Larry Ruzzo
Computational Biology
RNA Sequence, Structure and Function: Computational and Bioinformatic Methods
J. Gorodkin, W.L. Ruzzo, Methods in Molecular Biology, Humana Press, 2013.
(Springer Protocols, To Appear)
Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.
Z. Yao, A.P. Fong, Y. Cao, W.L. Ruzzo, R.C. Gentleman, S.J. Tapscott, Skeletal Muscle 3:1, 2013.
A Microbial Profiling Method for the Human Microbiota Using High-Throughput Sequencing
H.H.E. Tseng, M.A.J. Hullar, F. Li, J.W. Lampe, R. Sandstrom, A.K. Johnson, L.L. Strate, W.L. Ruzzo, J. Stamatoyannopoulos, Metagenomics 2, 2013.
Integration of 198 ChIP-seq Datasets Reveals Human cis-Regulatory Regions.
H. Bolouri, W.L. Ruzzo, Journal of computational biology : a journal of computational molecular cell biology 19:9, 2012.
Hardware Acceleration of Short Read Mapping
C.B. Olson, M. Kim, C. Clauson, B. Kogon, C. Ebeling, S. Hauck, W.L. Ruzzo, FCCM 2012: The 20th Annual IEEE International Symposium on Field-Programmable Custom Computing Machines, 2012.
(Best Paper Award)
Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain.
S.E. Seemann, S. Sunkin, M. Hawrylycz, W.L. Ruzzo, J. Gorodkin, BMC genomics 13:1, 2012.
DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy.
L.N. Geng, Z. Yao, L. Snider, A.P. Fong, J.N. Cech, J.M. Young, S.M. Maarel, W.L. Ruzzo, R.C. Gentleman, R. Tawil, S.J. Tapscott, Developmental cell 22:1, 2012.
An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.
E.C. Knouf, K. Garg, J.D. Arroyo, Y. Correa, D. Sarkar, R.K. Parkin, K. Wurz, K.C. O'Briant, A.K. Godwin, N.D. Urban, W.L. Ruzzo, R. Gentleman, C.W. Drescher, E.M. Swisher, M. Tewari, Nucleic acids research 40:2, 2012.
Genetic and epigenetic determinants of neurogenesis and myogenesis.
A.P. Fong, Z. Yao, J.W. Zhong, Y. Cao, W.L. Ruzzo, R.C. Gentleman, S.J. Tapscott, Developmental Cell 22:4, 2012.
A new approach to bias correction in RNA-Seq.
D.C. Jones, W.L. Ruzzo, X. Peng, M.G. Katze, Bioinformatics 28:7, 2012.
De novo prediction of structured RNAs from genomic sequences.
J. Gorodkin, I.L. Hofacker, E. Torarinsson, Z. Yao, J.H. Havgaard, W.L. Ruzzo, Trends in biotechnology 28:1, 2010.
Downloads: Abstract
Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.
Y. Cao, Z. Yao, D. Sarkar, M. Lawrence, G.J. Sanchez, M.H. Parker, K.L. MacQuarrie, J. Davison, M.T. Morgan, W.L. Ruzzo, R.C. Gentleman, S.J. Tapscott, Developmental cell 18:4, 2010.
Downloads: Abstract
Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.
P. Anandam, E. Torarinsson, W.L. Ruzzo, Bioinformatics (Oxford, England) 25:5, 2009.
Downloads: Abstract
Finding non-coding RNAs through genome-scale clustering.
H.H. Tseng, Z. Weinberg, J. Gore, R.R. Breaker, W.L. Ruzzo, Journal of bioinformatics and computational biology 7:2, 2009.
Downloads: Abstract
MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.
M. Bar, S.K. Wyman, B.R. Fritz, J. Qi, K.S. Garg, R.K. Parkin, E.M. Kroh, A. Bendoraite, P.S. Mitchell, A.M. Nelson, W.L. Ruzzo, C. Ware, J.P. Radich, R. Gentleman, H. Ruohola-Baker, M. Tewari, Stem cells (Dayton, Ohio) 26:10, 2008.
Downloads: Abstract
A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.
E.E. Regulski, R.H. Moy, Z. Weinberg, J.E. Barrick, Z. Yao, W.L. Ruzzo, R.R. Breaker, Molecular microbiology 68:4, 2008.
Downloads: Abstract
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.
Z. Weinberg, E.E. Regulski, M.C. Hammond, J.E. Barrick, Z. Yao, W.L. Ruzzo, R.R. Breaker, RNA (New York, N.Y.) 14:5, 2008.
Downloads: Abstract
Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.
E. Torarinsson, Z. Yao, E.D. Wiklund, J.B. Bramsen, C. Hansen, J. Kjems, N. Tommerup, W.L. Ruzzo, J. Gorodkin, Genome research 18:2, 2008.
Downloads: Abstract
Finding non-coding RNAs through genome-scale clustering
Tseng, Weinberg, Gore, Breaker, Ruzzo, Sixth Asia-Pacific Bioinformatics Conference, 2008.
