
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
Read moreI am interested in bioinformatics analysis of genomic sequence changes in prokaryotic (virus, bacteria etc) to eukaryotic organisms and genetic expression profiling in plants and animals. I like to develop computational pipelines and workflows for computational analysis of genetic sequences. My PhD work was focused on finding a method for low-cost HIV drug resistance test. I developed a python pipeline that takes in HIV genes (reverse transcriptase and protease) sequence data from samples collected from infected patients, quality controls the data, pools the sequences specific to a sample, maps the data to a standard reference sequence, determines the mutations in the HIV genetic sequences, infers drug resistance for the mutations based on Stanford HIV drug resistance mutation database and generates a patient specific drug resistance report.
I like exploring different bioinformatics open tools, learning the underlining algorithms of the tools and comparing the tools that are basically doing similar analysis.
ram_krishna.shrestha@tsl.ac.uk
+44 (0) 1603 450601
A workflow for simplified analysis of ATAC-cap-seq data in R. GigaScience, 2017, 1–7. DOI: 10.1093/gigascience/giy080
Read moreAbility 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.
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.
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.
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.
2013 – 2016 Core Bioinformatician, Earlham Institute, Norwich, UK