Shenzhen Bay Laboratory

Computational and Disease Genomics Lab


Peer Reviewed Publications

(The Lab member is the ^(co-)first or *(co-)corresponding author); H-index=25, Citations: 2333 (As of 07/11/2024)


Preprints

46. Zou XD^, Zhao ZZ^, Chen Y^, Xiong KW, Wang ZY, Chen SX, Chen H, Wei GH, Xu SH, Li W*, Ni Ting*, Li L*. Impact of Rare Non-coding Variants on Human Diseases through Alternative Polyadenylation Outliers. Research Square. Full text at Research Square


45. Chen WY, Wang ZY, Lin JX, Chen SX, Chen H, Ma XL, Zou XD, Li X, Wang YN, Qin YM, Ma XX, Qiao YB*, Li L*. Enhancer RNA transcriptome-wide association study reveals an atlas of pan-cancer susceptibility eRNAs. medRxiv. Full text at medRxiv


2024

44. Zhao ZZ^, Chen Y^, Zou XD^, Lin LM^, Zhou SL, Cheng XM, Yang GR, Xu QS, Gong LH, Li L*, Ni T*. (2024) Pan-cancer transcriptome analysis reveals widespread regulation through alternative tandem transcription initiation. Science Advances. 10, 28. Abstract    Full Paper

See Research Highlighted in BioArtMED (in Chinese)

[ Software ]

43. Zhang YW^, Gong LH^, Ding RF, Chen WY, Rong H, Li YG, Shameem F, Ali KA, Li L*, Liao Q*. (2024) eRNA-IDO: a one-stop platform for identification, interactome discovery and functional annotation of. enhancer RNAs. Genomics, Proteomics & Bioinformatics. (in press) Preprint at bioRxiv

[ Website ]


42. Lin P^, Chen WY^, Long ZL, Yu JC, Yang JY, Xia Z, Wu QL, Min XY, Tang J, Cui Y,Liu FY, Wang C, Zheng J, Li W, Rich J N, Li L*, Xie Q*. (2024) RBBP6 maintains glioblastoma stem cells through CPSF3-dependent alternative polyadenylation. Cell Discovery. 10, 32. Abstract    Full Paper

See Research Highlighted in SZBL


41. Chen H^, Wang ZY^, Gong LH, Wang QX, Chen WY, Wang J, Ma XL, Ding RF, Li X, Zou XD, Plass M, Lian C, Ni T, Wei GH, Li W, Deng L, Li L*. (2024) A distinct class of pan-cancer susceptibility genes revealed by alternative polyadenylation transcriptome-wide association study. Nature Communications. 15, 1729. Abstract    Full Paper

See Research Highlighted in BioArtMED (in Chinese)

[ Website ]   [ Software ]

2023

40. Li L^#, Ma XL, Cui Y, Rotival M, Chen WY, Zou XD, Ding RF, Qin YM, Wang QX, Quintana-Murci L, Li W*. (2023) Immune-response 3′UTR alternative polyadenylation quantitative trait loci contribute to variation in human complex traits and diseases. Nature Communications. 14, 8347. #Lead Contact Abstract    Full Paper

[ Website ]


39. Ding RF^, Zou XD^, Qin YM, Gong LH, Chen H, Ma XL, Guang SH, Chen Yu, Gao Wang*, Li L*.(2023) xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs. Briefings in Bioinformatics. bbad440. Abstract    Full Paper

[ Software ]


38. Ding RF^, Wang QX^, Gong LH^, Zhang T, Zou XD, Xiong KW, Liao Q, Plass M, Li L*.(2023) scQTLbase: an integrated human single-cell eQTL database. Nucleic Acids Research. gkad781, https://doi.org/10.1093/nar/gkad781. Abstract    Full Paper

See Research Highlighted in news (in Chinese)

[ Website ]

2022

37. Zhou H.J., Li L, Li YM, Li W, Li Jessica J. (2022) PCA outperforms popular hidden variable inference methods for QTL mapping. Genome Biology. 23, 210. Abstract    Full Paper

See Research Highlighted in BioArtMED (in Chinese)

[ Software ]


