Ding P, Sakai T, Shrestha RK, Perez NM, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG (2020)
Chromatin accessibility landscapes activated by cell surface and intracellular immune receptors. bioRxiv preprint June 18, 2020 doi: https://doi.org/10.1101/2020.06.17.157040
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Langner T, Harant A, Gómez-Luciano LB, Shrestha RK, Win J, Kamoun S (2020)
Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus. bioRxiv preprint Jan 11, 2020 doi: https://doi.org/10.1101/2020.01.10.901983
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Ding P, Ngou BPM, Furzer OJ, Sakai T, Shrestha RK, MacLean D, Jones JDG (2020)
High-resolution Expression Profiling of Selected Gene Sets during Plant Immune Activation. Plant Biotechnol J. 2020 Jan 8. doi: 10.1111/pbi.13327.
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Ding P, Ngou BPM, Oliver J. Furzer OJ, Sakai T, Shrestha RK, MacLean D, Jones JDG (2019)
High-resolution Expression Profiling of Selected Gene Sets during Plant Immune Activation. bioRxiv preprint Sep 23, 2019 doi: https://doi.org/10.1101/775973
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Shrestha RK, Ding P, Jones JDG, MacLean D (2018)
A workflow for simplified analysis of ATAC-cap-seq data in R. GigaScience, 2017, 1–7. DOI: 10.1093/gigascience/giy080
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Scheepers C, Shrestha RK, Lambson BE, Jackson KJ, Wright IA, Naicker D, Goosen M, Berrie L, Ismail A, Garrett N, Abdool Karim Q, Abdool Karim SS, Moore PL, Travers SA, Morris L (2015)
Ability To Develop Broadly Neutralizing HIV-1 Antibodies Is Not Restricted by the Germline Ig Gene Repertoire. J Immunol. 194(9):4371-8. doi: 10.4049/jimmunol.1500118.
Shrestha RK, Lubinsky B, Bansode VB, Moinz MB, McCormack GP, Travers SA (2014)
QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform. BMC Bioinformatics. 2014 Jan 30;15:33. doi: 10.1186/1471-2105-15-33.
Bansode V, McCormack GP, Crampin AC, Ngwira B, Shrestha RK, French N, Glynn JR, Travers SA (2013)
Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing. BMC Infect Dis. 2013 Jan 30;13:52. doi: 10.1186/1471-2334-13-52.
Crous S, Shrestha RK, Travers SA (2012)
Appraising the performance of genotyping tools in the prediction of coreceptor tropism in HIV-1 subtype C viruses. BMC Infect Dis. 2012 Sep 2;12:203. doi: 10.1186/1471-2334-12-203.