Junior Bioinformatician

Providence Health & Services Santa Monica , CA 90405

Posted 4 weeks ago

Providence is calling a Junior Bioinformatician (Full Time, Day Shift) to John Wayne Cancer Institute in Santa Monica, CA.

We are seeking a Junior Bioinformatician who will be under the direction of the Department Administrative Manager and the Sequencing Center, the Junior Bioinformatician will provide analysis and computing support for cancer-related research including microarray and next-generation sequencing (NGS) data (genomic, transcriptomic, epigenomic, and proteomic) analysis.

In this position you will have the following responsibilities:

  • Analyze next-generation sequencing data using open-source tools

  • Able to interact with organization system hardware, software, infrastructure, and IT individuals routinely

  • Develop analysis pipelines for next generation sequencing data generated from the Illumina HiSeq 2500 and MiSeq platforms

  • Use open-source and/or develop tools for data processing and data visualization

  • Use open-source and/or develop tools to integrate analysis performed on multiple platforms to derive biological meaning

  • Work effectively with many people at various levels of the organization

  • Handle multiple tasks, appropriately prioritize, and complete on schedule

  • Maintain patient confidentiality and privacy in accordance to research and hospital policy (HIPAA)

  • Be a team player and support MD, PhDs and research technicians in bioinformatics analysis

  • Be able to provide data analysis reports in a timely manner

  • Assist in manuscript and grant writing related to bioinformatics

  • Fax, photocopy, and other administrative duties

Required qualifications for this position include:

  • Bachelor's Degree in Biology, Bioinformatics, Computational Biology, or a related field

  • Experience in processing and managing raw data generated from:

  • Expression, SNP, and DNA methylation microarrays

  • Whole-genome and targeted (exome and/or gene panel) sequencing

  • Transcriptomic (mRNA-seq and smRNA-seq) sequencing

  • Epigenomic (Methyl-seq and ChIP-seq) sequencing

  • Other Next Generation Sequencing (NGS) techniques

  • Experience with NGS data generated on Illumina sequencing instruments, including the HiSeq and MiSeq platforms

  • Experience using open source genomic analysis tools including SAMtools, Picard, GATK, BWA, MuTect, BEDtools, VCFtools, among others.

  • Experience using open source tools for the annotation and interpretation of genomic variants, such as ANNOVAR, VEP, SnpEff, among others.

  • Experience in transcriptome analysis, including differential expression analysis using DESeq2, edgeR, limma, or similar.

  • Experience in and understanding of the organization and utilization of public databases such as The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO-NCBI), ENCODE project, ArrayExpress (EMBL-EBI) among others

  • Experience working with large-scale NGS data in high performance cluster computing environments

  • Experience in at least one of the following scripting languages: bash, Python, or Perl

  • Experience in statistical analyses using R/Bioconductor

  • Unix/Linux system administration experience

  • Experience in biostatistics and bioinformatics

  • Self-starter who can manage multiple tasks in a multi-task translational research environment

  • Must be able to work cohesively with research personnel from multiple disciplines in human translational research

  • A good understanding of the next generation sequencing workflow

  • Ability to select and perform the most appropriate experimental design, analytical workflow, and analytic technique for different NGS data types

  • Ability to perform the appropriate analyses that may include: identifying SNPs, somatic variants, differential expression, alternative splicing, fusion genes, indels, structural variants, and copy number variations

  • Efficient organizational skills to catalogue, regulate, and maintain integrity of data

  • Excellent demonstrated oral and written communication skills

  • Ability to read, interpret, and apply scientific literature

  • Knowledge of basic genetics

  • Knowledge of basic statistics

Preferred qualifications for this position include:

  • Experience using cloud computing platforms such as Amazon and/or Google

  • Experience using Cancer Genomics Cloud (CGC) resources

  • Knowledge of human genetics

  • Knowledge of cancer and molecular biology

  • Publications that demonstrate knowledge and application of genomic analyses

About the hospital you will serve:

The John Wayne Cancer Institute at Providence Saint John's Health Center is a cancer research institute dedicated to the understanding and curing of cancer in order to eliminate patient suffering worldwide. The Institute's mission is accomplished by conducting innovative research focused on biological mechanisms to provide new understandings of the cause, diagnosis, control, and cure of cancer; training the next generation of surgical scientists who study and treat cancer; and researching unique experimental treatment services to rapidly develop and test new forms of diagnosis and therapy in order to improve the quality of life and expected survival of those afflicted with cancer.


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Junior Bioinformatician

Providence Health & Services