Lei Chen, Ph.D., Principal Investigator
Shanghai Institute of Immunology
Shanghai Jiao Tong University School of Medicine
Phone: 021-63846590-776734
Email: lei.chen@sjtu.edu.cn
Dr. Chen's lab studies the complex immune system and its interaction with human microbiota through analysis of sequencing data. One focus is to use single cell RNA-seq to dissect immune cell heterogeneity, track their developmental lineages. Another focus is human gut microbiota, how their compositions are correlated with intestinal health or disease.
Education:
Aug 2010 Ph.D. in Structural and Computational Biology and Molecular Biophysics from Baylor College of Medicine at Houston, USA.
Jul 2005 B.Sc. in Biology from Fudan University at Shanghai, China.
Work Experience:
Nov 2016-Present PI, Shanghai Jiaotong University School of Medicine.
Mar 2014-Nov 2016 Bioinformatics Analyst, The Jackson Labs for Genomic Medicine.
Aug 2010-Mar 2014 Postdoc, Washington University in St Louis.
Apr 2008-Aug 2010 Research Assistant, Washington University at St Louis.
Publications:
1. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, Leopold SR, Hanson BM, Agresta HO, Gerstein M, Sodergren E, Weinstock GM. Nat Commun. 2019 Nov 6;10(1):5029.
2. Longitudinal multi-omics of host-microbe dynamics in prediabetes. Zhou W, Sailani MR, Contrepois K, Zhou Y, Ahadi S, Leopold SR, Zhang MJ, Rao V, Avina M, Mishra T, Johnson J, Lee-McMullen B, Chen S, Metwally AA, Tran TDB, Nguyen H, Zhou X, Albright B, Hong BY, Petersen L, Bautista E, Hanson B, Chen L, Spakowicz D, Bahmani A, Salins D, Leopold B, Ashland M, Dagan-Rosenfeld O, Rego S, Limcaoco P, Colbert E, Allister C, Perelman D, Craig C, Wei E, Chaib H, Hornburg D, Dunn J, Liang L, Rose SMS, Kukurba K, Piening B, Rost H, Tse D, McLaughlin T, Sodergren E, Weinstock GM, Snyder M. Nature. 2019 May;569(7758):663-671.
3. Acylglycerol Kinase Maintains Metabolic State and Immune Responses of CD8+ T Cells. Hu Z, Qu G, Yu X, Jiang H, Teng XL, Ding L, Hu Q, Guo X, Zhou Y, Wang F, Li HB, Chen L, Jiang J, Su B, Liu J, Zou Q. Cell Metab. 2019 Aug 6;30(2):290-302.e5.
4. Metabolic regulation of T cell development by Sin1-mTORC2 is mediated by pyruvate kinase M2. Ouyang X, Han Y, Qu G, Li M, Wu N, Liu H, Arojo O, Sun H, Liu X, Liu D, Chen L, Zou Q, Su B. J Mol Cell Biol. 2019 Feb 1;11(2):93-106.
5. Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota. Cignarella F, Cantoni C, Ghezzi L, Salter A, Dorsett Y, Chen L, Phillips D, Weinstock GM, Fontana L, Cross AH, Zhou Y, Piccio L. Cell Metab. 2018 Jun 5;27(6):1222-1235.e6.
6. Extensive Gene Amplification as a Mechanism for Piperacillin-Tazobactam Resistance in Escherichia coli. Schechter LM, Creely DP, Garner CD, Shortridge D, Nguyen H, Chen L, Hanson BM, Sodergren E, Weinstock GM, Dunne WM Jr, van Belkum A, Leopold SR. MBio. 2018 Apr 24;9(2). pii: e00583-18. doi: 10.1128/mBio.00583-18.
7. Community characteristics of the gut microbiomes of competitive cyclists. Petersen LM, Bautista EJ, Nguyen H, Hanson BM, Chen L, Lek SH, Sodergren E, Weinstock GM. Microbiome. 2017 Aug 10;5(1):98.
8. Phenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study. Zhou Y, Burnham CA, Hink T, Chen L, Shaikh N, Wollam A, Sodergren E, Weinstock GM, Tarr PI, Dubberke ER. J Clin Microbiol. 2014 Dec;52(12):4260-6.
9. TIGRA: a targeted iterative graph routing assembler for breakpoint assembly. Chen K, Chen L, Fan X, Wallis J, Ding L, Weinstock G. Genome Res. 2014 Feb;24(2):310-7.
