Dr Ram Krishna Shrestha

Computational Biologist
Bioinformatics

I 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.

Publications

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

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

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.