Sr Scientist, NGS and Bioinformatics Core

AlivaMab Biologics; San Diego (CA); On-site; USD 144,000 - 176,000; Full time

Job summary

AlivaMab Biologics seeks a leader to head the NGS and Bioinformatics Core, overseeing antibody sequencing, repertoire analysis, and AI/ML data workflows. You will collaborate with Protein Sciences, Antibody Engineering, and Discovery teams, ensuring data quality and informing strategic decisions.

Reporting to the Associate Director of Antibody Engineering, you will drive new technology initiatives and data-driven insights.

Qualifications

• PhD in a life sciences field and strong bioinformatics focus.
• 5+ years experience in biotech/pharma or academia with NGS data analysis.
• Hands-on experience applying NGS tools to antibody sequencing and repertoires.
• Proficient Python coding for bioinformatics workflows.
• Experience applying AI/ML to antibody data (sequence/epitope).
• Knowledge of human immune repertoire and immunoglobulin genes.
• Experience with NGS library prep, sequencing platforms, QC.
• Familiarity with single-cell workflows (10X Genomics) a plus.
• Interest in ML/AI for antibody discovery and development.

Responsibilities

• Lead development and implementation of bioinformatics pipelines for antibody sequences and repertoires.
• Apply AI/ML methods for sequence analyses and sequence-epitope prediction.
• Oversee end-to-end NGS workflow from library to downstream analysis; ensure data quality.
• Propose and lead new tech initiatives to expand sequencing capabilities and tools.
• Act as SME in bioinformatics, training cross-functional teams.
• Keep abreast of field announcements; critique claims for management.
• Collaborate with project leads on sequencing and computational reports.
• Interact with external partners to present data and answer questions.
• Maintain scientific independence with proactive communication with stakeholders.
• Generate and manage records in ELN and develop SOPs.

Skills

PhD level biology/biotech

5+ years biopharma/academic bioinfo/NG

Bioinformatics with NGS data analysis

Python coding

AI/ML for antibody analysis

Immunology knowledge

NGS library prep / QC

Single-cell sequencing (10X)

ML for antibody discovery

Education

PhD in Molecular Biology, Biochemistry, Bioinformatics, Computational Biology, or related Life Sciences

Tools

Python

NGS analysis tools

10X Genomics

Job description

AlivaMab Biologics is seeking an outstanding individual to serve as the head of the NGS and Bioinformatics Core, enabling antibody discovery and engineering projects through oversight of Next-Generation Sequencing (NGS) workflows, bioinformatics, and computational analysis to thoroughly examine antibody repertoires, broadening our understanding of sequence and functional diversity and therapeutic potential of biologics. The individual will also have the opportunity and is expected to contribute to broader technology development and antibody engineering in collaboration with cross-functional teams, working closely with scientists in the Protein Sciences, Antibody Engineering, Antibody Discovery, and Project Management teams. This position will report to the Associate Director of Antibody Engineering.

Responsibilities

• Lead the ongoing development and implementation of enhanced bioinformatics pipelines and computational workflows for the analysis of antibody sequences and immune repertoires from NGS and other data sources
• Apply and advance AI/ML approaches for antibody sequence analyses and sequence-epitope prediction
• Manage and continuously improve the end-to-end NGS workflow (library generation, sequencing on Illumina MiSeq, QC, and downstream analysis), directing execution and safeguarding data quality
• Ideate, propose, and lead new technology initiatives to expand sequencing capabilities, data infrastructure, and analytical tools
• Serve as the primary subject matter expert in bioinformatics, computational analysis, and NGS, educating and supporting cross-functional teams on data interpretation and best practices
• Maintain awareness of major announcements in the field and provide critical analyses of strengths and weaknesses of such claims to senior management
• Collaborate with project leads on sequencing and computational analyses reports
• Serve as a subject matter expert for the team in interactions with external partners, presenting sequencing data, interpreting results, and addressing partner questions with clarity and confidence
• Operate with a high degree of scientific independence while maintaining proactive, open communication with stakeholders
• Generate, organize, and maintain meticulous records using Electronic Lab Notebooks and generate SOPs

Qualifications

Key Skills and Requirements:

• D. in Molecular Biology, Biochemistry, Bioinformatics, Computational Biology, or related Life Sciences
• Minimally, 5+ years of experience in biotech/pharma or an academic setting with a strong focus on bioinformatics, computational biology, and/or NGS data analysis
• Proficiency in bioinformatics with hands‑on experience applying NGS data analysis tools to antibody sequencing and immune repertoire workflows
• Proficient Python coding skills with experience in developing or customizing bioinformatics workflows for antibody sequencing and immune repertoire analysis
• Demonstrated experience applying AI/ML methods to antibody or protein sequence and structure data (e.g., sequence-epitope prediction, structure modeling)
• Understanding of the biology of the human immune repertoire and immunoglobulin genes
• Demonstrated initiative, insightfulness, and creativity in applications of AI/ML for analyses of antibody sequences and/or immune repertoires
• Knowledge and hands‑on experience in NGS library preparation, sequencing platforms, and QC methodologies
• Experience with single‑cell sequencing workflows, such as 10X Genomics, is a plus
• Experience with the applications of ML/AI to antibody drug discovery and development is a plus.
• Excellent troubleshooting, problem‑solving, and analytical skills
• Meticulous attention to detail, planning, and organizational skills with a history of timeline‑driven delivery
• Excellent communicator, highly effective in interacting with key internal and external stakeholders
• Team player and collaborative leader, with strong coaching and mentoring skills
• High functioning in an environment dedicated to exceptional quality and integrity

Salary Range: $144,000 - $176,000 annually

This range represents AlivaMab Biologics' good‑faith estimate of the base compensation for this position at the time of posting. Compensation offered will account for factors such as experience, education, and comprehensiveness of qualifications. The salary range excludes bonuses, equity, health benefits, PTO, other benefits, or any other forms of compensation that may be part of the total compensation package. Relocation assistance may be considered.