Larry Ruzzo

Computational Biology

RNA Sequence, Structure and Function: Computational and Bioinformatic Methods

J. Gorodkin, W.L. RuzzoMethods in Molecular BiologyHumana 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. TapscottSkeletal 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. StamatoyannopoulosMetagenomics 2, 2013.

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.

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

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)

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.

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.

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.

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.

A new approach to bias correction in RNA-Seq.

D.C. Jones, W.L. Ruzzo, X. Peng, M.G. KatzeBioinformatics 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. RuzzoTrends 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. TapscottDevelopmental cell 18:4, 2010.
Downloads: Abstract 

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

P. Anandam, E. Torarinsson, W.L. RuzzoBioinformatics (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. RuzzoJournal 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. TewariStem 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. BreakerMolecular 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. BreakerRNA (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. GorodkinGenome research 18:2, 2008.
Downloads: Abstract 

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.
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. MulvihillBMC 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. BreakerNucleic acids research 35:14, 2007.

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

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

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.
Downloads: Abstract 

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

Z. Weinberg, W.L. RuzzoBioinformatics (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. ClowesJournal 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. RuzzoBioinformatics (Oxford, England) 22:4, 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. BreakerRNA (New York, N.Y.) 11:5, 2005.

Searching for Non-coding RNA

W.L. RuzzoBrazilian 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. BreakerScience (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. SchwartzArteriosclerosis, 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. RuzzoBioinformatics (Oxford, England) 20 Suppl 1, 2004.
Downloads: Supplementary Data 

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

Weinberg,  RuzzoEighth Annual International Conference on Research in Computational Molecular Biology, 2004.

Improved gene selection for classification of microarrays.

J. Jaeger, R. Sengupta, W.L. RuzzoPacific 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. ReidNeoplasia (New York, N.Y.) 4:2, 2002.

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.

Principal component analysis for clustering gene expression data.

K.Y. Yeung, W.L. RuzzoBioinformatics (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. RuzzoBioinformatics (Oxford, England) 17:10, 2001.

Validating clustering for gene expression data.

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

Algorithms for a Simple Point Placement Problem

Redstone,  RuzzoAlgorithms and Complexity, 4th Italian Conference, 2000.

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.

A Linear Time Algorithm for Finding All Maximal Scoring Subsequences

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

Computational Complexity Theory

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

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

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

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

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

Barnes,  RuzzoComputational Complexity 6:1, 1997.

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

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

Pointers versus Arithmetic in PRAMs

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

Time-Space Tradeoffs for Undirected Graph Traversal by Graph Automata

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

Lower Bounds on the Length of Universal Traversal Sequences

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

Results on Communication Complexity Classes

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

Low Overhead Parallel Schedules for Task Graphs

R.J. Anderson, P. Beame, W.L. RuzzoSPAA, 1990.

The iterated mod problem

H.J. Karloff, W.L. RuzzoInformation 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. TompaSIAM Journal on Computing 18:3, 1989.

The Power of Parallel Pointer Manipulation

T.W. Lam, W.L. RuzzoSPAA, 1989.

Space-bounded hierarchies and probabilistic computations

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

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.

On uniform circuit complexity

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

Tree-size bounded alternation

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

Improved time and space bounds for Boolean matrix multiplication

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

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.

Protection in operating systems

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