W. Larry Ruzzo

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.

Selected Publications:

Kuppusamy KT, Jones DC, Sperber H, Madan A, Fischer KA, Rodriguez ML, Pabon L, Zhu WZ, Tulloch NL, Yang X, Sniadecki NJ, Laflamme MA, Ruzzo WL, Murry CE, Ruohola-Baker H. Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes. Proc Natl Acad Sci U S A. 2015 May 26;112(21):E2785-94. doi: 10.1073/pnas.1424042112. Epub 2015 May 11.
PubMed PMID: 25964336; PubMed Central PMCID: PMC4450404.

Jones DC, Ruzzo WL, Peng X, Katze MG. A new approach to bias correction in RNA-Seq. Bioinformatics. 2012 Apr 1;28(7):921-8. doi:
10.1093/bioinformatics/bts055. Epub 2012 Jan 28. PubMed PMID: 22285831; PubMed Central PMCID: PMC3315719.

Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, Gentleman RC, Tapscott SJ. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.
Dev Cell. 2010 Apr 20;18(4):662-74. doi: 10.1016/j.devcel.2010.02.014. PubMed
PMID: 20412780; PubMed Central PMCID: PMC2910615.

Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL. De novo prediction of structured RNAs from genomic sequences. Trends Biotechnol. 2010 Jan;28(1):9-19. doi: 10.1016/j.tibtech.2009.09.006. Epub 2009 Nov 26. Review.
PubMed PMID: 19942311; PubMed Central PMCID: PMC4712260.

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. 2008 Feb;18(2):242-51. Epub 2007
Dec 20. PubMed PMID: 18096747; PubMed Central PMCID: PMC2203622.

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. PubMed PMID:
17621584; PubMed Central PMCID: PMC1950547.

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.
PubMed 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. PubMed PMID: 15472076.

Additional Publications

additional publication listings available via PubMed