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About the MacArthur Lab

We are a tight-knit research group jointly based as Massachusetts General Hospital and the Broad Institute of Harvard and MIT, and leveraging the largest genomic data sets in the world and cutting-edge analysis methods to make sense of human genetic variation. We’re committed to open data and open-source code, as well as experimenting with new methods of communication. Working with us is a chance to learn from experts in computational biology, large-scale genomics, variant interpretation, software development and clinical genomics, as well as to make a difference to the lives of hundreds of families affected by rare diseases.


Associate Computational Biologist II.

Despite recent advances in genomic technologies, the majority of families affected by rare genetic diseases still cannot be given a precise molecular diagnosis. We are seeking a creative and self-motivated candidate to play a key role in developing computational methods to improve the diagnosis of rare disease. These tools will be applied to thousands of families affected by rare diseases, many of whom have been waiting for many years for a formal genetic diagnosis for their disease, and used to make new discoveries that can then be clinically validated and returned to families.

In this role you will design and implement code to analyze RNA, genome, and exome sequencing data at scale in three essential areas of interest:

  1. Identifying unusual splicing and gene expression in RNA-seq (transcriptome) data to identify genetic causes of previously unsolved rare disease cases
  2. Identifying structural variants in whole-genome sequencing data
  3. Accurately detecting sequence repeat expansions in genome and exome data

Our group is an interdisciplinary team of academic trainees, computational biologists, software developers and other personnel, engaged in the design, development, and deployment of cutting-edge genomic technologies at exceptional scale to characterize and interpret the impact of human genetic variation. As part of our methods development group, you will have the opportunity to make substantial contributions to patients and families affected by rare disease, as well as to participate in the vibrant research environment at the Broad Institute, with its close links to MIT, Harvard, and the Harvard-affiliated hospitals across Boston. You will have access to data sets of unprecedented scale, including genome and exome sequencing data from hundreds of thousands of reference individuals and thousands of rare disease families, and to colleagues with deep expertise in genetics, computational biology, software development, and machine learning.

The responsibilities of this role align closely with the mission of the Broad to transform medicine and human health through cross-disciplinary collaboration and the development of pioneering technologies to analyze scientific data on an unprecedented scale.

Primary Responsibilities:

    • Implementing, benchmarking, and optimizing existing computational algorithms to address research questions and analysis objectives
    • Writing new algorithms to handle data in cases where no satisfactory methods exist
    • Regularly contributing code to our public GitHub repository and participating in team-based code review
    • Monitoring and assessing current, relevant scientific literature related to the group’s analysis aims, in order to understand emerging practices and to ensure the group continues to employ optimal methods
    • Initiating consultations with scientists, software engineers, and mathematicians within and external to the Broad with relevant specific expertise in the course of evaluating existing methods and developing novel ones
    • Soliciting and implementing software feature requests from critical stakeholders, including variant analysts within the group, fellow members of the software engineering and methods development team, external clinical collaborators, and other end-users
    • Designing clear, appealing, and accessible figures, readouts, and/or user interfaces that provide analytical insight into the data for clinical researchers using our online analysis platform; and implementing an automatic workflow for producing such reports
    • Presenting results at regular intervals at lab and project team meetings, including meetings with external collaborators as well as institute, national, and/or international conferences as appropriate
    • Contributing code, figures, and text to team presentations and publications, including, as appropriate, leading and coordinating manuscript writing for the candidate’s first-author publications

Characteristics and Qualifications

The role will require an independent and highly motivated candidate with the ambition to establish a significant body of code that advances the discovery of the genetic causes of rare disease.

You will have an interest in developing domain expertise in computational methods for analyzing next-generation sequencing data, as well as an interest in the technical aspects of deploying these methods at scale.

We are looking for someone who:

    • Is able to write clean, efficient, robust, and usable code, with demonstrated proficiency in one of the following: Linux, Perl, Python, Java, C++, Matlab, or R, with a preference towards Linux, Python, and R
    • Has a BS or MS degree and 0-2 years experience in computer science, engineering, physics, mathematics, statistics, biology, or related fields
    • Has demonstrated experience in quantitative (statistical, mathematical, computational) research with large data sets; skill and experience with statistical analysis and/or computational biology is strongly preferred
    • Has fluency with human genetics and next-generation sequencing data; ideally will have prior experience with algorithms relevant to RNA-Seq analysis
    • Exhibits strong initiative and the ability to take ownership of assigned tasks and projects
    • Listens, communicates, and collaborates well with team members, clinicians, software developers, and research scientists
    • Demonstrates excellent written and oral presentation skills
    • Manages time well and is able to respond to shifting priorities in a fast-paced and rapidly changing environment

Please apply via Broad Institute careers site.


