Author

A. McPherson

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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Cancer Biology· 9 Immunology· 1

Signature Assays, Organisms & Methods

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Organism:human· 9 Research Focus:clustering· 8 Research Focus:differential expression· 7 Approach:statistical model· 7 Assay:whole-genome sequencing· 6 Research Focus:gene regulatory network inference· 5 Research Focus:cell type annotation· 3 Approach:deep learning· 3

Frequent Co-Authors

S. P. Shah· 7 shared A. C. Weiner· 5 shared M. J. Williams· 5 shared S. Aparicio· 5 shared D. Lai· 4 shared N. Rusk· 4 shared B. Wang· 3 shared D. Grewal· 3 shared

Activity by Year

2016-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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7 shared papersCancer Biology

S. P. Shah

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10 papers

Recent·Most cited

Luminal breast epithelial cells from wildtype and BRCA mutation carriers harbor copy number alterations commonly associated with breast cancer

M. J. Williams, M. U. Oliphant, V. Au, C. Liu, C. Baril, C. O'Flanagan, D. Lai, S. Beatty, M. Van Vliet, J. C. Liu, L. O'Connor, W. L. Goh, A. Pollaci, A. C. Weiner, D. Grewal, , S. Aparicio

The paper analyzes copy number alterations in breast epithelial cells from BRCA mutation carriers and wildtype individuals, finding lineage-specific CNAs that mirror cancer genomes.

bioRxiv · May 1, 2024 · PreprintCancer Biology

VICTree - a Variational Inference method for Clonal Tree reconstruction

H. Melin, V. Zampinetti, A. McPherson, J. Lagergren

VICTree is a variational inference method for clonal tree reconstruction that uses a Tree-structured Mixture Hidden Markov Model and evaluates on cancer datasets.

bioRxiv · Feb 14, 2024 · PreprintCancer Biology

Single-cell DNA replication dynamics in genomically unstable cancers

A. C. Weiner, M. J. Williams, H. Shi, I. Vazquez-Garcia, S. Salehi, N. Rusk, S. Aparicio, S. P. Shah, A. McPherson

The paper develops a method to infer DNA replication states from single-cell sequencing and analyzes replication dynamics in aneuploid cancers, finding correlations between replication timing and copy number changes.

bioRxiv · Apr 10, 2023Cancer Biology

Exploiting allele-specific transcriptional effects of subclonal copy number alterations for genotype-phenotype mapping in cancer cell populations

H. Shi, M. J. Williams, G. Satas, A. C. Weiner, A. McPherson, S. P. Shah

This paper develops TreeAlign to map subclonal copy number alterations to transcriptional phenotypes in cancer cells, showing improved accuracy in clone-specific gene expression analysis.

bioRxiv · Jan 10, 2023 · PreprintCancer Biology

Adenovirus-Vectored SARS-CoV-2 Vaccine Expressing S1-N Fusion Protein

M. S. Khan, E. Kim, A. McPherson, F. J. Weisel, S. Huang, T. W. Kenniston, E. Percivalle, I. Cassaniti, F. Baldanti, M. Meisel, A. Gambotto

This paper develops a novel adenovirus-vectored SARS-CoV-2 vaccine expressing S1-N fusion protein, showing improved immunogenicity in mice against SARS-CoV-2 variants.

bioRxiv · May 9, 2022Immunology

Chemotherapy Signatures Map Evolution of Therapy-Related Myeloid Neoplasms

B. T. Diamond, B. Ziccheddu, K. H. Maclachlan, J. Taylor, E. Boyle, J. Arrango Ossa, J. T. Jahn, M. Affer, T. M. Totiger, D. G. Coffey, J. Watts, S. X. Lu, N. Bolli, K. Bolton, J. H. Park, , F. Maura

The paper reconstructs the evolutionary history of therapy-related myeloid neoplasms using chemotherapy-associated mutational signatures and identifies distinct mutational patterns linked to different chemotherapies.

bioRxiv · Apr 26, 2022 · PreprintCancer Biology

Evolutionary tracking of cancer haplotypes at single-cell resolution

M. J. Williams, T. Funnell, C. O'Flanagan, A. McPherson, S. Salehi, I. Vazquez-Garcia, F. Kabeer, H. Lee, T. Masud, P. Eirew, D. Yap, B. Wang, J. Brimhall, J. Biele, J. Ting, , S. P. Shah

The paper tracks cancer haplotypes at single-cell resolution, revealing allele-specific alterations and their role in structural variation evolution in human tumors.

bioRxiv · Jun 4, 2021 · PreprintCancer Biology

The impact of mutational processes on structural genomic plasticity in cancer cells

T. Funnell, C. H. O'Flanagan, M. J. Williams, A. McPherson, S. McKinney, F. Kabeer, H. Lee, T. Masud, P. Eirew, D. Yap, A. W. Zhang, J. L. P. Lim, B. Wang, J. Brimhall, J. Biele, , S. Aparicio

The paper analyzes structural genomic variations in cancer cells to understand how mutational processes influence cell-to-cell genomic diversity and tumor evolution.

bioRxiv · Jun 3, 2021 · PreprintCancer Biology

Single cell fitness landscapes induced by genetic and pharmacologic perturbations in cancer

S. Salehi, F. Kabeer, N. Ceglia, M. Andronescu, M. Williams, K. R. Campbell, T. Masud, B. Wang, J. Biele, J. Brimhall, J. Ting, A. W. Zhang, C. H. OFlanagan, F. Dorri, N. Rusk, , S. P. Shah

This study develops a quantitative fitness model to analyze clonal dynamics in cancer under genetic and pharmacologic perturbations, revealing how mutations and drug resistance shape tumor evolution.

bioRxiv · May 8, 2020Cancer Biology

E-scape: Interactive visualization of single cell phylogenetics and spatio-temporal evolution in cancer

M. A. Smith, C. Nielsen, F. C. Chan, A. McPherson, A. Roth, H. Farahani, D. Machev, A. Steif, S. P. Shah

E-scape provides an interactive visualization tool for analyzing cancer clonal dynamics and spatio-temporal evolution using integrated mutation, phylogenetic, and imaging data.

bioRxiv · Nov 20, 2016Cancer Biology