Lu ZHANG

2024

A multi-modal deep language model for contaminant removal from metagenome-assembled genomes

Zou, B., Wang, J., Ding, Y., Zhang, Z., Huang, Y., Fang, X., Cheung, K. C., See, S. & Zhang, L., Oct 2024, In: Nature Machine Intelligence. 6, 10, p. 1245–1255 11 p.

Research output: Contribution to journal › Journal article › peer-review

Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity

Zhang, Z., Xiao, J., Wang, H., Yang, C., Huang, Y., Yue, Z., Chen, Y., Han, L., Yin, K., Lyu, A., Fang, X. & Zhang, L., 31 May 2024, In: Nature Communications. 15, 1, 18 p., 4631.

Research output: Contribution to journal › Journal article › peer-review

Open Access

1 Citation (Scopus)

LRTK: a platform agnostic toolkit for linked-read analysis of both human genome and metagenome

Yang, C., Zhang, Z., Huang, Y., Xie, X., Liao, H., Xiao, J., Veldsman, W. P., Yin, K., Fang, X. & Zhang, L., 13 Jun 2024, In: GigaScience. 13, 13 p., giae028.

Research output: Contribution to journal › Journal article › peer-review

Open Access

1 Citation (Scopus)

Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer

Zou, S., Yang, C., Zhang, J., Zhong, D., Meng, M., Zhang, L., Chen, H. & Fang, L., 18 Feb 2024, In: Journal of Translational Medicine. 22, 13 p., 175.

Research output: Contribution to journal › Journal article › peer-review

Open Access

8 Citations (Scopus)

Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection

Veldsman, W. P., Yang, C., Zhang, Z., Huang, Y., Chowdhury, D. & Zhang, L., 17 Jan 2024, In: Viruses. 16, 1, 15 p., 134.

Research output: Contribution to journal › Journal article › peer-review

Open Access

1 Citation (Scopus)

生成式人工智能对临床实践指南制订、评价和应用的影响

Translated title of the contribution: The Impact of Generative Artificial Intelligence on the Development,Evaluation,and Application of Clinical Practice Guidelines罗旭飞, 吕晗, 宋再伟, 刘辉, 王郅翔, 李昊东, 王晔, 朱迪, 张璐 & 陈耀龙, 20 Sept 2024, In: 协和医学杂志. 15, 5, p. 1173-1181 9 p.

Research output: Contribution to journal › Journal article › peer-review

2023

Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute

Xu, K., Cheong, C. W., Veldsman, W. P., Lyu, A., Cheung, W. K. & Zhang, L., May 2023, In: Briefings in Bioinformatics. 24, 3, 12 p., bbad124.

Research output: Contribution to journal › Journal article › peer-review

4 Citations (Scopus)

A comprehensive investigation of statistical and machine learning approaches for predicting complex human diseases on genomic variants

Wang, C., Zhang, J., Veldsman, W. P., Zhou, X. & Zhang, L., Jan 2023, In: Briefings in Bioinformatics. 24, 1, 15 p., bbac552.

Research output: Contribution to journal › Journal article › peer-review

Benchmarking genome assembly methods on metagenomic sequencing data

Zhang, Z., Yang, C., Veldsman, W. P., Fang, X. & Zhang, L., Mar 2023, In: Briefings in Bioinformatics. 24, 2, 17 p., bbad087.

Research output: Contribution to journal › Journal article › peer-review

13 Citations (Scopus)

Benchmarking multi-platform sequencing technologies for human genome assembly

Wang, J., Veldsman, W. P., Fang, X., Huang, Y., Xie, X., Lyu, A. & Zhang, L., Sept 2023, In: Briefings in Bioinformatics. 24, 5, bbad300.

Research output: Contribution to journal › Journal article › peer-review

Open Access

2 Citations (Scopus)

Gut microbiota-derived tryptamine and phenethylamine impair insulin sensitivity in metabolic syndrome and irritable bowel syndrome

Zhai, L., Xiao, H., Lin, C., Wong, H. L. X., Lam, Y. Y., Gong, M., Wu, G., Ning, Z., Huang, C., Zhang, Y., Yang, C., Luo, J., Zhang, L., Zhao, L., Zhang, C., Lau, J.Y.-N., Lu, A., Lau, L.-T., Jia, W. & Zhao, L. & 1 others, Bian, Z.-X., 17 Aug 2023, In: Nature Communications. 14, 1, 14 p., 4986.

Research output: Contribution to journal › Journal article › peer-review

Open Access

34 Citations (Scopus)

Ruminococcus gnavus plays a pathogenic role in diarrhea-predominant irritable bowel syndrome by increasing serotonin biosynthesis

Zhai, L., Huang, C., Ning, Z., Zhang, Y., Zhuang, M., Yang, W., Wang, X., Wang, J., Zhang, L., Xiao, H., Zhao, L., Asthana, P., Lam, Y. Y., Chow, C. F. W., Huang, J. D., Yuan, S., Chan, K. M., Yuan, C. S., Lau, J. Y. N. & Wong, H. L. X. & 1 others, Bian, Z. X., 11 Jan 2023, In: Cell Host and Microbe. 31, 1, p. 33-44.e5 12 p.

