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Items: 46


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

Palpant NJ, Wang Y, Hadland B, Zaunbrecher RJ, Redd M, Jones D, Pabon L, Jain R, Epstein J, Ruzzo WL, Zheng Y, Bernstein I, Margolin A, Murry CE.

Cell Rep. 2017 Aug 15;20(7):1597-1608. doi: 10.1016/j.celrep.2017.07.067.


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

Hecker N, Seemann SE, Silahtaroglu A, Ruzzo WL, Gorodkin J.

Sci Rep. 2017 Jul 18;7(1):5776. doi: 10.1038/s41598-017-06200-4.


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

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.

Genome Res. 2017 Aug;27(8):1371-1383. doi: 10.1101/gr.208652.116. Epub 2017 May 9.


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

Palpant NJ, Pabon L, Roberts M, Hadland B, Jones D, Jones C, Moon RT, Ruzzo WL, Bernstein I, Zheng Y, Murry CE.

Development. 2015 Sep 15;142(18):3198-209. doi: 10.1242/dev.117010. Epub 2015 Jul 7.


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

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.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):E2785-94. doi: 10.1073/pnas.1424042112. Epub 2015 May 11.


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

Peng X, Pipes L, Xiong H, Green RR, Jones DC, Ruzzo WL, Schroth GP, Mason CE, Palermo RE, Katze MG.

J Med Primatol. 2014 Oct;43(5):317-28. doi: 10.1111/jmp.12125. Epub 2014 May 8.


De novo discovery of structured ncRNA motifs in genomic sequences.

Ruzzo WL, Gorodkin J.

Methods Mol Biol. 2014;1097:303-18. doi: 10.1007/978-1-62703-709-9_15. Review.


Concepts and introduction to RNA bioinformatics.

Gorodkin J, Hofacker IL, Ruzzo WL.

Methods Mol Biol. 2014;1097:1-31. doi: 10.1007/978-1-62703-709-9_1. Review.


Discriminative motif analysis of high-throughput dataset.

Yao Z, Macquarrie KL, Fong AP, Tapscott SJ, Ruzzo WL, Gentleman RC.

Bioinformatics. 2014 Mar 15;30(6):775-83. doi: 10.1093/bioinformatics/btt615. Epub 2013 Oct 25.


A microbial profiling method for the human microbiota using high-throughput sequencing.

Tseng HH, Hullar MA, Li F, Lampe JW, Sandstrom R, Johnson AK, Strate LL, Ruzzo WL, Stamatoyannopoulos J.

Metagenomics (Cairo). 2013;2:235646.


Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.

Yao Z, Fong AP, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ.

Skelet Muscle. 2013 Apr 8;3(1):8. doi: 10.1186/2044-5040-3-8.


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

Jones DC, Ruzzo WL, Peng X, Katze MG.

Nucleic Acids Res. 2012 Dec;40(22):e171. doi: 10.1093/nar/gks754. Epub 2012 Aug 16.


Integration of 198 ChIP-seq datasets reveals human cis-regulatory regions.

Bolouri H, Ruzzo WL.

J Comput Biol. 2012 Sep;19(9):989-97. doi: 10.1089/cmb.2012.0100. Epub 2012 Aug 16.


Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain.

Seemann SE, Sunkin SM, Hawrylycz MJ, Ruzzo WL, Gorodkin J.

BMC Genomics. 2012 May 31;13:214. doi: 10.1186/1471-2164-13-214.


Genetic and epigenetic determinants of neurogenesis and myogenesis.

Fong AP, Yao Z, Zhong JW, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ.

Dev Cell. 2012 Apr 17;22(4):721-35. doi: 10.1016/j.devcel.2012.01.015. Epub 2012 Mar 22.


A new approach to bias correction in RNA-Seq.

Jones DC, Ruzzo WL, Peng X, Katze MG.

Bioinformatics. 2012 Apr 1;28(7):921-8. doi: 10.1093/bioinformatics/bts055. Epub 2012 Jan 28.


DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy.

Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R, Tapscott SJ.

Dev Cell. 2012 Jan 17;22(1):38-51. doi: 10.1016/j.devcel.2011.11.013. Epub 2011 Dec 29.


An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.

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.

Nucleic Acids Res. 2012 Jan;40(2):499-510. doi: 10.1093/nar/gkr731. Epub 2011 Sep 14.


Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL, Gentleman RC, Tapscott SJ.

Dev Cell. 2010 Apr 20;18(4):662-74. doi: 10.1016/j.devcel.2010.02.014.


De novo prediction of structured RNAs from genomic sequences.

Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL.