A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.
Z. Yao, J. Barrick, Z. Weinberg, S. Neph, R. Breaker, M. Tompa, W.L. Ruzzo, PLoS computational biology 3:7, 2007.
Downloads: Abstract
A Marfan syndrome gene expression phenotype in cultured skin fibroblasts.
Z. Yao, J.C. Jaeger, W.L. Ruzzo, C.Z. Morale, M. Emond, U. Francke, D.M. Milewicz, S.M. Schwartz, E.R. Mulvihill, BMC genomics 8, 2007.
Downloads: Abstract
Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.
Z. Weinberg, J.E. Barrick, Z. Yao, A. Roth, J.N. Kim, J. Gore, J.X. Wang, E.R. Lee, K.F. Block, N. Sudarsan, S. Neph, M. Tompa, W.L. Ruzzo, R.R. Breaker, Nucleic acids research 35:14, 2007.
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.
J.A. Eisen, R.S. Coyne, M. Wu, D. Wu, M. Thiagarajan, J.R. Wortman, J.H. Badger, Q. Ren, P. Amedeo, K.M. Jones, L.J. Tallon, A.L. Delcher, S.L. Salzberg, J.C. Silva, B.J. Haas, W.H. Majoros, M. Farzad, J.M. Carlton, R.K. Smith, J. Garg, R.E. Pearlman, K.M. Karrer, L. Sun, G. Manning, N.C. Elde, A.P. Turkewitz, D.J. Asai, D.E. Wilkes, Y. Wang, H. Cai, K. Collins, A.B. Stewart, S.R. Lee, K. Wilamowska, Z. Weinberg, W.L. Ruzzo, D. Wloga, J. Gaertig, J. Frankel, C.C. Tsao, M.A. Gorovsky, P.J. Keeling, R.F. Waller, N.J. Patron, M.J. Cherry, N.A. Stover, C.J. Krieger, C. Toro, H.F. Ryder, S.C. Williamson, R.A. Barbeau, E.P. Hamilton, E. Orias, PLoS biology 4:9, 2006.
Downloads: Abstract
Sequence-based heuristics for faster annotation of non-coding RNA families.
Z. Weinberg, W.L. Ruzzo, Bioinformatics (Oxford, England) 22:1, 2006.
Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophy.
P.C.H. Hsieh, R.D. Kenagy, E.R. Mulvihill, J.P. Jeanette, X. Wang, C.M.C. Chang, Z. Yao, W.L. Ruzzo, S. Justice, K.L. Hudkins, C.E. Alpers, S. Berceli, A.W. Clowes, Journal of vascular surgery : official publication, the Society for Vascular Surgery [and] International Society for Cardiovascular Surgery, North American Chapter 43:1, 2006.
CMfinder--a covariance model based RNA motif finding algorithm.
Z. Yao, Z. Weinberg, W.L. Ruzzo, Bioinformatics (Oxford, England) 22:4, 2006.
A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.
Z. Yao, W.L. Ruzzo, BMC bioinformatics 7 Suppl 1, 2006.
6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.
J.E. Barrick, N. Sudarsan, Z. Weinberg, W.L. Ruzzo, R.R. Breaker, RNA (New York, N.Y.) 11:5, 2005.
Searching for Non-coding RNA
W.L. Ruzzo, Brazilian Symposium on Bioinformatics, 2005.
A glycine-dependent riboswitch that uses cooperative binding to control gene expression.
M. Mandal, M. Lee, J.E. Barrick, Z. Weinberg, G.M. Emilsson, W.L. Ruzzo, R.R. Breaker, Science (New York, N.Y.) 306:5694, 2004.
Atherosclerotic plaque smooth muscle cells have a distinct phenotype.
E.R. Mulvihill, J. Jaeger, R. Sengupta, W.L. Ruzzo, C. Reimer, S. Lukito, S.M. Schwartz, Arteriosclerosis, thrombosis, and vascular biology 24:7, 2004.
Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy.
Z. Weinberg, W.L. Ruzzo, Bioinformatics (Oxford, England) 20 Suppl 1, 2004.
Downloads: Supplementary Data
Faster Genome Annotation of Non-coding RNA Families Without Loss of Accuracy
Weinberg, Ruzzo, Eighth Annual International Conference on Research in Computational Molecular Biology, 2004.
Improved gene selection for classification of microarrays.
J. Jaeger, R. Sengupta, W.L. Ruzzo, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2003.
Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae.
M.T. Barrett, K.Y. Yeung, W.L. Ruzzo, L. Hsu, P.L. Blount, R. Sullivan, H. Zarbl, J. Delrow, P.S. Rabinovitch, B.J. Reid, Neoplasia (New York, N.Y.) 4:2, 2002.
Pre-mRNA secondary structure prediction aids splice site prediction.
D.J. Patterson, K. Yasuhara, W.L. Ruzzo, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 2002.
