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Research Objectives:

To create knowledge structures in order to apply logical reasoning to biological knowledge across large data sets. One particular biological organism of interest is Plasmodium falciparum, a causative agent of human malaria. In addition to having a potential impact on human health, another reason for studying parasites is that they are interesting from a modeling perspective due to complex host-parasite interactions and lifecycle changes.

Malaria Resources:

PlasmoCyc: a knowledge base of Plasmodium falciparum metabolism.

PlasmoDB: a database of Plasmodium sequences, annotations, and functional assignments.

Malaria Transcriptome Database: from the Derisi lab at UCSF.

Biological Ontology Resources:

Gene Ontology: a controlled vocabulary for annotation of gene products by molecular function, biological process, and cellular component.

Gene Ontology in Protege: tools for importing Gene Ontology into a Protege project. Tools also available for importing GO format annotations into an existing Protege Project.

Publications:

Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB. Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery. Genome Research. 2004 14(5):917-24. link

Yeh I, Karp PD, Noy NF, Altman RB. Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics 2003 19(2):241-8. pdf

Peleg M, Yeh I, Altman RB. Modeling biological processes using workflow and Petri Net models. Bioinformatics 2002 18(6):825-37. link

Presentations:

BCATS 2002; Speaker: Using a Pathway/Genome Database for Plasmodium falciparum to find novel drug targets

Bioontologies 2002; Speaker: An Ontology for Subcellular Localization.

ISMB 2002; Poster: PlasmoCyc: A Pathway/Genome Database for Malaria

PSB 2002; Poster: Application of Protege-2000 to Gene Ontology

Malaria Bioinformatics International Workshop 2000,2001; Tutorial: Metabolic Pathways for the Malaria Parasite

Research Funding:

Burroughs Wellcome Fund

National Institute of General Medical Sciences through the Medical Scientist Training Program

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