LSP Bibliography

1.
Balabin H, Hoyt CT, Birkenbihl C, Gyori BM, Bachman J, Kodamullil AT, Plöger PG, Hofmann-Apitius M, Domingo-Fernández D. STonKGs: A Sophisticated Transformer Trained on Biomedical Text and Knowledge Graphs. Bioinformatics. 2022 Jan 5;btac001. PMID: 34986221
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Fröhlich F, Gerosa L, Muhlich J, Sorger PK. Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance. 2022 Feb 18 [cited 2022 Feb 25]; Available from: http://biorxiv.org/lookup/doi/10.1101/2022.02.17.480899
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Jessup J, Krueger R, Warchol S, Hoffer J, Muhlich J, Ritch CC, Gaglia G, Coy S, Chen Y-A, Lin J-R, Santagata S, Sorger PK, Pfister H. Scope2Screen: focus+context techniques for pathology tumor assessment in multivariate image data. IEEE Trans Vis Comput Graph. 2022 Jan;28(1):259–269. PMCID: PMC8805697
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Launonen I-M, Lyytikäinen N, Casado J, Anttila EA, Szabó A, Haltia U-M, Jacobson CA, Lin JR, Maliga Z, Howitt BE, Strickland KC, Santagata S, Elias K, D’Andrea AD, Konstantinopoulos PA, Sorger PK, Färkkilä A. Single-cell tumor-immune microenvironment of BRCA1/2 mutated high-grade serous ovarian cancer. Nat Commun. 2022 Feb 11;13(1):835. PMCID: PMC8837628
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Palmer AC, Izar B, Hwangbo H, Sorger PK. Predictable clinical benefits without evidence of synergy in trials of combination therapies with Immune-checkpoint Inhibitors. Clin Cancer Res. 2022 Jan 15;28(2):368–377. PMID: 35045958
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Plana D, Palmer AC, Sorger PK. Independent drug action in combination therapy: implications for precision oncology. Cancer Discov. 2022 Mar 1;12(3):606–624. PMCID: PMC8904281
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Plana D, Fell G, Alexander BM, Palmer AC, Sorger PK. Cancer patient survival can be parametrized to improve trial precision and reveal time-dependent therapeutic effects. Nat Commun. 2022 Feb 15;13(1):873. PMCID: PMC8847344
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Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen Y-A, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin J-R, 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. MITI minimum information guidelines for highly multiplexed tissue images. Nat Methods. 2022 Mar;19(3):262–267. PMID: 35277708
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Schink SJ, Christodoulou D, Mukherjee A, Athaide E, Brunner V, Fuhrer T, Bradshaw GA, Sauer U, Basan M. Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing. Mol Syst Biol. 2022 Jan;18(1):e10704. PMID: 34994048
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Scholten B, Simón LG, Krishnan S, Vermeulen R, Pronk A, Gyori BM, Bachman JA, Vlaanderen J, Stierum R. Automated Network Assembly of Mechanistic Literature for Informed Evidence Identification to Support Cancer Risk Assessment. Environ Health Perspect. 2022 Mar;130(3):37002. PMID: 35238605
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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. Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium. Commun Biol. 2022 Feb 11;5(1):129. PMCID: PMC8837632
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Abtahi S, Gliksman NR, Heneghan JF, Nilsen SP, Muhlich JL, Copeland J, Rozbicki E, Allan C, Dudeja PK, Turner JR. A Simple Method for Creating a High-Content Microscope for Imaging Multiplexed Tissue Microarrays. Curr Protoc. 2021 Apr;1(4):e68. PMCID: PMC8103673
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AlQuraishi M, Sorger PK. Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms. Nat Methods. 2021 Oct;18(10):1169–1180. PMCID: PMC8793939
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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. A crisis-responsive framework for medical device development applied to the COVID-19 pandemic. Front Digit Health. 2021 Mar;3:617106. PMCID: PMC8064560
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Bi WL, Santagata S. Skull Base Tumors: Neuropathology and Clinical implications. Neurosurgery. 2021 Jun 23;nyab209. PMID: 34164689
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Bouatta N, Sorger P, AlQuraishi M. Protein structure prediction by AlphaFold2: are attention and symmetries all you need? Acta Crystallogr D Struct Biol. 2021 Aug 1;77(Pt 8):982–991. PMCID: PMC8329862
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Břinda K, Baym M, Kucherov G. Simplitigs as an efficient and scalable representation of de Bruijn graphs. Genome Biol. 2021 Apr 6;22(1):96. PMCID: PMC8025321
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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. Antigen dominance hierarchies shape TCF1+ progenitor CD8 T cell phenotypes in tumors. Cell. 2021 Sep 16;184(19):4996-5014.e26. PMCID: PMC8522630
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Chowdhury R, Bouatta N, Biswas S, Rochereau C, Church GM, Sorger PK, AlQuraishi M. Single-sequence protein structure prediction using language models from deep learning. bioRxiv [Internet]. 2021 Aug 4 [cited 2021 Dec 28]; Available from: http://biorxiv.org/lookup/doi/10.1101/2021.08.02.454840
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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. Analysis of SteraMist ionized hydrogen peroxide technology in the sterilization of N95 respirators and other PPE. Sci Rep. 2021 Jan 21;11(1):2051. PMCID: PMC7819989
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Doherty LM, Mills CE, Boswell SA, Liu X, Hoyt CT, Gyori BM, Buhrlage SJ, Sorger PK. Integrating multi-omics data reveals function and therapeutic potential of deubiquitinating enzymes. bioRxiv [Internet]. 2021 Aug 9 [cited 2021 Dec 28]; Available from: http://biorxiv.org/lookup/doi/10.1101/2021.08.06.455458
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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, Rusakiewicz S, Doucey M-A, Dangaj Laniti D, Coukos G. Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation. Cancer Cell. 2021 Dec 13;39(12):1623-1642.e20. PMCID: PMC8861565
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Färkkilä A, Rodríguez A, Oikkonen J, Gulhan DC, Nguyen H, Domínguez J, Ramos S, Mills CE, Pérez-Villatoro F, Lazaro J-B, Zhou J, Clairmont CS, Moreau LA, Park PJ, Sorger PK, Hautaniemi S, Frias S, D’Andrea AD. Heterogeneity and Clonal Evolution of Acquired PARP Inhibitor Resistance in TP53- and BRCA1-Deficient Cells. Cancer Res. 2021 May 15;81(10):2774–2787. PMCID: PMC8323804
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Fröhlich F, Weindl D, Schälte Y, Pathirana D, Paszkowski Ł, Lines GT, Stapor P, Hasenauer J. AMICI: high-performance sensitivity analysis for large ordinary differential equation models. Bioinformatics. 2021 Apr 2;btab227. PMCID: PMC8545331
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Goldberg J, Pastorello RG, Vallius T, Davis J, Cui YX, Agudo J, Waks AG, Keenan T, McAllister SS, Tolaney SM, Mittendorf EA, Guerriero JL. The Immunology of Hormone Receptor Positive Breast Cancer. Front Immunol. 2021;12:674192. PMCID: PMC8202289
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Gross SM, Dane MA, Smith RL, Devlin K, McLean I, Derrick D, Mills C, Subramanian K, London AB, Torre D, Erdem C, Lyons N, Natoli T, Pessa S, Lu X, Mullahoo J, Li J, Adam M, Wassie B, Liu M, Kilburn D, Liby TA, Bucher E, Sanchez-Aguila C, Daily K, Omberg L, Wang Y, Jacobson C, Yapp C, Chung M, Vidovic D, Lu Y, Schurer S, Lee A, Pillai A, Subramanian A, Papanastasiou M, Fraenkel E, Feiler HS, Mills GB, Jaffe J, Ma’ayan A, Birtwistle MR, Sorger PK, Korkola JE, Gray JW, Heiser LM. A LINCS microenvironment perturbation resource for integrative assessment of ligand-mediated molecular and phenotypic responses. 2021 Aug 9; Available from: http://biorxiv.org/lookup/doi/10.1101/2021.08.06.455429
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Gyori BM, Bachman JA. From knowledge to models: Automated modeling in systems and synthetic biology. Current Opinion in Systems Biology. 2021;28:100362.
