Available Positions

The Ideker Laboratory is in continual open recruitment for excellent postdoctoral scholars, graduate students, and software engineers. To apply, please send a current CV and references to Dr. Trey Ideker (tideker@ucsd.edu).

PhD Students

Prof. Ideker receives a large volume of emails asking about how to join the Ideker Lab. If you are a student who wants to be admitted to UCSD graduate programs, please directly check out the website of the BISB, BMS, Bioengineering, or CS programs. If you've already been admitted to a UCSD PhD program, please do the following before contacting Prof. Ideker: please watch Prof. Ideker's talk at AACR 2018 , read our Research page, and read some of our papers on the projects that interest you.

Postdoctoral Fellows

We are recruiting bioinformatics postdocs and senior research scientists to three recently funded NIH cell mapping centers: the Cancer Cell Map Initiative (CCMI), the Psychiatric Cell Map Initiative (PCMI) and the Host Pathogen Map Initiative (HPMI). The goal of these positions is to use data generated by the centers to develop advanced computational models of cell biology for use in translating patient data to successful therapies. Currently, there is much interest in building intelligent systems for this purpose, under the banner of precision medicine. However, the current machine learning models face particular challenges when applied to biology, including handling of extreme data heterogeneity and lack of mechanistic insight into predictions. The premise of the CCMI, PCMI and HPMI is to address these challenges by building machine learning systems that are trained to learn not only biological function but also biological structure. Further vision and details for this research are described in this Perspective article in Cell

Applicants must have a PhD in bioinformatics, computer science or a related discipline, a strong background in machine learning and bioinformatics, and a history of productive publication.

Software Engineers

The Ideker Lab is involved in development of several bioinformatic resources for network analysis that are widely used by the biological research community. The best known is Cytoscape (http://www.cytoscape.org), a collaborative open-source software project. Cytoscape is a leading workstation-based platform for visualizing and processing complex networks. It is widely used with approximately 17,000 downloads per month. NDEx, the Network Data Exchange (http://ndexbio.org), is another major project, a public web resource for sharing, storing, accessing, and publishing biological knowledge as computable networks.

Cytoscape Cyberinfrastructure Programmer

The Cytoscape Cyberinfrastructure  Programmer will assist in creating and maintaining elements of the Cytoscape and NDEx, work flexibly across multiple technologies (both front-end, back-end, and database), and acquire skills in new programming languages and environments, packages, and databases. Also, under supervision, the Programmer will assist in maintenance and development of existing code bases, including Cytoscape and its apps. Other responsibilities will be to assist in system administration of public and internal servers. Software deployment and distribution and assist in database management, backup, migration, and recovery. The CI Programmer will interface with colleagues from project sponsors, and with collaborators in the UCSD community and worldwide.

For more information and to apply, please visit: https://jobs.ucsd.edu/bulletin/job.aspx?jobnum_in=96165

System Administrator and Project Coordinator

The System Administrator and Project Coordinator (SAPC) will manage, maintain and extend the computing infrastructure, both hardware and software, and they will support the users of that infrastructure. They will work with the software development team to deploy and administrate cloud hosted websites and services, including usage analysis and reporting. Finally, the SAPC will coordinate the software release process for the web and desktop products of the software development team, including the management of issue tracking and user bug reporting.

Additional responsibilities will include labinfrastructure system administration, working with stakeholders to design hardware and software solutions as the infrastructure evolves to meet new demands, providing lab user support, assisting in the IT issues encountered when installing or maintaining scientific instruments in the wet lab, managing user accounts and commercial software used in the lab, cloud website and service system administration, and coordination of software release process and issue tracking. 

For more information and to apply, please visit: https://jobs.ucsd.edu/bulletin/job.aspx?jobnum_in=95903