Akhil Kumar

I am a Research Fellow at the Perumal Lab, part of the School of Biological Sciences at Indian Institute of Technology (IIT) Delhi, where I use bioinformatics tools to understand viral pathogens’ sequencing data. My project advisor is Vivekanandan Perumal. Before this, I was an undergraduate at the Chemical Engineering Department, Indian Institute of Technology (IIT) Delhi.

Email / GitHub / Google Scholar / LinkedIn / CV

Research

I'm interested in developing and using bioinformatics tools to understand sequencing data.

Changing dynamics of CpG depletion in SARS-CoV-2 genomes over time and the role of various selection pressures

Akhil Kumar, Nishank Goyal, Nandhini Saranathan, Sonam Dhamija, Saurabh Saraswat, Manoj B Menon, Perumal Vivekanandan
Molecular Biology and Evolution, 2022
paper / code /

Investigated the changing dynamics of CpG depletion in SARS-CoV-2 genomes over time and role of various selection pressures. Led the computational work, clearly defined the objectives beforehand, advocated the use of best-programming practices. Successfully tested all custom written functions, classes by designing exhaustive test-cases for unit testing before using them. Single-handedly refactored the code repository for our project to enhance execution speed, improve code design and readability. Mastered the use of Python, attained proficiency in the use of regular expressions, version control, and test-driven development.

Other Projects

These include unpublished research work from internships, coursework, and side projects.

	Temporal evolution of mono- and dinucleotides in human mitochondrial DNA Perumal Lab, Indian Institute of Technology Delhi Independent study 2019-11-28 slides / Inspected temporal evolution of mono- and dinucleotides in human mtDNA by analysing sequences dated back to 50k BC. Developed boxplots for samples from earliest-, middle- and latest-period; conducted statistical tests to compare their medians. Our findings suggested that lighter strand is becoming heavier, and a slight bias toward GC-rich sequences in ancient reads.
	In-silico design of small ligand molecules to inhibit early-stage insulin aggregation nucleation Multiscale Modeling Group, Indian Institute of Technology Delhi Coursework 2019-11-24 slides / Assisted with the in-silico design of small ligand molecules to inhibit early-stage insulin aggregation nucleation. Identified EGCG and polyoxometalates as the putative ligands through extensive literature review, programmed their structures. Performed targeted docking of EGCG into a partially folded intermediate of insulin using Gray lab’s ROSIE server.
	Systematic construction and validation of kinetic model from metabolic networks Biomolecular Computational Group, Indian Institute of Science Bangalore Summer Internship 2019-07-15 slides / Investigated existing kinetic modelling approaches to translate metabolic networks of interest into a dynamic model. Designed a convenience kinetics based dynamic model comprising 92 reactions, 110 species using complex pathway simulator. Distributed the reactions across 4 compartments and simulated its dynamic characterstics; examined robustness of the model.
	Single-cell transcriptomic data analysis Srinivas Group, University of Oxford Summer Internship 2018-07-24 code / Analysed single-cell transcriptomic data collected from early mouse embryo mutant carrying a mutation in ASPP-2 gene. Processed sequence data files, mapped sequence reads, performed quality control on the individual cells, normalized the data. Identified cell sub-types using an unbiased hierarchical clustering algorithm and expression values for biological marker genes. NOTE: The code repository for this project is private, please contact me for access.