Yukun Tan

Soluble Immune Factor Profiles in Blood and CSF Associated with LRRK2 Mutations and Parkinson's Disease

This study identifies immune factor profiles in blood and CSF associated with LRRK2 mutations and Parkinson's disease, showing distinct changes in serum and CSF markers.

Literature-scaled immunological gene set annotation using AI-powered immune cell knowledge graph (ICKG)

The paper constructs an immune cell knowledge graph (ICKG) using AI to annotate immunological gene sets more accurately than existing methods.

Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles

The paper constructs immune-specific gene sets using non-negative matrix factorization on bulk RNA-seq data to improve immune subtype analysis and ICB response prediction.

novoRNABreak: local assembly for novel splice junction and fusion transcript detection from RNA-seq data

novoRNABreak detects novel splice junctions and fusion transcripts in cancer RNA-seq data with high sensitivity and efficiency.

Monopogen: single nucleotide variant calling from single cell sequencing

Monopogen calls single nucleotide variants from single-cell sequencing data, achieving high accuracy in germline variant detection and enabling ancestry inference and variant association analysis.

Characterizing transition cells in developmental processes from scRNA-seq data

The paper models scRNA-seq data from developmental processes using SDEs to identify transition cells that explain heterogeneity and predict cell fate in early tumorigenesis.

PALLAS: Penalized mAximum LikeLihood and pArticle Swarms for inference of gene regulatory networks from time series data

PALLAS infers gene regulatory networks from time series data using penalized maximum likelihood and particle swarms, showing efficiency and accuracy in synthetic and real data.