Research Topics
Species | Zizhen YaoSummaryAffiliation: University of Washington Country: USA Publications
| Collaborators
|
Detail Information
Publications
CMfinder--a covariance model based RNA motif finding algorithmZizhen Yao
Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195 2350, USA
Bioinformatics 22:445-52. 2006..We have used this approach to obtain highly accurate covariance models of known RNA motifs based on small numbers of related sequences, which identified homologs in deeply-diverged species...- A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous dataZizhen Yao
Department of Computer Science and Engineering, AC101 Paul G Allen Center, University of Washington, Seattle WA 98195, USA
BMC Bioinformatics 7:S11. 2006..As a variety of functional genomic and proteomic techniques become available, there is an increasing need for functional analysis methodologies that integrate heterogeneous data sources... - A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotesZizhen Yao
Department of Computer Science and Engineering, University of Washington, Seattle, Washington, USA
PLoS Comput Biol 3:e126. 2007..Of the ncRNA candidates not in Rfam, we find compelling evidence that some of them are functional, and analyze several potential ribosomal protein leaders in depth... - A Marfan syndrome gene expression phenotype in cultured skin fibroblastsZizhen Yao
Department of Pathology, University of Washington, Seattle, Washington 98195, USA
BMC Genomics 8:319. 2007..This syndrome constitutes a significant identifiable subtype of aortic aneurysmal disease, accounting for over 5% of ascending and thoracic aortic aneurysms... - DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophyLinda N Geng
Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Dev Cell 22:38-51. 2012..These findings suggest specific mechanisms of FSHD pathology and identify candidate biomarkers for disease diagnosis and progression... - Genetic and epigenetic determinants of neurogenesis and myogenesisAbraham P Fong
Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Department of Pediatrics, University of Washington, School of Medicine, Seattle, WA 98105, USA
Dev Cell 22:721-35. 2012..These findings demonstrate that the differentiation program is genetically determined by E box sequence, whereas cell lineage epigenetically determines the availability of E boxes for each differentiation program... - Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogrammingYi Cao
Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
Dev Cell 18:662-74. 2010..Therefore, in addition to regulating muscle gene expression, MyoD binds genome wide and has the ability to broadly alter the epigenome in myoblasts and myotubes... - Polycomb-mediated repression during terminal differentiation: what don't you want to be when you grow up?Melissa L Conerly
Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
Genes Dev 25:997-1003. 2011..789-794) in Genes & Development of the role of the polycomb group protein Ezh2 in muscle stem cells, and discuss the implications for general lineage restriction... - Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophyPatrick C H Hsieh
Department of Bioengineering, University of Washington, Seattle, WA 98195-6410, USA
J Vasc Surg 43:150-8. 2006..CONCLUSIONS: Increased BMPs (particularly BMP4) coupled with decreased noggin may promote high shear stress-mediated graft neointimal atrophy by inhibiting SMC proliferation and increasing SMC death... - Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipelineZasha Weinberg
Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520 8103, USA
Nucleic Acids Res 35:4809-19. 2007..These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered... - A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolismElizabeth E Regulski
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
Mol Microbiol 68:918-32. 2008..Furthermore, we identify variants of this RNA that are likely to be triggered by the related tungsten cofactor (Tuco), which carries tungsten in place of molybdenum as the metal constituent... - Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regionsElfar Torarinsson
Section for Genetics and Bioinformatics, IBVH, Faculty of Life Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
Genome Res 18:242-51. 2008.... - The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitchesZasha Weinberg
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520 8103, USA
RNA 14:822-8. 2008..Our findings support the view that RNA has considerable structural versatility and reveal that riboswitches exploit this potential to expand the scope of RNA in genetic regulation...