Research Scientist, Bioinformatics

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Job Summary

The Ismagilov Lab at the California Institute of Technology is looking for a Research Scientist, Bioinformatics to join a fast-paced ~20-person interdisciplinary laboratory team. The research agenda includes development of scientific knowledge and technologies to impact human health, in particular in areas of emerging human pathogens, human host-microbe interactions, and human immune response to infection.

The Research Scientist, Bioinformatics will work with the PI to execute the laboratory's ambitious research agenda. The position will support the PI, students, and postdoctoral researchers via several avenues: bioinformatics and computational tools, assistance with research projects, acquisition of research funding, and personnel recruitment and training. The successful candidate will have a strong drive to advance the frontiers of knowledge, to develop new technologies through rigorous science, to have significant impact on human health, and to guide and mentor the next generation of researchers.

Essential Job Duties

Bioinformatic Responsibilities:

• Deploy and maintain the state-of-the-art computational tools, including NGS bioinformatic pipelines, that are developed by the lab, its collaborators, and other leaders in the field.
• Collaborate with students/postdocs in the lab and with external collaborators to improve the accuracy, efficiency, and usability of computational pipelines.
• Collaborate with students/postdocs in quality control assessment and troubleshooting of microbial sequencing.
• Collaborate with students/postdocs in the analyses (e.g., mapping, gene expression, variant calling, MAG assembly, etc.) and interpretation of both RNA and DNA next generation sequencing (NGS) datasets containing human and microbial sequences from complex clinical samples. Examples of datasets include Illumina short read shotgun metagenomes, long read shotgun metagenomes, RNA-Seq, 16S/ITS Amplicon sequencing.
• Collaborate with students/postdocs to design appropriately powered experiments and to perform statistical analyses.
• Train students on lab’s computational pipelines and the use of Caltech’s high-performance computing cluster.
• Work with Caltech’s IT to ensure proper data and computing management.

Group Research Roles:

• Assist with the execution of research in the laboratory to enable timely accomplishment of research goals.
• Assist students and postdocs with project design and execution, implementation and troubleshooting.
• Identify project bottlenecks and suggest strategies to improve workflows.
• Assist students and postdocs in identifying and engaging internal and external resources to facilitate project execution.
• Along with the PI and members of the lab team, assist with the preparation of the technical sections of grant proposals following the directions established by the PI.
• Has the opportunity to conduct research in collaboration with the members of the lab; has the opportunity to co-author and/or write journal articles, procedural guides or manuals; has the opportunity to present research work at seminars and conferences.
• Assist with generating data for grant proposals, grant reports, patents, and publications.
• Assist the PI in recruitment, evaluation, and training of research personnel, including students and postdocs.

Basic Qualifications

General Qualifications:

• Ph.D. in bioengineering, computational biology, bioinformatics, biology, molecular biology, or related field OR a Master’s in bioengineering, computational biology, bioinformatics, biology, molecular biology, or related fields with 2 + years of industry or academic experience.
• A record of independent research accomplishments.
• Broad, interdisciplinary mindset along with flexibility and willingness to continue learning.
• Ability to do rigorous research, including thoughtful study design and selection of appropriate controls and appropriate analysis methods.
• Effective technical communication skills, including scientific writing and data visualization.
• Experience managing project deliverables for multiple concurrent projects involving multiple researchers and collaborators.
• Experience training and supervising junior colleagues leading to positive outcomes in colleagues’ education and accomplishments.
• Strong critical-thinking skills.
• Excellent fact-based decision-making skills.
• Ability to solve complex problems.
• Ability to manage multiple priorities and deadlines.
• Must be self-motivated, take initiative, and lead; must be able to work independently and multi-task.
• Excellent communication skills, both oral and written.
• Excellent interpersonal skills. Able to work with a diverse and interdisciplinary group of researchers and external collaborators.
• A strong desire to collaborate with and mentor the next generation of researchers.

Bioinformatic Qualifications:

• Strong quantitative skills and strong comprehension of statistics.
• Strong computational skills.
• Strong understanding of the fundamental principles on which bioinformatic pipelines are built. 
• Computational experience with NGS datasets.
• Experience with high-performance computing, including bash scripting.

Preferred Qualifications

• Experience with microbial bioinformatics. 
• Computational experience analyzing samples to identify microbial (bacteria, fungi, and virus) taxonomy, metagenomic assembled genomes (MAGs), and functional gene analysis.
• Experience with analysis of long-read sequencing datasets.
• Proficiency in Python.
• Familiarity with and interest in modern Al tools.
• Familiarity with grant proposal preparation. 

Required Documents

• CV
• Statement describing candidate’s aspirations and qualifications, including: (1) relevant technical depth and expertise, 2) experience in mentoring and supporting junior researchers, and 3) record of productivity, especially in complex projects.