36. Ma XL^, Cheng SM^, Ding RF, Zhao ZZ, Zou XD, Guang SH, Wang QX, Jing H, Chen Yu, Ting Ni, Li L*. (2022) ipaQTL-atlas: an atlas of intronic polyadenylation quantitative trait loci across human tissues. Nucleic Acids Research. 51(D1), D1046-D1052. Abstract     Full Paper

See Research Highlighted in BioArtMED (in Chinese)

[ Website ]


35. Zou XD^, Ding RF^, Chen WY, Wang G, Cheng SM, Wang Q, Li W*, Li L*. (2022) Using population-scale transcriptomic and genomic data to map 3′UTR alternative polyadenylation quantitative trait loci. STAR Protocols. 3(3), 101566. Abstract    Full Paper

See Research Highlighted in news (in Chinese)

[ Software ]


34. Li L*, Li YM, Zou XD, Peng FD, Cui Y, Eric JW, Li W. (2022) Population-Scale Genetic Control of Alternative Polyadenylation and its Association with Human Diseases. Quantitative Biology. 20(1), 44-54. Abstract    Full Paper

See featured on the Cover of Quantitative Biology, Research Highlighted in QB (in Chinese)


33. Cui Y, Peng FL, Wang D, Li YM, Li JS, Li L*, Li W*. (2022) 3′aQTL-atlas: an atlas of 3′UTR alternative polyadenylation quantitative trait loci across human normal tissues. Nucleic Acids Research. 50(D1), D39-D45. Abstract    Full Paper

See Research Highlighted in BioArt (in Chinese)

[ Website ]


2021

32. Zhang ZH, Liu XP, Li L, Yang Y, Yang JG, Wang Y, Wu JJ, Wu XD, Shan L, Pei F, Liu JY, Wang S, Li W, Sun LY, LiangJ, Shang YF. (2021) SNP rs4971059 Predisposes to Breast Carcinogenesis and Chemoresistance via TRIM46-mediated HDAC1 degradation. The EMBO Journal. 40(19), e107974. Abstract    Full Paper


31. Sheng Y, Wei JB, Yu F, Xu HZ, Yu CJ, Wu Q, Liu Y, Li L, Cui XL, Gu XY, Shen B, Li W, Huang Y, Sumita BM, He C, Qian ZJ. (2021) A Critical Role of Nuclear m6A Reader YTHDC1 in Leukemogenesis by Regulating MCM Complex-Mediated DNA Replication. Blood. 138(26), 2838-2852. Abstract    Full Paper

See Research Highlighted in BioArt (in Chinese)


30. Zhang ZC, Yan CC, Li K, Bao SQ, Li L, Chen L, Zhao JT, Sun J, Zhou M. (2021) Pan-cancer characterization of long non-coding RNA modifiers of tumor immune microenvironment reveals de novo tumor subtypes with biologically and clinically different behaviors. npj Genomic Medicine. 6(1): 52. Abstract    Full Paper


29. Gao Y, Li L, Amos CI,Li W. (2021) Analysis of alternative polyadenylation from single-cell RNA-seq using scDaPars reveals cell subpopulations invisible to gene expression. Genome Research. 31(10), 1856-1866. Abstract    Full Paper

See Research Highlighted in GenomeWeb.com


28. Li L, Huang K, Gao YP, Cui Y, Wang G, Nathan D, Li YM, Chen YE, Ji P, Peng F, William K, Wagner EJ, Li W. (2021) An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability. Nature Genetics. 53: 994–1005. Abstract    Full Paper

See Previewed in Trends in Genetics, Highlighted in BioArt (in Chinese), Trends in Genetics, ebiotrade


2020

27. Venturini E, Svensson SL, Maaß S, Gelhausen R, Eggenhofer F, Li L, Cain AK, Parkhill J, Becher D, Backofen R, Barquist L, Sharma CM, Westermann AJ, Vogel J. (2020) A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence. MicroLife. 1(1): uqaa002. Abstract    Full Paper

