Publications
Center Preprints
Multi range ERK responses shape the proliferative trajectory of single cells following oncogene induced senescence.
Chen JY, Hug C, Reyes J, Tian C, Gerosa L, Fröhlich F, Ponsioen B, Snippert HJG, Spencer SL, Jambhekar A, Sorger PK, Lahav G.
bioRxiv. 2022 Oct 7. doi: 10.1101/2022.10.06.511142.
Multi-modal digital pathology for colorectal cancer diagnosis by high-plex immunofluorescence imaging and traditional histology of the same tissue section.
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.
bioRxiv. 2022 Sept 30. doi: 10.1101/2022.09.28.509927.
Paired evaluation defines performance landscapes for machine learning models.
Nariya MK, Mills CE, Sorger PK, Sokolov A.
bioRxiv. 2022 Sept 12. doi: 10.1101/2022.09.07.507020.
Automated assembly of molecular mechanisms at scale from text mining and curated databases.
Bachman JA, Gyori BM, Sorger PK.
bioRxiv. 2022 Aug 31. doi: 10.1101/2022.08.30.505688.
Lymphocyte networks are dynamic cellular communities in the immunoregulatory landscape of lung adenocarcinoma.
Gaglia G, Burger M, Ritch CC, Rammos D, Dai Y, Crossland GE, Tavana SZ, Warchol S, Jaeger AM, Naranjo S, Coy S, Johnson A, Krueger R, Lin JR, Pfister H, Sorger PK, Jacks T, Santagata S.
bioRxiv. 2022 Aug 13. doi: 10.1101/2022.08.11.503237.
KINOMO: A non-negative matrix factorization framework for recovering intra- and inter-tumoral heterogeneity from single-cell RNA-seq data.
Tagore S, Wang Y, Biermann J, Rabadan R, Azizi E, Izar B.
bioRxiv. 2022 May 4. doi: 10.1101/2022.05.02.490362.
Fc-engineered antibodies leverage neutrophils to drive control of Mycobacterium tuberculosis.
Irvine EB, Peters JM, Lu R, Grace PS, Sixsmith J, Wallace A, Schneider M, Shin S, Karpinski W, Hsiao JC, van Woudenbergh E, Casadevall A, Bryson BD, Cavacini L, Alter G, Fortune SM.
bioRxiv. 2022 May 1. doi: 10.1101/2022.05.01.490220.
Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance.
Fröhlich F, Gerosa L, Muhlich J, Sorger PK.
bioRxiv. 2022 Feb 18; doi: 10.1101/2022.02.17.480899.
Micro-region transcriptomics of fixed human tissue using Pick-Seq.
Maliga Z, Nirmal AJ, Ericson NG, Boswell SA, U’Ren L, Podyminogin R, Chow J, Chen Y-A, Chen AA, Weinstock DM, Lian CG, Murphy GF, Kaldjian EP, Santagata S, Sorger PK.
bioRxiv. 2021 Mar 19. doi: 10.1101/2021.03.18.431004.
Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung.
Kalocsay M, Maliga Z, Nirmal AJ, Eisert RJ, Bradshaw GA, Solomon IH, Chen Y-A, Pelletier RJ, Jacobson CA, Mintseris J, Padera RF, Martinot AJ, Barouch DH, Santagata S, Sorger PK.
bioRxiv. 2020 Oct 14. doi: 10.1101/2020.10.14.339952.
2023 Publications
Multiplexed 3D atlas of state transitions and immune interactions 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. doi: 10.1016/j.cell.2022.12.028. PMID: 36669472. NIHMSID: 1863463.
Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks.
Lakrisenko P, Stapor P, Grein S, Paszkowski Ł, Pathirana D, Fröhlich F, Lines GT, Weindl D, Hasenauer J.
PLoS Comput Biol. 2023 Jan 3;19(1):e1010783. doi: 10.1371/journal.pcbi.1010783. PMID: 36595539; PMCID: PMC9838866.
Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens.
Wang Y, Fan JL, Melms JC, Amin AD, Georgis Y, Barrera I, Ho P, Tagore S, Abril-Rodríguez G, He S, Jin Y, Biermann J, Hofree M, Caprio L, Berhe S, Khan SA, Henick BS, Ribas A, Macosko EZ, Chen F, Taylor AM, Schwartz GK, Carvajal RD, Azizi E, Izar B.
Nat Genet. 2023 Jan;55(1):19-25. doi: 10.1038/s41588-022-01268-9. Epub 2023 Jan 9. PMID: 36624340.
2022 Publications
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.
Nat Commun. 2022 Dec 10;13(1):7652. doi: 10.1038/s41467-022-35157-w. PMID: 36496454; PMCID: PMC9741618.
UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues.
Yapp C, Novikov E, Jang WD, Vallius T, Chen YA, Cicconet M, Maliga Z, Jacobson CA, Wei D, Santagata S, Pfister H, Sorger PK.
Commun Biol. 2022 Nov 18;5(1):1263. doi: 10.1038/s42003-022-04076-3. PMID: 36400937. PMCID: PMC9674686.
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.
Nat Commun. 2022 Nov 14;13(1):6918. doi: 10.1038/s41467-022-34536-7. PMID: 36376301; PMCID: PMC9663587.
Spatial genomics maps the structure, nature and evolution of cancer clones.
Lomakin A, Svedlund J, Strell C, Gataric M, Shmatko A, Rukhovich G, Park JS, Ju YS, Dentro S, Kleshchevnikov V, Vaskivskyi V, Li T, Bayraktar OA, Pinder S, Richardson AL, Santagata S, Campbell PJ, Russnes H, Gerstung M, Nilsson M, Yates LR.
Nature. 2022 Nov;611(7936):594-602. doi: 10.1038/s41586-022-05425-2. Epub 2022 Nov 9. PMID: 36352222; PMCID: PMC9668746.
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.
Nat Biotechnol. 2022 Nov;40(11):1617-1623. doi: 10.1038/s41587-022-01432-w. Epub 2022 Oct 3. Erratum in: Nat Biotechnol. 2022 Oct 17;: PMID: 36192636. NIHMSID: 1830988.
Exploiting endogenous and therapy-induced apoptotic vulnerabilities in immunoglobulin light chain amyloidosis with BH3 mimetics.
Fraser CS, Spetz JKE, Qin X, Presser A, Choiniere J, Li C, Yu S, Blevins F, Hata AN, Miller JW, Bradshaw GA, Kalocsay M, Sanchorawala V, Sarosiek S, Sarosiek KA.
Nat Commun. 2022 Oct 2;13(1):5789. doi: 10.1038/s41467-022-33461-z. PMID: 36184661. PMCID: PMC9527241.
Oncometabolite d-2HG alters T cell metabolism to impair CD8+ T cell function.
Notarangelo G, Spinelli JB, Perez EM, Baker GJ, Kurmi K, Elia I, Stopka SA, Baquer G, Lin JR, Golby AJ, Joshi S, Baron HF, Drijvers JM, Georgiev P, Ringel AE, Zaganjor E, McBrayer SK, Sorger PK, Sharpe AH, Wucherpfennig KW, Santagata S, Agar NYR, Suvà ML, Haigis MC.
Science. 2022 Sep 30;377(6614):1519-1529. doi: 10.1126/science.abj5104. Epub 2022 Sep 29. PMID: 36173860. PMCID: PMC9629749.
