Walter L. Ruzzo - Publications

Affiliations: 
Computer Science and Engineering University of Washington, Seattle, Seattle, WA 
Area:
Computer Science, Bioinformatics Biology, Microbiology Biology

40 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F, Nielsen H, Tommerup N, Ruzzo WL, Gorodkin J. The identification and functional annotation of RNA structures conserved in vertebrates. Genome Research. PMID 28487280 DOI: 10.1101/Gr.208652.116  0.52
2015 Palpant NJ, Pabon L, Roberts M, Hadland B, Jones D, Jones C, Moon RT, Ruzzo WL, Bernstein I, Zheng Y, Murry CE. Inhibition of β-catenin signaling respecifies anterior-like endothelium into beating human cardiomyocytes. Development (Cambridge, England). PMID 26153229 DOI: 10.1242/Jcs.180588  1
2015 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. Proceedings of the National Academy of Sciences of the United States of America. 112: E2785-94. PMID 25964336 DOI: 10.1073/Pnas.1424042112  1
2014 Peng X, Pipes L, Xiong H, Green RR, Jones DC, Ruzzo WL, Schroth GP, Mason CE, Palermo RE, Katze MG. Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. Journal of Medical Primatology. 43: 317-28. PMID 24810475 DOI: 10.1111/Jmp.12125  1
2014 Yao Z, Macquarrie KL, Fong AP, Tapscott SJ, Ruzzo WL, Gentleman RC. Discriminative motif analysis of high-throughput dataset. Bioinformatics (Oxford, England). 30: 775-83. PMID 24162561 DOI: 10.1093/Bioinformatics/Btt615  1
2013 Yao Z, Fong AP, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ. Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites. Skeletal Muscle. 3: 8. PMID 23566431 DOI: 10.1186/2044-5040-3-8  1
2013 McVicar N, Ruzzo WL, Hauck S. Accelerating ncRNA homology search with FPGAs Acm/Sigda International Symposium On Field Programmable Gate Arrays - Fpga. 43-52. DOI: 10.1145/2435264.2435276  1
2012 Jones DC, Ruzzo WL, Peng X, Katze MG. Compression of next-generation sequencing reads aided by highly efficient de novo assembly. Nucleic Acids Research. 40: e171. PMID 22904078 DOI: 10.1093/Nar/Gks754  1
2012 Fong AP, Yao Z, Zhong JW, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ. Genetic and epigenetic determinants of neurogenesis and myogenesis. Developmental Cell. 22: 721-35. PMID 22445365 DOI: 10.1016/J.Devcel.2012.01.015  1
2012 Jones DC, Ruzzo WL, Peng X, Katze MG. A new approach to bias correction in RNA-Seq. Bioinformatics (Oxford, England). 28: 921-8. PMID 22285831 DOI: 10.1093/Bioinformatics/Bts055  1
2012 Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R, Tapscott SJ. DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Developmental Cell. 22: 38-51. PMID 22209328 DOI: 10.1016/J.Devcel.2011.11.013  1
2012 Knouf EC, Garg K, Arroyo JD, Correa Y, Sarkar D, Parkin RK, Wurz K, O'Briant KC, Godwin AK, Urban ND, Ruzzo WL, Gentleman R, Drescher CW, Swisher EM, Tewari M. An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription. Nucleic Acids Research. 40: 499-510. PMID 21917857 DOI: 10.1093/Nar/Gkr731  1
2010 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. Developmental Cell. 18: 662-74. PMID 20412780 DOI: 10.1016/J.Devcel.2010.02.014  1
2010 Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL. De novo prediction of structured RNAs from genomic sequences. Trends in Biotechnology. 28: 9-19. PMID 19942311 DOI: 10.1016/J.Tibtech.2009.09.006  0.52
2009 Tseng HH, Weinberg Z, Gore J, Breaker RR, Ruzzo WL. Finding non-coding RNAs through genome-scale clustering. Journal of Bioinformatics and Computational Biology. 7: 373-88. PMID 19340921 DOI: 10.1142/S0219720009004126  1
2009 Anandam P, Torarinsson E, Ruzzo WL. Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies. Bioinformatics (Oxford, England). 25: 668-9. PMID 19136551 DOI: 10.1093/Bioinformatics/Btp006  1
2008 Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM, Ruzzo WL, Ware C, Radich JP, Gentleman R, Ruohola-Baker H, et al. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells (Dayton, Ohio). 26: 2496-505. PMID 18583537 DOI: 10.1634/Stemcells.2008-0356  1
2008 Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. Rna (New York, N.Y.). 14: 822-8. PMID 18369181 DOI: 10.1261/Rna.988608  1
