Tianxiao Li

Generative AI Guided Design of High-Affinity T cell Receptors

This paper introduces TCRPPO2, an AI-driven framework for optimizing TCR affinity, showing improved activity in engineered TCRs against tumor antigens.

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

Constructing a multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and co-infecting microbes

This paper constructs a multiple-layer interactome for SARS-CoV-2 by integrating human genes, miRNAs, and co-infecting microbes to identify potential drug targets.

Latent-space embedding of expression data identifies gene signatures from sputum samples of asthmatic patients

The paper identifies gene signatures predictive of asthma severity using a denoising autoencoder and random forest classifier applied to sputum gene expression data.

Approaches for integrating heterogeneous RNA-seq data reveals cross-talk between microbes and genes in asthmatic patients

The paper integrates heterogeneous RNA-seq data from asthmatic patients to uncover gene-microbe interactions and their clinical associations.

TopicNet: a framework for measuring transcriptional regulatory network change

TopicNet measures transcriptional regulatory network change by abstracting gene regulatory topics and quantifying rewiring scores between cellular states, revealing TFs with significant network connectivity changes and their impact on cancer survival.

GRAM: A generalized model to predict the molecular effect of a non-coding variant in a cell-type specific manner

GRAM predicts the molecular effect of non-coding variants in a cell-type specific manner using SELEX and expression profiles, achieving high performance on MPRA and luciferase assays.