Professor
M.D., Harvard Medical School, 1989
Ph.D., Harvard University, 1989

Genome informatics; bioinformatics; mapping; software; World Wide Web

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Today, the desktop computer has become an indispensable part of the biologist’s tool chest. The success of the Human Genome Project has created an information explosion. Billions of bits of data on everything from genetic-linkage information, through physical and genetic maps, to nucleotide and protein sequences and structures are stashed in databases around the globe waiting for the right key to unlock them. Meanwhile, new technologies such as DNA microarrays and high-throughput genotyping are transforming laboratory experimentation, creating an information overload that traditional laboratory techniques cannot handle. Our lab is taking a proactive approach to the genome information explosion by developing databases, data analysis tools, and user interfaces to organize, manage, and visualize that vast body of information.

One current project is a database of human single nucleotide polymorphisms, or SNPs, and their genotypes in three world populations. The information in this database will be used to create a “haplotype map” allowing rapid identification of genetically-determined traits such as disease susceptibility.

Another project is WormBase, a database of the C. elegans genome and biology. This database contains extensive information on the organism’s genes, genetic interactions, cellular anatomy and nervous system, and gives users quick access to the large C. elegans literature.

A third project is Gramene, a comparative mapping resource for rice and other monocots. When finished, researchers will be able to use the rice genomic sequence to identify candidate genes of interest in maize, wheat, and other grains.

A fourth project is Reactome, an interactive database of fundamental biological pathways in the human.

Please visit the Stein Lab home page.

Selected Publications

Stein L.D., et al. 2004. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1: E45.

Stein, L., Sternberg, P., Mangone, M., Durbin, R., Thierry-Mieg, J., and Spieth, J. 2001. WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 29: 82–86.

The SNP Consortium. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928–933.

Stein, L.D., and Thierry-Mieg, J. 1998. Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases. Genome Res. 8: 1308–1315.

Hudson, T.J., Stein, L.D., Gerety, S.S., Ma, J., Castle, A.B., Silva, J., Slonim, D.K., Baptista, R., Kruglyak, L., Xu, S.H., et al., and E.S. Lander. 1995. An STS-based map of the human genome. Science 270: 1945–1954.