D. Lee

Lab-in-the-loop therapeutic antibody design with deep learning

This paper introduces a machine learning framework for therapeutic antibody design that integrates computational methods with experimental validation, resulting in significantly improved binding affinity for multiple targets.

Wide-field bond-selective fluorescence imaging: from single-molecule to cellular imaging beyond video-rate

This paper introduces WF-BonFIRE, a wide-field bond-selective fluorescence imaging technique that achieves single-molecule sensitivity and kilohertz speeds for live-cell and bacterial imaging.

De Novo Design of Integrin α5β1 Modulating Proteins for Regenerative Medicine

The paper designs de novo proteins called NeoNectins that specifically bind integrin α5β1, enhancing cell attachment and tissue integration in biomaterials.

Multispectral live-cell imaging with uncompromised spatiotemporal resolution

The paper introduces a multispectral imaging approach for live-cell imaging, enabling accurate unmixing of low signal-to-noise ratio data at video rates.

Spatial Transcriptomics Reveals Spatially Diverse Cancer-Associated Fibroblast in Lung Squamous Cell Carcinoma Linked to Tumor Progression

This study uses spatial transcriptomics to analyze cancer-associated fibroblasts in lung squamous cell carcinoma, linking their spatial organization to tumor progression and patient outcomes.

Combinatorial characterization of bacterial taxa-driven differences in the microbiome of oyster reefs

The paper characterizes microbial differences in oyster reef ecosystems by analyzing abundance and diversity across soil, biofilm, and oysters in four sites, identifying distinct taxa and their associations with environmental factors.

Amino Acid-Dependent Material Properties of Tetrapeptide Condensates

This study investigates how different amino acids affect the physical properties of tetrapeptide condensates, revealing significant variations in phase behavior and material properties.

SCO-pH: Microfluidic dynamic phenotyping platform for high-throughput screening of single cell acidification

SCO-pH enables high-throughput single-cell acidification analysis by compartmentalizing cells in microfluidic droplets and measuring extracellular pH changes to distinguish metabolic states.

Viral evolution prediction identifies broadly neutralizing antibodies against existing and prospective SARS-CoV-2 variants

This paper predicts SARS-CoV-2 RBD evolution using deep mutational scanning to identify broadly neutralizing antibodies effective against existing and prospective variants.

Inhibition of HDAC7 reprograms the histone H3.3 landscape to induce heterochromatin spreading and DNA replication defects in cancer cells.

This study shows that inhibiting HDAC7 alters H3.3 deposition and chromatin structure, leading to DNA replication defects and increased sensitivity to DNA damage in cancer cells.

Single cell-guided prenatal derivation of primary epithelial organoids from the human amniotic and tracheal fluids.

The paper derives epithelial organoids from human amniotic and tracheal fluids to model congenital malformations and predict disease outcomes.

A genome-wide arrayed CRISPR screen identifies PLSCR1 as an intrinsic barrier to SARS-CoV-2 entry that recent virus variants have evolved to resist

The paper identifies PLSCR1 as a host factor restricting SARS-CoV-2 entry, which recent variants have evolved to bypass, through a CRISPR screen and integration of genetic studies.

Intermittent energy restriction inhibits tumor growth and enhances paclitaxel response in a transgenic mouse model of endometrial cancer

This study shows that intermittent energy restriction (IER) reduces tumor growth and improves paclitaxel response in a mouse model of endometrial cancer compared to low-fat diet.

A Novel Therapeutic Approach using CXCR3 Blockade to Treat Immune Checkpoint Inhibitor-mediated Myocarditis

This study identifies CXCR3-CXCL9/10 axis as a therapeutic target for ICI-mediated myocarditis using mouse models and human patient data.

Beta-cell adaptation to metabolic stresses requires prolactin receptor signaling

This study shows that prolactin receptor signaling protects beta-cells from metabolic stress by maintaining incretin receptor expression and insulin secretion.