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Gyori BM, Hoyt CT, Steppi A. Gilda: biomedical entity text normalization with machine-learned disambiguation as a service. 2021 Sep 11; Available from: http://biorxiv.org/lookup/doi/10.1101/2021.09.10.459803
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Hemming ML, Coy S, Lin J-R, Andersen JL, Przybyl J, Mazzola E, Abdelhamid Ahmed AH, van de Rijn M, Sorger PK, Armstrong SA, Demetri GD, Santagata S. HAND1 and BARX1 act as transcriptional and anatomic determinants of malignancy in gastrointestinal stromal tumor. Clin Cancer Res. 2021 Mar 15;27(6):1706–1719. PMCID: PMC7956056
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Ietswaart R, Gyori BM, Bachman JA, Sorger PK, Churchman LS. GeneWalk identifies relevant gene functions for a biological context using network representation learning. Genome Biol. 2021 Feb 2;22(1):55. PMCID: PMC7852222
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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 J-A, Brownfield D, Jia H, Sarosiek KA. Age-dependent regulation of SARS-CoV-2 cell entry genes and cell death programs correlates with COVID-19 severity. Sci Adv. 2021 Aug 18;7(34):eabf8609. PMCID: PMC8373124
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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. Opposing immune and genetic mechanisms shape oncogenic programs in synovial sarcoma. Nat Med. 2021 Feb;27(2):289–300. PMCID: PMC8817899
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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. Discovery and resistance mechanism of a selective CDK12 degrader. Nat Chem Biol. 2021 Jun;17(6):675–683. PMCID: PMC8590456
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Kassamali B, Yu Z, Davis C, Carmack M, Bui A-TN, Said JT, Plana D, Yang H, Sorger P, LeBoeuf NR, LaChance AH. Conversion of existing UVB phototherapy units to UVC germicidal chambers for N95 decontamination: lessons learned. Photobiomodul Photomed Laser Surg. 2021 Feb;39(2):83–85. PMCID: PMC8106246
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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. Clinical efficacy and molecular response correlates of the WEE1 inhibitor adavosertib combined with cisplatin in patients with metastatic triple-negative breast cancer. Clin Cancer Res. 2021 Feb 15;27(4):983–991. PMCID: PMC7887044
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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. Targeting Pin1 renders pancreatic cancer eradicable by synergizing with immunochemotherapy. Cell. 2021 Sep 2;184(18):4753-4771.e27. PMCID: PMC8557351
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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. De novo powered air-purifying respirator design and fabrication for pandemic response. Front Bioeng Biotechnol. 2021 Sep 6;9:690905. PMCID: PMC8450396
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Lee J, Vernet A, Gruber NG, Kready KM, Burrill DR, Way JC, Silver PA. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Eng Des Sel. 2021 Feb 15;34:gzab025. PMID: 34725710
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Leipzig J, Nüst D, Hoyt CT, Ram K, Greenberg J. The role of metadata in reproducible computational research. Patterns (N Y). 2021 Sep 10;2(9):100322. PMCID: PMC8441584
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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 J-A, Li P, Pauli C, Gottesdiener L, DiPardo BJ, Hollmann TJ, Merghoub T, Wen HY, Reis-Filho JS, Riaz N, Su S-SM, Kalbasi A, Vasan N, Powell SN, Wolchok JD, Elemento O, Swanton C, Shoushtari AN, Parkes EE, Izar B, Bakhoum SF. Metastasis and immune evasion from extracellular cGAMP hydrolysis. Cancer Discov. 2021 May;11(5):1212–1227. PMCID: PMC8102348
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Lin J-R, Wang S, Coy S, Tyler M, Yapp C, Chen Y-A, Heiser CN, Lau KS, Santagata S, Sorger PK. Multiplexed 3D atlas of state transitions and immune interactions in colorectal cancer. bioRxiv [Internet]. 2021 Apr 2 [cited 2021 Dec 28]; Available from: http://biorxiv.org/lookup/doi/10.1101/2021.03.31.437984
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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. Micro-region transcriptomics of fixed human tissue using Pick-Seq. bioRxiv [Internet]. 2021 Mar 19 [cited 2021 Mar 19]; Available from: http://biorxiv.org/lookup/doi/10.1101/2021.03.18.431004
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Mancuso CP, Lu Z-X, Qian J, Boswell SA, Springer M. A Semi-Quantitative Isothermal Diagnostic Assay Utilizing Competitive Amplification. Anal Chem. 2021 Jun 28;acs.analchem.1c01576. PMID: 34180655
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McAvoy M, Bui A-TN, Hansen C, Plana D, Said JT, Yu Z, Yang H, Freake J, Van C, Krikorian D, Cramer A, Smith L, Jiang L, Lee KJ, Li SJ, Beller B, Huggins K, Short MP, Yu SH, Mostaghimi A, Sorger PK, LeBoeuf NR. 3D Printed frames to enable reuse and improve the fit of N95 and KN95 respirators. BMC Biomed Eng. 2021 Jun 7;3(1):10. PMCID: PMC8182357
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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. Targeting immunosuppressive macrophages overcomes PARP inhibitor resistance in BRCA1-associated triple-negative breast cancer. Nat Cancer. 2021 Jan;2(1):66–82. PMCID: PMC7963404
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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, Tsai EJ, Zorn E, Markowitz GS, Schwabe RF, Schwartz RE, Elemento O, Saqi A, Hibshoosh H, Que J, Izar B. A molecular single-cell lung atlas of lethal COVID-19. Nature. 2021 Jul;595(7865):114–119. PMCID: PMC8814825
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Mills CE, Subramanian K, Hafner M, Niepel M, Gerosa L, Chung M, Victor C, Gaudio B, Yapp C, Sorger PK. Multiplexed and reproducible high content screening of live and fixed cells using the Dye Drop method. bioRxiv [Internet]. 2021 Aug 28 [cited 2021 Dec 28]; Available from: http://biorxiv.org/lookup/doi/10.1101/2021.08.27.457854
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Muhlich J, Chen Y-A, Russell D, Sorger PK. Stitching and registering highly multiplexed whole slide images of tissues and tumors using ASHLAR software. bioRxiv [Internet]. 2021 Apr 21 [cited 2021 Dec 28]; Available from: http://biorxiv.org/lookup/doi/10.1101/2021.04.20.440625
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Nirmal AJ, Maliga Z, Vallius T, Quattrochi B, Chen AA, Jacobson CA, Pelletier RJ, Yapp C, Arias-Camison R, Chen Y-A, Lian CG, Murphy GF, Santagata S, Sorger PK. The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution. 2021 May 23 [cited 2021 Jun 29]; Available from: http://biorxiv.org/lookup/doi/10.1101/2021.05.23.445310
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Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel J-M, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Modos D, Treveil A, Olbei M, De Meulder B, Ballereau S, Dugourd A, Naldi A, Noël V, Calzone L, Sander C, Demir E, Korcsmaros T, Freeman TC, Augé F, Beckmann JS, Hasenauer J, Wolkenhauer O, Wilighagen EL, Pico AR, Evelo CT, Gillespie ME, Stein LD, Hermjakob H, D’Eustachio P, Saez-Rodriguez J, Dopazo J, Valencia A, Kitano H, Barillot E, Auffray C, Balling R, Schneider R, COVID-19 Disease Map Community. COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. Mol Syst Biol. 2021 Oct;17(10):e10387. PMCID: PMC8524328
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Owen SV, Wenner N, Dulberger CL, Rodwell EV, Bowers-Barnard A, Quinones-Olvera N, Rigden DJ, Rubin EJ, Garner EC, Baym M, Hinton JCD. Prophages encode phage-defense systems with cognate self-immunity. Cell Host Microbe. 2021 Nov 10;29(11):1620-1633.e8. PMCID: PMC8585504
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Patiño-Galindo JÁ, Filip I, Chowdhury R, Maranas CD, Sorger PK, AlQuraishi M, Rabadan R. Recombination and lineage-specific mutations linked to the emergence of SARS-CoV-2. Genome Med. 2021 Aug 6;13(1):124. PMCID: PMC8343217
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Pettit ME, Boswell SA, Qian J, Novak R, Springer M. Accessioning and automation compatible anterior nares swab design. J Virol Methods. 2021 May 10;114153. PMCID: PMC8108477
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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. Assessing the filtration efficiency and regulatory status of N95s and nontraditional filtering face-piece respirators available during the COVID-19 pandemic. BMC Infect Dis. 2021 Jul 29;21(1):712. PMCID: PMC8319695
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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. Melanoma cell intrinsic GABAA receptor enhancement potentiates radiation and immune checkpoint inhibitor response by promoting direct and T cell-mediated antitumor activity. Int J Radiat Oncol Biol Phys. 2021 Mar 15;109(4):1040–1053. PMCID: PMC8329598
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Rashid R, Chen Y-A, Hoffer J, Muhlich JL, Lin J-R, Krueger R, Pfister H, Mitchell R, Santagata S, Sorger PK. Narrative online guides for the interpretation of digital-pathology images and tissue-atlas data. Nat Biomed Eng. 2021 Nov 8; PMID: 34750536
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Rodriguez S, Sahin A, Schrank BR, Al-Lawati H, Costantino I, Benz E, Fard D, Albers AD, Cao L, Gomez AC, Evans K, Ratti E, Cudkowicz M, Frosch MP, Talkowski M, Sorger PK, Hyman BT, Albers MW. Genome-encoded cytoplasmic double-stranded RNAs, found in C9ORF72 ALS-FTD brain, propagate neuronal loss. Sci Transl Med. 2021 Jul 7;13(601):eaaz4699. PMID: 34233951
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Rodriguez S, Hug C, Todorov P, Moret N, Boswell SA, Evans K, Zhou G, Johnson NT, Hyman BT, Sorger PK, Albers MW, Sokolov A. Machine learning identifies candidates for drug repurposing in Alzheimer’s disease. Nat Commun. 2021 Feb 15;12(1):1033. PMCID: PMC7884393
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Schapiro D, Sokolov A, Yapp C, Chen Y-A, Muhlich JL, Hess J, Creason AL, Nirmal AJ, Baker GJ, Nariya MK, Lin J-R, 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. MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging. Nat Methods. 2021 Nov 25; PMID: 34824477
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Schmucker R, Farina G, Faeder J, Fröhlich F, Saglam AS, Sandholm T. Combination treatment optimization using a pan-cancer pathway model. PLoS Comput Biol. 2021 Dec 28;17(12):e1009689. PMCID: PMC8747684
1.
