Principal Scientist, Bioinformatics

Back to jobs New Principal Scientist, Bioinformatics Fremont, California Apply At Alamar, we are passionate about enabling our customers to make scientific discoveries that translate into clinical outcomes and benefit patients. Our team is growing quickly as we develop innovative approaches to measure critical protein biomarkers from liquid samples that can enable the earliest possible detection of disease. We believe the next frontier in biology is enabled by measuring proteins at higher sensitivity in highly multiplexed assays at the push of a button, which is something only Alamar can do. As we build our team, we seek collaborative, driven, intellectually curious people committed to solving complex challenges. Our culture rewards accountability and cross functional teamwork because we believe this enables the kind of breakthrough thinking that will accelerate our mission. We are seeking a Principal Scientist, Bioinformatics to lead the design, development, and implementation of bioinformatics pipelines and computational tools that drive our molecular diagnostics and assay development programs. This role serves as a senior technical leader bridging computational biology, algorithm development, and wet-lab product development in a fast-paced, innovation-driven environment.   Key Responsibilities Multi-omics & Biomarker Discovery Analyze large-scale datasets to identify disease-specific biomarkers including mutation and methylation signatures Develop computational models and scoring tools that integrate multi-omic data (gene expression, clinical variables) for disease risk stratification Apply machine learning approaches to protein expression data for applications such as tissue-of-origin classification and multi-cancer early detection Cross-Functional Collaboration & Product Development Partner with product management, wet-lab scientists, and manufacturing teams to define new products, set specifications, design studies, analyze data, and guide product development decisions Ensure bioinformatics deliverables comply with quality management systems and applicable regulatory frameworks (FDA, CLIA) Interact with key customers as a technical resource, providing support and incorporating product feedback Team Leadership & Mentorship Establish best practices for computational workflows, code quality, and reproducible analysis within the bioinformatics group Represent bioinformatics capabilities and strategy in cross-functional and leadership discussions  Required Qualifications Ph.D. in Bioinformatics, Computational Biology, Molecular Biology, Genomics, or a closely related field 12+ years of progressive bioinformatics experience in the diagnostics, life sciences, or biotechnology industry, with at least 5 years in a leadership or senior technical role Deep expertise in NGS data analysis (whole genome, targeted panels, RNA-seq, methylation) and associated tools (BWA, samtools, STAR, variant callers) Strong programming proficiency in Python and/or R, with experience in at least one additional language (e.g., C++, PHP) Demonstrated ability to apply statistical and machine learning methods to genomic, proteomic or clinical datasets Experience working in a regulated environment (FDA, CLIA, ISO 13485, or equivalent QMS) Track record of peer-reviewed publications in relevant fields Preferred Qualifications Experience with biomarker discovery using public datasets (TCGA, GEO) and translating findings into clinical assay products Background in protein analysis tools and databases (PDB, Pfam, InterPro, SignalP) Experience engaging directly with customers a scientist in a customer-facing technical role Technical Environment Languages: Python, R, Perl, C++ Databases: Oracle, PostgreSQL, MySQL Platforms: Linux, Unix ML/Statistics: R, Python-based ML framework What You’ll Bring A strategic mindset that connects computational innovation to product and clinical impact The ability to operate across the full spectrum from hands-on algorithm development to team leadership and cross-functional strategy Deep domain expertise spanning molecular diagnostics, oncology genomics, and assay development A collaborative, customer-oriented approach to building tools and products that solve real problems The base salary range for this full-time position is $150,000 - $170,000 + bonus + equity + benefits. 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