J. H. Lee

Rapid generation of antibody conformational ensembles using machine learning

This paper introduces Cadense, a machine learning framework that generates antibody conformational ensembles from sequence, capturing dynamic properties and improving docking accuracy.

The Power of Partnership: Democratizing Genetic Prevalence to Empower Patient Advocacy

The paper estimates genetic prevalence for 22 autosomal recessive conditions using gnomAD data and develops a tool to democratize these calculations, highlighting the dynamic nature of prevalence estimates.

Spatial mapping reveals unique cellular interactions and enhanced tertiary lymphoid structures in responders to anti-PD-1 therapy in mucosal head and neck cancers.

The paper identifies immune landscape differences in responders and non-responders to anti-PD-1 therapy in head and neck cancers using spatial mapping.

High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation

Human vascular organoids with a mosaic AKT1 mutation recapitulate Proteus syndrome

This paper creates a vascular organoid model with an AKT1 mutation to study Proteus syndrome and finds AKT inhibitors reverse vascular malformations.

Cannabis sativa (Hemp) seed-derived peptides WVYY and PSLPA modulate the Nrf2 signaling pathway in human keratinocytes

This study investigates the antioxidant and antibacterial effects of hemp seed-derived peptides WVYY and PSLPA, showing their activation of the Nrf2 signaling pathway in human keratinocytes.

Orally delivered biodegradable targeted inflammation resolving pectin-coated nanoparticles induce anastomotic healing post intestinal surgery

This paper develops pectin-coated nanoparticles that deliver an inflammation-resolving peptide to the colon post-surgery, improving anastomotic healing in a murine model of colitis.

Chitinase 3-like-1 (CHI3L1) Inhibits Innate Anti-Tumor and Tissue Remodeling ImmuneResponses by Regulating CD47-SIRPα and CD24-Siglec10-Mediated Phagocytosis

This study shows CHI3L1 inhibits macrophage phagocytosis by modulating CD47-SIRPα and CD24-Siglec10 pathways, contributing to immune evasion in cancer and COPD.

Chromatinization Modulates Topoisomerase II Processivity

This study shows that chromatin enhances topoisomerase II processivity under both high and low torsional stress, with topo II relaxing over 6000 DNA turns on plectonemic DNA.

Functional immune state classification of unlabeled live human monocytes using holotomography and machine learning

This study uses holotomography and machine learning to classify functional immune states of human monocytes, achieving high accuracy in identifying hyper-inflammatory and immune-suppressed states.

Glycan heterogeneity as a cause of the persistent fraction in HIV-1 neutralization

This study investigates how glycan heterogeneity on HIV-1 Env contributes to persistent infectivity despite neutralizing antibody (NAb) treatment, showing that glycan variants affect antibody binding and neutralization efficacy.

Liquid plug propagation in computer-controlled microfluidic airway-on-a-chip with semi-circular microchannels

This paper presents a lung-on-a-chip device that enables systematic study of liquid plug dynamics in distal airways, showing effects of surfactant, viscosity, and channel geometry on plug propagation and epithelial cell injury.

Evolutionary spread of protein L-(iso)aspartyl O-methyltransferases guides the discovery of distinct isoaspartate-containing peptides, pimtides

The paper identifies a new RiPP subclass, pimtides, by analyzing the evolutionary spread of PIMT enzymes and their role in modifying precursor peptides.

In Vitro Modeling of CD8 T Cell Exhaustion Enables CRISPR Screening to Reveal a Role for BHLHE40

The paper establishes an in vitro model of CD8 T cell exhaustion and uses CRISPR screening to identify BHLHE40 as a regulator of T cell exhaustion differentiation.

Oomycete effector AVRblb2 targets cyclic nucleotide-gated channels through calcium sensors to suppress pattern-triggered immunity

This study identifies AVRblb2 as an effector that targets CNGC channels via CaM/CML proteins to suppress PTI in plants.