Shimada K, Bachman JA, Muhlich JL, Mitchison TJ. shinyDepMap, a tool to identify targetable cancer genes and their functional connections from Cancer Dependency Map data. Elife. 2021 Feb 8;10:e57116. PMCID: PMC7924953
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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. Vascular disease and thrombosis in SARS-CoV-2-infected rhesus macaques. Cell. 2020 Nov 25;183(5):1354-1366.e13. PMCID: PMC7546181
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Berginski ME, Moret N, Liu C, Goldfarb D, Sorger PK, Gomez SM. The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. Nucleic Acids Res. 2020 Oct 20;49(D1):D529–D535. PMCID: PMC7778917
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Bhola PD, Ahmed E, Guerriero JL, Sicinska E, Su E, Lavrova E, Ni J, Chipashvili O, Hagan T, Pioso MS, McQueeney K, Ng K, Aguirre AJ, Cleary JM, Cocozziello D, Sotayo A, Ryan J, Zhao JJ, Letai A. High-throughput dynamic BH3 profiling may quickly and accurately predict effective therapies in solid tumors. Sci Signal. 2020 Jun 16;13(636). PMCID: PMC8023011
1.
Břinda K, Callendrello A, Ma KC, MacFadden DR, Charalampous T, Lee RS, Cowley L, Wadsworth CB, Grad YH, Kucherov G, O’Grady J, Baym M, Hanage WP. Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing. Nat Microbiol. 2020;5(3):455–464. PMCID: PMC7044115
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Chopra SS, Jenney A, Palmer A, Niepel M, Chung M, Mills C, Sivakumaren SC, Liu Q, Chen J-Y, Yapp C, Asara JM, Gray NS, Sorger PK. Torin2 exploits replication and checkpoint vulnerabilities to cause death of PI3K-activated triple-negative breast cancer cells. Cell Syst. 2020 Jan 22;10(1):66-81.e11. PMCID: PMC7000271
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Coy S, Rashid R, Stemmer-Rachamimov A, Santagata S. An update on the CNS manifestations of neurofibromatosis type 2. Acta Neuropathol. 2020 Apr;139(4):643–665. PMCID: PMC7038792
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Cunningham JM, Koytiger G, Sorger PK, AlQuraishi M. Biophysical prediction of protein-peptide interactions and signaling networks using machine learning. Nat Methods. 2020 Feb;17(2):175–183. PMCID: PMC7004877
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Drijvers JM, Sharpe AH, Haigis MC. The effects of age and systemic metabolism on anti-tumor T cell responses. Elife. 2020 Nov 10;9:e62420. PMCID: PMC7655106
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Drouin A, Wallbillich N, Theberge M, Liu S, Katz J, Bellovoda K, Se Yun Cheon S, Gootkind F, Bierman E, Zavras J, Berberich MJ, Kalocsay M, Guastaldi F, Salvadori N, Troulis M, Fusco DN. Impact of Zika virus on the human type I interferon osteoimmune response. Cytokine. 2020 Oct 29;137:155342. PMID: 33130337
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Du G, Rao S, Gurbani D, Henning NJ, Jiang J, Che J, Yang A, Ficarro SB, Marto JA, Aguirre AJ, Sorger PK, Westover KD, Zhang T, Gray NS. Structure-Based Design of a Potent and Selective Covalent Inhibitor for SRC Kinase That Targets a P-Loop Cysteine. J Med Chem. 2020 Jan 30; PMID: 31935084
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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. Immunogenomic profiling determines responses to combined PARP and PD-1 inhibition in ovarian cancer. Nat Commun. 2020 Mar 19;11(1):1459. PMCID: PMC7081234
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Gaglia G, Rashid R, Yapp C, Joshi GN, Li CG, Lindquist SL, Sarosiek KA, Whitesell L, Sorger PK, Santagata S. HSF1 phase transition mediates stress adaptation and cell fate decisions. Nat Cell Biol. 2020 Feb;22(2):151–158. PMCID: PMC7135912
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Geisinger E, Mortman NJ, Dai Y, Cokol M, Syal S, Farinha A, Fisher DG, Tang AY, Lazinski DW, Wood S, Anthony J, van Opijnen T, Isberg RR. Antibiotic susceptibility signatures identify potential antimicrobial targets in the Acinetobacter baumannii cell envelope. Nat Commun. 2020 09;11(1):4522. PMCID: PMC7481262
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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. Receptor-driven ERK pulses reconfigure MAPK signaling and enable persistence of drug-adapted BRAF-mutant melanoma cells. Cell Syst. 2020 Nov 18;11(5):478-494.e9. PMCID: PMC8009031
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Gevertz JL, Greene JM, Sanchez-Tapia CH, Sontag ED. A novel COVID-19 epidemiological model with explicit susceptible and asymptomatic isolation compartments reveals unexpected consequences of timing social distancing. J Theor Biol. 2020 Nov 23;110539. PMID: 33242489
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Hafner A, Reyes J, Stewart-Ornstein J, Tsabar M, Jambhekar A, Lahav G. Quantifying the Central Dogma in the p53 Pathway in Live Single Cells. Cell Syst. 2020 Jun 24;10(6):495-505.e4. PMCID: PMC7413213
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Hemming ML, Nathenson MJ, Lin J-R, Mei S, Du Z, Malik K, Marino-Enriquez A, Jagannathan JP, Sorger PK, Bertagnolli M, Sicinska E, Demetri GD, Santagata S. Response and mechanisms of resistance to larotrectinib and selitrectinib in metastatic undifferentiated sarcoma harboring oncogenic fusion of NTRK1. JCO Precis Oncol. 2020 Feb 14;4:79–90. PMCID: PMC7055910
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Hoffer J, Rashid R, Muhlich JL, Chen Y-A, Russell DPW, Ruokonen J, Krueger R, Pfister H, Santagata S, Sorger PK. Minerva: a light-weight, narrative image browser for multiplexed tissue images. J Open Source Softw. 2020 Oct 15;5(54):2579. PMCID: PMC7989801
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Izar B, Tirosh I, Stover EH, Wakiro I, Cuoco MS, Alter I, Rodman C, Leeson R, Su M-J, Shah P, Iwanicki M, Walker SR, Kanodia A, Melms JC, Mei S, Lin J-R, 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. A single-cell landscape of high-grade serous ovarian cancer. Nat Med. 2020 Aug;26(8):1271–1279. PMCID: PMC7723336
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Kalocsay M, Berberich M, Everley R, Nariya M, Chung M, Gaudio B, Victor C, Bradshaw G, Hafner M, Sorger PK, Mills C, Subramanian K. Proteomic profiling of breast cancer cell lines and models. 2020 Dec 15; Available from: http://biorxiv.org/lookup/doi/10.1101/2020.12.15.422823
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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. Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung. bioRxiv [Internet]. 2020 Oct 15 [cited 2020 Dec 5]; Available from: http://biorxiv.org/lookup/doi/10.1101/2020.10.14.339952
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Krueger R, Beyer J, Jang W-D, Kim NW, Sokolov A, Sorger PK, Pfister H. Facetto: combining unsupervised and supervised learning for hierarchical phenotype analysis in multi-channel image data. IEEE Trans Vis Comput Graph. 2020 Jan;26(1):227–237. PMCID: PMC7045445
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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. Automated measurements of key morphological features of human embryos for IVF. Med Image Comput Comput Assist Interv. 2020 Oct;12265:25–35. PMCID: PMC7732604
