Publications

• Diersheide KJ*, Battaglia RA*, Li G-W.
  How do bacteria tune transcription termination efficiency?
  Current Opinion in Microbiology 82:102557 (2024).

• McCain JSP, Britten GL, Hackett SR, Follows MJ, Li G-W.
  Microbial reaction rate estimation using proteins and proteomes.
  BioRxiv, 2024.08.13.607198 (2024).

• Schaening-Burgos C, Hannah LeBlanc, Christian Fagre, Li G-W*, Gilbert W*.
  RluA is the major mRNA pseudouridine synthase in Escherichia coli.
  PLOS Genetics 20:e1011100 (2024).

• Dierksheide KJ, Li G-W.
  A historical sequence deletion in a commonly used Bacillus subtilis chromosome integration vector generates undetected loss-of-function mutations.
  Microbiology 170:1455 (2024).

• Savinov A, Swanson S, Keating AE, Li G-W.
  High-throughput computational discovery of inhibitory protein fragments with AlphaFold.
  BioRxiv, 2023.12.19.572389 (2023).

• Parker ML, Rubien J, McCormick DM, Li G-W.
  Molecular Time Capsules Enable Transcriptomic Recording in Living Cells.
  BioRxiv, 2023.10.12.562053 (2023).

• Taggart JC, Lalanne JB, Durand S, Braun F, Condon C, Li G-W.
  A high-resolution view of RNA endonuclease cleavage in Bacillus subtilis.
  BioRxiv, 2023.03. 12.532304 (2023).

• Johnson GE†, Parker DJ†, Lalanne JB, Parker ML, LI G-W. †equal contribution
  BaM-seq and TBaM-seq, highly multiplexed and targeted RNA-seq protocols for rapid, low-cost library generation from bacterial samples.
  NAR Genomics and Bioinformatics 5:lqad017 (2023). [PDF]

• Herzel L, Stanley JA, Yao CC, Li G-W.
  Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome.
  Nucleic Acids Research 50:5029 (2022). [PDF][Supplement]

• Lalanne JB, Li G-W.
  First-principles model of optimal translation factors stoichiometry.
  eLife 10:e69222 (2021). [PDF][Data]

• Taggart JC†, Lalanne JB†, Li G-W. †equal contribution
  Quantitative Control for Stoichiometric Protein Synthesis.
  Annual Review of Microbiology 75:243 (2021). [PDF]

• McCormick DM†, Lalanne JB†, Lan TCT, Rouskin S, Li G-W. †equal contribution
  Differential translation of mRNA isoforms transcribed with distinct sigma factors.
  RNA 27:791 (2021). [PDF][Supplement]

• Mori M, Zhang Z, Banaei‐Esfahani A, Lalanne JB, Okano H, Collins BC, Schmidt A, Schubert OT, Lee, DS, Li G-W, Aebersold R, Hwa T, Ludwig C.
  From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions.
  Molecular Systems Biology 17:e9536 (2021). [PDF][Supplement]

• Lalanne JB, Parker DJ, Li G-W.
  Spurious regulatory connections dictate the expression-fitness landscape of translation factors.
  Molecular Systems Biology 17:e10302 (2021). [PDF][Supplement]

• Johnson GE†, Lalanne JB†, Peters ML, Li G-W. †equal contribution
  Functionally uncoupled transcription-translation in Bacillus subtilis.
  Nature 585:124 (2020). [PDF][Supplement](Trends in Microbiology, Nature Reviews Microbiology, MIT News, Science in Boston)

• Parker DJ, Lalanne JB, Kimura S, Johnson GE, Waldor MK, Li G-W.
  Growth optimized aminoacyl-tRNA synthetase levels prevent maximal tRNA charging.
  Cell Systems 11:121 (2020). [PDF][Supplement](MIT Biology News)

• Taggart JC†, Zauber H†, Selbach M*, Li GW*, McShane E*. †equal contributions, *corresponding authors
  Keeping the proportions of protein complex components in check.
  Cell Systems 10:125 (2020). [PDF][Supplement1][Supplement2]

• Harden TT, Herlambang KS, Chamberlain M, Lalanne JC, Wells CD, Li GW, Landick R, Hochschild A, Kondev J, Gelles J.
  Alternative transcription cycle for bacterial RNA polymerase.
  Nature Communications 11:1 (2020).

• Parker DJ†, Demetci P†, Li GW. †equal contributions
  Rapid accumulation of motility-activating mutations in resting liquid culture of Escherichia coli.
  Journal of Bacteriology 19:e00259 (2019).

• Burton AT, DeLoughery A, Li GW, Kearns DB.
  Transcriptional regulation and mechanism of SigN (ZpdN), a pBS32-encoded sigma factor in Bacillus subtilis.
  mBio 10:e01899 (2019).

