Senior Bioinformatics Programmer

Position Summary

The Molecular Pathology Lab at NYU Langone Health with the Applied Bioinformatics Laboratories (ABL) is seeking a highly motivated individual to join the clinical bioinformatics team. The successful candidate will be primarily responsible for enhancing or developing new automated workflows/pipelines within a Nextflow environment for bioinformatic tools utilizing Next Generation Sequencing (NGS) data in clinical diagnostic assays.

Job 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

Preferred Qualifications

• 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)

Minimum Qualifications

• 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
• Familiarity with 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