Trends Biotechnol. 2010 Jan;28(1):9-19. doi: 10.1016/j.tibtech.2009.09.006. Epub 2009 Nov 26. Review.


Finding non-coding RNAs through genome-scale clustering.

Tseng HH, Weinberg Z, Gore J, Breaker RR, Ruzzo WL.

J Bioinform Comput Biol. 2009 Apr;7(2):373-88.


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

Anandam P, Torarinsson E, Ruzzo WL.

Bioinformatics. 2009 Mar 1;25(5):668-9. doi: 10.1093/bioinformatics/btp006. Epub 2009 Jan 9.


MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.

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, Tewari M.

Stem Cells. 2008 Oct;26(10):2496-505. doi: 10.1634/stemcells.2008-0356. Epub 2008 Jun 26.


The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.

Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR.

RNA. 2008 May;14(5):822-8. doi: 10.1261/rna.988608. Epub 2008 Mar 27.


A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism.

Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR.

Mol Microbiol. 2008 May;68(4):918-32. doi: 10.1111/j.1365-2958.2008.06208.x. Epub 2008 Mar 19.


Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J.

Genome Res. 2008 Feb;18(2):242-51. Epub 2007 Dec 20.


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

Wang AX, Ruzzo WL, Tompa M.

BMC Bioinformatics. 2007 Oct 26;8:417.


A Marfan syndrome gene expression phenotype in cultured skin fibroblasts.

Yao Z, Jaeger JC, Ruzzo WL, Morale CZ, Emond M, Francke U, Milewicz DM, Schwartz SM, Mulvihill ER.

BMC Genomics. 2007 Sep 12;8:319.


Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline.

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.

Nucleic Acids Res. 2007;35(14):4809-19. Epub 2007 Jul 9.


A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes.

Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL.

PLoS Comput Biol. 2007 Jul;3(7):e126.


Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

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, Majoros WH, Farzad M, Carlton JM, Smith RK Jr, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E.

PLoS Biol. 2006 Sep;4(9):e286.


Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophy.

Hsieh PC, Kenagy RD, Mulvihill ER, Jeanette JP, Wang X, Chang CM, Yao Z, Ruzzo WL, Justice S, Hudkins KL, Alpers CE, Berceli S, Clowes AW.

J Vasc Surg. 2006 Jan;43(1):150-8.


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

Yao Z, Weinberg Z, Ruzzo WL.

Bioinformatics. 2006 Feb 15;22(4):445-52. Epub 2005 Dec 15.


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

Weinberg Z, Ruzzo WL.

Bioinformatics. 2006 Jan 1;22(1):35-9. Epub 2005 Nov 2.


6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.

Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR.

RNA. 2005 May;11(5):774-84. Epub 2005 Apr 5.


A glycine-dependent riboswitch that uses cooperative binding to control gene expression.

Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR.

Science. 2004 Oct 8;306(5694):275-9. Erratum in: Science. 2004 Nov 26;306(5701):1477.


Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy.

Weinberg Z, Ruzzo WL.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i334-41.


Atherosclerotic plaque smooth muscle cells have a distinct phenotype.

Mulvihill ER, Jaeger J, Sengupta R, Ruzzo WL, Reimer C, Lukito S, Schwartz SM.

Arterioscler Thromb Vasc Biol. 2004 Jul;24(7):1283-9. Epub 2004 May 13.


Improved gene selection for classification of microarrays.

Jaeger J, Sengupta R, Ruzzo WL.

Pac Symp Biocomput. 2003:53-64.


Pre-mRNA secondary structure prediction aids splice site prediction.

Patterson DJ, Yasuhara K, Ruzzo WL.

Pac Symp Biocomput. 2002:223-34.


Transcriptional analyses of Barrett's metaplasia and normal upper GI mucosae.

Barrett MT, Yeung KY, Ruzzo WL, Hsu L, Blount PL, Sullivan R, Zarbl H, Delrow J, Rabinovitch PS, Reid BJ.

Neoplasia. 2002 Mar-Apr;4(2):121-8.


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

Yeung KY, Fraley C, Murua A, Raftery AE, Ruzzo WL.

Bioinformatics. 2001 Oct;17(10):977-87.


Principal component analysis for clustering gene expression data.

Yeung KY, Ruzzo WL.

Bioinformatics. 2001 Sep;17(9):763-74.


Validating clustering for gene expression data.

Yeung KY, Haynor DR, Ruzzo WL.

Bioinformatics. 2001 Apr;17(4):309-18.


A linear time algorithm for finding all maximal scoring subsequences.

Ruzzo WL, Tompa M.

Proc Int Conf Intell Syst Mol Biol. 1999:234-41.


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