J. S. Lee

Responses to membrane potential-modulating ionic solutions measured by magnetic resonance imaging of cultured cells and in vivo rat cortex

This study uses MRI to measure responses of cultured cells and in vivo rat cortex to ionic solutions that modulate membrane potential, finding changes in T2 relaxation time and bound-to-free water proton ratio.

Ribonanza: deep learning of RNA structure through dual crowdsourcing

The paper introduces RibonanzaNet, a deep learning model trained on crowdsourced RNA chemical mapping data to predict RNA structure and related properties.

Genome-wide CRISPR screen identifies KEAP1 perturbation as a vulnerability of ARID1A-deficient cells

The paper identifies KEAP1 as a genetic dependency in ARID1A-deficient clear cell ovarian carcinoma cells through a genome-wide CRISPR screen, showing KEAP1 perturbation leads to growth inhibition.

Evolutionary arms race between SARS-CoV-2 and interferon signaling via dynamic interaction with autophagy.

This study identifies how SARS-CoV-2 evolves to counteract host interferon signaling through interactions with autophagy pathways.

2D and 3D multiplexed subcellular profiling of nuclear instability in human cancer

The paper shows nuclear rupture is common in cancer, especially glioblastoma, and links it to lamin proteins and immune signaling.

A tryptophan metabolite modulates the host response to bacterial infection via kainate receptors

The paper identifies 3-hydroxy-kynurenine as a tryptophan metabolite that enhances host survival during bacterial infection by modulating kainate receptors in macrophages.

Identification of hyperosmotic stress-responsive genes in Chinese hamster ovary cells via genome-wide virus-free CRISPR/Cas9 screening

The paper identifies hyperosmotic stress-responsive genes in CHO cells using CRISPR/Cas9 screening and validates their role in stress resistance and protein production.

A Compensatory RNase E Variation Increases Iron Piracy and Virulence in Multidrug-Resistant Pseudomonas aeruginosa during Macrophage Infection

This study shows that a compensatory RNase E mutation in P. aeruginosa increases siderophore production and macrophage ferroptosis, contributing to virulence and potentially being targeted by gallium therapy.

Relative infectivity of the SARS-CoV-2 Omicron variant in human alveolar cells

This study compares the infectivity of SARS-CoV-2 variants in human alveolar cells, finding Omicron (BA.1) to be 3-5-fold more infectious than other variants at early infection.

Transcriptomics based prediction of survival and response to therapy in malignant mesothelioma

The paper identifies a 48-gene prognostic signature and synthetic-lethality profiles predictive of survival and therapy response in mesothelioma using transcriptomic and exomic data from 122 patients.

Antibodies targeting conserved non-canonical antigens and endemic coronaviruses associate with favorable outcomes in severe COVID-19

The paper identifies antibody responses against non-canonical and endemic coronavirus antigens as predictors of favorable outcomes in severe COVID-19.

Differential neutralization and inhibition of SARS-CoV-2 variants by antibodies elicited by COVID-19 mRNA vaccines

This study evaluates how well antibodies from mRNA vaccines neutralize SARS-CoV-2 variants, finding that Omicron shows the most escape but booster doses maintain moderate neutralizing activity.

Pyrimidine biosynthesis inhibitors synergize with nucleoside analogs to block SARS-CoV-2 infection

The paper screens 18,000 drugs for antiviral activity against SARS-CoV-2, identifies synergistic combinations of pyrimidine biosynthesis inhibitors and nucleoside analogs, and validates their efficacy in vitro and in vivo.

A landscape of synergistic drug combinations in non-small-cell lung cancer

The paper identifies synergistic drug combinations in non-small-cell lung cancer cell lines, finding that synergy often arises from sensitizing resistant models through dual pathway targeting.

Efficacy of double-stranded RNA for the large-scale control and prevention of sacbrood virus in Apis cerana (Hymenoptera: Apidae) apiaries

This study tests the efficacy of double-stranded RNA targeting VP1 to control and prevent sacbrood virus in Apis cerana apiaries, showing increased survival rates and safe mitigation of the virus.