Spatial dissection of cellular heterogeneity and functional crosstalk in the tumor microenvironments of gastric cancers

This study uses spatial transcriptomics to analyze gastric cancer tumor microenvironments, identifying subtypes and functional interactions between cell types that correlate with clinical outcomes.

PI4KIII3β inhibition reduces rhinovirus associated cell shedding and ciliary dysfunction

This study shows that inhibiting PI4KIIIβ reduces rhinovirus replication and ciliated cell loss in respiratory epithelial cultures from healthy and COPD patients.

Understanding epistatic networks in the B1 -lactamases through coevolutionary statistical modeling and deep mutational scanning

The paper uses coevolutionary analysis and deep mutational scanning to study epistatic networks in B1-lactamases, revealing both conserved and specific interactions across homologs.

Comparative single-cell transcriptomic atlases reveal conserved and divergent features of drosophilid central brains

This study compares single-cell transcriptomes of central brains across three Drosophila species to identify conserved and divergent features linked to ecological specialization.

Ultra-Long-Term Delivery of Hydrophilic Drugs Using Injectable In Situ Cross-Linked Depots

This paper develops an injectable platform for ultra-long-term hydrophilic drug delivery, achieving sustained release over six months in vivo.

AGAMOUS-like 6 and MYB DOMAIN PROTEIN 80 regulate the development of female and male cones in Pinus densiflora S. et Z.

This study identifies hub genes regulating female and male cone development in Pinus densiflora by analyzing transcriptomes across developmental stages.

Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response

This study shows BET inhibition reduces E6 and E7 expression in HPV-16 HNSCC, with variable effects on p53 and Rb, and induces G1 arrest and apoptosis.

Pre-clinical Evaluation of Biomarkers for Early Detection of Nephrotoxicity Following Alpha-particle Radioligand Therapy

This study evaluates urinary NGAL as a non-invasive biomarker for early detection of tubular damage and long-term nephrotoxicity from alpha-particle radioligand therapy in mice.

A Novel Subtype of Myeloproliferative Neoplasms Driven by a MYC-Alarmin Axis

This study identifies a MYC-S100A9 axis driving triple negative myelofibrosis and shows it is a therapeutic target.

Nuclear speckles regulate HIF-2α programs and correlate with patient survival in kidney cancer

This study shows nuclear speckles vary in cancer, correlate with survival in kidney cancer, and are regulated by HIF-2 through speckle targeting motifs.

TESOGENASE, An Engineered Nuclease Editor for Enhanced Targeted Genome Integration

The paper introduces enGager, a system that enhances ssDNA-mediated genome integration by fusing Cas9 with ssDNA-binding proteins, achieving up to 6-fold efficiency improvements for large transgene knock-in.

Modulation of cannabinoid receptor 2 alters neuroinflammation and reduces formation of alpha-synuclein aggregates in a rat model of nigral synucleinopathy

This study shows that targeting CB2 with SMM-189 reduces alpha-synuclein aggregates and neuroinflammation in a rat model of Parkinson's disease.

Enhanced functionalities of immune cells separated by microfludic lattice: assessment based on holotomography

This study compares microfluidic and centrifugation methods for isolating white blood cells, finding microfluidic separation better preserves cell functionality.

Anti-muscle Atrophy Effects of Lactobacillus reuteri ATG-F4 and Its Impact on Intestinal Microbiota and Metabolites: Implications for Prophylaxis and Therapy

This study shows that Lactobacillus reuteri ATG-F4 reduces muscle atrophy by altering gut microbiota and metabolites, with anti-inflammatory effects.

Piperidine CD4-mimetic compounds expose vulnerable Env epitopes sensitizing HIV-1-infected cells to ADCC

The paper describes piperidine-based CD4-mimetic compounds that expose HIV-1 Env epitopes, increasing sensitivity to ADCC by targeting Asp368.