Author

P. Bradley

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Immunology· 4 Microbiology· 4 Biophysics· 2

Signature Assays, Organisms & Methods

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Organism:human· 6 Research Focus:cell type annotation· 5 Research Focus:differential expression· 4 Approach:experimental assay· 4 Approach:statistical model· 4 Approach:deep learning· 3 Assay:scRNA-seq· 3 Research Focus:gene regulatory network inference· 2

Frequent Co-Authors

Z. Iqbal· 3 shared A. Souquette· 2 shared J. C. Crawford· 2 shared P. G. Thomas· 2 shared S. Schattgen· 2 shared T. M. Walker· 2 shared A. A. Votintseva· 1 shared A. Chatterjee· 1 shared

Activity by Year

2016-2022 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 16 mutual co-author links

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3 shared papersMicrobiology

Z. Iqbal

Mutual co-authors in cluster

Author profile →

10 papers

Recent·Most cited

Statistical inference reveals the role of length, breathing, and nucleotide identity in V(D)J nucleotide trimming

M. L. Russell, N. Simon, P. Bradley, F. A. Matsen

The paper uses a probabilistic model to analyze TCRβ repertoire data and identifies sequence features that predict nucleotide trimming during V(D)J recombination.

bioRxiv · Dec 8, 2022Immunology

Learning the shape of protein micro-environments with a holographic convolutional neural network

M. N. Pun, A. Ivanov, Q. Bellamy, Z. Montague, C. LaMont, P. Bradley, J. Otwinowski, A. Nourmohammad

This paper introduces H-CNN, a machine learning model that predicts mutation impacts on protein function using structural and evolutionary data.

bioRxiv · Oct 31, 2022 · PreprintBiophysics

MR1-restricted T cell clonotypes are associated with 'resistance' to M.tuberculosis infection

D. L. Cross, E. D. Layton, K. K. Yu, M. T. Smith, M. S. Aguilar, S. Li, H. Mayanja-Kizza, C. M. Stein, W. H. Boom, T. R. Hawn, P. Bradley, E. Newell, C. Seshadri

The paper identifies MR1-restricted T cell clonotypes associated with resistance to M. tuberculosis infection in a cohort of Ugandan individuals.

bioRxiv · Oct 12, 2022 · PreprintImmunology

TCR meta-clonotypes for biomarker discovery with tcrdist3: identification of public, HLA-restricted SARS-CoV-2 associated TCR features

K. Mayer-Blackwell, S. Schattgen, L. Cohen-Lavi, J. C. Crawford, A. Souquette, J. A. Gaevert, T. Hertz, P. G. Thomas, P. Bradley, A. Fiore-Gartland

The paper introduces meta-clonotypes for TCR analysis, identifies HLA-restricted SARS-CoV-2 TCR features, and develops tcrdist3 for repertoire analysis.

bioRxiv · Dec 24, 2020Immunology

Linking T cell receptor sequence to transcriptional profiles with clonotype neighbor graph analysis (CoNGA)

S. Schattgen, K. Guion, J. C. Crawford, A. Souquette, A. Martinez Barrio, M. J. T. Stubbington, P. G. Thomas, P. Bradley

The paper introduces CoNGA, a graph-theoretic method to analyze relationships between TCR sequences and gene expression in T cells, revealing known and novel associations across human and mouse datasets.

bioRxiv · Jun 4, 2020Immunology

Ancient MAPK ERK7 is regulated by an unusual inhibitory scaffold required for Toxoplasma apical complex biogenesis

P. S. Back, W. J. O'Shaughnessy, A. S. Moon, P. S. Dewangan, J. L. Wohlschlegel, J. Sha, P. Bradley, M. L. Reese

The paper identifies AC9 as an essential scaffold for ERK7 regulation during apical complex biogenesis in Toxoplasma gondii, revealing a novel inhibitory mechanism for an ancient MAPK.

Proceedings of the National Academy of Sciences · May 14, 2020Peer-reviewedMicrobiology

A novel multi SNP based method for the identification of subspecies and associated lineages and sub-lineages of the Mycobacterium tuberculosis complex by whole genome sequencing

S. I. W. Lipworth, R. Jajou, H. de Neeling, P. Bradley, W. van der Hoek, G. Maphalala, M. Bonnet, E. Sanchez-Padilla, R. Diel, S. Niemann, Z. Iqbal, G. Smith, T. Peto, D. Crook, T. M. Walker, D. van Soolingen

This paper introduces SNP-IT, a method using whole genome sequencing to identify subspecies and lineages of Mycobacterium tuberculosis complex, revealing high prevalence of M. orygis in UK clinical isolates.

bioRxiv · Jan 5, 2018Microbiology

The global distribution and spread of the mobilized colistin resistance gene mcr-1

R. Wang, L. van Dorp, L. Shaw, P. Bradley, Q. Wang, X. Wang, L. Jin, Q. Zhang, Y. Liu, A. Rieux, T. Dorai-Schneiders, L. A. Weinert, Z. Iqbal, X. Didelot, H. Wang, F. Balloux

The paper analyzes the global spread of the mcr-1 gene by sequencing isolates and phylogenetic analysis, finding all mcr-1 elements originated from a single mobilization event in the mid-2000s.

bioRxiv · Nov 17, 2017Microbiology

The Rosetta all-atom energy function for macromolecular modeling and design

R. F. Alford, A. Leaver-Fay, J. R. Jeliazkov, M. J. O'Meara, F. P. DiMaio, H. Park, M. V. Shapovalov, P. D. Renfrew, V. K. Mulligan, K. Kappel, J. W. Labonte, M. S. Pacella, R. Bonneau, P. Bradley, R. L. Dunbrack, , J. J. Gray

The paper explains the Rosetta all-atom energy function, its mathematical models, and its application to biomolecular modeling and design, including new capabilities for membrane proteins and other macromolecules.

bioRxiv · Feb 7, 2017Biophysics

Same-day diagnostic and surveillance data for tuberculosis via whole genome sequencing of direct respiratory samples.

A. A. Votintseva, P. Bradley, L. Pankhurst, C. del Ojo Elias, M. Loose, K. Nilgiriwala, A. Chatterjee, E. G. Smith, N. Sanderson, T. M. Walker, M. R. Morgan, D. H. Wyllie, A. S. Walker, T. E. Peto, D. W. Crook, Z. Iqbal

This paper develops a low-cost WGS method for TB diagnosis and surveillance using direct respiratory samples, achieving rapid results with high concordance with reference labs.

bioRxiv · Dec 19, 2016Microbiology