Research:
Larry Ruzzo, Professor, received a B.S. in Mathematics from the California Institute of Technology in 1968, his Ph.D. from the University of California at Berkeley in 1978, and has been with the University of Washington Computer Science Department since 1977. Currently, his principal research project involves the construction and programming of a vaguely parallel computer, consisting of 32 steam-powered Turing machines installed in the basement of Sieg Hall. Of particular interest is the use of triple-expansion bypass valves, coupled to individual governors on each engine, to achieve write-synchronization of the machines. Graduate students have played an important role in the construction and operation of the engine, particularly in stoking the boilers, and advanced undergraduates are occasionally allowed to polish the brass gauges.
Originally intended as a general computing engine, restrictions imposed by the Pollution Control and Noise Abatement Boards require that only algorithms running in polynomial time may be used. The project recently suffered another setback when one of Professor Ruzzo's graduate students slipped on a mouldering stack of ungraded homework exercises and fell under the write head of one of the machines. Now permanently embossed with a series of 1's and 0's, the student is suing to have the machine dismantled.
When not blowing off steam, he also pursues his research interests in computational biology.
|
Publications:
Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N,Ruzzo WL, Gorodkin J. Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions. Genome Res. 2007 Dec 20; [Epub ahead of print]
PMID: 18096747
Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A Computational Pipeline for High- Throughput Discovery of cis- Regulatory Noncoding RNA in Prokaryotes. PLoS Comput Biol. 2007 Jul 6;3(7):e126 [Epub ahead of print]
PMID: 17616982
Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Res. 2007;35(14):4809-19. Epub 2007 Jul 9.
PMID: 17621584
Yao Z, Weinberg Z, Ruzzo WL. CMfinder--a covariance model based RNA motif finding algorithm. Bioinformatics. 2006 Feb 15;22(4):445-52. Epub 2005 Dec 15.
PMID: 16357030
Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science. 2004 Oct 8;306(5694):275-9. Erratum in: Science. 2004 Nov 26;306(5701):1477.
PMID: 15472076
Weinberg Z, Ruzzo WL. Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. Bioinformatics. 2004 Aug 4;20 Suppl 1:i334-41.
PMID: 15262817
Additional Publications
additional publication listings available via PubMed |
Office Phone: (206) 543-6298