(Senior) Bioinformatics Data Engineer, Omics Pipelines, Translational and Quantitative Sciences D...
Company: Genmab
Location: Princeton
Posted on: October 18, 2024
Job Description:
Job DescriptionAt Genmab, we're committed to building
extra[not]ordinary futures together, by developing antibody
products and pioneering, knock-your-socks-off therapies that change
the lives of patients and the future of cancer treatment and
serious diseases. From our people who are caring, candid, and
impact-driven to our business, which is innovative and rooted in
science, we believe that being proudly unique, determined to be our
best, and authentic is essential to fulfilling our purpose.The
RoleThe successful candidate will contribute to the mission of the
global data engineering function and be responsible for many
aspects of data including creation of data-as-a-product,
architecture, access, classification, standards, integration, and
pipelines. Although your role will involve a diverse set of
data-related responsibilities, your key focus will be on the
creation of bioinformatics pipelines to process bulk and single
cell genomics and transcriptomics data for the enablement and
downstream interpretation of Translational and Quantitative
Sciences functions, including Data Science, Translational Medicine,
Precision Medicine, and Translational Research. You will have a
balance of subject matter expertise in life science data,
terminology and processes and technical expertise for hands-on
implementation. You will be expected to create workflows to
standardize and automate data, connect systems, enable tracking of
data, implement triggers and data cataloging. With your experience
in the Research domain, you will possess knowledge of diverse assay
types such as IHC, flow cytometry, cytokine data, but specialize in
genomics and transcriptomics. Your ultimate goal will be to place
data at the fingertips of stakeholders and enable science to go
faster. You will join an enthusiastic, agile, fast-paced and
explorative global data engineering team.Responsibilities
- Design, implement and manage ETL data pipelines that process
and transform vast amounts of scientific data from public, internal
and partner sources into various repositories on a cloud platform
(AWS)
- Incorporate bioinformatic tools and libraries to the processing
pipelines for omics assays such as bulk and single cell RNASeq
- Enhance end-to-end workflows with automation that rapidly
accelerate data flow with pipeline management tools such as Step
Functions, Airflow, or Databricks Workflows in combination with
specialized bioinformatics pipeline tools such as WDL, Nextflow, or
Snakemake
- Implement and maintain bespoke databases for scientific data
(RWE, in-house labs, CRO data) and consumption by analysis
applications and AI products
- Innovate and advise on the latest technologies and standard
methodologies in Data Engineering and Data Management, including
recent advancements with GenAI, and latest bioinformatics tools,
modules and techniques in RNA sequencing analysis
- Manage relationships and project coordination with external
parties such as Contract Research Organizations (CRO) and vendor
consultants / contractors
- Define and contribute to data engineering practices for the
group, establishing shareable templates and frameworks, determining
best usage of specific cloud services and tools, and working with
vendors to provision cutting edge tools and technologies
- Collaborate with stakeholders to determine best-suited data
enablement methods to optimize the interpretation of the data,
including creating presentations and leading tutorials on data
usage as appropriate
- Apply value-balanced approaches to the development of the data
ecosystem and pipeline initiatives
- Proactively communicate data ecosystem and pipeline value
propositions to partnering collaborators, specifically around data
strategy and management practices
- Participate in GxP validation processesRequirements
- BS/MS in Computer Science, Bioinformatics, or a related field
with 5+ years of software engineering experience (8+ years for
senior role) or a PhD in Computer Science, Bioinformatics or a
related field and 2+ years of software engineering experience (5+
years for senior role)
- Excellent skills and deep knowledge of ETL pipeline, automation
and workflow managements tools such as Airflow, AWS Glue, AWS Step
Functions, and CI/CD is a must. Strong preference specifically for
AWS Step Functions and Lambda.
- Excellent skills with bioinformatics pipeline tools and
troubleshooting for quality such as Snakemake, WDL, and Nextflow.
Strong preference for Nextflow.