• Lalanne JB, Taggart JC, Guo MS, Herzel L, Schieler A, Li GW.
  Evolutionary convergence of pathway-specific enzyme expression stoichiometry.
  Cell 173:749 (2018). (MIT News)

• Taggart JC, Li GW.
  Production of protein-complex components is stoichiometric and lacks general feedback regulation in eukaryotes.
  Cell Systems 7:580 (2018). (MIT News)

• DeLoughery A, Lalanne JB, Losick R, Li GW.
  Maturation of polycistronic mRNA by the endoribonuclease RNase Y and its associated Y-complex in Bacillus subtilis.
  PNAS 115:E5585 (2018).

• Zhang Y†, Burkhardt DH†, Rouskin S†, Li GW*, Weissman JS*, Gross CA*. †equal contributions, *corresponding authors
  A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation.
  Molecular Cell 70:274 (2018).

• Johnson GE, Li GW.
  Genome-wide quantitation of protein synthesis rates in bacteria.
  Methods in Enzymology 612:225 (2018).

• Babina AM, Parker DJ, Li GW, Meyer MM.
  Fitness advantages conferred by the L20-interacting RNA cis-regulator of ribosomal protein synthesis in Bacillus subtilis
  RNA 24:1133 (2018).

• Lalanne JB, Li GW.
  Enzyme pathways call for precise recipes.
  Cell Systems 6:397 (2018).

• Burkhardt DH†, Rouskin S†, Zhang Y†, Li GW*, Weissman JS*, Gross CA*.†equal contributions, *corresponding authors
  Operon mRNAs are organized into ORF-centric structures that predict translation efficiency.
  eLife 6: e22037 (2017).

• DeFrancesco AS, Masloboeva N, Syed AK, DeLoughery A, Bradshaw N, Li GW, Gilmore MS, Walker S, Losick R.
  Genome-wide screen for genes involved in eDNA release during biofilm formation by Staphylococcus aureus.
  PNAS 114:E5969 (2017).

• Schrader JM, Li GW, Childers WS, Perez AM, Weissman JS, Shapiro L, McAdams HH.
  Dynamic translation regulation in Caulobacter cell cycle control.
  PNAS 113: E6859 (2016).

• Li GW.
  How do bacteria tune translation efficiency?
  Current opinion in microbiology 24: 66 (2015).

Before MIT

• Li GW, Burkhardt D, Gross CA, Weissman JS.
  Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources.
  Cell  157: 624 (2014).

• Schrader JM, Zhou B, Li GW, Lasker K, Childers WS, William B, Long T, Crosson S, McAdams HH, Weissman JS, Shapiro L.
  The coding and noncoding architecture of the Caulobacter crescentus genome.
  PLoS Genetics 10: e1004463 (2014).

• Chen B, Gilbert La, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B.
  Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.
  Cell 155: 1479 (2013).

• O’Connor PBF, Li GW, Weissman JS, Atkins JF, Baranov PV. rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments.
  Bioinformatics 29: 1488 (2013).

• Li GW, Oh E, Weissman JS.
  The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria.
  Nature  484: 538 (2012).

• Brandman O, Stewart-Ornstein J, Wong D, Larson A, Williams CC, Li GW, Zhou S, King D, Shen PS, Weibezahn J, Dunn JG, Rouskin S, Inada T, Frost A, Weissman JS.
  A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress.
  Cell 151: 1042 (2012).

• Wang W*, Li GW*, Chen C*, Xie XS, Zhuang X.  *equal contribution
  Chromosome organization by a nucleoid-associated protein in live bacteria.
  Science  333: 1445 (2011)

• Li GW, Xie XS.
  Central dogma at the single-molecule level in living cells
  Nature  475: 308 (2011).

• Taniguchi Y*, Choi PJ*, Li GW*, Chen H* et al.  *equal contribution
  Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.
  Science  329: 533 (2010).

• Li GW, Elf J.
  Single molecule approaches to transcription factor kinetics in living cells.
  FEBS letters 583: 3979 (2009).

• Li GW, Berg OG, Elf J.
  Effects of macromolecular crowding and DNA looping on gene regulation kinetics.
  Nature Physics  5: 294 (2009).

• Xie XS, Choi PJ, Li GW, Lee NK, Lia G.
  Single-molecule approach to molecular biology in living bacterial cells.
  Annual Reviews of Biophysics 37:417 (2008).

• Elf J*, Li GW*, Xie XS.  *equal contribution
  Probing transcription factor dynamics at the single-molecule level in a living cell.
  Science 316: 1191 (2007).