Available Positions

The Ideker Laboratory in the Department of Medicine at UC San Diego is in open recruitment​ for​ the following positions. See Research Overview page for additional details about the objectives of Ideker Laboratory. 

PhD and Postdoctoral Recruitment

Candidates for Postdoctoral Scholar, Graduate Student, and Rotation Student positions should have applicable education in bioinformatics, computational biology, mathematics, physics, molecular biology or related discipline. To apply, please send a current CV and references to Dr. Trey Ideker​ (tideker@ucsd.edu​). 

Project: Using a hierarchical cellular model to analyze tumor genetic mutations

The candidate will explore whether a hierarchical cell model we have recently constructed for predicting growth of simple cells can be translated to predict aggressiveness of human cancer. The model will be provided, along with access to tumor exomes from both public and internal sources. The goal is to determine whether and to what extent the model can be used to analyze a patient's exome. If so, this project could be readily developed in multiple future directions.

Project: Experimental mapping of the DNA damage response

Cell colonies on agar grow in a near linear fashion with growth rates reflective of their "fitness". The laboratory has developed an experimental platform that can make continuous measurements of growth rates via time-lapse image capture of thousands of specific genetic mutant strains, enabling us to determine the relevance of every gene in the response to stimuli such as DNA damage via radiation or chemotherapy. In this project the candidate will grow ~50,000 cell colonies in parallel and capture their growth curves using digital images and intermittent radiation exposure. The project includes working in Matlab for the analysis of growth curves and the elucidation of DNA damage response pathways.

Project: Computing a minimal set of genes required for life

A long standing question in biology is how many (and which) genes are required for life. This essential core set of genes, or minimal genome, makes up the cell's “life support system” or “chassis and power supply” on which more complex functions and processes are built. This set of genes is of keen interest in the field Synthetic Biology, which aims to synthesize the complete minimal genome of an organism and add additional functions to this genome for biotechnological, pharmaceutical and agricultural ends. This project will attempt to use our whole-cell model of the networks and pathways in a cell to predict which genes and gene combinations are essential for life and, conversely, which genes and gene combinations can be removed. If successful, this project will be able to predict minimal genomes for synthesis and testing. It will also address whether there actually is a single “minimal genome” or whether there exist many different configurations all of which are near or at the global minimum.


 

Cytoscape Cyberinfrastructure Developer

We’re looking for a few highly skilled and versatile software engineers that can join our team to create a SOA-based distributed system (called the Cytoscape Cyberinfrastructure or “CI”) that will enable analyses of biological networks to deliver medical decisions, practices and products tailored to individual patients. Today, we work with Java, Javascript, Golang, Python, R, React, REST, Docker, Kubernetes, OpenCL and machine learning platforms – tomorrow’s stack will be team-defined responsive to emergent CI requirements. The CI Developer will create and maintain elements of the CI, will need to work flexibly across multiple technologies, both front-end, back-end, and database, and will need to rapidly acquire skills in new programming languages and environments, packages, and databases.

Please visit the UC San Diego Jobs portal for additional details and to apply for this position: 
https://jobs.ucsd.edu/bulletin/job.aspx?jobnum_in=88300 


 

NDEx Senior Developer

The NDEx Senior Developer will be one of the primary software engineers for the NDEx project, an open-source bioinformatics software project that provides infrastructure and applications to support the effective use of biological networks by the research, pharmaceutical, and clinical communities. The NDEx platform enables sharing, storing, accessing, and publishing biological knowledge as computable networks. The project manages a public website using the NDEx platform, providing a global resource for scientists and organizations (see www.ndexbio.org for more details). It creates applications based on the platform and helps other researches build their own applications using NDEx services. 

The NDEx Senior Developer will be a key technical expert for the NDEx development team, solving problems that are both technically and scientifically challenging for a large and varied community of users. The NDEx Senior Developer will work with front-end interface, and back-end service and database technologies and must be able to rapidly acquire skills in new programming languages, packages, and databases.

Please visit the UC San Diego Jobs portal for additional details and to apply for this position: