Publications

Center Preprints

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.
Single cell spatial analysis reveals the topology of immunomodulatory purinergic signaling in glioblastoma.
Coy S, Wang S, Stopka SA, Lin J-R, Rashid R, Yapp C, Ritch CC, Khadka P, Regan M, Hwang J, Wen PY, Bandopadhayay P, Ligon KL, Agar NY, Sorger PK, Touat M, Santagata S.
bioRxiv. 2022 Jan 12; doi: 10.1101/2022.01.12.475925.
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.
bioRxiv. 2021 Dec 6; doi: 10.1101/2021.12.05.471248.
Multiplexed and reproducible high content screening of live and fixed cells using the Dye Drop method.
Mills CE, Subramanian K, Hafner M, Niepel M, Gerosa L, Chung M, Victor C, Gaudio B, Yapp C, Sorger PK.
bioRxiv. 2021 Aug 28. doi: 10.1101/2021.08.27.457854.
Drug repurposing of metformin for Alzheimer’s disease: Combining causal inference in medical records data and systems pharmacology for biomarker identification.
Charpignon M-L, Vakulenko-Lagun B, Zheng B, Magdamo C, Su B, Evans K, Rodriguez S, Sokolov A, Boswell S, Sheu Y-H, Somai M, Middleton L, Hyman BT, Betensky RA, Finkelstein SN, Welsch RE, Tzoulaki I, Blacker D, Das S, Albers MW.
medRxiv. 2021 Aug 12; doi: 10.1101/2021.08.10.21261747.
Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes.
Doherty LM, Mills CE, Boswell SA, Liu X, Hoyt CT, Gyori BM, Buhrlage SJ, Sorger PK.
bioRxiv. 2021 Aug 9. doi: 10.1101/2021.08.06.455458.
Single-sequence protein structure prediction using language models from deep learning.
Chowdhury R, Bouatta N, Biswas S, Rochereau C, Church GM, Sorger PK, AlQuraishi M.
bioRxiv. 2021 Aug 4. doi: 10.1101/2021.08.02.454840.
Tumor cells dictate anti-tumor immune responses by altering pyruvate utilization and succinate signaling in CD8+ T cells.
Elia I, Rowe J, Joshi S, Johnson S, Notarangelo G, Kurmi K, Freeman GJ, Sharpe A, Haigis MC.
SSRN Journal. 2021 May 27; doi: 10.2139/ssrn.3854520.
Fides: reliable trust-region optimization for parameter estimation of ordinary differential equation models.
Fröhlich F, Sorger PK.
bioRxiv. 2021 May 22. doi: 10.1101/2021.05.20.445065.
Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR software.
Muhlich J, Chen Y-A, Russell D, Sorger PK.
bioRxiv. 2021 Apr 21. doi: 10.1101/2021.04.20.440625.
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.
bioRxiv. 2021 Apr 4. doi: 10.1101/2021.04.02.438285.
Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer.
Lin J-R, Wang S, Coy S, Tyler M, Yapp C, Chen Y-A, Heiser CN, Lau KS, Santagata S, Sorger PK.
bioRxiv. 2021 Apr 2. doi: 10.1101/2021.03.31.437984.
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.

2022 Publications

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. PMID: 35298263.
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.
PyBioPAX: biological pathway exchange in Python.
Gyori BM, Hoyt CT.
J Open Source Softw. 2022 Mar 11;7(71):4136. doi: 10.21105/joss.04136. NIHMS: NIHMS1788994.
Independent drug action in combination therapy: implications for precision oncology.
Plana D, Palmer AC, Sorger PK.
Cancer Discov. 2022 Mar 1;12(3):606-624. doi: 10.1158/2159-8290.CD-21-0212. PubMed PMID: 34983746; PMCID: PMC8904281.
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.
Time-series transcriptomics and proteomics reveal alternative modes to decode p53 oscillations.
Jiménez A, Lu D, Kalocsay M, Berberich MJ, Balbi P, Jambhekar A, Lahav G.
Mol Syst Biol. 2022 Mar;18(3):e10588. doi: 10.15252/msb.202110588. PMID: 35285572. PMCID: PMC8919251.
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.
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.
Nat Commun. 2022 Feb 15;13(1):873. doi: 10.1038/s41467-022-28410-9. PMID: 35169116. PMCID: PMC8847344.
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.
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.
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.

