L. Hong

An integrative approach to protein sequence design through multiobjective optimization

This paper introduces an evolutionary multiobjective optimization framework for protein sequence design, combining AlphaFold2 and ProteinMPNN to improve sequence recovery in complex design problems.

Thymidine Phosphorylase Promotes the Formation of Abdominal Aortic Aneurysm in Mice Fed a Western Diet

This study shows that TYMP promotes abdominal aortic aneurysm (AAA) in mice fed a Western diet by enhancing inflammation, thrombosis, and MMP2 activation while inhibiting vascular smooth muscle cell function.

Discovery of Alkenyl Oxindole as a Novel PROTAC Moiety for Targeted Protein Degradation via CRL4DCAF11 Recruitment

The paper develops JQ1-alkenyl oxindole conjugates that degrade BRD4 via the ubiquitin-proteasome system and recruits CRL4DCAF11, identifying HL435 as a potent antitumor lead.

A 3-component module maintains sepal flatness in Arabidopsis

The paper identifies a 3-component module involving VIP4, ARF3, and VANGUARD1 that maintains sepal flatness in Arabidopsis by regulating cell wall stiffness and growth balance.

Semantical and Geometrical Protein Encoding Toward Enhanced Bioactivity and Thermostability

This paper introduces a pre-training framework that combines sequential and geometric encoders to improve protein variant prediction for enhanced bioactivity and thermostability.

Protein Engineering with Lightweight Graph Denoising Neural Networks

This study introduces a lightweight graph neural network for protein engineering that predicts fitness and guides the design of effective mutants with improved physicochemical properties.

Growth couples temporal and spatial fluctuations of tissue properties during morphogenesis

The paper investigates spatiotemporal fluctuations in plant tissue growth, showing that growth couples temporal and spatial variations through a mechanism called fluctuation stretching.

Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K

The paper investigates the onset of anharmonicity in a protein and its surface water around 200 K, finding they are decoupled, with the protein's transition being intrinsic and the water's being a resolution effect.

CaCO3 Nanoparticles Delivering MicroRNA-200c Suppress Oral Squamous Cell Carcinoma

This study evaluates CaCO3-based nanoparticles delivering miR-200c to suppress OSCC growth and metastasis in vitro and in vivo.

Small molecule nitroalkenes inhibit RAD51-mediated homologous recombination and amplify triple-negative breast cancer cell killing by DNA-directed therapies.

This paper identifies nitroalkenes that inhibit RAD51-mediated homologous recombination, enhancing DNA damage in triple-negative breast cancer cells and showing potential as anticancer agents.

A conditional protein diffusion model generates artificial programmable endonuclease sequences with enhanced activity

This paper introduces CPDiffusion, a conditional protein diffusion model that generates artificial endonuclease sequences with enhanced activity without labeled data.

Hypoxia-sensing by the Histone Demethylase UTX (KDM6A) Controls Colitogenic CD4+ T cell Fate and Mucosal Inflammation

This study shows that UTX, an oxygen-sensitive histone demethylase, modulates colitis severity by affecting CD4+ T cell function and epigenetic regulation under hypoxia.

A Medium Chain Fatty Acid, 6-hydroxyhexanoic acid (6-HHA), Protects Against Obesity and Insulin Resistance

This paper identifies 6-hydroxyhexanoic acid (6-HHA), a medium chain fatty acid from Streptococcus gordonii, as a compound that reduces obesity and insulin resistance in mice fed a high-fat diet.

Mn2+-Induced Structural Flexibility Enhances the Entire Catalytic Cycle and the Cleavage of Mismatches in Prokaryotic Argonaute Proteins

This study shows that Mn2+ enhances pAgo protein flexibility, improving catalytic efficiency and mismatch cleavage through structural changes.

De Novo Design of Peptide Binders to Conformationally Diverse Targets with Contrastive Language Modeling

This paper designs short, target-binding linear peptides using a contrastive learning framework, demonstrating effective binding and degradation of conformationally diverse proteins.

Circulating Microparticles: Optimization and Standardization of Isolation Protocols and Reassessment of Their Characteristics and Functions

This study optimizes MP isolation protocols, identifies 3000g as critical for composition, and reveals functional differences between traditional and new MPs.

Microsporidia dressing up: the spore polaroplast transport through the polar tube and transformation into the sporoplasm membrane

This study investigates the formation of the sporoplasm membrane during microsporidia spore germination, revealing that the polaroplast transforms into the sporoplasm membrane via the polar tube.

TRAF4 is crucial for the propagation of ST2+ memory Th2 cells in IL-33-mediated type 2 airway inflammation

This study shows TRAF4 is essential for ST2+ memory Th2 cell proliferation in IL-33-driven type 2 airway inflammation, revealing its role in AKT/mTOR and ERK1/2 signaling and gene expression.

Extracellular matrix stiffness regulates fibroblast differentiation by influencing DNA methyltransferase 1 expression through microtubule polymerization

This study shows that extracellular matrix stiffness influences fibroblast differentiation by modulating DNMT1 expression via microtubule polymerization.

Single-Cell RNA-seq of Heart Reveals Intercellular Communication Drivers of Myocardial Fibrosis in Diabetic Mice

This study uses single-cell RNA-seq to identify intercellular communication drivers of myocardial fibrosis in diabetic mice, highlighting key ligand-receptor interactions and fibroblast subpopulations involved in fibrosis.

A cooperative switch within the KaiC hexamer revealed by cryo-EM

The paper uses cryo-EM to reveal cooperative conformational changes in KaiC hexamers that enable switch-like phosphorylation responses.

Kinetic model of small RNA-mediated regulation suggests that a small RNA can regulate co-transcriptionally

The paper develops a kinetic model to study sRNA-mediated gene regulation, revealing co-transcriptional regulation and identifying binding as a rate-limiting step.

A giant cell enhancer achieves cell-type specificity through activation via TCP and repression by Dof transcription factors

Development of a vaccine against the newly emerging COVID-19 virus based on the receptor binding domain displayed on virus-like particles

This study develops a vaccine candidate against SARS-CoV-2 using virus-like particles displaying the receptor binding domain, which induces neutralizing antibodies in mice.

Insulin dissociates by diverse mechanisms of coupled unfolding and unbinding

This study uses molecular dynamics simulations to investigate insulin dimer dissociation mechanisms, revealing multipathway behavior with conformational selection and induced fit as limiting cases.

Timing of organ initiation is crucial for robust organ size

The paper shows that DRMY1 regulates sepal size in Arabidopsis by controlling organ initiation timing and growth.

The MEK1/2 pathway as a therapeutic target in high-grade serous ovarian carcinoma

This study investigates MEK1/2 pathway activity in high-grade serous ovarian carcinoma and shows that its inhibition reduces tumor growth but promotes stem-like properties, suggesting potential resistance mechanisms.

RIPK3 upregulation confers robust proliferation and collateral cystine-dependence on breast cancer recurrence

This study identifies RIPK3 upregulation in recurrent breast tumors, showing it promotes proliferation but also creates dependence on cystine, offering new therapeutic targets.

Morphological plant modeling: Unleashing geometric and topological potential within the plant sciences

This paper discusses the importance of mathematical modeling in plant morphology and outlines challenges and opportunities for integrating geometric and topological approaches in plant science research and education.