Location: New York, NY
Cap-Exempt H-1B Position — No lottery required
**Description** This position will serve as a senior computational scientist responsible for the analysis, integration, and interpretation of large-scale single-cell, multiomic, and genomic datasets generated by the laboratory. The individual will play a central role in transforming raw sequencing data into biologically interpretable models of human brain development and neuropsychiatric disease. The role includes end-to-end ownership of computational workflows spanning raw sequencing processing, genotype-based demultiplexing, single-cell and spatial transcriptomic analysis, and multiomic data integration. The scientist will lead the development and maintenance of reproducible analysis pipelines and will be responsible for ensuring consistency across large, heterogeneous datasets derived from multiple genetic and pharmacologic disease models. A major component of the position involves integrating diverse datasets—including scRNA-seq, snATAC-seq, multiome, and spatial transcriptomics—with human fetal and postmortem reference atlases to define conserved and disease-specific cell states. The individual will also contribute to the identification of regulatory programs and candidate signaling pathways for experimental validation in organoid systems. This role requires close collaboration with experimental scientists to iteratively refine hypotheses, prioritize perturbation targets, and guide experimental design based on computational findings. https://profiles.icahn.mssm.edu/deepak-kaji **Responsibilities** **Data Processing & Infrastructure** - Process raw sequencing data (FASTQ), including alignment and quantification for single-cell and single-nucleus assays - Perform genotype-based demultiplexing using tools such as cellsnp-lite and Vireo (or related methods) - Build and maintain reproducible, well-documented analysis pipelines - Genotype & VCF Handling (critical component) - Generate, curate, and harmonize VCFs from whole-genome sequencing and SNP array data - Perfo