Associate Computational Scientist - Dr. Sachet Ashok Shukla's laboratory

University of Texas MD Anderson Cancer Center
Houston, Texas
Closing date
Oct 8, 2022

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Health Sciences
Organization Type
The primary purpose of the Associate Computational Scientist position is to assist in the analysis and development of algorithms and software for scientific problems.

Analyze Next-generation Sequencing Data and Deploy Immunogenomic Tools:
**Run somatic mutation, copy number and transcriptional alteration pipelines on matched tumor/normal pairs whole exome/genome and RNA-seq data. **Run clonality estimation and mutational phylogeny inference tools. **Perform single-point and serial analysis of single-cell RNA-seq, ATAC-seq, CITE-seq and TCR/BCR-seq data. **Create pipelines comprising a wide-ranging suite of in-house and external immune deconvolution, HLA inference, neoantigen prediction, T- and B-cell repertoire analysis software. **Write custom scripts to improve immunogenic methods developed in the lab. Package tools using Docker and Conda applications.

Assisting & Teaching Others:
** Assists other laboratory personnel with animal experiments as necessary, to include: injection of cancer cells, assessing tumor size, and harvesting tumors. ** Helps laboratory manager teach techniques to graduate students, surgical fellows, and other research personnel.

Support Ongoing Research Projects:
**Provide bioinformatic and basic statistical support to ongoing research projects including differential gene expression/mutation analysis, gene set enrichment and pathway analysis, custom sequence alignments etc. **Download and analyze publicly available datasets such as TCGA, CCLE, GTEx and GEO. **Generate custom visualizations of analytical results. **Organize data and document and code developed for each project **Other duties as assigned.

Analytical Thinking - Gather relevant information systematically; break down problems into simple components; make sound decisions.

Innovative Thinking - Approach problems with curiosity and open-mindedness; offer new ideas, solutions and/or options.

Technical/Functional Expertise - Demonstrate technical proficiency required to do the job; possess up-to-date knowledge in the profession; provide technical expertise to others.

Service Orientation
Provide service to our stakeholders, including patients, caregivers, colleagues and each other, in a safe, courteous, accountable, efficient and innovative manner to include:
• Promoting inclusiveness and collegiality that demonstrates respect and professionalism to our stakeholders at all times
• Modeling safe, ethical behavior that mitigates risk to the institution through sound business practices, and adherence to MD Anderson's Standards of Conduct, institutional policies and procedures
• Responding to requests in a timely manner while proactively communicating expectations for procedures, service arrival, or project deliverables to stakeholders
• Using the steps to HEAL (Hear, Empathize, Address and Learn) the relationship when service recovery is needed

Education Required: Bachelor's degree in Biomedical Engineering, Electrical Engineering, Physics, Applied Mathematics or related field. Education Preferred: Master's degree in a related field. Experience: Three years experience in scientific software development/analysis. With preferred degree, one year of required experience. Preferred Experience: None. 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.

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