Gene‐Wei Li

The paper clarifies bacterial mRNA decay kinetics by resolving full-length mRNAs, revealing first-order decay and 5'-dependent decay mechanisms.

The paper identifies new Rae1 cleavage sites and shows that ribosome stalling and collisions trigger mRNA decay in Bacillus subtilis, with sequence context influencing cleavage efficiency.

The paper shows that long-range mRNA folding affects ribosome binding site accessibility, leading to gene expression regulation and sequence evolution constraints.

This study uses AI to design protein fragments that regulate biomolecular condensates, showing success in multiple targets and revealing new interaction mechanisms.

The paper identifies a new feature of bacterial intrinsic transcription terminators, showing that dinucleotides at the edges of the transcription bubble are critical for termination efficiency.

The paper investigates transcription termination in cyanobacteria, finding that most transcription units lack canonical intrinsic terminators and suggesting novel termination mechanisms.

An all-atom diffusion model unifying biomolecular structure prediction and sequence-structure generation designs experimentally validated nanobodies, mini-proteins, and linear or cyclic peptides across 26 diverse targets.

The paper shows that purine bias in bacterial genes prevents premature transcription termination by evading Rho-dependent termination, leading to biased codon usage in species with runaway transcription.

The paper estimates microbial reaction rates using proteomic data, finding that global proteomes can predict reaction rates with high accuracy without needing detailed mechanistic knowledge.

The paper identifies a 227-bp deletion in a commonly used Bacillus subtilis integration vector that causes undetected loss-of-function mutations in the ldh gene.

The paper identifies RluA as the main pseudouridine synthase in E. coli mRNAs, showing it modifies 31 of 44 high-confidence sites through a sequence and structural motif.

This paper introduces molecular time capsules to capture and preserve transcriptomic data from living cells, enabling retrospective analysis of gene expression during cellular transitions.

The paper identifies endonucleolytic cleavage sites in Bacillus subtilis using transcriptome-wide mapping and deep mutational scanning, revealing distinct sequence determinants for different endoribonucleases.

The paper quantifies mRNA decay fragments in E. coli, revealing that most cellular RNAs are decay intermediates, which can skew estimates of functional mRNA abundance.