Visinity: Visual Spatial Neighborhood Analysis for Multiplexed Tissue Imaging Data.
Warchol S, Krueger R, Nirmal AJ, Gaglia G, Jessup J, Ritch CC, Hoffer J, Muhlich J, Burger ML, Jacks T, Santagata S, Sorger PK, Pfister H.
IEEE Trans Vis Comput Graph. 2022 Sep 28;PP. doi: 10.1109/TVCG.2022.3209378. Epub ahead of print. PMID: 36170403. NIHMSID:1851534.
Design principles to assemble drug combinations for effective tuberculosis therapy using interpretable pairwise drug response measurements.
Larkins-Ford J, Degefu YN, Van N, Sokolov A, Aldridge BB.
Cell Rep Med. 2022 Sep 20;3(9):100737. doi: 10.1016/j.xcrm.2022.100737. Epub 2022 Sep 8. PMID: 36084643. PMCID: PMC9512659.
Metabolic analyses reveal dysregulated NAD+ metabolism and altered mitochondrial state in ulcerative colitis.
Kang YH, Tucker SA, Quevedo SF, Inal A, Korzenik JR, Haigis MC.
PLoS One. 2022 Aug 17;17(8):e0273080. doi: 10.1371/journal.pone.0273080. PMID: 35976971. PMCID: PMC9385040.
Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma.
Coy S, Wang S, Stopka SA, Lin JR, Yapp C, Ritch CC, Salhi L, Baker GJ, Rashid R, Baquer G, Regan M, Khadka P, Cole KA, Hwang J, Wen PY, Bandopadhayay P, Santi M, De Raedt T, Ligon KL, Agar NYR, Sorger PK, Touat M, Santagata S.
Nat Commun. 2022 Aug 16;13(1):4814. doi: 10.1038/s41467-022-32430-w. PMID: 35973991. PMCID: PMC9381513.
Spatial intra-tumor heterogeneity is associated with survival of lung adenocarcinoma patients.
Wu HJ, Temko D, Maliga Z, Moreira AL, Sei E, Minussi DC, Dean J, Lee C, Xu Q, Hochart G, Jacobson CA, Yapp C, Schapiro D, Sorger PK, Seeley EH, Navin N, Downey RJ, Michor F.
Cell Genom. 2022 Aug 10;2(8). doi: 10.1016/j.xgen.2022.100165. PMID: 36419822. PMCID: PMC9681138.
Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies.
Reichart D, Lindberg EL, Maatz H, Miranda AMA, Viveiros A, Shvetsov N, Gärtner A, Nadelmann ER, Lee M, Kanemaru K, Ruiz-Orera J, Strohmenger V, DeLaughter DM, Patone G, Zhang H, Woehler A, Lippert C, Kim Y, Adami E, Gorham JM, Barnett SN, Brown K, Buchan RJ, Chowdhury RA, Constantinou C, Cranley J, Felkin LE, Fox H, Ghauri A, Gummert J, Kanda M, Li R, Mach L, McDonough B, Samari S, Shahriaran F, Yapp C, Stanasiuk C, Theotokis PI, Theis FJ, van den Bogaerdt A, Wakimoto H, Ware JS, Worth CL, Barton PJR, Lee YA, Teichmann SA, Milting H, Noseda M, Oudit GY, Heinig M, Seidman JG, Hubner N, Seidman CE.
Science. 2022 Aug 5;377(6606):eabo1984. doi: 10.1126/science.abo1984. Epub 2022 Aug 5. PMID: 35926050. PMCID: PMC9528698.
Tumor cells dictate anti-tumor immune responses by altering pyruvate utilization and succinate signaling in CD8+ T cells.
Elia I, Rowe JH, Johnson S, Joshi S, Notarangelo G, Kurmi K, Weiss S, Freeman GJ, Sharpe AH, Haigis MC.
Cell Metab. 2022 Aug 2;34(8):1137-1150.e6. doi: 10.1016/j.cmet.2022.06.008. Epub 2022 Jul 11. PMID: 35820416. PMCID: PMC9357162.
Early on-treatment transcriptional profiling as a tool for improving pathological response prediction in HER2-positive inflammatory breast cancer.
Pernas S, Guerriero JL, Naumenko S, Goel S, Regan MM, Hu J, Harrison BT, Lynce F, Lin NU, Partridge A, Morikawa A, Hutchinson J, Mittendorf EA, Sokolov A, Overmoyer B.
Ther Adv Med Oncol. 2022 Jul 30;14:17588359221113269. doi: 10.1177/17588359221113269. PMID: 35923923; PMCID: PMC9340890.
Dissecting the treatment-naive ecosystem of human melanoma brain metastasis.
Biermann J, Melms JC, Amin AD, Wang Y, Caprio LA, Karz A, Tagore S, Barrera I, Ibarra-Arellano MA, Andreatta M, Fullerton BT, Gretarsson KH, Sahu V, Mangipudy VS, Nguyen TTT, Nair A, Rogava M, Ho P, Koch PD, Banu M, Humala N, Mahajan A, Walsh ZH, Shah SB, Vaccaro DH, Caldwell B, Mu M, Wünnemann F, Chazotte M, Berhe S, Luoma AM, Driver J, Ingham M, Khan SA, Rapisuwon S, Slingluff CL Jr, Eigentler T, Röcken M, Carvajal R, Atkins MB, Davies MA, Agustinus A, Bakhoum SF, Azizi E, Siegelin M, Lu C, Carmona SJ, Hibshoosh H, Ribas A, Canoll P, Bruce JN, Bi WL, Agrawal P, Schapiro D, Hernando E, Macosko EZ, Chen F, Schwartz GK, Izar B.
Cell. 2022 Jul 7;185(14):2591-2608.e30. doi: 10.1016/j.cell.2022.06.007. PMID: 35803246. PMCID: PMC9677434.
A human breast atlas integrating single-cell proteomics and transcriptomics.
Gray GK, Li CM, Rosenbluth JM, Selfors LM, Girnius N, Lin JR, Schackmann RCJ, Goh WL, Moore K, Shapiro HK, Mei S, D'Andrea K, Nathanson KL, Sorger PK, Santagata S, Regev A, Garber JE, Dillon DA, Brugge JS.
Dev Cell. 2022 Jun 6;57(11):1400-1420.e7. doi: 10.1016/j.devcel.2022.05.003. Epub 2022 May 25. PMID: 35617956; PMCID: PMC9202341.
Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data.
Rashid R, Chen YA, Hoffer J, Muhlich JL, Lin JR, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK.
Nat Biomed Eng. 2022 May;6(5):515-526. doi: 10.1038/s41551-021-00789-8. PMID: 34750536. PMCID: PMC9079188.
Overcoming differential tumor penetration of BRAF inhibitors using computationally guided combination therapy.
Ng TSC, Hu H, Kronister S, Lee C, Li R, Gerosa L, Stopka SA, Burgenske DM, Khurana I, Regan MS, Vallabhaneni S, Putta N, Scott E, Matvey D, Giobbie-Hurder A, Kohler RH, Sarkaria JN, Parangi S, Sorger PK, Agar NYR, Jacene HA, Sullivan RJ, Buchbinder E, Mikula H, Weissleder R, Miller MA.
Sci Adv. 2022 Apr 29;8(17):eabl6339. doi: 10.1126/sciadv.abl6339. PMID: 35486732. PMCID: PMC9054019.