Research output: Contribution to journal › Journal article › peer-review

55 Citations (Scopus)

2022

A Bayesian factorization method to recover single-cell RNA sequencing data

Wen, Z.-H., Langsam, J. L., Zhang, L., Shen, W. & Zhou, X., 24 Jan 2022, In: Cell Reports Methods. 2, 1, 18 p., 100133.

Research output: Contribution to journal › Journal article › peer-review

Open Access

4 Citations (Scopus)

A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization

Wang, H., Wan, H. T., Wu, B., Jian, J., Ng, A. H. M., Chung, C.Y.-L., Chow, E.Y.-C., Zhang, J., Wong, A. O. L., Lai, K. P., Chan, T. F., Zhang, E. L. & Wong, C.K.-C., 8 Dec 2022, In: GigaScience. 11, giac120.

Research output: Contribution to journal › Journal article › peer-review

Open Access

6 Citations (Scopus)

Automated filtering of genome-wide large deletions through an ensemble deep learning framework

Hu, Y., Mangal, S., Zhang, L. & Zhou, X., Oct 2022, In: Methods. 206, p. 77-86 10 p.

Research output: Contribution to journal › Journal article › peer-review

Open Access

1 Citation (Scopus)

dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data

Xu, Y., Chen, J., Lyu, A., Cheung, W. K. & Zhang, L., Nov 2022, In: Briefings in Bioinformatics. 23, 6, 10 p., bbac424.

Research output: Contribution to journal › Journal article › peer-review

7 Citations (Scopus)

Hepatic metabolism gene expression and gut microbes in offspring, subjected to in-utero PFOS exposure and postnatal diet challenges

Shi, F., Almerick T Boncan, D., Wan, H. T., Chan, T. F., Zhang, E. L., Lai, K. P. & Wong, C. K. C., Dec 2022, In: Chemosphere. 308, Part 1, 22 p., 136196.

Research output: Contribution to journal › Journal article › peer-review

Open Access

5 Citations (Scopus)

2021

Aquila_stLFR: diploid genome assembly based structural variant calling package for stLFR linked-reads

Liu, Y. H., Grubbs, G. L., Zhang, L., Fang, X., Dill, D. L., Sidow, A. & Zhou, X., 16 Jun 2021, In: Bioinformatics advances. 1, 1, 3 p., vbab007.

Research output: Contribution to journal › Journal article › peer-review

Open Access

6 Citations (Scopus)

Aquila enables reference-assisted diploid personal genome assembly and comprehensive variant detection based on linked reads

Zhou, X., Zhang, L., Weng, Z., Dill, D. L. & Sidow, A., 17 Feb 2021, In: Nature Communications. 12, 1, 12 p., 1077.

Research output: Contribution to journal › Journal article › peer-review

Open Access

7 Citations (Scopus)

Characterizing Enterotypes in Human Metagenomics: A Viral Perspective

Song, L., Zhang, L. & Fang, X., 29 Sept 2021, In: Frontiers in Microbiology. 12, 13 p., 740990.

Research output: Contribution to journal › Journal article › peer-review

Open Access

4 Citations (Scopus)

DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data

Chen, J., Cheong, C. W., Lan, L., Zhou, X., Liu, J., Lyu, A., Cheung, W. K. & Zhang, L., Nov 2021, In: Briefings in Bioinformatics. 22, 6, 14 p., bbab325.

Research output: Contribution to journal › Journal article › peer-review

Open Access

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39 Citations (Scopus)

39 Downloads (Pure)

METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs

Zhang, Z. & Zhang, L., 22 Jul 2021, In: BMC Bioinformatics. 22, Suppl. 10, 13 p., 378.

Research output: Contribution to journal › Journal article › peer-review

Open Access

16 Citations (Scopus)

2020

A comprehensive investigation of metagenome assembly by linked-read sequencing

Zhang, L., Fang, X., Liao, H., Zhang, Z., Zhou, X., Han, L., Chen, Y., Qiu, Q. & Li, S. C., 11 Nov 2020, In: Microbiome. 8, 1, 11 p., 156.

Research output: Contribution to journal › Journal article › peer-review

Open Access

13 Citations (Scopus)

De novo diploid genome assembly for genome-wide structural variant detection

Zhang, L., Zhou, X., Weng, Z. & Sidow, A., 1 Mar 2020, In: NAR Genomics and Bioinformatics. 2, 1, 10 p., lqz018.

Research output: Contribution to journal › Journal article › peer-review

Open Access

8 Citations (Scopus)

2019

Assessment of human diploid genome assembly with 10x Linked-Reads data

Zhang, L., Zhou, X., Weng, Z. & Sidow, A., 1 Nov 2019, In: GigaScience. 8, 11, 11 p., giz141.

