Highlighted Publications

Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance

Fröhlich F, Gerosa L, Muhlich J, Sorger PK.
Molecular Systems Biology. 2023 Jan 26;e10988. PMID: 36700386

Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma

Gaglia G, Burger ML, Ritch CC, Rammos D, Dai Y, Crossland GE, Tavana SZ, Warchol S, Jaeger AM, Naranjo S, Coy S, Nirmal AJ, Krueger R, Lin JR, Pfister H, Sorger PK, Jacks T, Santagata S.
Cancer Cell. 2023 Apr 8; 871-886. PMID: 37059105

Automated assembly of molecular mechanisms at scale from text mining and curated databases

Bachman JA, Gyori BM, Sorger PK.
Mol Syst Biol. 2023 May 9;19(5):e11325. PMCID: PMC10167483.

High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers

Lin JR, Chen YA, Campton D, Cooper J, Coy S, Yapp C, Tefft JB, McCarty E, Ligon KL, Rodig SJ, Reese S, George T, Santagata S, Sorger PK
Nature Cancer. 2023 Jul;4(7):1036-1052. PMID: 37349501

Sequential apoptotic and multiplexed proteomic evaluation of single cancer cells

Lecky E, Mukherji A, German R, Antonellis G, Lin JR, Yorsz M, McQueeney KE, Ryan J, Ng K, Sicinska E, Sorger PK, Letai A, Bhola PD.
Science Advances. 2023 Jun 23;9(25): eadg4128. PMID: 37352344

Multiplexed 3D atlas of state transitions and immune interaction in colorectal cancer

Lin JR, Wang S, Coy S, Chen YA, Yapp C, Tyler M, Nariya MK, Heiser CN, Lau KS, Santagata S, Sorger PK.
Cell. 2023 Jan 19;186(2):363-381.e19. PMID: 36669472

Causal inference in medical records and complementary systems pharmacology for metformin drug repurposing towards dementia

Charpignon ML, Vakulenko-Lagun B, Zheng B, Magdamo C, Su B, Evans K, Rodriguez S, Sokolov A, Boswell S, Sheu YH, Somai M, Middleton L, Hyman BT, Betensky RA, Finkelstein SN, Welsch RE, Tzoulaki I, Blacker D, Das S, Albers MW.
Nature Communications. 2022 Dec 10;13(1):7652. PMCID: PMC9741618

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.

Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques

Baaijens JA, Zulli A, Ott IM, Nika I, van der Lugt MJ, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy KA, Ghaeli N, Imakaev M, Mckenzie-Bennett MF, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer ML, Simen BB, Yale SARS-CoV-2 Genomic Surveillance Initiative, Hanage WP, Grubaugh ND, Peccia J, Baym M.
Genome Biology. 2022 Nov 8;23(1):236. PMCID: PMC9643916

Single-sequence protein structure prediction using a language model and deep learning

Chowdhury R, Bouatta N, Biswas S, Floristean C, Kharkar A, Roy K, Rochereau C, Ahdritz G, Zhang J, Church GM, Sorger PK, AlQuraishi M.
Nature Biotechnology. 2022 Nov;40(11):1617–1623. PMID: 36192636

Multiplexed and reproducible high content screening of live and fixed cells using Dye Drop

Mills CE, Subramanian K, Hafner M, Niepel M, Gerosa L, Chung M, Victor C, Gaudio B, Yapp C, Nirmal AJ, Clark N, Sorger PK.
Nature Communications. 2022 Nov 14;13(1):6918. PMCID: PMC9663587

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

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.

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.

Cancer patient survival can be parametrized to improve trial precision and reveal time-dependent therapeutic effects

Plana D, Fell G, Alexander BM, Palmer AC, Sorger PK.
Nature Communications. 2022 Feb 15;13(1):873. PMCID: PMC8847344

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.

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.

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.

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.

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.