Copper induces cell death by targeting lipoylated TCA cycle proteins.
Tsvetkov P, Coy S, Petrova B, Dreishpoon M, Verma A, Abdusamad M, Rossen J, Joesch-Cohen L, Humeidi R, Spangler RD, Eaton JK, Frenkel E, Kocak M, Corsello SM, Lutsenko S, Kanarek N, Santagata S, Golub TR.
Science. 2022 Mar 18;375(6586):1254-1261. doi: 10.1126/science.abf0529. Epub 2022 Mar 17. Erratum in: Science. 2022 Apr 22;376(6591):eabq4855. PMID: 35298263. PMCID: PMC9273333.
Natural and designed proteins inspired by extremotolerant organisms can form condensates and attenuate apoptosis in human cells.
Veling MT, Nguyen DT, Thadani NN, Oster ME, Rollins NJ, Brock KP, Bethel NP, Lim S, Baker D, Way JC, Marks DS, Chang RL, Silver PA.
ACS Synth Biol. 2022 Mar 18;11(3):1292-1302. doi: 10.1021/acssynbio.1c00572. PMID: 35176859. PMCID: PMC9651988.
Phase 2 study of pembrolizumab in patients with recurrent and residual high-grade meningiomas.
Brastianos PK, Kim AE, Giobbie-Hurder A, Lee EQ, Wang N, Eichler AF, Chukwueke U, Forst DA, Arrillaga-Romany IC, Dietrich J, Corbin Z, Moliterno J, Baehring J, White M, Lou KW, Larson J, de Sauvage MA, Evancic K, Mora J, Nayyar N, Loeffler J, Oh K, Shih HA, Curry WT, Cahill DP, Barker FG, Gerstner ER, Santagata S.
Nat Commun. 2022 Mar 14;13(1):1325. doi: 10.1038/s41467-022-29052-7. PMID: 35289329. PMCID: PMC8921328.
Temporal and spatial topography of cell proliferation in cancer.
Gaglia G, Kabraji S, Rammos D, Dai Y, Verma A, Wang S, Mills CE, Chung M, Bergholz JS, Coy S, Lin JR, Jeselsohn R, Metzger O, Winer EP, Dillon DA, Zhao JJ, Sorger PK, Santagata S.
Nat Cell Biol. 2022 Mar;24(3):316-326. doi: 10.1038/s41556-022-00860-9. PMID: 35292783. PMCID: PMC8959396.
MITI minimum information guidelines for highly multiplexed tissue images.
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA; Human Tumor Atlas Network, Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK.
Nat Methods. 2022 Mar;19(3):262-267. doi: 10.1038/s41592-022-01415-4. PMID: 35277708. PMCID: PMC9009186.
MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging.
Schapiro D, Sokolov A, Yapp C, Chen YA, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin JR, Maliga Z, Jacobson CA, Hodgman MW, Ruokonen J, Farhi SL, Abbondanza D, McKinley ET, Persson D, Betts C, Sivagnanam S, Regev A, Goecks J, Coffey RJ, Coussens LM, Santagata S, Sorger PK.
Nat Methods. 2022 Mar;19(3):311-315. doi: 10.1038/s41592-021-01308-y. PMID: 34824477. PMCID: PMC8916956.
Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.
Vickovic S, Schapiro D, Carlberg K, Lötstedt B, Larsson L, Hildebrandt F, Korotkova M, Hensvold AH, Catrina AI, Sorger PK, Malmström V, Regev A, Ståhl PL.
Commun Biol. 2022 Feb 11;5(1):129. doi: 10.1038/s42003-022-03050-3. PMID: 35149753. PMCID: PMC8837632.
Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer.
Launonen IM, Lyytikäinen N, Casado J, Anttila EA, Szabó A, Haltia UM, Jacobson CA, Lin JR, Maliga Z, Howitt BE, Strickland KC, Santagata S, Elias K, D'Andrea AD, Konstantinopoulos PA, Sorger PK, Färkkilä A.
Nat Commun. 2022 Feb 11;13(1):835. doi: 10.1038/s41467-022-28389-3. PMID: 35149709. PMCID: PMC8837628.
Predictable clinical benefits without evidence of synergy in trials of combination therapies with immune-checkpoint inhibitors.
Palmer AC, Izar B, Hwangbo H, Sorger PK.
Clin Cancer Res. 2022 Jan 15;28(2):368-377. doi: 10.1158/1078-0432.CCR-21-2275. PMID: 35045958. PMCID: PMC9068233.
Multimodal platform for assessing drug distribution and response in clinical trials.
Lopez BGC, Kohale IN, Du Z, Korsunsky I, Abdelmoula WM, Dai Y, Stopka SA, Gaglia G, Randall EC, Regan MS, Basu SS, Clark AR, Marin BM, Mladek AC, Burgenske DM, Agar JN, Supko JG, Grossman SA, Nabors LB, Raychaudhuri S, Ligon KL, Wen PY, Alexander B, Lee EQ, Santagata S, Sarkaria J, White FM, Agar NYR.
Neuro Oncol. 2022 Jan 5;24(1):64-77. doi: 10.1093/neuonc/noab197. PMID: 34383057. PMCID: PMC8730776.
Activity of PD-1 blockade with nivolumab among patients with recurrent atypical/anaplastic meningioma: phase II trial results.
Bi WL, Nayak L, Meredith DM, Driver J, Du Z, Hoffman S, Li Y, Lee EQ, Beroukhim R, Rinne M, McFaline-Figueroa R, Chukwueke U, McCluskey C, Gaffey S, Cherniack AD, Stefanik J, Doherty L, Taubert C, Cifrino M, LaFrankie D, Graillon T, Wen PY, Ligon KL, Al-Mefty O, Huang RY, Muzikansky A, Chiocca EA, Santagata S, Dunn IF, Reardon DA.
Neuro Oncol. 2022 Jan 5;24(1):101-113. doi: 10.1093/neuonc/noab118. PMID: 34015129. PMCID: PMC8730772.
A community-based approach to image analysis of cells, tissues and tumors.
CSBC/PS-ON Image Analysis Working Group, Vizcarra JC, Burlingame EA, Hug CB, Goltsev Y, White BS, Tyson DR, Sokolov A.
Comput Med Imaging Graph. 2022 Jan;95:102013. doi: 10.1016/j.compmedimag.2021.102013. PMID: 34864359. PMCID: PMC8761177.
Scope2Screen: focus+context techniques for pathology tumor assessment in multivariate image data.
Jessup J, Krueger R, Warchol S, Hoffer J, Muhlich J, Ritch CC, Gaglia G, Coy S, Chen Y, Lin J, Santagata S, Sorger PK, Pfister H.
IEEE Trans Vis Comput Graph. 2022 Jan;28(1):259-269. doi: 10.1109/TVCG.2021.3114786. PMID: 34606456. PMCID: PMC8805697.
2021 Publications
Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation.
Duraiswamy J, Turrini R, Minasyan A, Barras D, Crespo I, Grimm AJ, Casado J, Genolet R, Benedetti F, Wicky A, Ioannidou K, Castro W, Neal C, Moriot A, Renaud-Tissot S, Anstett V, Fahr N, Tanyi JL, Eiva MA, Jacobson CA, Montone KT, Westergaard MCW, Svane IM, Kandalaft LE, Delorenzi M, Sorger PK, Färkkilä A, Michielin O, Zoete V, Carmona SJ, Foukas PG, Powell DJ Jr, Rusakiewicz S, Doucey MA, Dangaj Laniti D, Coukos G.
