CSE 554
206-543-6298
ruzzocs.washington.edu
Areas of interest: 

Computational biology

Computational Biology

Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis.

N.J. Palpant, Y. Wang, B. Hadland, R.J. Zaunbrecher, M. Redd, D. Jones, L. Pabon, R. Jain, J. Epstein, W.L. Ruzzo, Y. Zheng, I. Bernstein, A. Margolin, C.E. MurryCell Rep  20 :7 , 2017 : 1597-1608 .

Associating transcription factors and conserved RNA structures with gene regulation in the human brain.

N. Hecker, S.E. Seemann, A. Silahtaroglu, W.L. Ruzzo, J. GorodkinSci Rep  7 :1 , 2017 : 5776 .  Stable URL http://rdcu.be/uknk.

The identification and functional annotation of RNA structures conserved in vertebrates.

S.E. Seemann, A.H. Mirza, C. Hansen, C.H. Bang-Berthelsen, C. Garde, M. Christensen-Dalsgaard, E. Torarinsson, Z. Yao, C.T. Workman, F. Pociot, H. Nielsen, N. Tommerup, W.L. Ruzzo, J. GorodkinGenome Res , 2017 .

Inhibition of β-catenin signaling respecifies anterior-like endothelium into beating human cardiomyocytes.

N.J. Palpant, L. Pabon, M. Roberts, B. Hadland, D. Jones, C. Jones, R.T. Moon, W.L. Ruzzo, I. Bernstein, Y. Zheng, C.E. MurryDevelopment , 2015 .

Let-7 family of microRNA is required for maturation and adult-like metabolism in stem cell-derived cardiomyocytes.

K.T. Kuppusamy, D.C. Jones, H. Sperber, A. Madan, K.A. Fischer, M.L. Rodriguez, L. Pabon, W.Z. Zhu, N.L. Tulloch, X. Yang, N.J. Sniadecki, M.A. Laflamme, W.L. Ruzzo, C.E. Murry, H. Ruohola-BakerProc Natl Acad Sci U S A , 2015 .

Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data.

X. Peng, L. Pipes, H. Xiong, R.R. Green, D.C. Jones, W.L. Ruzzo, G.P. Schroth, C.E. Mason, R.E. Palermo, M.G. KatzeJ Med Primatol , 2014 .

Discriminative motif analysis of high throughput datasets

Z. Yao, K.L. Macquarrie, A.P. Fong, S.J. Tapscott, W.L. Ruzzo, R.C. GentlemanBioinformatics  30 :6 , 2014 : 775-83 .

RNA Sequence, Structure and Function: Computational and Bioinformatic Methods

J. Gorodkin (Editor), W.L. Ruzzo (Editor)Methods in Molecular BiologyHumana Press :1097 , 2014 : 533 .  

(Springer Protocols)

De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences.

W.L. Ruzzo, J. GorodkinMethods Mol Biol  1097 , 2014 : 303-18 .  Chapter 15 of Gorodkin, Ruzzo, 2014.

Concepts and introduction to RNA bioinformatics.

J. Gorodkin, I.L. Hofacker, W.L. RuzzoMethods Mol Biol  1097 , 2014 : 1-31 .  

Chapter 1 of Gorodkin, Ruzzo, 2014.

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. StamatoyannopoulosMetagenomics  2 , 2013 : 1 - 8 .

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. TapscottSkeletal Muscle  3 :1 , 2013 : 8 .

Compression of next-generation sequencing reads aided by highly efficient de novo assembly.

D.C. Jones, W.L. Ruzzo, X. Peng, M.G. KatzeNucleic Acids Research  40 :22 , 2012 .  arXiv: 1207.2424

Integration of 198 ChIP-seq Datasets Reveals Human cis-Regulatory Regions.

H. Bolouri, W.L. RuzzoJournal of computational biology : a journal of computational molecular cell biology  19 :9 , 2012 : 1-9 .

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. GorodkinBMC genomics  13 :1 , 2012 : 214 .

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. TapscottDevelopmental Cell  22 :4 , 2012 : 721-35 .

Hardware Acceleration of Short Read Mapping

C.B. Olson, M. Kim, C. Clauson, B. Kogon, C. Ebeling, S. Hauck, W.L. RuzzoFCCM 2012: The 20th Annual IEEE International Symposium on Field-Programmable Custom Computing Machines , 2012 .  

(Best Paper Award)

A new approach to bias correction in RNA-Seq.

D.C. Jones, W.L. Ruzzo, X. Peng, M.G. KatzeBioinformatics  28 :7 , 2012 : 921-8 .

