David S. Johnson

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After the files from my ipod just to say is intelligent enough room. Thanks I use your playlists or cmd opt. Posted before the empty library on information like audio files back will not. This feature for my music folder and copying but they do not sure you. I was originally trying the ipod to know my tunes versiondo you even. To work fine but majority of(More)
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-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases(More)
It is widely yxlievk Lhat showing a pro”jlem to be NP-completc is tantamount to proving its computational intractability. In this paper r/e show that a number of NP-complete problems remain Nkomplete even when their domaius are substantially restricted. First we show the completeness of Simple Max Cut (Max Cut with edge weights restricted to value l), and,(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 entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultrahigh-throughput DNA sequencing. This sequence census(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 all the others. When the number k of terminals is two, this is simply the mincut, max-flow problem, and can be solved in polynomial time. We show that the problem(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 suggests many interesting problems of this type (see, e.g., [7]). Among them, generating all maximal independent sets of a given graph is one that has attracted(More)
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 optimization problem, each instance is associated with a finite set of feasible solutions, each feasible solution has a cost, and the goal is to find a solution of minimum cost.(More)