Cancer Cell. 2021 Dec 13;39(12):1623-1642.e20. doi: 10.1016/j.ccell.2021.10.008. Epub 2021 Nov 4. PMID: 34739845. PMCID: PMC8861565.
Robust IgM responses following intravenous vaccination with Bacille Calmette-Guérin associate with prevention of Mycobacterium tuberculosis infection in macaques.
Irvine EB, O'Neil A, Darrah PA, Shin S, Choudhary A, Li W, Honnen W, Mehra S, Kaushal D, Gideon HP, Flynn JL, Roederer M, Seder RA, Pinter A, Fortune S, Alter G.
Nat Immunol. 2021 Dec;22(12):1515-1523. doi: 10.1038/s41590-021-01066-1. PMID: 34811542. PMCID: PMC8642241.
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 Nov 17;12(11):1046-1063.e7. doi: 10.1016/j.cels.2021.08.004. PMID: 34469743. PMCID: PMC8617591.
Antigen dominance hierarchies shape TCF1+ progenitor CD8 T cell phenotypes in tumors.
Burger ML, Cruz AM, Crossland GE, Gaglia G, Ritch CC, Blatt SE, Bhutkar A, Canner D, Kienka T, Tavana SZ, Barandiaran AL, Garmilla A, Schenkel JM, Hillman M, de Los Rios Kobara I, Li A, Jaeger AM, Hwang WL, Westcott PMK, Manos MP, Holovatska MM, Hodi FS, Regev A, Santagata S, Jacks T.
Cell. 2021 Sep 16;184(19):4996-5014.e26. doi: 10.1016/j.cell.2021.08.020. PMID: 34534464. PMCID: PMC8522630.
De novo powered air-purifying respirator design and fabrication for pandemic response.
Kothakonda A, Atta L, Plana D, Ward F, Davis C, Cramer A, Moran R, Freake J, Tian E, Mazor O, Gorelik P, Van C, Hansen C, Yang H, Li Y, Sinha MS, Li J, Yu SH, LeBoeuf NR, Sorger PK.
Front Bioeng Biotechnol. 2021 Sep 6;9:690905. doi: 10.3389/fbioe.2021.690905. PMID: 34552915. PMCID: PMC8450396.
Spatially organized multicellular immune hubs in human colorectal cancer.
Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N.O
Cell. 2021 Sep 2;184(18):4734-4752.e20. doi: 10.1016/j.cell.2021.08.003. PMID: 34450029. PMCID: PMC8772395.
Targeting Pin1 renders pancreatic cancer eradicable by synergizing with immunochemotherapy.
Koikawa K, Kibe S, Suizu F, Sekino N, Kim N, Manz TD, Pinch BJ, Akshinthala D, Verma A, Gaglia G, Nezu Y, Ke S, Qiu C, Ohuchida K, Oda Y, Lee TH, Wegiel B, Clohessy JG, London N, Santagata S, Wulf GM, Hidalgo M, Muthuswamy SK, Nakamura M, Gray NS, Zhou XZ, Lu KP.
Cell. 2021 Sep 2;184(18):4753-4771.e27. doi: 10.1016/j.cell.2021.07.020. PMID: 34388391. PMCID: PMC8557351.
Developmental stage classification of embryos using two-stream neural network with linear-chain conditional random field.
Lukyanenko S, Jang WD, Wei D, Struyven R, Kim Y, Leahy B, Yang H, Rush A, Ben-Yosef D, Needleman D, Pfister H.
Med Image Comput Comput Assist Interv. 2021 Sep-Oct;12908:363-372. doi: 10.1007/978-3-030-87237-3_35. PMID: 34671767. PMCID: PMC8526069.
Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 disease severity.
Inde Z, Croker BA, Yapp C, Joshi GN, Spetz J, Fraser C, Qin X, Xu L, Deskin B, Ghelfi E, Webb G, Carlin AF, Zhu YP, Leibel SL, Garretson AF, Clark AE, Duran JM, Pretorius V, Crotty-Alexander LE, Li C, Lee JC, Sodhi C, Hackam DJ, Sun X, Hata AN, Kobzik L, Miller J, Park JA, Brownfield D, Jia H, Sarosiek KA.
Sci Adv. 2021 Aug 18;7(34):eabf8609. doi: 10.1126/sciadv.abf8609. PMID: 34407940. PMCID: PMC8373124
Assessing the filtration efficiency and regulatory status of N95s and nontraditional filtering face-piece respirators available during the COVID-19 pandemic.
Plana D, Tian E, Cramer AK, Yang H, Carmack MM, Sinha MS, Bourgeois FT, Yu SH, Masse P, Boyer J, Kim M, Mo J, LeBoeuf NR, Li J, Sorger PK.
BMC Infect Dis. 2021 Jul 29;21(1):712. doi: 10.1186/s12879-021-06008-8. PMID: 34325673. PMCID: PMC8319695.
Computing the Riemannian curvature of image patch and single-cell RNA sequencing data manifolds using extrinsic differential geometry.
Sritharan D, Wang S, Hormoz S.
Proc Natl Acad Sci. 2021 Jul 20;118(29):e2100473118. doi: 10.1073/pnas.2100473118. PMID: 34272279. PMCID: PMC8307776.
COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.
Delorey TM, Ziegler CGK, Heimberg G, Normand R, Yang Y, Segerstolpe Å, Abbondanza D, Fleming SJ, Subramanian A, Montoro DT, Jagadeesh KA, Dey KK, Sen P, Slyper M, Pita-Juárez YH, Phillips D, Biermann J, Bloom-Ackermann Z, Barkas N, Ganna A, Gomez J, Melms JC, Katsyv I, Normandin E, Naderi P, Popov YV, Raju SS, Niezen S, Tsai LT, Siddle KJ, Sud M, Tran VM, Vellarikkal SK, Wang Y, Amir-Zilberstein L, Atri DS, Beechem J, Brook OR, Chen J, Divakar P, Dorceus P, Engreitz JM, Essene A, Fitzgerald DM, Fropf R, Gazal S, Gould J, Grzyb J, Harvey T, Hecht J, Hether T, Jané-Valbuena J, Leney-Greene M, Ma H, McCabe C, McLoughlin DE, Miller EM, Muus C, Niemi M, Padera R, Pan L, Pant D, Pe'er C, Pfiffner-Borges J, Pinto CJ, Plaisted J, Reeves J, Ross M, Rudy M, Rueckert EH, Siciliano M, Sturm A, Todres E, Waghray A, Warren S, Zhang S, Zollinger DR, Cosimi L, Gupta RM, Hacohen N, Hibshoosh H, Hide W, Price AL, Rajagopal J, Tata PR, Riedel S, Szabo G, Tickle TL, Ellinor PT, Hung D, Sabeti PC, Novak R, Rogers R, Ingber DE, Jiang ZG, Juric D, Babadi M, Farhi SL, Izar B, Stone JR, Vlachos IS, Solomon IH, Ashenberg O, Porter CBM, Li B, Shalek AK, Villani AC, Rozenblatt-Rosen O, Regev A.
Nature. 2021 Jul;595(7865):107-113. doi: 10.1038/s41586-021-03570-8. PMID: 33915569. PMCID: PMC8919505.
A molecular single-cell lung atlas of lethal COVID-19.
