Pattern Genomics, a Madison, CT based startup company, is seeking full-time bioinformatics student interns for summer 2014.  Pattern Genomics has developed a proprietary bioinformatics platform called Daydreamer™ for large-scale comparative genomics and molecular diagnostic design.  Our initial focus is in infectious disease, where our system allows us to load hundreds of pathogen genomes that are labeled as belonging to two or more subtypes and find patterns of markers that distinguish between the subtypes.  We have successfully applied the technology to important disease detection problems such as methicillin-resistant Staphylococcus aureus and toxigenic Clostridium difficile.  As with many early-stage computing companies, Pattern Genomics operates as a virtual organization and would be an ideal opportunity for interns who intend to stay in the central Connecticut area over the summer.  Access to appropriate computing resources would be provided.

We are interested in supporting two different types of internships.  For students whose primary interest is in computer science and bioinformatics algorithms, there are many opportunities to enhance our Daydreamer™ platform.  The platform is written in C++ for Linux systems, and makes use of multithreading and distributed computation with MPI.  Topics could include improving the efficiency of our distributed sequence analysis methods or providing additional approaches to finding discriminating patterns and reducing them to molecular assay designs.  Expertise with C++, Linux development, data structures and algorithms are required; knowledge of molecular biology is a plus but not necessary.

For students whose main interest in the application of bioinformatics, we are interested in supporting research into relevant molecular diagnostic topics such as Carbapenem-resistant Enterobacteriaceae (CRE) detection.  Such a project may involve scripting or minor changes to our code, but would focus primarily understanding the application area, performing computational data analysis, and interpreting the results in the context of existing knowledge.  The goal would be to use Daydreamer™ and other tools to identify relevant gene sequences and design a detection assay design that could be tested in the lab.  For this position, expertise with computational genomics and sequence analysis tools are required, but only basic Linux and programming skills are needed.

Please contact Daniel Fasulo by email at daniel.fasulo@patterngenomics.com for more information or to apply.