Gene-Wei Li

Gene-Wei Li

Associate Professor of Biology; Investigator, Howard Hughes Medical Institute

Gene-Wei Li investigates how quantitative information regarding precise proteome composition is encoded in and extracted from bacterial genomes.

617-324-6703

Phone

68-223

Office

gwli@mit.edu

Email

Building 68 - Koch Biology Building

Location

Lab Website
Cindy Woolley

Assistant

617-253-6060

Assistant Phone

Education

  • PhD, 2010, Harvard University
  • SB, 2004, Physics, National Tsinghua University

Research Summary

We seek to understand the optimization of bacterial proteomes at both mechanistic and systems levels. Our work combines high-precision assays, genome-wide measurements, and quantitative/biophysical modeling. Ongoing projects focus on the design principles of transcription, translation, and RNA maturation machineries in the face of competing cellular processes.

Awards

  • Smith Odyssey Award, 2020
  • MIT Committed to Caring Award, 2020
  • NSF Career Award, 2019
  • Pew Biomedical Scholar, 2017
  • Smith Family Award for Excellence in Biomedical Research, 2017
  • NIGMS R35 Maximizing Investigator Research Award, 2017
  • Sloan Research Fellowship, 2016
  • Searle Scholar, 2016
  • NIH Pathway to Independence Award, 2013

Key Publications

  1. Functionally uncoupled transcription-translation in Bacillus subtilis. Johnson, GE, Lalanne, JB, Peters, ML, Li, GW. 2020. Nature 585, 124-128.
    doi: 10.1038/s41586-020-2638-5PMID:32848247
  2. Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging. Parker, DJ, Lalanne, JB, Kimura, S, Johnson, GE, Waldor, MK, Li, GW. 2020. Cell Syst 11, 121-130.e6.
    doi: 10.1016/j.cels.2020.07.005PMID:32726597
  3. Production of Protein-Complex Components Is Stoichiometric and Lacks General Feedback Regulation in Eukaryotes. Taggart, JC, Li, GW. 2018. Cell Syst 7, 580-589.e4.
    doi: 10.1016/j.cels.2018.11.003PMID:30553725
  4. Maturation of polycistronic mRNAs by the endoribonuclease RNase Y and its associated Y-complex in Bacillus subtilis. DeLoughery, A, Lalanne, JB, Losick, R, Li, GW. 2018. Proc Natl Acad Sci U S A 115, E5585-E5594.
    doi: 10.1073/pnas.1803283115PMID:29794222
  5. Evolutionary Convergence of Pathway-Specific Enzyme Expression Stoichiometry. Lalanne, JB, Taggart, JC, Guo, MS, Herzel, L, Schieler, A, Li, GW. 2018. Cell 173, 749-761.e38.
    doi: 10.1016/j.cell.2018.03.007PMID:29606352

Recent Publications

  1. How do bacteria tune transcription termination efficiency? Julia Dierksheide, K, Battaglia, RA, Li, GW. 2024. Curr Opin Microbiol 82, 102557.
    doi: 10.1016/j.mib.2024.102557PMID:39423561
  2. Author Correction: From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions. Mori, M, Zhang, Z, Banaei-Esfahani, A, Lalanne, JB, Okano, H, Collins, BC, Schmidt, A, Schubert, OT, Lee, DS, Li, GW et al.. 2024. Mol Syst Biol 20, 1257-1259.
    doi: 10.1038/s44320-024-00062-5PMID:39354190
  3. RluA is the major mRNA pseudouridine synthase in Escherichia coli. Schaening-Burgos, C, LeBlanc, H, Fagre, C, Li, GW, Gilbert, WV. 2024. PLoS Genet 20, e1011100.
    doi: 10.1371/journal.pgen.1011100PMID:39241085
  4. Microbial reaction rate estimation using proteins and proteomes. McCain, JSP, Britten, GL, Hackett, SR, Follows, MJ, Li, GW. 2024. bioRxiv , .
    doi: 10.1101/2024.08.13.607198PMID:39185172
  5. A historical sequence deletion in a commonly used Bacillus subtilis chromosome integration vector generates undetected loss-of-function mutations. Dierksheide, KJ, Li, GW. 2024. Microbiology (Reading) 170, .
    doi: 10.1099/mic.0.001455PMID:38602388
  6. A historical sequence deletion in a commonly used Bacillus subtilis chromosome integration vector generates undetected loss-of-function mutations. Dierksheide, KJ, Li, GW. 2024. bioRxiv , .
    doi: 10.1101/2024.01.04.574214PMID:38260694
  7. High-throughput discovery of inhibitory protein fragments with AlphaFold. Savinov, A, Swanson, S, Keating, AE, Li, GW. 2024. bioRxiv , .
    doi: 10.1101/2023.12.19.572389PMID:38187731
  8. Molecular Time Capsules Enable Transcriptomic Recording in Living Cells. Parker, M, Rubien, J, McCormick, D, Li, GW. 2023. bioRxiv , .
    doi: 10.1101/2023.10.12.562053PMID:37905077
  9. BaM-seq and TBaM-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation from bacterial samples. Johnson, GE, Parker, DJ, Lalanne, JB, Parker, ML, Li, GW. 2023. NAR Genom Bioinform 5, lqad017.
    doi: 10.1093/nargab/lqad017PMID:36879903
  10. Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome. Herzel, L, Stanley, JA, Yao, CC, Li, GW. 2022. Nucleic Acids Res 50, 5029-5046.
    doi: 10.1093/nar/gkac295PMID:35524564

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