Positions Available

Research Programmer Position

The NANOtumor project is an NIH funded 5 year project with the objective to develop in vivo tools for detection and treatment of cancer in humans. This is a collaborative effort involving the University of California, San Diego (UCSD), Moores UCSD Cancer Center, UC-Santa Barbara, UC-Riverside, the Burnham Institute, market research organization NanoBioNexus, and five corporate partners: General Electric Company, Honeywell, Nanogen, Irvine Sensors Corporation, and Enterprise Partners Venture Capital.

Specific projects of this CCNE include development of

Tumor-homing peptide-nanoparticle complexes Porous nanoparticles for drug and sensor delivery Computational methods for monitoring tumor progression and response using data from nanoparticle-delivered sensors Enzyme-sensitive nanoparticle coatings to increase tumor-targeting capabilities of smart nanoparticle platforms

There are several projects with the several laboratories involved. The research programmer serves as a member of the informatics component and is responsible for a) development of data acquisition and storage system, b) building tools for enabling experimental design, and c) analysis of data upon generation. This position requires an expert in bioinformatics, computer software and programming, familiarity with biology, especially cancer-related biology and strong skills in communication. Incumbent will work with minimal supervision and will be expected to write documentation, contribute content for reports, and make presentations describing work.


  1. Advanced experience in the use of Java technology, particularly Servlets and JSPs, Java Swings and database programming

  2. Advanced degree in computer science, or a master’s degree in biochemistry/Life Sciences with at least 5 years of relevant software development experience, or comparable combination of education and experience. Ph.D. desirable

  3. Demonstrated experience using OC4J as well as with IDEs such as Eclipse

  4. Strong demonstrated experience with Struts, Hibernate 3, EJB 3.0, Java Swings, Perl, Unix, Linux, SQL, MSSQL, Oracle, PC/Windows, Rational Software Modeler, Eclipse 3.0 and above, ER Studio, TOAD ,Ant, Java Web Star

2-3 Postdoctoral Positions 

2 Research Programmer Positions

The positions are available for the following projects.


The major objective of this multiinvestigator multiinstitution project is the identification and characterization of mammalian lipids in normal and diseased states. The cells of choice are macrophages. Work in this project will entail both proteomic annotations and lipid pathway reconstructions. For more information about LIPID MAPS, visit the website;http://www.lipidmaps.org

NanoTUMOR project

The major objective of this Center project is the development of nanodevices for detection, monitoring and treatment of cancer. The posted job of Research Programmer is to coordinate data deposition using CaNanoLab architecture and to analyze cellular and phenotypic data from cancer measurements. Required qualifications include web and database experience and familiarity with biology.

Gene networks controlling macrophage-adipocyte interactions

This project  deals with identification and characterization of gene networks in adipocytes and macrophages associated with insulin action. This is a Program Project Grant  involving Professors Chris Glass, Geoff Rosenfeld, Jerry Olefsky and me. We are making systematic genome wide measurements using Chip, ChIP-chip and digital sequencing methods to explore transcriptional changes in adipocytes and macrophages from normal and diseased animals. The work proposed involves using systems biology approaches towards identification and reconstruction of networks, including development of novel strategies.

Reconstruction of networks involved in differentiation of stem cells into cardiomyocytes

This is a systems biology project associated with reconstruction of networks involved in differentiation of murine embryonic stem cells into cardiomyocytes. My co-PIs on this R33 project are Mark Mercola (an embryologist and stem cell biologist) and Juan Carlos Belmonte (a stem cell biologist). We are systematically carrying out both proteomic and gene expression measurements longitudinally with differentiation at various stages. The proposed work will involve analysis of the large data and reconstruction and modeling of networks

Job applications can be sent by email to Professor Subramaniam at shankar@ucsd.edu