Shenzhen Bay Laboratory

Computational and Disease Genomics Lab

Peer Reviewed Publications

(The Lab member is the ^(co-)first or *(co-)corresponding author); H-index=19, Citations: 1447 (As of 05/14/2022)


37. 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. (accepted).

[ Website ]

36. 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. (accepted). Full text at Genome Biology

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. Full text at STAR Protocols

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. Full text at Quantitative Biology

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. Full text at Nucleic Acids Research

See Research Highlighted in BioArt (in Chinese)

[ Website ]


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. Full text at The EMBO Journal

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. Full text at Blood

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. Full text at npj Genomic Medicine

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. Full text at Genome Research

See Research Highlighted in

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. Full text at Nature Genetics

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


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. Full text at MicroLife

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. Full text at Nature Communications

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. Full text at Molecular Cell

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


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. Full text at Oncogene

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. Full text at Journal Of Clinical Investigation

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. Full text at The FASEB Journal

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


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. Full text at Molecular Cell

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. Full text at Nature Genetics

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. Full text at Nucleic Acids Research

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. Full text at International Journal of Medicinal Mushrooms

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


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. Full text at Nucleic Acids Research

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. Full text at Journal of Proteomics

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. Full text at Molecular Cell

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. Full text at Nature Microbiology

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


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. Full text at The EMBO Journal

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. Full text at Mycological Progress

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. Full text at Applied Microbiology and Biotechnology

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. Full text at Plos One

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. Full text at BMC Genomics

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. Full text at Applied and Environmental Microbiology

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. Full text at Journal of Proteome Research

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. Full text at Nucleic Acids Research

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. Full text at Genome announcements

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. Full text at Journal of bacteriology

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) Full text at BMC Research Notes

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) Full text at BMC Research Notes