TL
Tak-Wah Lam
AlgorithmsbioinformaticsSoftwareHigh-Throughput Nucleotide SequencingNanoporesq-bio.GNcs.DSGenomicsComputational BiologyGenetic Variation
On Valency
published · living versionsW_yhpv267m·v1 · currentpublished
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
with Dinghua Li, Chi-Man Liu, Ruibang Luo, Kunihiko Sadakane
1 version
W_26xzgw86·v1published
Preprints & journals
89 papers in the corpus · 2003–2026ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.42387002 · Zheng, Zhenxian, Chen, Lei, Su, Junhao et al.2026 · 6 citationsNature methods. 2026;23(8):1507-1520
ASDA: Automated Skill Distillation and Adaptation for Financial Reasoning2603.16112v2 · Tik Yu Yim, Wenting Tan, Sum Yee Chan et al.2026 · 0 citationsarXiv
Correction: Protein domain-specific genotype-phenotype correlation study of neurofibromatosis type 1.41741723 · Ou, Min, Ho, Strphanie Kl, Luk, Ho-Ming et al.2026 · 0 citationsScientific reports. 2026;16(1)
Protein domain-specific genotype-phenotype correlation study of neurofibromatosis type 1.41398366 · Ou, Min, Ho, Strphanie Kl, Luk, Ho-Ming et al.2026 · 3 citationsScientific reports. 2025;16(1):2709
Primary prevention cardiovascular disease risk prediction model for contemporary Chinese (1°P-CARDIAC): Model derivation and validation using a hybrid statistical and machine-learning approach.40720453 · Zhou, Yekai, Lin, Celia Jiaxi, Yu, Qiuyan et al.2025 · 6 citationsPloS one. 2025;20(7):e0322419
AutoPM3: enhancing variant interpretation via LLM-driven PM3 evidence extraction from scientific literature.40586923 · Li, Shumin, Wang, Yiding, Liu, Chi-Man et al.2025 · 8 citationsBioinformatics (Oxford, England). 2025;41(7)
Survival estimate models of cancer patients with spinal metastases: big data analytics to aid daily clinical practice (abridged secondary publication).40605570 · Kwan, K Y H, Cheung, C L, Cheung, K M C et al.2025 · 0 citationsHong Kong medical journal = Xianggang yi xue za zhi. 2025;31 Suppl 3(3):12-13
Repun: an accurate small variant representation unification method for multiple sequencing platforms.39584701 · Zheng, Zhenxian, Ren, Yingxuan, Chen, Lei et al.2024 · 5 citationsBriefings in bioinformatics. 2024;26(1)
Development and validation of a tool to stratify the treatment effect of low-dose aspirin in patients with cardiovascular disease: VISTA (Vascular Intervention Stratification Tool for Aspirin)10.1101/2024.06.07.24308636v1 · Zhou, Y., Blais, J. E., Chan, E. W. et al.2024 · 3 citationsmedRxiv
Development and validation of risk prediction model for recurrent cardiovascular events among Chinese: the Personalized CARdiovascular DIsease risk Assessment for Chinese model.38774379 · Zhou, Yekai, Lin, Celia Jiaxi, Yu, Qiuyan et al.2024 · 12 citationsEuropean heart journal. Digital health. 2024;5(3):363-370
ClusterV-Web: a user-friendly tool for profiling HIV quasispecies and generating drug resistance reports from nanopore long-read data.38282975 · Su, Junhao, Li, Shumin, Zheng, Zhenxian et al.2024 · 4 citationsBioinformatics advances. 2024;4(1):vbae006
Development and validation of risk prediction model for recurrent cardiovascular events among Chinese: P-CARDIAC model10.1101/2023.10.17.23297127v1 · Zhou, Y., Lin, J., Yu, Q. et al.2023 · 0 citationsmedRxiv
Integrated modeling framework reveals co-regulation of transcription factors, miRNAs and lncRNAs on cardiac developmental dynamics.37705079 · Li, Shumin, Yan, Bin, Wu, Binbin et al.2023 · 9 citationsStem cell research & therapy. 2023;14(1):247
ClairS: a deep-learning method for long-read somatic small variant calling10.1101/2023.08.17.553778v1 · Zheng, Z., Su, J., Chen, L. et al.2023 · 25 citationsbioRxiv
