Summary
My name is Asish Kumar Swain, I am currently a PhD candidate at the Indian Institute of Technology, Jodhpur, India. My research interests focus on the analysis and algorithm development in single-cell and spatial transcriptomics. Additionally, I have over six years of experience in various subdomains of computational biology and data science.
Education
Indian Institute of Technology (IIT), Jodhpur, India (2021 – Present)
Ph.D, Computational Biology (Topic: Algorithm development in spatial and single-cell omics; CGPA: 8.77/10)
Indian Institute of Science Education & Research (IISER), Mohali, India (2015 – 2020)
BS-MS Dual Degree (Biological Science)
Research Interests
- Single-cell and spatial transcriptomics
- Computational biology and data science
- Algorithm development in omics data analysis
Technical Competencies
- Programming Languages: Python, R, Bash, LATEX
- Bioinformatics: scRNA-seq, spatial, GWAS, multi-omics
- Frameworks: Seurat, ScanPy, Scikit-learn, Pytorch, Docker
- Statistics: Math models, ML, DL, CNN, GNN
- Operating Systems: Debian, Ubuntu, CentOS, MacOS, Windows
- Wet-lab: Basic molecular biology techniques
Abbr: GWAS: Genome Wide Association Studies; ML: Machine Learning; DL: Deep Learning; CNN: Convolution Neural Net; GNN: Graph Neural Net.
Research Experience
Indian Institute of Technology (IIT), Jodhpur, India (2021 – Present)
- Development of scalable spot deconvolution and clustering method for low-resolution spatial omics (Completed).
- Development of unsupervised automated cell type annotation tool for single-cell omics (Completed).
- Gene enhancement algorithm development for image-based spatial omics (Ongoing).
- Integration of GWAS and single cell multi-omics datasets (Ongoing).
Indian Institute of Science Education & Research (IISER), Mohali, India (2015 – 2020)
- Molecular modelling and network analysis in folate family proteins across eukaryotes.
- Malaria cell image detection using convolution neural network. (Link)
Invited Talks
- “Spatialprompt: Spatially aware scalable and accurate tool for spot deconvolution and clustering in spatial transcriptomics”, Human Cell Atlas-pre-meeting, Kolkata, India (2023)
- Spot deconvolution and clustering in spatial transcriptomics, Asian Student Council Symposium (2024)
- “Computational Methods for Analyzing, Modelling and Predicting the behaviour of exploitative or applicatory biological systems”, V.V.P Engg College, Rajkot, India (2022)
- Resource person in basic molecular techniques workshops by AIIMS, Jodhpur, India (2021 & 2022)
Conferences
- Poster presentation: Human Cell Atlas - General Meeting, Milan, Italy (2024)
- Poster presentation: Human Cell Atlas - Asia, Kolkata, India (2023)
- Poster presentation: Indian Cancer Genome Atlas, Pune, India (2023)
Fellowship and Achievements
- Awarded travel grant ($1000) - Human Cell Atlas General Meeting, Milan, Italy (2024)
- Awarded travel grant ($400) - Human Cell Atlas Asia, Kolkata, India (2023)
- Qualified GATE-BT (Graduate Aptitude Test in Engineering - Biotechnology) (2020)
- Qualified NET-LS (National Eligibility Test for Lectureship in India) (2020)
- DST: INSPIRE Fellow (2015-2020)
- Qualified JEE Mains and AIPMT (2015)
- Qualified NEST exam (All India Rank: 1024) (2015)
Teaching Assistantship
- Designs in Omics Experiments, IIT Jodhpur (2023)
- Statistics and Data Analysis Lab, IIT Jodhpur (2023)
- Intro to Bio-Eng: Theory & Lab, IIT Jodhpur (2022)
- Computational and Systems Biology, IIT Jodhpur (2022)
- Supervised 10+ B.Tech and master’s students for projects related to computational biology.