Zhiyuan Li

The paper models how sequential signaling pulses guide cell fate decisions in a hierarchical system, revealing design principles for robust fate navigation.

The paper introduces CIM, a method to predict CFM-Rec interactions from genomic data, revealing topological patterns in microbial communities.

This study identifies PBP2 subtype SBPs as the primary siderophore recognizers in Gram-positive bacteria through genome-wide analysis of 16,232 genomes.

This paper introduces the Hyper Solution Landscape (HSL) method to analyze cell fate decisions by exploring gene regulatory network configurations and their dynamic changes.

The paper introduces TFA (Transcription Factor Activity) to infer TF-TF interactions with high fidelity, outperforming expression-based methods and revealing isoform-level heterogeneity in regulatory circuits.

This paper introduces a genome-based pipeline to predict pyoverdine structures and their receptors in Pseudomonas using pHMMs and co-evolutionary analysis, validated across 14,230 genomes.

The paper investigates why waste-product cross-feeding persists in microbial communities by developing a mathematical model showing that intracellular metabolite toxicity can make cross-feeding evolutionarily stable.

The paper develops a framework to trace siderophore biosynthesis to primary metabolism and applies it to identify metabolic differences between beneficial and pathogenic bacteria.

The paper develops a functional-space framework to analyze siderophore biosynthesis across bacteria, revealing ecological drivers over phylogenetic constraints.

The paper develops a co-evolution algorithm to predict bacterial iron interaction networks based on siderophore synthetase-receptor gene pairs across Pseudomonas genomes, revealing habitat- and pathogen-specific interactions.

The paper identifies recombination-enhancing variants in marine symbionts using a phylogeny-deviation approach, finding genes that improve recombination efficiency in Escherichia coli.

The paper develops a bioinformatic pipeline to predict bacterial siderophore structures and receptors from genome sequences, revealing significant diversity in pyoverdines and their receptors.

The paper develops an AI-driven method to label tubulin isotypes in vivo across species, enabling precise visualization of microtubule dynamics and pathogenic variants without disrupting cellular processes.

This study develops a mathematical model to simulate the emergence of complexity in multicellular systems through cell division and lateral inhibition, using C. elegans as an example.

SIDERITE identifies new iron-binding molecules by analyzing chemical structures and confirming their iron-binding ability through experimental validation.

The paper shows that moderate cheating in microbial communities supports biodiversity by creating self-sustaining exploitation cycles, while excessive cheating leads to system collapse.

This study constructs a logic-incorporated gene regulatory network model to analyze how regulatory logic and noise influence cell fate decisions in differentiation and reprogramming.

The paper introduces a standardized NRPS architecture using conserved motifs, leading to new subtype classifications, novel motifs, and insights into reengineering challenges.

The paper quantifies translational regulation in E. coli across 12 conditions, revealing gene-specific and cross-condition variability in translation efficiency.

This study models microbial metabolic trade-offs in a chemostat to show how dynamic fitness landscapes enable ecological and evolutionary stable coexistence.

The paper quantifies and phenotypes early embryonic morphogenesis in C. elegans using a reference embryo and system-level phenotyping methods to analyze 1818 mutant embryos.