Computational Antibody Repertoire Analysis Co-Op

Boehringer Ingelheim GmbH; Ridgefield (CT); Hybrid; USD 33,000 - 45,000; Full time

Benefits offered by this job

Medical coverage

Paid time off

Paid holidays

Disability and life insurance

Other company-sponsored benefits

Job summary

Boehringer Ingelheim is offering a Computational Antibody Repertoire Analysis Co-Op to work on a state-of-the-art NGS pipeline for prioritizing antibody hits. You will gain experience with somatic hypermutation modeling, immune-repertoire data, and comparative analyses across platforms.

You will collaborate with BI scientists to benchmark models, develop reproducible workflows, and translate computational results into experimentally testable hypotheses. This is a paid co-op in the United States.

Qualifications

• Enrolled student in good academic standing in a relevant field.
• Must be legally authorized to work in the United States.
• Experience with Python or R for scientific data analysis.
• Familiarity with immunology and immune repertoire sequencing.
• Undergraduate students must have completed at least 12 credit hours at current college or university.
• Graduate and advanced degree students must have completed at least 9 credit hours at current college or university.

Responsibilities

• Curate, quality-control, and analyze antibody repertoire sequencing datasets.
• Benchmark somatic hypermutation models and related methods.
• Evaluate model calibration, performance, uncertainty, and generalization.
• Apply immune-repertoire tools (Immcantation, Shazam, Dowser) to characterize clonotypes.
• Contribute to end-to-end sequence-prioritization workflow.
• Explore SHM-based features with protein language models or ML approaches.
• Develop reproducible analyses with version-controlled code and docs.
• Collaborate with computational and lab scientists to define validation datasets.
• Summarize results and recommendations in presentations and reports.

Skills

Python

R

Immunology

AIRR standards

HPC/Cloud

Git workflows

Single-cell V(D)J

Single-cell VDJ data

HPC / Cloud

Protein language models

Education

Undergrad/Grad student in a related field

GPA 3.0 preferred

Related field major/minor

12 credit hours (undergrad)

9 credit hours (grad)

Tools

Shazam

Dowser

Change-O

IgBLAST

MiXCR

Job description

Description

Are you passionate about computational immunology and applying immune repertoire science to improve biotherapeutic discovery efficiency? As a Computational Antibody Repertoire Analysis Co-Op in Biotherapeutics Research, you will actively participate in an ambitious project that will build a state-of-the-art NGS computational pipeline that will enable prioritization of antibody hits to decrease non-binder and low affinity binder attrition. You will learn to use somatic hypermutation models to infer B cell evolutionary trajectories and predict the most evolved clones within clonotype families from immune repertoires deriving from BI's humanized mouse model.

You will work with BI scientists to benchmark computational models and help develop a reproducible pipeline that enriches for likely antigen binders and ranks higher-affinity candidates within expanded clonotype families. This role offers hands-on experience with single-cell and bulk immune-repertoire data, antibody lineage analysis, model evaluation, scientific software development, and translation of computational results into experimentally testable hypotheses.

As an employee of Boehringer Ingelheim, you will actively contribute to the discovery, development and delivery of our products to our patients and customers. Our global presence provides opportunities for all employees to collaborate internationally, offering visibility and opportunity to directly contribute to the company’s success. We realize that our strength and competitive advantage lie with our people. We support our employees in a number of ways to foster a healthy working environment, meaningful work, diversity and inclusion, mobility, networking and work-life balance. Our competitive compensation and benefit programs reflect Boehringer Ingelheim's high regard for our employees.

Duties & Responsibilities

• Curate, quality-control, and analyze antibody repertoire sequencing datasets generated using platforms such as 10x Genomics and SMART-seq/BCR-seq.
• Benchmark somatic hypermutation models and related computational methods using predefined training and held-out test datasets.
• Evaluate model calibration, predictive performance, uncertainty, and generalization across experimental platforms, immunization conditions, and mouse background strains.
• Apply immune-repertoire analysis tools, including components of the Immcantation framework such as Shazam and Dowser, to characterize clonotypes, lineage relationships, mutation patterns, and selection signatures.
• Contribute to an end-to-end sequence-prioritization workflow that ranks likely antigen binders and higher-affinity variants within clonotype families.
• Explore whether SHM-based features can be complemented by protein language models or other machine-learning approaches.
• Develop reproducible analyses using version-controlled code, documented software environments, configuration files, test datasets, and quality-control reports.
• Collaborate with computational and laboratory scientists to define validation datasets and compare computational rankings with binding and affinity measurements.
• Summarize results, limitations, and recommendations in clear presentations, technical documentation, and a final project report.

Requirements

• Must be a current undergraduate, graduate or advanced degree student in good academic standing.
• Student must be enrolled at an accredited college or university for the duration of the co-op.
• Overall cumulative minimum GPA from last completed quarter/semester 3.0 GPA (on a 4.0 scale) preferred.
• Major or minor in related field of co-op.
• Undergraduate students must have completed at least 12 credit hours at current college or university.
• Graduate and advanced degree students must have completed at least 9 credit hours at current college or university.

Desired Skills, Experience and Abilities

• Experience programming in Python or R for scientific data analysis, including data wrangling, visualization, and statistical evaluation.
• Familiarity with biological sequence analysis, genomics, immunology, antibody biology, or immune-repertoire sequencing.
• Understanding of core statistical and machine-learning concepts, including training and test partitions, benchmarking, model calibration, and performance metrics.
• Ability to work with command-line tools and reproducible software practices such as Git, environment management, and workflow documentation.
• Strong analytical, troubleshooting, communication, and presentation skills.
• Ability to work independently while collaborating effectively with multidisciplinary and geographically distributed teams.
• Curiosity, scientific rigor, and a willingness to learn new computational methods and biological concepts.
• Experience with immunoglobulin sequence annotation, clonotype assignment, phylogenetic or lineage analysis, or somatic hypermutation modeling.
• Familiarity with AIRR Community standards, the Immcantation ecosystem, or tools such as Change-O, Shazam, Dowser, IgBLAST, or MiXCR.
• Experience analyzing single-cell V(D)J data, particularly 10x Genomics datasets, and bulk antibody repertoire sequencing data.
• Experience using high-performance computing, cloud computing, containers, workflow managers, SQL, or data visualization platforms.
• Interest in protein language models, antibody candidate prioritization, or computational support of wet-lab validation.

Eligibility Requirements

• Must be legally authorized to work in the United States without restriction.
• Must be willing to take a drug test and post-offer physical (if required)
• Must be 18 years of age or older

Compensation Data

This position offers an hourly rate of $24 to $33 commensurate with the level of degree program in which an applicant is actively enrolled. We continuously review market data and may adjust salary ranges as needed in the future.

Benefits include

• medical coverage
• paid time off
• paid holidays
• disability and life insurance benefits
• other company-sponsored benefits

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