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Liu Y, Ferguson FM, Li L, Kuljanin M, Mills CE, Subramanian K, Harshbarger W, Gondi S, Wang J, Sorger PK, Mancias JD, Gray NS, Westover KD. Chemical Biology Toolkit for DCLK1 Reveals Connection to RNA Processing. Cell Chem Biol. 2020 Oct 15;27(10):1229-1240.e4. PMCID: PMC8053042
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Lyashenko E, Niepel M, Dixit PD, Lim SK, Sorger PK, Vitkup D. Receptor-based mechanism of relative sensing and cell memory in mammalian signaling networks. Elife. 2020 Jan 21;9:e50342. PMCID: PMC7046471
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Magid SA, Jang W-D, Schapiro D, Wei D, Tompkin J, Sorger PK, Pfister H. Channel embedding for informative protein identification from highly multiplexed images. Med Image Comput Comput Assist Interv. 2020 Oct;12265:3–13. PMCID: PMC7713713
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Mallela A, Nariya MK, Deeds EJ. Crosstalk and ultrasensitivity in protein degradation pathways. PLoS Comput Biol. 2020 Dec;16(12):e1008492. PMCID: PMC7793289
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Melms JC, Vallabhaneni S, Mills CE, Yapp C, Chen J-Y, 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. Inhibition of haspin kinase promotes cell-intrinsic and extrinsic antitumor activity. Cancer Res. 2020 Feb 15;80(4):798–810. PMCID: PMC7029677
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Mostaghimi A, Antonini M-J, 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. Regulatory and safety considerations in deploying a locally fabricated, reusable face shield in a hospital responding to the COVID-19 pandemic. Med (N Y). 2020 Dec 18;1(1):139-151.e4. PMCID: PMC7304404
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Palmer AC, Plana D, Sorger PK. Comparing the efficacy of cancer therapies between subgroups in basket trials. Cell Syst. 2020 Nov 18;11(5):449-460.e2. PMCID: PMC8022348
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Palmer AC, Plana D, Gao H, Korn JM, Yang G, Green J, Zhang X, Velazquez R, McLaughlin ME, Ruddy DA, Kowal C, Muszynski 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. A proof of concept for biomarker-guided targeted therapy against ovarian cancer based on patient-derived tumor xenografts. Cancer Res. 2020 Oct 1;80(19):4278–4287. PMCID: PMC7541581
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Pena A-M, Chen X, Pence IJ, Bornschlögl T, Jeong S, Grégoire S, Luengo GS, Hallegot P, Obeidy P, Feizpour A, Chan KF, Evans CL. Imaging and quantifying drug delivery in skin - Part 2: Fluorescence andvibrational spectroscopic imaging methods. Adv Drug Deliv Rev. 2020 Jan 1;153:147–168. PMCID: PMC7483684
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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. Impact of sequencing radiation therapy and immune checkpoint inhibitors in the treatment of melanoma brain metastases. Int J Radiat Oncol Biol Phys. 2020 Sep 1;108(1):157–163. PMCID: PMC7839060
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Qian J, Lu Z-X, Mancuso CP, Jhuang H-Y, Del Carmen Barajas-Ornelas R, Boswell SA, Ramírez-Guadiana FH, Jones V, Sonti A, Sedlack K, Artzi L, Jung G, Arammash M, Pettit ME, Melfi M, Lyon L, Owen SV, Baym M, Khalil AS, Silver PA, Rudner DZ, Springer M. Barcoded microbial system for high-resolution object provenance. Science. 2020 05;368(6495):1135–1140. PMID: 32499444
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Qu J, Steppi A, Zhong D, Hao J, Wang J, Lung P-Y, Zhao T, He Z, Zhang J. Triage of documents containing protein interactions affected by mutations using an NLP based machine learning approach. BMC Genomics. 2020 Nov 10;21(1):773. PMCID: PMC7654050
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Revach O-Y, Liu S, Jenkins RW. Targeting TANK-binding kinase 1 (TBK1) in cancer. Expert Opin Ther Targets. 2020 Oct 5;1–14. PMID: 32962465
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Rozenblatt-Rosen O, Regev A, Oberdoerffer P, Nawy T, Hupalowska A, Rood JE, Ashenberg O, Cerami E, Coffey RJ, Demir E, Ding L, Esplin ED, Ford JM, Goecks J, Ghosh S, Gray JW, Guinney J, Hanlon SE, Hughes SK, Hwang ES, Iacobuzio-Donahue CA, Jané-Valbuena J, Johnson BE, Lau KS, Lively T, Mazzilli SA, Pe’er D, Santagata S, Shalek AK, Schapiro D, Snyder MP, Sorger PK, Spira AE, Srivastava S, Tan K, West RB, Williams EH, Human Tumor Atlas Network. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell. 2020 Apr 16;181(2):236–249. PMCID: PMC7376497
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Russell-Goldman E, Murphy GF. The Pathobiology of Skin Aging: New Insights into an Old Dilemma. Am J Pathol. 2020 Jul;190(7):1356–1369. PMCID: PMC7481755
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Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells. Nat Cell Biol. 2020 Apr;22(4):372–379. PMCID: PMC7185069
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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 M-J, 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. A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med. 2020 May;26(5):792–802. PMCID: PMC7220853
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Steppi A, Gyori BM, Bachman JA. Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature. J Open Source Softw. 2020 Jan 16;5(45):1708. PMCID: PMC7182313
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Teng M, Jiang J, He Z, Kwiatkowski NP, Donovan KA, Mills CE, Victor C, Hatcher JM, Fischer ES, Sorger PK, Zhang T, Gray NS. Development of CDK2 and CDK5 Dual Degrader TMX-2172. Angew Chem Int Ed Engl. 2020 Aug 10;59(33):13865–13870. PMCID: PMC7703486
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Tran AP, Ali Al-Radhawi M, Kareva I, Wu J, Waxman DJ, Sontag ED. Delicate Balances in Cancer Chemotherapy: Modeling Immune Recruitment and Emergence of Systemic Drug Resistance. Front Immunol. 2020;11:1376. PMCID: PMC7338613
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Tsabar M, Mock CS, Venkatachalam V, Reyes J, Karhohs KW, Oliver TG, Regev A, Jambhekar A, Lahav G. A Switch in p53 Dynamics Marks Cells That Escape from DSB-Induced Cell Cycle Arrest. Cell Rep. 2020 Aug 4;32(5):107995. PMCID: PMC7521664
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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. Considerations for the selection and use of disinfectants against SARS-CoV-2 in a health care setting. Open Forum Infect Dis. 2020 Sep;7(9):ofaa396. PMCID: PMC7499694
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Williams AL, Fitzgerald JE, Ivich F, Sontag ED, Niedre M. Short-Term Circulating Tumor Cell Dynamics in Mouse Xenograft Models and Implications for Liquid Biopsy. Front Oncol. 2020;10:601085. PMCID: PMC7677561
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Zervantonakis IK, Poskus MD, Scott AL, Selfors LM, Lin J-R, Dillon DA, Pathania S, Sorger PK, Mills GB, Brugge JS. Fibroblast-tumor cell signaling limits HER2 kinase therapy response via activation of MTOR and antiapoptotic pathways. Proc Natl Acad Sci USA. 2020 Jul 14;117(28):16500–16508. PMCID: PMC7368275