Melms JC, Biermann J, Huang H, Wang Y, Nair A, Tagore S, Katsyv I, Rendeiro AF, Amin AD, Schapiro D, Frangieh CJ, Luoma AM, Filliol A, Fang Y, Ravichandran H, Clausi MG, Alba GA, Rogava M, Chen SW, Ho P, Montoro DT, Kornberg AE, Han AS, Bakhoum MF, Anandasabapathy N, Suárez-Fariñas M, Bakhoum SF, Bram Y, Borczuk A, Guo XV, Lefkowitch JH, Marboe C, Lagana SM, Del Portillo A, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B.
Nature. 2021 Jul;595(7865):114-119. doi: 10.1038/s41586-021-03569-1. PMID: 33915568. PMCID: PMC8814825.
3D Printed frames to enable reuse and improve the fit of N95 and KN95 respirators.
McAvoy M, Bui AN, 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. doi: 10.1186/s42490-021-00055-7. PMID: 34099062. PMCID: PMC8182357.
Evolution of delayed resistance to immunotherapy in a melanoma responder.
Liu D, Lin JR, Robitschek EJ, Kasumova GG, Heyde A, Shi A, Kraya A, Zhang G, Moll T, Frederick DT, Chen YA, Wang S, Schapiro D, Ho LL, Bi K, Sahu A, Mei S, Miao B, Sharova T, Alvarez-Breckenridge C, Stocking JH, Kim T, Fadden R, Lawrence D, Hoang MP, Cahill DP, Malehmir M, Nowak MA, Brastianos PK, Lian CG, Ruppin E, Izar B, Herlyn M, Van Allen EM, Nathanson K, Flaherty KT, Sullivan RJ, Kellis M, Sorger PK, Boland GM.
Nat Med. 2021 Jun;27(6):985-992. doi: 10.1038/s41591-021-01331-8. PMID: 33941922. PMCID: PMC8474080.
Discovery and resistance mechanism of a selective CDK12 degrader.
Jiang B, Gao Y, Che J, Lu W, Kaltheuner IH, Dries R, Kalocsay M, Berberich MJ, Jiang J, You I, Kwiatkowski N, Riching KM, Daniels DL, Sorger PK, Geyer M, Zhang T, Gray NS.
Nat Chem Biol. 2021 Jun;17(6):675-683. doi: 10.1038/s41589-021-00765-y. PMID: 33753926. PMCID: PMC8590456.
Metastasis and immune evasion from extracellular cGAMP hydrolysis.
Li J, Duran MA, Dhanota N, Chatila WK, Bettigole SE, Kwon J, Sriram RK, Humphries MP, Salto-Tellez M, James JA, Hanna MG, Melms JC, Vallabhaneni S, Litchfield K, Usaite I, Biswas D, Bareja R, Li HW, Martin ML, Dorsaint P, Cavallo JA, Li P, Pauli C, Gottesdiener L, DiPardo BJ, Hollmann TJ, Merghoub T, Wen HY, Reis-Filho JS, Riaz N, Su SM, Kalbasi A, Vasan N, Powell SN, Wolchok JD, Elemento O, Swanton C, Shoushtari AN, Parkes EE, Izar B, Bakhoum SF.
Cancer Discov. 2021 May;11(5):1212-1227. doi: 10.1158/2159-8290.CD-20-0387. PMID: 33372007. PMCID: PMC8102348.
Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment.
Pauken KE, Shahid O, Lagattuta KA, Mahuron KM, Luber JM, Lowe MM, Huang L, Delaney C, Long JM, Fung ME, Newcomer K, Tsai KK, Chow M, Guinn S, Kuchroo JR, Burke KP, Schenkel JM, Rosenblum MD, Daud AI, Sharpe AH, Singer M.
J Exp Med. 2021 Apr 5;218(4):e20200920. doi: 10.1084/jem.20200920. PMID: 33651880. PMCID: PMC7933992.
AMICI: high-performance sensitivity analysis for large ordinary differential equation models.
Fröhlich F, Weindl D, Schälte Y, Pathirana D, Paszkowski Ł, Lines GT, Stapor P, Hasenauer J.
Bioinformatics. 2021 Apr 2;37(20):3676–7. doi: 10.1093/bioinformatics/btab227. PMID: 33821950; PMCID: PMC8545331.
Time resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling.
Vemulapalli V, Chylek LA, Erickson A, Pfeiffer A, Gabriel KH, LaRochelle J, Subramanian K, Cao R, Stegmaier K, Mohseni M, LaMarche MJ, Acker MG, Sorger PK, Gygi SP, Blacklow SC.
Elife. 2021 Mar 23;10:e64251. doi: 10.7554/eLife.64251. PMID: 33755016. PMCID: PMC8024022.
HAND1 and BARX1 Act as transcriptional and anatomic determinants of malignancy in gastrointestinal stromal tumor.
Hemming ML, Coy S, Lin JR, Andersen JL, Przybyl J, Mazzola E, Abdelhamid Ahmed AH, van de Rijn M, Sorger PK, Armstrong SA, Demetri GD, Santagata S.
Clin Cancer Res. 2021 Mar 15;27(6):1706-1719. doi: 10.1158/1078-0432.CCR-20-3538. PMID: 33451979. PMCID: PMC7956056.
Melanoma cell intrinsic GABAA receptor enhancement potentiates radiation and immune checkpoint inhibitor response by promoting direct and T cell-mediated antitumor activity.
Pomeranz Krummel DA, Nasti TH, Kaluzova M, Kallay L, Bhattacharya D, Melms JC, Izar B, Xu M, Burnham A, Ahmed T, Li G, Lawson D, Kowalski J, Cao Y, Switchenko JM, Ionascu D, Cook JM, Medvedovic M, Jenkins A, Khan MK, Sengupta S.
Int J Radiat Oncol Biol Phys. 2021 Mar 15;109(4):1040-1053. doi: 10.1016/j.ijrobp.2020.10.025. PMID: 33289666. PMCID: PMC8329598.
A crisis-responsive framework for medical device development applied to the COVID-19 pandemic.
Antonini M-J, Plana D, Srinivasan S, Atta L, Achanta A, Yang H, Cramer AK, Freake J, Sinha MS, Yu SH, LeBoeuf NR, Linville-Engler B, Sorger PK.
Front Digit Health. 2021 Mar;3:617106. doi: 10.3389/fdgth.2021.617106. PMID: 33899045. PMCID: PMC8064560.
Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion.
Frangieh CJ, Melms JC, Thakore PI, Geiger-Schuller KR, Ho P, Luoma AM, Cleary B, Jerby-Arnon L, Malu S, Cuoco MS, Zhao M, Ager CR, Rogava M, Hovey L, Rotem A, Bernatchez C, Wucherpfennig KW, Johnson BE, Rozenblatt-Rosen O, Schadendorf D, Regev A, Izar B.
Nat Genet. 2021 Mar;53(3):332-341. doi: 10.1038/s41588-021-00779-1. PMID: 33649592. PMCID: PMC8376399.
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.
Clinical efficacy and molecular response correlates of the WEE1 inhibitor adavosertib combined with cisplatin in patients with metastatic triple-negative breast cancer.
Keenan TE, Li T, Vallius T, Guerriero JL, Tayob N, Kochupurakkal B, Davis J, Pastorello R, Tahara RK, Anderson L, Conway J, He MX, Shannon E, Godin RE, Sorger PK, D'Andrea A, Overmoyer B, Winer EP, Mittendorf EA, Van Allen EM, Shapiro GI, Tolaney SM.
