Taushif Khan

Clinical and Cross-Domain Validation of an LLM-Guided, Literature-Based Gene Prioritization Framework

The paper validates an LLM-guided gene prioritization framework for sepsis and tests its generalizability to obesity and infection using clinical and proteomic data.

Automating Candidate Gene Prioritization with Large Language Models: From Naive Scoring to Literature-Grounded Validation

This paper develops a framework using large language models for gene prioritization, validated against literature, identifying 30 high-confidence therapeutic candidates for sepsis.

Deep functional profiling of gene sets using Large Language Models: A blueprint for tailored, context-aware functional annotation

This paper introduces a method using Large Language Models to perform deep functional profiling of gene sets, demonstrating its ability to uncover detailed immune functions and improve upon traditional annotation tools.

Automating Candidate Gene Prioritization with Large Language Models: Development and Benchmarking of an API-Driven Workflow Leveraging GPT-4

This paper develops an API-driven workflow using GPT-4 to automate candidate gene prioritization, demonstrating high consistency and scalability in identifying sepsis-related genes.

Tackling the Complexity of Spatial Transcriptomics Data Interpretation with Large Language Models

This study uses large language models to analyze spatial transcriptomics data from a murine melanoma model, identifying immunosuppressive mechanisms in the tumor microenvironment.

Initial TCR Signal Strength Imprints GATA3 and Tbet Expression Driving T-helper Cell Fate Decisions

The paper shows that initial TCR signal strength sets early expression of GATA3 and Tbet, influencing Th2 differentiation, while cytokine signals modulate later differentiation outcomes.

Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens

The paper examines how HLA class II gene diversity influences antibody responses to common pathogens in an Arab cohort, finding that heterozygosity and synergistic allele effects enhance immunity.

ProLego: tool for extracting and visualizing topological modules in protein structures

ProLego extracts and visualizes topological modules in protein structures using a database of non-redundant topologies.

Indoril: An I-PV Add-On For Visualization Of Point Mutations On 3D Cartesian Coordinates

Indoril is an I-PV add-on that visualizes point mutations on 3D Cartesian coordinates to help researchers understand their impact on protein structure.