Research output per year
Research output per year
Research output
- 1 - 50 out of 103 results
Search results
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2025
GOPhage: protein function annotation for bacteriophages by integrating the genomic context
Guan, J., Ji, Y., Peng, C., Zou, W., Tang, X., Shang, J. & Sun, Y., Jan 2025, In: Briefings in Bioinformatics. 26, 1, bbaf014.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile17 Downloads (CityUHK Scholars) -
MOSTPLAS: A Self-correction Multi-label Learning Model for Plasmid Host Range Prediction
Zou, W., Ji, Y., Guan, J. & Sun, Y., Mar 2025, In: Bioinformatics. 41, 3, btaf075.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile3 Downloads (CityUHK Scholars) -
RTTAP: 基於短讀長的全感染組分類分析流程
Translated title of the contribution :RTTAP: A Read-based Total-infectome Taxonomic Analysis Pipeline Research output: Patents, Agreements and Assignments › RGC 51 - Patents (CityUHK)
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2024
Accelerating de novo SINE annotation in plant and animal genomes
Liao, H., Sun, Y. & Ou, S., 2024, In: Mobile DNA. 15, 24.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile7 Downloads (CityUHK Scholars) -
Accurate and efficient protein embedding using multi-teacher distillation learning
Shang, J., Peng, C., Ji, Y., Guan, J., Cai, D., Tang, X. & Sun, Y., Sept 2024, In: Bioinformatics. 40, 9, btae567.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile1 Citation (Scopus)8 Downloads (CityUHK Scholars) -
Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities
Charon, J., Olendraite, I., Forgia, M., Chong, L. C., Hillary, L. S., Roux, S., Kupczok, A., Debat, H., Sakaguchi, S., Tahzima, R., Nakagawa, S., Babaian, A., Abroi, A., Bejerman, N., Ben Mansour, K., Brown, K., Butkovic, A., Cervera, A., Charriat, F. & Chen, G. & 27 others, , 2024, In: Frontiers in Virology. 4, 1371958.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile4 Citations (Scopus)22 Downloads (CityUHK Scholars) -
Identifying ARG-carrying bacteriophages in a lake replenished by reclaimed water using deep learning techniques
Wang, D., Shang, J., Lin, H., Liang, J., Wang, C., Sun, Y., Bai, Y. & Qu, J., 1 Jan 2024, In: Water Research. 248, 120859.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
11 Citations (Scopus) -
PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure
Ji, Y., Shang, J., Guan, J., Zou, W., Liao, H., Tang, X. & Sun, Y., 2024, In: GigaScience. 13, 17 p., giae104.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile11 Downloads (CityUHK Scholars) -
Quantum Modeling for Simulating Biological Stochastic Processes
Ho, L. Y. L., PAN, L., MENG, F., Ho, K. T. M., LIU, F., Wu, M.-T., Lei, P., Bhachu, G., Dahlsten, O., SUN, Y., Lee, P.-H. & TAN, G. Y. A., 2024, (Presented).Research output: Conference Papers › Poster › peer-review
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Quantum modeling simulates nutrient effect of bioplastic polyhydroxyalkanoate (PHA) production in Pseudomonas putida
Ho, L. Y. L., Pan, L., Meng, F., Ho, K. T. M., Liu, F., Wu, M.-T., Lei, H. I., Bhachu, G., Wang, X., Dahlsten, O., Sun, Y., Lee, P.-H. & Tan, G. Y. A., 2024, In: Scientific Reports. 14, 18255.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile1 Citation (Scopus)30 Downloads (CityUHK Scholars) -
RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes
Chen, G., Jiang, J. & Sun, Y., 2024, In: GigaScience. 13, giae059.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile42 Downloads (CityUHK Scholars) -
SegVir: Reconstruction of Complete Segmented RNA Viral Genomes from Metatranscriptomes
Tang, X., Shang, J., Chen, G., Chan, K. H. K., Shi, M. & Sun, Y., Aug 2024, In: Molecular Biology and Evolution. 41, 8, msae171.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile1 Citation (Scopus)12 Downloads (CityUHK Scholars) -
The clinical outcome of COVID-19 is strongly associated with microbiome dynamics in the upper respiratory tract
