
Daly GM, Leggett RM, Rowe W, Stubbs S, Wilkinson M, Ramirez-Gonzalez RH, Caccamo M, Bernal W, Heeney JL. Host Subtraction, Filtering and Assembly Validations for Novel Viral Discovery Using Next Generation Sequencing Data. PLoS One 2015;10:e0129059. [PMID: 26098299 PMCID: PMC4476701 DOI: 10.1371/journal.pone.0129059] [Citation(s) in RCA: 25] [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: 09/10/2014] [Accepted: 05/04/2015] [Indexed: 12/18/2022]  Open
12
Powell D, Knibb W, Remilton C, Elizur A. De-novo transcriptome analysis of the banana shrimp (Fenneropenaeus merguiensis) and identification of genes associated with reproduction and development. Mar Genomics 2015;22:71-8. [PMID: 25936497 DOI: 10.1016/j.margen.2015.04.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/20/2015] [Accepted: 04/20/2015] [Indexed: 01/07/2023]
13
Xu X, Liu T, Ren X, Liu B, Yang J, Chen L, Wei C, Zheng J, Dong J, Sun L, Zhu Y, Jin Q. Proteogenomic Analysis of Trichophyton rubrum Aided by RNA Sequencing. J Proteome Res 2015;14:2207-18. [PMID: 25868943 DOI: 10.1021/acs.jproteome.5b00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
14
Laumer CE, Hejnol A, Giribet G. Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation. eLife 2015;4:e05503. [PMID: 25764302 PMCID: PMC4398949 DOI: 10.7554/elife.05503] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/06/2015] [Indexed: 12/25/2022]  Open
15
Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biol 2014. [PMID: 25608678 DOI: 10.1101/006338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]  Open
16
Li B, Fillmore N, Bai Y, Collins M, Thomson JA, Stewart R, Dewey CN. Evaluation of de novo transcriptome assemblies from RNA-Seq data. Genome Biol 2014;15:553. [PMID: 25608678 PMCID: PMC4298084 DOI: 10.1186/s13059-014-0553-5] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 10/30/2014] [Indexed: 01/16/2023]  Open
17
Marchant A, Mougel F, Almeida C, Jacquin-Joly E, Costa J, Harry M. De novo transcriptome assembly for a non-model species, the blood-sucking bug Triatoma brasiliensis, a vector of Chagas disease. Genetica 2014;143:225-39. [PMID: 25233990 DOI: 10.1007/s10709-014-9790-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/01/2014] [Indexed: 11/29/2022]
18
Wang C, Grohme MA, Mali B, Schill RO, Frohme M. Towards decrypting cryptobiosis--analyzing anhydrobiosis in the tardigrade Milnesium tardigradum using transcriptome sequencing. PLoS One 2014;9:e92663. [PMID: 24651535 PMCID: PMC3961413 DOI: 10.1371/journal.pone.0092663] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 02/25/2014] [Indexed: 11/18/2022]  Open
19
Vázquez-Castellanos JF, García-López R, Pérez-Brocal V, Pignatelli M, Moya A. Comparison of different assembly and annotation tools on analysis of simulated viral metagenomic communities in the gut. BMC Genomics 2014;15:37. [PMID: 24438450 PMCID: PMC3901335 DOI: 10.1186/1471-2164-15-37] [Citation(s) in RCA: 63] [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: 03/13/2013] [Accepted: 01/16/2014] [Indexed: 02/07/2023]  Open
20
A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems. EvoDevo 2013;4:16. [PMID: 23731568 PMCID: PMC3748831 DOI: 10.1186/2041-9139-4-16] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 03/14/2013] [Indexed: 11/10/2022]  Open
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