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Quantitative analysis of complex protein mixtures using isotope-coded affinity tags
TLDR
An approach for the accurate quantification and concurrent sequence identification of the individual proteins within complex mixtures based on isotope-coded affinity tags and tandem mass spectrometry is described. Expand
Identification of RIP1 kinase as a specific cellular target of necrostatins.
TLDR
Necroptosis is a cellular mechanism of necrotic cell death induced by apoptotic stimuli in the form of death domain receptor engagement by their respective ligands under conditions where apoptotic execution is prevented and necrostatins are established as the first-in-class inhibitors of RIP1 kinase, the key upstream kinase involved in the activation of necroptosis. Expand
RNAi-Mediated Targeting of Heterochromatin by the RITS Complex
TLDR
The purification of an RNAi effector complex termed RITS (RNA-induced initiation of transcriptional gene silencing) that is required for heterochromatin assembly in fission yeast is described and a mechanism for the role of the RNAi machinery and small RNAs in targeting of heterochROMatin complexes and epigenetic genesilencing at specific chromosomal loci is suggested. Expand
Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS
TLDR
The AQUA strategy was used to quantify low abundance yeast proteins involved in gene silencing, quantitatively determine the cell cycle-dependent phosphorylation of Ser-1126 of human separase protein, and identify kinases capable of phosphorylating Ser-1501 of separase in an in vitro kinase assay. Expand
Two RNAi Complexes, RITS and RDRC, Physically Interact and Localize to Noncoding Centromeric RNAs
TLDR
Findings reveal a physical and functional link between Rdp1 and RITS and suggest that noncoding RNAs provide a platform for siRNA-dependent localization of RNAi complexes to specific chromosome regions. Expand
A probability-based approach for high-throughput protein phosphorylation analysis and site localization
TLDR
A large-scale phosphorylation data set is provided with a measured error rate as determined by the target-decoy approach, an approach to maximize data set sensitivity by efficiently distracting incorrect peptide spectral matches (PSMs) is demonstrated, and a probability-based score is presented, the Ascore, that measures the probability of correct phosphorylated site localization based on the presence and intensity of site-determining ions in MS/MS spectra. Expand
Large-scale phosphorylation analysis of mouse liver
TLDR
It is demonstrated that a combination of tandem phosphopeptide enrichment methods, high performance MS, and optimized database search/data filtering strategies is a powerful tool for surveying the phosphoproteome. Expand
Steps in Assembly of Silent Chromatin in Yeast: Sir3-Independent Binding of a Sir2/Sir4 Complex to Silencers and Role for Sir2-Dependent Deacetylation
TLDR
A stepwise model for the assembly of silent chromatin domains in Saccharomyces cerevisiae is supported by results at the rDNA repeats and at the Sir2/Sir4 complex. Expand
HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms.
TLDR
This work shows that Swi6 and Chp2 exist in nonoverlapping complexes and make distinct contributions to silencing, and suggests that different HP1 proteins ensure full heterochromatic gene silencing through largely non overlapping inhibitory mechanisms. Expand
Dicer-dependent endothelial microRNAs are necessary for postnatal angiogenesis
TLDR
Reduction of endothelial miRNAs by cell-specific inactivation of Dicer reduces postnatal angiogenic response to a variety of stimuli, including exogenous VEGF, tumors, limb ischemia, and wound healing. Expand
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