Xie, L. (Co-first Author), Luo, G. (Co-first Author), Yang, Z., Wu, W.-C., Chen, J., Ren, Y., Zeng, Z., Ye, G., Pan, Y., Zhao, W.-J., Chen, Y.-Q., Hou, W., Sun, Y., Guo, D., Yang, Z., Li, J., Holmes, E. C., Li, Y., Chen, L. & Shi, M., Mar 2024, In: Journal of Infection. 88, 3, 106118.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile4 Citations (Scopus)24 Downloads (CityUHK Scholars) -
Towards more accurate microbial source tracking via non-negative matrix factorization (NMF)
Huang, Z. (Co-first Author), Cai, D. (Co-first Author) & Sun, Y., Jul 2024, ISMB 2024 Proceedings. Oxford University Press, p. i68-i78 (Bioinformatics; vol. 40, no. Supplement_1).Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review
Open AccessFile2 Citations (Scopus)34 Downloads (CityUHK Scholars) -
Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review
Yu, R., Huang, Z., Lam, T. Y. C. & Sun, Y., Jul 2024, In: Briefings in Bioinformatics. 25, 4, bbae292.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile2 Citations (Scopus)24 Downloads (CityUHK Scholars) -
ViraLM: empowering virus discovery through the genome foundation model
Peng, C. (Co-first Author), Shang, J. (Co-first Author), Guan, J., Wang, D. & Sun, Y., Dec 2024, In: Bioinformatics. 40, 12, btae704.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile3 Citations (Scopus)2 Downloads (CityUHK Scholars) -
VirID: Beyond Virus Discovery — An Integrated Platform for Comprehensive RNA Virus Characterization
Yang, Z. (Co-first Author), Shan, Y. (Co-first Author), Liu, X., Chen, G., Pan, Y., Gou, Q., Zou, J., Chang, Z., Zeng, Q., Yang, C., Kong, J., Sun, Y., Li, S., Zhang, X., Wu, W.-C., Li, C., Peng, H., Holmes, E. C., Guo, D. & Shi, M., Oct 2024, In: Molecular Biology and Evolution. 41, 10, msae202.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile16 Downloads (CityUHK Scholars) -
VirTAXA: Enhancing RNA virus taxonomic classification with remote homology search and tree-based validation
Zhu, Y., Chen, G. & Sun, Y., Oct 2024, In: Bioinformatics. 40, 10, btae575.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile17 Downloads (CityUHK Scholars) -
2023
AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data
Yu, R., Cai, D. & Sun, Y., Jan 2023, In: Bioinformatics. 39, 1, 8 p., btac827.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile3 Citations (Scopus)68 Downloads (CityUHK Scholars) -
Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients
Zhang, F., Gia, A., Chen, G., Gong, L., Behary, J., Hold, G. L., Zekry, A., Tang, X., Sun, Y., El-Omar, E. & Jiang, X.-T., Jan 2023, In: Viruses. 15, 1, 13 p.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile1 Citation (Scopus)54 Downloads (CityUHK Scholars) -
GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data
Liao, H., Shang, J. & Sun, Y., Dec 2023, In: Bioinformatics. 39, 12, btad747.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile2 Citations (Scopus)34 Downloads (CityUHK Scholars) -
Global prevalence of SARS-CoV-2 3CL protease mutations associated with nirmatrelvir or ensitrelvir resistance
Ip, J. D., Chu, A.W.-H., Chan, W.-M., Leung, R.C.-Y., Abdullah, S. M. U., Sun, Y. & To, K.K.-W., May 2023, In: eBioMedicine. 91, 104559.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile69 Citations (Scopus)59 Downloads (CityUHK Scholars) -
High-resolution strain-level microbiome composition analysis from short reads
Liao, H. (Co-first Author), Ji, Y. (Co-first Author) & Sun, Y., 2023, In: Microbiome. 11, 183.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile14 Citations (Scopus)39 Downloads (CityUHK Scholars) -
HMMPolish: a coding region polishing tool for TGS-sequenced RNA viruses
Yu, R., Abdullah, S. M. U. & Sun, Y., Sept 2023, In: Briefings in Bioinformatics. 24, 5, bbad264.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile1 Citation (Scopus)48 Downloads (CityUHK Scholars) -
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer
