Bioinformatics Analyst

Primary Responsibilities

• Implement, document, and maintain standardized computational pipelines for analysis of multi-omics datasets, with particular emphasis on bulk RNA-seq and integration with proteomic, metabolomic, and lipidomic data.
• Build computational workflows based on genome-scale metabolic network models for identifying metabolic biomarkers, context-specific metabolic model reconstruction, and performing constraint-based flux analyses to generate mechanistic hypotheses.
• Apply established machine learning workflows for multi-omics integration, including feature selection, phenotype classification, latent network inference, and survival prediction using methods such as random forests, mixed graphical models, and related statistical learning techniques.
• Adapt computational pipelines for efficient execution on a high-performance computing (HPC) environment, including workflow automation and parallel computing.
• Apply these computational methods to collaborative studies investigating metabolic adaptations across multiple disease models, including diabetes, cancer dormancy, immune cell development, and neurodegenerative disease.
• Interpret computational results through collaboration with experimental scientists to generate biologically meaningful and experimentally testable hypotheses.
• Contribute to dissemination of methods and results through manuscripts and presentations.

Required Qualifications

• Bachelor's or Master's degree in Bioinformatics, Computational Biology, Biomedical Engineering, Computer Science, Applied Mathematics, or a related quantitative discipline, and at least 2 years of computational research experience after graduation.
• Strong programming experience in Python, MATLAB, and R.
• Experience developing reproducible computational analysis pipelines.
• Experience working in Linux/Unix environments and with version control systems.
• Familiarity with high-performance computing environments, workflow automation, and parallel computing.
• Excellent written and verbal scientific communication skills.
• Ability to work largely independently but with periodic guidance from PI and more senior lab members.

Preferred Qualifications

• Experience analyzing next-generation sequencing data, particularly RNA-seq.
• Familiarity with metabolomics, proteomics, lipidomics, or other multi-omics datasets.
• Experience applying machine learning methods to biological data.
• Experience with genome-scale metabolic modeling, constraint-based modeling, COBRA Toolbox/COBRApy, or related systems biology methods.
• Prior experience contributing to collaborative biomedical research and scientific publications.

Research Environment

The successful candidate will join an interdisciplinary research team in the Department of Systems & Computational Biology developing computational methods that integrate network biology, systems metabolism, and machine learning. The position provides opportunities to collaborate with multiple laboratories generating state-of-the-art multi-omics datasets and to develop computational tools with broad applicability across diverse disease models.

Current collaborative projects include studies of inflammatory responses in pancreatic islets, stress-induced alterations in thymic epithelial cells, metabolic reprogramming during breast cancer dormancy, and neurodegenerative disease associated with microglial dysfunction.

Appointment

This is a full-time, grant-funded appointment expected to last one to two years, contingent upon continued funding. Successful performance is expected to result in substantial contributions to multiple collaborative projects and co-authorship on peer-reviewed publications. The position also offers excellent experience for individuals interested in pursuing graduate study or careers in computational biology, bioinformatics, systems biology, or biomedical data science.

The Chang Lab at Albert Einstein College of Medicine is seeking a highly motivated Bioinformatics Analyst to join a collaborative…