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Items: 1 to 50 of 171

1.

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes.

Lin JR, Izar B, Wang S, Yapp C, Mei S, Shah PM, Santagata S, Sorger PK.

Elife. 2018 Jul 11;7. pii: e31657. doi: 10.7554/eLife.31657.

2.

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

Bachman JA, Gyori BM, Sorger PK.

BMC Bioinformatics. 2018 Jun 28;19(1):248. doi: 10.1186/s12859-018-2211-5.

3.

Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases.

Sampattavanich S, Steiert B, Kramer BA, Gyori BM, Albeck JG, Sorger PK.

Cell Syst. 2018 Jun 27;6(6):664-678.e9. doi: 10.1016/j.cels.2018.05.004. Epub 2018 Jun 6.

4.

A High Content Screen in Macrophages Identifies Small Molecule Modulators of STING-IRF3 and NFkB Signaling.

Koch PD, Miller HR, Yu G, Tallarico JA, Sorger PK, Wang Y, Feng Y, Thomas JR, Ross NT, Mitchison T.

ACS Chem Biol. 2018 Apr 20;13(4):1066-1081. doi: 10.1021/acschembio.7b01060. Epub 2018 Mar 19.

5.

Inflammatory but not mitogenic contexts prime synovial fibroblasts for compensatory signaling responses to p38 inhibition.

Jones DS, Jenney AP, Joughin BA, Sorger PK, Lauffenburger DA.

Sci Signal. 2018 Mar 6;11(520). pii: eaal1601. doi: 10.1126/scisignal.aal1601.

PMID:
29511118
6.

Multiplexed immunofluorescence reveals potential PD-1/PD-L1 pathway vulnerabilities in craniopharyngioma.

Coy S, Rashid R, Lin JR, Du Z, Donson AM, Hankinson TC, Foreman NK, Manley PE, Kieran MW, Reardon DA, Sorger PK, Santagata S.

Neuro Oncol. 2018 Jul 5;20(8):1101-1112. doi: 10.1093/neuonc/noy035.

PMID:
29509940
7.

Small-Molecule Screen Identifies De Novo Nucleotide Synthesis as a Vulnerability of Cells Lacking SIRT3.

Gonzalez Herrera KN, Zaganjor E, Ishikawa Y, Spinelli JB, Yoon H, Lin JR, Satterstrom FK, Ringel A, Mulei S, Souza A, Gorham JM, Benson CC, Seidman JG, Sorger PK, Clish CB, Haigis MC.

Cell Rep. 2018 Feb 20;22(8):1945-1955. doi: 10.1016/j.celrep.2018.01.076.

8.

Combination Cancer Therapy Can Confer Benefit via Patient-to-Patient Variability without Drug Additivity or Synergy.

Palmer AC, Sorger PK.

Cell. 2017 Dec 14;171(7):1678-1691.e13. doi: 10.1016/j.cell.2017.11.009.

PMID:
29245013
9.

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations.

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 JR, 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.

Cell Syst. 2018 Jan 24;6(1):13-24. doi: 10.1016/j.cels.2017.11.001. Epub 2017 Nov 29. Review.

PMID:
29199020
10.

From word models to executable models of signaling networks using automated assembly.

Gyori BM, Bachman JA, Subramanian K, Muhlich JL, Galescu L, Sorger PK.

Mol Syst Biol. 2017 Nov 24;13(11):954. doi: 10.15252/msb.20177651.

11.

Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics.

Hafner M, Heiser LM, Williams EH, Niepel M, Wang NJ, Korkola JE, Gray JW, Sorger PK.

Sci Data. 2017 Nov 7;4:170166. doi: 10.1038/sdata.2017.166.

12.

Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling.

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.

Nat Commun. 2017 Oct 30;8(1):1186. doi: 10.1038/s41467-017-01383-w.

13.

GRcalculator: an online tool for calculating and mining dose-response data.

Clark NA, Hafner M, Kouril M, Williams EH, Muhlich JL, Pilarczyk M, Niepel M, Sorger PK, Medvedovic M.

BMC Cancer. 2017 Oct 24;17(1):698. doi: 10.1186/s12885-017-3689-3.

14.

Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane.

