Thomas Girke, Ph.D.

Degrees

Research Interests

The research in my group focuses on the development of novel tools and algorithms for comparative genomics, data mining, cellular network analysis, quanitative systems modeling and drug discovery. One of our major projects is the development of predictive cheminformatics tools for the discovery of novel bioactive compounds for chemical genomics research and drug discovery. The publicly available ChemMine database is part of this effort.

Another research focus is the integration and modeling of large-scale 'omics' data from model organisms, such as gene expression profiling, proteomics and regulatory network data. For these analyses we develop and utilize a variety of comparative genomics, network analysis and machine learning approaches.

My group also develops and maintains a variety of research databases that are part of the Systomics Network.

Group Members

See group page.

Selected Publications

See publication page.

Teaching

• Bioinformatic manuals
• Bioinformatic workshops
• Genetics 240A
• Genetics 240B: Bioinformatics Tools,   Microarray Analysis
• Bioinfo Core Short (PDF)
• Bioinfo Core Long (PDF)

Open Positions

Postdoctoral position in comparative genomics

This position requires several years of experience in computational biology, statistics, database design and data mining with strong publications records in several of these areas. The candidate should be proficient in at least one of the common programming languages that are used in bioinformatics: C, Python, Java, Perl or R. Experience with web and database programming is also beneficial. To apply for this position, please email your CV and a statement of research interests to thomas.girke@ucr.edu.

Postdoctoral position in cheminformatics

This position requires experience in computational chemistry, drug-informatics, QSAR/phramacophore modeling and data mining with strong publications records in several of these areas. The candidate should be proficient in at least one of the common programming languages that are used in cheminformatics: C, Python, Java, Perl or R. Experience with web and database programming is also beneficial. To apply for this position, please email your CV and a statement of research interests to thomas.girke@ucr.edu.

Undergraduate research positions

Several postions are available for undergraduate students who are interested in participating in challenging database and software development projects for various research projects in bioinformatics and cheminformatics. The required skills are experience with open-source databases (MySQL/PostgreSQL), application and web programming with Python, Perl and/or Java. The minimum time commitment is 15-20h per week for a period of at least 18 months. Full-time employment during the summer break is possible. To apply for these positions, please email your CV with a detailed outline of your computational skills to thomas.girke@ucr.edu.

Lab Meeting

Girke Lab Meeting

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