Publications
Peer Reviewed
- A.C. Weiner, M.J. Williams, H. Shi, I. Vazquez-Garcia, S. Salehi, N. Rusk, S. Aparicio, S.P. Shah, A. McPherson, “Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data”, Nature Communications. 2024. doi: https://doi.org/10.1038/s41467-024-52544-7.
- M.J. Williams, M.U.J. Oliphant, V. Au, …, A.C. Weiner, …, S.P. Shah, J.S. Brugge, S. Aparicio, “Luminal breast epithelial cells of wildtype and BRCA mutation carriers harbor copy number alterations commonly associated with breast cancer”, Nature Genetics. 2024. doi: https://doi.org/10.1038/s41588-024-01988-0.
- M. Kim, A. Gorelick, …, A.C. Weiner, …, S.P. Shah, E. Reznik, “Single cell mtDNA dynamics in tumors is driven by ongoing co-regulation of nuclear and mitochondrial genomes”, Nature Genetics. 2024; 56: 889-899. doi: https://doi.org/10.1038/s41588-024-01724-8.
- H. Shi, M.J. Williams, G. Satas, A.C. Weiner, A. McPherson, S.P. Shah, “Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells”, Nature Communications. 2024; 15: 2482. doi: https://doi.org/10.1038/s41467-024-46710-0.
- T. Funnell, C.H. O’Flanagan, M.J. Williams, …, A.C. Weiner, … S.P. Shah, S. Aparicio, “Single-cell genomic variation induced by mutational processes in cancer”, Nature. 2022; 612: 106115. doi: https://doi.org/10.1038/s41586-022-05249-0.
- A.M. Farhat∗, A.C. Weiner∗, C. Posner, Z.S. Kim, B. Orcutt-Jahns, S.M. Carlson, A.S. Meyer, “Modeling cell-specific dynamics and regulation of the common gamma chain cytokines”, Cell Reports. 2021; 35: 109044. doi: https://doi.org/10.1016/j.celrep.2021.109044.
Preprints
- A. McPherson, I. Vazquez-Garcia, M. Myers, …, A.C. Weiner, …, S.P. Shah, “Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer”, Nature (in review). bioRxiv doi: https://doi.org/10.1101/2024.07.11.602772.
- K.N. Dinh , I. Vazquez-Garcia , A. Chan , R. Malhotra , A.C. Weiner, A. McPherson, S. Tavare, “CINner: modeling and simulation of chromosomal instability in cancer at single-cell resolution”. PLOS Comp Biol (in review). bioRxiv doi: https://doi.org/10.1101/2024.04.03.587939.