Clin Cancer Res. 2021 Feb 15;27(4):983-991. doi: 10.1158/1078-0432.CCR-20-3089. PMID: 33257427. PMCID: PMC7887044.
Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma.
Jerby-Arnon L, Neftel C, Shore ME, Weisman HR, Mathewson ND, McBride MJ, Haas B, Izar B, Volorio A, Boulay G, Cironi L, Richman AR, Broye LC, Gurski JM, Luo CC, Mylvaganam R, Nguyen L, Mei S, Melms JC, Georgescu C, Cohen O, Buendia-Buendia JE, Segerstolpe A, Sud M, Cuoco MS, Labes D, Gritsch S, Zollinger DR, Ortogero N, Beechem JM, Petur Nielsen G, Chebib I, Nguyen-Ngoc T, Montemurro M, Cote GM, Choy E, Letovanec I, Cherix S, Wagle N, Sorger PK, Haynes AB, Mullen JT, Stamenkovic I, Rivera MN, Kadoch C, Wucherpfennig KW, Rozenblatt-Rosen O, Suvà ML, Riggi N, Regev A.
Nat Med. 2021 Feb;27(2):289-300. doi: 10.1038/s41591-020-01212-6. PMID: 33495604. PMCID: PMC8817899.
Conversion of existing UVB phototherapy units to UVC germicidal chambers for N95 decontamination: lessons learned.
Kassamali B, Yu Z, Davis C, Carmack M, Bui AN, Said JT, Plana D, Yang H, Sorger P, LeBoeuf NR, LaChance AH.
Photobiomodul Photomed Laser Surg. 2021 Feb;39(2):83-85. doi: 10.1089/photob.2020.4968. PMID: 33481669. PMCID: PMC8106246.
Pharmacologic screening identifies metabolic vulnerabilities of CD8+ T cells.
Drijvers JM, Gillis JE, Muijlwijk T, Nguyen TH, Gaudiano EF, Harris IS, LaFleur MW, Ringel AE, Yao CH, Kurmi K, Juneja VR, Trombley JD, Haigis M, Sharpe AH.
Cancer Immunol Res. 2021 Feb;9(2):184-199. doi: 10.1158/2326-6066.CIR-20-0384. PMID: 33277233. PMCID: PMC7864883.
Mammalian cell proliferation requires noncatalytic functions of O-GlcNAc transferase.
Levine ZG, Potter SC, Joiner CM, Fei GQ, Nabet B, Sonnett M, Zachara NE, Gray NS, Paulo JA, Walker S.
Proc Natl Acad Sci U S A. 2021 Jan 26;118(4):e2016778118. doi: 10.1073/pnas.2016778118. PMID: 33419956. PMCID: PMC7848692.
PEtab – interoperable specification of parameter estimation problems in systems biology.
Schmiester L, Schälte Y, Bergmann FT, Camba T, Dudkin E, Egert J, Fröhlich F, Fuhrmann L, Hauber AL, Kemmer S, Lakrisenko P, Loos C, Merkt S, Müller W, Pathirana D, Raimúndez E, Refisch L, Rosenblatt M, Stapor PL, Städter P, Wang D, Wieland FG, Banga JR, Timmer J, Villaverde AF, Sahle S, Kreutz C, Hasenauer J, Weindl D.
PLoS Comput Biol. 2021 Jan 26;17(1):e1008646. doi: 10.1371/journal.pcbi.1008646. PMID: 33497393. PMCID: PMC7864467.
Analysis of SteraMist ionized hydrogen peroxide technology in the sterilization of N95 respirators and other PPE.
Cramer AK, Plana D, Yang H, Carmack MM, Tian E, Sinha MS, Krikorian D, Turner D, Mo J, Li J, Gupta R, Manning H, Bourgeois FT, Yu SH, Sorger PK, LeBoeuf NR.
Sci Rep. 2021 Jan 21;11(1):2051. doi: 10.1038/s41598-021-81365-7. PMID: 33479334. PMCID: PMC7819989.
Concurrent dexamethasone limits the clinical benefit of immune checkpoint blockade in glioblastoma.
Iorgulescu JB, Gokhale PC, Speranza MC, Eschle BK, Poitras MJ, Wilkens MK, Soroko KM, Chhoeu C, Knott A, Gao Y, Lim-Fat MJ, Baker GJ, Bonal DM, Nguyen QD, Grant GRL, Ligon KL, Sorger PK, Chiocca EA, Anderson AC, Kirschmeier PT, Sharpe AH, Freeman GJ, Reardon DA.
Clin Cancer Res. 2021 Jan 1;27(1):276-287. doi: 10.1158/1078-0432.CCR-20-2291. PMID: 33239433. PMCID: PMC8034990.
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 J-R, 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. PMID: 33738458. PMCID: PMC7963404.
2020 Publications
Obesity shapes metabolism in the tumor microenvironment to suppress anti-tumor immunity.
Ringel AE, Drijvers JM, Baker GJ, Catozzi A, García-Cañaveras JC, Gassaway BM, Miller BC, Juneja VR, Nguyen TH, Joshi S, Yao C-H, Yoon H, Sage PT, LaFleur MW, Trombley JD, Jacobson CA, Maliga Z, Gygi SP, Sorger PK, Rabinowitz JD, Sharpe AH, Haigis MC.
Cell. 2020 Dec 23;183(7):1848-1866.e26. doi: 10.1016/j.cell.2020.11.009. PMID: 33301708. PMCID: PMC8064125.
Regulatory and safety considerations in deploying a locally fabricated, reusable face shield in a hospital responding to the COVID-19 pandemic.
Mostaghimi A, Antonini MJ, Plana D, Anderson PD, Beller B, Boyer EW, Fannin A, Freake J, Oakley R, Sinha MS, Smith L, Van C, Yang H, Sorger PK, LeBoeuf NR, Yu SH.
Med (N Y). 2020 Dec 18;1(1):139-151.e4. doi: 10.1016/j.medj.2020.06.003. PMID: 32838357. PMCID: PMC7304404.
Vascular disease and thrombosis in SARS-CoV-2-infected rhesus macaques.
Aid M, Busman-Sahay K, Vidal SJ, Maliga Z, Bondoc S, Starke C, Terry M, Jacobson CA, Wrijil L, Ducat S, Brook OR, Miller AD, Porto M, Pellegrini KL, Pino M, Hoang TN, Chandrashekar A, Patel S, Stephenson K, Bosinger SE, Andersen H, Lewis MG, Hecht JL, Sorger PK, Martinot AJ, Estes JD, Barouch DH.
Cell. 2020 Nov 25;183(5):1354-1366.e13. doi: 10.1016/j.cell.2020.10.005. PMID: 33065030. PMCID: PMC7546181.
Receptor-driven ERK pulses reconfigure MAPK signaling and enable persistence of drug-adapted BRAF-mutant melanoma cells.
Gerosa L, Chidley C, Fröhlich F, Sanchez G, Lim SK, Muhlich J, Chen J-Y, Vallabhaneni S, Baker GJ, Schapiro D, Atanasova MI, Chylek LA, Shi T, Yi L, Nicora CD, Claas A, Ng TSC, Kohler RH, Lauffenburger DA, Weissleder R, Miller MA, Qian W-J, Wiley HS, Sorger PK.
