Scientist, Systems Immunology

AbbVie Inc.; Cambridge (MA); On-site; USD 120,000 - 180,000; Full time

Job summary

AbbVie Inc. in Cambridge, MA is seeking a Computational Immunology Scientist to develop computational approaches for disease biology and drug responses using multiomics data.

You will integrate scRNA-seq, scATAC-seq, TCR/BCR, bulk RNA-seq, and proteomics to characterize cell states and identify therapeutic opportunities. The role involves collaboration across teams, contributing to publications and regulatory filings, and working in a multidisciplinary environment to advance AbbVie's immunology

Qualifications

• BS or MS degree in computational biology, bioinformatics, genomics, biostatistics, computer science, or related quantitative field.
• Typically 5-7+ years (BS) or 2-5+ years (MS) of relevant experience.
• Hands-on scRNA-seq analysis experience or scATAC-seq/TCR/BCR analysis desired.
• Proficiency in Python and/or R; Linux computing environment experience.
• Familiarity with tools like Scanpy, AnnData, Cell Ranger, scvi-tools, DESeq2, GSEA, WGCNA.

Responsibilities

• Analyze scRNA-seq, scATAC-seq, and TCR/BCR data with QC, integration, clustering, and annotations.
• Integrate cohorts with reference atlases, perform differential expression and pathway analyses.
• Analyze multiomics data to prioritize targets and biomarkers; document workflows; leverage cloud/HPC.
• Collaborate with internal/external scientists; communicate findings and contribute to publications.

Skills

Python

R

Linux

Scanpy

AnnData

Cell Ranger

scvi-tools

DESeq2

GSEA

WGCNA

AWS

SLURM

Education

BS or MS in computational biology or related field

Tools

Python

R

Linux

Job description

About AbbVie

AbbVie's mission is to discover and deliver innovative medicines and solutions that solve serious health issues today and address the medical challenges of tomorrow. We strive to have a remarkable impact on people's lives across several key therapeutic areas including immunology, oncology and neuroscience - and products and services in our Allergan Aesthetics portfolio. For more information about AbbVie, please visit us at www.abbvie.com . Follow @abbvie on LinkedIn, Facebook , Instagram , X and YouTube.

AbbVie Immunology is expanding its discovery Systems Immunology team in Cambridge, Massachusetts. The team is focused on identifying new targets for the treatment of autoimmune and chronic inflammatory diseases through computational analysis of human disease tissue-derived datasets and validating targets using humanized experimental approaches.

We are seeking a highly motivated and skilled individual to join our team as a Computational Immunology Scientist. The successful candidate will develop and implement computational approaches to understand disease biology and drug responses using high-throughput molecular profiling data. This role will involve integrating single-cell RNA-seq, scATAC-seq, TCR/BCR repertoire, bulk RNA-seq, and Olink proteomics data to characterize disease-associated cell states, investigate gene regulatory networks, and identify therapeutic opportunities.

The scientist will work in a multidisciplinary team analyzing multiomics datasets to derive insights into immunological diseases and identify novel therapeutic targets relevant to patient cohorts and AbbVie pipeline drugs. The candidate will also contribute to scientific conference presentations, peer-reviewed publications of translational findings, new drug applications, and regulatory filings.

This position will be based in Cambridge, Massachusetts, and requires passion, attention to detail, prior hands-on experience, and teamwork.

Key Responsibilities

• Analyze scRNA-seq, and CITE-seq, datasets, including quality control, integration, clustering, and cell-type and cell-state annotation.
• Integrate patient cohorts with reference atlases and perform differential expression, abundance, and pathway analyses, accounting for donor variation and study design.
• Analyze scATAC-seq data to identify differential accessibility, transcription factor motifs, and candidate regulatory programs; integrate accessibility with gene expression to infer peak-to-gene relationships.
• Analyze TCR/BCR repertoires, including clonotype assignment, clonal expansion, diversity, V(D)J usage, and sharing across tissues or time points; link clonotypes to matched single-cell profiles.
• Analyze bulk RNA-seq and Olink proteomics data and integrate multiomics findings to support target prioritization and biomarker hypotheses; maintain documented, version-controlled workflows and evaluate methods using cloud or high-performance computing.
• Collaborate with internal and external scientists to prioritize hypotheses for validation, communicate findings and limitations, and contribute to presentations and publications.

BS or MS degree in computational biology, bioinformatics, genomics, biostatistics, computer science, or a related quantitative field with typically 5-7+ years (BS) or 2-5+ years (MS) of relevant experience.

Hands-on scRNA-seq analysis experience or experience with scATAC-seq or TCR/BCR analysis, with interest in developing expertise across both.

Proficiency in Python and/or R and experience working in Linux-based computing environments.

Experience with commonly used bioinformatics tools and frameworks such as Scanpy, AnnData, Cell Ranger, scvi-tools, DESeq2, GSEA, WGCNA, or related methods.

Working knowledge of statistical analysis, multiple-testing correction, batch effects, and biological replication in high-dimensional datasets.

Ability to translate biological questions into analyses, interpret and communicate results critically, collaborate effectively, and manage multiple priorities with attention to detail.

Demonstrated ability to work collaboratively, manage multiple priorities, and deliver high-quality analyses with attention to detail.

Preferred Qualifications

• Experience analyzing Olink or other high-plex proteomics datasets.
• Experience with CITE-seq, ATAC-seq, spatial transcriptomics, or integrative multi-omics analysis.
• Experience building or benchmarking machine-learning models, including convolutional neural networks, autoencoders, generative models, transfer learning, or foundation models.
• Experience with cloud or high-performance computing, including AWS and/or SLURM.
• Understanding of immunology and inflammatory disease biology; experience supporting target discovery with experimental teams and communicating research through presentations, publications, or reports.
• Evidence of scientific communication through presentations, posters, publications, technical reports, or related research contributions.

Position will be filled at level commensurate with extent of education, experience, and accomplishment— Scientist I or Scientist II

Applicable only to applicants applying to a position in any location with pay disclosure requirements under state or local law:

The compensation range described below is the range of possible base pay compensation that the Company believes in good faith it will pay for this role at the time of this posting based on the job grade for this position. Individual compensation paid within this range will depend on many factors including geographic location, and we may ultimately pay more or less than the posted range. This range may be modified in the future.

We offer a comprehensive package of benefits including paid time off (vacation, holidays, sick), medical/dental/vision insurance and 401(k) to eligible employees.

This job is eligible to participate in our short-term incentive programs.

Note: No amount of pay is considered to be wages or compensation until such amount is earned, vested, and determinable. The amount and availability of any bonus, commission, incentive, benefits, or any other form of compensation and benefits that are allocable to a particular employee remains in the Company's sole and absolute discretion unless and until paid and may be modified at the Company’s sole and absolute discretion, consistent with applicable law.

AbbVie is an equal opportunity employer and is committed to operating with integrity, driving innovation, transforming lives and serving our community. Equal Opportunity Employer/Veterans/Disabled.

US & Puerto Rico only - to learn more, visit https://www.abbvie.com/join-us/equal-employment-opportunity-employer.html

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https://www.abbvie.com/join-us/reasonable-accommodations.html