We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seqâ€¦ (More)

In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entireâ€¦ (More)

In the Multiterminal Cut problem we are given an edge-weighted graph and a subset of the vertices called terminals, and asked for a minimum weight set of edges that separates each terminal from allâ€¦ (More)

Generating all configurations that satisfy a given specification (e.g., all permutations of n objects that do not fix any object) is a well-studied problem in combinatorics [6]. Graph theory suggestsâ€¦ (More)

26th Annual Symposium on Foundations of Computerâ€¦

1985

One of the few general approaches to difficult combinatorial optimization problems that has met with empirical success is local (or neighborhood> search. In a typical combinatorial optimizationâ€¦ (More)