The Center for Infection and Immunity at Columbia University Irving Medical Center (CUIMC) and the Mailman School of Public Health is hiring for the position of Staff Associate (Bioinformatics) to join one of the world's largest and most advanced center for basic and translational science, with a global network of researchers, focused on chronic and infectious diseases, microbial surveillance, discovery and diagnosis in humans and wildlife. The successful candidate will be part of a talented team of bioinformaticians and statisticians that work on the development and maintenance of clinical pipelines for FDA and New York State Clinical Laboratory Evaluation Program (CLEP) approval of microbial diagnostic assays. The candidate will participate in the data analysis and integration of single-cell/bulk RNA-Seq and other multi-omics datasets for large-scale studies on Chronic Fatigue Syndrome/Myalgic Encephalomyelitis (ME/CFS) with the goal of unraveling the underlying host-response mechanisms that will lead to methods for diagnosing, treating, and preventing ME/CFS.
The candidate will write programs for data analysis of Next Generation Sequencing (NGS) data generated from a variety of sequencing-based applications and perform data processing using on-site high-performance clusters (HPC) and Amazon Cloud. Ability to write code in Python, R and Shell scripting using containerization and workflow management tools would be considered a plus. The candidate will be responsible for maintaining the existing pipelines and genomic databases. The various high-impact projects will provide opportunities to participate in manuscript and grant writing.
Provide bioinformatics support for multi-omics analysis in a large and dynamic laboratory - 50%
Provide support for projects related to microbial detection and discovery - 30%
Manage databases and data - 10%
Contribute to publications and research grants - 5%
Perform other related duties as assigned - 5%
Candidate must possess the following for consideration:
Bachelor's degree in computer science, bioinformatics, or related field
Minimum of 4-6 year's related experience
Knowledge of commonly used bioinformatics tools and algorithms, writing pipelines for analysis of NGS datasets generated using Illumina sequencing platform, along with strong programming and analytical skills.
Experience in NGS experimental design, data quality control, mapping software such as Bowtie, BWA and STAR, genome annotations from major bioinformatics resources (ENSEMBL, EMBL, NCBI). RNA-Seq data analysis using featureCounts, DESeq2, cellranger and Seurat package would be desirable.
Knowledge and experience working with basic statistical analysis, supervised and unsupervised techniques in R.
High proficiency in scripting languages, such as Python, Bash and R in an academic or industrial environment.
Ability to work in Linux environments consisting of high-performance clusters or Amazon Cloud. Familiarity with SGE or Slurm schedulers, resource management, multi-threading tools.
Familiarity with Gene Set Enrichment Analysis or Ingenuity Pathway analysis
Thank you for your interest in the Columbia University Center for Infection and Immunity (CII). If interested and qualified for this position, please submit a CV and Cover Letter to link provided.
Columbia University is an Equal Opportunity Employer / Disability / Veteran
Columbia University is one of the world's most important centers of research and at the same time a distinctive and distinguished learning environment for undergraduates and graduate students in many scholarly and professional fields. The University recognizes the importance of its location in New York City and seeks to link its research and teaching to the vast resources of a great metropolis. It seeks to attract a diverse and international faculty and student body, to support research and teaching on global issues, and to create academic relationships with many countries and regions. It expects all areas of the university to advance knowledge and learning at the highest level and to convey the products of its efforts to the world.