| Year |
Citation |
Score |
| 2023 |
Ng TT, Su J, Lao HY, Lui WW, Chan CT, Leung AW, Jim SH, Lee LK, Shehzad S, Tam KK, Leung KS, Tang F, Yam WC, Luo R, Siu GK. Long-Read Sequencing with Hierarchical Clustering for Antiretroviral Resistance Profiling of Mixed Human Immunodeficiency Virus Quasispecies. Clinical Chemistry. PMID 37537871 DOI: 10.1093/clinchem/hvad108 |
0.337 |
|
| 2023 |
Yu H, Zheng Z, Su J, Lam TW, Luo R. Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP. Bmc Bioinformatics. 24: 308. PMID 37537536 DOI: 10.1186/s12859-023-05434-6 |
0.409 |
|
| 2023 |
Su J, Lui WW, Lee Y, Zheng Z, Siu GK, Ng TT, Zhang T, Lam TT, Lao HY, Yam WC, Tam KK, Leung KS, Lam TW, Leung AW, Luo R. Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling. Scientific Reports. 13: 5237. PMID 37002338 DOI: 10.1038/s41598-023-32378-x |
0.322 |
|
| 2023 |
Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, ... ... Luo R, et al. The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 186: 1493-1511.e40. PMID 37001506 DOI: 10.1016/j.cell.2023.02.018 |
0.581 |
|
| 2023 |
Li S, Yan B, Li TKT, Lu J, Gu Y, Tan Y, Gong F, Lam TW, Xie P, Wang Y, Lin G, Luo R. Ultra-low-coverage genome-wide association study-insights into gestational age using 17,844 embryo samples with preimplantation genetic testing. Genome Medicine. 15: 10. PMID 36788602 DOI: 10.1186/s13073-023-01158-7 |
0.413 |
|
| 2022 |
Zhou Y, Leung AW, Ahmed SS, Lam TW, Luo R. Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing. Bmc Bioinformatics. 23: 465. PMID 36344913 DOI: 10.1186/s12859-022-05025-x |
0.454 |
|
| 2022 |
Li Q, Yan B, Lam TW, Luo R. Assembly-free discovery of human novel sequences using long reads. Dna Research : An International Journal For Rapid Publication of Reports On Genes and Genomes. PMID 36308393 DOI: 10.1093/dnares/dsac039 |
0.51 |
|
| 2022 |
Su J, Zheng Z, Ahmed SS, Lam TW, Luo R. Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks. Briefings in Bioinformatics. PMID 35849103 DOI: 10.1093/bib/bbac301 |
0.377 |
|
| 2022 |
Teng JLL, Ma Y, Chen JHK, Luo R, Foo CH, Li TT, Fong JYH, Yao W, Wong SSY, Fung KSC, Lau SKP, Woo PCY. Streptococcus sp. nov. Infection Associated with Guinea Pigs. Microbiology Spectrum. e0001422. PMID 35510851 DOI: 10.1128/spectrum.00014-22 |
0.368 |
|
| 2022 |
Leung AW, Leung HC, Wong CL, Zheng ZX, Lui WW, Luk HM, Lo IF, Luo R, Lam TW. ECNano: A cost-effective workflow for target enrichment sequencing and accurate variant calling on 4800 clinically significant genes using a single MinION flowcell. Bmc Medical Genomics. 15: 43. PMID 35246132 DOI: 10.1186/s12920-022-01190-3 |
0.392 |
|
| 2022 |
Gularte-Mérida R, Smith S, Bowman AS, da Cruz Paula A, Chatila W, Bielski CM, Vyas M, Borsu L, Zehir A, Martelotto LG, Shia J, Yaeger R, Fang F, Gardner R, Luo R, et al. Same-Cell Co-Occurrence of RAS Hotspot and BRAF V600E Mutations in Treatment-Naive Colorectal Cancer. Jco Precision Oncology. 6: e2100365. PMID 35235413 DOI: 10.1200/PO.21.00365 |
0.361 |
|
| 2022 |
Ou M, Leung HC, Leung AW, Luk HM, Yan B, Liu CM, Tong TM, Mok MT, Ko WM, Law WC, Lam TW, Lo IF, Luo R. HKG: an open genetic variant database of 205 Hong Kong cantonese exomes. Nar Genomics and Bioinformatics. 4: lqac005. PMID 35156024 DOI: 10.1093/nargab/lqac005 |
