Roujia Li

Enigma: An Efficient Model for Deciphering Regulatory Genomics

Enigma is an efficient regulatory genomics model that achieves competitive performance with state-of-the-art models while significantly reducing computational cost.

FlashRNA: An Efficient Model for Regulatory Genomics

FlashRNA improves computational efficiency for genomic sequence-to-function models while maintaining or enhancing predictive performance across multiple tasks.

Comprehensively Testing the Function of Missense Variation in the STK11 Tumour Suppressor

This study functionally tests STK11 missense variants in mammalian cells, identifying pathogenic variants and providing insights for clinical interpretation.

Empowering rare variant burden-based gene-trait association studies via optimized computational predictor choice

The paper evaluates computational predictors for rare variant burden tests and identifies two top predictors that enhance gene-trait association discovery in the UK Biobank.

A missense variant effect map for the human tumour suppressor protein CHK2

The paper creates a functional map of all possible missense variants in CHK2 to assess their impact on cancer risk.

A comprehensive map of human glucokinase variant activity

This study maps human glucokinase variant activity using a yeast complementation assay, identifying activity patterns linked to disease and providing insights for variant interpretation and therapeutic development.

A map of binary SARS-CoV-2 protein interactions implicates host immune regulation and ubiquitination

The paper maps binary SARS-CoV-2 protein interactions with host proteins, identifying key processes like immune signaling and ubiquitination, and suggests therapeutic targets.

Global BioID-based SARS-CoV-2 proteins proximal interactome unveils novel ties between viral polypeptides and host factors involved in multiple COVID19-associated mechanisms

Proximity-dependent biotinylation (BioID) of 28 SARS-CoV-2 proteins in human cells maps 5,415 proximal interactions with 2,128 host targets across basal and poly(I:C) conditions.

TrackSig: reconstructing evolutionary trajectories of mutations in cancer

TrackSig estimates mutation evolutionary trajectories from bulk tumor sequencing data, showing improved accuracy in detecting subclonal populations and signature activity changes compared to baseline methods.

A reference map of the human protein interactome

The paper presents HuRI, a comprehensive human protein-protein interaction map, and demonstrates its utility in understanding cellular function and disease mechanisms.