Highlighted Publications
Development and validation of time-to-event models to predict metastatic recurrence of localized cutaneous melanoma
Wan G, Leung BW, DeSimone MS, Nguyen N, Rajeh A, Collier MR, Rashdan H, Roster K, Zhou X, Moseley CB, Nirmal AJ, Pelletier RJ, Maliga Z, Marko-Varga G, Németh IB, Tsao H, Asgari MM, Gusev A, Stagner AM, Lian CG, Hurlbert MS, Liu F, Yu KH, Sorger PK, Semenov YR.
J Am Acad Dermatol. 2023 Oct 3;S0190-9622(23)02881–5. PMID: 37797836
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
Multi-range ERK responses shape the proliferative trajectory of single cells following oncogene induction.
Chen JY, Hug C, Reyes J, Tian C, Gerosa L, Fröhlich F, Ponsioen B, Snippert HJG, Spencer SL, Jambhekar A, Sorger PK, Lahav G.
Cell Rep. 2023 Mar 28;42(3):112252. PMCID: PMC10153468
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
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
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.
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.
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.
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.