A short ERK5 isoform modulates nucleocytoplasmic shuttling of active ERK5 and associates with poor survival in breast cancer

This paper identifies a short ERK5 isoform that promotes extranuclear localization of active ERK5, driving EMT and poor survival in breast cancer.

Bifurcated monocyte states are predictive of mortality in severe COVID-19

The paper identifies bifurcated monocyte states in severe COVID-19 patients that predict mortality, with distinct cytokine and interferon gene modules associated with survival or death.

Transmission of one predicts another: Apathogenic proxies for transmission dynamics of a fatal virus

The paper uses apathogenic FIV transmission data to predict pathogenic FeLV transmission dynamics in Florida panthers, showing comparable accuracy to traditional methods.

Tetherin antagonism by SARS-CoV-2 enhances virus release: multiple mechanisms including ORF3a-mediated defective retrograde traffic

This study shows SARS-CoV-2 evades tetherin restriction by multiple mechanisms, including ORF3a disrupting tetherin localization and Spike protein reducing tetherin levels, enhancing viral release.

SUMO-specific protease 2 (SENP2) suppresses browning of white adipose tissue through C/EBPβ modulation

This study shows that SENP2 suppresses white adipose tissue browning by modulating C/EBPβ, leading to increased thermogenic gene expression and resistance to obesity in mice.

Single-cell Transcriptome of Bronchoalveolar Lavage Fluid Reveals Dynamic Change of Macrophages During SARS-CoV-2 Infection in Ferrets

This study uses single-cell RNA sequencing to track macrophage dynamics in SARS-CoV-2-infected ferrets over time, revealing distinct subpopulations and functional changes.

RNF5 Regulation of RBBP4 Defines Acute Myeloid Leukemia Growth and Susceptibility to Histone Deacetylase Inhibitors

This study shows RNF5 promotes AML growth by regulating RBBP4 and epigenetic pathways, and its inhibition enhances sensitivity to HDAC inhibitors, suggesting it as a therapeutic target and biomarker.

Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2

The paper screens FDA-approved drugs against SARS-CoV-2 in different cell types, identifying three FDA-approved antivirals with potential for clinical use.

scRNA-seq analysis of colon and esophageal tumors uncovers abundant microbial reads in myeloid cells undergoing proinflammatory transcriptional alterations

The paper develops a computational pipeline to identify microbial reads in scRNA-seq data and finds that microbial reads are enriched in myeloid cells with proinflammatory transcriptional changes.

A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes

The paper uses a CRISPR-Cas9 screen in Chinese hamster ovary cells to identify glutamine-sensitive genes, revealing a novel lipase involved in TCA cycle regulation.

Synthetic lethality across normal tissues is strongly associated with cancer risk, onset, and tumor suppressor specificity

The paper quantifies synthetic lethality in normal tissues and links it to cancer risk, onset, and tumor suppressor specificity using GTEx transcriptomics data.

Whole exome precision oncology targeting synthetic lethal vulnerabilities across the tumor transcriptome

This paper predicts patient response to cancer therapies using computationally derived genetic interactions across multiple tumor transcriptomics datasets.

Integrated computational and experimental identification of p53, KRAS and VHL mutant selection associated with CRISPR-Cas9 editing

The paper identifies p53, KRAS, and VHL mutations as being selected during CRISPR-Cas9 editing through computational and experimental analysis.

Intense light-mediated circadian cardioprotection via transcriptional reprogramming of the endothelium

This study identifies circadian PER2 amplitude enhancement in endothelial cells as a novel cardioprotective strategy that mimics HIF1A metabolic adaptation during myocardial ischemia.

Higher prevalence of homologous recombination-deficiency in lung squamous carcinoma from African Americans

The paper compares genomic features between African American and European American lung cancers, finding higher genomic instability and homologous recombination-deficiency in African American tumors.