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Samuel H. Kim

dblp:185/8538 · DBLP profile ↗
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1ranked-venue papers
0as first author
0since 2021 · last 2016
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Theoretical computer science
1 paper
Graph algorithms and graph theory · 100%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › sequence analysis › sequence assembly
genome assembly
0.212016
Information-optimal genome assembly via sparse read-overlap graphs · Bioinform. 2016
Bioinformatics and computational biology › sequence analysis › sequence assembly › genome assembly › de novo assembly
overlap-graph assembly
0.212016
Information-optimal genome assembly via sparse read-overlap graphs · Bioinform. 2016
Graph algorithms and graph theory › graph traversal
eulerian path
0.112016
Information-optimal genome assembly via sparse read-overlap graphs · Bioinform. 2016
Graph algorithms and graph theory
graph algorithms
0.112016
Information-optimal genome assembly via sparse read-overlap graphs · Bioinform. 2016

Methods — techniques the papers use, named apart from their topics

not-so-greedy algorithm · 0.5information feasibility analysis · 0.5
YearPublicationVenuePosition
2016 Information-optimal genome assembly via sparse read-overlap graphs
abstract
MOTIVATION: In the context of third-generation long-read sequencing technologies, read-overlap-based approaches are expected to play a central role in the assembly step. A fundamental challenge in assembling from a read-overlap graph is that the true sequence corresponds to a Hamiltonian path on the graph, and, under most formulations, the assembly problem becomes NP-hard, restricting practical approaches to heuristics. In this work, we avoid this seemingly fundamental barrier by first setting the computational complexity issue aside, and seeking an algorithm that targets information limits In particular, we consider a basic feasibility question: when does the set of reads contain enough information to allow unambiguous reconstruction of the true sequence? RESULTS: Based on insights from this information feasibility question, we present an algorithm-the Not-So-Greedy algorithm-to construct a sparse read-overlap graph. Unlike most other assembly algorithms, Not-So-Greedy comes with a performance guarantee: whenever information feasibility conditions are satisfied, the algorithm reduces the assembly problem to an Eulerian path problem on the resulting graph, and can thus be solved in linear time. In practice, this theoretical guarantee translates into assemblies of higher quality. Evaluations on both simulated reads from real genomes and a PacBio Escherichia coli K12 dataset demonstrate that Not-So-Greedy compares favorably with standard string graph approaches in terms of accuracy of the resulting read-overlap graph and contig N50. AVAILABILITY: Available at github.com/samhykim/nsg CONTACT: [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Ilan Shomorony, Samuel H. Kim, Thomas A. Courtade, David Tse
Bioinform.2