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Alley EC, Khimulya G, Biswas S, AlQuraishi M, Church GM. Unified rational protein engineering with sequence-based deep representation learning. Nat Methods. 2019 Dec;16(12):1315–1322. PMCID: PMC7067682
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Chopra SS, Jenney A, Palmer A, Niepel M, Chung M, Mills C, Sivakumaren SC, Liu Q, Chen J-Y, Yapp C, Asara JM, Gray NS, Sorger PK. Combined inhibition of mTOR and PIKKs exploits replicative and checkpoint vulnerabilities to induce death of PI3K-activated triple-negative breast cancer cells. bioRxiv [Internet]. 2019 Jul 12;700625. Available from: http://biorxiv.org/lookup/doi/10.1101/700625
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Du Z, Lin J-R, Rashid R, Maliga Z, Wang S, Aster JC, Izar B, Sorger PK, Santagata S. Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging. Nat Protoc. 2019 Oct;14(10):2900–2930. PMCID: PMC6959005
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Ferguson FM, Doctor ZM, Ficarro SB, Browne CM, Marto JA, Johnson JL, Yaron TM, Cantley LC, Kim ND, Sim T, Berberich MJ, Kalocsay M, Sorger PK, Gray NS. Discovery of Covalent CDK14 Inhibitors with Pan-TAIRE Family Specificity. Cell Chem Biol [Internet]. 2019 Jun 20;26(6):804-817.e12. Available from: https://www.cell.com/cell-chemical-biology/abstract/S2451-9456(19)30070-4 PMCID: PMC6588450
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Hafner M, Mills CE, Subramanian K, Chen C, Chung M, Boswell SA, Everley RA, Liu C, Walmsley CS, Juric D, Sorger PK. Multiomics profiling establishes the polypharmacology of FDA-approved CDK4/6 inhibitors and the potential for differential clinical activity. Cell Chem Biol. 2019 Aug 15;26(8):1067-1080.e8. PMCID: PMC6936329
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Hoyt CT, Domingo-Fernández D, Aldisi R, Xu L, Kolpeja K, Spalek S, Wollert E, Bachman J, Gyori BM, Greene P, Hofmann-Apitius M. Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. Database. 2019 Jan 1;2019:baz068.
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Li Z, Pinch BJ, Olson CM, Donovan KA, Nowak RP, Mills CE, Scott DA, Doctor ZM, Eleuteri NA, Chung M, Sorger PK, Fischer ES, Gray NS. Development and Characterization of a Wee1 Kinase Degrader. Cell Chem Biol. 2019 Nov 13;27(1):57-65.e9. PMCID: PMC6980656
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Liu B, Gyori BM, Thiagarajan PS. Statistical Model Checking-Based Analysis of Biological Networks. In: Liò P, Zuliani P, editors. Automated Reasoning for Systems Biology and Medicine [Internet]. Cham: Springer International Publishing; 2019. p. 63–92. Available from: https://doi.org/10.1007/978-3-030-17297-8_3
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Moret N, Clark NA, Hafner M, Wang Y, Lounkine E, Medvedovic M, Wang J, Gray N, Jenkins J, Sorger PK. Cheminformatics Tools for Analyzing and Designing Optimized Small-Molecule Collections and Libraries. Cell Chem Biol. 2019 May 16;26(5):765-777.e3. PMCID: PMC6526536
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Niepel M, Hafner M, Mills CE, Subramanian K, Williams EH, Chung M, Gaudio B, Barrette AM, Stern AD, Hu B, Korkola JE, LINCS Consortium, Gray JW, Birtwistle MR, Heiser LM, Sorger PK. A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines. Cell Syst. 2019 Jul 5;9(1):35-48.e5. PMCID: PMC6700527
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Olson CM, Liang Y, Leggett A, Park WD, Li L, Mills CE, Elsarrag SZ, Ficarro SB, Zhang T, Düster R, Geyer M, Sim T, Marto JA, Sorger PK, Westover KD, Lin CY, Kwiatkowski N, Gray NS. Development of a Selective CDK7 Covalent Inhibitor Reveals Predominant Cell-Cycle Phenotype. Cell Chem Biol. 2019 Jun 20;26(6):792-803.e10. PMCID: PMC6588464
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Palmer AC, Chidley C, Sorger PK. A curative combination cancer therapy achieves high fractional cell killing through low cross-resistance and drug additivity. Elife. 2019 Nov 19;8:e50036. PMCID: PMC6897534
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Pavkovic M, Pantano L, Gerlach CV, Brutus S, Boswell SA, Everley RA, Shah JV, Sui SH, Vaidya VS. Multi omics analysis of fibrotic kidneys in two mouse models. Scientific Data. 2019 Jun 14;6(1):92.
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Rao S, Du G, Hafner M, Subramanian K, Sorger PK, Gray NS. A multitargeted probe-based strategy to identify signaling vulnerabilities in cancers. J Biol Chem. 2019 May 24;294(21):8664–8673. PMCID: PMC6544847
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Rashid R, Gaglia G, Chen Y-A, Lin J-R, Du Z, Maliga Z, Schapiro D, Yapp C, Muhlich J, Sokolov A, Sorger P, Santagata S. Highly multiplexed immunofluorescence images and single-cell data of immune markers in tonsil and lung cancer. Sci Data. 2019 Dec 17;6(1):323. PMCID: PMC6917801
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Song Y, Subramanian K, Berberich MJ, Rodriguez S, Latorre IJ, Luria CM, Everley R, Albers MW, Mitchison TJ, Sorger PK. A dynamic view of the proteomic landscape during differentiation of ReNcell VM cells, an immortalized human neural progenitor line. Sci Data. 2019 Feb 19;6:190016. PMCID: PMC6380223
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Todorov PV, Gyori BM, Bachman JA, Sorger PK. INDRA-IPM: interactive pathway modeling using natural language with automated assembly. Bioinformatics. 2019 May 9; PMID: 31070726
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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. Adaptation of human iPSC-derived cardiomyocytes to tyrosine kinase inhibitors reduces acute cardiotoxicity via metabolic reprogramming. Cell Syst. 2019 May 22;8(5):412-426.e7. PMCID: PMC6657491
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Wang S, Lin J-R, Sontag ED, Sorger PK. Inferring reaction network structure from single-cell, multiplex data, using toric systems theory. PLoS Comput Biol. 2019 Dec;15(12):e1007311. PMCID: PMC6919632
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Bachman JA, Gyori BM, Sorger PK. FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. BMC Bioinformatics. 2018 Jun 28;19(1):248. PMCID: PMC6022344
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Cokol M, Li C, Chandrasekaran S. Chemogenomic model identifies synergistic drug combinations robust to the pathogen microenvironment. PLoS Comput Biol. 2018 Dec 31;14(12):e1006677. PMCID: PMC6329523
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Cokol-Cakmak M, Bakan F, Cetiner S, Cokol M. Diagonal Method to Measure Synergy Among Any Number of Drugs. J Vis Exp. 2018 Jun 21;(136). PMID: 29985330
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Coy S, Rashid R, Lin J-R, Du Z, Donson AM, Hankinson TC, Foreman NK, Manley PE, Kieran MW, Reardon DA, Sorger PK, Santagata S. Multiplexed Immunofluorescence Reveals Potential PD-1/PD-L1 Pathway Vulnerabilities in Craniopharyngioma. Neuro Oncol [Internet]. 2018 Mar 2;20(8):1101–1112. Available from: https://academic-oup-com.ezp-prod1.hul.harvard.edu/neuro-oncology/advance-article/doi/10.1093/neuonc/noy035/4917565 PMCID: PMC6280314