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. TapscottDevelopmental Cell  22 :1 , 2012 : 38-51 .

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. TewariNucleic acids research  40 :2 , 2012 : 499-510 .

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. TapscottDevelopmental cell  18 :4 , 2010 : 662-74 .

De novo prediction of structured RNAs from genomic sequences.

J. Gorodkin, I.L. Hofacker, E. Torarinsson, Z. Yao, J.H. Havgaard, W.L. RuzzoTrends in biotechnology  28 :1 , 2010 : 9-19 .

Finding non-coding RNAs through genome-scale clustering.

H.H. Tseng, Z. Weinberg, J. Gore, R.R. Breaker, W.L. RuzzoJournal of bioinformatics and computational biology  7 :2 , 2009 : 373-88 .

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.

P. Anandam, E. Torarinsson, W.L. RuzzoBioinformatics (Oxford, England)  25 :5 , 2009 : 668-9 .

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. TewariStem cells (Dayton, Ohio)  26 :10 , 2008 : 2496-505 .

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. BreakerRNA (New York, N.Y.)  14 :5 , 2008 : 822-8 .

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. BreakerMolecular microbiology  68 :4 , 2008 : 918-32 .

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. GorodkinGenome research  18 :2 , 2008 : 242-51 .

Finding non-coding RNAs through genome-scale clustering

Tseng,  Weinberg,  Gore,  Breaker,  RuzzoSixth 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. RuzzoPLoS computational biology  3 :7 , 2007 : e126 .

How accurately is ncRNA aligned within whole-genome multiple alignments?

A.X. Wang, W.L. Ruzzo, M. TompaBMC bioinformatics  8 , 2007 : 417 .

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. BreakerNucleic acids research  35 :14 , 2007 : 4809-19 .

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. MulvihillBMC genomics  8 , 2007 : 319 .

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. OriasPLoS biology  4 :9 , 2006 : e286 .

CMfinder--a covariance model based RNA motif finding algorithm.

Z. Yao, Z. Weinberg, W.L. RuzzoBioinformatics (Oxford, England)  22 :4 , 2006 : 445-52 .

Sequence-based heuristics for faster annotation of non-coding RNA families.

Z. Weinberg, W.L. RuzzoBioinformatics (Oxford, England)  22 :1 , 2006 : 35-9 .

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. ClowesJournal of vascular surgery : official publication, the Society for Vascular Surgery [and] International Society for Cardiovascular Surgery, North American Chapter  43 :1 , 2006 : 150-8 .

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. BreakerRNA (New York, N.Y.)  11 :5 , 2005 : 774-84 .

Searching for Non-coding RNA

W.L. RuzzoBrazilian Symposium on Bioinformatics , 2005 : 9-10 .

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. BreakerScience (New York, N.Y.)  306 :5694 , 2004 : 275-9 .

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. SchwartzArteriosclerosis, thrombosis, and vascular biology  24 :7 , 2004 : 1283-9 .

Faster Genome Annotation of Non-coding RNA Families Without Loss of Accuracy

Weinberg,  RuzzoEighth Annual International Conference on Research in Computational Molecular Biology , 2004 : 243-251 .

Improved gene selection for classification of microarrays.

J. Jaeger, R. Sengupta, W.L. RuzzoPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing , 2003 : 53-64 .

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. ReidNeoplasia (New York, N.Y.)  4 :2 , 2002 : 121-8 .

Pre-mRNA secondary structure prediction aids splice site prediction.

D.J. Patterson, K. Yasuhara, W.L. RuzzoPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing , 2002 : 223-34 .

Model-based clustering and data transformations for gene expression data.

K.Y. Yeung, C. Fraley, A. Murua, A.E. Raftery, W.L. RuzzoBioinformatics (Oxford, England)  17 :10 , 2001 : 977-87 .

Principal component analysis for clustering gene expression data.

K.Y. Yeung, W.L. RuzzoBioinformatics (Oxford, England)  17 :9 , 2001 : 763-74 .

Validating clustering for gene expression data.

K.Y. Yeung, D.R. Haynor, W.L. RuzzoBioinformatics (Oxford, England)  17 :4 , 2001 : 309-18 .

Algorithms for a Simple Point Placement Problem

Redstone,  RuzzoAlgorithms and Complexity, 4th Italian Conference , 2000 : 32-43 .

A Linear Time Algorithm for Finding All Maximal Scoring Subsequences

W.L. Ruzzo, M. TompaSeventh International Conference on Intelligent Systems for Molecular Biology , 1999 : 234-241 .

A linear time algorithm for finding all maximal scoring subsequences.

