Publications | Paul G. Allen School of Computer Science & Engineering

Contact

Walter L (Larry) Ruzzo

CSE 554

206-543-6298

ruzzo

cs.washington.edu

Areas of interest:

Computational biology

Computational Biology Computational Complexity Theory

Computational Biology

Does rapid sequence divergence preclude RNA structure conservation in vertebrates?

S.E. Seemann, A.H. Mirza, C.H. Bang-Berthelsen, C. Garde, M. Christensen-Dalsgaard, C.T. Workman, F. Pociot, N. Tommerup, J. Gorodkin, W.L. Ruzzo, Nucleic Acids Res, 2022 .

https://www.ncbi.nlm.nih.gov/pubmed/35188540?dopt=Abstract

Polee: RNA-Seq analysis using approximate likelihood.

D.C. Jones, W.L. Ruzzo, NAR Genom Bioinform 3:2, 2021 : lqab046.

https://www.ncbi.nlm.nih.gov/pubmed/34056596?dopt=Abstract

Spatial modeling of prostate cancer metabolic gene expression reveals extensive heterogeneity and selective vulnerabilities.

Y. Wang, S. Ma, W.L. Ruzzo, Sci Rep 10:1, 2020 : 3490.

https://www.ncbi.nlm.nih.gov/pubmed/32103057?dopt=Abstract

Metabolic Control over mTOR-Dependent Diapause-like State

A.M. Hussein, Y. Wang, J. Mathieu, L. Margaretha, C. Song, D.C. Jones, C. Cavanaugh, J.W. Miklas, E. Mahen, M.R. Showalter, W.L. Ruzzo, O. Fiehn, C.B. Ware, A. Blau, H. Ruohola-Baker, Developmental Cell 52:2, 2020 : 236 - 250.e7.

Identification and characterization of novel conserved RNA structures in Drosophila.

R. Kirsch, S.E. Seemann, W.L. Ruzzo, S.M. Cohen, P.F. Stadler, J. Gorodkin, BMC Genomics 19:1, 2018 : 899.

http://www.ncbi.nlm.nih.gov/pubmed/30537930?dopt=Abstract

Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana.

J.A. Koester, C.T. Berthiaume, N. Hiranuma, M.S. Parker, V. Iverson, R. Morales, W.L. Ruzzo, V. Armbrust, Sci Rep 8:1, 2018 : 10492.

http://www.ncbi.nlm.nih.gov/pubmed/30002405?dopt=Abstract

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. Murry, Cell Rep 20:7, 2017 : 1597-1608.

http://www.ncbi.nlm.nih.gov/pubmed/28813672?dopt=Abstract

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. Gorodkin, Sci Rep 7:1, 2017 : 5776. Stable URL http://rdcu.be/uknk.

http://www.ncbi.nlm.nih.gov/pubmed/28720872?dopt=Abstract

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. Gorodkin, Genome Res, 2017 .

http://www.ncbi.nlm.nih.gov/pubmed/28487280?dopt=Abstract

Isolator: accurate and stable analysis of isoform-level expression in RNA-Seq experiments

D.C. Jones, K.T. Kuppusamy, N.J. Palpant, X. Peng, C.E. Murry, H. Ruohola-Baker, W.L. Ruzzo, 2016 . bioRxiv

Cis-Compound Mutations are Prevalent in Triple Negative Breast Cancer and Can Drive Tumor Progression

N. Hiranuma, J. Liu, C. Song, J. Goldsmith, M.O. Dorschner, C.C. Pritchard, K.A. Burton, E.M. Mahen, S. Blau, F.M. Senecal, W.L. Monsky, S. Parker, S.C. Schmechel, S.K. Allison, V.K. Gadi, S.R. Salama, A.J. Radenbaugh, M. Goldman, J.M. Johnsen, S. Heimfeld, V. Komashko, M. LaMadrid-Hermannsfeldt, Z. Duan, S.C. Benz, P. Soon-Shiong, D. Haussler, J. Zhu, W.L. Ruzzo, W.S. Noble, A. Blau, bioRxiv, 2016 .

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. Murry, Development, 2015 .

http://www.ncbi.nlm.nih.gov/pubmed/26153229?dopt=Abstract

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-Baker, Proc Natl Acad Sci U S A, 2015 .

http://www.ncbi.nlm.nih.gov/pubmed/25964336?dopt=Abstract

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. Katze, J Med Primatol, 2014 .

http://www.ncbi.nlm.nih.gov/pubmed/24810475?dopt=Abstract

Discriminative motif analysis of high throughput datasets

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

http://www.ncbi.nlm.nih.gov/pubmed/24162561?dopt=Abstract

RNA Sequence, Structure and Function: Computational and Bioinformatic Methods

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

(Springer Protocols)

De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences.

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

http://www.ncbi.nlm.nih.gov/pubmed/24639166?dopt=Abstract

Concepts and introduction to RNA bioinformatics.

