Yili Qian

A data-driven modeling framework for mapping genotypes to synthetic microbial community functions

This paper introduces a data-driven model to predict synthetic microbial community functions from genetic features, enabling predictions for new species not included in training data.

Human gut microbiota interactions shape the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile

This study shows how human gut microbiota interactions influence the long-term growth and evolutionary adaptations of C. difficile, including metabolic shifts and reduced disease severity.

Elucidating human gut microbiota interactions that robustly inhibit diverse Clostridioides difficile strains across different nutrient landscapes

This study identifies gut microbiota interactions that inhibit C. difficile strains across nutrient environments, highlighting strain variability and nutrient context as key factors.

Building subtraction operators and controllers via molecular sequestration

The paper demonstrates how subtraction can be achieved through molecular sequestration in a chemical reaction network and presents two feedback control architectures based on this principle.

Building molecular band-pass filters via molecular sequestration

The paper designs synthetic gene circuits that function as band-pass filters using molecular sequestration, showing improved performance with combined Incoherent Feed-Forward Loop and Negative Feedback motifs.

High-throughput single-cell sequencing of multiple invertible promoters reveals a strong determinant of bacterial population heterogeneity

The paper uses high-throughput single-cell sequencing to show promoter inversion rates drive population heterogeneity in Bacteroides spp.

Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles

This paper develops synthetic phosphorylation-based signaling networks in mammalian cells that are tunable, precise, and robust to perturbations.

Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

The paper identifies PULs in B. uniformis that influence fitness and community interactions through glycan degradation and butyrate production.

Species richness determines C. difficile invasion outcome in synthetic human gut communities

This study shows that species richness in synthetic human gut communities determines the outcome of C. difficile invasion, with mechanisms like acidification and resource competition playing key roles.

dCas9 regulator to neutralize competition in CRISPRi circuits

This paper introduces a dCas9 regulator that reduces competition among sgRNAs in CRISPRi circuits, enabling independent gene repression control.

An endoribonuclease-based feedforward controller for decoupling resource-limited genetic modules in mammalian cells

This paper develops an endoribonuclease-based feedforward loop to improve modularity in genetic systems by reducing resource competition in mammalian cells.

A quasi-integral controller for adaptation of genetic modules to variable ribosome demand

This paper designs a quasi-integral feedback controller to maintain gene expression levels despite changes in ribosome availability, showing it prevents expression reduction when a resource competitor is activated.

A Model for Resource Competition in CRISPR-Mediated Gene Repression

The paper develops a model to analyze resource competition in CRISPR-mediated gene repression networks and shows how hidden interactions affect network function based on the number of repressors.

Realizing ‘integral control’ in living cells: How to overcome leaky integration due to dilution?

This paper proposes a design principle for integral controllers in genetic circuits that mitigates dilution-induced memory loss, demonstrating it with synthetic circuits for gene expression adaptation.

Resource Competition Shapes the Response of Genetic Circuits

The paper investigates how resource competition affects genetic circuits in E. coli and provides a model to mitigate unintended behaviors by tuning resource demand coefficients.

A Dynamical Model for the Low Efficiency of Induced Pluripotent Stem Cell Reprogramming

This paper develops a dynamical model of transcriptional circuitry to explain the low efficiency of induced pluripotent stem cell reprogramming.