Ji, Y., Shang, J., Tang, X. & Sun, Y., May 2023, In: Bioinformatics. 39, 5, btad283.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile8 Citations (Scopus)82 Downloads (CityUHK Scholars) -
LncRNA-Top: Controlled Deep Learning Approaches for LncRNA Gene Regulatory Relationship Annotations across Different Platforms
Xie, W., Chen, X., Zheng, Z., Wang, F., Zhu, X., Lin, Q., Sun, Y. & Wong, K.-C., 17 Nov 2023, In: iScience. 26, 11, 108197.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile69 Downloads (CityUHK Scholars) -
PhaBOX: A web server for identifying and characterizing phage contigs in metagenomic data
Shang, J., Peng, C., Liao, H., Tang, X. & Sun, Y., 2023, In: Bioinformatics Advances. 3, 1, vbad101.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile42 Citations (Scopus)24 Downloads (CityUHK Scholars) -
PhaGenus: genus-level classification of bacteriophages using a Transformer model
Guan, J., Peng, C., Shang, J., Tang, X. & Sun, Y., Nov 2023, In: Briefings in Bioinformatics. 24, 6, bbad408.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
6 Citations (Scopus) -
PhaTYP: predicting the lifestyle for bacteriophages using BERT
Shang, J., Tang, X. & Sun, Y., Jan 2023, In: Briefings in Bioinformatics. 24, 1, bbac487.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile92 Citations (Scopus)83 Downloads (CityUHK Scholars) -
PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer
Shang, J., Peng, C., Tang, X. & Sun, Y., Jun 2023, ISMB/ECCB 2023 Proceedings. Oxford University Press, p. i30-i39 (Bioinformatics; vol. 39, no. Supplement_1).Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review
Open AccessFile7 Citations (Scopus)34 Downloads (CityUHK Scholars) -
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer
Tang, X., Shang, J., Ji, Y. & Sun, Y., 25 Aug 2023, In: Nucleic Acids Research. 51, 15, e83.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile30 Citations (Scopus)64 Downloads (CityUHK Scholars) -
Quantum Like System for Phenotypic Switch in the Context of Industrial Bioplastic Synthesis
Ho, L., Pan, L., Hui, S., Vicera, C., Wu, M.-T., Zhuang, H., Sun, Y., Lee, P.-H. & Tan, G. Y. A., 17 Jun 2023, (Presented).Research output: Conference Papers › RGC 33 - Other conference paper › peer-review
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VirBot: an RNA viral contig detector for metagenomic data
Chen, G., Tang, X., Shi, M. & Sun, Y., Mar 2023, In: Bioinformatics. 39, 3, btad093.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile11 Citations (Scopus)60 Downloads (CityUHK Scholars) -
Virus classification for viral genomic fragments using PhaGCN2
Jiang, J.-Z., Yuan, W.-G., Shang, J., Shi, Y.-H., Yang, L.-L., Liu, M., Zhu, P., Jin, T., Sun, Y. & Yuan, L.-H., Jan 2023, In: Briefings in Bioinformatics. 24, 1, bbac505.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
60 Citations (Scopus) -
2022
Accurate identification of bacteriophages from metagenomic data using Transformer
Shang, J., Tang, X., Guo, R. & Sun, Y., Jul 2022, In: Briefings in Bioinformatics. 23, 4, bbac258.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile32 Citations (Scopus)77 Downloads (CityUHK Scholars) -
AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes
Li, Y., Jiang, N. & Sun, Y., Feb 2022, In: Plant Physiology. 188, 2, p. 955-970Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile10 Citations (Scopus)70 Downloads (CityUHK Scholars) -
Artificial Intelligence in Meta-optics
Chen, M. K., Liu, X., Sun, Y. & Tsai, D. P., 12 Oct 2022, In: Chemical Reviews. 122, 19, p. 15356–15413 58 p.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile146 Citations (Scopus)177 Downloads (CityUHK Scholars) -
CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model
Shang, J. & Sun, Y., Sept 2022, In: Briefings in Bioinformatics. 23, 5, bbac182.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile55 Citations (Scopus)95 Downloads (CityUHK Scholars) -
Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.)