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de Souza CF, Sabedot TS, Malta TM, Stetson L, Morozova O, Sokolov A, Laird PW, Wiznerowicz M, Iavarone A, Snyder J, deCarvalho A, Sanborn Z, McDonald KL, Friedman WA, Tirapelli D, Poisson L, Mikkelsen T, Carlotti CG, Kalkanis S, Zenklusen J, Salama SR, Barnholtz-Sloan JS, Noushmehr H. A Distinct DNA Methylation Shift in a Subset of Glioma CpG Island Methylator Phenotypes during Tumor Recurrence. Cell Rep. 2018 Apr 10;23(2):637–651. PMID: 29642018
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Dunn IF, Du Z, Touat M, Sisti MB, Wen PY, Umeton R, Dubuc AM, Ducar M, Canoll PD, Severson E, Elvin JA, Ramkissoon SH, Lin J-R, Cabrera L, Acevedo B, Sorger PK, Ligon KL, Santagata S, Reardon DA. Mismatch repair deficiency in high-grade meningioma: a rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade. JCO Precis Oncol. 2018 Nov 27;2018. PMCID: PMC6383717
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Gonzalez Herrera KN, Zaganjor E, Ishikawa Y, Spinelli JB, Yoon H, Lin J-R, Satterstrom FK, Ringel A, Mulei S, Souza A, Gorham JM, Benson CC, Seidman JG, Sorger PK, Clish CB, Haigis MC. Small-Molecule Screen Identifies De Novo Nucleotide Synthesis as a Vulnerability of Cells Lacking SIRT3. Cell Rep. 2018 Feb 20;22(8):1945–1955. PMID: 29466723
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Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D. Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability. Nature. 2018 Jul 23;560(7719):504–508. PMCID: PMC6287498
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Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su M-J, Melms JC, Leeson R, Kanodia A, Mei S, Lin J-R, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget M-A, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A. A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. Cell. 2018 Nov 1;175(4):984-997.e24. PMCID: PMC6410377
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Keenan AB, Jenkins SL, Jagodnik KM, Koplev S, He E, Torre D, Wang Z, Dohlman AB, Silverstein MC, Lachmann A, Kuleshov MV, Ma’ayan A, Stathias V, Terryn R, Cooper D, Forlin M, Koleti A, Vidovic D, Chung C, Schürer SC, Vasiliauskas J, Pilarczyk M, Shamsaei B, Fazel M, Ren Y, Niu W, Clark NA, White S, Mahi N, Zhang L, Kouril M, Reichard JF, Sivaganesan S, Medvedovic M, Meller J, Koch RJ, Birtwistle MR, Iyengar R, Sobie EA, Azeloglu EU, Kaye J, Osterloh J, Haston K, Kalra J, Finkbiener S, Li J, Milani P, Adam M, Escalante-Chong R, Sachs K, Lenail A, Ramamoorthy D, Fraenkel E, Daigle G, Hussain U, Coye A, Rothstein J, Sareen D, Ornelas L, Banuelos M, Mandefro B, Ho R, Svendsen CN, Lim RG, Stocksdale J, Casale MS, Thompson TG, Wu J, Thompson LM, Dardov V, Venkatraman V, Matlock A, Van Eyk JE, Jaffe JD, Papanastasiou M, Subramanian A, Golub TR, Erickson SD, Fallahi-Sichani M, Hafner M, Gray NS, Lin J-R, Mills CE, Muhlich JL, Niepel M, Shamu CE, Williams EH, Wrobel D, Sorger PK, Heiser LM, Gray JW, Korkola JE, Mills GB, LaBarge M, Feiler HS, Dane MA, Bucher E, Nederlof M, Sudar D, Gross S, Kilburn DF, Smith R, Devlin K, Margolis R, Derr L, Lee A, Pillai A. The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations. Cell Syst [Internet]. 2018 Jan 24;6(1):13–24. Available from: https://www.cell.com/cell-systems/abstract/S2405-4712(17)30490-8 PMCID: PMC5799026
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Lin J-R, Izar B, Wang S, Yapp C, Mei S, Shah PM, Santagata S, Sorger PK. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. Elife. 2018 Jul 11;7. PMCID: PMC6075866
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Shimada K, Reznik E, Stokes ME, Krishnamoorthy L, Bos PH, Song Y, Quartararo CE, Pagano NC, Carpizo DR, deCarvalho AC, Lo DC, Stockwell BR. Copper-Binding Small Molecule Induces Oxidative Stress and Cell-Cycle Arrest in Glioblastoma-Patient-Derived Cells. Cell Chem Biol. 2018 Mar 7; PMID: 29576531
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Spady ES, Wyche TP, Rollins NJ, Clardy J, Way JC, Silver PA. Mammalian Cells Engineered To Produce New Steroids. Chembiochem. 2018 Sep 4;19(17):1827–1833. PMCID: PMC6156985
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Wang J, Erazo T, Ferguson FM, Buckley DL, Gomez N, Muñoz-Guardiola P, Diéguez-Martínez N, Deng X, Hao M, Massefski W, Fedorov O, Offei-Addo NK, Park PM, Dai L, DiBona A, Becht K, Kim ND, McKeown MR, Roberts JM, Zhang J, Sim T, Alessi DR, Bradner JE, Lizcano JM, Blacklow SC, Qi J, Xu X, Gray NS. Structural and Atropisomeric Factors Governing the Selectivity of Pyrimido-benzodiazipinones as Inhibitors of Kinases and Bromodomains. ACS Chem Biol. 2018 Sep 21;13(9):2438–2448. PMCID: PMC6333101
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Weinstein ZB, Kuru N, Kiriakov S, Palmer AC, Khalil AS, Clemons PA, Zaman MH, Roth FP, Cokol M. Modeling the impact of drug interactions on therapeutic selectivity. Nat Commun. 2018 Aug 27;9(1):3452. PMCID: PMC6110842
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Cardenas-Gonzalez M, Srivastava A, Pavkovic M, Bijol V, Rennke HG, Stillman IE, Zhang X, Parikh S, Rovin BH, Afkarian M, de Boer IH, Himmelfarb J, Waikar SS, Vaidya VS. Identification, Confirmation, and Replication of Novel Urinary MicroRNA Biomarkers in Lupus Nephritis and Diabetic Nephropathy. Clin Chem. 2017 Jun 30; PMID: 28667184
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Carlin DE, Paull EO, Graim K, Wong CK, Bivol A, Ryabinin P, Ellrott K, Sokolov A, Stuart JM. Prophetic Granger Causality to infer gene regulatory networks. PLoS One. 2017;12(12):e0170340. PMCID: PMC5718405
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Cokol M, Kuru N, Bicak E, Larkins-Ford J, Aldridge BB. Efficient measurement and factorization of high-order drug interactions in Mycobacterium tuberculosis. Sci Adv. 2017 Oct;3(10):e1701881. PMCID: PMC5636204
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Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin J-R, Boswell SA, Shah P, Rotem A, Garraway LA, Sorger PK. Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state. Mol Syst Biol [Internet]. 2017 Jan 9;13(1):905. Available from: http://www.ncbi.nlm.nih.gov/pubmed/28069687 PMCID: PMC5248573
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Ferguson FM, Doctor ZM, Chaikuad A, Sim T, Kim ND, Knapp S, Gray NS. Characterization of a highly selective inhibitor of the Aurora kinases. Bioorg Med Chem Lett. 2017 Sep 15;27(18):4405–4408. PMID: 28818446
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Froehlich F, Kessler T, Weindl D, Shadrin A, Schmiester L, Hache H, Muradyan A, Schuette M, Lim J-H, Heinig M, Theis F, Lehrach H, Wierling C, Lange B, Hasenauer J. Efficient parameterization of large-scale mechanistic models enables drug response prediction for cancer cell lines. bioRxiv [Internet]. 2017 Aug 9;174094. Available from: http://www.biorxiv.org/content/early/2017/08/09/174094
