A. Chen

C4 Grasses Employ Distinct Strategies to Acclimate Rubisco Activase to Heat Stress

This study investigates how different C4 grasses regulate rubisco activase under heat stress, revealing species-specific adaptations in isoform abundance and biochemical regulation.

Solid/liquid coexistence during aging of FUS condensates

The paper shows that FUS condensates during aging exhibit solid/liquid coexistence, with the transition initiated at the interface between dense and dilute phases.

3D CentroidNet: Nuclei Centroid Detection With Vector Flow Voting

This paper introduces a 3D nuclei centroid detection method using vector flow voting, achieving better performance than existing methods on real microscopy data.

NISNet3D: Three-Dimensional Nuclear Synthesis and Instance Segmentation for Fluorescence Microscopy Images

NISNet3D is a deep learning model for 3D nuclear segmentation in fluorescence microscopy images, trained on synthetic data and compared to eight existing methods.

High-throughput single-molecule quantification of individual base stacking energies in nucleic acids

This study measures individual base stacking energies in DNA and RNA using a custom Centrifuge Force Microscope, finding stronger stacking between purines and weaker between pyrimidines, with implications for DNA nanostructures, enzymatic ligation, and MD simulations.

DINAVID: A Distributed and Networked Image Analysis System for Volumetric Image Data

DINAVID provides a cloud-based system for remote 3D microscopy image analysis and visualization, designed to handle large datasets and improve accessibility.

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball patterned arrays

This study develops Stereo-seq, a high-resolution spatial transcriptomic method, to analyze mouse organogenesis and map developmental disease loci.

An Ensemble Learning and Slice Fusion Strategy for Three-Dimensional Nuclei Instance Segmentation

This paper introduces EMR-CNN, a 3D nuclei segmentation method that avoids ground truth annotations and uses ensemble learning and slice fusion for efficient and accurate results.

Assignment of structural transitions during mechanical unwrapping of nucleosomes and their disassembly products

This study uses optical tweezers and FRET to identify DNA segments unwrapped during nucleosome mechanical transitions, revealing distinct low- and high-force unwrapping processes.

Mechanism-based crosslinking probes capture E. coli ketosynthase FabB in conformationally-distinct catalytic states.

The paper solves crystal structures of E. coli FabB in complex with crosslinked ACPs to elucidate its catalytic mechanism and conformational states.

Global Spatial Transcriptome of Macaque Brain at Single-Cell Resolution

The paper creates a 3-D cell type atlas of the monkey brain using single-cell spatial transcriptomics and identifies molecular markers for neocortical layers and subregions.

Modeling predicts mechanisms altered by mutations of the SARS-CoV-2 delta and omicron variants

The paper models how mutations in SARS-CoV-2 delta and omicron variants alter viral load and infection outcomes by simulating different mechanistic changes.

Novel plasma exosome biomarkers for prostate cancer progression in co-morbid metabolic disease

This study identifies plasma exosomal miRNAs associated with T2D that induce EMT and immune checkpoint expression in prostate cancer cells.

40 new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds.

This paper describes 40 new Ichthyornis specimens, revealing detailed postcranial morphology and phylogenetic placement within the avian stem group.

Single-nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma

This study uses snRNA-seq and Stereo-seq to analyze the immunological microenvironment of cervical squamous cell carcinoma, identifying immune cell clusters and their associations with tumor progression and patient survival.

Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift

This study shows that Omicron variant's spike protein has enhanced ACE2 binding and reduces neutralizing activity, but some broadly neutralizing antibodies remain effective.

Directing iPSC Differentiation into iTenocytes using Combined Scleraxis Overexpression and Cyclic Loading

This study differentiates iPSC-derived MSCs into tenocytes using Scleraxis overexpression and mechanical stretch, showing improved tendon marker expression and ECM alignment compared to BM-MSCs.

Syrbactin-class dual constitutive- and immuno-proteasome inhibitor TIR-199 impedes myeloma-mediated bone degeneration in vivo.

This study characterizes TIR-199, a proteasome inhibitor that effectively targets myeloma and shows in vivo activity against bone degeneration.

Spatially-resolved transcriptomics analyses of invasive fronts in solid tumors

This study uses spatial transcriptomics to analyze invasive fronts in solid tumors, identifying immune cell enrichment, metabolic changes, and poor prognosis factors.

Single-cell Stereo-seq enables cell type-specific spatial transcriptome characterization in Arabidopsis leaves

This study introduces scStereo-seq, a method for single-cell spatial transcriptome profiling in Arabidopsis leaves, revealing cell type-specific spatial gene expression gradients and developmental trajectories.

Prevalence, persistence, and genetics of antibody responses to protein toxins and virulence factors

The paper uses PhIP-Seq with a ToxScan library to profile antibody responses to toxins and virulence factors in 1,000 individuals, finding MHC-II locus associations and novel anti-flagellin links to juvenile dermatomyositis.

Stem cell quiescence requires PRC2/PRC1-mediated mitochondrial checkpoint

The paper shows that PRC2/PRC1-mediated mitochondrial checkpoint regulates quiescence in Drosophila GSCs and human iPSCs through mitophagy and mitochondrial dynamics.

Genome-wide CRISPR activation screen identifies novel receptors for SARS-CoV-2 entry

This study identifies novel SARS-CoV-2 receptors through a CRISPR activation screen, revealing LDLRAD3, TMEM30A, and CLEC4G as functional receptors independent of ACE2.

SARS-CoV-2 immune evasion by variant B.1.427/B.1.429

This study evaluates how the B.1.427/B.1.429 SARS-CoV-2 variant evades neutralizing antibodies through mutations in the RBD and NTD, showing reduced neutralization by both vaccine-induced and infection-derived antibodies.

High-resolution single-molecule long-fragment rRNA gene amplicon sequencing for uncultured bacterial and fungal communities

This study develops a method to sequence nearly full-length rRNA genes from environmental samples, achieving high accuracy and coverage in microbial community analysis.

Structure and mechanistic analyses of the gating mechanism of elongating ketosynthases

The paper investigates the gating mechanism of elongating ketosynthases by analyzing structural and functional data from AcpP-FabF complexes.

Survival and Inactivation by Advanced Oxidative Process of Foodborne Viruses in Model Low-Moisture Foods

This study examines viral survival in low-moisture foods and evaluates the effectiveness of an advanced oxidative process for virus inactivation.

N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2

The paper identifies a conserved antigenic supersite on the SARS-CoV-2 N-terminal domain recognized by neutralizing antibodies and shows its vulnerability to mutations in variants.

In vitro analysis of colistin and ciprofloxacin antagonism of Pseudomonas aeruginosa phage PEV2 infection activities

This study evaluates how colistin and ciprofloxacin affect the infection activities of Pseudomonas aeruginosa phage PEV2, finding that colistin significantly interferes while ciprofloxacin has minimal impact.

An adaptive optics module for deep tissue multiphoton imaging in vivo

This paper develops an adaptive optics module for multiphoton imaging in vivo, enabling high-resolution visualization of neural structures and calcium responses in deep brain and spinal cord regions of mice.