Quantifying conformational changes in the TCR:pMHC-I binding interface

Authors: Benjamin McMaster, Christopher J. Thorpe, Jamie Rossjohn, Charlotte M. Deane, Hashem Koohy

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: TCR, MHC, peptide, HLA, conformational changes, T cell antigen specificity, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1491656/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/2331d3c5d2894b149ead1b291cba1917

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

Authors: Chloe H. Lee, Jaesung Huh, Paul R. Buckley, Myeongjun Jang, Mariana Pereira Pinho, Ricardo A. Fernandes, Agne Antanaviciute, Alison Simmons, Hashem Koohy

Source: Genome Medicine, Vol 15, Iss 1, Pp 1-24 (2023)

Subject Terms: Immunogenicity, CD8 + T-cell epitopes, Deep learning, Transfer learning, Computational immunology, Epitope prediction, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/e4fa26aaefb94dcb8391be6331e31555

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

Authors: Dan Hudson, Alex Lubbock, Mark Basham, Hashem Koohy

Source: ImmunoInformatics, Vol 13, Iss , Pp 100033- (2024)

Subject Terms: T cell antigen specificity, T cell receptor repertoire analysis, Clustering models, Deorphanizing TCRs, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S266711902400003X; https://doaj.org/toc/2667-1190

Access URL: https://doaj.org/article/0bd38d5ba5934f918697625493f3305a

Dual RNA sequencing reveals dendritic cell reprogramming in response to typhoidal Salmonella invasion

Authors: Anna Aulicino, Agne Antanaviciute, Joe Frost, Ana Sousa Geros, Esther Mellado, Moustafa Attar, Marta Jagielowicz, Philip Hublitz, Julia Sinz, Lorena Preciado-Llanes, Giorgio Napolitani, Rory Bowden, Hashem Koohy, Hal Drakesmith, Alison Simmons

Source: Communications Biology, Vol 5, Iss 1, Pp 1-17 (2022)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/26c225ac2f684651825e4bab14553e42

HLA variants have different preferences to present proteins with specific molecular functions which are complemented in frequent haplotypes

Authors: Vadim Karnaukhov, Wayne Paes, Isaac B. Woodhouse, Thomas Partridge, Annalisa Nicastri, Simon Brackenridge, Dmitrii Shcherbinin, Dmitry M. Chudakov, Ivan V. Zvyagin, Nicola Ternette, Hashem Koohy, Persephone Borrow, Mikhail Shugay

Source: Frontiers in Immunology, Vol 13 (2022)

Subject Terms: HLA, gene ontologies and pathways, molecular function, protein, mass spectrometry, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2022.1067463/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/8f742cced08646d3ae70b82baf33b46c

To what extent does MHC binding translate to immunogenicity in humans?

Authors: Chloe H. Lee, Agne Antanaviciute, Paul R. Buckley, Alison Simmons, Hashem Koohy

Source: ImmunoInformatics, Vol 3, Iss , Pp 100006- (2021)

Subject Terms: Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2667119021000069; https://doaj.org/toc/2667-1190

Access URL: https://doaj.org/article/e773dc3678264aaea0771eece7ab591b

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

Authors: Chloe H. Lee, Mariana Pereira Pinho, Paul R. Buckley, Isaac B. Woodhouse, Graham Ogg, Alison Simmons, Giorgio Napolitani, Hashem Koohy

Source: Frontiers in Immunology, Vol 11 (2020)

Subject Terms: cross-reactivity, antigen presentation, predict immunogenicity, epitopes, CD8+ T cell recognition, COVID-19, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2020.579480/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/cb5d6cdd7c3f41198aaa107f502f7680

Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors

Authors: Chloe H. Lee, Mariolina Salio, Giorgio Napolitani, Graham Ogg, Alison Simmons, Hashem Koohy

Source: Frontiers in Immunology, Vol 11 (2020)

Subject Terms: T cell cross reactivity, T cell specificity, epitope, antigen presentation, adaptive immune system, antigen specificity, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2020.565096/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/7ebdfb8b811347709b53843cc76d9ae5

In silico identification of vaccine targets for 2019-nCoV [version 2; peer review: 3 approved]

Authors: Chloe H. Lee, Hashem Koohy

Source: F1000Research, Vol 9 (2020)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/9-145/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/88c126f2005240259c44a9a29ef8d0c2

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

Authors: Hashem Koohy, Daniel J. Bolland, Louise S. Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jeremy Denizot, Raquel Manzano Garcia, Steven W. Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip Hawkins, Len Stephens, Sarah Elderkin, Mikhail Spivakov, Peter Fraser, Anne E. Corcoran, Patrick D. Varga-Weisz

Source: Genome Biology, Vol 19, Iss 1, Pp 1-24 (2018)

Subject Terms: Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-018-1489-y; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/6176506a0b014dd1a2e2a5beb2a2e029

In silico identification of vaccine targets for 2019-nCoV [version 1; peer review: 2 approved]

Authors: Chloe Hyun-Jung Lee, Hashem Koohy

Source: F1000Research, Vol 9 (2020)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/9-145/v1; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/2e9c296c9e1b490ab1122e742090068e

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

Authors: Daniel J. Bolland, Hashem Koohy, Andrew L. Wood, Louise S. Matheson, Felix Krueger, Michael J.T. Stubbington, Amanda Baizan-Edge, Peter Chovanec, Bryony A. Stubbs, Kristina Tabbada, Simon R. Andrews, Mikhail Spivakov, Anne E. Corcoran

Source: Cell Reports, Vol 15, Iss 11, Pp 2475-2487 (2016)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124716305885; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/2754b12283b14484b5441338b9c3ac7a

The rise and fall of machine learning methods in biomedical research [version 2; referees: 2 approved]

Authors: Hashem Koohy

Source: F1000Research, Vol 6 (2018)

Subject Terms: Bioinformatics, Statistical Methodologies & Health Informatics, Medicine, Science

File Description: electronic resource

Relation: https://f1000research.com/articles/6-2012/v2; https://doaj.org/toc/2046-1402

Access URL: https://doaj.org/article/fa61c0ecf6354dd8b6caa7f765401b27

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

Authors: Louise S. Matheson, Daniel J. Bolland, Peter Chovanec, Felix Krueger, Simon Andrews, Hashem Koohy, Anne E. Corcoran

Source: Frontiers in Immunology, Vol 8 (2017)

Subject Terms: V(D)J recombination, immunoglobulin kappa, epigenetic regulation, chromatin state, PU.1, IKAROS, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: http://journal.frontiersin.org/article/10.3389/fimmu.2017.01550/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/308388b4b3d8483f8570a4664004ecad

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

Authors: Hashem Koohy, Thomas A Down, Mikhail Spivakov, Tim Hubbard

Source: PLoS ONE, Vol 9, Iss 5, p e96303 (2014)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24810143/?tool=EBI; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/72529f33aa2046fc876b6f845a6a1978

Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.

Authors: Hashem Koohy, Thomas A Down, Tim J Hubbard

Source: PLoS ONE, Vol 8, Iss 7, p e69853 (2013)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23922824/?tool=EBI; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/07f3562fbdd9490287ef1b6281a41eec