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Fusco DN, Pratt H, Kandilas S, Cheon SS, Lin W, Cronkite DA, Basavappa M, Jeffrey KL, Anselmo A, Sadreyev R, Yapp C, Shi X, O’Sullivan JF, Gerszten RE, Tomaru T, Yoshino S, Satoh T, Chung RT. HELZ2 Is an IFN Effector Mediating Suppression of Dengue Virus. Front Microbiol [Internet]. 2017;8:240. Available from: https://www.ncbi.nlm.nih.gov/pubmed/28265266
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Gerlach CV, Vaidya VS. MicroRNAs in injury and repair. Arch Toxicol [Internet]. 2017 Aug;91(8):2781–2797. Available from: http://link.springer.com/10.1007/s00204-017-1974-1 PMCID: PMC5843992
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Goel S, DeCristo MJ, Watt AC, BrinJones H, Sceneay J, Li BB, Khan N, Ubellacker JM, Xie S, Metzger-Filho O, Hoog J, Ellis MJ, Ma CX, Ramm S, Krop IE, Winer EP, Roberts TM, Kim H-J, McAllister SS, Zhao JJ. CDK4/6 inhibition triggers anti-tumour immunity. Nature. 2017 Aug 16; PMID: 28813415
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Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, Bivol A, Bunte K, Carlin D, Chopra S, Deran A, Ellrott K, Gopalacharyulu P, Graim K, Kaski S, Khan SA, Newton Y, Ng S, Pahikkala T, Paull E, Sokolov A, Tang H, Tang J, Wennerberg K, Xie Y, Zhan X, Zhu F, Broad-DREAM Community, Aittokallio T, Mamitsuka H, Stuart JM, Boehm JS, Root DE, Xiao G, Stolovitzky G, Hahn WC, Margolin AA. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Syst. 2017 Nov 22;5(5):485-497.e3. PMCID: PMC5814247
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Gyori BM, Bachman JA, Subramanian K, Muhlich JL, Galescu L, Sorger PK. From word models to executable models of signaling networks using automated assembly. Mol Syst Biol [Internet]. 2017 Nov 24;13(11):954. Available from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5731347/ PMCID: PMC5731347
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Hafner M, Niepel M, Subramanian K, Sorger PK. Designing Drug-Response Experiments and Quantifying their Results. Curr Protoc Chem Biol. 2017 Jun 19;9(2):96–116. PMCID: PMC5729909
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Lin J-R. Multiplexed Single-Cell Imaging: Past, Present, and Future. ASSAY and Drug Development Technologies. 2017;15(1):8–10.
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Logsdon MM, Ho P-Y, Papavinasasundaram K, Richardson K, Cokol M, Sassetti CM, Amir A, Aldridge BB. A Parallel Adder Coordinates Mycobacterial Cell-Cycle Progression and Cell-Size Homeostasis in the Context of Asymmetric Growth and Organization. Curr Biol. 2017 Nov 6;27(21):3367-3374.e7. PMCID: PMC5687851
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Mason DJ, Stott I, Ashenden S, Weinstein ZB, Karakoc I, Meral S, Kuru N, Bender A, Cokol M. Prediction of Antibiotic Interactions Using Descriptors Derived from Molecular Structure. J Med Chem. 2017 May 11;60(9):3902–3912. PMID: 28383902
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Niepel M, Hafner M, Chung M, Sorger PK. Measuring Cancer Drug Sensitivity and Resistance in Cultured Cells. Curr Protoc Chem Biol. 2017 Jun 19;9(2):55–74. PMCID: PMC5538315
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Niepel M, Hafner M, Duan Q, Wang Z, Paull EO, Chung M, Lu X, Stuart JM, Golub TR, Subramanian A, Ma’ayan A, Sorger PK. Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. Nat Commun. 2017 Oct 30;8(1):1186. PMCID: PMC5662764
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Paek J, Kalocsay M, Staus DP, Wingler L, Pascolutti R, Paulo JA, Gygi SP, Kruse AC. Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling. Cell. 2017 Apr 6;169(2):338-349.e11. PMCID: PMC5514552
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Subramanian K, Tyson JJ. Spatiotemporal Models of the Asymmetric Division Cycle of Caulobacter crescentus. In: Tassan J-P, Kubiak JZ, editors. Asymmetric Cell Division in Development, Differentiation and Cancer [Internet]. Cham: Springer International Publishing; 2017. p. 23–48. Available from: http://link.springer.com/10.1007/978-3-319-53150-2_2
1.
Tan L, Gurbani D, Weisberg EL, Hunter JC, Li L, Jones DS, Ficarro SB, Mowafy S, Tam C-P, Rao S, Du G, Griffin JD, Sorger PK, Marto JA, Westover KD, Gray NS. Structure-guided development of covalent TAK1 inhibitors. Bioorg Med Chem [Internet]. 2017 Feb 1;25(3):838–846. Available from: http://www.ncbi.nlm.nih.gov/pubmed/28011204 PMCID: PMC5484537
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Tanguturi SK, Trippa L, Ramkissoon SH, Pelton K, Knoff D, Sandak D, Lindeman NI, Ligon AH, Beroukhim R, Parmigiani G, Wen PY, Ligon KL, Alexander BM. Leveraging molecular datasets for biomarker-based clinical trial design in glioblastoma. Neuro-oncology. 2017 Feb 20;
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Viswanathan VS, Ryan MJ, Dhruv HD, Gill S, Eichhoff OM, Seashore-Ludlow B, Kaffenberger SD, Eaton JK, Shimada K, Aguirre AJ, Viswanathan SR, Chattopadhyay S, Tamayo P, Yang WS, Rees MG, Chen S, Boskovic ZV, Javaid S, Huang C, Wu X, Tseng Y-Y, Roider EM, Gao D, Cleary JM, Wolpin BM, Mesirov JP, Haber DA, Engelman JA, Boehm JS, Kotz JD, Hon CS, Chen Y, Hahn WC, Levesque MP, Doench JG, Berens ME, Shamji AF, Clemons PA, Stockwell BR, Schreiber SL. Dependency of a therapy-resistant state of cancer cells on a lipid peroxidase pathway. Nature. 2017 27;547(7664):453–457. PMCID: PMC5667900
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Wang Y, Woehrstein JB, Donoghue N, Dai M, Avendaño MS, Schackmann RCJ, Zoeller JJ, Wang SSH, Tillberg PW, Park D, Lapan SW, Boyden ES, Brugge JS, Kaeser PS, Church GM, Agasti SS, Jungmann R, Yin P. Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues. Nano Lett [Internet]. 2017 Oct 11;17(10):6131–6139. Available from: https://doi.org/10.1021/acs.nanolett.7b02716
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Zhou J, Ramanathan R, Wong W-F, Thiagarajan PS. Automated Property Synthesis of ODEs Based Bio-pathways Models. In: Feret J, Koeppl H, editors. Computational Methods in Systems Biology. Cham: Springer International Publishing; 2017. p. 265–282.
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AlQuraishi M, Sorger PK. Reproducibility will only come with data liberation. Sci Transl Med [Internet]. 2016 May 18;8(339):339ed7. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27194726 PMCID: PMC5084089
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Cárdenas-González M, Jacobo Estrada T, Rodríguez-Muñoz R, Barrera-Chimal J, Bobadilla NA, Barbier OC, Del Razo LM. Sub-chronic exposure to fluoride impacts the response to a subsequent nephrotoxic treatment with gentamicin: Fluoride exposure impacts the response to treatment with gentamicin. Journal of Applied Toxicology. 2016;36(2):309–319.
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Goel S, Wang Q, Watt AC, Tolaney SM, Dillon DA, Li W, Ramm S, Palmer AC, Yuzugullu H, Varadan V, Tuck D, Harris LN, Wong K-K, Liu XS, Sicinski P, Winer EP, Krop IE, Zhao JJ. Overcoming Therapeutic Resistance in HER2-Positive Breast Cancers with CDK4/6 Inhibitors. Cancer Cell. 2016;29(3):255–269.
1.
