Akanksha Sharma

CSIR-IHBT is one of 37 premier national research laboratories within India's Council of Scientific and Industrial Research (CSIR), the country's largest publicly-funded research organization. CSIR is equivalent t to

Project Associate I (Computational Biology) at CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT) (2024-01 – Present)

CSIR-IHBT is one of 37 premier national research laboratories within India's Council of Scientific and Industrial Research (CSIR), the country's largest publicly-funded research organization. CSIR is equivalent to organizations like CNRS (France) or Max Planck Society (Germany) in structure and mission. Supervisor: Dr. Ravi Shankar (Senior Principal Scientist)

• Developing Transformer-based deep learning model to predict DNA methylation states from RNA-seq data, using PyTorch to implement multi-head attention mechanisms for capturing long-range genomic dependencies
• Developed and deployed three public web servers for the research community (PTF-Vac, CTF-BIND, CritiCal-C), integrating deep learning models with user-friendly interfaces (HTML, CSS, JavaScript, Flask). These tools are currently in active use by researchers internationally.
• Performed bulk RNA-Seq analysis: quality control, read alignment, differential expression analysis, functional annotation, and pathway enrichment using Bioconductor packages in R
• Conducted whole-genome bisulfite sequencing (WGBS-seq) analysis: methylation calling, differential methylation analysis, integration with gene expression data
• Independently studied single-cell multi-omics sequencing through hands-on analysis of publicly available datasets: processed and integrated paired single-cell RNA-seq and single-cell WGBS-seq data from human colorectal cancer to understand cell-type-specific regulatory mechanisms
• Integrated multi-omics data to improve gene regulatory network inference, co-authoring paper in Current Plant Biology (IF 4.5, Q1)
• Conducted molecular dynamics simulations using GROMACS to study protein-DNA interactions and regulatory mechanisms
• Managed Linux-based bioinformatics pipelines and server infrastructure for computational research projects

Research Intern at Indian Institute of Science Education and Research (IISER), Bhopal (2023-05 – 2023-07)

IISER Bhopal is one of seven IISERs established by India's Ministry of Education for advanced scientific research and education, modeled after institutions like Caltech in the US. Project: Knowledge Graphs for Biomedical Data. Supervisor: Prof. Parthiban Srinivasan

• Integrated diverse genomic information from scientific databases (NCBI, Ensembl, UniProt), research literature, and clinical records
• Standardized and harmonized data formats across multiple heterogeneous datasets
• Applied text mining and natural language processing techniques for automated biomedical information extraction
• Created comprehensive knowledge graph schemas for structured representation of biomedical relationships

Master of Science (M.Sc.) in Human Genomics – Panjab University (2022-07)

Bachelor of Science (B.Sc.) in Bioinformatics (Honours) – GGDSD College-32 (affiliated with Panjab University) (2020-07)

Clinical Research Training in Medical Research – Post Graduate Institute of Medical Education and Research (PGIMER) (2022-03 – 2022-04)