Bioinformatics Specialist - Doudna Lab


HHMI is currently seeking a talented, teamwork-oriented Bioinformatics Specialist for a full-time opportunity to join the lab of Professor and Nobel Laureate Jennifer Doudna at the University of California, Berkeley.

The California Institute for Quantitative Biosciences (QB3) is one of four Governor Gray Davis Institutes for Science and Innovation established in 2000 to ensure the future of the California economy by promoting research and innovation. QB3 is a cooperative effort between the state of California, private industry, venture capital, and the University of California campuses at Berkeley, San Francisco, and Santa Cruz. As a unit within QB3, the Doudna lab is a large, highly collaborative team that pursues mechanistic understanding of fundamental biological processes involving RNA molecules. Research in the lab is currently focused on bacterial immunity via CRISPR-Cas systems. They utilize diverse techniques including structural biology, high-throughput sequencing, biochemistry, molecular biology, and eukaryotic cell culture. For more information about the Doudna lab, please visit and

The Bioinformatics Specialist is an organized, creative problem solver who will focus on supporting research projects within the laboratory by working with lab members to analyze bacterial and human genomic and transcriptomic data from next-generation sequencing experiments. This role will have the unique opportunity to work with a diverse group of lab members and the ability to contribute to several different projects, including preparing reports to share with laboratory members at weekly meetings to promote a strong base of shared knowledge in the lab and ensure understanding between different arms of a given project. Intellectual or technical contributions made to a research project that is to be published will warrant authorship. The lab also has flexibility to allow for a partially remote work schedule.

Essential Duties:

Design and implement bioinformatic pipelines to handle next-generation sequencing data from both prokaryotic and eukaryotic samples.

Handle both genomic (DNA-seq) and transcriptomic (RNA-seq) datasets (and potentially metagenomic datasets).

Perform statistical analyses and plots using R.

Perform differential gene expression analyses on RNA-seq data.

Map genome deletions/insertions/mutations (and potentially transcriptomic mutations).

Store, organize, curate, and relocate datasets/files on the server.



A bachelor’s degree in bioinformatics, computational biology, computer science, biostatistics, or a closely related area is required.


A minimum of 3 years of experience with next-generation DNA-seq/RNA-seq data analysis in academia, industry, or equivalent training is required.

Strong experience and skill with programming in R, Python, and/or equivalent programming languages is required.

Experience with sequencing pipelines such as Illumina, DESeq, Bowtie, SAMtools, BAMtools, BEDtools, or alternatives is required.

Familiarity with common plotting methods (scatter, box, CDF, volcano) to represent/summarize results is preferred.

Knowledge, Skills, and Abilities

Basic understanding of biology to communicate with peers and understand their questions.

Ability to communicate technical information to an audience not versed in bioinformatics and/or programming.

Interest in contributing to scientific studies and manuscripts and comfort in being responsible for writing bioinformatic methods.

Strong sense of self-motivation with an ability to work well both independently and as part of a team.

Ability to organize and manage multiple bioinformatics projects simultaneously.

Ability to interact positively with all team members and comfort working in a large, diverse, collaborative lab environment.

Ability to work efficiently, meet deadlines, and be adaptable to changing priorities.

Application Instructions:
Please attach the following information (preferably as a single PDF document) as part of your application.

Résumé/CV emphasizing prior experience

Cover letter outlining specific interest in this role and the Doudna lab

Contact information for three references

Physical Requirements:

Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet).

Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.

Please Note:

This job description sets forth the job’s principal duties, responsibilities, and requirements; it should not be construed as an exhaustive statement, however. Unless they begin with the word “may,” the Essential Duties and Responsibilities described above are “essential functions” of the job, as defined by the Americans with Disabilities Act.

HHMI is an Equal Opportunity Employer


Start date

As soon as possible

How to Apply