Turning multi-omic data into therapeutic insight: 5+ years postdoctoral research across single-cell and spatial genomics, 10 peer-reviewed publications, and 2,000,000+ single cells analyzed across 10+ projects spanning immuno-oncology and cardiovascular immunology.

📧 nayanchoton1789@gmail.com · 🔗 LinkedIn · 🆔 ORCID 0000-0002-4564-872X

Flagship

• 🧬 bioinformatics-portfolio — variant analysis, scRNA-seq (Seurat + Scanpy), scATAC-seq, spatial transcriptomics, and a checkpoint-blockade biomarker (AUROC 0.86) built from raw GEO data

Single-cell & multi-omics

• scATAC-WNN-multimodal — 10x Multiome RNA+ATAC integration via WNN, chromVAR TF motif scoring
• cite-seq-wnn-trajectory — CITE-seq WNN integration + Monocle3 pseudotime

Functional genomics & perturbation

• crispr-mageck-screen — MAGeCK CRISPR screen hit-calling + GO/KEGG enrichment
• perturb-seq-deep-learning — PyTorch classifier predicting CRISPRi guide identity from expression (44.0% vs. 30.8% baseline)

Bulk sequencing pipelines

• nf-variant-pipeline — Nextflow germline + somatic (Mutect2) variant calling
• bulk-rnaseq-star-deseq2 — STAR→DESeq2 Snakemake DAG with SLURM, SQL, Spark, and a verified Airflow DAG
• bulk-chipseq-pipeline — Input-controlled ChIP-seq, 67% biological-replicate concordance
• bulk-atacseq-pipeline — Tn5 shift, fragment-size & TSS-enrichment QC, MACS3 peak calling
• cutandrun-pipeline — bowtie2 + MACS3 peak calling on public CUT&Tag data

• Containers — Docker/Singularity profiles in nf-variant-pipeline; pinned biocontainers per rule in every Snakemake DAG; Dockerfiles in cite-seq-wnn-trajectory, crispr-mageck-screen, perturb-seq-deep-learning and spatial-visium-squidpy
• HPC (SLURM + Apptainer) — SLURM job scripts and a Docker/Apptainer runtime switch across the pipeline repos, e.g. bulk-rnaseq-star-deseq2, bulk-chipseq-pipeline, bulk-atacseq-pipeline, cutandrun-pipeline
• AWS (EC2 + S3) — one-shot launcher scripts that run an analysis on an EC2 instance, sync results to S3 and terminate, e.g. aws/launch_ec2.sh; Nextflow awsbatch profile in nf-variant-pipeline
• Workflow engines — Nextflow, Snakemake, Airflow DAG, PySpark

• spatial-visium-squidpy — 10x Visium mouse brain with Scanpy + Squidpy: Leiden clustering, neighborhood enrichment, co-occurrence, Moran's I, ligand-receptor inference; Docker, SLURM and EC2 run scripts

• Yepuri G, Ramirez LM, et al. DIAPH1-MFN2 interaction regulates mitochondria-SR/ER contact and modulates ischemic/hypoxic stress. Nature Communications, 2023.
• Hasan SN, Sharma A, et al. Bcl11b prevents catastrophic autoimmunity by controlling multiple aspects of a regulatory T cell gene expression program. Science Advances, 2019.
• Kim CJ, Lee CG, et al. The transcription factor Ets1 suppresses T follicular helper type 2 cell differentiation to halt systemic lupus erythematosus. Immunity, 2018.

Full list (10 peer-reviewed papers) on ORCID.