0.324 |
|
| 2021 |
Xie S, Leung AW, Zheng Z, Zhang D, Xiao C, Luo R, Luo M, Zhang S. Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era. Innovation (New York, N.Y.). 2: 100153. PMID 34901902 DOI: 10.1016/j.xinn.2021.100153 |
0.703 |
|
| 2021 |
Li Q, Tian S, Yan B, Liu CM, Lam TW, Li R, Luo R. Building a Chinese pan-genome of 486 individuals. Communications Biology. 4: 1016. PMID 34462542 DOI: 10.1038/s42003-021-02556-6 |
0.52 |
|
| 2020 |
Leung CM, Li D, Xin Y, Law WC, Zhang Y, Ting HF, Luo R, Lam TW. MegaPath: sensitive and rapid pathogen detection using metagenomic NGS data. Bmc Genomics. 21: 500. PMID 33349238 DOI: 10.1186/s12864-020-06875-6 |
0.372 |
|
| 2020 |
Liu L, Wang Y, Che Y, Chen Y, Xia Y, Luo R, Cheng SH, Zheng C, Zhang T. High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method. Microbiome. 8: 155. PMID 33158461 DOI: 10.1186/s40168-020-00937-3 |
0.491 |
|
| 2020 |
Zhang Y, Liu CM, Leung HCM, Luo R, Lam TW. CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning. Iscience. 23: 101128. PMID 32422594 DOI: 10.1016/J.Isci.2020.101128 |
0.567 |
|
| 2020 |
Jiao F, Luo R, Dai X, Liu H, Yu G, Han S, Lu X, Su C, Chen Q, Song Q, Meng C, Li F, Sun H, Zhang R, Hui T, et al. Chromosome-level reference genome and population genomic analysis provide insight into the evolution and improvement of domesticated mulberry (Morus alba L). Molecular Plant. PMID 32422187 DOI: 10.1016/j.molp.2020.05.005 |
0.377 |
|
| 2020 |
Luo R, Wong C, Wong Y, Tang C, Liu C, Leung C, Lam T. Exploring the limit of using a deep neural network on pileup data for germline variant calling Nature Machine Intelligence. 2: 220-227. DOI: 10.1038/S42256-020-0167-4 |
0.511 |
|
| 2019 |
Luo R, Sedlazeck FJ, Lam TW, Schatz MC. A multi-task convolutional deep neural network for variant calling in single molecule sequencing. Nature Communications. 10: 998. PMID 30824707 DOI: 10.1038/S41467-019-09025-Z |
0.6 |
|
| 2018 |
Mai H, Zhang Y, Li D, Leung HC, Luo R, Wong CK, Ting HF, Lam TW. AC-DIAMOND v1: Accelerating large-scale DNA-protein alignment. Bioinformatics (Oxford, England). PMID 29771282 DOI: 10.1093/Bioinformatics/Bty391 |
0.374 |
|
| 2017 |
Luo R, Sedlazeck FJ, Darby CA, Kelly SM, Schatz MC. LRSim: A Linked-Reads Simulator Generating Insights for Better Genome Partitioning. Computational and Structural Biotechnology Journal. 15: 478-484. PMID 29213995 DOI: 10.1016/J.Csbj.2017.10.002 |
0.686 |
|
| 2017 |
Luo R, Zimin A, Workman R, Fan Y, Pertea G, Grossman N, Wear MP, Jia B, Miller H, Casadevall A, Timp W, Zhang SX, Salzberg SL. First Draft Genome Sequence of the Pathogenic Fungus Lomentospora prolificans (formerly Scedosporium prolificans). G3 (Bethesda, Md.). PMID 28963165 DOI: 10.1534/G3.117.300107 |
0.666 |
|
| 2017 |
Luo R, Schatz MC, Salzberg SL. 16GT: a fast and sensitive variant caller using a 16-genotype probabilistic model. Gigascience. PMID 28637275 DOI: 10.1093/Gigascience/Gix045 |
0.653 |
|
| 2016 |
Liu B, Liu CM, Li D, Li Y, Ting HF, Yiu SM, Luo R, Lam TW. BASE: a practical de novo assembler for large genomes using long NGS reads. Bmc Genomics. 17: 499. PMID 27586129 DOI: 10.1186/S12864-016-2829-5 |
0.518 |
|
| 2016 |
Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, Yamashita H, Lam TW. MEGAHIT v1.0: A Fast and Scalable Metagenome Assembler driven by Advanced Methodologies and Community Practices. Methods (San Diego, Calif.). PMID 27012178 DOI: 10.1016/J.Ymeth.2016.02.020 |
0.4 |
|
| 2015 |
Ou M, Ma R, Cheung J, Lo K, Yee P, Luo T, Chan TL, Au CH, Kwong A, Luo R, Lam TW. database.bio: a web application for interpreting human variations. Bioinformatics (Oxford, England). PMID 26315902 DOI: 10.1093/Bioinformatics/Btv500 |
0.387 |
|
| 2015 |
González-Beltrán A, Li P, Zhao J, Avila-Garcia MS, Roos M, Thompson M, van der Horst E, Kaliyaperumal R, Luo R, Lee TL, Lam TW, Edmunds SC, Sansone SA, Rocca-Serra P. From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. Plos One. 10: e0127612. PMID 26154165 DOI: 10.1371/Journal.Pone.0127612 |
0.301 |
|
| 2015 |
Cao H, Wu H, Luo R, Huang S, Sun Y, Tong X, Xie Y, Liu B, Yang H, Zheng H, Li J, Li B, Wang Y, Yang F, Sun P, et al. De novo assembly of a haplotype-resolved human genome. Nature Biotechnology. 33: 617-22. PMID 26006006 DOI: 10.1038/Nbt.3200 |
0.59 |
|
| 2015 |
Zhang Z, Mao L, Chen H, Bu F, Li G, Sun J, Li S, Sun H, Jiao C, Blakely R, Pan J, Cai R, Luo R, Van de Peer Y, Jacobsen E, et al. Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber. The Plant Cell. 27: 1595-604. PMID 26002866 DOI: 10.1105/Tpc.114.135848 |
0.389 |
|
| 2015 |
Luo R, Cheung J, Wu E, Wang H, Chan SH, Law WC, He G, Yu C, Liu CM, Zhou D, Li Y, Li R, Wang J, Zhu X, Peng S, et al. MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC). Bmc Bioinformatics. 16: S10. PMID 25952019 DOI: 10.1186/1471-2105-16-S7-S10 |
0.382 |
|
| 2015 |
Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics (Oxford, England). 31: 1674-6. PMID 25609793 DOI: 10.1093/Bioinformatics/Btv033 |
0.389 |
|
| 2014 |
Luo R, Wong YL, Law WC, Lee LK, Cheung J, Liu CM, Lam TW. BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU. Peerj. 2: e421. PMID 24949238 DOI: 10.7717/Peerj.421 |
0.549 |
|
| 2014 |
Wang W, Wang P, Xu F, Luo R, Wong MP, Lam TW, Wang J. FaSD-somatic: a fast and accurate somatic SNV detection algorithm for cancer genome sequencing data. Bioinformatics (Oxford, England). 30: 2498-500. PMID 24833803 DOI: 10.1093/Bioinformatics/Btu338 |
0.522 |
|
| 2014 |
Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics (Oxford, England). 30: 1660-6. PMID 24532719 DOI: 10.1093/Bioinformatics/Btu077 |
0.547 |
|
| 2013 |
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, ... ... Luo R, et al. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species. Gigascience. 2: 10. PMID 23870653 DOI: 10.1186/2047-217X-2-10 |
0.738 |
|
| 2013 |
Luo R, Wong T, Zhu J, Liu CM, Zhu X, Wu E, Lee LK, Lin H, Zhu W, Cheung DW, Ting HF, Yiu SM, Peng S, Yu C, Li Y, et al. SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner. Plos One. 8: e65632. PMID 23741504 DOI: 10.1371/Journal.Pone.0065632 |
0.506 |
|
| 2013 |
Luo R, Wong T, Zhu J, Liu C, Zhu X, Wu E, Lee L, Lin H, Zhu W, Cheung DW, Ting H, Yiu S, Peng S, Yu C, Li Y, et al. Correction: SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner Plos One. 8. DOI: 10.1371/Annotation/823F3670-Ed17-41Ec-Ba51-B50281651915 |
0.368 |
|
| 2012 |