See Research Highlighted in Science Daily


26. Yang SK, Huang X, Lin WW, Min J, Miller DJ, Mayasundari A, Rodrigues P, Griffith EC, Gee CT, Li L, Li W, Lee RE, Rankovic Z, Chen TS, Potts PR. (2020) Structural basis for substrate recognition and chemical inhibition of oncogenic MAGE ubiquitin ligases. Nature Communications. 11(1): 1-14. Abstract    Full Paper


25. Yang SW^, Li L^, Connelly JP, Porter SN, Kodali K, Gan HY, Park JM, Tacer KF, Tillman H, Peng JM, Shondra MP, Li W, Potts PR. (2020) A Cancer-Specific Ubiquitin Ligase Drives mRNA Alternative Polyadenylation by Ubiquitinating the mRNA 3′End Processing Complex. Molecular Cell. 77(6): 1206-1221. Abstract    Full Paper

See Research Highlighted in BioArt (in Chinese), Featured on the Cover of Molecular Cell


2019

24. Chu YA, Elrod N, Wang CJ, Li L, Chen T, Routh A, Xia Z, Li W, Eric JW, Ji P. (2019) Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients. Oncogene. 38(21): 4154–4168. Abstract    Full Paper


23. Weng T, Ko J, Masamha CP, Xia Z, Xiang Y, Chen NY, Molina JG, Collum S, Mertens TC, Luo F, Philip K, Davies J, Huang J, Wilson C, Thandavarayan RA, Bruckner BA, Jyothula SS, Volcik KA, Li L, Han L, Li W, Assassi S, Karmouty-Quintana H, Wagner EJ, Blackburn MR. (2019) Cleavage factor 25 deregulation contributes to pulmonary fibrosis through alternative polyadenylation. Journal Of Clinical Investigation. 129(5): 1984-1999. Abstract    Full Paper


22. Hollenhorst MI, Jurastow I, Nandigama R, Appenzeller S, Li L, Vogel J, Wiederhold S, Althaus M, Empting M, Altmüller J, Hirsch AK. (2019) Tracheal brush cells release acetylcholine in response to bitter tastants for paracrine and autocrine signaling. The FASEB Journal. 34(1): 316-332. Abstract    Full Paper

See selected as the "paper of the month" in December by The German Anatomical Society, and one of Top Downloaded Paper for 2018-2019


2018

21. Holmqvist E, Li L, Bischler T, Barquist L, Vogel J. (2018) Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3′Ends. Molecular Cell. 70(5): 971-982. Abstract    Full Paper


20. Park HJ, Ji P, Kim S, Xia Z, Rodriguez B, Li L, Su JZ, Chen KF, Chioniso PM, Baillat D, Camila RF, Shyu A, Joel RN, Eric JW, Li W. (2018) 3′UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk. Nature Genetics. 50(6): 783–789. Abstract    Full Paper

See Research Highlighted in Nature Reviews Molecular Cell Biology, Recommended by Faculty of 1000


19. Feng X^, Li L^, Wagner EJ, Li W. (2018) TC3A: The Cancer 3′UTR Atlas. Nucleic Acids Research. 46(D1): 1027–1030. Abstract    Full Paper


18. Gong W, Li L, Zhou Y, Bian Y, Kwan H, Cheung M, Xiao Y. (2018) Detection of Quantitative Trait Loci Underlying Yield-Related Traits in Shiitake Culinary-Medicinal Mushroom, Lentinus edodes (Agaricomycetes). International Journal of Medicinal Mushrooms. 20(5): 451-458. Abstract    Full Paper


17. Li L, Konrad UF, Chao YJ. (2018) Computational Analysis of RNA–Protein Interactions via Deep Sequencing. Methods in Molecular Biology. 1751: 171-182. Abstract    Full Paper


2017

16. Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C, Vogel J. (2017) The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. Nucleic Acids Research. 45(10): 6147–6167. Abstract    Full Paper


15. Fan B, Li YL, Li L, Peng XJ, Bu C, Wu XQ, Borriss R. (2017) Malonylome analysis of rhizobacterium Bacillus amyloliquefaciens FZB42 reveals involvement of lysine malonylation in polyketide synthesis and plant-bacteria interactions. Journal of Proteomics. 154: 1-12. Abstract    Full Paper