Cerbin, S., Ou, S., Li, Y., Sun, Y. & Jiang, N., Oct 2022, In: Plant Journal. 112, 1, p. 172-192Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile4 Citations (Scopus)38 Downloads (CityUHK Scholars) -
HaploDMF: viral Haplotype reconstruction from long reads via Deep Matrix Factorization
Cai, D., Shang, J. & Sun, Y., 15 Dec 2022, In: Bioinformatics. 38, 24, p. 5360–5367Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile6 Citations (Scopus)53 Downloads (CityUHK Scholars) -
Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework
Zhu, Y., Shang, J., Peng, C. & Sun, Y., 2022, In: Frontiers in Microbiology. 13, 1032186.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile64 Citations (Scopus)202 Downloads (CityUHK Scholars) -
RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data
Tang, X., Shang, J. & Sun, Y., Mar 2022, In: Briefings in Bioinformatics. 23, 2, bbac011.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile3 Citations (Scopus)66 Downloads (CityUHK Scholars) -
Reconstructing viral haplotypes using long reads
Cai, D. & Sun, Y., 15 Apr 2022, In: Bioinformatics. 38, 8, p. 2127–2134 8 p.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
8 Citations (Scopus) -
Seismic Hazard Determination Method And System
ZUKERMAN, M. (Inventor), WANG, Z. (Inventor), Wang, Gang (Inventor), WANG, Y. (Inventor), WANG, X. (Inventor), MORAN, W. (Inventor), WANG, Q. (Inventor) & SUN, Y. (Inventor), 15 Nov 2022, Patent No. US11,500,125, Priority No. 16/889,663Research output: Patents, Agreements and Assignments › RGC 51 - Patents (CityUHK)
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VirStrain: a strain identification tool for RNA viruses
Liao, H., Cai, D. & Sun, Y., 2022, In: Genome Biology. 23, 1, 38.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile9 Citations (Scopus)76 Downloads (CityUHK Scholars) -
2021
Bacteriophage classification for assembled contigs using Graph Convolutional Network
Shang, J., Jiang, J. & Sun, Y., Jul 2021, ISMB/ECCB 2021 Proceedings. Oxford University Press, p. i25-i33 9 p. (Bioinformatics; vol. 37, no. Suppl. 1).Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review
Open AccessFile77 Citations (Scopus)72 Downloads (CityUHK Scholars) -
Characterizing the Host Coral Proteome of Platygyra carnosa Using Suspension Trapping (S-Trap)
Ma, H., Liao, H., Dellisanti, W., Sun, Y., Chan, L. L. & Zhang, L., 5 Mar 2021, In: Journal of Proteome Research. 20, 3, p. 1783–1791Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
5 Citations (Scopus) -
CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning
Shang, J. & Sun, Y., May 2021, In: Methods. 189, p. 95-103 9 p.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
39 Citations (Scopus) -
Improving protein domain classification for third-generation sequencing reads using deep learning
Du, N., Shang, J. & Sun, Y., 2021, In: BMC Genomics. 22, 251.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile6 Citations (Scopus)68 Downloads (CityUHK Scholars) -
Machine learning for the analysis of multi-omics data
Sun, Y., May 2021, In: Methods. 189, p. 1-2Research output: Journal Publications and Reviews › Editorial Preface
4 Citations (Scopus)