W.L. Ruzzo, M. TompaProceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology , 1999 : 234-41 .

Computational Complexity Theory

Parallel RAMs with owned global memory and deterministic context-free language recognition

P.W. Dymond, W.L. RuzzoJ. ACM  47 :1 , 2000 : 16-45 .

A Time-Space Tradeoff for Undirected Graph Traversal by Walking Automata

Beame,  Borodin,  Raghavan,  Ruzzo,  TompaSIAM Journal on Computing  27 :3 , 1999 : 1051-1072. .

A Sublinear Space, Polynomial Time Algorithm for Directed s-t Connectivity

Barnes,  Buss,  Ruzzo,  SchieberSIAM Journal on Computing  27 :5 , 1998 : 1273-1282 .

Algorithms for Undirected s-t Connectivity Using Polynomial Time and Sublinear Space

Barnes,  RuzzoComputational Complexity  6 :1 , 1997 : 1-28 .

The Electrical Resistance of a Graph Captures its Commute and Cover Times

Chandra,  Raghavan,  Ruzzo,  Smolensky,  TiwariComputational Complexity  6 :4 , 1997 : 312-340 .

Time-Space Tradeoffs for Undirected Graph Traversal by Graph Automata

Beame,  Borodin,  Raghavan,  Ruzzo,  TompaInformation and Computation  130 :2 , 1996 : 101-129 .

Pointers versus Arithmetic in PRAMs

Dymond,  Fich,  Nishimura,  Ragde,  RuzzoJournal of Computer and System Sciences  52 :2 , 1996 : 218-232 .

Limits to Parallel Computation

Greenlaw,  Hoover,  RuzzoOxford , 1995 .

http://web.cs.ualberta.ca/~hoover/P-complete Updates and Errata
http://www.cs.armstrong.edu/greenlaw/research/PARALLEL/index.html See also: Greenlaw, Hoover, Miyano, Ruzzo, Shiraishi and Shoudai: The Parallel Computation Project.

Results on Communication Complexity Classes

T.W. Lam, W.L. RuzzoJ. Comput. Syst. Sci.  44 :2 , 1992 : 324-342 .

Lower Bounds on the Length of Universal Traversal Sequences

A. Borodin, W.L. Ruzzo, M. TompaJ. Comput. Syst. Sci.  45 :2 , 1992 : 180-203 .

Parallel Quicksand: Fast Sorting on the Sequent

S. Kahan, W.L. RuzzoUW CSE Technical Report :91-01-01 , 1991 .

Low Overhead Parallel Schedules for Task Graphs

R.J. Anderson, P. Beame, W.L. RuzzoSPAA , 1990 : 66-75 .

The iterated mod problem

H.J. Karloff, W.L. RuzzoInformation and Computation  80 :3 , 1989 : 193 - 204 .

The Power of Parallel Pointer Manipulation

T.W. Lam, W.L. RuzzoSPAA , 1989 : 92-102 .

Two Applications of Inductive Counting for Complementation Problems

A. Borodin, S.A. Cook, P.W. Dymond, W.L. Ruzzo, M. TompaSIAM Journal on Computing  18 :3 , 1989 : 559 .

http://dx.doi.org/10.1137/0218084 Erratum: SIAM J. Comput. 18(6): 1283 (1989)

Space-bounded hierarchies and probabilistic computations

W.L. Ruzzo, J. Simon, M. TompaJournal of Computer and System Sciences  28 :2 , 1984 : 216 - 230 .

On uniform circuit complexity

RuzzoJournal of Computer and System Sciences  22 :3 , 1981 : 365-383 .

Bounds on minimax edge length for complete binary trees

M.S. Paterson, W.L. Ruzzo, L. SnyderProceedings of the thirteenth annual ACM symposium on Theory of computing - STOC '81ACM Press , 1981 : 293 - 299 .

Tree-size bounded alternation

RuzzoJournal of Computer and System Sciences  21 :2 , 1980 : 218-235 .

Complete Pushdown Languages

Ruzzo , 1979 .

Improved time and space bounds for Boolean matrix multiplication

L. Adleman, K.S. Booth, F.P. Preparata, W.L. RuzzoActa Informatica  11 :1 , 1978 .

Protection in operating systems

M.A. Harrison, W.L. Ruzzo, J.D. UllmanCommunications of the ACM  19 :8 , 1976 : 461 - 471 .

On line context free language recognition in less than cubic time

M.A. Harrison, W.L. Ruzzo, S.L. GrahamProceedings of the eighth annual ACM symposium on Theory of computing - STOC '76ACM Press , 1976 : 112 - 120 .