Research output: Contribution to journal › Journal article › peer-review

Open Access

16 Citations (Scopus)

Assessment of network module identification across complex diseases

Choobdar, S., Ahsen, M. E., Crawford, J., Tomasoni, M., Fang, T., Lamparter, D., Lin, J., Hescott, B., Hu, X., Mercer, J., Natoli, T., Narayan, R., Aicheler, F., Amoroso, N., Arenas, A., Azhagesan, K., Baker, A., Banf, M., Batzoglou, S. & Baudot, A. & 30 others, Bellotti, R., Bergmann, S., Boroevich, K. A., Brun, C., Cai, S., Caldera, M., Calderone, A., Cesareni, G., Chen, W., Chichester, C., Cowen, L., Crawford, J., Cui, H., Dao, P., De Domenico, M., Dhroso, A., Didier, G., Divine, M., del Sol, A., Fang, T., Feng, X., Flores-Canales, J. C., Fortunato, S., Gitter, A., Gorska, A., Guan, Y., Guénoche, A., Gómez, S., Zhang, L. & The DREAM Module Identification Challenge Consortium, 1 Sept 2019, In: Nature Methods. 16, 9, p. 843-852 10 p.

Research output: Contribution to journal › Journal article › peer-review

Open Access

182 Citations (Scopus)

2018

Coding mutations in NUS1 contribute to Parkinson's disease

Guo, J. F., Zhang, L., Li, K., Mei, J. P., Xue, J., Chen, J., Tang, X., Shen, L., Jiang, H., Chen, C., Guo, H., Wu, X. L., Sun, S. L., Xu, Q., Sun, Q. Y., Chan, P., Shang, H. F., Wang, T., Zhao, G. H. & Liu, J. Y. & 20 others, Xie, X. F., Jiang, Y. Q., Liu, Z. H., Zhao, Y. W., Zhu, Z. B., Li, J. D., Hu, Z. M., Yan, X. X., Fang, X. D., Wang, G. H., Zhang, F. Y., Xia, K., Liu, C. Y., Zhu, X. W., Yue, Z. Y., Li, S. C., Cai, H. B., Zhang, Z. H., Duan, R. H. & Tang, B. S., Oct 2018, In: Proceedings of the National Academy of Sciences of the United States of America. 115, 45, p. 11567-11572 6 p.

Research output: Contribution to journal › Journal article › peer-review

Open Access

73 Citations (Scopus)

HAPDeNovo: A haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data

Zhou, X., Batzoglou, S., Sidow, A. & Zhang, L., 18 Jun 2018, In: BMC Genomics. 19, 467.

Research output: Contribution to journal › Journal article › peer-review

Open Access

9 Citations (Scopus)

Thermally Activated Delayed Fluorescence Host for High Performance Organic Light-Emitting Diodes

Zhang, L. & Cheah, K. W., 1 Dec 2018, In: Scientific Reports. 8, 1, 8832.

Research output: Contribution to journal › Journal article › peer-review

Open Access

32 Citations (Scopus)

2017

The snp-set based association study identifies ITGA1 as a susceptibility gene of attention-deficit/hyperactivity disorder in Han Chinese

Liu, L., Zhang, L., Li, H. M., Wang, Z. R., Xie, X. F., Mei, J. P., Jin, J. L., Shi, J., Sun, L., Li, S. C., Tan, Y. L., Yang, L., Wang, J., Yang, H. M., Qian, Q. J. & Wang, Y. F., 15 Aug 2017, In: Translational Psychiatry. 7, 8, e1201.

Research output: Contribution to journal › Journal article › peer-review

Open Access

8 Citations (Scopus)

2015

Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies

Li, X., Fan, D., Zhang, W., Liu, G., Zhang, L., Zhao, L., Fang, X., Chen, L., Dong, Y., Chen, Y., Ding, Y., Zhao, R., Feng, M., Zhu, Y., Feng, Y., Jiang, X., Zhu, D., Xiang, H., Feng, X. & Li, S. & 4 others, Wang, J., Zhang, G., Kronforst, M. R. & Wang, W., 10 Sept 2015, In: Nature Communications. 6, 10 p., 8212.

Research output: Contribution to journal › Journal article › peer-review

Open Access

149 Citations (Scopus)

2012

Association of CD247 with systemic lupus erythematosus in Asian populations

Li, R., Yang, W., Zhang, J., Hirankarn, N., Pan, H. F., Mok, C. C., Chan, T. M., Wong, R. W. S., Mok, M. Y., Lee, K. W., Wong, S. N., Leung, A. M. H., Li, X. P., Avihingsanon, Y., Lee, T. L., Ho, M. H. K., Lee, P. P. W., Wong, W., Wong, C. M. & Ng, I. & 19 others, Yang, J., Li, P. H., Zhang, Y., Zhang, L., Li, W., Baum, L., Kwan, P., Rianthavorn, P., Deekajorndej, T., Suphapeetiporn, K., Shotelersuk, V., Garcia-Barceló, M. M., Cherny, S. S., Tam, P.-H., Sham, P. C., Lau, C. S., Shen, N., Lau, Y. L. & Ye, D.-Q., Jan 2012, In: Lupus. 21, 1, p. 75-83 9 p.

Research output: Contribution to journal › Journal article › peer-review

33 Citations (Scopus)

Lu ZHANG, Dr

Research Output

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