RL
Ruibang Luo
bioinformaticsSoftwareHigh-Throughput Nucleotide SequencingGenomicsGenome, Humanq-bio.GNAlgorithmsDeep LearningNanoporesSequence Analysis, DNA
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, Kunihiko Sadakane, Tak-Wah Lam
1 version
W_26xzgw86·v1published
Preprints & journals
125 papers in the corpus · 2009–2026Telomere-to-telomere CHM13 reference reveals missing truth variants and improves deep learning-based variant calling in long-read sequencing data.42845716 · Zheng, Zhenxian, He, Minggao, Yu, Xian et al.2026 · 0 citationsQuantitative biology (Beijing, China). 2026;14(4):e70051
Leveraging ONT move table values for signal aware variant calling.42635225 · Yu, Xian, Zheng, Zhenxian, Chen, Lei et al.2026 · 2 citationsBioinformatics (Oxford, England). 2026;42(Suppl 2)
xDecoder unlocks the potential of genomic foundation models for few-shot personal gene expression prediction.42521815 · Li, Shumin, Luo, Ruibang, Huang, Yuanhua2026 · 0 citationsMolecular systems biology. 2026
Spatial omics in the AI era: Technologies, algorithmic ecosystems, biological applications, and large model perspectives.42491402 · Wang, Haoxiu, Yang, Xinwang, Wang, Siheng et al.2026 · 0 citationsiMeta. 2026;5(3):e70146
ClairS: 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
HOPE: Interpretable Histology Analysis with Spatial Omics-Derived Signatures for Precision Oncology10.64898/2026.06.03.729847v1 · Wang, T., Bieniosek, M., Krpicak, T. J. et al.2026 · 0 citationsbioRxiv
A complete human pancreatic cancer genome.42146349 · Wagner, Justin, Keskus, Ayse G, Oshima, Keisuke K et al.2026 · 4 citationsbioRxiv : the preprint server for biology. 2026
Accelerated long-read variant calling with Clair3 for whole-genome sequencing.41967838 · Zheng, Zhenxian, He, Minggao, Yu, Xian et al.2026 · 3 citationsBioinformatics (Oxford, England). 2026;42(5)
Gungnir codec enabling high error-tolerance and low-redundancy DNA storage through substantial computing power.41932957 · Zhang, Jingcheng, Chen, Lei, Sun, Jinlin et al.2026 · 1 citationNature communications. 2026;17(1)
EPInformer: scalable and integrative prediction of gene expression from promoter-enhancer sequences with multimodal epigenomic profiles.41832145 · Lin, Jiecong, Li, Zhijian, Zhao, Yajie et al.2026 · 4 citationsNature communications. 2026;17(1)
DECODE: deep learning-based common deconvolution framework for various omics data.41772096 · Zhao, Tianyi, Liu, Renjie, Sun, Yuzhi et al.2026 · 12 citationsNature methods. 2026;23(3):596-608
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)
Correction to "Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids".41709733 · Xue, Yan, Su, Junhao, Chao, Yiming et al.2026 · 0 citationsAdvanced science (Weinheim, Baden-Wurttemberg, Germany). 2026;13(22):e74435
Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.41560697 · Xue, Yan, Su, Junhao, Chao, Yiming et al.2026 · 2 citationsAdvanced science (Weinheim, Baden-Wurttemberg, Germany). 2026;13(17):e18084
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
Modeling patient tissues at molecular resolution with Eva10.64898/2025.12.10.693553v2 · Liu, Y., Sharma, R., Bieniosek, M. et al.2025 · 1 citationbioRxiv
LongPhase-S: purity estimation and variant recalibration with somatic haplotying for long-read sequencing10.1101/2025.11.20.689492v1 · Ho, M.-E., Zheng, Z., Luo, R. et al.2025 · 2 citationsbioRxiv
Clair-Mosaic: A deep-learning method for long-read mosaic small variant calling10.1101/2025.10.31.685831v1 · Chen, L., Zheng, Z., He, M. et al.2025 · 1 citationbioRxiv
ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling.41173866 · Chen, Lei, Zheng, Zhenxian, Su, Junhao et al.2025 · 21 citationsNature communications. 2025;16(1):9630
Author Correction: cuteFC: regenotyping structural variants through an accurate and efficient force-calling method.40954496 · Jiang, Tao, Cao, Shuqi, Liu, Yadong et al.2025 · 0 citationsGenome biology. 2025;26(1):280
Real-time raw signal genomic analysis using fully integrated memristor hardware.40940455 · He, Peiyi, Wang, Shengbo, Mao, Ruibin et al.2025 · 2 citationsNature computational science. 2025;5(10):940-951
Toward owner governance in genomic data privacy with Governome.40930087 · Zhang, Jingcheng, Zhou, Yekai, Ren, Yingxuan et al.2025 · 2 citationsCell reports methods. 2025;5(9):101171
Guess till correct: Gungnir codec enabling high error-tolerance and low-redundancy DNA storage through substantial computing power10.1101/2025.08.29.673174v1 · Zhang, J., Chen, L., Sun, J. et al.2025 · 0 citationsbioRxiv
Optimizing long term disease prevention with reinforcement learning: a framework for precision lipid control.40866452 · Zhou, Yekai, Luo, Ruibang, Blais, Joseph Edgar et al.2025 · 5 citationsNPJ digital medicine. 2025;8(1):553
