We are seeking a highly skilled analyst/programmer interested in joining a computational genomics laboratory at the intersection of cutting-edge genomics and systems biology of kidney disease. The applicant will use their skills in high-performance, large scale computing and a deep understanding of statistical genetics at the genome-wide level to make original contributions to a diverse set of scientific projects that seek to understand the molecular pathogenesis of glomerular disease using human-based genotype and gene expression data. The applicant will work with a multidisciplinary research team made up of nephrologists, computational geneticists, genetic epidemiologists, bioinformaticians, and wet-bench researchers.
Within a cluster computer and linux environment, the applicant will work with genome-wide genotyping, sequencing, and transcriptomic data for processing, alignment, transfer, management, generation and analysis of genome-wide genotype files derived from patients with nephrotic syndrome, kidney disease and healthy controls. The applicant will use established computational programs for data generation and analysis. The position requires an individual capable of communicating with students and researchers, handling and prioritizing tasks across multiple projects, and working independently on critical tasks. The applicant must have excellent written and oral communication skills, strong analytical skills, excellent judgment, and the ability to work under deadlines with general guidance.
- Development of computer scripts/programs for the processing of genomic data, including quality control, statistical analysis, and functional interpretation.
- Creation, troubleshooting, and execution of specialized, custom computer scripts and programs to process and analyze genome-wide genetic and transcriptomic data.
- Maintenance and management of sequence data and analysis results. Analysis of next-generation sequencing data (whole genome sequencing, targeted DNA sequencing, and RNA-seq) using computer programs. ?
- Installation and execution of established analysis pipelines for the identification of genome variants including SNPs, indels, and structural variants.?
- Analysis of SNP data.
- Analysis of data and results, communication with external collaborators, and contributions to the preparation of manuscripts, grants, and presentations is required.
- MA/MS in computer science, bioinformatics, biostatistics, or a related field
- 2-3 years computer research experience
- Experience working as computational genomics researcher as a student or as a job with demonstrated expertise in bioinformatics.
- Experience with Unix/Linux and working with large datasets in a cluster-computing environment using job schedulers is required Experience with a language such as python, perl, shell scripting, or sed/awk is required, and the knowledge of lower-level language such as C/C++ or Java
- A working knowledge of basic principles of genetics/genomics such as gene structure, gene transcription is required
- A critical qualification is a strong desire to contribute to a cutting-edge research program that combines computational approaches with genomics data to gain insights into the basic biology of genomes, evolution, population variation, and the genetic basis of phenotypic variation.
- Experience with high-throughput genomic data, such as microarray, RNA-seq, DNA sequencing data
- Knowledge of standard software for genomic and genetic analysis such as BLAST, BWA, samtools, GATK, PLINK, Bowtie, Cufflink, or BLAT
- Basic statistics/data analysis abilities and experience with R
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