Data Scientist (Bioinformatics Developer) - Next Generation Sequencing (NGS)

The Department of Molecular Diagnostics at MD Anderson Cancer Center is at the forefront of precision oncology, leveraging advanced genomic technologies to deliver clinically actionable insights that directly impact patient care. The department supports a wide range of next-generation sequencing (NGS)–based assays and computational platforms that enable accurate diagnosis, prognostication, and treatment selection for cancer patients in a highly regulated clinical environment.

As a Data Scientist (Bioinformatics Developer), you will develop, implement, and maintain clinical informatics applications and bioinformatics pipelines that support molecular diagnostic testing and genomic reporting. Working closely with molecular diagnostics scientists, bioinformaticians, pathologists, software engineers, and clinical stakeholders, you will translate complex biological and clinical questions into scalable, reproducible computational solutions.

In this role, you will support and enhance enterprise-level platforms such as the OncoSeek genomics annotation and reporting engine, which has been used at MD Anderson for clinical NGS reporting for over a decade. You will also contribute to the development and ongoing maintenance of the MDLConductor laboratory informatics system (LIS), integrating laboratory workflows with hospital informatics systems and automating critical processes such as sample tracking, labeling, robotic storage, quantitation, and plate-based workflows. Your work will directly enable high-throughput, high-fidelity clinical laboratory operations.

You will design and implement algorithms and statistical methods for interpreting genomic data, including variant detection, differential expression, pathway analysis, and other advanced analytics. This position requires deep expertise in bioinformatics theory and hands-on data analysis, along with the ability to apply these methods to real-world clinical datasets in compliance with laboratory and regulatory standards.

The role includes developing and maintaining bioinformatics pipelines for a broad range of NGS applications, including whole genome, whole exome, whole transcriptome, targeted sequencing, single-cell sequencing, liquid biopsy analysis, and minimal residual disease detection. You will perform and optimize key analytical steps such as quality control, alignment, variant calling, annotation, and reporting, adapting pipelines to meet evolving clinical and research needs.

You will also integrate existing bioinformatics tools and databases into custom workflows, evaluate emerging technologies, and incorporate new methods to improve efficiency, accuracy, and reproducibility. Maintaining thorough documentation, version control, and software development best practices is essential to ensure transparency and long-term sustainability of analytical pipelines.

Collaboration is central to this role. You will actively participate in interdisciplinary project teams, contribute to scientific discussions, present work in meetings and seminars, and provide training and technical support to laboratory staff, precision oncology scientists, pathologists, and clinicians. Through these interactions, you will help drive innovation, support clinical decision-making, and expand the effective use of genomics and artificial intelligence in cancer care.

MD Anderson offers a comprehensive total rewards package, including paid medical benefits, generous paid time off, retirement plans, and additional benefits, providing stability and long-term career growth within one of the world’s leading cancer centers.

**The ideal candidate will have a PHD, NGS & C#/.NET experience**  

JOB SPECIFIC COMPETENCIES

Development, Optimization, Deployment and Maintenance of Clinical Informatics Applications and Bioinformatics Pipelines

Support functional development of the OncoSeek genomics annotation and reporting engine which has been used to generate genomic next-generation sequencing panel reports at MD Anderson since 2012.

Support, develop and maintain MDLConductor laboratory informatics system(LIS) and applications for MDL.  Specific efforts include but are not limited to, integrate MDL LIS with hospital informatics system, develop automated rack label and vial label printing with real-time Micronics tube mapping for stock tube management for all derivative sample types (e.g. DNA, RNA, cDNA), coordinate interfacing with existing robotic sample storage (ASR), quantitation devices (Synergy), and robotic fluid handlers for plate setups & core laboratory workflows.

Design and implement algorithms and statistical methods for the interpretation of genomic data, including identification of genetic variants, differential expression analysis, and pathway analysis. This requires a deep understanding of both bioinformatics theory and practical applications to derive meaningful insights from complex genomic datasets.
 

Collaborate with molecular diagnostics professionals to understand project requirements, propose solutions, and provide technical support for data analysis and interpretation. This involves actively engaging with project teams to translate biological questions into computational workflows and troubleshooting issues that arise during data analysis.

Develop Bioinformatics pipelines for various next generation sequencing (NGS) applications such as whole transcriptome sequencing(WTS), whole genome sequencing (WGS), exome sequencing (WES), targeted sequencing, single-cell sequencing, liquid biopsy analysis, and minimal residual disease (MRD) detection. This includes adapting existing pipelines and developing new methodologies to address the specific requirements and challenges associated with each application. This also includes processing and analyzing NGS and other genomic data, including tasks such as quality control, alignment, variant calling, and annotation. 

Integrate existing bioinformatics tools and databases into custom workflows to address specific clinical application needs and improve analysis efficiency. This includes evaluating the suitability of available tools and databases for particular analyses and developing scripts or wrappers to automate data processing tasks and facilitate reproducibility. This involves staying up-to-date with the latest tools and methods in the field and integrating them into existing pipelines to ensure accurate and efficient analysis, and actively monitoring scientific literature, attending conferences, and participating in online forums and community discussions to identify emerging trends and technologies relevant to genomics research.

Maintain documentation and version control for developed software and pipelines, ensuring reproducibility and transparency of analyses. This includes writing comprehensive documentation for code and pipelines, managing code repositories using version control systems such as Git, and adhering to best practices for software development and data management.

Participate in team meetings, seminars, and training sessions to share knowledge and best practices in bioinformatics analysis. This includes presenting updates on ongoing projects, leading discussions on relevant topics in bioinformatics, and providing training to team members on new tools and methods.

Provide support and training to other team members, including laboratory staff, precision oncology scientists, bioinformaticians, pathologists and clinical oncologists, on the use of bioinformatics tools and data analysis techniques. This involves offering guidance on experimental design, data preprocessing, and interpretation of results, as well as troubleshooting issues and answering technical questions to facilitate productive collaborations across disciplines.