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Providence Health & Services Senior Bioinformatician in Santa Monica, California


Providence is calling a Senior Bioinformatician for Full-Time Day Shift to Providence Saint John's Cancer Institute in Santa Monica, CA.

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Please upload a current resume reflecting all relevant experience.

In this position you will:

  • Provide analysis and computing support for cancer-related research including microarray and next-generation sequencing (NGS) data (genomic, transcriptomic, epigenomic, and proteomic) analysis.


Required qualifications for this position include:

  • Ph.D. in Genetics, Cancer Biology, Bioinformatics, Computational Biology, or a related field or equivalent education/experience.

  • Equivalent experience in sequencing analysis.

  • Experience in processing and managing raw data generated from expression, SNP, and DNA methylation 450k/850K Epics microarrays; Whole-genome and targeted (exome and/or gene panel) sequencing; Transcriptomic (mRNA-seq and smRNA-seq) sequencing; Epigenomic (Methyl-seq and ChIP-seq, ATAC-seq) sequencing and; Other Next Generation Sequencing (NGS) techniques.

  • Experience with NGS data generated on Illumina sequencing instruments, including the NextSeq 550 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 other cancer databases (nucleic acids, proteomics, etc.).

  • 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. Must have understanding of TCGA-GDC portal and GDC FireBrowse and CaBioPortal cancer databases access and analysis.

  • 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. Ability to communicate with investigators on analysis outputs.

  • Excellent demonstrated oral and written communication skills.

  • Ability to read, interpret, and apply scientific literature.

  • Knowledge of bioinformatics.

  • Knowledge of basic statistics

  • Knowledge of human genetics.

  • Knowledge of human cancers and molecular biology.

  • Publication that demonstrate knowledge and application of genomic analyses.

Preferred qualifications for this position include:

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

  • Experience using Cancer Genomics Cloud (CGC) resources.

About the hospital you will serve:

The Saint John's 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.

We offer comprehensive, best-in-class benefits to our caregivers. For more information, visit

Our Mission

As expressions of God’s healing love, witnessed through the ministry of Jesus, we are steadfast in serving all, especially those who are poor and vulnerable.

About Us

Providence is a comprehensive not-for-profit network of hospitals, care centers, health plans, physicians, clinics, home health care and services continuing a more than 100-year tradition of serving the poor and vulnerable. Providence is proud to be an Equal Opportunity Employer. Providence does not discriminate on the basis of race, color, gender, disability, veteran, military status, religion, age, creed, national origin, sexual identity or expression, sexual orientation, marital status, genetic information, or any other basis prohibited by local, state, or federal law.

Schedule: Full-time

Shift: Day

Job Category: Research

Location: California-Santa Monica

Req ID: 324608