Cell Syst. 2020 Nov 18;11(5):478-494.e9. doi: 10.1016/j.cels.2020.10.002. PMID: 33113355. PMCID: PMC8009031.
Minerva: a light-weight, narrative image browser for multiplexed tissue images.
Hoffer J, Rashid R, Muhlich JL, Chen Y-A, Russell DPW, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK.
J Open Source Softw. 2020 Oct 15;5(54):2579. doi: 10.21105/joss.02579. PMID: 33768192. PMCID: PMC7989801.
A proof of concept for biomarker-guided targeted therapy against ovarian cancer based on patient-derived tumor xenografts.
Palmer AC, Plana D, Gao H, Korn JM, Yang G, Green J, Zhang X, Velazquez R, McLaughlin ME, Ruddy DA, Kowal C, Goldovitz J, Bullock C, Rivera S, Rakiec DP, Elliott G, Fordjour P, Meyer R, Loo A, Kurth E, Engelman JA, Bitter H, Sellers WR, Williams JA, Sorger PK.
Cancer Res. 2020 Oct 1;80(19):4278-4287. doi: 10.1158/0008-5472.CAN-19-3850. PMID: 32747364. PMCID: PMC7541581.
MitoEM dataset: large-scale 3D mitochondria instance segmentation from EM images.
Wei D, Lin Z, Franco-Barranco D, Wendt N, Liu X, Yin W, Huang X, Gupta A, Jang WD, Wang X, Arganda-Carreras I, Lichtman JW, Pfister H.
Med Image Comput Comput Assist Interv. 2020 Oct;12265:66-76. doi: 10.1007/978-3-030-59722-1_7. PMID: 33283212. PMCID: PMC7713709.
Channel embedding for informative protein identification from highly multiplexed images.
Magid SA, Jang W-D, Schapiro D, Wei D, Tompkin J, Sorger PK, Pfister H.
Med Image Comput Comput Assist Interv. 2020 Oct;12265:3-13. doi: 10.1007/978-3-030-59722-1_1. PMID: 33283211. PMCID: PMC7713713.
Automated measurements of key morphological features of human embryos for IVF.
Leahy BD, Jang W-D, Yang HY, Struyven R, Wei D, Sun Z, Lee KR, Royston C, Cam L, Kalma Y, Azem F, Ben-Yosef D, Pfister H, Needleman D.
Med Image Comput Comput Assist Interv. 2020 Oct;12265:25-35. doi: 10.1007/978-3-030-59722-1_3. PMID: 33313603. PMCID: PMC7732604.
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. PMID: 32898474. PMCID: PMC7565356.
Impact of sequencing radiation therapy and immune checkpoint inhibitors in the treatment of melanoma brain metastases.
Pomeranz Krummel DA, Nasti TH, Izar B, Press RH, Xu M, Lowder L, Kallay L, Rupji M, Rosen H, Su J, Curran W, Olson J, Weinberg B, Schniederjan M, Neill S, Lawson D, Kowalski J, Khan MK, Sengupta S.
Int J Radiat Oncol Biol Phys. 2020 Sep 1;108(1):157-163. doi: 10.1016/j.ijrobp.2020.01.043. PMID: 32057994. PMCID: PMC7839060.
Considerations for the selection and use of disinfectants against SARS-CoV-2 in a health care setting.
Tyan K, Levin A, Avalos-Pacheco A, Plana D, Rand EA, Yang H, Maliszewski LE, Chylek LA, Atta L, Tye MA, Carmack MM, Oglesby NS, Burgin S, Yu SH, LeBoeuf NR, Kemp JM.
Open Forum Infect Dis. 2020 Aug 31;7(9):ofaa396. doi: 10.1093/ofid/ofaa396. PMID: 32989420. PMCID: PMC7499694.
SARS-CoV-2 infection protects against rechallenge in rhesus macaques.
Chandrashekar A, Liu J, Martinot AJ, McMahan K, Mercado NB, Peter L, Tostanoski LH, Yu J, Maliga Z, Nekorchuk M, Busman-Sahay K, Terry M, Wrijil LM, Ducat S, Martinez DR, Atyeo C, Fischinger S, Burke JS, Slein MD, Pessaint L, Van Ry A, Greenhouse J, Taylor T, Blade K, Cook A, Finneyfrock B, Brown R, Teow E, Velasco J, Zahn R, Wegmann F, Abbink P, Bondzie EA, Dagotto G, Gebre MS, He X, Jacob-Dolan C, Kordana N, Li Z, Lifton MA, Mahrokhian SH, Maxfield LF, Nityanandam R, Nkolola JP, Schmidt AG, Miller AD, Baric RS, Alter G, Sorger PK, Estes JD, Andersen H, Lewis MG, Barouch DH.
Science. 2020 Aug 14;369(6505):812-817. doi: 10.1126/science.abc4776. PMID: 32434946. PMCID: PMC7243369.
Two stream active query suggestion for active learning in connectomics.
Lin Z, Wei D, Jang W-D, Zhou S, Chen X, Wang X, Schalek R, Berger D, Matejek B, Kamentsky L, Peleg A, Haehn D, Jones T, Parag T, Lichtman J, Pfister H.
Comput Vis ECCV. 2020 Aug;12363:103-120. doi: 10.1007/978-3-030-58523-5_7. PMID 33345257. PMCID: PMC7746018.
A single-cell landscape of high-grade serous ovarian cancer.
Izar B, Tirosh I, Stover EH, Wakiro I, Cuoco MS, Alter I, Rodman C, Leeson R, Su MJ, Shah P, Iwanicki M, Walker SR, Kanodia A, Melms JC, Mei S, Lin JR, Porter CBM, Slyper M, Waldman J, Jerby-Arnon L, Ashenberg O, Brinker TJ, Mills C, Rogava M, Vigneau S, Sorger PK, Garraway LA, Konstantinopoulos PA, Liu JF, Matulonis U, Johnson BE, Rozenblatt-Rosen O, Rotem A, Regev A.
Nat Med. 2020 Aug;26(8):1271-1279. doi: 10.1038/s41591-020-0926-0. PMID: 32572264. PMCID: PMC7723336.
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A.
Nat Med. 2020 May;26(5):792-802. doi: 10.1038/s41591-020-0844-1. PMID: 32405060. PMCID: PMC7220853.
Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism.
Schauer NJ, Liu X, Magin RS, Doherty LM, Chan WC, Ficarro SB, Hu W, Roberts RM, Iacob RE, Stolte B, Giacomelli AO, Perera S, McKay K, Boswell SA, Weisberg EL, Ray A, Chauhan D, Dhe-Paganon S, Anderson KC, Griffin JD, Li J, Hahn WC, Sorger PK, Engen JR, Stegmaier K, Marto JA, Buhrlage SJ.
Sci Rep. 2020 Mar 24;10(1):5324. doi: 10.1038/s41598-020-62076-x. PMID: 32210275; PMCID: PMC7093416.
Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer.
Färkkilä A, Gulhan DC, Casado J, Jacobson CA, Nguyen H, Kochupurakkal B, Maliga Z, Yapp C, Chen Y-A, Schapiro D, Zhou Y, Graham JR, Dezube BJ, Munster P, Santagata S, Garcia E, Rodig S, Lako A, Chowdhury D, Shapiro GI, Matulonis UA, Park PJ, Hautaniemi S, Sorger PK, Swisher EM, D’Andrea AD, Konstantinopoulos PA.