2021 Publications

Combination treatment optimization using a pan-cancer pathway model.
Schmucker R, Farina G, Faeder J, Fröhlich F, Saglam AS, Sandholm T.
PLoS Comput Biol. 2021 Dec 28;17(12):e1009689. doi: 10.1371/journal.pcbi.1009689. PMID: 34962919. PMCID: PMC8747684.
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.
Translational biophotonics with Raman imaging: clinical applications and beyond.
Pence IJ, Evans CL.
Analyst. 2021 Oct 25;146(21):6379-6393. doi: 10.1039/d1an00954k. PMID: 34596653. PMCID: PMC8543123.
Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms.
AlQuraishi M, Sorger PK.
Nat Methods. 2021 Oct;18(10):1169-1180. doi: 10.1038/s41592-021-01283-4. PMID: 34608321; PMCID: PMC8793939.
Dynamic high-pass filtering and multi-spectral attention for image super-resolution.
Magid SA, Zhang Y, Wei D, Jang W-D, Lin Z, Fu Y, Pfister H.
Proc IEEE Int Conf Comput Vis. 2021 Oct;2021:4268-4277. doi: 10.1109/iccv48922.2021.00425. PubMed PMID: 35368831. PMCID: PMC8969883.
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
Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2.
Patiño-Galindo JÁ, Filip I, Chowdhury R, Maranas CD, Sorger PK, AlQuraishi M, Rabadan R.
Genome Med. 2021 Aug 6;13(1):124. doi: 10.1186/s13073-021-00943-6. PMID: 34362430. PMCID: PMC8343217.
Protein structure prediction by AlphaFold2: are attention and symmetries all you need?
Bouatta N, Sorger P, AlQuraishi M.
Acta Crystallogr D Struct Biol. 2021 Aug 1;77(Pt 8):982-991. doi: 10.1107/S2059798321007531. PMID: 34342271. PMCID: PMC8329862.
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.
shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data.
Shimada K, Bachman JA, Muhlich JL, Mitchison TJ.
Elife. 2021 Feb 8;10:e57116. doi: 10.7554/eLife.57116. PMID: 33554860. PMCID: PMC7924953.
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.
Comparing the efficacy of cancer therapies between subgroups in basket trials.
Palmer AC, Plana D, Sorger PK.
Cell Syst. 2020 Nov 18;11(5):449-460.e2. doi: 10.1016/j.cels.2020.09.003. PMID: 33220857. PMCID: PMC8022348.
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.
The effects of age and systemic metabolism on anti-tumor T cell responses.
Drijvers JM, Sharpe AH, Haigis MC.
Elife. 2020 Nov 10;9:e62420. doi: 10.7554/eLife.62420. PMID: 33170123. PMCID: PMC7655106.
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.
Personal protective equipment for COVID-19: distributed fabrication and additive manufacturing.
Sinha MS, Bourgeois FT, Sorger PK.
Am J Public Health. 2020 Aug;110(8):1162-1164. doi: 10.2105/AJPH.2020.305753. PMID 32552025. PMCID: PMC7349433.
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.
An update on the CNS manifestations of neurofibromatosis type 2.
Coy S, Rashid R, Stemmer-Rachamimov A, Santagata S.
Acta Neuropathol. 2020 Apr;139(4):643-665. doi: 10.1007/s00401-019-02029-5. PMID: 31161239. PMCID: PMC7038792.
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.
Biophysical prediction of protein-peptide interactions and signaling networks using machine learning.
Cunningham JM, Koytiger G, Sorger PK, AlQuraishi M.
