Faraz Khan

-Applied probabilistic modeling and GRN inference to investigate inflammatory bowel disease (IBD), identifying cell-state transitions and transcription factor-driven regulatory programs underlying intestinal inflammation. -Fine-tuned and applied sequence-to-function (S2F) models to infer cis-regulatory logic, identifying sequence drivers of inflammatory gene expression and translating attribution maps into mechanistic GRN insights. -Curated and integrated multi-omics datasets to benchmark GRN and sequence-to-function models, improving model interpretability and robustness. -Constructed scalable pipelines in Snakemake to extract fine-mapped GWAS signals and integrate them with QTL colocalization, enabling robust causal gene and variant prioritization.

-At Grey Wolf Therapeutics, part of the Molecule 2 Medicine ecosystem, developed bioinformatic pipelines and novel computational methods for diverse multi-omic datasets, providing unique biological insights for ongoing drug discovery and development programs.

-Development of pipelines for NGS data analysis, including mutational calling, Single-Cell RNA-seq, ChIP peak calling and methylation, variant annotation and prioritisation, as well as multi-layer data integration strategy and tools.

Genome assembly, Genome upgrading, variant calling and genome annotation.

Analysis, mining and interpretation of DNA and RNA-sequencing projects in several species involving quality control, alignment, transcript assembly, quantification, expression analysis, variant calling, annotation, network and pathway analysis.

Specialized in bioinformatics applications within agricultural omics, gained expertise in genomic and transcriptomic data analysis and statistical modeling.