Demo Data from EDBT 2026 / reviewers in the wild / expert
Audrey M. V. Ah-Fong
dblp:222/4622
· DBLP profile ↗
1ranked-venue papers
0as first author
0since 2021 · last 2018
—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% |
Topics — the 2 heaviest of 2, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › sequence analysis › sequence assembly
genome assembly |
0.3 | 1 | 2018 | Novo&Stitch: accurate reconciliation of genome assemblies via optical maps · Bioinform. 2018 |
Bioinformatics and computational biology › sequence analysis › sequence assembly › genome assembly
optical map alignment |
0.1 | 1 | 2018 | Novo&Stitch: accurate reconciliation of genome assemblies via optical maps · Bioinform. 2018 |
Methods — techniques the papers use, named apart from their topics
optical map alignment · 0.3
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2018 | Novo&Stitch: accurate reconciliation of genome assemblies via optical mapsabstractMotivation: De novo genome assembly is a challenging computational problem due to the high repetitive content of eukaryotic genomes and the imperfections of sequencing technologies (i.e. sequencing errors, uneven sequencing coverage and chimeric reads). Several assembly tools are currently available, each of which has strengths and weaknesses in dealing with the trade-off between maximizing contiguity and minimizing assembly errors (e.g. mis-joins). To obtain the best possible assembly, it is common practice to generate multiple assemblies from several assemblers and/or parameter settings and try to identify the highest quality assembly. Unfortunately, often there is no assembly that both maximizes contiguity and minimizes assembly errors, so one has to compromise one for the other. Results: The concept of assembly reconciliation has been proposed as a way to obtain a higher quality assembly by merging or reconciling all the available assemblies. While several reconciliation methods have been introduced in the literature, we have shown in one of our recent papers that none of them can consistently produce assemblies that are better than the assemblies provided in input. Here we introduce Novo&Stitch, a novel method that takes advantage of optical maps to accurately carry out assembly reconciliation (assuming that the assembled contigs are sufficiently long to be reliably aligned to the optical maps, e.g. 50 Kbp or longer). Experimental results demonstrate that Novo&Stitch can double the contiguity (N50) of the input assemblies without introducing mis-joins or reducing genome completeness. Availability and implementation: Novo&Stitch can be obtained from https://github.com/ucrbioinfo/Novo_Stitch. Weihua Pan, Steve Wanamaker, Audrey M. V. Ah-Fong, Howard S. Judelson, Stefano Lonardi |
Bioinform. | 3 |