Wei Wang

CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription

ProteinAligner: A Multi-modal Pretraining Framework for Protein Foundation Models

ProteinAligner improves protein function and property prediction by integrating sequence, structure, and literature text modalities in a multi-modal pretraining framework.

Miniaturizing, Modifying, and Magnifying Nature's Proteins with Raygun

Raygun is a generative AI framework that miniaturizes, modifies, and expands proteins while preserving function and structural integrity, validated through cell-based experiments.

TUnA: An uncertainty aware transformer model for sequence-based protein-protein interaction prediction

TUnA is a Transformer model that predicts protein-protein interactions from sequence data and provides uncertainty estimates for unseen sequences, improving reliability.

APOE3-R136S mutation confers resilience against tau pathology via cGAS-STING-IFN inhibition

The R136S mutation on APOE3 enhances resistance to tau-related pathology and toxicity by downregulating the cGAS-STING-IFN signaling pathway.

For antibody sequence generative modeling, mixture models may be all you need

This paper introduces a simple generative model, SAM, for antibody sequence modeling that outperforms complex models and provides fast, interpretable tools for antibody sequence analysis.

Novel Ser74 of NF-kappaB/CgIkappaBalpha Phosphorylated by MAPK/ERK Regulates Temperature Adaptation in Oysters

The paper identifies a novel phosphorylation site (Ser74) in oyster NF-kappaB/CgI{kappa}B regulated by MAPK/ERK that mediates thermal adaptation through ubiquitin-proteasome degradation and nuclear translocation of CgREL.

Multi-ancestry genome-wide meta-analysis in Parkinson's disease

This paper conducts a multi-ancestry genome-wide meta-analysis of Parkinson's disease, identifying 78 independent loci and 23 genes associated with PD risk.

ADAM10 mediates macroglial cell fate decisions in the developing brain

The paper shows ADAM10 regulates macroglial cell fate by promoting astrocyte generation and inhibiting oligodendrocyte production in developing brains.

Dynamic fluctuations of the locus coeruleus-norepinephrine system underlie sleep state transitions

This study investigates how locus coeruleus-norepinephrine system activity and astrocytic responses change during sleep states, revealing dynamic fluctuations in norepinephrine levels and their relationship to sleep processes.

Generative pretraining from large-scale transcriptomes: Implications for single-cell deciphering and clinical translation

The paper introduces tGPT, a generative model for integrating large-scale single-cell transcriptomes, showing its effectiveness in clustering, trajectory inference, and linking gene patterns to clinical outcomes.

A framework for integrated clinical risk assessment using population sequencing data

This paper integrates monogenic, polygenic, and clinical risk factors to predict disease risk for carriers of rare variants, identifying elevated risk in 18.22% of UK Biobank participants for breast cancer, familial hypercholesterolemia, and colorectal cancer.

Brain endothelial cell tissue-nonspecific alkaline phosphatase (TNAP) activity promotes maintenance of barrier integrity via the ROCK pathway

This study shows that TNAP activity in brain endothelial cells maintains barrier integrity via the ROCK pathway, and its inhibition leads to barrier dysfunction.

Transduction catalysis:doxorubicin accelerates and enhances rAAV-mediated gene expression in the cortex of mouse, cat and monkey

This study shows doxorubicin enhances rAAV-mediated gene expression in the cortex of mice, cats, and monkeys, with effects observed across multiple serotypes and without significant cytotoxicity.

Genome-wide association analysis and replication in 810,625 individuals identifies novel therapeutic targets for varicose veins

This study identifies 49 genetic signals associated with varicose veins through a large GWAS and replication, highlighting potential therapeutic targets and biological pathways.

Exploring the Changing Landscape of Cell-to-Cell Variation After CTCF Knockdown via Single Cell RNA-seq

The paper investigates how CTCF knockdown affects genome-wide cell-to-cell variation using single-cell RNA-seq, finding increased expression noise and enrichment of transcription factor-related genes in CTCF-KD cells.

Neurogenin regulates effectors of migratory neuron cell behaviors in Ciona

The paper identifies candidate genes regulated by Neurogenin in Ciona's bipolar tail neurons, suggesting conserved roles in neuronal migration and development.

DTI-CDF: a CDF model towards the prediction of DTIs based on hybrid features

DTI-CDF improves drug-target interaction prediction by integrating hybrid features into a cascade deep forest model, achieving higher performance than existing methods.

The RNA-binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria

This study identifies Armitage as a protein linking piRNA amplification in nuage to phased piRNA production on mitochondria in Drosophila.

Paralogues of the PXY and ER receptor kinases enforce radial patterning in plant vascular tissue.

This study identifies a signaling network involving ER, PXY, PXL1, and PXL2 that coordinates radial patterning and expansion in plant vascular tissue through intertissue signaling.

Contextual Regression: An Accurate and Conveniently Interpretable Nonlinear Model for Mining Discovery from Scientific Data

The paper introduces contextual regression, a nonlinear model that combines interpretability and accuracy, demonstrating its effectiveness on simulated data and open chromatin prediction.

Sulforaphane modulates microRNA expression in colon cancer cells to implicate the regulation of oncogenes CDC25A, HMGA2 and MYC

This study investigates how sulforaphane affects microRNA expression in colon cancer and non-cancer cells, identifying potential targets like CDC25A, HMGA2, and MYC.

GSKB: A gene set database for pathway analysis in mouse

The paper creates a gene set database for pathway analysis in mouse, enabling pathway analysis and meta-analysis of gene expression signatures.

Assessment of single cell RNA-seq normalization methods

This study evaluates seven single cell RNA-seq normalization methods using diluted RNA data, finding that methods incorporating spike-in ERCC RNA outperform those without.

Assessing the measurement transfer function of single-cell RNA sequencing

This study evaluates the performance of three scRNA-seq methods through controlled experiments, finding they reliably detect genes above 5-10 molecules with linear measurement transfer functions.

Systematic identification of cooperation between DNA binding proteins in 3D space

The paper introduces a method to identify both cis- and trans-cooperation between DNA-binding proteins using ChIP-seq and Hi-C data, revealing new insights into 3D chromosomal interactions.

Targeted mutations on 3D hub loci alter spatial interaction environment

The paper identifies cancer-specific genotype variations that target 3D chromosomal hubs, altering local interactions and revealing principles of genome organization.

The Effectiveness of China’s National Forest Protection Program and National-level Nature Reserves, 2000 to 2010: PREPRINT

This study evaluates China's National Forest Protection Program and National-level Nature Reserves from 2000 to 2010, finding reduced deforestation rates within protected areas despite overall losses.

Full-genome evolutionary histories of selfing, splitting and selection in Caenorhabditis

This study uses whole-genome sequencing of C. briggsae isolates to infer population history, selection effects, and speciation dynamics across different geographic groups.

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

This study investigates the early stages of diploidization in Capsella bursa-pastoris, finding that gene loss is not rapid but rather associated with reduced selection efficacy due to demographic and genomic factors.