Tian Yu

Language models reveal evidence gaps in variants of uncertain significance

The paper uses language models to analyze ClinVar variant summaries, identifying evidence gaps in Variants of Uncertain Significance and reclassifying some as likely benign or pathogenic.

Extracting and calibrating evidence of variant pathogenicity from population biobank data

The paper uses population biobank data to identify and calibrate evidence of variant pathogenicity for 41 genes, finding that 2.6% of participants have rare variants with moderate or stronger evidence of pathogenicity.

Deaminase-mediated chromatin accessibility profiling with single-allele resolution

The paper introduces ACCESS-ATAC, a method that improves TF binding site prediction resolution and reveals allele-specific co-occupancy patterns in HepG2 and K562 cells.

Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification

This paper improves variant effect quantification in base editing screens by integrating genotypic and phenotypic data using a Bayesian network called BEAN.

Systematic elucidation of genetic mechanisms underlying cholesterol uptake

This study identifies 21 genes whose rare variants affect LDL-C levels by altering cholesterol uptake, using CRISPR screening and co-essentiality analysis.

Maternal transmission of a paramutant phenotype requires intact DNMT2 functions in the male germline

The paper investigates the role of DNMT2 in maternal transmission of a paramutant phenotype through the male germline.

Efficient multiplex genome editing using CRISPR-Mb3Cas12a in mice

This study demonstrates that CRISPR-Mb3Cas12a can efficiently edit the mouse genome with minimal off-target effects and without requiring the TTTV PAM sequence.

Template switching causes artificial junction formation and false identification of circular RNAs

The paper identifies artificial junction sequences formed by reverse transcriptases, leading to false circular RNA identification, and proposes methods to distinguish true circular RNAs.