Bioinformatics Analyst II

About the Company: Theiagen Genomics is an innovative technology company dedicated to transforming public health and pathogen genomics through advanced technology solutions and a collaborative work culture. At Theiagen we aim to work with state IT and bring these computing resources outside the state infrastructure. Leveraging the affordability, scalability, and security of cloud computing environments resulting in cutting edge technology that can drive your public health interventions. We are a team of experts across academia, government and industry careers who have come together to deliver a world-leading service covering a diverse range of microbial genomics applications. Interested in joining the cause? About The Job: Theiagen is a thriving startup at an exciting stage of growth. Having developed organically, we are now seeking a structured approach to scale effectively. Theiagen is looking to add a Bioinformatics Analyst II to our growing team. We are looking for a Bioinformatics Analyst II to support development efforts to maintain and expand Theiagen's bioinformatics solutions, ensuring the core functionality and stability of our software used in pathogen genomics, under the direction of their Public Health Team Lead. Key Responsibilities Training Development and Delivery • Lead the development and delivery of Theiagen training workshops, managing--with minimal supervision--all aspects from material preparation to logistics and communication with external partners. Subject Matter Expert (SME) Support • Lead SME support for external partners, overseeing activities to support genomic investigations (e.g., pathogen outbreaks) to ensure timely and effective solutions that address partner needs. Process Improvement and Best Practices • Ensure the adherence to, and continuous improvement of, internal training and support practices. Communication and Collaboration • Serve as a bridge between partners and the development team, ensuring that partner needs are translated and implemented effectively. • Regularly communicate with their Public Health Team Lead to summarize critical information, ensuring alignment on project statuses, challenges, and milestones for informed decision-making. Mentorship and Team Development • Mentor junior members of the team, fostering a culture of learning and technical excellence within the team. • Perform other duties as assigned. Skills, Knowledge and Expertise • Masters or doctoral degree in bioinformatics, biostatistics, computer science, microbiology, molecular biology, or related field • Demonstrated expertise applying bioinformatics tools and workflows to answer complex biological questions, particularly in pathogen genomics. • Advanced proficiency in using bioinformatics tools for tasks such as genome assembly, annotation, taxonomic classification, and antimicrobial resistance detection. • Deep knowledge of statistical approaches and bioinformatics pipelines for analyzing next-generation sequencing (NGS) data. • Proficiency with genomic epidemiology methods, including phylogenetics, outbreak investigation tools, and MLST typing. • Proven ability to lead and manage multiple projects independently or within a collaborative team environment. • Excellent written and verbal communication, with experience presenting technical results to diverse audiences. • Effective judgment and advanced problem-solving skills with minimal supervision. • Strong motivation and demonstrated impact in public health initiatives. Preferred Skills: • Comprehensive knowledge of public health laboratory processes and workflows, including validation and verification of bioinformatics workflows for decision-making. • Expertise in interpreting bioinformatics results and providing actionable public health insights. • Significant experience analyzing pathogen genomics datasets for public health applications (e.g., SARS-CoV-2, Mycobacterium tuberculosis, antimicrobial resistance, or HAIs). • Advanced experience with cloud-based bioinformatics platforms (e.g., Terra.bio, Galaxy) and workflow orchestration tools (e.g., Nextflow, WDL, or Snakemake). • Hands-on expertise in using visualization and reporting tools to clearly communicate results to stakeholders. • Proficiency in shell scripting and working in UNIX/Linux environments. • Leadership experience mentoring junior team members and fostering technical excellence. Benefits • Competitive Compensation • Paid Time Off • Fully remote work (Must be able to provide proof of ability to work in the US upon hire-does not offer sponsorship at this time) • Company supplied phone and computer • Medical, Dental, Vision coverage/stipend • 401(k) with company match • Flexible Spending Accounts • Employee Assistance Program • Employee Discount Program Why Join Theiagen Genomics? • Be part of a passionate team driving innovation in the pathogen genomics space. • Competitive salary, comprehensive benefits, and opportunities for professional development. • A culture that values diversity, collaboration, and a commitment to excellence. Theiagen Genomics is an equal opportunity employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability or veteran status.