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For: Lin HN, Hsu WL. DART: a fast and accurate RNA-seq mapper with a partitioning strategy. Bioinformatics 2018;34:190-197. [PMID: 28968831 PMCID: PMC5860201 DOI: 10.1093/bioinformatics/btx558] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/29/2017] [Accepted: 09/03/2017] [Indexed: 01/13/2023]  Open
Number Cited by Other Article(s)
1
Pronozin AY, Karetnikov DI, Shmakov NA, Bocharnikova ME, Afonnikova SD, Afonnikov DA, Kolchanov NA. CropGene: a software package for the analysis of genomic and transcriptomic data of agricultural plants. Vavilovskii Zhurnal Genet Selektsii 2025;29:320-329. [PMID: 40264806 PMCID: PMC12011622 DOI: 10.18699/vjgb-25-35] [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: 11/27/2024] [Revised: 01/15/2025] [Accepted: 01/15/2025] [Indexed: 04/24/2025]  Open
2
Ngoh IA, Mane K, Manneh J, Bojang F, Jawara AS, Akenji TN, Anong DN, D’Alessandro U, Amambua-Ngwa A. Transcriptome analysis reveals molecular targets of erythrocyte invasion phenotype diversity in natural Plasmodium falciparum isolates from Cameroon. FRONTIERS IN PARASITOLOGY 2024;3:1370615. [PMID: 39817175 PMCID: PMC11731687 DOI: 10.3389/fpara.2024.1370615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/24/2024] [Indexed: 01/18/2025]
3
Miller JR, Adjeroh DA. Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq. BMC Bioinformatics 2024;25:109. [PMID: 38475727 DOI: 10.1186/s12859-024-05728-3] [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: 07/28/2023] [Accepted: 03/01/2024] [Indexed: 03/14/2024]  Open
4
Fenn A, Tsoy O, Faro T, Rößler FM, Dietrich A, Kersting J, Louadi Z, Lio CT, Völker U, Baumbach J, Kacprowski T, List M. Alternative splicing analysis benchmark with DICAST. NAR Genom Bioinform 2023;5:lqad044. [PMID: 37260511 PMCID: PMC10227362 DOI: 10.1093/nargab/lqad044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 04/13/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023]  Open
5
Gerasimova SV, Kolosovskaya EV, Vikhorev AV, Korotkova AM, Hertig CW, Genaev MA, Domrachev DV, Morozov SV, Chernyak EI, Shmakov NA, Vasiliev GV, Kochetov AV, Kumlehn J, Khlestkina EK. WAX INDUCER 1 Regulates β-Diketone Biosynthesis by Mediating Expression of the Cer-cqu Gene Cluster in Barley. Int J Mol Sci 2023;24:ijms24076762. [PMID: 37047735 PMCID: PMC10095013 DOI: 10.3390/ijms24076762] [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: 02/21/2023] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023]  Open
6
Yamamoto N, Tong W, Lv B, Peng Z, Yang Z. The Original Form of C4-Photosynthetic Phosphoenolpyruvate Carboxylase Is Retained in Pooids but Lost in Rice. FRONTIERS IN PLANT SCIENCE 2022;13:905894. [PMID: 35958195 PMCID: PMC9358456 DOI: 10.3389/fpls.2022.905894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
7
Glagoleva AY, Vikhorev AV, Shmakov NA, Morozov SV, Chernyak EI, Vasiliev GV, Shatskaya NV, Khlestkina EK, Shoeva OY. Features of Activity of the Phenylpropanoid Biosynthesis Pathway in Melanin-Accumulating Barley Grains. FRONTIERS IN PLANT SCIENCE 2022;13:923717. [PMID: 35898231 PMCID: PMC9310326 DOI: 10.3389/fpls.2022.923717] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
8
Approaches in Gene Coexpression Analysis in Eukaryotes. BIOLOGY 2022;11:biology11071019. [PMID: 36101400 PMCID: PMC9312353 DOI: 10.3390/biology11071019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 11/22/2022]
9
Alser M, Rotman J, Deshpande D, Taraszka K, Shi H, Baykal PI, Yang HT, Xue V, Knyazev S, Singer BD, Balliu B, Koslicki D, Skums P, Zelikovsky A, Alkan C, Mutlu O, Mangul S. Technology dictates algorithms: recent developments in read alignment. Genome Biol 2021;22:249. [PMID: 34446078 PMCID: PMC8390189 DOI: 10.1186/s13059-021-02443-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 07/28/2021] [Indexed: 01/08/2023]  Open
10
Long noncoding RNAs are involved in multiple immunological pathways in response to vaccination. Proc Natl Acad Sci U S A 2019;116:17121-17126. [PMID: 31399544 PMCID: PMC6708379 DOI: 10.1073/pnas.1822046116] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
11
Van den Berge K, Hembach KM, Soneson C, Tiberi S, Clement L, Love MI, Patro R, Robinson MD. RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021255] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
12
Gurunathan S, Qasim M, Park C, Yoo H, Choi DY, Song H, Park C, Kim JH, Hong K. Cytotoxicity and Transcriptomic Analysis of Silver Nanoparticles in Mouse Embryonic Fibroblast Cells. Int J Mol Sci 2018;19:ijms19113618. [PMID: 30453526 PMCID: PMC6275036 DOI: 10.3390/ijms19113618] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/27/2018] [Accepted: 11/13/2018] [Indexed: 12/16/2022]  Open
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