Systems Biology Institute

Engineered Orthogonal Translation Systems from Metagenomic Libraries Expand the Genetic Code

Abstract Genetic code expansion with noncanonical amino acids (ncAAs) opens new opportunities for the design and engineering of proteins by broadening their chemical repertoire. Unfortunately, ncAA incorporation into proteins is limited both by a small collection of orthogonal am...

Starvation suppression in dense scale-free metabolic networks: Dynamical mean-field analysis of catalytic reaction networks

Cellular metabolic networks exhibit scale-free topologies with power-law degree distributions across diverse organisms. Although such topologies are often linked to mutational robustness and evolutionary advantage, their role in metabolic dynamics remains unclear. Using dynamical...

Hydraulicity in Organic Polymers Enabled by Hydrophobization Upon Water‐Triggered Curing of Hydrophilic Chains

Water-curing capability of cementitious materials, commonly known as hydraulicity, is key to their widespread use through simply mixing powder with water to form desired robust structures. However, hydraulicity has been difficult to achieve for organic materials due to the lack o...

Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies

Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable, in part because existing computational models do not fully capture the metabolic compatibility between donor and recip...

Cellulose-fueled extracellular electron transfer in termite gut microbes

ABSTRACT Termites decompose billions of tons of lignocellulosic material annually through the cellulolytic metabolism of their gut microbiota. However, the mechanisms by which cellulose degradation drives anaerobic metabolism of the gut microbiome remain poorly understood. Here,...

SPINK1-COL18A1 crosstalk shapes epigenome and drives cancer stemness in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a devastating cancer with an increasing incidence and extremely dismal prognosis. Discovery and mechanistic understanding of the genetic and epigenetic drivers of PDAC is therefore of critical importance. Here, we uncover serine protease...

Systematic prioritization of candidate genes in camptothecin biosynthesis using multi‐omics and deep learning

Abstract Camptothecin (CPT), a plant‐derived monoterpene indole alkaloid first identified in Camptotheca acuminata , is a drug precursor widely used for cancer chemotherapeutics. However, the full set of genes responsible for CPT biosynthesis remains unclear, hindering efforts to...