Ben T. Jordan

This paper introduces PTM-POSE, a computational pipeline to analyze how alternative splicing affects post-translational modifications, and finds that 32% of PTMs are excluded from at least one Ensembl isoform.

Biosurfer identifies sources of protein isoform diversity by analyzing long-read RNA-seq data, revealing common mechanisms like alternative transcription start sites and 'ragged codons'.

The paper introduces LRP-IS-PRM, a method using long-read RNAseq to inform targeted proteomics with IS-PRM, identifying five new protein isoforms in human stem cells.

IsoBayes infers protein isoform presence and abundance using Bayesian methods integrating proteomics and transcriptomics data, showing good sensitivity and specificity in simulations and real datasets.

The paper uses long-read proteogenomics to characterize protein isoform diversity in HUVECs, identifying novel transcripts and isoforms with potential functional implications.

KSTAR predicts patient-specific kinase activities from phosphoproteomic data, improving comparison across labs and identifying tissue-specific profiles and treatment responses.

The paper benchmarks variant callers on long-read RNA-seq data and proposes a pipeline to improve their performance using spliced alignment files.

KinPred unifies and sustains kinase-substrate predictions by standardizing reference proteomes, mapping substrates and kinases, and filtering for the human phosphoproteome.