Kai Wang

A protein language model for domain, functional site, and variant effect prediction

PALM, a protein language model, predicts domain, functional site, and variant effects with high accuracy using curated sequence data and outperforms existing models in multiple benchmarks.

Analysis of Rare Coding Variation Identifies New Genetic Contributors to Schizophrenia

Ultra-rare damaging coding variants in 87,959 schizophrenia cases and 150,587 controls implicate 40 genes (16 exome-wide, 24 at 5% FDR), half overlapping autism, developmental delay or bipolar genes.

PubMind: Literature-Based Genetic Variant Extraction and Functional Annotation Using Large Language Models

PubMind extracts and annotates genetic variant functionality from biomedical literature using LLMs, creating a database with over 1.3 million variants.

Dissecting the relationship between haplotypes around ATXN2 CAG repeats and the number of CAA interruptions by long-read sequencing

This study uses long-read sequencing to analyze haplotypes and CAA interruptions in ATXN2 CAG repeats, finding ethnicity-specific and ALS-specific associations.

LongAllele: a joint inference framework for allele-specific analysis on long-read bulk and single-cell RNA sequencing

LongAllele jointly infers haplotypes and performs allele-specific analysis on long-read bulk and single-cell RNA-seq data, revealing context-dependent cis-regulatory effects and high-impact variants.

Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing

SCOTCH improves isoform-level gene expression characterization using long-read single-cell RNA sequencing by refining sub-exon boundaries and reducing false positives.

Long-Read Transcriptome Sequencing and Functional Validation Reveals Novel and Oncogenic Gene Fusions in Fusion Panel-Negative Gliomas

The paper identifies novel oncogenic gene fusions in fusion-negative gliomas using long-read sequencing and functional validation in Drosophila.

Distinct cellular DNA methylation mechanisms underlie common and rare genetic risk for brain disorders

The paper identifies distinct DNA methylation mechanisms for common and rare noncoding genetic risk in brain disorders using deep learning and single-nucleus DNAm data.

Noncoding de novo mutations in SCN2A are associated with autism spectrum disorders

The paper identifies noncoding de novo mutations in SCN2A associated with autism spectrum disorders using two statistical methods on large-scale sequencing data.

NRCAM variant defined by microexon skipping is a targetable cell surface proteoform in high-grade gliomas

The paper identifies a NRCAM proteoform with skipped microexons as a targetable surface antigen in pHGG and demonstrates its utility in immunotherapy.

A Comparative Evaluation of Computational Models for RNA modification detection using Nanopore sequencing with RNA004 Chemistry

This study compares two RNA modification detection models, Dorado and m6Anet, using RNA004 sequencing data, finding Dorado has higher recall but both have high false discovery rates for m6A and pseudouridine.

LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data

LongReadSum provides fast, comprehensive quality control and signal summarization for long-read sequencing data across multiple platforms and formats.

Functional analysis of ESRP1/2 gene variants and CTNND1 isoforms in orofacial cleft pathogenesis

The paper functionally tests ESRP1/2 variants and CTNND1 isoforms in orofacial cleft models, finding some variants are benign and showing CTNND1's role in palatogenesis.

Running ahead of evolution - AI based simulation for predicting future high-risk SARS-CoV-2 variants

This paper develops an AI-based simulation method to predict future high-risk SARS-CoV-2 variants by simulating RBD mutations and screening potential variants efficiently.

precisionFDA Truth Challenge V2: Calling variants from short- and long-reads in difficult-to-map regions

The paper evaluates variant calling in difficult genomic regions using short- and long-read sequencing, showing improved performance with new methods and multi-technology approaches.

LIQA: Long-read Isoform Quantification and Analysis

LIQA quantifies isoform expression and detects differential alternative splicing in long-read RNA-seq data, outperforming existing methods in low-coverage and biased read scenarios.

A computational method for direct imputation of cell type-specific expression profiles and cellular compositions from bulk-tissue RNA-Seq in brain disorders

CellR imputes cell type-specific expression profiles and cellular compositions from bulk RNA-Seq data in brain disorders, showing improved accuracy and stability compared to existing methods.

Detection of Base Analogs Incorporated During DNA Replication by Nanopore Sequencing

This paper demonstrates the use of nanopore sequencing to detect thymidine analogs incorporated during DNA replication, enabling high-resolution analysis of replication fork dynamics.

Implications of error-prone long-read whole-genome shotgun sequencing on characterizing reference microbiomes

This study evaluates the feasibility of using error-prone long-read sequencing for microbiome characterization, showing high accuracy in assembly and abundance estimation.

Phen2Gene: Rapid Phenotype-Driven Gene Prioritization for Rare Diseases

Phen2Gene prioritizes genes based on HPO terms for rare diseases, outperforming existing tools in speed and accuracy for clinical diagnosis.

Gene expression in patient-derived neural progenitors implicates WNT5A signaling in the etiology of schizophrenia

The paper identifies differentially expressed genes in schizophrenia-associated neural progenitor cells, implicating WNT5A signaling in schizophrenia etiology.

NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks

NanoCaller improves SNP and indel detection in difficult genomic regions using long-read sequencing and haplotype-aware deep learning.

Dosage effect of multiple genes accounts for multisystem disorder of myotonic dystrophy type 1

This study shows that reduced gene dosage in multiple genes causes multisystem disorders in DM1 by creating mouse models with multigene mutations.

LinkedSV for detection of mosaic structural variants from linked-read exome and genome sequencing data

LinkedSV detects mosaic structural variants from linked-read sequencing data, outperforming existing tools and identifying SVs missed by conventional sequencing methods.

Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD)

This paper develops a single-molecule optical mapping method for quantitative D4Z4 repeat analysis in FSHD, showing concordance with Southern blot and improved haplotype resolution.

Deconvolution of Transcriptional Networks Identifies TCF4 as a Master Regulator in Schizophrenia

The paper deconvolves transcriptional networks in schizophrenia to identify TCF4 as a master regulator potentially dysregulated in the disease.

NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data

NanoMod detects DNA modifications from Nanopore sequencing data by comparing signal distributions between modified and unmodified samples.

iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing cancer driver genes in personal genomes

iCAGES identifies personalized cancer driver genes and predicts therapies by integrating genomic data and biological knowledge, achieving high accuracy in mutation and gene classification.

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.