Bioinformaticists: Dongmei Zuo, Yanhui Hu, and Helen Taycher.
Systems: Michael Collins

The mission of HIP Bioinformatics group is to do Bioinformatics support for various high-throughput operations at Harvard Institute of Proteomics from clone production, clone sequence analysis, clone distribution to clone utilization in different functional assays.

“FLEXGene” is an oracle database with web-based user interface to track the creation of FLEX clones at high-throughput cloning pipeline. “ACE” is an automatic sequence analysis package with web-based user interface to support high-throughput clone validation. “PlasmID” is for on-line clone ordering and for supporting the automatic clone storage and retrieval system. Dongmei is the lead developer for “FLEXGene” and “PlasmID” while Helen is the lead developer for “ACE”.

“MedGene” is a text mining project designed to develop the automated extraction of biomedical knowledge from Medline database to create a human gene-to-disease co-occurrence network for all named human genes and all human diseases by automated analysis of MeSH indexes, title and abstracts in millions of Medline records. Users can review most reported genes related to any human disease and vice versa in ranking order. “BioGene” is an extension of “MedGene” to extract the associations of gene and biological terms (such as cell cycle and hela cells) from pubmed literature. Yanhui is the lead developer for “MedGene” and “BioGene”.

"FLEXProt" is a protein database to track experiments of high-throughput protein purification and functional studies. It can also facilitate interpretation of experimental results in high-throughput manner and help to analyze factors that may affect experimental outcome. Yanhui is the lead developer for “FLEXProt”.

In addition, a few other web-based handy tools were developed by previous members. "PCR Oligo Generator" was developed to generate 5' and 3' primers in batch mode for full length gene cloning. “DNA Polymorphism Detector” is a web-based tool to distinguish real sequence discrepancies from polymorphism changes during clone sequence validation. “BatchBlast” is a blast parser developed using JavaCC technology.