880 citations · 1.1k across the 10 of their papers we have counts for
7 papers · 1 filter
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
Nicholas H. Putnam, Brendan O'Connell, Jonathan C. Stites +7
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by pr…
Retrotransposon mobilization in cancer genomes
Tracy Ballinger, Adam D. Ewing, David Haussler
The Cancer Genome Atlas project was initiated by the National Cancer Institute in order to characterize the genomes of hundreds of tumors of various cancer types. While much effort…
Canonical, Stable, General Mapping using Context Schemes
Adam Novak, Yohei Rosen, David Haussler +1
Motivation: Sequence mapping is the cornerstone of modern genomics. However, most existing sequence mapping algorithms are insufficiently general. Results: We introduce context sch…
Mapping to a Reference Genome Structure
Benedict Paten, Adam Novak, David Haussler
To support comparative genomics, population genetics, and medical genetics, we propose that a reference genome should come with a scheme for mapping each base in any DNA string to…
RADIA: RNA and DNA Integrated Analysis for Somatic Mutation Detection
Amie J. Radenbaugh, Singer Ma, Adam Ewing +4
The detection of somatic single nucleotide variants is a crucial component to the characterization of the cancer genome. Mutation calling algorithms thus far have focused on compar…
Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs
Daniel R. Zerbino, Tracy Ballinger, Benedict Paten +2
The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are r…
A Unifying Model of Genome Evolution Under Parsimony
Benedict Paten, Daniel R. Zerbino, Glenn Hickey +1
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutio…