J. Zhu

PulseDIA improves DIA-MS specificity and sensitivity by using gas phase fractionation, achieving higher protein identification rates in cancer proteomics.

The paper describes the UCSC Xena platform, which enables secure visualization and analysis of both public and private cancer genomics data through web-based tools and hubs.

The paper identifies diverse flanking sequences of blaNDM in specific plasmids from E. coli isolated from poultry, highlighting the role of IS26 in plasmid evolution.

This study analyzes the vagino-cervical microbiome of 516 women using metagenomic shotgun sequencing to explore how pregnancy, delivery, and contraception influence microbiome composition.

The paper shows that Syntrophus aciditrophicus can use direct interspecies electron transfer via conductive pili, challenging the belief that hydrogen/formate transfer is the primary mechanism in syntrophic communities.

This study identifies MUC5AC as a driver of COPD exacerbation severity by amplifying virus-induced airway inflammation through ATP release.

This study shows CD155/CD96 promotes immunosuppression in LUAD by inhibiting antitumor immune responses and up-regulating CD96 in CD8 T cells, with potential therapeutic implications.

This study compares the efficacy of new bio-pesticides and conventional chemical pesticides against Tetranychus cinnabarinus, finding abamectin to be the most effective.

The paper analyzes bacterial diversity succession in compost made from pig manure and wood chips using 16S rRNA gene analysis, showing shifts in microbial phyla over composting stages.

This study identifies two distinct LUSC subtypes driven by Sox2 partnerships with Brn2 or p63, revealing lineage heterogeneity and potential therapeutic targets.

This study tracks the development of a potent ZIKV-specific antibody in a convalescent human, revealing limited somatic hypermutation and high germline identity.

The paper develops a method to detect inorganic polyphosphates in plants using a dye and binding domain, finding that higher plants lack large polyP stores.

This paper introduces a scalable method for inferring phylogenetic networks from multi-locus data, achieving accurate results at a larger scale than existing methods.

The paper uses shotgun metagenomics to analyze the gut microbiome in AS patients, finding enriched bacterial epitopes linked to HLA-B27 and effects of TNFi therapy and host genotype on microbiome composition.

This study identifies CHAD domains as specific inorganic polyphosphate binding modules across bacteria, archaea, and eukaryotes, revealing their structural and functional roles in polyP metabolism and localization.

This study identifies VIH1 and VIH2 as bifunctional enzymes regulating phosphate homeostasis in Arabidopsis by modulating PP-InsP levels in response to ATP concentration changes.

This study shows that indole pulses in E. coli regulate cytoplasmic pH in a memory-like manner, maintaining pH at 7.2 during stationary phase and protecting against stress.

The paper examines factors influencing gut microbiota density across mammals, disease states, and interventions, finding host and microbial factors shape density and impact health.

This paper demonstrates that gp41ECTO is the main source of HIV-1 envelope metastability and shows that stabilizing it improves nanoparticle assembly and induces more effective tier 2 neutralizing antibodies.

This study shows that β-lactam antibiotics increase MRSA pathogenicity by upregulating the tlpps gene cluster via SarA, leading to enhanced inflammation and infection severity.

This study shows PCDH7 promotes lung cancer growth in mice by accelerating KrasG12D-driven tumorigenesis and enhancing MAPK pathway activation, while its loss reduces tumor development and extends survival.

This study shows that S-nitrosylation of STIM1 by nNOS inhibits SOCE in cardiomyocytes by stabilizing the luminal domain and preventing oligomerization.

This paper introduces a pseudo-likelihood method for inferring phylogenetic networks from bi-allelic markers, demonstrating scalability and robustness on simulated and biological data.

This study identifies sFRP2 as an oncogenic driver in P53-mutant osteosarcoma through autocrine and paracrine mechanisms, showing its role in promoting tumor growth and poor survival.

The paper describes the evolution and features of PhyloNet, a software package for inferring phylogenetic networks from genetic data.

This paper introduces a Bayesian method for inferring phylogenetic networks from bi-allelic markers, demonstrating good accuracy and robustness on simulated and empirical data.

This study shows that disruption of the EIHM in Magnaporthe oryzae leads to effector re-location and a lifestyle switch during rice blast disease, identifying key infection phases and host cell responses.

This study shows PD-1 inhibits T cell activation by preferentially dephosphorylating CD28 over TCR, revealing CD28 as a primary target for PD-1-mediated suppression.