Computational Scientist - Bioinformatics

Led by Prof. Bissan Al-Lazikani, Director of Therapeutics Data Science, the intelligent and ever-learning A3D3a platform is part of the new initiative in Therapeutics Data Science and part of our ambitious Institute for Data Science in Oncology at MD Anderson. A3D3a will accelerate the discovery and impact of novel therapies for cancer by enabling novel opportunities for optimized therapies for patients with a focus on rare and hard-to-treat cancers through the development of novel machine learning and AI technologies.

JOB SPECIFIC COMPETENCIES
Carry out preparation, clean-up, and quality control of biological data, including whole exome sequencing, whole genome sequencing, and RNA sequencing from both bulk and single-cell datasets.
• Develop and maintain pipelines for bioinformatics and statistical analyses of aforementioned data types; activities to include handling raw data, evaluating outputs, optimizing parameters and summarizing findings.
• Deploy bioinformatics pipelines in high performance computing environments.
• Visualize data and interpret results, including implementation of approaches suchas variant calling, functional annotation, gene set enrichment, and pathway annotation.
• Maintain knowledge of latest bioinformatic approaches and genomic technologies and implement these where appropriate
• Present results at multidisciplinary project meetings.
• Produce output for scientific publications and co-author said publications.
• Prepare written reports, manuscripts, and grant applications with investigators.
• Work closely with the team and collaborators to discover novel therapeutic opportunities for cancer patients.

Expected Skills
• Deep knowledge of bioinformatics tools and their implementation as part of pipelines, particularly for whole genome sequencing, whole exome sequencing, and RNA sequencing data, in both bulk and single-cell contexts.
• Demonstrated experience and understanding of genomic technologies and analysis of data generated.
• Analyzing and interpreting outputs to identify insights and hypotheses from data.
• Understanding of essential statistical methodologies required for bioinformatics analyses.
• Addressing challenges in bioinformatics as well as mitigation strategies including bias, batch correction, etc.
• Applying data clustering (e.g., t-SNE, UMAP, novel approaches) and basic machine learning techniques to complement bioinformatic analyses
• Utilizing High Performance Computing to run large-scale analyses.
• Deploying pipelining tools (e.g., Nextflow or similar).
• Unix, R, Python or other scripting/programming languages.

Service Orientation
1. Conduct research and interactions with colleagues in a reliable, responsive, safe, friendly and courteous manner.
2. Promotes inclusiveness and collegiality by demonstrating respect and professionalism to others at all times
3. Models safe, ethical behavior, mitigating risk to the institution through sound business practices, and adherence to MD Anderson's Standards of Conduct, institutional policies and procedures.
4. Meets time and attendance expectations and responds to requests in a timely manner, communicating expectations for procedures, service arrival, or project deliverables to coworkers.
5. Admits when wrong, apologize and take steps to resolve a situation to help to coworkers before being asked.

Other duties as assigned.

EDUCATION:
Required: Bachelor's degree in Biomedical Engineering, Electrical Engineering, Physics, Applied Mathematics or related field.

Preferred: Master's degree or PhD with a concentration in Science, Engineering or related field.

EXPERIENCE:
Required: Five years experience in scientific software development/analysis. With Master's degree, three years experience required. With PhD, one year of experience required.

Preferred: One year of postdoctoral experience.

It is the policy of The University of Texas MD Anderson Cancer Center to provide equal employment opportunity without regard to race, color, religion, age, national origin, sex, gender, sexual orientation, gender identity/expression, disability, protected veteran status, genetic information, or any other basis protected by institutional policy or by federal, state or local laws unless such distinction is required by law. http://www.mdanderson.org/about-us/legal-and-policy/legal-statements/eeo-affirmative-action.html