Paul J. S. Skipp

Identification of pre-existing ubiquitous neoantigen-reactive tumor-infiltrating T-cells in a patient with metastatic pancreatic neuroendocrine tumor

This study identifies a ubiquitous neoantigen-reactive T-cell response across multiple metastatic sites in a patient with pancreatic neuroendocrine tumor, supporting the use of mutation-sharing status for neoantigen selection in immunotherapy.

Immunopeptidomics-guided identification of functional neoantigens in non-small cell lung cancer

The paper identifies functional neoantigens in NSCLC patients using immunopeptidomics, achieving an 83% success rate in eliciting immune responses.

PathPinpointR: Predicting the progression of sc-RNAseq samples through reference trajectories.

PathPinpointR predicts scRNA-seq sample positions along reference trajectories using switching-gene events to assign pseudo-time values.

Identification of natural Zika virus peptides presented on the surface of paediatric brain tumour cells by HLA classI

This paper identifies 19 ZIKV peptides presented on paediatric brain tumour cells via HLA-I, showing their potential for developing epitope-specific immunotherapies.

Comparative analysis of protein expression between oesophageal adenocarcinoma and normal adjacent tissue

This study compares protein expression between oesophageal adenocarcinoma and normal adjacent tissue using proteomics to identify differentially expressed proteins and pathways.

Comparative analysis of transcriptomic and proteomic expression between two non-small cell lung cancer subtypes

The paper compares transcriptomic and proteomic expression between two NSCLC subtypes to identify potential therapeutic targets and biomarkers.

Knockdown proteomics reveals USP7 as a regulator of cell-cell adhesion in colorectal cancer via AJUBA

This study identifies USP7 as a regulator of cell-cell adhesion in colorectal cancer through its interaction with Ajuba, showing reduced adhesion upon USP7 or Ajuba knockdown.

Distinct immune responses in patients infected with influenza or SARS-CoV-2, and in COVID-19 survivors, characterised by transcriptomic and cellular abundance differences in blood.

The paper compares immune responses in influenza and SARS-CoV-2 infected patients and COVID-19 survivors using transcriptomic data, identifying distinct immune signatures and prognostic indicators.

A novel isoform of ACE2 is expressed in human nasal and bronchial respiratory epithelia and is upregulated in response to RNA respiratory virus infection

The paper identifies a novel short ACE2 isoform expressed in respiratory epithelia that is upregulated by interferon and RNA virus infection but not SARS-CoV-2, and shows reduced SARS-CoV-2 binding affinity.

An integrated model system to gain mechanistic insights into biofilm formation and antimicrobial resistance development in Pseudomonas aeruginosa MPAO1

The paper validates a model system to identify genes involved in biofilm formation and antibiotic resistance in Pseudomonas aeruginosa MPAO1 using genomics and experimental approaches.