Nat Commun. 2020 Mar 19;11(1):1459. doi: 10.1038/s41467-020-15315-8. PMID: 32193378. PMCID: PMC7081234.
Inhibition of haspin kinase promotes cell-intrinsic and extrinsic anti-tumor activity.
Melms JC, Vallabhaneni S, Mills CE, Yapp C, Chen JY, Morelli E, Waszyk P, Kumar S, Deming D, Moret N, Rodriguez S, Subramanian K, Rogava M, Cartwright ANR, Luoma A, Mei S, Brinker TJ, Miller DM, Spektor A, Schadendorf D, Riggi N, Wucherpfennig KW, Sorger PK, Izar B.
Cancer Res. 2020 Feb 15;80(4):798-810. doi: 10.1158/0008-5472.CAN-19-2330. PMID: 31882401. PMCID: PMC7029677.
Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1.
Hemming ML, Nathenson MJ, Lin JR, Mei S, Du Z, Malik K, Marino-Enriquez A, Jagannathan JP, Sorger PK, Bertagnolli M, Sicinska E, Demetri GD, Santagata S.
JCO Precision Oncology. 2020 Feb 14;4:79-90. doi: 10.1200/po.19.00287. PMID: 32133433. PMCID: PMC7055910.
HSF1 phase transition mediates stress adaptation and cell fate decision.
Gaglia G, Rashid R, Yapp C, Joshi GN, Li C, Lindquist SL, Sarosiek KA, Whitesell L, Sorger PK, Santagata S.
Nat Cell Biol. 2020 Feb;22(2):151-158. doi.org/10.1038/s41556-019-0458-3. PMID: 32015439. PMCID: PMC7135912.
Torin2 exploits replication and checkpoint vulnerabilities to cause death of PI3K-activated triple-negative breast cancer cells.
Chopra SS, Jenney A, Palmer A, Niepel M, Chung M, Mills C, Sivakumaren SC, Liu Q, Chen JY, Yapp C, Asara JM, Gray NS, Sorger PK.
Cell Syst. 2020 Jan 22;10(1):66-81.e11. doi: 10.1016/j.cels.2019.11.001. PMID 31812693. PMCID: PMC7000271.
Imaging and quantifying drug delivery in skin – Part 2: fluorescence and vibrational spectroscopic imaging methods.
Pena AM, Chen X, Pence I, Bornschlögl T, Jeong S, Grégoire S, Luengo GS, Hallegot P, Obeidy P, Feizpour A, Chan KF, Evans CL.
Adv Drug Deliv Rev. 2020 Jan 1;153:147-168. doi: 10.1016/j.addr.2020.03.003. PMID: 32217069. PMCID: PMC7483684.
Facetto: combining unsupervised and supervised learning for hierarchical phenotype analysis in multi-channel image data.
Krueger R, Beyer J, Jang WD, Kim NW, Sokolov A, Sorger PK, Pfister H.
IEEE Trans Vis Comput Graph. 2020 Jan;26(1):227-237. doi: 10.1109/TVCG.2019.2934547. PMID: 31514138. PMCID: PMC7045445.
2019 Publications
Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer.
Rashid R, Gaglia G, Chen YA, Lin JR, Du Z, Maliga Z, Schapiro D, Yapp C, Muhlich J, Sokolov A, Sorger P, Santagata S.
Sci Data. 2019 Dec 17;6(1):323. doi: 10.1038/s41597-019-0332-y. PMID: 31848351. PMCID: PMC6917801.
PTPN2 regulates the generation of exhausted CD8+ T cell subpopulations and restrains tumor immunity.
LaFleur MW, Nguyen TH, Coxe MA, Miller BC, Yates KB, Gillis JE, Sen DR, Gaudiano EF, Al Abosy R, Freeman GJ, Haining WN, Sharpe AH.
Nat Immunol. 2019 Oct;20(10):1335-1347. doi: 10.1038/s41590-019-0480-4. PMID: 31527834. PMCID: PMC6754306.
Targeted treatment of papillary craniopharyngiomas harboring BRAF V600E mutations.
Juratli TA, Jones PS, Wang N, Subramanian M, Aylwin SJB, Odia Y, Rostami E, Gudjonsson O, Shaw BL, Cahill DP, Galanis E, Barker FG 2nd, Santagata S, Brastianos PK.
Cancer. 2019 Sep 1;125(17):2910-2914. doi: 10.1002/cncr.32197. PMID: 31314136. PMCID: PMC7032527.
Multiomics profiling establishes the polypharmacology of FDA approved CDK4/6 inhibitors and the potential for differential clinical activity.
Hafner M, Mills CE, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Liu C, Walmsley CS, Juric D, Sorger PK.
Cell Chem Biol. 2019 Aug 15;26(8):1067-1080.e8. doi: 10.1016/j.chembiol.2019.05.005. PMID: 31178407. PMCID: PMC6936329.
Leveraging compound promiscuity to Identify targetable cysteines within the kinome.
Rao S, Gurbani D, Du G, Everley RA, Browne CM, Chaikuad A, Tan L, Schröder M, Gondi S, Ficarro SB, Sim T, Kim ND, Berberich MJ, Knapp S, Marto JA, Westover KD, Sorger PK, Gray NS.
Cell Chem Biol. 2019 Jun 20;26(6):818-829.e9. doi: 10.1016/j.chembiol.2019.02.021. PMID: 30982749. PMCID: PMC6634314.
Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma.
Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R.
Nat Commun. 2019 Jun 3;10(1):2400. doi: 10.1038/s41467-019-10307-9. PMID: 31160565. PMCID: PMC6546744.
Adaptation of human iPSC-derived cardiomyocytes to tyrosine kinase inhibitors reduces acute cardiotoxicity via metabolic reprogramming.
Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK.
Cell Syst. 2019 May 22;8(5):412-426.e7. doi: 10.1016/j.cels.2019.03.009. PMID: 31078528. PMCID: PMC6657491.
Characterizing ABC-transporter substrate-likeness using a clean-slate genetic background.
Sokolov A, Ashenden S, Sahin N, Lewis R, Erdem N, Ozaltan E, Bender A, Roth FP, Cokol M.
Front Pharmacol. 2019 Apr 25;10:448. doi: 10.3389/fphar.2019.00448. PMID: 31105571. PMCID: PMC6494965.
Biomarker-driven strategy for MCL1 inhibition in T-cell lymphomas.
Koch R, Christie AL, Crombie JL, Palmer AC, Plana D, Shigemori K, Morrow SN, Van Scoyk A, Wu W, Brem EA, Secrist JP, Drew L, Schuller AG, Cidado J, Letai A, Weinstock DM.
Blood. 2019 Feb 7;133(6):566-575. doi: 10.1182/blood-2018-07-865527. PMID: 30498064. PMCID: PMC6367646.
2018 Publications
Mismatch repair deficiency in high-grade meningioma: a rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade.
Dunn IF, Du Z, Touat M, Sisti MB, Wen PY, Umeton R, Dubuc AM, Ducar M, Canoll PD, Severson E, Elvin JA, Ramkissoon S.H, Lin JR, Cabrera L, Acevedo B, Sorger PK, Ligon KL, Santagata S, Reardon DA.
JCO Precis Oncol. 2018. doi: 10.1200/PO.18.00190. PMID: 30801050. PMCID: PMC6383717.