Hi, I am Lei.

Computational Transcriptomics in Infection and Cancer

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Three research interests about Lei.

RNA Systems Biology

Single Cell RNA-seq ( Nature Microbiology 2017), RNA transcription ( NAR 2017), RNA processing ( EMBO Journal 2016, Molecular Cell 2018), RNA translation, RNA decay ( Molecular Cell 2017),Non-coding RNAs (NAR 2013)

Genetic basis of human diseases

Alternative polyadenylation (NAR 2017, Molecular Cell 2020)

Bioinformatics algorithm and tools development

DaPars2, sPepfinder, BSRD database (NAR 2013), FUNdue


     Selected Publications

    24. Seung Wook Y^, Li L^ , Connelly J, Porter S, Kodali K, Gan H, Park J, Tacer K, Tillman, H, Peng J, Pruett-Miller S, Li W, Ryan Pott. (2020) A cancer-specific ubiquitin ligase drives alternative polyadenylation by targeting PCF11. Molecular Cell. doi: 10.1016/j.molcel.2019.12.022 (^ co-first author) Full text at Molecular Cell

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

    23. Chu Y, Elrod N, Wang C, Li L , Chen T, Routh A, Xia Z, Li W, Wagner EJ, Ji P.(2019) Nudt21 regulates the alternative polyadenylation of Pak1 and is predictive in the prognosis of glioblastoma patients. Oncogene. 38(21), p.4154 Full text at Oncogene

    22. 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

    21. Park HJ, Ji P, Kim S, Xia Z, Rodriguez B, Li L , Su J, Chen K, Masamha CP, Baillat D, Fontes CR, Shyu AB, Neilson JR, Wagner EJ, Li W. (2018) 3ʹ-UTR Shortening Represses Tumor Suppressor Genes in trans by Disrupting ceRNA Crosstalk. Nature Genetics. 50(6), 783 Full text at Nature Genetics

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

    20. Feng X ^, Li L ^ , Wagner EJ, Li W. (2017) TC3A: The Cancer 3’ UTR Atlas. Nucleic Acids Research. 46(D1), D1027-D1030. ( ^ co-first author) Full text at NAR

    19. Li L , Förstner KU, Chao Y. (2017) Computational analysis of RNA-protein interactions via deep sequencing. Methods in Molecular Biology. 2018; 1751:171-182. Full text

    18. 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 NAR

    17. Chao Y, Li L , Girodat D, Förstner KU, Said N, Corcoran C, Smiga M, Papenfort K, Reinhardt R, Wieden HJ, Luisi BF, Vogel J. (2017) In vivo cleavage map illuminates the central role of RNase E in coding and noncoding RNA pathways. Molecular Cell. 65(1):39-51. Full text at Molecular Cell

       See Previewed in Molecular Cell , Recommended by Faculty of 1000

    16. Saliba AE, Li L , Westermann AJ, Appenzeller S, Stapels DAC, Schulte LN, Helaine S, Vogel J. (2017) Single cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella. Nature Microbiology. 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)

    15. 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 EMBO Journal

    14. 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. 15:1135. Full text at BMC Genomics

    13. Li L , Huang D, Cheung MK, Nong W, Huang Q, Kwan HS. (2013) BSRD: a repository for bacterial small regulatory RNA. Nucleic Acids Research. vol. 41. D233-238. Full text at NAR

     Other Publications

    12. 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. J Clin Invest. 129(5):1984-1999. Full text at The JCI

    11. 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

    10. Fan B, Li YL, Li L ,Peng XJ, Bu C, Wu XQ, Borriss R. (2016) 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

    9. 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

    8. 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

    7. 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

    6. Krysciak D, Grote J, Orbegoso MR, Utpatel C, Förstner KU, Li L , Schmeisser C, Krishnan HB, Streit WR. (2014) RNA-seq in 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 AEM

    5. 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

    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 GA

    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. 6319-6320. Full text at JB

    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) German Escherichia coli O104:H4 outbreak: whole-genome phylogeny without alignment. BMC Research Notes. 4, 533. (Highly accessed) Full text at BMC Research Notes

     Further information regarding Publications

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Lei Li, PhD

Lei Li Assistant Researcher in Prof. Wei Li's lab at The Department of Biological Chemistry , University of California, Irvine . Before he was a Postdoctoral Associate in Prof. Jörg Vogel's lab at University of Würzburg, Germany. He received his PhD in Computational biology at The Chinese University of Hong Kong. His research interests intersect at bioinformatics, RNA biology, with the goal of design and apply bioinformatics approaches to decipher biological questions that related to human health.

Email: lei.li.bioinfo [at] gmail.com (or) lei.li [at] uci.edu
ORCID: 0000-0003-3924-2544
Twitter: @LeiLi_bioinfo