Home Faculty and Research Faculty by Name Gerald Rubin

Gerald Rubin

Howard Hughes Investigator and MacArthur Professor of Genetics, Genomics and Development

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Research Interests

We are interested in developing the biological and computer-based tools needed to analyze and efficiently utilize the vast amount of information being derived from the mapping and sequencing of the Drosophila genome to address issues in genome organization and function, development and evolution.

Current Projects

Genome research. We have a number of projects underway to approach biological problems such as gene regulation and function at a genome-wide level in Drosophila. For example, we are using expression micro-arrays and in situ hybridization to study global patterns of gene expression and regulation. In addition, we are developing computer-based tools to analyze, visualize and store genomic DNA sequences in relation to genetic and other biological information.

Selected Publications

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. [B.P. Berman, Y. Nibu, B.D. Pfeiffer, P. Tomancak, S.E. Celniker, M. Levine, G.M. Rubin, and M.B. Eisen (2002) Proc. Natl. Acad. Sci. USA 99, 757-762]

The draft sequences. Comparing species. [G.M. Rubin (2001) Nature 409, 820-821]

Drosophila neuralized is a ubiquitin ligase that promotes the internalization and degradation of Delta. [E.C. Lai, G.A. Deblandre, C. Kintner, and G.M. Rubin (2001) Developmental Cell 1, 783-794]

mus304 encodes a novel DNA damage checkpoint protein required during Drosophila development. [M.H. Brodsky, J.J. Sekelsky, G. Tsang, R.S. Hawley, and G.M. Rubin (2000) Genes and Development 14, 666-678]

Drosophila p53 binds a damage response element at the reaper locus. [M.H. Brodsky, W. Nordstrom, G. Tsang, E. Kwan, G.M. Rubin, and J.M. Abrams (2000) Cell 101, 103-113]

Gene ontology: tool for the unification of biology. [M. Ashburner et al. (2000) Nature Genetics 25, 25-28]

The Genome Sequence of Drosophila melanogaster. [M. D. Adams et al.(2000) Science 287, 2185-2195]

Comparative Genomics of the Eukaryotes. [G. M. Rubin et al. (2000) Science 287, 2204-2215]

A Drosophila Complementary DNA Resource. [G. M. Rubin, L. Hong, P. Brokstein, M. Evans-Holm, E. Frise, M. Stapleton, and D.A. Harvey (2000) Science 287, 2222-2224]

A misexpression screen identifies genes that can modulate RAS1 pathway signaling in Drosophila melanogaster. [A.M. Huang and G.M. Rubin (2000) Genetics 156, 1219-1230]

An exploration of the sequence of a 2.9-megabase region of the genome of Drosophila melanogaster - The `Adh' region. [M. Ashburner, S. Misra, J. Roote, S. Lewis, R. Blazej, T. Davis, C. Doyle, R. Galle, R. George, N. Harris, G. Hartzell, D. Harvey, L. Hong, K. Houston, R. Hoskins, G. Johnson, C. Martin, A. Moshrefi, M. Palazzolo, M. Reese, A. Spradling, G. Tsang, K. Wan, K. Whitelaw, B. Kimmel, S. Celniker and G.M. Rubin (1999) Genetics 153, 179-219]

The BDGP gene disruption project: single P element insertions mutating 25% of vital Drosophila genes. [A.C. Spradling, D. Stern, A. Beaton, E.J. Rhem, T. Laverty, N. Mozden, S. Misra and G.M. Rubin (1999) Genetics 153, 135-177]

CNK, a RAF-binding multidomain protein required for RAS signaling. [M. Therrien, A. M. Wong, and G. M. Rubin. (1998) Cell 95, 343-353]

A high throughput screen to identify secreted and transmembrance proteins involved in Drosophila embryogenesis. [C. C. Kopczynski, J. N. Noordermeer, T. L. Serano, W. Y. Chen, J. D. Pendleton, S. Lewis, C. S. Goodman, and G. M. Rubin (1998) Proc. Natl. Acad. Sci. USA 95, 9973-9978]

BioViews: Java-based tools for genomic data visualization. [G. A. Helt, S. Lewis, A. E. Loraine, and G. M. Rubin (1998) Genome Research 8, 291-305]

PHYL acts to down-regulate TTL88, a transcriptional repressor of neuronal cell fates, by a SINA-dependent mechanism. [A. H. Tang, T. Neufeld, E. Kwan,and G. M. Rubin (1997) Cell 90, 459-467]

The role of genome project in determining gene function insights from model organisms. [G. L. G. Miklos and G. M. Rubin (1996) Cell 86, 521-529]

Yan functions as a general inhibitor of differentiation and is negatively regulated by activation of the Ras1/MAPK pathway in Drosophila. [I. Rebay and G. M. Rubin (1995) Cell 81, 857-866]

Ksr, a novel protein kinase required for Ras signal transduction. [M. Therrien, H. C. Chang, N. H. Solomon, F. D. Karim, D. A. Wassarrman, and G. M. Rubin (1995) Cell 83, 879-888]

Determination of neuronal cell fate: Lessons from the R7 neuron of Drosophila. [S. L. Zipursky and G. M. Rubin (1994) Ann. Rev. of Neuroscience 17, 373-97]

Analysis of genetics mosaics in developing and adult Drosophila tissue. [T. Xu and G. M. Rubin (1993) Development 117, 1223-1237]

Ras1and a putative guanine nucleotide exchange factor perform crucial steps in signaling by the Sevenless protein tyrosine kinase. [M. A. Simon, D. D. L. Bowtell, G. S. Dodson, T. R. Laverty, and G. M. Rubin (1991) Cell 67, 701-716]

Genetic transformation of Drosophila with transposable element vectors. [G. M. Rubin and A. C. Spradling (1982) Science 218, 348-353]

† † Currently on administrative leave (Serving as Vice-President and Director of Planning for Janelia Farm Campus, HHMI)

Last Updated 2003-09-05