Center-Authored Papers

Filters: Author is Ruzzo, Walter L  [Clear All Filters]
Journal Article
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
Hecker N, Seemann SE, Silahtaroglu A, Ruzzo WL, Gorodkin J.  2017.  Associating transcription factors and conserved RNA structures with gene regulation in the human brain.. Scientific reports. 7(1):5776. Abstract
Palpant NJ, Wang Y, Hadland B, Zaunbrecher RJ, Redd M, Jones D, Pabon L, Jain R, Epstein J, Ruzzo WL et al..  2017.  Chromatin and Transcriptional Analysis of Mesoderm Progenitor Cells Identifies HOPX as a Regulator of Primitive Hematopoiesis.. Cell reports. 20(7):1597-1608. Abstract
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
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
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
Yao Z, MacQuarrie KL, Fong AP, Tapscott SJ, Ruzzo WL, Gentleman RC.  2013.  Discriminative motif analysis of high-throughput dataset.. Bioinformatics (Oxford, England). 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
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
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
Seemann SE, Mirza AH, Hansen C, Bang-Berthelsen CH, Garde C, Christensen-Dalsgaard M, Torarinsson E, Yao Z, Workman CT, Pociot F et al..  2017.  The identification and functional annotation of RNA structures conserved in vertebrates.. Genome research. Abstract
Palpant NJ, Pabon L, Roberts M, Hadland B, Jones D, Jones C, Moon RT, Ruzzo WL, Bernstein I, Zheng Y et al..  2015.  Inhibition of β-catenin signaling respecifies anterior-like endothelium into beating human cardiomyocytes.. Development (Cambridge, England). 142(18):3198-209. Abstract
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
Kuppusamy KT, Jones DC, Sperber H, Madan A, Fischer KA, Rodriguez ML, Pabon L, Zhu W-Z, Tulloch NL, Yang X et al..  2015.  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. 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
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
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
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