14. Chao YJ, Li L, Girodat D, Konrad UF, Corcoran C, Śmiga M, Papenfort K, Reinhardt R, Wieden H, Ben FL, Vogel J. (2017) In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. Molecular Cell. 65(1): 39-51. Abstract    Full Paper

See Previewed in Molecular Cell, Recommended by Faculty of 1000


13. Saliba A, Li L, Alexander JW, Appenzeller S, Daphne AC, Leon NS, Helaine S, Vogel J. (2017) Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella. Nature Microbiology. 2(2): 16206. Abstract    Full Paper

See Reports in Science Daily, selected as the "paper of the month" in December 2016 by The German Society for Hygiene and Microbiology (DGHM)


2016

12. Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J. (2016) Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo. The EMBO Journal. 35(9): 991-1011. Abstract    Full Paper


11. Xiang X, Li C, Li L, Bian Y, Kwan HS, Nong W, Cheung MK, Xiao Y. (2016) Genetic diversity and population structure of Chinese Lentinula edodes revealed by InDel and SSR markers. Mycological Progress. 15(4): 37. Abstract    Full Paper


10. Gong WB, Li L, Zhou Y, Bian YB, Kwan HS, Cheung MK, Xiao Y. (2016) Genetic dissection of fruiting body-related traits using quantitative trait loci mapping in Lentinula edodes. Applied Microbiology and Biotechnology. 100(12): 5437-5452. Abstract    Full Paper


Before 2015

9. Fan B, Li L, Chao Y, Förstner KU, Vogel J, Borriss R, Wu XQ. (2015) dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42. Plos One. 10(11): e0142002. Abstract    Full Paper


8. Li L, Wong HC, Nong W, Cheung MK, Law PT, Kam KM, Kwan HS. (2014) Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus. BMC Genomics. 15(1): 1135. Abstract    Full Paper


7. Krysciak D, Grote J, Orbegoso MR, Utpatel C, Förstner KU, Li L, Schmeisser C, Krishnan HB, Streit WR. (2014) RNA Sequencing Analysis of the Broad-Host-Range Strain Sinorhizobium fredii NGR234 Identifies a Large Set of Genes Linked to Quorum Sensing-Dependent Regulation in the Background of a traI and ngrI Deletion Mutant. Applied and Environmental Microbiology. 80(18): 5655-5671. Abstract    Full Paper


6. Huang Q, Chang J, Cheung MK, Nong W, Li L, Lee MT, Kwan HS. (2014) Human proteins with target sites of multiple post-translational modification types are more prone to be involved in disease. Journal of Proteome Research. 13(6): 2735-2748. Abstract    Full Paper


5. Li L, Huang D, Cheung MK, Nong W, Huang Q, Kwan HS. (2013) BSRD: a repository for bacterial small regulatory RNA. Nucleic Acids Research. 41(D1): 233-238. Abstract    Full Paper


4. Cheng CK, Au CH, Li L, Nong W, Law PT, Cheung WM, Ling JM, Kwan HS. (2013) Genome sequences of Salmonella enterica serotype Typhimurium blood clinical isolate ST4848/06 and stool isolate ST1489/06. Genome announcements. 1(5): e00823-13. Abstract    Full Paper


3. Li L, Cheng CK, Cheung MK, Law PT, Ling JM, Kam KM, Cheung WM, Kwan HS. (2012) Draft Genome Sequence of Salmonella enterica Serovar Typhimurium ST1660/06, a Multidrug-Resistant Clinical Strain Isolated from a Diarrheic Patient. Journal of bacteriology. 194(22): 6319-6320. Abstract    Full Paper


2. Jiang J, Li J, Kwan HS, Au CH, Law PT, Li L, Kam KM, Ling JM, Leung FC. (2012) A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation. BMC Research Notes. 5(1): 80. (Highly accessed) Abstract    Full Paper


1. Cheung MK, Li L, Nong W, Kwan HS. (2011) 2011 German Escherichia coli O104:H4 outbreak: whole-genome phylogeny without alignment. BMC Research Notes. 4: 533. (Highly accessed) Abstract    Full Paper