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Yuk Kei Wan

dblp:345/8202 · DBLP profile ↗
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2ranked-venue papers
0as first author
2since 2021 · last 2025
0000-0003-1774-261XORCID · corroborated

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

Applied, interdisciplinary, general and emerging computing · 2 · 2 since 2021

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
2 papers
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › sequence analysis
nanopore sequencing
0.912025
Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis · Bioinform. 2025
Bioinformatics and computational biology
gene regulation
0.712023
Translation Rate Prediction and Regulatory Motif Discovery with Multi-task Learning · RECOMB 2023
Bioinformatics and computational biology › sequence analysis › motif discovery
regulatory motif discovery
0.712023
Translation Rate Prediction and Regulatory Motif Discovery with Multi-task Learning · RECOMB 2023

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

move table analysis · 0.9multi-task learning · 0.7
YearPublicationVenuePosition
2025 Leveraging basecaller's move table to generate a lightweight k-mer model for nanopore sequencing analysis
abstract
MOTIVATION: Nanopore sequencing by Oxford Nanopore Technologies (ONT) enables direct analysis of DNA and RNA by capturing raw electrical signals. Different nanopore chemistries have varied k-mer lengths, current levels, and standard deviations, which are stored in "k-mer models." In cases where official models are lacking or unsuitable for specific sequencing conditions, tailored k-mer models are crucial to ensure precise signal-to-sequence alignment, analysis and interpretation. The process of transforming raw signal data into nucleotide sequences, known as basecalling, is a fundamental step in nanopore sequencing. RESULTS: In this study, we leverage the move table produced by ONT's basecalling software to create a lightweight de novo k-mer model for RNA004 chemistry. We demonstrate the validity of our custom k-mer model by using it to guide signal-to-sequence alignment analysis, achieving high alignment rates (97.48%) compared to larger default models. Additionally, our 5-mer model exhibits similar performance as the default 9-mer models another analysis, such as detection of m6A RNA modifications. We provide our method, termed Poregen, as a generalizable approach for creation of custom, de novo k-mer models for nanopore signal data analysis. AVAILABILITY AND IMPLEMENTATION: Poregen is an open source package under an MIT license: https://github.com/hiruna72/poregen.
Hiruna Samarakoon, Yuk Kei Wan, Sri Parameswaran, Jonathan Göke, Hasindu Gamaarachchi, Ira W. Deveson
Bioinform.2
2023 Translation Rate Prediction and Regulatory Motif Discovery with Multi-task Learning
Weizhong Zheng, John H. C. Fong, Yuk Kei Wan, Athena H. Y. Chu, Yuanhua Huang, Alan S. L. Wong, Joshua W. K. Ho
RECOMB3