Dr Justin P. Whalley
Senior Bioinformatician
Dr Justin P. Whalley is currently (2023) a member of the faculty of the Chicago Medical School at Rosalind Franklin University of Medicine and Science.
He was a senior bioinformatician in the Knight Group from 2017 to 2022 and Research Member of Common Room at Kellogg College. He was the lead for the Extreme Response Functional Genomics project, as well as the head of Integration (Tensors) working group for the COVID-19 Multi-omic Blood Atlas (COMBAT).
Publications from his time in the group concentrated on immunity and the host response to infection. This included work on CRISPR/Cas9, epigenetics, long read technologies, tensor decomposition and imputation.
His teaching responsibilities included the Introduction to Statistics module to first year DPhil in Genomic Medicine and Statistics students, and the Data Science in Python module to the Masters in Modelling for Global Health students.
He was heavily involved in public engagement and led the group that won the Wellcome Centre for Human Genetics "Excellence in Public Engagement for Projects" 2019 prize.
Recent publications
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Pleural fluid proteomics from patients with pleural infection shows signatures of diverse neutrophilic responses: The Oxford Pleural Infection Endotyping Study (TORPIDS-2)
Journal article
Kanellakis NI. et al, (2025), European Respiratory Journal, 2500010 - 2500010
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High-throughput mass spectrometry maps the sepsis plasma proteome and differences in patient response
Journal article
Mi Y. et al, (2024), Science Translational Medicine, 16
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Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs
Journal article
Weeratunga P. et al, (2023), Nature Communications, 14
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Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance
Journal article
Amarasinghe HE. et al, (2023), BMC Genomics, 24
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SARS-CoV-2 infection induces a long-lived pro-inflammatory transcriptional profile
Journal article
Zhang J-Y. et al, (2023), Genome Medicine, 15
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A Transcriptomic Approach to Understand Patient Susceptibility to Pneumonia After Abdominal Surgery
Journal article
Torrance HD. et al, (2023), Annals of Surgery
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A transcriptomic approach to understand patient susceptibility to pneumonia after abdominal surgery
Preprint
Torrance HD. et al, (2023)
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Systemic 4-1BB stimulation augments extrafollicular memory B cell formation and recall responses duringPlasmodiuminfection
Preprint
Caloba C. et al, (2023)
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Unbiased single cell spatial analysis localises inflammatory clusters of immature neutrophils-CD8 T cells to alveolar progenitor cells in fatal COVID-19 lungs
Preprint
Weeratunga P. et al, (2022)
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Epigenomic analysis reveals a dynamic and context-specific macrophage enhancer landscape associated with innate immune activation and tolerance
Journal article
Zhang P. et al, (2022), Genome Biology, 23