A mathematical concept known as a de Bruijn graph turns the formidable challenge of
assembling a contiguous genome from billions of short sequencing reads into a tractable …

Limitations of genome sequencing techniques have led to dozens of assembly algorithms,
none of which is perfect. A number of methods for comparing assemblers have been …

… A vertex w precedes (follows) vertex v in a graph G if there exists an edge from w to v (from
v to w) in G. indegree(v) (outdegree(v)) is the the number of vertices preceding (following) v. A …

… Let A SDP be the set of anchors of length K SDP that are exact matches between the read
and the genome interval g s ,…,g f . Sparse dynamic programming finds the largest subset of …

… Given a weighted graph G and a positive integer t, we define G t as the graph obtained
from G by breaking all edges longer than t. To break the de Bruijn graph into subnetworks, we …

The genome organizations of eight phylogenetically distinct species from five mammalian
orders were compared in order to address fundamental questions relating to mammalian …

… Let G be a directed acyclic graph (DAG) with vertex set V and edge set E. For vertices v and
w in G, we define v ≺ w if there exists a directed path from v to w in G. A mapping f : V → V,E …

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled,
mapped, and annotated with a comparative approach that involved cross-reference to …

Although analysis of genome rearrangements was pioneered by Dobzhansky and Sturtevant
65 years ago, we still know very little about the rearrangement events that produced the …

… G b N b = 9.6 Mb, where G b = 2,707 Mb is the overall length of syntenic blocks. The bin size
is 2.5 Mb. (Center) The same histogram superimposed with the 190 hidden synteny blocks …