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  • Influence
Linda in context
How can a system that differs sharply from all currently fashionable approaches score any kind of success? Here's how.
PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
A general scoring approach to address unique challenges in ChIP-seq data analysis is described, based on the observation that sites of potential binding are strongly correlated with signal peaks in the control, likely revealing features of open chromatin. Expand
De novo mutations revealed by whole-exome sequencing are strongly associated with autism
It is shown, using whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with autism spectrum disorders and carry large effects. Expand
Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome
High-throughput and massive paired-end mapping (PEM) was used to map SVs in an African and in a putatively European individual and identified shared and divergent SVs relative to the reference genome, documenting that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. Expand
Linda and Friends
Linda consists of a few simple operators designed to support and simplify the construction of explicitly-parallel programs, which is to make it largely unnecessary to think about the coupling between parallel processes. Expand
De novo mutations in histone modifying genes in congenital heart disease
Comparing the incidence of de novo mutations in severe CHD cases and controls by analysing exome sequencing of parent–offspring trios suggests that several hundreds of genes collectively contribute to approximately 10% of severeCHD. Expand
How to write parallel programs: a guide to the perplexed
A framework for parallel programming is presented, based on three conceptual classes for understanding parallelism and three programming paradigms for implementing parallel programs, which are useful on many kinds of parallel machine, and each can be expressed in several different parallel programming languages. Expand
How to write parallel programs - a first course
This straightforward tutorial explains why parallelism is a powerful and proven way to run programs fast and provides the instruction that will transform ordinary programmers into parallel programmers. Expand
PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data
Paired-End Mapper demonstrated high structural variant reconstruction efficiency for PEMer's coverage-adjusted multi-cutoff scoring-strategy and showed its relative insensitivity to base-calling errors. Expand