Wei Li

scPCIP: cross-species annotation of plant cell types with conserved gene programs

scPCIP annotates plant cell types across species using conserved gene programs, outperforming marker-based and deep-learning methods in held-out datasets.

Preclinical Development and Safety of Laterally Spreading Dual AAV.SPR-MYO7A Vectors for the Treatment of Usher Syndrome Type 1B

This paper develops and tests dual AAV vectors for treating USH1B by reconstituting full-length MYO7A expression, showing safety and efficacy in non-human primates.

Janusein and EB Cooperate to Enhance Microtubule Plus-end Catastrophe

This study identifies Janusein as a microtubule-associated protein that cooperates with EB proteins to enhance microtubule plus-end catastrophe.

Interspecific hybrids reveal a deeply conserved nuclear role of EIF1A-family proteins in zygotic genome activation

The paper uses interspecific hybrid embryos to identify EIF1A-family proteins as conserved nuclear regulators of zygotic genome activation across mammals.

Repetitive transcranial magnetic stimulation targeting motor cortical region induces cell-type-specific transcriptional reprogramming and behavioral recovery in non-human primate model of Rett syndrome

This study shows that rTMS targeting the motor cortex in a non-human primate model of Rett syndrome improves behavioral outcomes and induces cell-type-specific transcriptional changes.

Pan-cancer nucleosome landscapes reveal tumor heterogeneity and inform cell-free DNA-based detection

The paper characterizes nucleosome organization across 23 cancer types using ATAC-seq and shows its utility for cancer classification and detection using cell-free DNA.

Transient tubular membrane injury is converted into persistent fibrosis through a macrophage-fibroblast relay

This paper identifies a macrophage-fibroblast relay mechanism that converts transient tubular membrane injury into persistent fibrosis following acute kidney injury.

Systemic tumor-cell reprogramming converts solid tumors into in situ biofactories for immunotherapy

LENTRA reprograms tumor cells to produce therapeutic molecules, inducing antitumor immunity and durable immune memory in mouse models and patient-derived explants.

The RNA modification N6-methyladenosine restrains SIRPα to license myeloid efferocytosis in atherosclerosis

This study identifies the m6A-SIRP axis as a regulator of efferocytosis in atherosclerosis, showing myeloid m6A loss increases plaque instability.

Spatially Confined Phase Separation Promotes Local Tubulin Availability to Stabilize Ciliary Microtubule Growth

This study identifies RAT-1 as a regulator of ciliary microtubule dynamics through spatially confined phase separation that stabilizes tubulin availability for MT growth.

Integrating structural and biological evidence to rerank ESMFold2 protein-protein interactions

The paper develops a framework to rerank protein-protein interactions using structural and biological evidence, improving prediction accuracy over structural-only methods.

Mammalian TMC Family Proteins are Mechanically Gated Ion Channels

The paper identifies TMC3-8 as mechanosensitive ion channels by showing their plasma membrane localization and stretch-activated currents in cultured cells.

Full-length transcriptome atlas of Panax vietnamensis var. fuscidiscus reveals novel genes and alternative splicing in tissue-specific biosynthesis of ocotillol-type saponins

This study constructs the first full-length transcriptome atlas of Panax vietnamensis var. fuscidiscus, identifying novel genes and extensive alternative splicing events related to OCT-type saponin biosynthesis.

Healed predation scar on a Cambrian apex predator

The paper reports a healed predation scar on a Cambrian apex predator, providing evidence of trophic complexity in Cambrian food webs.

Mapping Enteric Neural Circuits by Anterograde Transsynaptic Tracing

The paper introduces mWmC, a viral tracer for mapping enteric neuronal circuits, showing it selectively labels postsynaptic neurons without affecting other cell types.

A Diploid Panax Genome Reveals Ginsenoside Diversity Driven by UGT Diversification and Network Rewiring, Rather Than Gene Family Expansion

This paper presents a diploid Panax genome and shows ginsenoside diversity arises from UGT diversification and rewired networks, not gene family expansion.

A high-quality, chromosome-scale genome assembly of the shade-tolerant wild rice, Oryza granulata

This paper presents a high-quality chromosome-scale genome assembly of Oryza granulata, a shade-tolerant wild rice, using PacBio, Hi-C, and Illumina sequencing.

Salivary microRNA Profiling of Long COVID Subjects Reveals Host-Encoded Regulators of Inflammation and Viral Persistence

This study identifies salivary miRNAs that regulate inflammation and SARS-CoV-2 persistence in long COVID patients.

MeCP2 is Necessary in Cerebellar Purkinje Cells for Precise Network Dynamics During Associative Motor Learning

This study shows that MeCP2 in Purkinje cells is critical for precise timing and coordination in cerebellar learning but not for general motor behaviors.

Telomere maintaining germline and somatic variants in thyroid cancer and melanoma

The paper examines the mutual exclusivity and clinical associations of germline long-telomere syndrome variants and somatic TERT promoter mutations in thyroid cancer and melanoma, finding they are mutually exclusive but have distinct clinical impacts.

ATF2 phosphorylation is a core transcriptional driver of neuron apoptosis

The paper identifies ATF2 phosphorylation as a key driver of neuron apoptosis and shows that inhibiting ATF2 protects neurons in culture and in vivo.

cfMIND: A read-level methylation framework for accurate non- invasive disease detection using cell-free DNA

cfMIND improves non-invasive disease detection by analyzing read-level methylation signals from cell-free DNA, achieving high accuracy even at low sequencing depth and across diverse cancers.

Epigenetic and 3D Genome Changes Drive Primary Trastuzumab Resistance in HER2+ Breast Cancer

This study identifies epigenetic and 3D genome changes as key drivers of primary trastuzumab resistance in HER2+ breast cancer through integrative analysis of chromatin architecture and histone modifications.

DNA Data Storage Architecture via Ligation of Dynamic DNA Bytes

This paper introduces a modular DNA storage system using dynamic DNA bytes that enables reconfigurable, rewritable data storage with CRUD operations and error correction.

Toward Computationally Complete Spatial Omics

COSIE is a computational framework that integrates multiple spatial omics modalities to generate high-resolution molecular landscapes, outperforming existing methods across diverse datasets.

Tissue- and Age-Specific Transcriptomic and Metabolomic Analysis Reveals Regulatory Mechanisms of Ginsenoside Biosynthesis in Panax notoginseng

This study identifies tissue- and age-specific transcriptional regulators of ginsenoside biosynthesis in Panax notoginseng using transcriptomics and metabolomics.

Evolutionary Divergence of Structure-Function Coupling between Human and Macaque: Spatial Patterns and Transcriptomic Basis

This study compares structural-functional coupling patterns between human and macaque brains, finding species-specific differences linked to evolutionary adaptations in gene expression and cognitive function.

Anti-σ28 factor FlgM secretion regulates Vibrio cholerae adaptability in adult mice through quorum sensing and methionine metabolism

This study shows that FlgM secretion in V. cholerae affects host adaptability through quorum sensing and methionine metabolism, linking motility loss to increased virulence.

Progranulin deficiency induces lipid droplet accumulation in microglia via a STAT3-GPAT3 axis

This study shows that PGRN deficiency causes lipid droplet accumulation in microglia through the STAT3-GPAT3 axis, and identifies potential therapeutic strategies.

DNACSE: Enhancing Genomic LLMs with Contrastive Learning for DNA Barcode Identification

DNACSE improves DNA barcode identification by fine-tuning DNA language models with contrastive learning, achieving higher accuracy and clustering performance than existing methods.