Author

J. M. Dempster

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

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Cancer Biology· 6

Signature Assays, Organisms & Methods

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Organism:human· 6 Assay:CRISPR screen· 4 Research Focus:drug response / drug discovery· 3 Approach:experimental assay· 3 Research Focus:gene regulatory network inference· 3 Approach:statistical model· 3 Assay:bulk RNA-seq· 2 Research Focus:differential expression· 2

Frequent Co-Authors

D. E. Root· 5 shared A. Tsherniak· 4 shared F. Vazquez· 4 shared J. S. Boehm· 3 shared T. R. Golub· 3 shared A. Goodale· 2 shared J. Krill-Burger· 2 shared M. Kazachkova· 2 shared

Activity by Year

2019-2022 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 38 mutual co-author links

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5 shared papersCancer Biology

D. E. Root

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Author profile →

6 papers

Recent·Most cited

Mapping the landscape of genetic dependencies in chordoma

T. Sharifnia, M. J. Wawer, A. Goodale, Y. Lee, M. Kazachkova, J. M. Dempster, S. Muller, J. Levy, D. M. Freed, J. Sommer, J. Kalfon, F. Vazquez, W. C. Hahn, D. E. Root, P. A. Clemons, S. L. Schreiber

This study identifies essential genes in chordoma using CRISPR screens, revealing new therapeutic targets like PTPN11 and confirming known dependencies such as TBXT.

bioRxiv · Aug 17, 2022Cancer Biology

Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal

J. M. Krill-Burger, J. M. Dempster, A. A. Borah, B. R. Paolella, D. E. Root, T. R. Golub, J. S. Boehm, W. Hahn, J. M. McFarland, F. Vazquez, A. Tsherniak

This study compares CRISPR-Cas9 and RNAi screens to identify cancer vulnerabilities, finding that RNAi better detects pan-dependencies while CRISPR identifies more dependencies overall.

bioRxiv · Mar 2, 2022Cancer Biology

Non-canonical open reading frames encode functional proteins essential for cancer cell survival

J. R. Prensner, O. M. Enache, V. Luria, K. Krug, K. R. Clauser, J. M. Dempster, A. Karger, L. Wang, K. Stumbraite, V. M. Wang, G. Botta, N. J. Lyons, A. Goodale, Z. Kalani, B. Fritchman, , T. R. Golub

The paper identifies non-canonical open reading frames (ORFs) that encode functional proteins essential for cancer cell survival, with one example, GREP1, showing preferential essentiality in breast cancer.

bioRxiv · Mar 10, 2020 · PreprintCancer Biology

Gene expression has more power for predicting in vitro cancer cell vulnerabilities than genomics

J. M. Dempster, J. Krill-Burger, A. Warren, J. McFarland, J. S. Boehm, F. Vazquez, W. Hahn, T. Golub, A. Tsherniak

This study compares DNA- and expression-based models for predicting cancer cell viability and finds expression models are more accurate and interpretable.

bioRxiv · Feb 21, 2020 · PreprintCancer Biology

Extracting Biological Insights from the Project Achilles Genome-Scale CRISPR Screens in Cancer Cell Lines

J. M. Dempster, J. Rossen, M. Kazachkova, J. Pan, G. Kugener, D. E. Root, A. Tsherniak

The paper describes updates to the Project Achilles processing pipeline for CRISPR screens in cancer cell lines, including quality control improvements and dependency score calculations.

bioRxiv · Jul 31, 2019 · PreprintCancer Biology

Agreement between two large pan-cancer CRISPR-Cas9 gene dependency datasets

J. M. Dempster, C. Pacini, S. Pantel, F. M. Behan, T. Green, J. Krill-Burger, C. M. Beaver, S. T. Younger, V. Zhivich, H. Najgebauer, F. Allen, E. Goncalves, R. Shepherd, J. G. Doench, K. Yusa, , A. Tsherniak

This study compares two large pan-cancer CRISPR-Cas9 screens, finding high concordance in gene dependencies despite differences in protocols and reagents.

bioRxiv · Jun 4, 2019Cancer Biology