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AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.
Rashid U, Wu C, Shiller J, Smith K, Crowhurst R, Davy M, Chen TH, Carvajal I, Bailey S, Thomson S, Deng CH. Rashid U, et al. Among authors: thomson s. Bioinformatics. 2024 Aug 2;40(8):btae477. doi: 10.1093/bioinformatics/btae477. Bioinformatics. 2024. PMID: 39078114 Free PMC article.
A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.
Pilkington SM, Crowhurst R, Hilario E, Nardozza S, Fraser L, Peng Y, Gunaseelan K, Simpson R, Tahir J, Deroles SC, Templeton K, Luo Z, Davy M, Cheng C, McNeilage M, Scaglione D, Liu Y, Zhang Q, Datson P, De Silva N, Gardiner SE, Bassett H, Chagné D, McCallum J, Dzierzon H, Deng C, Wang YY, Barron L, Manako K, Bowen J, Foster TM, Erridge ZA, Tiffin H, Waite CN, Davies KM, Grierson EP, Laing WA, Kirk R, Chen X, Wood M, Montefiori M, Brummell DA, Schwinn KE, Catanach A, Fullerton C, Li D, Meiyalaghan S, Nieuwenhuizen N, Read N, Prakash R, Hunter D, Zhang H, McKenzie M, Knäbel M, Harris A, Allan AC, Gleave A, Chen A, Janssen BJ, Plunkett B, Ampomah-Dwamena C, Voogd C, Leif D, Lafferty D, Souleyre EJF, Varkonyi-Gasic E, Gambi F, Hanley J, Yao JL, Cheung J, David KM, Warren B, Marsh K, Snowden KC, Lin-Wang K, Brian L, Martinez-Sanchez M, Wang M, Ileperuma N, Macnee N, Campin R, McAtee P, Drummond RSM, Espley RV, Ireland HS, Wu R, Atkinson RG, Karunairetnam S, Bulley S, Chunkath S, Hanley Z, Storey R, Thrimawithana AH, Thomson S, David C, Testolin R, Huang H, Hellens RP, Schaffer RJ. Pilkington SM, et al. Among authors: thomson s. BMC Genomics. 2018 Apr 16;19(1):257. doi: 10.1186/s12864-018-4656-3. BMC Genomics. 2018. PMID: 29661190 Free PMC article.
First Chromosome-Scale Assembly and Deep Floral-Bud Transcriptome of a Male Kiwifruit.
Tahir J, Crowhurst R, Deroles S, Hilario E, Deng C, Schaffer R, Le Lievre L, Brendolise C, Chagné D, Gardiner SE, Knaebel M, Catanach A, McCallum J, Datson P, Thomson S, Brownfield LR, Nardozza S, Pilkington SM. Tahir J, et al. Among authors: thomson s. Front Genet. 2022 May 16;13:852161. doi: 10.3389/fgene.2022.852161. eCollection 2022. Front Genet. 2022. PMID: 35651931 Free PMC article. No abstract available.
High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content.
Montanari S, Thomson S, Cordiner S, Günther CS, Miller P, Deng CH, McGhie T, Knäbel M, Foster T, Turner J, Chagné D, Espley R. Montanari S, et al. Among authors: thomson s. Front Plant Sci. 2022 Sep 23;13:965397. doi: 10.3389/fpls.2022.965397. eCollection 2022. Front Plant Sci. 2022. PMID: 36247546 Free PMC article.
Identification and Characterization of Innate Immunity in Actinidia melanandra in Response to Pseudomonas syringae pv. actinidiae.
Hemara LM, Chatterjee A, Yeh SM, Chen RKY, Hilario E, Lievre LL, Crowhurst RN, Bohne D, Arshed S, Patterson HR, Barrett-Manako K, Thomson S, Allan AC, Brendolise C, Chagné D, Templeton MD, Tahir J, Jayaraman J. Hemara LM, et al. Among authors: thomson s. Plant Cell Environ. 2025 Feb;48(2):1037-1050. doi: 10.1111/pce.15189. Epub 2024 Oct 13. Plant Cell Environ. 2025. PMID: 39400369 Free PMC article.
1,350 results