Publications — Radcliffe Department of Medicine

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Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity?

McMaster B. et al, (2024), Nat Methods

A robust deep learning workflow to predict CD8 + T-cell epitopes.

Lee CH. et al, (2023), Genome Med, 15

A comparison of clustering models for inference of T cell receptor antigen specificity

Hudson D. et al, (2023)

Can we predict T cell specificity with digital biology and machine learning?

Hudson D. et al, (2023), Nat Rev Immunol, 1 - 11

SARS-CoV-2 peptides bind to NKG2D and increase NK cell activity.

Kim H. et al, (2021), Cell Immunol, 371

Spatiotemporal analysis of human intestinal development at single-cell resolution.

Fawkner-Corbett D. et al, (2021), Cell, 184, 810 - 826.e23

Single-cell atlas of colonic CD8+ T cells in ulcerative colitis.

Corridoni D. et al, (2020), Nat Med, 26, 1480 - 1490

In silico identification of vaccine targets for 2019-nCoV.

Lee CH. and Koohy H., (2020), F1000Res, 9

Potential CD8+ T Cell Cross-Reactivity Against SARS-CoV-2 Conferred by Other Coronavirus Strains.

Lee CH. et al, (2020), Front Immunol, 11

Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors.

Lee CH. et al, (2020), Front Immunol, 11

Discovery of a CD10-negative B-progenitor in human fetal life identifies unique ontogeny-related developmental programs.

O'Byrne S. et al, (2019), Blood, 134, 1059 - 1071

Colonic epithelial cell diversity in health and inflammatory bowel disease.

Parikh K. et al, (2019), Nature, 567, 49 - 55

Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease.

Kinchen J. et al, (2018), Cell, 175, 372 - 386.e17

Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells.

Koohy H. et al, (2018), Genome Biol, 19

Local Chromatin Features Including PU.1 and IKAROS Binding and H3K4 Methylation Shape the Repertoire of Immunoglobulin Kappa Genes Chosen for V(D)J Recombination.

Matheson LS. et al, (2017), Front Immunol, 8

The rise and fall of machine learning methods in biomedical research.

Koohy H., (2017), F1000Res, 6

Two Mutually Exclusive Local Chromatin States Drive Efficient V(D)J Recombination.

Bolland DJ. et al, (2016), Cell Rep, 15, 2475 - 2487

A new phosphate-starvation response in fission yeast requires the endocytic function of myosin I.

Petrini E. et al, (2015), J Cell Sci, 128, 3707 - 3713

A comparison of peak callers used for DNase-Seq data.

Koohy H. et al, (2014), PLoS One, 9

A lesson from the ice bucket challenge: using social networks to publicize science.

Koohy H. and Koohy B., (2014), Front Genet, 5

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