Emission of floral volatiles is facilitated by cell-wall non-specific lipid transfer proteins

The paper shows that cell-wall non-specific lipid transfer proteins (nsLTPs) facilitate the emission of volatile organic compounds (VOCs) from plant cells to the cuticle.

Physics of sliding on water predicts morphological and behavioral allometry across a wide range of body sizes in water striders (Gerridae)

The paper models sliding physics on water to predict morphological and behavioral allometry in water striders across body sizes, confirming predictions with species observations.

SARS-CoV-2 multi-antigen protein microarray for detailed characterization of antibody responses in COVID-19 patients

This study develops a SARS-CoV-2 multi-antigen protein microarray to analyze antibody responses in COVID-19 patients, showing higher S IgG levels and reactivity to the S1 RBD but not S2 heptad repeat domain.

DNA-Stimulated Liquid-Liquid Phase Separation by Eukaryotic Topoisomerase II Modulates Catalytic Function

This study shows that DNA-induced phase separation of eukaryotic type IIA topoisomerases switches their function from DNA unlinking to catenation.

Q-SHINE: a versatile sensor for glutamine measurement via ligand-induced dimerization

The paper introduces Q-SHINE, a sensor for measuring glutamine levels through ligand-induced dimerization, enabling accurate detection in bio-fluids and living cells.

Efficient isolation of rare B cells using next-generation antigen barcoding

This paper introduces a method for efficiently isolating rare antigen-specific B cells using next-generation antigen barcoding and a computational framework, demonstrating its ability to recover thousands of mAbs, including rare HIV broadly neutralizing antibodies.

SARS-CoV-2 Spike N-Terminal Domain modulates TMPRSS2-dependent viral entry and fusogenicity

This study examines how mutations in the SARS-CoV-2 Spike N-Terminal Domain affect viral entry and fusogenicity, showing context-dependent modulation of spike function.

A Phytophthora nucleolar effector, Pi23226, targets to host ribosome biogenesis for necrotrophic cell death

This study identifies Pi23226, a Phytophthora effector that targets host ribosome biogenesis, inducing nucleolar stress and cell death to promote pathogenicity.

High-dimensional and spatial analysis reveals immune landscape dependent progression in cutaneous squamous cell carcinoma

This study compares immune landscapes of non-progressing and progressing cutaneous squamous cell carcinomas to identify immune features associated with metastasis.

Long-lasting germinal center responses to a priming immunization with continuous proliferation and somatic mutation

This study shows that germinal center B cells can persist and continue to mutate for 29 weeks after a single immunization, leading to long-lasting antibody responses.

Deep Learning-based Automated Rare Sperm Identification from Testes Biopsies

The paper develops a CNN to detect rare sperm in testis biopsies, achieving an 85.2% F1 score, which could improve IVF-ICSI success rates for NOA patients.

Mechanically active integrins direct cytotoxic secretion at the immune synapse

This study identifies integrin mechanotransduction as essential for directing cytotoxic secretion at the immune synapse, showing that mechanical forces from LFA-1 guide lytic granule fusion and cytotoxicity.

Application of an integrated computational antibody engineering platform to design SARS-CoV-2 neutralizers

The paper designs SARS-CoV-2 neutralizing antibodies using a computational platform to improve binding affinity and developability, and introduces trispecific formats and Fc modifications to enhance efficacy and reduce risk.

Vaccine genetics of IGHV1-2 VRC01-class broadly neutralizing antibody precursor naive human B cells

The paper screens naive B cells for VRC01-class broadly neutralizing antibody precursors using a germline-targeting immunogen and single-cell BCR sequencing, finding common germline variation affecting gene usage.

Kasugamycin is a novel chitinase 1 inhibitor with strong antifibrotic effects on pulmonary fibrosis

This study identifies Kasugamycin as a novel CHIT1 inhibitor with strong antifibrotic effects in pulmonary fibrosis models.