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Items: 1 to 20 of 43


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.

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