Selected papers

Understanding Language Model Scaling on Protein Fitness Prediction

Hou et al 2026
Nature Computational Science

Molecular dynamics simulations of intrinsically disordered protein regions enable biophysical interpretation of variant effect predictors

Zafar et al 2026
HGG Advances

Protein language models trained on biophysical dynamics inform mutation effects

Hou et al 2026
PNAS

Antisense oligonucleotides to KIF1A polymorphisms expand targets and rescue patient-derived neurons in vitro

Zuccaro et al 2025
Nature Communications

MotifAE Reveals Functional Motifs from Protein Language Model: Unsupervised Discovery and Interpretability Analysis

Hou et al 2025b
bioRxiv

Disrupted endosomal trafficking of the Vangl-Celsr polarity complex underlies congenital anomalies in trachea-esophageal morphogenesis

Edwards et al 2025
Developmental Cell

PreMode predicts mode of action of missense variants by deep graph representation learning of protein sequence and structural context

Zhong et al 2025
Nature Communications

G2VTCR: predicting antigen binding specificity by Weisfeiler-Lehman graph embedding of T cell receptor sequences

Wang et al 2025
bioRxiv

A probabilistic graphical model for estimating selection coefficientsof nonsynonymous variants from human population sequence data

Zhao et al 2025
Nature Communications

Common variants increase risk for congenital diaphragmatic hernia within the context of de novo variants

Qiao et al 2024
AJHG

SABRE: Self-Attention Based model for predicting T-cell Receptor Epitope Specificity

Wang and Shen 2023
bioRxiv

VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants

Zhong et al 2023
Communications Biology

Rare predicted loss of function alleles in Bassoon (BSN) are associated with obesity

Zhu et al 2023
npj Genomic Medicine

SHINE: Protein Language Model based Pathogenicity Prediction for Inframe Insertion and Deletion Variants

Fan et al 2023
Briefings in Bioinformatics

Predicting functional effect of missense variants using graph attention neural networks

Zhang et al 2022
Nature Machine Intelligence

Accurate in silico confirmation of rare copy number variant calls from exome sequencing data using transfer learning

Tan and Shen 2022
Nucleic acids research

AlphaCluster: Coevolutionary driven residue-residue interaction models enable quantifiable clustering analysis of de novo variants to enhance predictions of pathogenicity

Obiajulu et al 2022
Research Square

Integrating de novo and inherited variants in over 42,607 autism cases identifies mutations in new moderate risk genes

Zhou et al 2022
Nature Genetics

Statistical models of the genetic etiology of congenital heart disease

Zhong & Shen 2022
Current Opinion in Genetics & Development

Identification and validation of novel candidate risk genes in endocytic vesicular trafficking associated with esophageal atresia and tracheoesophageal fistulas

Zhong et al 2022
HGG Advances

Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene

Qiao et al 2021
AJHG

Imputing cognitive impairment in SPARK, a large autism cohort

Shu et al 2022
Autism Research

Predicting localized affinity of RNA binding proteins to transcripts with convolutional neural networks

Kitaygorodsky et al 2021
bioRxiv

Rare variant analysis of 4,241 pulmonary arterial hypertension cases from an international consortium implicate FBLN2, PDGFD and rare de novo variants in PAH

Zhu et al 2021
Genome Medicine

Penetrance of breast cancer genes from the eMERGE III Network

Fan et al 2021
JNCI Cancer Spectrum

Functional interrogation of DNA damage response variants with base editing screens

Cuella-Martin et al 2021
Cell

MVP predicts pathogenicity of missense variants by deep learning

Qi et al 2021
Nature Communications

Template-based prediction of protein structure with deep learning

Zhang et al 2020
BMC Genomics

Genomic analyses implicate noncoding de novo variants in congenital heart disease

Richter et al 2020
Nature Genetics

Likely damaging de novo variants in congenital diaphragmatic hernia patients are associated with worse clinical outcomes

Qiao et al 2020
Genetics in Medicine

Novel Candidate Genes in Esophageal Atresia/Tracheoesophageal Fistula Identified by Exome Sequencing

Wang et al 2020
EJHG

Dissecting Autism Genetic Risk Using Single-cell RNA-seq Data

Chen et al 2020
bioRxiv

EM-mosaic detects mosaic point mutations that contribute to congenital heart disease.

Hsieh et al 2020
Genome medicine

Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes.

Feliciano et al 2019
NPJ genomic medicine

Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose.

Ma et al 2019
BMC molecular and cell biology

De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders.

Qi et al 2018
PLoS genetics

Quantifying size and diversity of the human T cell alloresponse.

DeWolf et al 2018
JCI insight

Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease.

Zhu et al 2018
Genome medicine

Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders.

Han et al 2018
Nature communications

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites.

Kumar et al 2017
Cell reports

Lineage specification of human dendritic cells is marked by IRF8 expression in hematopoietic stem cells and multipotent progenitors.

Lee et al 2017
Nature immunology

A Cell Type-Specific Expression Signature Predicts Haploinsufficient Autism-Susceptibility Genes.

Zhang and Shen 2016
Human mutation

Deep Genetic Connection Between Cancer and Developmental Disorders.

Qi et al 2016
Human mutation

Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire.

Sims et al 2016
PNAS

De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies.

Homsy et al 2015
Science

Increased burden of de novo predicted deleterious variants in complex congenital diaphragmatic hernia.

Yu et al 2015
Human molecular genetics

Tracking donor-reactive T cells: Evidence for clonal deletion in tolerant kidney transplant patients.

Morris et al 2015
Science translational medicine

Spatial map of human T cell compartmentalization and maintenance over decades of life.

Thome et al 2014
Cell

CANOES: detecting rare copy number variants from whole exome sequencing data.

Backenroth et al 2014
Nucleic acids research

All Papers