Senior Bioinformatics Programmer
About The Position
NYU Grossman School of Medicine is seeking a Sr. Bioinformatics Programmer to join the Department of Molecular Pathology, specifically within the Applied Bioinformatics Laboratories (ABL) and the Molecular Pathology Lab. This role focuses on Clinical Genomics and Precision Medicine within a Molecular Diagnostics environment. The successful candidate will be responsible for developing and maintaining computational pipelines, creating bioinformatic tools for clinical Next Generation Sequencing (NGS) based diagnostics in collaboration with clinicians, and performing bioinformatics analysis of patient genomic, epigenomic, and transcriptomic data. This position offers an opportunity to work in an innovative environment, develop new analysis tools and pipelines, analyze complex datasets, and contribute to cutting-edge NGS-based cancer diagnostics, clinical genomics, and precision medicine.
Requirements
- M.Sc. plus a minimum of 3 years’ experience in Bioinformatics, Computer Science, Programming, Software Development, or related field
- Previous experience with NGS data and associated bioinformatics tools
- Experience in Unix/Linux systems including high-performance computing environments
- Strong programming skills in Python, R, shell scripting
- Proficiency in Nextflow, Django, Docker and Singularity containers
- Work experience and algorithm understanding of standard software tools used to generate and manipulate FASTQ, BAM, VCF files including but not limited to BWA, GATK, Picard, samtools, bcftools
- Knowledge in the analysis of SNV, Indel, CNV and structural variants for both somatic and germline disease, additional understanding of variant annotation
- Familiarity with various NGS QC principles
- Knowledge of biology, cancer genomics or an understanding of key and complex biological concepts
- Detail-oriented, well-organized and an interest in clinical sequencing and disease related or cancer genomics
- Ability to work independently (e.g., recommend new software or bioinformatic tools, find papers relevant to the subject, assess methods, implement methods, and apply them to datasets to reproduce results)
- Team oriented with excellent written and verbal communication skills
- Ability to function in a multidisciplinary team including MD’s and PhD’s
- Qualified candidates must be able to effectively communicate with all levels of the organization.
Nice To Haves
- Expert in creating customized sequencing analysis pipelines, in applications for data analysis, and executing standard bioinformatics pipelines (relevant examples in a GitHub repository).
- Basic knowledge and understanding of software engineering concepts
- Knowledge of algorithms, data structures, machine learning
- Prior experience working in CLIA environment is a plus
- Experience in variant calling benchmarking and clinical validation analysis (e.g. concordance, limit of detection, assay reproducibility)
- Experience with running workflows on public cloud (GCP / AWS)
- Experience with developing and querying databases using SQL queries
- Experience with web-development (HTML, CSS, JavaScript, TypeScript and related)
Responsibilities
- Enhance or develop new automated workflows/pipelines within a nextflow environment for bioinformatic tools utilizing next generation sequencing data in clinical diagnostic assays
- Use existing bioinformatics pipelines to analyze the molecular patient data generated in the clinical lab
- Oversee systems support for existing bioinformatics pipelines and develop new pipelines to support new molecular assays
- Support the team in its common clinical genomics and precision medicine goals
- Perform quality control of the generated sequencing data and develop solutions to enhance future performance
- Perform different types of data analysis relating to the genomics-based approaches utilized by the lab, in an independent fashion.
- Develop new methods for multi-omics data analysis and integration
- Work with bioinformatics scientists and clinical pathologists to analyze and interpret patient NGS results for better potential treatment options
- Work with lab users to analyze biomedical data and address clinical needs using bioinformatics techniques and tools
- Work with MCIIT and HPC team to provide current and future solutions for server, storage and other requirements.
Benefits
- financial security benefits
- a generous time-off program
- employee resources groups for peer support
- holistic employee wellness program, which focuses on seven key areas of well-being: physical, mental, nutritional, sleep, social, financial, and preventive care.
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What This Job Offers
Job Type
Full-time
Career Level
Senior
