Computational Biologist & Project Manager in Genomics (Biostatistician 2)

🔍 School of Medicine, Stanford, California, United States

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📅   : 2 days ago Post Date

📅   : 107087 Requisition #

The Engreitz and Kundaje Labs are seeking a Computational Biologist / Project Manager (Biostatistician 2) to join the Department of Genetics to map the regulatory wiring of the human genome to discover genetic mechanisms of disease. 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. The Engreitz and Kundaje Labs have developed new experimental approaches and computational methods that could enable mapping this regulatory wiring at massive scale (see Fulco et al. Nature Genetics 2019, Schnitzler & Kang et al. Nature 2024, Avsec et al. Nature Genetics 2021, Pampari et al. bioRxiv 2024). We invent new tools combining single-cell genomics, CRISPR perturbations, and machine learning to assemble regulatory maps of the human genome and uncover mechanisms of complex diseases. For more information and recent work, see https://www.engreitzlab.org and https://kundajelab.github.io/)

Project overview: We aim to develop and apply computational models to interpret the function of any noncoding variant or protein-coding gene in the human genome, across many human cell types in the body. Toward this goal, we are leading highly collaborative projects in two NIH-funded Consortia: MorPhiC (https://morphic.bio) and IGVF (https://www.igvf.org). MorPhiC aims to characterize the functions of genes through CRISPR perturbations and predictive modeling (Adli et al. Nature 2025). IGVF aims to characterize the impact of genomic variation on function by combining single-cell mapping, genomic perturbations, and predictive models (IGVF Consortium, Nature 2024). This position will involve improving predictive models of variants, enhancers, and genes and applying them to large single-cell and CRISPR datasets generated by MorPhiC and IGVF to create a comprehensive catalog of the regulatory wiring of the genome.

We are looking for creative and passionate people at any stage in their careers, including computational biologists, bioinformaticians and software engineers. Candidates will train to lead and design team science computational projects that push the boundaries of genomic technology and reveal the functions of genetic elements associated with human diseases.

Our laboratories are co-located in the Department of Genetics and Biomedical Innovations Building at Stanford University. Our department 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 ideal candidate should have expertise in bioinformatics and computational biology workflows; statistical methods in data analysis, with applications to high-throughput sequencing or other biological assays; fundamentals of software engineering; strong knowledge of molecular biology and genomics; fluency in Unix and standard programming and data analysis languages (Python, R, or equivalent); interest in mentoring and training other lab members in computational biology and statistics; excellent communication, organization, and time management skills; and creativity and motivation.

Duties include:

Apply state-of-the-art machine learning models to large datasets, including single-cell and Perturb-seq datasets
Interpret model performance and results
Develop standards and pipelines to enable expand such analyses across additional datasets
Interface with collaborators at Stanford and in collaborating labs around the country to design and produce key methods and data analysis products
Track and manage contributions by other members of our labs to consortium activities
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

* - Other duties may also be assigned.

DESIRED QUALIFICATIONS:

Required: M.S. or Ph.D. in computational biology, genetics, computer science, statistics, math, molecular biology, or related field, or equivalent practical experience. Talented applicants of all levels are encouraged to apply.
Demonstrated expertise in statistical methods in data analysis, preferably with applications to high-throughput sequencing or other biological assays
Experience with data analysis and management, workflow management
Fluency in Unix, standard bioinformatics tools (Python, R, or equivalent), and a programming language (C/C++, Java)
Strong knowledge of molecular biology and functional genomics
Mentor and train other lab members in computational biology and statistics
Excellent communication, organization, and time management skills
Creative, organized, motivated, team player
A passion for science and sense of urgency to find new medicines to benefit patients

EDUCATION & EXPERIENCE (REQUIRED):

Master's degree in biostatistics, statistics or related field and at least 3 years of experience.

KNOWLEDGE, SKILLS AND ABILITIES (REQUIRED):

Proficient in at least two of R, SAS, SPSS, or STATA.
Skills in descriptive analysis, modeling of data, and graphic interfaces.
Outstanding ability to communicate technical information to both technical and non-technical audiences.
Demonstrated excellence in at least one area of expertise, which may include coordinating studies; statistical methodology such as missing data, survival analysis, statistical genetics, or informatics; statistical computing; database design (e.g., expertise in RedCAP or MySQL); graphical techniques (e.g., expertise in Illustrator).

CERTIFICATIONS & LICENSES:

None

PHYSICAL REQUIREMENTS*:

Frequently perform desk based computer tasks, seated work and use light/ fine grasping. \
Occasionally stand, walk, and write by hand, lift, carry, push pull objects that weigh up to 10 pounds.

* - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job.

WORKING CONDITIONS:

May work extended or non-standard hours based on project or business cycle needs.

The expected pay range for this position is $112,292 to $132,108 per annum. Stanford University provides pay ranges representing its good faith estimate of what the university reasonably expects to pay for a position. The pay offered to a selected candidate will be determined based on factors such as (but not limited to) the scope and responsibilities of the position, the qualifications of the selected candidate, departmental budget availability, internal equity, geographic location and external market pay for comparable jobs.

At Stanford University, base pay represents only one aspect of the comprehensive rewards package. The Cardinal at Work website (https://cardinalatwork.stanford.edu/benefits-rewards) provides detailed information on Stanford’s extensive range of benefits and rewards offered to employees. Specifics about the rewards package for this position may be discussed during the hiring process.

The job duties listed are typical examples of work performed by positions in this job classification and are not designed to contain or be interpreted as a comprehensive inventory of all duties, tasks, and responsibilities. Specific duties and responsibilities may vary depending on department or program needs without changing the general nature and scope of the job or level of responsibility. Employees may also perform other duties as assigned.
Consistent with its obligations under the law, the University will provide reasonable accommodations to applicants and employees with disabilities. Applicants requiring a reasonable accommodation for any part of the application or hiring process should contact Stanford University Human Resources at stanfordelr@stanford.edu. For all other inquiries, please submit a contact form.

Stanford is an equal employment opportunity and affirmative action employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

WORK STANDARDS (from JDL):

Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations.
Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned.
Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University's Administrative Guide, http://adminguide.stanford.edu.

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