8 sources for “John W. Hickey”

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PaperS7568

SPACEc: a streamlined, interactive Python workflow for multiplexed image processing and analysis

Yuqi Tan, Tim N Kempchen, Martin Becker, Maximilian Haist, Dorien Feyaerts, Jiaqi Liu, Marieta Toma, Yang Xiao, Graham Su, Andrew J Rech, Michael Hölzel, Rong Fan, John W Hickey, Garry P Nolan. ebi.ac.uk. November 27, 2025.

SPACEc combines spatial proteomics processing, cell annotation and neighbourhood analysis. Nolan is credited with supervision. The supplied article, static supplement and reporting form were reviewed; peer-review correspondence is partly read. Reused tissues, expert labels and nested cell counts limit independent replication. Computational comparisons depend on dataset, platform, normalization and metric definitions; funding does not establish a UAP programme.

Complete supplied main and static supplement text read; peer review partial

PaperS7679

Integration of spatial and single-cell data across modalities with weakly linked features

Shuxiao Chen, Bokai Zhu, Sijia Huang, John W Hickey, Kevin Z Lin, Michael Snyder, William J Greenleaf, Garry P Nolan, Nancy R Zhang, Zongming Ma. ebi.ac.uk. September 7, 2023.

This Nolan-coauthored study introduces MaxFuse, a computational method for aligning cell measurements across weakly linked data types. Benchmarks report gains on selected datasets; inferred spatial gene activity is distinguished from measurements actually made in each cell. Reused cell batches and tuned comparisons limit broader conclusions. The article explicitly attributes FDA Medical Countermeasures Initiative contracts and NIH support to Nolan, without reporting a secret approach or classified UAP programme.

Complete supplied XML text; original figures and supplements unreviewed

PaperS7524

Single-cell spatial pharmacobiology identifies conserved stromal barriers to therapeutic antibody delivery in human solid tumors

Guolan Lu, John W Hickey, Maximilian Haist, Xulei Qin, Emily Zhao, Abdullah Naveed, Erna Forgo, Marc-A Baertsch, Lucas Mani, Xavier Rovira-Clavé, Andrey Finegersh, Yury Goltsev, Chiara Caraccio, Nynke S van den Berg, Marisa Hom, Deana R Colburg, Brock A Martin, Christina S Kong, Natalie S Lui, George A Fisher, A Dimitrios Colevas, Robert B West, Greg M Thurber, George A Poultsides, Garry P Nolan, Eben L Rosenthal. ebi.ac.uk. June 3, 2026.

An exploratory oncology study examines antibody distribution and tissue organization in small, nested patient cohorts. Several nominal associations weaken after statistical correction or patient sensitivity checks. Alternate measurement on the same tissues adds a different method, without independent patient replication or proven clinical benefit.

Supplied manuscript, figures and supplement read

PaperS7706

High-throughput multiplexed serology via the mass-spectrometric analysis of isotopically barcoded beads

Alexandros P Drainas, David R McIlwain, Alec Dallas, Theresa Chu, Antonio Delgado-González, Maya Baron, Maria Angulo-Ibáñez, Angelica Trejo, Yunhao Bai, John W Hickey, Guolan Lu, Scott Lu, Jesus Pineda-Ramirez, Khamal Anglin, Eugene T Richardson, John C Prostko, Edwin Frias, Venice Servellita, Noah Brazer, Charles Y Chiu, Michael J Peluso, Jeffrey N Martin, Oliver F Wirz, Tho D Pham, Scott D Boyd, J Daniel Kelly, Julien Sage, Garry P Nolan, Xavier Rovira-Clavé. pmc.ncbi.nlm.nih.gov. February 12, 2025.

This serology technology article was reviewed only for descriptive background, author roles, funding, disclosures and bibliography. Aggregate assay counts do not establish independent participant counts or clinical performance; their target-count arithmetic remains unresolved within this scope. Nolan shares an acknowledged NIH award with Julien Sage and is a corresponding author/joint supervisor. Patent and company interests are declared. Results, Discussion, Methods and figure captions remain excluded; no UAP or private-approach inference follows.

