Z. Cao

The impact of model misspecification on phylogenetic network inference

This study evaluates how model misspecification affects phylogenetic network inference using simulated and biological data, finding that gene tree estimation error and substitution rate heterogeneity impact accuracy.

PLINDER: The protein-ligand interactions dataset and evaluation resource

PLINDER provides a large, annotated PLI dataset with diverse annotations and improved evaluation splits to better assess computational methods for drug design.

The effects of L-carnitine and fructose in improved Ham's F10 on sperm culture in idiopathic severe asthenospermia within 24h

This study evaluates the effects of L-carnitine and fructose in modified Ham's F10 medium on sperm motility in idiopathic severe asthenospermia patients within 24h, finding improved viability at specific concentrations and temperature.

Clostridium ablates tumors by degrading collagen mesh andinducing ferroptosis

This paper describes a Clostridium strain that degrades collagen and induces ferroptosis in tumors, leading to effective tumor destruction in mice.

Adipocyte microRNA-802 promotes adipose tissue inflammation and insulin resistance by modulating macrophages in obesity

This study shows that miR-802 in adipose tissue promotes inflammation and insulin resistance by modulating macrophage recruitment and polarization in obesity.

Feather degradation in Stenotrophomonas maltophilia relies on conversion and internalization of keratin monomer

This study shows Stenotrophomonas maltophilia degrades feathers by converting them into keratin monomers, which enter cells to trigger keratinase activity and complete hydrolysis.

Mathematical Modelling Indicates Th-cell Targeted Antibody-Dependent Cellular Cytotoxic Is a Crucial Obstacle Hurdling HIV Vaccine Development

This paper uses mathematical modeling to show that ADCC targeting Th cells hinders HIV vaccine development by damaging immune responses and reducing vaccine effectiveness.

PRMT5 deficiency disturbs Nur77 methylation to inhibit endometrial stromal cell differentiation in recurrent implantation failure

This study shows PRMT5 deficiency disrupts Nur77 methylation, impairing endometrial stromal cell differentiation and contributing to recurrent implantation failure.

Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination

This study identifies potent and broadly neutralizing antibodies against SARS-CoV-2 and related sarbecoviruses from a vaccinated donor, showing their efficacy against multiple variants and providing insights for therapeutic development.

Understanding Genome Structure Facilitates the Use of Wild Lentil Germplasm for Breeding: A Case Study with Shattering Loci

The paper identifies QTLs associated with pod shattering in lentil using genetic linkage maps and environmental data, aiding breeders in introgressing beneficial traits from wild relatives.

The receptor VLDLR binds East Equine Encephalitis virus through multiple distinct modes

This study identifies VLDLR as an EEEV receptor and characterizes its binding modes through cryo-EM and biochemical analyses, revealing mutations that enhance viral attachment.

Ubiquitin Ligase MARCH5 Regulates the Formation of Mitochondria Derived Pre-peroxisomes

This study identifies MARCH5 as a regulator of mitochondria-derived pre-peroxisomes by impeding PEX3-containing vesicle budding.

Exact solution of a three-stage model of stochastic gene expression including cell-cycle dynamics

This paper derives an exact solution for a three-stage stochastic gene expression model that includes cell-cycle dynamics, showing discrepancies with the classical model that ignores cell-cycle effects.

Dietary n-3 PUFA enhances DMI in transition cows by regulating taste transduction gene expression in liver associated with rumen microbial alteration

This study shows that dietary n-3 PUFA improves dry matter intake in transition cows by altering liver gene expression related to taste transduction and modifying rumen microbial composition.

Characterization of Tumor-Associated Endothelial Cells and the Development of a Prognostic Model in Pancreatic Ductal Adenocarcinoma

This study identifies a specific subset of tumor-associated endothelial cells in PDAC and develops a prognostic model, TaEMS, to predict patient outcomes based on immune and cellular pathway profiles.

The translocation mechanism of calcitriol through Helicobacter pylori lipid membrane and influence on water permeability

This study investigates how calcitriol and cholesterol translocate through H. pylori lipid membranes and their effects on water permeability using molecular dynamics simulations.

The structural basis of itch receptor MRGPRX1 activation

This study reports the cryo-EM structure of MRGPRX1 bound to an agonist, revealing its activation mechanism and guiding the design of specific modulators for itch and pain treatment.

Multiomics reveal that silk fibroin and sericin differentially potentiate the paracrine functions of mesenchymal stem cells and enhance tissue regeneration

This study uses multiomics to show that silk fibroin and sericin enhance mesenchymal stem cell paracrine activity and tissue regeneration through distinct pathways.

Sequential functional differentiation of luminal epithelial cells regulated by maternal and embryonic signaling in the mouse endometrium

The paper identifies maternal and embryonic signaling-driven differentiation of luminal epithelial cells in the mouse endometrium and shows conservation in humans.

A flexible network of lipid droplet associated proteins support embryonic integrity of C. elegans

The paper investigates the role of lipid droplet-associated proteins in C. elegans embryonic development, finding that SEIP-1 and other proteins redundantly support lipid barrier formation and embryonic survival.

Supporting per-locus substitution rates improves the accuracy of species networks and avoids spurious reticulations

The paper improves species network accuracy by supporting per-locus substitution rates, reducing spurious reticulations in phylogenetic inference.

RORA regulates neutrophil migration and activation in zebrafish

This study identifies miR-99 and ROR as regulators of neutrophil migration and anti-microbial defense in zebrafish.

Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species

The paper develops genome assemblies of wild and cultivated lentil species to reveal structural rearrangements affecting introgression breeding.

Spatial profiling of microbial communities by sequential FISH with error-robust encoding

This paper introduces SEER-FISH, a method for spatially profiling microbial communities with high multiplexity and accuracy, demonstrating its ability to quantify taxon abundance and map microbial biogeography.

Natural variations in the P-type ATPase heavy metal transporter ZmCd1 controlling cadmium accumulation in maize grains

This study identifies the ZmCd1 gene controlling cadmium accumulation in maize grains and develops molecular markers for breeding low-Cd maize varieties.

ALC1 links chromatin accessibility to PARP inhibitor response in homologous recombination deficient cells

This study identifies ALC1 as a key determinant of PARPi toxicity in HR-deficient cells by linking PARP-dependent chromatin remodeling to PARPi response.

Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes

This paper introduces a method to infer phylogenetic networks from polyploid data, minimizing deep coalescences and distinguishing between auto- and allo-polyploidy.

Phylogenomic assessment of the role of hybridization and introgression in trait evolution

The paper presents a phylogenomic method to assess hybridization and introgression's role in trait evolution, showing gene flow can lead to misleading trait evolution hypotheses.

An Antioxidant Enzyme Therapeutic for COVID-19

This paper describes a catalase-based therapeutic for COVID-19 that reduces oxidative stress and cytokine production in human and animal models without toxicity.

A membrane-depolarising toxin substrate of the Staphylococcus aureus Type VII secretion system mediates intra-species competition

This paper identifies TspA as a new T7SS substrate in S. aureus, showing it mediates intra-species competition by membrane depolarization and growth inhibition in vivo.