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Walter L. Ruzzo - Publications

Affiliations: 
Computer Science and Engineering University of Washington, Seattle, Seattle, WA 
Area:
Computer Science, Bioinformatics Biology, Microbiology Biology
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36 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
2022 Seemann SE, Mirza AH, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Workman CT, Pociot F, Tommerup N, Gorodkin J, Ruzzo WL. Does rapid sequence divergence preclude RNA structure conservation in vertebrates? Nucleic Acids Research. PMID 35188540 DOI: 10.1093/nar/gkac067  0.311
2021 Jones DC, Ruzzo WL. Polee: RNA-Seq analysis using approximate likelihood. Nar Genomics and Bioinformatics. 3: lqab046. PMID 34056596 DOI: 10.1093/nargab/lqab046  0.33
2018 Kirsch R, Seemann SE, Ruzzo WL, Cohen SM, Stadler PF, Gorodkin J. Identification and characterization of novel conserved RNA structures in Drosophila. Bmc Genomics. 19: 899. PMID 30537930 DOI: 10.1186/S12864-018-5234-4  0.456
2017 Hecker N, Seemann SE, Silahtaroglu A, Ruzzo WL, Gorodkin J. Associating transcription factors and conserved RNA structures with gene regulation in the human brain. Scientific Reports. 7: 5776. PMID 28720872 DOI: 10.1038/S41598-017-06200-4  0.413
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  0.465
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  0.308
2014 Ruzzo WL, Gorodkin J. De novo discovery of structured ncRNA motifs in genomic sequences. Methods in Molecular Biology (Clifton, N.J.). 1097: 303-18. PMID 24639166 DOI: 10.1007/978-1-62703-709-9_15  0.435
2014 Gorodkin J, Hofacker IL, Ruzzo WL. Concepts and introduction to RNA bioinformatics. Methods in Molecular Biology (Clifton, N.J.). 1097: 1-31. PMID 24639152 DOI: 10.1007/978-1-62703-709-9_1  0.45
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  0.326
2012 Bolouri H, Ruzzo WL. Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 989-97. PMID 22897152 DOI: 10.1089/Cmb.2012.0100  0.323
2012 Seemann SE, Sunkin SM, Hawrylycz MJ, Ruzzo WL, Gorodkin J. Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain. Bmc Genomics. 13: 214. PMID 22651826 DOI: 10.1186/1471-2164-13-214  0.448
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  0.333
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  0.446
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  0.307
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  0.323
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  0.453
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  0.642
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  0.347
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  0.62
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  0.644
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  0.455
2007 Wang AX, Ruzzo WL, Tompa M. How accurately is ncRNA aligned within whole-genome multiple alignments? Bmc Bioinformatics. 8: 417. PMID 17963514 DOI: 10.1186/1471-2105-8-417  0.316
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  0.663
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  0.647
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  0.564
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  0.588
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  0.315
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  0.642
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  0.636
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  0.635
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  0.582
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  0.59
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  0.582
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  0.59
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  0.602
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  0.59
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