Senior Bioinformatician - Sentinel

Job Summary

ACEGID is seeking to hire a Senior Bioinformatician to join its Sentinel team for pandemic preemption and genomic epidemiology, as well as human genetics. The successful applicant would join an interdisciplinary team of scientists, health professionals, and students, and will be primarily focused on leading high throughput processing and analysis of pathogen sequence data (including for SARS-CoV-2) as well as human genome sequence data being generated by ACEGID and its collaborators. This role will advance ongoing genomic surveillance, and human genomics sequencing and genotyping efforts at ACEGID in collaboration with regional public health organizations -- including NCDC, Africa CDC, WAHO, WHO, state and federal ministries of health-- as well as academic research centers and industrial partners to contribute to data sets, insights, and bioinformatic tools. We seek a highly motivated individual to work closely with researchers and collaborators from across the ACEGID and Sentinel networks. The ability to communicate effectively, work well in a team setting, and the demonstrated ability to learn, apply, extend, and pilot new computational methods are required. This individual will lead ACEGID’s bioinformatics analysis unit and will have a large role in ACEGID’s training and capacity-building programs centered around pathogen and human genome sequencing and genomic analysis. The position offers an opportunity to lead in a dynamic research environment in a fast-paced field of research, as well as further opportunities for professional advancement, skill development, and authorship on publications. We are seeking a bioinformatician with a deep passion for and experience in biomedical data analysis. Candidates will have a background in data science, software engineering, or bioinformatics and exposure to healthcare, public health, pharma, or the life sciences.

  • Minimum Qualification: MBA / MSc
  • Experience Level: Executive level
  • Experience Length: 4 years

Job Description/Requirements

Viral pandemics are one of the greatest risks to humanity. Despite taking giant leaps in technology and science, we are more vulnerable today than we were 100 years ago. From Ebola to COVID-19, pandemics have underscored the need for a systematic way of detecting and tracking outbreaks of many common and fatal infectious diseases. The necessary diagnostic tests either do not exist or are not available where the need is greatest — in the communities of lower-income countries, particularly those in West and Central Africa, which suffer continuously from a lack of diagnostic capacity. As a result, millions of infectious disease cases remain unidentified and uncontained, and outbreaks are only detected once so many people have become ill that the problem cannot be ignored — typically much too late to stop an epidemic.

To address this gap, our team is building and deploying Sentinel: a pandemic preemption system that detects viral threats in real-time and by way of checkups in rural clinics, allowing us to stop infectious diseases before they spread. This initiative has the potential to transform the world’s ability to detect viruses that cause outbreaks, radically improve the speed at which health authorities can respond, and significantly expand the geographic area covered by outbreak surveillance. This concept was first articulated through and largely funded by the Audacious Project, a collaborative approach to funding big ideas with the potential to create change at a thrilling scale. Sentinel is a global collaboration of clinicians, epidemiologists, geneticists, virologists, bioengineers, computer scientists, and public health operations experts led in a joint effort led by the African Center of Excellence for Genomics of Infectious Diseases (ACEGID) and the Broad Institute, supported by key partners, such as Fathom, Dimagi, and MASS Design.


Duties and Responsibilities

Computational Analysis:

  • Develop novel pipelines, programs, scripts, and code to implement new analytical approaches, visualizations, and data transformations as needed for ongoing research projects.
  • Develop new computational methods to integrate and interpret multi-omics data.
  • Distribute improved bioinformatic tools to a regional and global user base.
  • Execute genomic data analyses utilizing novel and existing cloud computing tools to deliver viral genomic data and analytic products to stakeholders, collaborators, funders, and the general public.
  • Design tools for effective communication, representation, and visualization of our data, findings, and insights to external collaborators and stakeholders.
  • Train and mentor junior bioinformaticians and research students who are part of ACEGID and Sentinel networks, including at partner sites across Africa.
  • Responding to routine project activity monitoring and reporting, the successful candidate should be able to generate high-quality visualizations of ACEGID sequencing output for reporting and other need-based purposes.
  • Maintain a large and complex database of ACEGID sequencing raw and processed files and provide useful extractions from the data for monitoring and reporting purposes.
  • Responsible for sharing ACEGID sequencing information to the greater scientific community including but not limited to GiSAID and Virological in an ethical standard science-based approach.

Hardware and Networking:

  • Work with IT Manager to build and deploy a high-performance computing cluster for onsite analysis.
  • Ensure that networking capability is sufficient to run onsite cloud-based analysis.
  • Manage queues for computing/analysis jobs submitted from across the ACEGID network.

Training:

  • Develop online and in-person training modules and materials across a variety of genomic analysis topics.
  • Lead a team of facilitators to deliver training workshops to researchers and public health professions from across Africa and beyond.

Data Visualization, Communications, and Reporting:

  • Develop and implement data visualization dashboards for internal and external use, in collaboration with technology partners, such as Fathom, Dimagi, etc.
  • Create a central repository for hosting all sequence data.
  • Provide status reports and feedback to the Center Director.

Requirements Knowledge, Skills & Abilities:

  • Demonstrated knowledge and experience in computer programming.
  • Strong troubleshooting skills and proven resourcefulness in researching solutions to technical problems.
  • Strong documentation skills to codify newly developed tools and pipelines.
  • Excellent interpersonal verbal and written communication skills.
  • Strong organizational savvy and attention to detail.
  • Ability to lead a team, manage multiple priorities and meet deadlines.
  • Ability to work independently to perform a wide range of duties under general guidance from supervisor; high level of integrity and dependability.
  • Deep understanding of molecular biology, troubleshooting issues with next-generation sequencing runs such as demultiplexing, clustering, and salvaging failed runs.
  • Hands-on knowledge of computer systems, security, network and systems administration, databases, and data storage systems.
  • Cross-cultural competency; ability to work with a diverse, global team.
  • English fluency.

Education and Experience:

  • Master’s degree in computational biology, bioinformatics, data science, computer science, or related field with 4+ years of experience in genomic analysis. A Ph.D. is a plus, but not required.
  • 3+ years of software development or data modeling experience is preferred, though exceptional candidates with less will be considered.
  • Background in computational genomics and statistical analysis using next-generation sequence data. Experience with cloud computing, distributed computing, and/or bioinformatics workflow languages required.
  • Knowledge of genomic sequencing, relevant bioinformatics tools (aligners, variant callers, etc), and public sequencing databases.
  • Strong practical experience with UNIX command-line environments and ability to code in at least two of Python, Java, and R. Comfort with containerized environments is preferred.
  • Experience with human WGS analysis, polygenic risk scores, Genome-Wide Association studies, and handling large volumes of data in complex workflows.
  • Experience with building analysis pipelines and products from scratch.
  • Experience in life sciences or healthcare with research questions, data mining, user experience design, metadata curation, or making data FAIR.
  • Experience working with an organization based in multiple locations, preferred; global experience a plus.
  • Must be flexible and able to respond to shifting priorities in a dynamic setting.

The deadline for applications is 10th November 2021. Only shortlisted candidates will be contacted

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