Principal component analysis for clustering gene expression data.
K.Y. Yeung, W.L. Ruzzo, Bioinformatics (Oxford, England) 17:9, 2001.
Model-based clustering and data transformations for gene expression data.
K.Y. Yeung, C. Fraley, A. Murua, A.E. Raftery, W.L. Ruzzo, Bioinformatics (Oxford, England) 17:10, 2001.
Validating clustering for gene expression data.
K.Y. Yeung, D.R. Haynor, W.L. Ruzzo, Bioinformatics (Oxford, England) 17:4, 2001.
Algorithms for a Simple Point Placement Problem
Redstone, Ruzzo, Algorithms and Complexity, 4th Italian Conference, 2000.
A linear time algorithm for finding all maximal scoring subsequences.
W.L. Ruzzo, M. Tompa, Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology, 1999.
A Linear Time Algorithm for Finding All Maximal Scoring Subsequences
W.L. Ruzzo, M. Tompa, Seventh International Conference on Intelligent Systems for Molecular Biology, 1999.
Computational Complexity Theory
Parallel RAMs with owned global memory and deterministic context-free language recognition
P.W. Dymond, W.L. Ruzzo, J. ACM 47:1, 2000.
A Time-Space Tradeoff for Undirected Graph Traversal by Walking Automata
Beame, Borodin, Raghavan, Ruzzo, Tompa, SIAM Journal on Computing 27:3, 1999.
A Sublinear Space, Polynomial Time Algorithm for Directed s-t Connectivity
Barnes, Buss, Ruzzo, Schieber, SIAM Journal on Computing 27:5, 1998.
Algorithms for Undirected s-t Connectivity Using Polynomial Time and Sublinear Space
Barnes, Ruzzo, Computational Complexity 6:1, 1997.
The Electrical Resistance of a Graph Captures its Commute and Cover Times
Chandra, Raghavan, Ruzzo, Smolensky, Tiwari, Computational Complexity 6:4, 1997.
Pointers versus Arithmetic in PRAMs
Dymond, Fich, Nishimura, Ragde, Ruzzo, Journal of Computer and System Sciences 52:2, 1996.
Time-Space Tradeoffs for Undirected Graph Traversal by Graph Automata
Beame, Borodin, Raghavan, Ruzzo, Tompa, Information and Computation 130:2, 1996.
Limits to Parallel Computation
Greenlaw, Hoover, Ruzzo, Oxford, 1995.
Downloads: Updates and Errata See also: Greenlaw, Hoover, Miyano, Ruzzo, Shiraishi and Shoudai: The Parallel Computation Project.
Lower Bounds on the Length of Universal Traversal Sequences
A. Borodin, W.L. Ruzzo, M. Tompa, J. Comput. Syst. Sci. 45:2, 1992.
Results on Communication Complexity Classes
T.W. Lam, W.L. Ruzzo, J. Comput. Syst. Sci. 44:2, 1992.
Low Overhead Parallel Schedules for Task Graphs
R.J. Anderson, P. Beame, W.L. Ruzzo, SPAA, 1990.
The iterated mod problem
H.J. Karloff, W.L. Ruzzo, Information and Computation 80:3, 1989.
Two Applications of Inductive Counting for Complementation Problems
A. Borodin, S.A. Cook, P.W. Dymond, W.L. Ruzzo, M. Tompa, SIAM Journal on Computing 18:3, 1989.
Downloads: Erratum: SIAM J. Comput. 18(6): 1283 (1989)
The Power of Parallel Pointer Manipulation
T.W. Lam, W.L. Ruzzo, SPAA, 1989.
Space-bounded hierarchies and probabilistic computations
W.L. Ruzzo, J. Simon, M. Tompa, Journal of Computer and System Sciences 28:2, 1984.
Bounds on minimax edge length for complete binary trees
M.S. Paterson, W.L. Ruzzo, L. Snyder, Proceedings of the thirteenth annual ACM symposium on Theory of computing - STOC '81, ACM Press, 1981.
On uniform circuit complexity
Ruzzo, Journal of Computer and System Sciences 22:3, 1981.
Tree-size bounded alternation
Ruzzo, Journal of Computer and System Sciences 21:2, 1980.
Complete Pushdown Languages
Ruzzo, 1979.
Improved time and space bounds for Boolean matrix multiplication
L. Adleman, K.S. Booth, F.P. Preparata, W.L. Ruzzo, Acta Informatica 11:1, 1978.
On line context free language recognition in less than cubic time
M.A. Harrison, W.L. Ruzzo, S.L. Graham, Proceedings of the eighth annual ACM symposium on Theory of computing - STOC '76, ACM Press, 1976.
Protection in operating systems
M.A. Harrison, W.L. Ruzzo, J.D. Ullman, Communications of the ACM 19:8, 1976.

Contact
Office: CSE554
Email:
ruzzo
cs
Phone: (206) 543-6298