10. Complete genome sequence of Treponema pallidum strain DAL-1. Zobaníková M, Mikolka P, Cejková D, Pospíšilová P, Chen L, Strouhal M, Qin X, Weinstock GM, Smajs D. Stand Genomic Sci. 2012 Oct 10;7(1):12-21.
11. Whole genome sequence of Treponema pallidum ssp. pallidum, strain Mexico A, suggests recombination between yaws and syphilis strains. Pětrošová H, Zobaníková M, Čejková D, Mikalová L, Pospíšilová P, Strouhal M, Chen L, Qin X, Muzny DM, Weinstock GM, Šmajs D. PLoS Negl Trop Dis. 2012;6(9):e1832.
12. A framework for human microbiome research. Human Microbiome Project Consortium. Nature. 2012 Jun 13;486(7402):215-21.
13. Structure, function and diversity of the healthy human microbiome. Human Microbiome Project Consortium. Nature. 2012 Jun 13;486(7402):207-14.
14. Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence. Cejková D, Zobaníková M, Chen L, Pospíšilová P, Strouhal M, Qin X, Mikalová L, Norris SJ, Muzny DM, Gibbs RA, Fulton LL, Sodergren E, Weinstock GM, Smajs D. PLoS Negl Trop Dis. 2012 Jan;6(1):e1471.
15. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel HR, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome Biol. 2011 Aug 29;12(8):R81.
16. Complete genome sequence of Treponema paraluiscuniculi, strain Cuniculi A: the loss of infectivity to humans is associated with genome decay. Šmajs D, Zobaníková M, Strouhal M, Čejková D, Dugan-Rocha S, Pospíšilová P, Norris SJ, Albert T, Qin X, Hallsworth-Pepin K, Buhay C, Muzny DM, Chen L, Gibbs RA, Weinstock GM. PLoS One. 2011;6(5):e20415.
17. A vertebrate case study of the quality of assemblies derived from next-generation sequences. Ye L, Hillier LW, Minx P, Thane N, Locke DP, Martin JC, Chen L, Mitreva M, Miller JR, Haub KV, Dooling DJ, Mardis ER, Wilson RK, Weinstock GM, Warren WC. Genome Biol. 2011;12(3):R31.
18. A catalog of reference genomes from the human microbiome. Human Microbiome Jumpstart Reference Strains Consortium. Science. 2010 May 21;328(5981):994-9.
19. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, Harris CC, McLellan MD, Fulton RS, Fulton LL, Abbott RM, Hoog J, Dooling DJ, Koboldt DC, Schmidt H, Kalicki J, Zhang Q, Chen L, Lin L, Wendl MC, McMichael JF, Magrini VJ, Cook L, McGrath SD, Vickery TL, Appelbaum E, Deschryver K, Davies S, Guintoli T, Lin L, Crowder R, Tao Y, Snider JE, Smith SM, Dukes AF, Sanderson GE, Pohl CS, Delehaunty KD, Fronick CC, Pape KA, Reed JS, Robinson JS, Hodges JS, Schierding W, Dees ND, Shen D, Locke DP, Wiechert ME, Eldred JM, Peck JB, Oberkfell BJ, Lolofie JT, Du F, Hawkins AE, O'Laughlin MD, Bernard KE, Cunningham M, Elliott G, Mason MD, Thompson DM Jr, Ivanovich JL, Goodfellow PJ, Perou CM, Weinstock GM, Aft R, Watson M, Ley TJ, Wilson RK, Mardis ER. Nature. 2010 Apr 15;464(7291):999-1005.
20. A SNP discovery method to assess variant allele probability from next-generation resequencing data. Shen Y, Wan Z, Coarfa C, Drabek R, Chen L, Ostrowski EA, Liu Y, Weinstock GM, Wheeler DA, Gibbs RA, Yu F. Genome Res. 2010 Feb;20(2):273-80.
21. Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF. Bourgogne A, Garsin DA, Qin X, Singh KV, Sillanpaa J, Yerrapragada S, Ding Y, Dugan-Rocha S, Buhay C, Shen H, Chen G, Williams G, Muzny D, Maadani A, Fox KA, Gioia J, Chen L, Shang Y, Arias CA, Nallapareddy SR, Zhao M, Prakash VP, Chowdhury S, Jiang H, Gibbs RA, Murray BE, Highlander SK, Weinstock GM. Genome Biol. 2008;9(7):R110.
22. The complete genome of an individual by massively parallel DNA sequencing. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. Nature. 2008 Apr 17;452(7189):872-6.