Partial descriptive XML; Results, Discussion and Methods excluded

PaperS7686

Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer

Magdalena Matusiak, John W. Hickey, David G.P. van IJzendoorn, Guolan Lu, Lukasz Kidziński, Shirley Zhu, Deana R.C. Colburg, Bogdan Luca, Darci J. Phillips, Sky W. Brubaker, Gregory W. Charville, Jeanne Shen, Kyle M. Loh, Derick K. Okwan-Duodu, Garry P. Nolan, Aaron M. Newman, Robert B. West, Matt van de Rijn. ebi.ac.uk. March 27, 2024.

This observational human-tissue study associates distinct macrophage populations with different colon-cancer outcomes: IL4I1 with favorable survival in two reported cohorts and SPP1 with unfavorable survival in one. Nested cells and tissue regions are not independent patients; no adjusted or prospectively validated clinical predictor is established. A reused breast-cancer treatment-response measure is T-cell receptor expansion, a surrogate. Nolan is a Resources coauthor. Public cancer-research grants name other recipients and establish no classified approach or UAP programme. Figures and supplements remain unreviewed.

Complete specialist supplied XML text; native graphics unreviewed

PaperS7692

Organization of the human intestine at single-cell resolution

John W. Hickey, Winston R. Becker, Stephanie A. Nevins, Aaron Horning, Almudena Espin Perez, Chenchen Zhu, Bokai Zhu, Bei Wei, Roxanne Chiu, Derek C. Chen, Daniel L. Cotter, Edward D. Esplin, Annika K. Weimer, Chiara Caraccio, Vishal Venkataraaman, Christian M. Schürch, Sarah Black, Maria Brbić, Kaidi Cao, Shuxiao Chen, Weiruo Zhang, Emma Monte, Nancy R. Zhang, Zongming Ma, Jure Leskovec, Zhengyan Zhang, Shin Lin, Teri Longacre, Sylvia K. Plevritis, Yiing Lin, Garry P. Nolan, William J. Greenleaf, Michael Snyder. pmc.ncbi.nlm.nih.gov. July 19, 2023.

This healthy-adult intestine atlas describes regional tissue composition and spatial organization in nine donors. Millions of cells and regional sections remain nested within donors. Predicted signalling and regulatory associations are hypotheses; subset validation overlaps one donor and does not establish a clinical or causal mechanism. Nolan is a corresponding coauthor and supervisor. Published funding and commercial disclosures provide ordinary research context, without establishing a classified approach or UAP programme.

Complete specialist supplied XML text; native apparatus unreviewed

PaperS7553

Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data

John W. Hickey, Yuqi Tan, Garry P. Nolan, Yury Goltsev. ebi.ac.uk. August 13, 2021.

The study compares 20 cell-annotation pipelines using four healthy-colon tissue blocks from one donor. Agreement improves with broader labels, but both reference sets use the same images and one explicitly favors a pipeline being evaluated. The authors recommend checking expression patterns and image locations when assigning cell types. Marker counts, a worked F-score example and several caption or settings inconsistencies remain documented. These results do not establish universal clinical accuracy or a UAP connection.

Supplied text and scoped apparatus read

PaperS7560

Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction

Julia Kennedy‐Darling, Salil S Bhate, John W Hickey, Sarah Black, Graham L Barlow, Gustavo Vazquez, Vishal G Venkataraaman, Nikolay Samusik, Yury Goltsev, Christian M Schürch, Garry P Nolan. ebi.ac.uk. March 10, 2021.

The authors demonstrate repeated three-color imaging of DNA-tagged antibodies on five human tissue sections from five donors. Millions of segmented cells do not become independent human subjects. Barcode and repeated-cycle validation experiments each have one experimental replicate. Cell-type assignment and spatial associations depend on segmentation, markers and manual annotation. Barcode counts, omitted sequences, reagent labels, geometry and timing remain inconsistent in the supplied material. Nolan is a cosenior and corresponding coauthor.

Complete supplied text and received apparatus read

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