Rimjhim Roy Choudhury

Responsibilities and Achievements

• Organization of Polyploid Summer School 2023

  (Live session link)

• DNA methylation analysis from long reads datasets
• Comparative transcriptomics of tetraploids

Technologies used:

• Unix
• Python
• R
• Slurm HPC
• Snakemake

I led a team of young bioinformaticians who worked on Mendelian randomization and rare variant GWAS analysis for various phenotypes related to heart, liver, kidney, metabolic and neurological diseases in the UKBiobank's 450,000 participant data. Our primary objective was to develop efficient pipelines that leverage the vast whole genome dataset of the UK Biobank to support research and provide valuable insights for the pharmaceutical industry in designing safer and more effective drugs, reducing the risk of adverse events. I also worked on a project to map genes and gene networks that predispose to NAFLD/NASH. I analysed the kidney and liver transcriptome of a population of mice generated by breeding different strains with varying levels of susceptibility to the disease.

Responsibilities and Achievements:

I was responsible for the bioinformatics team working under high-pressure to enhance the efficiency of bioinformatics projects within my research group through timely data generation and reporting to pharmaceutical companies. My main responsibilities are:

• Mendelian randomization and analysis of rare genetic variants to mitigate risks in drug development.
• Gene expression analysis of a genetically diverse mice population fed with western diet under thermoneutral conditions to induce liver disease.
• Mentoring Ph.D. students

Technologies used:

• UKBiobank
• DNAnexus
• Snakemake
• Slurm HPC
• R
• python
• Cloud computing

I studied the role of whole-genome duplication in the origin of S-locus supergene in Primulaceae. Worked with several genome assemblies and transcriptome datasets to investigate the lack of descending dysploidy and unbiased genome fractionation in ancient polyploids.

Responsibilities and Achievements

• I led the genome and repeat annotation for four Primulaceae genomes .
• I worked on analyzing the repeat content and subgenome gene content and expression fractionation in Androcaceae
• I was involved in analysis of TE based genome shock after hybridization of Primula species

Technologies used:

• Unix
• Python
• R
• Slurm HPC
• Snakemake

I worked on a complex polyploid plant genome trying to understand the relative impact of gene expression and transposon-mediated silencing on patterns of duplicated gene retention as well as the role of selection on retained duplicates.

Responsibilities and Achievements:

I was responsible for the bioinformatics management in the ecological genomics group at the University of Bern ensured smooth functioning of the bioinformatics projects. My main responsibilities are:

• The study of the impact of sequence turnover and conservation in shaping genome following whole-genome duplication.
• Annotation of transposable elements and genes
• Genome assembly using long read and linked read sequencing technologies
• Mentoring Ph.D. and masters students

Technologies used:

• Unix
• Python
• R
• Slurm HPC
• Pacbio
• 10x Genomics
• Illumina NovaSeq

During my successfully published Ph.D. thesis, I have worked on the development of various bioinformatics pipelines from annotation to variant calling related to large transposable element fragments in population datasets. I have also applied my pipeline on different datasets provided by collaborating groups. I have always challenged myself to find optimal solutions to complex problems.

Achievements:

• Transposable element annotation and characterization
• Population genomics of insertion/deletions related to transposable elements using whole-genome sequencing technology (Illumina-HiSeq) and their comparative analysis with SNPs from the same dataset
• Study of transposable element-mediated adaptive variation in alpine plant populations
• RNA-Seq and differential expression analysis

Technologies used:

• Phylogenomics
• Population Genomics
• Deseq2
• Python
• R
• Unix
• Platform LSF