X. Lu

The presenting HLA determines fidelity of SARS-CoV-2 spike protein epitope prediction

The paper compares epitope prediction methods across different HLA types and finds that prediction accuracy varies with HLA, suggesting broader HLA coverage improves epitope identification.

ClpP-dependent protein quality control supports antibiotic persistence in Campylobacter jejuni through bioenergetic homeostasis

This study identifies ClpP-dependent proteostasis as critical for antibiotic persistence in C. jejuni through bioenergetic homeostasis and metabolic remodeling.

NSP4 mutation T492I drives rapid evolution of SARS-CoV-2 toward Omicron

This study shows that the NSP4 T492I mutation increases SARS-CoV-2 mutation rates and accelerates the emergence of Omicron-like mutations.

Down regulation of Engase in Caenorhabditis elegans may improve its stresses adaptivity

This study shows that downregulating CeEngase in C. elegans enhances its adaptability to heat and osmotic stress.

Dynamic Human Gut Microbiome and Immune Shifts During an Immersive Psychosocial Therapeutic Program

The paper examines microbiome and immune changes in depression during a psychosocial intervention, finding a protective role for Prevotella-dominant microbiomes and reduced inflammation.

Deciphering the Preeclampsia-Specific Immune Microenvironment: The Role of Pro-inflammatory Macrophages

This study identifies pro-inflammatory macrophages as key regulators of the PE-specific immune microenvironment, linking them to Th17 and CD8+ T cell activation and gMDSC suppression in placental tissues.

A nanobody-enzyme fusion protein targeting PD-L1 and sialic acid exerts anti-tumor effects by affecting tumor associated macrophages

This study develops a nanobody-enzyme fusion protein targeting PD-L1 and sialic acid, showing anti-tumor effects by modulating tumor-associated macrophages.

On the discovered Cancer Driving Nucleotides (CDNs)-Distributions across genes, cancer types and patients

This study identifies Cancer Driving Nucleotides (CDNs) across cancer types and patients, finding that most remain unidentified and highlights the need for larger sample sizes to improve detection.

The theory of massively repeated evolution and full identifications of Cancer Driving Nucleotides (CDNs)

This study develops a theory to identify Cancer Driving Nucleotides (CDNs) by analyzing mutation recurrence across large cancer datasets, finding that mutations recurring at least three times are likely CDNs.

Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Non-structural Proteins Inhibitors

This study uses covalent DNA-encoded libraries to discover inhibitors targeting SARS-CoV-2 proteases 3CLpro and PLpro, identifying novel compounds with potent activity and unique binding modes.

Genotypic-phenotypic landscape computation based on first principle and deep learning

The paper develops a deep learning framework to map genotypes to fitness, applies it to predict viral mutations and immune escape, and computes the genotype-fitness landscape for SARS-CoV-2.

A Spatial Multi-Modal Dissection of Host-Microbiome Interactions within the Colitis Tissue Microenvironment

This study introduces MicroCart, a framework for spatial multi-omics analysis of host-microbiome interactions in colitis, revealing tissue-level immune responses and microbial shifts.

Imaging and quantification of prostate cancer-associated bone by polarization-sensitive optical coherence tomography

This study uses PS-OCT to differentiate bone tissue types in prostate cancer metastases by analyzing collagen organization and quantifying structural features.

Novel 3-D macrophage spheroid model reveals reciprocal regulation of immunomechanical stress and mechano-immunological response

This study shows macrophages generate mechanical stress in agarose gels and respond to environmental stiffness and cytokine signals.

Evaluation of the potential food allergy risks of recombinant human lactoferrin expressed in Komagataella phaffii

The paper assesses the allergenic risk of recombinant human lactoferrin produced in Komagataella phaffii using bioinformatics, glycan analysis, and simulated digestion, finding low allergenic potential.

Characterization of Recombinant Human Lactoferrin Expressed in Komagataella Phaffii

This study characterizes recombinant human lactoferrin produced in yeast, confirming its sequence, purity, glycosylation, structure, and thermal stability similar to native human milk lactoferrin.

Feedback loop regulation between viperin and viral hemorrhagic septicemia virus through competing protein degradation pathways

This study identifies a feedback loop between viperin and VHSV where viperin degrades viral proteins via autophagy, while viral N protein suppresses viperin via proteasome degradation.

Target-aware Molecule Generation for Drug Design Using a Chemical Language Model

This paper introduces TamGen, a chemical language model for target-aware molecule generation, and shows it produces high-quality compounds with inhibitory activity against Tuberculosis ClpP protease.

Broadly neutralizing antibody induction by non-stabilized SARS-CoV-2 Spike mRNA vaccination in nonhuman primates

Non-stabilized SARS-CoV-2 Spike mRNA vaccination in macaques induces B cell lineages targeting conserved epitopes on Omicron variants or cross-neutralizing epitopes on Sarbecoviruses.

Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies

This study uses molecular dynamics simulations to design HIV-1 immunogens that select for specific mutations in broadly neutralizing antibodies.

CRISPR-Cas13d screens identify KILR a breast cancer risk-associated lncRNA that regulates DNA replication and repair.

The paper identifies KILR, a breast cancer risk-associated lncRNA, and shows it regulates DNA replication and repair by sequestering RPA1.

Implantable nanophotonic neural probes for integrated patterned photostimulation and electrophysiology recording

This paper introduces implantable nanophotonic neural probes that enable patterned photostimulation and electrophysiology recording with minimal thermal damage.

NLRP3 Cys126 palmitoylation by ZDHHC7 Promotes Inflammasome Activation

This study identifies ZDHHC7-mediated palmitoylation of NLRP3 at Cys126 as critical for inflammasome activation, with implications for therapeutic targeting of inflammatory diseases.

Architecture and activation of human muscle phosphorylase kinase

The paper presents high-resolution cryo-EM structures of human muscle phosphorylase kinase, revealing its architecture and activation mechanism through conformational changes and allosteric regulation.

Identification and characterization of a beta-1,4 Galactosidase from Elizabethkingia meningoseptica and its application on living cell surface

This study identifies and characterizes a beta-1,4 galactosidase from Elizabethkingia meningoseptica that can remove galactose from living cell surfaces, named geGalaseI.

Epigenetic insights into GABAergic development in Dravet Syndrome iPSC and therapeutic implications

This study investigates epigenetic changes in GABAergic development using DS iPSCs and shows that VPA can rescue some chromatin abnormalities.

Cytoskeleton remodeling induced by SMYD2 methyltransferase drives breast cancer metastasis

This study identifies SMYD2 as a master regulator of breast cancer metastasis and shows that targeting the SMYD2-BCAR3-FMNL axis can prevent metastatic spread.

An optogenetic method for the controlled release of single molecules

This paper develops an optogenetic method to release single molecules in live cells, enabling controlled delivery of functional proteins and reconstitution of cellular functions at the single molecule level.

Acod1 Expression in Cancer Cells Promotes Immune Evasion through the Generation of Inhibitory Peptides

This study shows that Acod1 in cancer cells promotes immune evasion by releasing inhibitory peptides, not ITA, and that reducing Acod1 can make tumors responsive to PD-1 therapy.

Mutational order and epistasis determine the consequences of FBXW7 mutations during colorectal cancer evolution

This study shows that the order of FBXW7 and APC mutations affects colorectal cancer initiation, with FBXW7 mutations before APC preventing cancer-like features.