Publications

Submitted

Genomic, immunologic, and functional evolution of resistance to immunotherapy in a melanoma exceptional responder.
Liu D, Lin JR, Kasumova GG, Heyde A, Shi A, Kraya A, Zhang G, Moll T, Frederick DT, Chen YA, Schapiro D, Wang S, Bi K, Sahu A, Mei S, Miao B, Sharova T, Kim T, Fadden R, Lawrence D, Hoang MP, Cahill DP, Malehmir M, Lian C, Ruppin E, Izar B, Herlyn M, Nowak MA, Van Allen EM, Nathanson K, Flaherty KT, Sullivan RJ, Kellis M, Sorger PK, Boland GM.
Nat Med. [in revision]
Differentiating macrophages are regulated by PARP inhibitors and can be harnessed to overcome PARP-inhibitor resistance in BRCA-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, Gross BP, Rodig S, Santagata S, Garber JE, Tung N, Thaxton JE, Mittendorf EA, Sorger PK, Shapiro GI, Guerriero JL.
Nat Cancer. [in revision]

Center Preprints

Assessing the quality of nontraditional N95 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.
medRxiv. 2020 Jul 27. doi: 10.1101/2020.07.25.20161968. PMID: 32743596
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, Short M, Yu SH, Mostaghimi A, Sorger PK, LeBoeuf NR.
medRxiv. 2020 Jul 26:2020. doi: 10.1101/2020.07.20.20151019. PMID: 32743606.
Machine Learning Identifies Novel 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 B, Sorger PK, Albers MW, Sokolov A.
bioRxiv. 2020 May 16. doi: 10.1101/2020.05.15.098749.
Analysis of SteraMist ionized hydrogen peroxide technology in the sterilization of N95 respirators and other PPE: a quality improvement study.
Cramer A, Plana D, Yang HL, Carmack M, Tian E, Sinha MS, Krikorian D, Turner D, Mo J, Li J, Gupta R, Manning H, Bourgeois FT, Yu SH, Sorger P, LeBoeuf NR.
medRxiv. 2020 May 08. doi.org/10.1101/2020.04.19.20069997.
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, Pathirana D, Raimúndez E, Refisch L, Rosenblatt M, Stapor PL, Städter P, Wang D, Wieland F-G, Banga JR, Timmer J, Villaverde AF, Sahle S, Kreutz C, Hasenauer J, Weindl D.
arXiv. 2020 Apr 02.
Interpretative guides for interacting with tissue atlas and digital pathology data using the Minerva browser.
Rashid R, Chen YA, Hoffer J, Muhlich JL, Lin JR, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK.
bioRxiv. 2020 Mar 30. doi: 10.1101/2020.03.27.001834.
Channel embedding for informative protein identification from highly multiplexed images.
Magid SA, Jang WD, Schapiro D, Wei D, Tompkin J, Sorger PK, Pfister H.
bioRxiv. 2020 Mar 25. doi: 10.1101/2020.03.24.004085.
Combinatorial benefit without synergy in recent clinical trials of immune checkpoint inhibitors.
Palmer AC, Izar B, Sorger PK.
medRxiv. 2020 Feb 04. doi: 10.1101/2020.01.31.20019604.
Sporadic ERK pulses drive non-genetic resistance in drug-adapted BRAFV600E melanoma cells.
Gerosa L, Chidley C, Froehlich F, Sanchez G, Lim SK, Muhlich J, Chen J-Y, Baker GJ, Schapiro D, Shi T, Yi L, Nicora CD, Claas A, Lauffenburger DA, Qian W-J, Wiley HS, Sorger PK.
bioRxiv. 2019 Sep 8. doi: 10.1101/762294.
GeneWalk identifies relevant gene functions for a biological context using network representation learning.
Letswaart R, Gyori BM, Bachman JA, Sorger PK, Churchman LS.
bioRxiv. 2019 Sep 5. doi: 10.1101/755579.
Opposing immune and genetic forces shape oncogenic programs in synovial sarcoma.
Jerby-Arnon L, Neftel C, Shore ME, McBride MJ, Haas B, Izar B, Weissman HR, Volorio A, Boulay G, Cironi L, Richman AR, Broye LC, Gurski JM, Luo CC, Mylvaganam R, Nguyen L, Mei S, Melms J C, Georgescu C, Cohen O, Buendia-Buendia JE, Cuoco MS, Labes D, Zollinger DR, Beechem JM, Nielsen GP, Chebib I, Cote G, Choy E, Letovanec I, Cherix S, Wagle N, Sorger PK, Haynes AB, Mullen JT, Stamenkovic I, Rivera MN, Kadoch C, Rozenblatt-Rosen O, Suvà ML, Riggi N, Regev A.
bioRxiv. 2019 Aug 4. doi: 10.1101/724302.
Systemic immune response profiling with SYLARAS implicates a role for CD45R/B220+ CD8+ T cells in glioblastoma immunology.
Baker GJ, Muhlich JL, Palaniappan SK, Moore JK, Davis SH, Santagata S, Sorger PK.
Cell Syst. [in revision]
Comparing the efficacy of cancer therapies between subgroups in basket trials.
Palmer AC, Plana D, Sorger PK.
bioRxiv. 2018 Aug 28. doi: 10.1101/401620.

2020 Publications

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 Aug 3. doi: 10.1158/0008-5472.CAN-19-3850. PMID: 32747364.
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 Jun 22. doi: 10.1038/s41591-020-0926-0. PMID: 32572264.
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 Jun 19. doi: 10.1016/j.medj.2020.06.003. PMID: 32838357. PMCID: PMC7304404.
Personal Protective Equipment for COVID-19: Distributed Fabrication and Additive Manufacturing.
Sinha MS, Bourgeois FT, Sorger PK.
Am J Public Health. 2020 Jun 18:e1-e3. doi: 10.2105/AJPH.2020.305753. PMID 32552025. PMCID: PMC7349433.
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 May 20. doi: 10.1126/science.abc4776. PMID: 32434946. PMCID: PMC7243369.
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.
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 Mar 23;. doi: 10.1016/j.addr.2020.03.003. PMID: 32217069.
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.
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.
An update on the CNS manifestations of neurofibromatosis type 2.
Coy S, Rashid R, Stemmer-Rachamimov A, Santagata S.
Acta Neuropathol. 2019 Jun 4. doi: 10.1007/s00401-019-02029-5. PMID: 31161239. PMCID: PMC7038792.
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.