Hafner M, Niepel M, Chung M, Sorger PK. Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs. Nat Methods [Internet]. 2016 Jun 1;13(6):521–527. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27135972 PMCID: PMC4887336
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Lee JK, Phillips JW, Smith BA, Park JW, Stoyanova T, McCaffrey EF, Baertsch R, Sokolov A, Meyerowitz JG, Mathis C, Cheng D, Stuart JM, Shokat KM, Gustafson WC, Huang J, Witte ON. N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells. Cancer Cell. 2016 Apr 11;29(4):536–547. PMCID: PMC4829466
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Lin J-R, Fallahi-Sichani M, Chen J-Y, Sorger PK. Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging. Curr Protoc Chem Biol [Internet]. 2016 Dec 7;8(4):251–264. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27925668 PMCID: PMC5233430
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Pavkovic M, Vaidya VS. MicroRNAs and drug-induced kidney injury. Pharmacology & Therapeutics. 2016 Jul 1;163:48–57.
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Pavkovic M, Robinson-Cohen C, Chua AS, Nicoara O, Cárdenas-González M, Bijol V, Ramachandran K, Hampson L, Pirmohamed M, Antoine DJ, Frendl G, Himmelfarb J, Waikar SS, Vaidya VS. Detection of Drug-Induced Acute Kidney Injury in Humans Using Urinary KIM-1, miR-21, -200c, and -423. Toxicological Sciences [Internet]. 2016 [cited 2017 Jun 8];152(1):205–213. Available from: https://academic.oup.com/toxsci/article-lookup/doi/10.1093/toxsci/kfw077
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Pellegrini KL, Gerlach CV, Craciun FL, Ramachandran K, Bijol V, Kissick HT, Vaidya VS. Application of small RNA sequencing to identify microRNAs in acute kidney injury and fibrosis. Toxicology and Applied Pharmacology. 2016;312:42–52.
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Ramm S, Adler M, Vaidya VS. A High-Throughput Screening Assay to Identify Kidney Toxic Compounds. Curr Protoc Toxicol [Internet]. 2016 Aug 1;69:9.10.1-9.10.26. Available from: http://doi.wiley.com/10.1002/cptx.12 PMCID: PMC4981919
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Richardson K, Bennion OT, Tan S, Hoang AN, Cokol M, Aldridge BB. Temporal and intrinsic factors of rifampicin tolerance in mycobacteria. PNAS. 2016 Jul 19;113(29):8302–8307. PMCID: PMC4961206
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Sokolov A, Paull EO, Stuart JM. One-Class Detection of Cell States in Tumor Subtypes. Pac Symp Biocomput [Internet]. 2016 Jan 19;21:405–416. Available from: http://www.ncbi.nlm.nih.gov/pubmed/26776204 PMCID: 4856035
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Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM. Pathway-Based Genomics Prediction using Generalized Elastic Net. PLoS Comput Biol. 2016 Mar;12(3):e1004790. PMCID: PMC4784899
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Tan L, Gurbani D, Weisberg EL, Jones DS, Rao S, Singer WD, Bernard FM, Mowafy S, Jenney A, Du G, Nonami A, Griffin JD, Lauffenburger DA, Westover KD, Sorger PK, Gray NS. Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors. Bioorg Med Chem [Internet]. 2016 Dec 7;25(4):1320–1328. Available from: http://www.ncbi.nlm.nih.gov/pubmed/28038940 PMCID: PMC5484535
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Tirosh I, Izar B, Prakadan SM, Wadsworth MH, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin J-R, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CGK, Kazer SW, Gaillard A, Kolb KE, Villani A-C, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science [Internet]. 2016 Apr 8;352(6282):189–196. Available from: http://www.ncbi.nlm.nih.gov/pubmed/27124452 PMCID: PMC4944528

2015

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AlQuraishi M, Tang S, Xia X. An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system. BMC Bioinformatics [Internet]. 2015 Nov 19;16(1):390. Available from: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0819-2 PMCID: PMC4653904
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Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One [Internet]. 2015 May 22;10(5):e0128036. Available from: http://dx.doi.org/10.1371/journal.pone.0128036 https://www.ncbi.nlm.nih.gov/pubmed/26000737 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441430 http://dx.plos.org/10.1371/journal.pone.0128036
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Elia AE, Boardman AP, Wang DC, Huttlin EL, Everley RA, Dephoure N, Zhou C, Koren I, Gygi SP, Elledge SJ. Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response. Mol Cell. 2015 Sep;59(5):867–81.
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Fallahi-Sichani M, Moerke NJ, Niepel M, Zhang T, Gray NS, Sorger PK. Systematic analysis of BRAF(V600E) melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis. Mol Syst Biol [Internet]. 2015 Mar 31;11(3):797. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25814555 PMCID: PMC4380931
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Krukenberg KA, Kim S, Tan ES, Maliga Z, Mitchison TJ. Extracellular Poly(ADP-Ribose) Is a Pro-inflammatory Signal for Macrophages. Chemistry & Biology. 2015;22(4):446–452.
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Lin J-R, Fallahi-Sichani M, Sorger PK. Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method. Nat Commun [Internet]. 2015 Sep 25;6:8390. Available from: http://www.ncbi.nlm.nih.gov/pubmed/26399630 PMCID: PMC4587398
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Muntel J, Boswell SA, Tang S, Ahmed S, Wapinski I, Foley G, Steen H, Springer M. Abundance-based Classifier for the Prediction of Mass Spectrometric Peptide Detectability Upon Enrichment (PPA). Molecular & Cellular Proteomics [Internet]. 2015;14(2):430–440. Available from: http://www.mcponline.org/lookup/doi/10.1074/mcp.M114.044321
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Palmer AC, Toprak E, Baym M, Kim S, Veres A, Bershtein S, Kishony R. Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes. Nature Communications [Internet]. 2015 Jun 10;6:7385. Available from: http://www.nature.com/doifinder/10.1038/ncomms8385
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Pavkovic M, Riefke B, Frisk A-L, Gröticke I, Ellinger-Ziegelbauer H. Glomerulonephritis-Induced Changes in Urinary and Kidney MicroRNA Profiles in Rats. Toxicological Sciences. 2015;145(2):348–359.
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Pavkovic M, Riefke B, Frisk A-L, Gröticke I, Ellinger-Ziegelbauer H. Glomerulonephritis-induced changes in kidney gene expression in rats. Genom Data [Internet]. 2015 Dec;6:81–82. Available from: http://linkinghub.elsevier.com/retrieve/pii/S2213596015300131 PMCID: PMC4664719
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Xu X, Choi SH, Hu T, Tiyanont K, Habets R, Groot AJ, Vooijs M, Aster JC, Chopra R, Fryer C, Blacklow SC. Insights into Autoregulation of Notch3 from Structural and Functional Studies of Its Negative Regulatory Region. Structure. 2015;23(7):1227–1235.
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Chung JJ, Shim SH, Everley RA, Gygi SP, Zhuang X, Clapham DE. Structurally distinct Ca(2+) signaling domains of sperm flagella orchestrate tyrosine phosphorylation and motility. Cell. 2014 May;157(4):808–22.
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Palmer AC, Kishony R. Opposing effects of target overexpression reveal drug mechanisms. Nat Commun. 2014 Jul 1;5:4296. PMCID: PMC4408919
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Pellegrini KL, Han T, Bijol V, Saikumar J, Craciun FL, Chen WW, Fuscoe JC, Vaidya VS. MicroRNA-155 Deficient Mice Experience Heightened Kidney Toxicity When Dosed with Cisplatin. Toxicological Sciences. 2014 Oct 1;141(2):484–492.
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Everley RA, Kunz RC, McAllister FE, Gygi SP. Increasing throughput in targeted proteomics assays: 54-plex quantitation in a single mass spectrometry run. Anal Chem. 2013 Jun;85(11):5340–6.
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Orth JD, Kohler RH, Foijer F, Sorger PK, Weissleder R, Mitchison TJ. Analysis of mitosis and antimitotic drug responses in tumors by in vivo microscopy and single-cell pharmacodynamics. Cancer Res [Internet]. 2011 Jul 1;71(13):4608–16. Available from: http://www.ncbi.nlm.nih.gov/pubmed/21712408 PMCID: 3129392