Bloom, Joshua S, Khan, Zia, Kruglyak, Leonid, Singh, Mona, Caudy, Amy A
Abstract Background High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring...
Predicting gene function in a hierarchical context with an ensemble of classifiers (2008)
Guan, Yuanfang, Myers, Chad L, Hess, David C, Barutcuoglu, Zafer, Caudy, Amy A, Troyanskaya, Olga G
Abstract Background: The wide availability of genome-scale data for several organisms has stimulated interest in computational approaches to gene function prediction. Diverse machine learning methods...
Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells (2002)
Paddison, Patrick J., Caudy, Amy A., Bernstein, Emily, Hannon, Gregory J., Conklin, Douglas S.
Fragile X-related protein and VIG associate with the RNA interference machinery (2002)
Caudy, Amy A., Myers, Mike, Hannon, Gregory J., Hammond, Scott M.
Stable suppression of gene expression by RNAi in mammalian cells
Paddison, Patrick J., Caudy, Amy A., Hannon, Gregory J.
In a diverse group of organisms including plants, Caenorhabditis elegans, Drosophila, and trypanosomes, double-stranded RNA (dsRNA) is a potent trigger of gene silencing. In several model systems,...
Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells
Paddison, Patrick J., Caudy, Amy A., Bernstein, Emily, Hannon, Gregory J., Conklin, Douglas S.
RNA interference (RNAi) was first recognized in Caenorhabditis elegans as a biological response to exogenous double-stranded RNA (dsRNA), which induces sequence-specific gene silencing. RNAi...
Fragile X-related protein and VIG associate with the RNA interference machinery
Caudy, Amy A., Myers, Mike, Hannon, Gregory J., Hammond, Scott M.
RNA interference (RNAi) is a flexible gene silencing mechanism that responds to double-stranded RNA by suppressing homologous genes. Here, we report the characterization of RNAi effector complexes...
Stable suppression of gene expression by RNAi in mammalian cells
Paddison, Patrick J., Caudy, Amy A., Hannon, Gregory J.
In a diverse group of organisms including plants, Caenorhabditis elegans, Drosophila, and trypanosomes, double-stranded RNA (dsRNA) is a potent trigger of gene silencing. In several model systems,...
Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells
Paddison, Patrick J., Caudy, Amy A., Bernstein, Emily, Hannon, Gregory J., Conklin, Douglas S.
RNA interference (RNAi) was first recognized in Caenorhabditis elegans as a biological response to exogenous double-stranded RNA (dsRNA), which induces sequence-specific gene silencing. RNAi...
Fragile X-related protein and VIG associate with the RNA interference machinery
Caudy, Amy A., Myers, Mike, Hannon, Gregory J., Hammond, Scott M.
RNA interference (RNAi) is a flexible gene silencing mechanism that responds to double-stranded RNA by suppressing homologous genes. Here, we report the characterization of RNAi effector complexes...
Predicting gene function in a hierarchical context with an ensemble of classifiers
Guan, Yuanfang, Myers, Chad L, Hess, David C, Barutcuoglu, Zafer, Caudy, Amy A, Troyanskaya, Olga G
Predicting Cellular Growth from Gene Expression Signatures
Airoldi, Edoardo M., Huttenhower, Curtis, Gresham, David, Lu, Charles, Caudy, Amy A., Dunham, Maitreya J., ...
Maintaining balanced growth in a changing environment is a fundamental systems-level challenge for cellular physiology, particularly in microorganisms. While the complete set of regulatory and...
Hess, David C., Myers, Chad L., Huttenhower, Curtis, Hibbs, Matthew A., Hayes, Alicia P., Paw, Jadine, ...
Mitochondria are central to many cellular processes including respiration, ion homeostasis, and apoptosis. Using computational predictions combined with traditional quantitative experiments, we have...
Directing Experimental Biology: A Case Study in Mitochondrial Biogenesis
Hibbs, Matthew A., Myers, Chad L., Huttenhower, Curtis, Hess, David C., Li, Kai, Caudy, Amy A., ...
Computational approaches have promised to organize collections of functional genomics data into testable predictions of gene and protein involvement in biological processes and pathways. However, few...