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
OmicsNavigator: An auditable scientific partner for scalable hypothesis validation in spatial omics10.1101/2025.07.21.665821v2 · Li, Y., Vakharia, N., Liang, W. et al.2025 · 5 citationsbioRxiv
Assessing large-scale genomic language models in predicting personal gene expression: promises and limitations10.1101/2025.07.09.664024v1 · Li, S., Luo, R., Huang, Y.2025 · 1 citationbioRxiv
Author Correction: Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D.40295772 · Chen, Ying, Lin, Zhuo-Bin, Wang, Shao-Kai et al.2025 · 0 citationsNature structural & molecular biology. 2025;32(7):1318
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)
cuteFC: regenotyping structural variants through an accurate and efficient force-calling method.40514699 · Jiang, Tao, Cao, Shuqi, Liu, Yadong et al.2025 · 29 citationsGenome biology. 2025;26(1):166
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
Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D.40038455 · Chen, Ying, Lin, Zhuo-Bin, Wang, Shao-Kai et al.2025 · 4 citationsNature structural & molecular biology. 2025;32(7):1305-1317
Observational, causal relationship and shared genetic basis between cholelithiasis and gastroesophageal reflux disease: evidence from a cohort study and comprehensive genetic analysis.40139907 · Lyu, Yanlin, Tong, Shuangshuang, Huang, Wentao et al.2025 · 0 citationsGigaScience. 2025;14
Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data.39803537 · Zheng, Zhenxian, Yu, Xian, Chen, Lei et al.2025 · 25 citationsbioRxiv : the preprint server for biology. 2025
Unraveling the genetic susceptibility of irritable bowel syndrome: integrative genome-wide analyses in 845 492 individuals: a diagnostic study.39166955 · Huang, Wentao, Zhang, Lijun, Ma, Yuying et al.2025 · 9 citationsInternational journal of surgery (London, England). 2025;111(1):210-220
Optimizing long-term prevention of cardiovascular disease with reinforcement learning10.1101/2024.12.09.24318697v1 · Zhou, Y., Luo, R., Blais, J. E. et al.2024 · 0 citationsmedRxiv
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)
Sleep patterns, genetic susceptibility, and digestive diseases: a large-scale longitudinal cohort study.38781035 · Ma, Yuying, Yu, Shiyi, Li, Qinming et al.2024 · 24 citationsInternational journal of surgery (London, England). 2024;110(9):5471-5482
SARS-CoV-2 variants divergently infect and damage cardiomyocytes in vitro and in vivo.39095802 · Mok, Bobo Wing-Yee, Kwok, Maxwell, Li, Hung Sing et al.2024 · 9 citationsCell & bioscience. 2024;14(1):101
EPInformer: a scalable deep learning framework for gene expression prediction by integrating promoter-enhancer sequences with multimodal epigenomic data.39131276 · Lin, Jiecong, Luo, Ruibang, Pinello, Luca2026 · 13 citationsbioRxiv : the preprint server for biology. 2024
Towards a new standard in genomic data privacy: a realization of owner-governance10.1101/2024.07.23.604393v1 · Zhang, J., Ren, Y., Au, M. H. et al.2024 · 0 citationsbioRxiv
CellContrast: Reconstructing spatial relationships in single-cell RNA sequencing data via deep contrastive learning.39233694 · Li, Shumin, Ma, Jiajun, Zhao, Tianyi et al.2026 · 13 citationsPatterns (New York, N.Y.). 2024;5(8):101022
PET/CT deep learning prognosis for treatment decision support in esophageal squamous cell carcinoma.38913225 · Song, Jiangdian, Zhang, Jie, Liu, Guichao et al.2024 · 5 citationsInsights into imaging. 2024;15(1):161
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
Unveiling promising drug targets for autism spectrum disorder: insights from genetics, transcriptomics, and proteomics.39038939 · Jiang, Rui, Huang, Wentao, Qiu, Xinqi et al.2024 · 8 citationsBriefings in bioinformatics. 2024;25(4)
ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences.38725076 · Pei, Yao, Shum, Marcus Ho-Hin, Liao, Yunshi et al.2024 · 57 citationsMicrobiome. 2024;12(1):84
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
Investigating shared genetic architecture between inflammatory bowel diseases and primary biliary cholangitis.38721342 · Huang, Wentao, Jiang, Rui, Li, Sitao et al.2024 · 17 citationsJHEP reports : innovation in hepatology. 2024;6(6):101037
Adverse clinical outcomes and immunosuppressive microenvironment of RHO-GTPase activation pattern in hepatocellular carcinoma.38297333 · Yang, Qi, Zhuo, Zewei, Qiu, Xinqi et al.2024 · 10 citationsJournal of translational medicine. 2024;22(1):122
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
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