2008 Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Molecular Microbiology. 68: 918-32. PMID 18363797 DOI: 10.1111/J.1365-2958.2008.06208.X  1
2008 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 Research. 18: 242-51. PMID 18096747 DOI: 10.1101/Gr.6887408  0.52
2007 Yao Z, Jaeger JC, Ruzzo WL, Morale CZ, Emond M, Francke U, Milewicz DM, Schwartz SM, Mulvihill ER. A Marfan syndrome gene expression phenotype in cultured skin fibroblasts. Bmc Genomics. 8: 319. PMID 17850668 DOI: 10.1186/1471-2164-8-319  1
2007 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 Research. 35: 4809-19. PMID 17621584 DOI: 10.1093/Nar/Gkm487  1
2007 Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes. Plos Computational Biology. 3: e126. PMID 17616982 DOI: 10.1371/Journal.Pcbi.0030126  0.96
2007 Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes Plos Computational Biology. 3: 1212-1223. DOI: 10.1371/journal.pcbi.0030126  1
2006 Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, ... ... Ruzzo WL, et al. Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote. Plos Biology. 4: e286. PMID 16933976 DOI: 10.1371/Journal.Pbio.0040286  1
2006 Yao Z, Ruzzo WL. A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data. Bmc Bioinformatics. 7: S11. PMID 16723004 DOI: 10.1186/1471-2105-7-S1-S11  0.52
2006 Hsieh PCH, Kenagy RD, Mulvihill ER, Jeanette JP, Wang X, Chang CMC, Yao Z, Ruzzo WL, Justice S, Hudkins KL, Alpers CE, Berceli S, Clowes AW. Bone morphogenetic protein 4: Potential regulator of shear stress-induced graft neointimal atrophy Journal of Vascular Surgery. 43: 150-158. PMID 16414402 DOI: 10.1016/J.Jvs.2005.08.008  1
2006 Yao Z, Weinberg Z, Ruzzo WL. CMfinder--a covariance model based RNA motif finding algorithm. Bioinformatics (Oxford, England). 22: 445-52. PMID 16357030 DOI: 10.1093/Bioinformatics/Btk008  1
2006 Weinberg Z, Ruzzo WL. Sequence-based heuristics for faster annotation of non-coding RNA families. Bioinformatics (Oxford, England). 22: 35-9. PMID 16267089 DOI: 10.1093/Bioinformatics/Bti743  1
2005 Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. Rna (New York, N.Y.). 11: 774-84. PMID 15811922 DOI: 10.1261/Rna.7286705  1
2004 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 (New York, N.Y.). 306: 275-9. PMID 15472076 DOI: 10.1126/Science.1100829  1
2004 Weinberg Z, Ruzzo WL. Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy. Bioinformatics (Oxford, England). 20: i334-41. PMID 15262817 DOI: 10.1093/bioinformatics/bth925  1
2003 Jaeger J, Sengupta R, Ruzzo WL. Improved gene selection for classification of microarrays. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 53-64. PMID 12603017 DOI: 10.1142/9789812776303_0006  1
2002 Patterson DJ, Yasuhara K, Ruzzo WL. Pre-mRNA secondary structure prediction aids splice site prediction. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 223-34. PMID 11928478  1
2002 Barrett MT, Yeung KY, Ruzzo WL, Hsu L, Blount PL, Sullivan R, Zarbl H, Delrow J, Rabinovitch PS, Reid BJ. Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae. Neoplasia (New York, N.Y.). 4: 121-8. PMID 11896567 DOI: 10.1038/Sj.Neo.7900221  1
2001 Yeung KY, Fraley C, Murua A, Raftery AE, Ruzzo WL. Model-based clustering and data transformations for gene expression data. Bioinformatics (Oxford, England). 17: 977-87. PMID 11673243 DOI: 10.1093/Bioinformatics/17.10.977  1
2001 Yeung KY, Ruzzo WL. Principal component analysis for clustering gene expression data. Bioinformatics (Oxford, England). 17: 763-74. PMID 11590094 DOI: 10.1093/Bioinformatics/17.9.763  1
2001 Yeung KY, Haynor DR, Ruzzo WL. Validating clustering for gene expression data. Bioinformatics (Oxford, England). 17: 309-18. PMID 11301299 DOI: 10.1093/Bioinformatics/17.4.309  1
1996 Dymond PW, Fich FE, Nishimura N, Ragde P, Ruzzo WL. Pointers versus arithmetic in PRAMs Journal of Computer and System Sciences. 53: 218-232. DOI: 10.1006/Jcss.1996.0063  1
1978 Adleman L, Booth KS, Preparata FP, Ruzzo WL. Improved time and space bounds for Boolean matrix multiplication Acta Informatica. 11: 61-70. DOI: 10.1007/Bf00264600  1
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