Highlighted Publications

UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues.

Yapp C, Novikov E, Jang W-D, Vallius T, Chen Y-A, Cicconet M, Maliga Z, Jacobson CA, Wei D, Santagata S, Pfister H, Sorger PK.
Communications Biology. 2022 Nov 18;5(1):1263. PMID: 36400937. PMCID: PMC9674686.

The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution.

Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AC, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen Y-A, Lian CG, Murphy GF, Santagata S, Sorger PK.
Cancer Discovery. 2022 Apr 11; candisc.1357.2021. doi.org: 10.1158/2159-8290.CD-21-1357. PMID: 35404441. PMCID: PMC9167783.

Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.

Rashid R, Chen Y-A, Hoffer J, Muhlich JL, Lin J-R, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK.
Nature Biomedical Engineering. 2022 May;6(5): 515–526. PMID: 34750536. PMCID: 9079188.

Fides: Reliable trust-region optimization for parameter estimation of ordinary differential equation models

Fröhlich, F. & Sorger, PK.
PLoS Computational Biology. 2022 Jul 13;18(7):e1010322. PMID: 35830470. PMCID: PMC9312381

Systematic measurement of combination-drug landscapes to predict in vivo treatment outcomes for tuberculosis.

Larkins-Ford J, Greenstein T, Van N, Degefu YN, Olson MC, Sokolov A, Aldridge BB.
Cell Systems. 2021 Aug 21:S2405-4712(21)00292-1. doi: 10.1016/j.cels.2021.08.004. PMID: 34469743. PMCID: PMC8617591.

Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer.

Mehta, AK, Cheney, EM, Hartl, CA, Pantelidou, C, Oliwa, M, Castrillon, JA, Lin, JR, Hurst, KE, … Mittendorf EA, Sorger, PK, Shapiro, GI, Guerriero, JL.
Nature Cancer. 2021 Jan;2(1):66-82. doi: 10.1038/s43018-020-00148-7. PMID: 33738458. PMCID: PMC7963404.

SYLARAS: A platform for the statistical analysis and visual display of systemic immunoprofiling data and its application to glioblastoma.

Baker GJ, Muhlich JL, Palaniappan SK, Moore JK, Davis SH, Santagata S, Sorger PK.
Cell Systems. 2020 Sep 23;11(3):272-285.e9. doi: 10.1016/j.cels.2020.08.001. PMID: 32898474. PMCID: PMC7565356.

A switch in p53 dynamics marks cells that escape from DSB-induced cell cycle arrest.

Tsabar M, Mock CS, Venkatachalam V, Reyes J, Karhohs KW, Oliver TG, Regev A, Jambhekar A, Lahav G.
Cell Reports. 2020 Aug 4;32(5):107995. doi: 10.1016/j.celrep.2020.107995. 32(5):107995. PMID: 32755587; PMCID: PMC7521664.

Metabolic perturbations sensitize triple-negative breast cancers to apoptosis induced by BH3 mimetics.

Daniels VW, Zoeller JJ, van Gastel N, McQueeney KE, Parvin S, Potter DS, Fell GG, Ferreira VG, Yilma B, Gupta R, Spetz J, Bhola PD, Endress JE, Harris IS, Carrilho E, Sarosiek KA, Scadden DT, Brugge JS, Letai A.
Science Signaling. 2021 Jun 8;14(686):eabc7405. doi: 10.1126/scisignal.abc7405. PMID: 34103421. PMCID: PMC8285073.

Prophages encode phage-defense systems with cognate self-immunity.

Owen S V, Wenner N, Dulberger C, Rodwell E, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin, EJ, Garner EC, Baym, M, Hinton JCD.
Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8.

Machine learning identifies candidates for drug repurposing in Alzheimer’s disease.

Rodriguez S, Hug C, Todorov P, Moret N, Boswell SA, Evans K, Zhou G, Johnson NT, Hyman BT, Sorger PK, Albers MW, Sokolov A.
Nature Communications. 2021 Feb 15;12(1):1033. doi: 10.1038/s41467-021-21330-0. PMID: 33589615. PMCID: PMC7884393.