Gene-Wei Li

Gene-Wei Li

Associate Professor of Biology

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






Building 68 - Koch Biology Building


Cindy Woolley



Assistant Phone


  • 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.


  • 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. 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
  2. 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
  3. High-throughput computational discovery of inhibitory protein fragments with AlphaFold. Savinov, A, Swanson, S, Keating, AE, Li, GW. 2023. bioRxiv , .
    doi: 10.1101/2023.12.19.572389PMID:38187731
  4. 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
  5. 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
  6. 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
  7. First-principles model of optimal translation factors stoichiometry. Lalanne, JB, Li, GW. 2021. Elife 10, .
    doi: 10.7554/eLife.69222PMID:34590582
  8. Quantitative Control for Stoichiometric Protein Synthesis. Taggart, JC, Lalanne, JB, Li, GW. 2021. Annu Rev Microbiol 75, 243-267.
    doi: 10.1146/annurev-micro-041921-012646PMID:34343023
  9. 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.. 2021. Mol Syst Biol 17, e9536.
    doi: 10.15252/msb.20209536PMID:34032011
  10. Sigma factor dependent translational activation in Bacillus subtilis. McCormick, DM, Lalanne, JB, Lan, TCT, Rouskin, S, Li, GW. 2021. RNA 27, 791-804.
    doi: 10.1261/rna.078747.121PMID:33927010