The Department of Genetics is seeking a computational biologist and engineer (Life Science Research Professional 1) to join the Engreitz Laboratory to map the regulatory wiring of the human genome to discover genetic mechanisms of heart diseases. The Engreitz Lab launched at Stanford in 2020 and is part of the Department of Genetics and the Basic Science and Engineering (BASE) Initiative of the Moore Children’s Heart Center. The position is open, and a successful candidate could join immediately.
Lab overview: DNA regulatory elements in the human genome, which harbor thousands of genetic risk variants for common and rare diseases and could reveal targets for therapeutics that aim to precisely tune cellular functions — if only we could map the complex regulatory wiring that connects 2 million regulatory elements with 21,000 genes in thousands of cell types in the human body. We have recently developed new approaches that could enable mapping this regulatory wiring at massive scale (see Fulco et al. Science 2016, Fulco et al. Nature Genetics 2019, Nasser et al. Nature 2021, Bergman et al. Nature 2022). We invent new tools combining experimental and computational genomics, biochemistry, molecular biology, and human genetics to assemble regulatory maps of the human genome and uncover biological mechanisms of heart disease.
We are looking for creative and passionate people at any stage in their careers, including computational biologists and software engineers. Candidates will train to lead and design computational projects that push the boundaries of genomic technology and reveal the functions of genetic variants associated with human diseases.
Specific projects include: to develop and apply predictive models for enhancer-gene regulation, including leveraging the ABC and ENCODE-rE2G framework to capture enhancer synergies and genetic variant effect sizes; to develop and apply methods to systematically benchmark the performance of predictive models; to design and analyze large-scale single-cell CRISPR screens to chart gene regulatory connections and decipher molecular mechanisms of gene regulation. For more information and recent work, see www.engreitzlab.org.
The Engreitz Laboratory is a dynamic, interdisciplinary workplace that will provide unique access to cutting edge technologies and scientific thought, with the potential for widespread recognition of scientific contributions. We value a diversity of values, backgrounds, and approaches to solving problems.
The successful candidate for this position should have expertise in data analysis and software engineering, preferably with applications to high-throughput sequencing or other biological assays; enthusiasm for developing and applying computational approaches to learn fundamental mechanisms of gene regulation, and understand human disease; fluency in Unix, programming, and bioinformatics tools (Python, R, or equivalent); excellent communication, organization, and time management skills; and be a creative, organized, motivated team player.
Duties include:
- Collaborate with experimentalists and computational biologists to develop and apply functional genomics techniques to understand gene regulation and the genetic basis of heart disease
- Design and implement generalizable algorithms and tools for analysis of biological data, including high-throughput functional genomics assays
- Evaluate and recommend new emerging technologies, approaches, and problems
- Create scientifically rigorous visualizations, communications, and presentations of results
- Contribute to generation of protocols, publications, and intellectual property
- Maintain and organize computational infrastructure and resources
DESIRED QUALIFICATIONS:
- B.S. in computational biology, computer science, physics, statistics, math, molecular biology, or related field. Motivated applicants of all levels are encouraged to apply.
- Experience in collaborative software development and relevant platforms
- Demonstrated expertise in software engineering and/or statistical methods in data analysis, preferably with applications to high-throughput sequencing or other biological assays
- Enthusiasm for using computational approaches to learn fundamental mechanisms of gene regulation and understand human disease
- Excellent communication, organization, and time management skills
- Creative, organized, motivated, team player
EDUCATION & EXPERIENCE (REQUIRED):
- Bachelor's degree in related scientific field.
KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):
- General understanding of scientific principles. Demonstrated performance to use knowledge and skills when needed.
- Demonstrated ability to apply theoretical knowledge of science principles to problem solve work.
- Ability to maintain detailed records of experiments and outcomes.
- General computer skills and ability to quickly learn and master computer programs, databases, and scientific applications.
- Ability to work under deadlines with general guidance.
- Excellent organizational skills and demonstrated ability to accurately complete detailed work.
PHYSICAL REQUIREMENTS:
- Frequently stand, walk, twist, bend, stoop, squat, grasp lightly, use fine manipulation, grasp forcefully, perform desk-based computer tasks, use telephone, write by hand, lift, carry, push and pull objects weighing over 40 pounds.
- Occasionally sit, kneel, crawl, reach and work above shoulders, sort and file paperwork or parts.
- Rarely climb, scrub, sweep, mop, chop and mix or operate hand and foot controls.
- Must have correctible vision to perform duties of the job.
- Ability to bend, squat, kneel, stand, reach above shoulder level, and move on hard surfaces for up to eight hours.
- Ability to lift heavy objects weighing up to 50 pounds.
- Ability to work in a dusty, dirty, and odorous environment.
- Position may require repetitive motion.
- Sitting in place at computer for long periods of time with extensive keyboarding/dexterity.
- Occasionally use a telephone.
WORKING CONDITIONS:
- Some work may be performed in a laboratory or field setting
