Xingdong Feng

Learn More
To determine cancer pathway activities in nine types of primary tumors and NCI60 cell lines, we applied an in silica approach by examining gene signatures reflective of consequent pathway activation using gene expression data. Supervised learning approaches predicted that the Ras pathway is active in approximately 70% of lung adenocarcinomas but inactive in(More)
BACKGROUND In the Addona et al. paper (Nature Biotechnology 2009), a large-scale multi-site study was performed to quantify Multiple Reaction Monitoring (MRM) measurements of proteins spiked in human plasma. The unlabeled signature peptides derived from the seven target proteins were measured at nine different concentration levels, and their isotopic(More)
Multiple reaction monitoring (MRM) mass spectrometry coupled with stable isotope dilution (SID) and liquid chromatography (LC) is increasingly used in biological and clinical studies for precise and reproducible quantification of peptides and proteins in complex sample matrices. Robust LC-SID-MRM-MS-based assays that can be replicated across laboratories(More)
Susan E. Abbatiello‡, D. R. Mani‡, Birgit Schilling§, Brendan MacLean¶, Lisa J. Zimmerman , Xingdong Feng**, Michael P. Cusack§, Nell Sedransk**, Steven C. Hall‡‡, Terri Addona‡, Simon Allen‡‡, Nathan G. Dodder§§, Mousumi Ghosh¶¶, Jason M. Held§, Victoria Hedrick , H. Dorota Inerowicz , Angela Jackson, Hasmik Keshishian‡, Jong Won Kim, John S. Lyssand, C.(More)
Gene expression patterns can reflect gene regulations in human tissues under normal or pathologic conditions. Gene expression profiling data from studies of primary human disease samples are particularly valuable since these studies often span many years in order to collect patient clinical information and achieve a large sample size. Disease-to-Gene(More)
Linear regressions are commonly used to calibrate the signal measurements in proteomic analysis by mass spectrometry. However, with or without a monotone (e.g., log) transformation, data from such functional proteomic experiments are not necessarily linear or even monotone functions of protein (or peptide) concentration except over a very restricted range.(More)
Studies of gene expression in primary human disease tissue often span several years in order to achieve reasonably large sample sizes and to collect patient clinical information making this data particularly valuable. Due to the lack of a central repository, this data has only been available through disparate and non-publicly accessible sources following(More)
  • 1