Bioinformatics Analyst

Albert Einstein College of Medicine is seeking a highly motivated Bioinformatics Analyst to join the research group of Dr. Robert Burk. This role is central to translating large-scale sequencing datasets into rigorous, publication-ready results with direct relevance to chronic disease, cancer prevention, and infectious disease research.

Responsibilities

Design, implement, document, and maintain end-to-end NGS pipelines for microbiome and HPV genomics applications (e.g., 16S/ITS1 amplicon sequencing, shotgun metagenomics, viral/HPV sequencing, bisulfite sequencing, and viral integration analyses)

Perform robust QC, read processing, reference alignment, taxonomic and functional profiling, strain-level analyses where appropriate, and reproducible reporting for cohort-scale datasets

Harmonize sequencing outputs with clinical and epidemiologic metadata (including complex longitudinal designs), perform data cleaning and validation, and generate analysis-ready tables

Conduct and interpret statistical analyses using R and/or Python, including microbiome-specific methods (alpha/beta diversity, ordination, PERMANOVA, differential abundance) and epidemiologic modeling (regression and related approaches), with publication-quality visualizations

Lead defined analysis workstreams, set realistic milestones, communicate risks and dependencies early, and present progress and results in lab meetings and to collaborators

Diagnose and resolve complex issues (pipeline failures, batch effects, contamination artifacts, inconsistent metadata, compute bottlenecks). Improve robustness, scalability, and runtime efficiency on shared compute environments

Use version control (Git), structured documentation, and reproducible execution practices (workflow managers and/or containerization when appropriate). Maintain clear provenance from raw data to results

Propose fresh analytic ideas, evaluate new tools and methods, and contribute to interpretation and narrative framing of findings

Contribute figures, methods text, and analyses for manuscripts and grant applications

Preferred

Experience in microbiome bioinformatics (16S, ITS1, shotgun metagenomics) and/or viral genomics with familiarity with phylogenetics, or integration-related analyses

Experience working with protected clinical or epidemiologic data and with best practices for data security and governance

Experience analyzing large cohorts and handling confounding, batch effects, and complex study designs (longitudinal, nested case-control, matched studies)

Comfort translating analyses into clear figures, methods, and results text suitable for high-impact manuscripts

Microbiome bioinformatics

Viral genomics

Phylogenetics

Data security

Epidemiologic data

Data governance

Cohort analysis

Confounding handling

Batch effects

Complex study designs

Longitudinal studies

Nested case-control studies

Matched studies

Clear communication

Analytical thinking

Company

Medical school for biomedical research and education

Bronx, New York, USA

https://einsteinmed.edu/

Founded in 1953

1001-5000 employees

Qualifications

Bachelor's degree in bioinformatics, computational biology, biostatistics, epidemiology, computer science, or a related field; Master's or PhD preferred

Strong programming ability in R and/or Python, plus comfort working in a Unix/Linux environment (shell scripting, HPC-style workflows)

Demonstrated experience processing and analyzing NGS data, including building or extending pipelines rather than only running existing ones

Solid understanding of basic statistical concepts and the ability to translate scientific questions into appropriate analyses

Track record of independent problem solving, attention to detail, and producing reliable, well-documented outputs

Strong communication skills and a collaborative mindset for working with interdisciplinary teams

Experience in microbiome bioinformatics (16S, ITS1, shotgun metagenomics) and/or viral genomics with familiarity with phylogenetics, or integration-related analyses

Experience working with protected clinical or epidemiologic data and with best practices for data security and governance

Experience analyzing large cohorts and handling confounding, batch effects, and complex study designs (longitudinal, nested case-control, matched studies)

Comfort translating analyses into clear figures, methods, and results text suitable for high-impact manuscripts

Required skills

Containerization, Epidemiologic modeling, High-performance computing workflows, Independent problem solving, Microbiome bioinformatics, Next-generation sequencing (NGS) data processing, Phylogenetics, Pipeline development for NGS data, Python programming, R programming, Represents the skills you have, Shell scripting, Statistical analysis, Unix/Linux environment, Viral genomics, Workflow management, click on the tags

Preferred skills

(73), (83), (84), (88), (97), *2026, 2020, 2021, 2022, 2023, 2024, 2025, 3.9, 65, Accounting and Finance, Bronx, New York, USA, Customer Service and Support, Data Powered by, Distribution of Different Job Fields Receiving Sponsorship, Education and Training, Engineering and Development, Glassdoor, H1B Sponsorship, Legal and Compliance, Management and Executive, Marketing, Product Management, Represents job field similar to this job, Trends of Total Sponsorships, https://einsteinmed.edu/

Experience

Mid level