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

Chapter 1 of Gorodkin, Ruzzo, 2014.

http://www.ncbi.nlm.nih.gov/pubmed/24639152?dopt=Abstract

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 : 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. Tapscott, Skeletal Muscle 3:1, 2013 : 8.

http://www.ncbi.nlm.nih.gov/pubmed/23566431?dopt=Abstract

Accelerating ncRNA homology search with FPGAs

N. McVicar, W.L. Ruzzo, S. Hauck, the ACM/SIGDA international symposiumProceedings of the ACM/SIGDA international symposium on Field programmable gate arrays - FPGA '13, ACM Press, 2013 : 43.

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

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

http://www.ncbi.nlm.nih.gov/pubmed/22904078?dopt=Abstract Abstract

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 : 1-9.

http://www.ncbi.nlm.nih.gov/pubmed/22897152?dopt=Abstract

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 : 214.

http://www.ncbi.nlm.nih.gov/pubmed/22651826?dopt=Abstract

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 : 721-35.

http://www.ncbi.nlm.nih.gov/pubmed/22445365?dopt=Abstract

A new approach to bias correction in RNA-Seq.

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

http://www.ncbi.nlm.nih.gov/pubmed/22285831?dopt=Abstract

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)

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 : 38-51.

http://www.ncbi.nlm.nih.gov/pubmed/22209328?dopt=Abstract

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 : 499-510.

http://www.ncbi.nlm.nih.gov/pubmed/21917857?dopt=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 : 662-74.

http://www.ncbi.nlm.nih.gov/pubmed/20412780?dopt=Abstract Abstract

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 : 9-19.

http://www.ncbi.nlm.nih.gov/pubmed/19942311?dopt=Abstract 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 : 373-88.

http://www.ncbi.nlm.nih.gov/pubmed/19340921?dopt=Abstract Abstract

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

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

http://www.ncbi.nlm.nih.gov/pubmed/19136551?dopt=Abstract 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 : 2496-505.

http://www.ncbi.nlm.nih.gov/pubmed/18583537?dopt=Abstract 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 : 822-8.

http://www.ncbi.nlm.nih.gov/pubmed/18369181?dopt=Abstract 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 : 918-32.

http://www.ncbi.nlm.nih.gov/pubmed/18363797?dopt=Abstract 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 : 242-51.

http://www.ncbi.nlm.nih.gov/pubmed/18096747?dopt=Abstract 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 : e126.

http://www.ncbi.nlm.nih.gov/pubmed/17616982?dopt=Abstract Abstract

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

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

http://www.ncbi.nlm.nih.gov/pubmed/17963514?dopt=Abstract 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 : 319.

http://www.ncbi.nlm.nih.gov/pubmed/17850668?dopt=Abstract 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 : 4809-19.

http://www.ncbi.nlm.nih.gov/pubmed/17621584?dopt=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. Orias, PLoS biology 4:9, 2006 : e286.

http://www.ncbi.nlm.nih.gov/pubmed/16933976?dopt=Abstract Abstract

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

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

http://www.ncbi.nlm.nih.gov/pubmed/16357030?dopt=Abstract

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 : 150-8.

http://www.ncbi.nlm.nih.gov/pubmed/16414402?dopt=Abstract

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

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

http://www.ncbi.nlm.nih.gov/pubmed/16267089?dopt=Abstract

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 : S11.

http://www.ncbi.nlm.nih.gov/pubmed/16723004?dopt=Abstract

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 : 774-84.

http://www.ncbi.nlm.nih.gov/pubmed/15811922?dopt=Abstract

Searching for Non-coding RNA

W.L. Ruzzo, Brazilian 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. Breaker, Science (New York, N.Y.) 306:5694, 2004 : 275-9.

http://www.ncbi.nlm.nih.gov/pubmed/15472076?dopt=Abstract

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 : i334-41.

http://www.ncbi.nlm.nih.gov/pubmed/15262817?dopt=Abstract http://bio.cs.washington.edu/supplements/zasha-ISMB-2004/ Supplementary Data

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 : 1283-9.

http://www.ncbi.nlm.nih.gov/pubmed/15142862?dopt=Abstract

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 : 243-251.

Improved gene selection for classification of microarrays.

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

http://www.ncbi.nlm.nih.gov/pubmed/12603017?dopt=Abstract

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 : 121-8.

http://www.ncbi.nlm.nih.gov/pubmed/11896567?dopt=Abstract

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 : 223-34.

http://www.ncbi.nlm.nih.gov/pubmed/11928478?dopt=Abstract

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 : 977-87.

http://www.ncbi.nlm.nih.gov/pubmed/11673243?dopt=Abstract

Principal component analysis for clustering gene expression data.

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

http://www.ncbi.nlm.nih.gov/pubmed/11590094?dopt=Abstract

Validating clustering for gene expression data.

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

http://www.ncbi.nlm.nih.gov/pubmed/11301299?dopt=Abstract

Algorithms for a Simple Point Placement Problem

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

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 : 234-241.

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 : 234-41.

http://www.ncbi.nlm.nih.gov/pubmed/10786306?dopt=Abstract