742 citations · 1.5k across the 10 of their papers we have counts for
6 papers · 1 filter
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…
Comparative Assembly Hubs: Web Accessible Browsers for Comparative Genomics
Ngan Nguyen, Glenn Hickey, Brian J. Raney +6
We introduce a pipeline to easily generate collections of web accessible UCSC genome browsers interrelated by an alignment. Using the alignment, all annotations and the alignment i…
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…
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov +88
Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished g…