Senior Administrative Assistant.

We are looking for an experienced and motivated Administrative Assistant to support Dr. Daniel MacArthur, Co-Director of the Medical and Population Genetics Program and the Center for Mendelian Genomics at the Broad Institute. The successful candidate will work closely with Dr. MacArthur, providing comprehensive administrative support to him, his staff and the Center for Mendelian Genomics, who are spread between both the Broad Institute and his group at Massachusetts General Hospital.

What You’ll Do:

Provide effective and efficient administrative support for Dr. MacArthur and his staff. This includes:

  • Managing a complex and rapidly changing schedule via Google Calendar
  • Organizing and planning meetings and other special events
  • Managing travel arrangements for the Co-Director and his staff
  • Preparing financial, grant-related and administrative documents
  • On-boarding new staff and other administrative tasks as necessary

We are looking for candidates who have:

  • 2 to 5 years in an administrative support position
  • A bachelor’s degree or equivalent experience with administrative tasks
  • The ability to be discreet in handling confidential information and tactful in dealing with large volumes of scheduling and other requests from busy people
  • A sense of humor and ability to thrive in a fast paced and dynamic environment
  • Ability to multi-task and prioritize work by considering its risk, importance, urgency, and potential implications
  • High sense of urgency, drive and willingness to do what it takes to get the job done while also producing high-quality work
  • Ability to work independently or as part of a team
  • Excellent oral and written communications skills and excellent interpersonal skills
  • Exceptional proficiency in Microsoft Word, Excel, PowerPoint, and Google business apps (Gmail, Google Calendar and Google Drive)

What you’ll get:

  • Opportunities for professional development and career advancement
  • Colleagues who are intellectually curious, hard-working, and collaborative
  • A generous benefits package

Cool perks:

  • All the coffee and tea you can drink
  • On-site yoga and boot-camp classes
  • Frequent talks and events on science, art, law and policy

Please apply via Broad Institute careers site.


Sr. Software Engineer: Hail Team.

The Hail team’s mission is to build tools to enable rapid analysis and exploration of massive genetic datasets (10s of TB and tripling yearly). We are dedicated to open science and everything we do is open source. We currently develop in Scala, Spark, Python and C/C++ but will use any tools we need to get the job done.

You have a strong understanding of data structures and algorithms as well as an ability to quickly write clear, correct code to solve non-trivial but well-defined problems. You will contribute to design and implementation of a distributed system that is transforming the way biologists interact with their data. Key to our success is growing a strong and diverse team whose members enable and support the development and success of one another. Self-improvement is a fundamental part of our culture; we want to grow great engineers.

In the vein of building a diverse team, we are committed to giving equal consideration to candidates from underrepresented groups in software engineering. We know that many excellent candidates choose not to apply despite their capabilities and please allow us to enthusiastically counter this. We encourage applications from software engineers with at least two years of experience who are eager to grow personally and to support the growth of junior team-members.

This position will primarily support the Genome Aggregation Database (gnomAD) project. gnomAD is among the most comprehensive catalogues of human genetic variation in the world, consisting of tens of thousands of whole genomes and hundreds of thousands of exomes contributed by over one hundred research groups. Analysis results are shared publicly and have had sweeping impact on biomedical research and the clinical diagnosis of genetic disorders. gnomAD is set to triple in size this year, presenting major engineering and analytic challenges with huge scientific impact.

http://gnomad.broadinstitute.org/

https://www.theatlantic.com/science/archive/2015/09/genome-big-data-disease-genes/404356/

Responsibilities:

  • Work with the team, scientists, and analysts with diverse expertise to realize transformative scientific goals
  • Design, write, test, tune, document, deploy, maintain, and support new features, analysis methods, and infrastructure
  • Maintain computing infrastructure and software deployments
  • Constructively participate in the design and review of code

Requirements:

  • Bachelor’s degree in Computer Science or related field or equivalent experience
  • 2+ years of industry software engineering experience
  • Solid understanding of computer science fundamentals
  • Facility with “tools of the trade”, e.g., Unix system administration, shell scripting, build and deployment tools, version control, etc.
  • Ability to meet deadlines and work cooperatively in a multi-disciplinary environment
  • Experience with working with cloud deployments

Please apply via Broad Institute careers site.


Post-doctoral Fellows

We are looking for postdoc candidates with backgrounds in computational genomics or statistical genetics, ideally with direct experience in analyzing human sequencing data. Projects include identifying human knockouts, leveraging large human genetic data sets for drug target discovery, and improving the diagnosis of rare disease patients. Most importantly, we’re looking for people who are passionate about the translation of genomics into clinical practice, and have the right personality to work in a fast-paced and highly collaborative environment.

To apply, email Daniel with your CV.