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 1: 18. PMID 23587118 DOI: 10.1186/2047-217X-1-18 |
0.535 |
|
| 2012 |
Liu B, Yuan J, Yiu SM, Li Z, Xie Y, Chen Y, Shi Y, Zhang H, Li Y, Lam TW, Luo R. COPE: an accurate k-mer-based pair-end reads connection tool to facilitate genome assembly. Bioinformatics (Oxford, England). 28: 2870-4. PMID 23044551 DOI: 10.1093/Bioinformatics/Bts563 |
0.541 |
|
| 2012 |
Zhang G, Fang X, Guo X, Li L, Luo R, Xu F, Yang P, Zhang L, Wang X, Qi H, Xiong Z, Que H, Xie Y, Holland PW, Paps J, et al. The oyster genome reveals stress adaptation and complexity of shell formation. Nature. 490: 49-54. PMID 22992520 DOI: 10.1038/Nature11413 |
0.52 |
|
| 2012 |
Li X, Zhu J, Hu F, Ge S, Ye M, Xiang H, Zhang G, Zheng X, Zhang H, Zhang S, Li Q, Luo R, Yu C, Yu J, Sun J, et al. Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression. Bmc Genomics. 13: 300. PMID 22747568 DOI: 10.1186/1471-2164-13-300 |
0.338 |
|
| 2012 |
Liu CM, Wong T, Wu E, Luo R, Yiu SM, Li Y, Wang B, Yu C, Chu X, Zhao K, Li R, Lam TW. SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics (Oxford, England). 28: 878-9. PMID 22285832 DOI: 10.1093/Bioinformatics/Bts061 |
0.492 |
|
| 2012 |
Ho ES, Chow HC, Chan CT, Luo R, Leung HC, Yiu SM, Chin FY, Kwong YL, Leung AY. Whole Genome Sequencing On Donor Cell Leukemia in a Patient with Multiple Myeloma Identified Gene Mutations That May Provide Insights to Leukemogenesis. Blood. 120: 2414-2414. DOI: 10.1182/Blood.V120.21.2414.2414 |
0.46 |
|
| 2011 |
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, ... ... Luo R, et al. Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Research. 21: 2224-41. PMID 21926179 DOI: 10.1101/Gr.126599.111 |
0.726 |
|
| 2011 |
Li Y, Zheng H, Luo R, Wu H, Zhu H, Li R, Cao H, Wu B, Huang S, Shao H, Ma H, Zhang F, Feng S, Zhang W, Du H, et al. Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly. Nature Biotechnology. 29: 723-30. PMID 21785424 DOI: 10.1038/Nbt.1904 |
0.573 |
|
| 2011 |
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, ... ... Luo R, et al. Mapping copy number variation by population-scale genome sequencing. Nature. 470: 59-65. PMID 21293372 DOI: 10.1038/Nature09708 |
0.49 |
|
| 2010 |
Li Y, Zhu J, Tian G, Li N, Li Q, Ye M, Zheng H, Yu J, Wu H, Sun J, Zhang H, Chen Q, Luo R, Chen M, He Y, et al. The DNA methylome of human peripheral blood mononuclear cells. Plos Biology. 8: e1000533. PMID 21085693 DOI: 10.1371/Journal.Pbio.1000533 |
0.457 |
|
| 2010 |
Yi X, Liang Y, Huerta-Sanchez E, Jin X, Cuo ZX, Pool JE, Xu X, Jiang H, Vinckenbosch N, Korneliussen TS, Zheng H, Liu T, He W, Li K, Luo R, et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science (New York, N.Y.). 329: 75-8. PMID 20595611 DOI: 10.1126/Science.1190371 |
0.403 |
|
| 2010 |
Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, ... ... Luo R, et al. International network of cancer genome projects. Nature. 464: 993-8. PMID 20393554 DOI: 10.1038/Nature08987 |
0.408 |
|
| 2010 |
Li R, Li Y, Zheng H, Luo R, Zhu H, Li Q, Qian W, Ren Y, Tian G, Li J, Zhou G, Zhu X, Wu H, Qin J, Jin X, et al. Building the sequence map of the human pan-genome. Nature Biotechnology. 28: 57-63. PMID 19997067 DOI: 10.1038/Nbt.1596 |
0.598 |
|
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