Center-Authored Papers

Filters: Author is Ruzzo, Walter L  [Clear All Filters]
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2008
Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM et al..  2008.  MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.. Stem cells (Dayton, Ohio). 26(10):2496-505. Abstract
2010
Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL et al..  2010.  Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.. Developmental cell. 18(4):662-74. Abstract
2012
Bolouri H, Ruzzo WL.  2012.  Integration of 198 ChIP-seq Datasets Reveals Human cis-Regulatory Regions.. Journal of computational biology : a journal of computational molecular cell biology. 19(9):989-97. Abstract
Knouf EC, Garg K, Arroyo JD, Correa Y, Sarkar D, Parkin RK, Wurz K, O'Briant KC, Godwin AK, Urban ND et al..  2012.  An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription.. Nucleic acids research. 40(2):499-510. Abstract
Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R et al..  2012.  DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy.. Developmental cell. 22(1):38-51. Abstract
Seemann SE, Sunkin S, Hawrylycz M, Ruzzo WL, Gorodkin J.  2012.  Transcripts with in silico predicted RNA structure are enriched everywhere in the mouse brain.. BMC genomics. 13(1):214. Abstract
Jones DC, Ruzzo WL, Peng X, Katze MG.  2012.  Compression of next-generation sequencing reads aided by highly efficient de novo assembly.. Nucleic acids research. Abstract
Jones DC, Ruzzo WL, Peng X, Katze MG.  2012.  A new approach to bias correction in RNA-Seq.. Bioinformatics (Oxford, England). 28(7):921-928. Abstract
2013
Yao Z, Fong AP, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ.  2013.  Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.. Skeletal muscle. 3(1):8. Abstract
Yao Z, MacQuarrie KL, Fong AP, Tapscott SJ, Ruzzo WL, Gentleman RC.  2013.  Discriminative motif analysis of high-throughput dataset.. Bioinformatics (Oxford, England). Abstract
Tseng H-HE, Hullar MAJ, Li F, Lampe JW, Sandstrom R, Johnson AK, Strate LL, Ruzzo WL, Stamatoyannopoulos J.  2013.  A microbial profiling method for the human microbiota using high-throughput sequencing.. Metagenomics (Cairo, Egypt). 2:235646. Abstract
2014
Gorodkin J, Hofacker IL, Ruzzo WL.  2014.  Concepts and introduction to RNA bioinformatics.. Methods in molecular biology (Clifton, N.J.). 1097:1-31. Abstract
Ruzzo WL, Gorodkin J.  2014.  De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences.. Methods in molecular biology (Clifton, N.J.). 1097:303-18. Abstract
Peng X, Pipes L, Xiong H, Green RR, Jones DC, Ruzzo WL, Schroth GP, Mason CE, Palermo RE, Katze MG.  2014.  Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data.. Journal of medical primatology. Abstract
Amino Acid Motifs
Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL et al..  2010.  Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.. Developmental cell. 18(4):662-74. Abstract
Animals
Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL et al..  2010.  Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.. Developmental cell. 18(4):662-74. Abstract
APOPTOSIS
Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R et al..  2012.  DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy.. Developmental cell. 22(1):38-51. Abstract
April 2012
Fong AP, Yao Z, Zhong JW, Cao Y, Ruzzo WL, Gentleman RC, Tapscott SJ.  2012.  Genetic and epigenetic determinants of neurogenesis and myogenesis.. Developmental cell. 22(4):721-35. Abstract
April 2014
Gorodkin J, Hofacker IL, Ruzzo WL.  2014.  Concepts and introduction to RNA bioinformatics.. Methods in molecular biology (Clifton, N.J.). 1097:1-31. Abstract
Ruzzo WL, Gorodkin J.  2014.  De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences.. Methods in molecular biology (Clifton, N.J.). 1097:303-18. Abstract
Base Sequence
Bar M, Wyman SK, Fritz BR, Qi J, Garg KS, Parkin RK, Kroh EM, Bendoraite A, Mitchell PS, Nelson AM et al..  2008.  MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries.. Stem cells (Dayton, Ohio). 26(10):2496-505. Abstract
beta-Defensins
Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R et al..  2012.  DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy.. Developmental cell. 22(1):38-51. Abstract
Binding Sites
Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, MacQuarrie KL, Davison J, Morgan MT, Ruzzo WL et al..  2010.  Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.. Developmental cell. 18(4):662-74. Abstract
Biological Markers
Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R et al..  2012.  DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy.. Developmental cell. 22(1):38-51. Abstract
Blotting, Western
Geng LN, Yao Z, Snider L, Fong AP, Cech JN, Young JM, van der Maarel SM, Ruzzo WL, Gentleman RC, Tawil R et al..  2012.  DUX4 Activates Germline Genes, Retroelements, and Immune Mediators: Implications for Facioscapulohumeral Dystrophy.. Developmental cell. 22(1):38-51. Abstract