- Excellent skills and deep knowledge in Python, Pythonic design
and object-oriented programming is a must, including common Python
libraries such as pandas. Experience with R a plus
- Excellent understanding of different bioinformatics modules and
databases such as STAR, HISAT2, featureCounts, fastQC, RSeQC and
Cell Ranger and how they're used on different types of genomic and
transcriptomic data such as single cell transcriptomics
- Solid understanding of modern data architectures and their
implementation offerings such as Databricks' Delta Tables, Athena,
Glue, Iceberg, and their applications to Lakehouse and medallion
architecture.
- Experience working with clinical data and understanding of GxP
compliance and validation processes
- Proficiency with modern software development methodologies such
as Agile, source control, project management and issue tracking
with JIRA
- Proficiency with container strategies using Docker, Fargate,
and ECR
- Proficiency with AWS cloud computing services such as Lambda
functions, ECS, Batch and Elastic Load Balancer and other compute
frameworks such as Spark, EMR, and Databricks. Strong preference
for experience with AWS Omics.For US based candidates, the proposed
salary band for this position is as
follows:$114,375.00---$190,625.00The actual salary offer will
carefully consider a wide range of factors, including your skills,
qualifications, experience, and location. Also, certain positions
are eligible for additional forms of compensation, such as
bonuses.About You
- You are passionate about our purpose and genuinely care about
our mission to transform the lives of patients through innovative
cancer treatment
- You bring rigor and excellence to all that you do. You are a
fierce believer in our rooted-in-science approach to
problem-solving
- You are a generous collaborator who can work in teams with
diverse backgrounds
- You are determined to do and be your best and take pride in
enabling the best work of others on the team
- You are not afraid to grapple with the unknown and be
innovative
- You have experience working in a fast-growing, dynamic company
(or a strong desire to)
- You work hard and are not afraid to have a little fun while you
do soLocationsGenmab leverages the effectiveness of an agile
working environment, when possible, for the betterment of employee
work-life balance. Our offices are designed as open,
community-based spaces that work to connect employees while being
immersed in our state-of-the-art laboratories. Whether you're in
one of our collaboratively designed office spaces or working
remotely, we thrive on connecting with each other to innovate.About
GenmabGenmab is an international biotechnology company with a core
purpose guiding its unstoppable team to strive towards improving
the lives of patients through innovative and differentiated
antibody therapeutics. For more than 20 years, its passionate,
innovative and collaborative team has invented next-generation
antibody technology platforms and leveraged translational research
and data sciences, which has resulted in a proprietary pipeline
including bispecific T-cell engagers, next-generation immune
checkpoint modulators, effector function enhanced antibodies and
antibody-drug conjugates. To help develop and deliver novel
antibody therapies to patients, Genmab has formed 20+ strategic
partnerships with biotechnology and pharmaceutical companies. By
2030, Genmab's vision is to transform the lives of people with
cancer and other serious diseases with Knock-Your-Socks-Off (KYSO™)
antibody medicines.Established in 1999, Genmab is headquartered in
Copenhagen, Denmark with locations in Utrecht, the Netherlands,
Princeton, New Jersey, U.S. and Tokyo, Japan. Our commitment to
diversity, equity, and inclusionWe are committed to fostering
workplace diversity at all levels of the company and we believe it
is essential for our continued success. No applicant shall be
discriminated against or treated unfairly because of their race,
color, religion, sex (including pregnancy, gender identity, and
sexual orientation), national origin, age, disability, or genetic
information. Learn more about our commitments on our website.
Genmab is committed to protecting your personal data and privacy.
Please see our privacy policy for handling your data in connection
with your application on our website
https://www.genmab.com/privacy.Please note that if you are applying
for a position in the Netherlands, Genmab's policy for all
permanently budgeted hires in NL is initially to offer a fixed-term
employment contract for a year, if the employee performs well and
if the business conditions do not change, renewal for an indefinite
term may be considered after the fixed-term employment
contract.
Keywords: Genmab, East Brunswick , (Senior) Bioinformatics Data Engineer, Omics Pipelines, Translational and Quantitative Sciences D..., Engineering , Princeton, New Jersey
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