Genome instability-derived genes as a novel prognostic signature for lung adenocarcinoma.37655157 · Zhang, Xu, Lam, Tak-Wah, Ting, Hing-Fung2023 · 4 citationsFrontiers in cell and developmental biology. 2023;11:1224069
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP.37537536 · Yu, Huijing, Zheng, Zhenxian, Su, Junhao et al.2023 · 5 citationsBMC bioinformatics. 2023;24(1):308
Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling.37002338 · Su, Junhao, Lui, Wui Wang, Lee, YanLam et al.2023 · 28 citationsScientific reports. 2023;13(1):5237
Ultra-low-coverage genome-wide association study-insights into gestational age using 17,844 embryo samples with preimplantation genetic testing.36788602 · Li, Shumin, Yan, Bin, Li, Thomas K T et al.2023 · 13 citationsGenome medicine. 2023;15(1):10
MLProbs: A Data-Centric Pipeline for Better Multiple Sequence Alignment.35120007 · Kuang, Mengmeng, Zhang, Yong, Lam, Tak-Wah et al.2023 · 2 citationsIEEE/ACM transactions on computational biology and bioinformatics. 2023;20(1):524-533
Assembly-free discovery of human novel sequences using long reads.36308393 · Li, Qiuhui, Yan, Bin, Lam, Tak-Wah et al.2022 · 5 citationsDNA research : an international journal for rapid publication of reports on genes and genomes. 2022;29(6)
Symphonizing pileup and full-alignment for deep learning-based long-read variant calling.38177392 · Zheng, Zhenxian, Li, Shumin, Su, Junhao et al.2024 · 409 citationsNature computational science. 2022;2(12):797-803
Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing.36344913 · Zhou, Yekai, Leung, Amy Wing-Sze, Ahmed, Syed Shakeel et al.2022 · 15 citationsBMC bioinformatics. 2022;23(1):465
Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks.35849103 · Su, Junhao, Zheng, Zhenxian, Ahmed, Syed Shakeel et al.2022 · 36 citationsBriefings in bioinformatics. 2022;23(5)
Detecting structural variations with precise breakpoints using low-depth WGS data from a single oxford nanopore MinION flowcell.35296758 · Leung, Henry C M, Yu, Huijing, Zhang, Yifan et al.2022 · 11 citationsScientific reports. 2022;12(1):4519
ECNano: A cost-effective workflow for target enrichment sequencing and accurate variant calling on 4800 clinically significant genes using a single MinION flowcell.35246132 · Leung, Amy Wing-Sze, Leung, Henry Chi-Ming, Wong, Chak-Lim et al.2022 · 10 citationsBMC medical genomics. 2022;15(1):43
HKG: an open genetic variant database of 205 Hong Kong cantonese exomes.35156024 · Ou, Min, Leung, Henry Chi-Ming, Leung, Amy Wing-Sze et al.2024 · 4 citationsNAR genomics and bioinformatics. 2022;4(1):lqac005
Building a Chinese pan-genome of 486 individuals.34462542 · Li, Qiuhui, Tian, Shilin, Yan, Bin et al.2021 · 25 citationsCommunications biology. 2021;4(1):1016
RENET2: high-performance full-text gene-disease relation extraction with iterative training data expansion.34235433 · Su, Junhao, Wu, Ye, Ting, Hing-Fung et al.2021 · 22 citationsNAR genomics and bioinformatics. 2021;3(3):lqab062
ECNano: A Cost-Effective Workflow for Target Enrichment Sequencing and Accurate Variant Calling on 4,800 Clinically Significant Genes Using a Single MinION Flowcell10.1101/2021.04.05.438455v1 · Leung, A. W.-S., Leung, H. C.-M., Wong, C.-L. et al.2021 · 0 citationsbioRxiv
MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data.33349238 · Leung, Chi-Ming, Li, Dinghua, Xin, Yan et al.2021 · 15 citationsBMC genomics. 2020;21(Suppl 6):500
Tracking cytosine depletion in SARS-CoV-210.1101/2020.10.26.354787v1 · Luo, R., Wong, Y.-S., Lam, T.-W.2020 · 2 citationsbioRxiv
Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis.32948225 · Chan, Wai Sing, Au, Chun Hang, Chung, Yvonne et al.2021 · 28 citationsBMC research notes. 2020;13(1):444
