Associate Computational Scientist-Psychiatry Dr. 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
• Perform quality control, filtering, and format standardization across genotype sources
• Implement and troubleshoot imputation workflows and integration of mixed genotype datasets
• Ensure robust genotype–transcriptome linkage for accurate demultiplexing and downstream analyses
• Single-Cell & Multiomic Analysis
• Analyze scRNA-seq, snATAC-seq, multiome, and spatial transcriptomics datasets using modern frameworks (e.g., Scanpy, SnapATAC2, Squidpy, Pegasus or related tools)
• Perform dataset integration using probabilistic and deep learning approaches (e.g., scVI, scANVI or similar models)
• Conduct differential expression and variance partitioning analyses across complex designs (donor, condition, batch)
• Conduct trajectory inference and lineage mapping across developmental systems
• Integrative & Translational Analysis
• Map organoid-derived cell states to in vivo fetal and postmortem datasets
• Identify conserved transcriptional and regulatory programs across genetic and pharmacologic disease models
• Infer gene regulatory networks and candidate signaling pathways
• Qualifications
• Masters degree or equivalent in computational biology, bioinformatics, genomics, or a related field - Ph.D. in a scientific domain preferred.
• Beginner level, with some experience in a scientific/academic computing environment or equivalent preferred.
• Strong programming skills in Python (required); familiarity with R strongly preferred.
• Demonstrated experience working with single-cell genomics data.
• Strong quantitative and statistical background.
• Ability to work both independently and collaboratively in a highly iterative, interdisciplinary environment.
• Interest in biological interpretation and hypothesis generation, not just data processing.

Requirements

None specified.

Skills

Not specified.

Benefits

Not specified.

Pay

$72473 - $108709 Annually.

Schedule

Not specified.