The Center for Infection and Immunity is seeking a Sr. Programmer Analyst in Bioinformatics for developing pipelines to analyze large-scale gene expression datasets. The successful applicant will join a dynamic laboratory consisting of approximately 50 personnel at Columbia University and a global network of researchers that work on projects related to infectious disease surveillance and discovery in humans and wildlife, host response to infections, microbiome research, and large-scale studies on autism and chronic fatigue syndrome/myalgic encephalomyelitis.
The candidate is expected to demonstrate the following skills and experience:
Advanced knowledge of bioinformatics, statistics, systems biology, including biological pathway and network analysis, with working knowledge of writing pipelines for analysis of gene expression data from Illumina sequencing platform.
Thorough knowledge of NGS experimental design, data quality control, mapping software such as Bowtie, BWA or STAR, normalization and clustering methods, Tuxedo Suite tools such as Tophat and Cufflinks, Gene Set Enrichment Analysis, Ingenuity Pathway Analysis, and UCSC genome browser
Experience with genome annotations from major bioinformatics resources (NCBI, UCSC).
Ability to work in Unix environments consisting of high-performance clusters.
Advanced understanding of multi-threading tools (SGE, MPI), resource management, and allocation.
Broad knowledge scripting languages, such as Shell, Python, Perl, and R in an academic or industrial environment. Proficiency in R and Bioconductor packages is desirable.
Provide bioinformatics support for RNA-Seq analysis in a large and dynamic laboratory - 50%
Provide support for projects related to microbial detection and discovery - 30%
Manage databases - 10%
Contribute to publications and research grants - 5%
Perform other related duties as assigned - 5%
Bachelor's degree or equivalent in education and 4 years experience required.
Master???s or Ph.D. degree in epidemiology, biostatistics, public health, or a relevant field of study would substitute for experience
Advanced knowledge of bioinformatics, statistics, systems biology, including biological pathway and network analysis, with working knowledge of writing pipelines for analysis of gene expression data from Illumina sequencing platform. Proficiency in R and Bioconductor packages is desirable.
Equal Opportunity Employer / Disability / Veteran
Columbia University is committed to the hiring of qualified local residents.
Internal Number: 516390
About Columbia University
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.