Nat Methods. 2020 Feb;17(2):175-183. doi: 10.1038/s41592-019-0687-1. PMID: 31907444. PMCID: PMC7004877.
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.
Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks.
Lyashenko E, Niepel M, Dixit PD, Lim SK, Sorger PK, Vitkup D.
Elife. 2020 Jan 21;9. doi: 10.7554/eLife.50342. PMID: 31961323. PMCID: PMC7046471.
Adeft: acromine-based disambiguation of entities from text with applications to the biomedical literature.
Steppi A, Gyori BM, Bachman JA.
Journal of Open Source Software. 2020 Jan 16;5(45): 1708. doi: 10.21105/joss.01708. PMID: 32337477. PMCID: PMC7182313.
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.
Inferring reaction network structure from single-cell, multiplex data, using toric systems theory.
Wang S, Lin JR, Sontag ED, Sorger PK.
PLoS Comput Biol. 2019 Dec 6;15(12):e1007311. doi: 10.1371/journal.pcbi.1007311. PMID: 31809500. PMCID: PMC6919632.
Unified rational protein engineering with sequence-based deep representation learning.
Alley EC, Khimulya G, Biswas S, AlQuraishi M, Church GM.
Nat Methods. 2019 Dec;16(12):1315-1322. doi: 10.1038/s41592-019-0598-1. PMID: 31636460. PMCID: PMC7067682.
A curative combination cancer therapy achieves high fractional cell killing through low cross-resistance and drug additivity.
Palmer AC, Chidley C, Sorger PK.
Elife. 2019 Nov 19;8. pii: e50036. doi: 10.7554/eLife.50036. PMID: 31742555. PMCID: PMC6897534.
AlphaFold at CASP13.
AlQuraishi M.
Bioinformatics. 2019 Nov 1;35(22):4862-4865. doi: 10.1093/bioinformatics/btz422. PMID: 31116374. PMCID: PMC6907002.
CXCR3: here to stay to enhance cancer immunotherapy?
Rogava M, Izar B.
EBioMedicine. 2019 Nov;49:11-12. doi: 10.1016/j.ebiom.2019.09.044. PMID: 31690542. PMCID: PMC6945198.
Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging.
Du Z, Lin JR, Rashid R, Maliga Z, Wang S, Aster JC, Izar B, Sorger PK, Santagata S.
Nat Protoc. 2019 Oct;14(10):2900-2930. doi: 10.1038/s41596-019-0206-y. PMID: 31534232. PMCID: PMC6959005.
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.
T cell activation depends on extracellular alanine.
Ron-Harel N, Ghergurovich JM, Notarangelo G, LaFleur MW, Tsubosaka Y, Sharpe AH, Rabinowitz JD, Haigis MC.
Cell Rep. 2019 Sep 17;28(12):3011-3021.e4. doi: 10.1016/j.celrep.2019.08.034. PMID: 31533027. PMCID: PMC6934407.
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.
ProteinNet: a standardized data set for machine learning of protein structure.
AlQuraishi M.
BMC Bioinformatics. 2019 Jun 11;20(1):311. doi: 10.1186/s12859-019-2932-0. PMID: 31185886. PMCID: PMC6560865.
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.
A multitargeted probe-based strategy to identify signaling vulnerabilities in cancers.
Rao S, Du G, Hafner M, Subramanian K, Sorger PK, Gray NS.
J Biol Chem. 2019 May 24;294(21):8664-8673. doi: 10.1074/jbc.RA118.006805. PMID: 30858179. PMCID: PMC6544847.
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.
End-to-end differentiable learning of protein structure.
AlQuraishi M.
Cell Syst. 2019 Apr 24;8(4):292-301.e3. doi: 10.1016/j.cels.2019.03.006. PMID: 31005579. PMCID: PMC6513320.
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.