Bioinformatics Scientist

Sanford Burnham Prebys Medical Discovery Institute
San Diego, CA
Closing date
Sep 26, 2023

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Organization Type
Bioinformatics Scientist

A full-time, academically minded staff-level Bioinformatics Scientist position is available in Dr. Jerold Chuns lab at the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California. The position will be central to several teams in the lab that require bioinformatics and will interface with current bioinformatics personnel. The Chun lab is located at the heart of the biomedical research hub in La Jolla, California, and the position encompasses ongoing collaborations with UCSD, other academic institutions, and pharmaceutical partners. The focus of this position will be bioinformatic approaches to understanding mosaic neural genomes RNA and DNA in single cells of the brain. Representative publications:
  1. Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain Science 2016 Vol. 352 Issue 6293 Pages 1586-90. PMC5038589
  2. Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain Nat Biotechnol 2018 Vol. 36 Issue 1 Pages 70-80. PMC5951394
  3. Submegabase copy number variations arise during cerebral cortical neurogenesis as revealed by single-cell whole-genome sequencing Proc Natl Acad Sci U S A 2018 Vol. 115 Issue 42 Pages 10804-10809. PMC6196524
  4. Somatic APP gene recombination in Alzheimer's disease and normal neurons. Nature 2018 Vol. 563 Issue 7733 Pages 639-645. PMC6391999

Primary Responsibilities:

-Analyze next generation sequencing (NGS, short-read) and especially third generation sequencing (long-read) datasets (genomic and transcriptomic)

-Develop new informatic approaches and pipelines in coordination with other researchers in the lab

-Help to maintain and update existing informatics pipelines and lab Github repository

-Manage and organize large sequencing datasets produced by the lab

Required Qualifications:

-Mastery of command line operations and Linux/Unix operating environments

-Familiarity with high performance computing cluster-based analysis

-Fluency with coding in Python, R, and similar languages

-Experience customizing pipelines, algorithms, and quality control metrics for data analysis

-Attention to detail with accuracy

-Ability to communicate effectively in English and to work in a fast-paced environment

-Good social skills

Preferred Qualifications:

-Experience with long-read sequencing (Pacific Biosciences (PacBio) and/or Oxford Nanopore Technologies) and analysis is strongly preferred.

-Knowledge of next generation sequencing toolsets (fastqc, STAR, bwa, samtools, GATK, etc.)

-Familiarity with NCBI, UCSC Genome browser, Integrated Genomics Viewer

-Experience with single-cell sequencing (10x Genomics) and analysis

Masters degree in computer science or bioinformatics plus three years of direct experience is required. PhD-level of experience is preferred. Should be willing and excited to learn about ongoing science.
The expected hiring range for this position is $101,785.00 - $152,677.00/year, commensurate with relevant experience.

Sanford Burnham Prebys Medical Discovery Institute is an Equal Opportunity employer M/F/Veteran/Disability committed to the hiring, advancement and fair treatment of all individuals. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability, protected veteran status, or any other protected status as designated by federal, state or local law. For additional information about your rights as an applicant, click HERE.

Sanford Burnham Prebys Medical Discovery Institute will not discharge or in any other manner discriminate against employees or applicants because they have inquired about, discussed, or disclosed their own pay or the pay of another employee or applicant. However, employees who have access to the compensation information of other employees or applicants as a part of their essential job functions cannot disclose the pay of other employees or applicants to individuals who do not otherwise have access to compensation information, unless the disclosure is (a) in response to a formal complaint or charge, (b) in furtherance of an investigation, proceeding, hearing, or action, including an investigation conducted by the employer, or (c) consistent with the contractors legal duty to furnish information.

Sanford Burnham Prebys Medical Discovery Institute is an Equal Opportunity Employer M/F/Veteran/Disability committed to the hiring, advancement and fair treatment of all individuals.
Department: Chun Lab Location: San Diego, CA

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