To take advantage of the potential quantitative benefits offered by tandem mass spectrometry,
we have modified the method in which tandem mass spectrum data are acquired in '…

We have developed pLink, software for data analysis of cross-linked proteins coupled with
mass-spectrometry analysis. pLink reliably estimates false discovery rate in cross-link …

Structure-specific endonucleases resolve DNA secondary structures generated during DNA
repair and recombination. The yeast 5′ flap endonuclease Slx1-Slx4 has received …

The mechanosensitive Piezo channels function as key eukaryotic mechanotransducers.
However, their structures and mechanogating mechanisms remain unknown. Here we …

We describe pLink 2, a search engine with higher speed and reliability for proteome-scale
identification of cross-linked peptides. With a two-stage open search strategy facilitated by …

DAF-2, an insulin receptor–like protein, regulates metabolism, development, and aging in
Caenorhabditis elegans. In a quantitative proteomic study, we identified 86 proteins that were …

Necrosis can be induced by stimulating death receptors with tumor necrosis factor (TNF) or
other agonists; however, the underlying mechanism differentiating necrosis from apoptosis is …

Like apoptosis, oncogene-induced senescence is a barrier to tumor development. However,
relatively little is known about the signaling pathways mediating the senescence response. …

MicroRNAs (miRNAs) regulate gene expression for diverse functions, but only a limited
number of mRNA targets have been experimentally identified. We show that GW182 family …

We present a sequence-tag-based search engine, Open-pFind, to identify peptides in an
ultra-large search space that includes coeluting peptides, unexpected modifications and …