4 papers
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…
NAPX: A Polynomial Time Approximation Scheme for the Noah's Ark Problem
G. Hickey, P. Carmi, A. Maheshwari +1
The Noah's Ark Problem (NAP) is an NP-Hard optimization problem with relevance to ecological conservation management. It asks to maximize the phylogenetic diversity (PD) of a set o…