Research

Highlighted Publications

Changing fitness effects of mutations through long-term bacterial evolution

Couce A, Limdi A, Magnan M, Owen SV, Herren CM, Lenski RE, Tenaillon O, Baym M

Science. 2024 Jan 26;383(6681):eadd1417. PMID: 38271521

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

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

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.

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

NIH Director's Blog

Association Between Regulatory Submission Characteristics and Recalls of Medical Devices Receiving 510(k) Clearance.

Everhart AO, Sen S, Stern AD, Zhu Y, Karaca-Mandic P.

JAMA. 2023;329(2):144–156. doi:10.1001/jama.2022.22974. PMID: 36625811

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.

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

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.

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

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

US Food and Drug Administration Approval of High-risk Cardiovascular Devices for Use in Children and Adolescents, 1977-2021.

Wunnava S, Miller TA, Narang C, Nathan M, Bourgeois FT.

JAMA. 2022;328(6):580–582. doi: 10.1001/jama.2022.10041. PMID: 35943478 PMCID: PMC9364120.

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 Syst. 2021 Aug 21:S2405-4712(21)00292-1. doi: 10.1016/j.cels.2021.08.004. Epub ahead of print. PMID: 34469743.

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, de Oliveira Taveira M, Johnson NT, Oldham WM, Kalocsay M, Berberich MJ, Boswell SA, Kothari A, Johnson S, Dillon DA, Lipschitz M, Rodig S, Santagata S, Garber JE, Tung N, Yélamos J, Thaxton JE, Mittendorf EA, Sorger PK, Shapiro GI, Guerriero JL.

Nat Cancer. 2021 Jan;2(1):66-82. doi: 10.1038/s43018-020-00148-7. Epub 2020 Dec 14. 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 Syst. 2020 Sep 23;11(3):272-285.e9. doi: 10.1016/j.cels.2020.08.001. Epub 2020 Sep 7. PMID: 32898474; PMCID: PMC7565356.

Evaluation of publication of pediatric drug trials.

Srivastav A, and Bourgeois FT.

JAMA Network Open. 2021 April 1; 4(4): e215829.

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.

Sci Signal. 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, SV, 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 November 10; 29(11): 1620-1633.e8. doi:10.1016/j.chom.2021.09.002. PMID: 34597593 PMCID: PMC8585504

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.

Nat Commun. 2021 Feb 15;12(1):1033. doi: 10.1038/s41467-021-21330-0. PMID: 33589615; PMCID: PMC7884393.

3D Printed frames to enable reuse and improve the fit of N95 and KN95 respirators.

McAvoy M, Bui A-TN, Hansen C, Plana D, Said JT, Yu Z, Yang H, Freake J, Van C, Krikorian D, Cramer A, Smith L, Jiang L, Lee KJ, Li SJ, Beller B, Huggins K, Short MP, Yu SH, Mostaghimi A, Sorger PK, LeBoeuf NR.

BMC Biomed Eng. 2021 Jun 7;3(1):10. PMCID: PMC8182357

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 Rep. 2020 Aug 4;32(5):107995. doi: 10.1016/j.celrep.2020.107995. Erratum in: Cell Rep. 2020 Nov 10;33(6):108392. PMID: 32755587; PMCID: PMC7521664.