Research Investigator - Dr. Sachet Ashok Shukla's Laboratory

SUMMARY

The Shukla lab is a highly translational group focused on antigen discovery and development of personalized immunotherapies. We develop computational approaches and deploy state-of-the-art technologies and experimental assays to elucidate mechanisms underlying immunogenicity, immune escape and clinical outcomes to cancer immunotherapy. We are seeking highly motivated and skilled computational biologists who will work within an interdisciplinary team comprising computational scientists, software engineers, oncologists, and immunologists on tumor immunity projects across cancer types.

We are recruiting a highly motivated, organized and enthusiastic Research Investigator who will conduct analysis of data generated from high-throughput biological profiling technologies including bulk and single-cell sequencing. The candidate will build pipelines for detection of somatic alterations, phylogenetic inference and immunogenomic characterization using whole exome and RNA-seq data. The candidate will analyze data from single-cell sequencing experiments including scRNA-seq, CITE-seq, ATAC-seq and TCR-seq to answer key scientific questions and provide bioinformatic support to ongoing research efforts. The ideal candidate will have formal training and experience in analysis of high-throughput data using statistical or machine learning methods, and strong programming skills. Prior knowledge of cancer biology or immunology is a plus. Software development experience is desirable but not required. Must thrive in an academic/professional atmosphere, where interdisciplinary teams are central to project success.

Dr. Shukla is deeply committed to the career growth and success of each member of the laboratory. Computational lab members will also have access to the rich expertise and technologies the institutional ECLIPSE platform where Dr. Shukla will serve as the Computational Director, as well as the benefit of collaborating with leading external computational groups.

We are looking for an enthusiastic, self-motivated, independent thinker with a tremendous work ethic. The position will require great planning and organizational skills. An ability to work well with others as part of a cohesive team, take initiative, and creatively problem solve are a must.

CORE VALUES

Caring: By our words and actions we demonstrate caring toward everyone.

• We are sensitive to the concerns of our patients, their loved ones and our colleagues.
• We are respectful and courteous to each other and practice cultural humility.
• We promote and reward teamwork and inclusion.

Integrity: We work together with professionalism to merit the trust of our colleagues and those we serve in all that we do.

• We hold ourselves, and each other, accountable for our work - decisions and data - and for practicing our values and ethics.
• We advocate for diversity and equity for our workforce, for those we serve and for our community.
• We communicate frequently, honestly, openly and responsibly.

Discovery: We embrace creativity and seek new knowledge from diverse perspectives.

• We encourage continuous learning, seeking out information and new ideas.
• We team with each other to identify and resolve problems.
• We seek personal growth and enable others to do so.

Safety: We provide a safe environment - physically and psychologically - for our patients, for our colleagues and for our community.

• We create a sense of security and empowerment and are committed to keeping one another free from harm.
• We embrace a framework and best practices for the highest quality of care and service.
• We inspire trust by modeling excellence in our work and acceptance of each person's contributions.

Stewardship: We protect and preserve our institutional reputation and the precious resources - people, time, financial and environmental - entrusted to us.

• We prioritize the health and well-being of each other.
• We act responsibly to safeguard the institution's finances.
• We ensure the proper care and use of time, data, materials, equipment and property afforded to us.

JOB SPECIFIC COMPETENCIES

Analyze next-generation sequencing data

• 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

Deploy immunogenomic tools

• 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

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

Bachelor's degree in Biomedical Engineering, Electrical Engineering, Physics, Applied Mathematics or related field. Preferred Education: Master's degree (M.S.) or Doctorate degree (PhD) in Computational Biology, Computer Science, Engineering, Applied Mathematics, Biostatistics or a related discipline with BS/MS in Immunology, Cancer Biology or a related discipline. Five years of experience in scientific software development/analysis or experimental research work. With preferred degree, three years of required experience. Preferred Experience: Proficiency in scripting/statistical computing. Experience manipulating datasets/high performance computing. Familiarity with data normalization/analysis of batch effects. Development of statistical algorithms and comprehensive assessments for analysis. Collaboration with bench biologists, next-generation sequencing analytics, pathway/networ, and transcriptional regluator networks. 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