Minimizing the risk of reporting false positives in large-scale RNAi screens (2006)
Echeverri, Christophe J, Beachy, Philip A, Baum, Buzz, Boutros, Michael, Buchholz, Frank, Chanda, Sumit K, ...
Large-scale RNA interference (RNAi)-based analyses, very much as other 'omic' approaches, have inherent rates of false positives and negatives. The variability in the standards of care applied to...
Systematic behavioral modeling of nonlinear microwave/RF circuits in the time (2003)
David E. Root, John Wood, Nick Tufillaro, Dominique Schreurs, Er Pekker
A powerful and systematic approach to behavioral modeling of nonlinear microwave/RF circuits in the time domain is presented, integrating several techniques from nonlinear dynamical systems analysis....
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
Kelley, Brian P., Sharan, Roded, Karp, Richard M., Sittler, Taylor, Root, David E., Stockwell, Brent R., ...
We implement a strategy for aligning two protein–protein interaction networks that combines interaction topology and protein sequence similarity to identify conserved interaction pathways and...
Detecting Spatial Patterns in Biological Array Experiments
ROOT, DAVID E., KELLEY, BRIAN P., STOCKWELL, BRENT R.
Chemical genetic screening and DNA and protein microarrays are among a number of increasingly important and widely used biological research tools that involve large numbers of parallel experiments...
Global analysis of large-scale chemical and biological experiments
Root, David E, Kelley, Brian P, Stockwell, Brent R
Research in the life sciences is increasingly dominated by high-throughput data collection methods that benefit from a global approach to data analysis. Recent innovations that facilitate such...
Biological Mechanism Profiling Using an Annotated Compound Library
Root, David E., Flaherty, Stephen P., Kelley, Brian P., Stockwell, Brent R.
We present a method for testing many biological mechanisms in cellular assays using an annotated library of 2036 small organic molecules. This annotated compound library represents a large-scale...
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
Kelley, Brian P., Sharan, Roded, Karp, Richard M., Sittler, Taylor, Root, David E., Stockwell, Brent R., ...
We implement a strategy for aligning two protein–protein interaction networks that combines interaction topology and protein sequence similarity to identify conserved interaction pathways and...