Jing Chen

Transient diquat inclusion and carboxylate-rim binding to carboxymethyl-α-cyclodextrin: a molecular dynamics study

This study uses molecular dynamics to show that diquat binds to carboxymethyl-α-cyclodextrin mainly through dynamic rim interactions rather than persistent cavity inclusion.

Why 627 BindCraft2 trajectories produced zero binders

The paper reports that two BindCraft2 campaigns produced no binders despite high interface confidence, identifying issues with confidence metrics and a disabled feature.

Cross-Tissue Inflammatory Convergence Supports a Putative Muscle-Brain Axis in Alzheimer's Disease

The paper identifies shared inflammatory pathways between aging skeletal muscle and Alzheimer's disease brain tissue, detectable in peripheral blood, and prioritizes candidate regulators.

A T2T Benchmark Reveals How Reference Choice Shapes Human Genome Interpretation

This paper benchmarks how reference genome choice affects human genome interpretation by comparing T2T references and finding ancestry-matched references provide more accurate variant discovery.

Zfp719 is a transcription factor important for maintenance of hearing in mice

The paper investigates the role of Zfp719 in hearing maintenance in mice, finding that its mutation leads to progressive hearing loss and outer hair cell degeneration.

Forensic Identification of Confiscated Helmeted Hornbill (Rhinoplax vigil) Casques and Implications for Individual Quantification in Wildlife Crimes

This study improves forensic identification of helmeted hornbill casques by combining morphology and DNA barcoding to better estimate the number of individuals involved in wildlife crimes.

A variational sparse Gaussian-process method for detecting spatially variable genes and cellular interactions from spatial transcriptomics

VISGP identifies spatially variable genes and cellular interactions from spatial transcriptomics data, outperforming existing methods in detecting ligand-receptor pairs.

HESTA: a curated and reusable database for the human early organogenesis spatiotemporal transcriptome atlas

The paper presents a spatiotemporal transcriptome database of human embryogenesis, providing spatial gene expression and substructure data across 50 developing organs.

Structural Basis for Sarbecovirus Rc-o319 Spike Adaptation to Rhinolophus cornutus Bat ACE2 and Constraints on Switching to Human ACE2

This study characterizes the Rc-o319 S-protein's adaptation to R. cornutus ACE2 and identifies structural constraints limiting its ability to bind human ACE2.

ExMODE: A Multi-Omics Repository for Extremophile Adaptation and Bioprospecting

ExMODE is a multi-omics database for extremophiles that integrates and standardizes data to enable comparative analysis and bioprospecting.

TcrDesign: De novo design of epitope specific full-length T cell receptors

TcrDesign generates experimentally validated, functional, full-length TCRs using deep learning, achieving state-of-the-art performance in binding prediction and sequence generation.

CEACAM5/6+ Tumor Cells and IL-1β+ Macrophages Drive Resistance to Chemo-immunotherapy in Gastric Cancer

The paper identifies two resistance mechanisms in gastric cancer to chemo-immunotherapy, involving CEACAM5/6+ tumor cells and IL-1β+ macrophages, and suggests them as biomarkers and therapeutic targets.

Assessment of the Genetic Architecture at Early-Stage Drought Tolerance in Wheat Using UAV-Based Multispectral Imaging

This study uses UAV-based multispectral imaging to assess drought tolerance in wheat, identifying candidate genes and QTNs associated with early-stage drought stress.

A high-throughput immunopeptidome platform for MHC II alleles to characterize antigen-specific CD4 + T cells

The paper develops EliteMHCII, a high-throughput platform to identify MHC II epitopes and assess peptide binding affinity, showing high-affinity peptides correlate with strong CD4+ T cell responses.

Increased Inflammation as well as Decreased Endoplasmic Reticulum Stress and Translation Differentiate Pancreatic Islets of Pre-symptomatic Stage 1 Type 1 Diabetes and Non-diabetic Cases

Laser-microdissected islets of 3 multiple-autoantibody-positive stage 1 type 1 diabetes donors versus matched controls show 202 altered proteins: immune and glycolytic up, translation and ER-stress proteins down.

Distinct Binding Modes of Inter-Spike Cross-Linking Suggest a Supplementary Mechanism for SARS-CoV-2 Antibody Neutralization

This study uses cryo-EM to show that the W328-6H2 antibody forms different structures with SARS and Omicron BA.1 spike proteins, revealing a supplementary neutralization mechanism beyond RBD-Fab binding.

RhlR, but not RhlI, allows P. aeruginosa bacteria to evade Drosophila Tep4- mediated opsonization

This study shows that RhlR, not RhlI, enables P. aeruginosa to evade Drosophila Tep4-mediated opsonization, highlighting a RhlI-independent immune evasion mechanism.