Identification of Cooperative Gene Regulation Among Transcription Factors, LncRNAs, and MicroRNAs in Diabetic Nephropathy Progression.33088282 · Chen, Ling, Wu, Binbin, Wang, Shaobin et al.2020 · 12 citationsFrontiers in genetics. 2020;11:1008
CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning.32422594 · Zhang, Yifan, Liu, Chi-Man, Leung, Henry C M et al.2021 · 8 citationsiScience. 2020;23(5):101128
Potential utility of metagenomic sequencing for improving etiologic diagnosis of infective endocarditis.31691592 · Chan, Wai-Sing, Au, Chun-Hang, Leung, Henry Chi-Ming et al.2020 · 17 citationsFuture cardiology. 2019;15(6):411-424
A multi-task convolutional deep neural network for variant calling in single molecule sequencing.30824707 · Luo, Ruibang, Sedlazeck, Fritz J, Lam, Tak-Wah et al.2019 · 186 citationsNature communications. 2019;10(1):998
Draft Genome Sequence of Helicobacter cinaedi, Compiled by Direct Whole-Genome Sequencing of a Blood Culture-Positive Isolate in Hong Kong.30533780 · Chan, Wai-Sing, Au, Chun-Hang, Leung, Henry Chi-Ming et al.2020 · 2 citationsMicrobiology resource announcements. 2018;7(18)
AC-DIAMOND v1: accelerating large-scale DNA-protein alignment.29771282 · Mai, Huijun, Zhang, Yifan, Li, Dinghua et al.2019 · 17 citationsBioinformatics (Oxford, England). 2018;34(21):3744-3746
Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants10.1101/311985v2 · Luo, R., Lam, T.-W., Schatz, M.2018 · 7 citationsbioRxiv
Transcriptome Analysis of Acute Phase Liver Graft Injury in Liver Transplantation.29642405 · Lee, Nikki P, Wu, Haiyang, Ng, Kevin T P et al.2020 · 13 citationsBiomedicines. 2018;6(2)
MegaGTA: a sensitive and accurate metagenomic gene-targeted assembler using iterative de Bruijn graphs.29072142 · Li, Dinghua, Huang, Yukun, Leung, Chi-Ming et al.2018 · 17 citationsBMC bioinformatics. 2017;18(Suppl 12):408
Serine peptidase inhibitor Kazal type 1 (SPINK1) as novel downstream effector of the cadherin-17/β-catenin axis in hepatocellular carcinoma.28631187 · Shek, Felix H, Luo, Ruibang, Lam, Brian Y H et al.2018 · 13 citationsCellular oncology (Dordrecht, Netherlands). 2017;40(5):443-456
A simple and economical method for improving whole genome alignment.28589863 · Mai, Huijun, Lam, Tak-Wah, Ting, Hing-Fung2018 · 5 citationsBMC genomics. 2017;18(Suppl 4):362
PnpProbs: a better multiple sequence alignment tool by better handling of guide trees.27585754 · Ye, Yongtao, Lam, Tak-Wah, Ting, Hing-Fung2017 · 2 citationsBMC bioinformatics. 2016;17 Suppl 8:285
BASE: a practical de novo assembler for large genomes using long NGS reads.27586129 · Liu, Binghang, Liu, Chi-Man, Li, Dinghua et al.2017 · 11 citationsBMC genomics. 2016;17 Suppl 5:499
MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.27012178 · Li, Dinghua, Luo, Ruibang, Liu, Chi-Man et al.2018 · 2,095 citationsMethods (San Diego, Calif.). 2016;102:3-11
database.bio: a web application for interpreting human variations.26315902 · Ou, Min, Ma, Ricky, Cheung, Jeanno et al.2016 · 9 citationsBioinformatics (Oxford, England). 2015;31(24):4035-7
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.26154165 · González-Beltrán, Alejandra, Li, Peter, Zhao, Jun et al.2016 · 41 citationsPloS one. 2015;10(7):e0127612
Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.26161257 · Luo, Ruibang, Liu, Binghang, Xie, Yinlong et al.2016 · 269 citationsGigaScience. 2015;4:30
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.25609793 · Li, Dinghua, Liu, Chi-Man, Luo, Ruibang et al.2015 · 9,932 citationsBioinformatics (Oxford, England). 2015;31(10):1674-6
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