Werbin JL, Avendaño MS, Becker V, Jungmann R, Yin P, Danuser G, Sorger PK.

Sci Rep. 2017 Sep 22;7(1):12150. doi: 10.1038/s41598-017-12257-y.

15.

Designing Drug-Response Experiments and Quantifying their Results.

Hafner M, Niepel M, Subramanian K, Sorger PK.

Curr Protoc Chem Biol. 2017 Jun 19;9(2):96-116. doi: 10.1002/cpch.19.

16.

Measuring Cancer Drug Sensitivity and Resistance in Cultured Cells.

Niepel M, Hafner M, Chung M, Sorger PK.

Curr Protoc Chem Biol. 2017 Jun 19;9(2):55-74. doi: 10.1002/cpch.21.

17.

Alternative drug sensitivity metrics improve preclinical cancer pharmacogenomics.

Hafner M, Niepel M, Sorger PK.

Nat Biotechnol. 2017 Jun 7;35(6):500-502. doi: 10.1038/nbt.3882. No abstract available.

18.

Fundamental trade-offs between information flow in single cells and cellular populations.

Suderman R, Bachman JA, Smith A, Sorger PK, Deeds EJ.

Proc Natl Acad Sci U S A. 2017 May 30;114(22):5755-5760. doi: 10.1073/pnas.1615660114. Epub 2017 May 12.

19.

Deletion of the MAD2L1 spindle assembly checkpoint gene is tolerated in mouse models of acute T-cell lymphoma and hepatocellular carcinoma.

Foijer F, Albacker LA, Bakker B, Spierings DC, Yue Y, Xie SZ, Davis S, Lutum-Jehle A, Takemoto D, Hare B, Furey B, Bronson RT, Lansdorp PM, Bradley A, Sorger PK.

Elife. 2017 Mar 20;6. pii: e20873. doi: 10.7554/eLife.20873.

20.

Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de-differentiated state.

Fallahi-Sichani M, Becker V, Izar B, Baker GJ, Lin JR, Boswell SA, Shah P, Rotem A, Garraway LA, Sorger PK.

Mol Syst Biol. 2017 Jan 9;13(1):905. doi: 10.15252/msb.20166796.

21.

Studies of TAK1-centered polypharmacology with novel covalent TAK1 inhibitors.

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.

Bioorg Med Chem. 2017 Feb 15;25(4):1320-1328. doi: 10.1016/j.bmc.2016.11.034. Epub 2016 Dec 7.

22.

Structure-guided development of covalent TAK1 inhibitors.

Tan L, Gurbani D, Weisberg EL, Hunter JC, Li L, Jones DS, Ficarro SB, Mowafy S, Tam CP, Rao S, Du G, Griffin JD, Sorger PK, Marto JA, Westover KD, Gray NS.

Bioorg Med Chem. 2017 Feb 1;25(3):838-846. doi: 10.1016/j.bmc.2016.11.035. Epub 2016 Dec 9.

23.

Cyclic Immunofluorescence (CycIF), A Highly Multiplexed Method for Single-cell Imaging.

Lin JR, Fallahi-Sichani M, Chen JY, Sorger PK.

Curr Protoc Chem Biol. 2016 Dec 7;8(4):251-264. doi: 10.1002/cpch.14.

24.

Profiling drugs for rheumatoid arthritis that inhibit synovial fibroblast activation.

Jones DS, Jenney AP, Swantek JL, Burke JM, Lauffenburger DA, Sorger PK.

Nat Chem Biol. 2017 Jan;13(1):38-45. doi: 10.1038/nchembio.2211. Epub 2016 Oct 31.

25.

Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

Shi T, Niepel M, McDermott JE, Gao Y, Nicora CD, Chrisler WB, Markillie LM, Petyuk VA, Smith RD, Rodland KD, Sorger PK, Qian WJ, Wiley HS.

Sci Signal. 2016 Jul 12;9(436):rs6. doi: 10.1126/scisignal.aaf0891.

26.

Reproducibility will only come with data liberation.

AlQuraishi M, Sorger PK.

Sci Transl Med. 2016 May 18;8(339):339ed7. doi: 10.1126/scitranslmed.aaf0968. No abstract available.

27.

Growth rate inhibition metrics correct for confounders in measuring sensitivity to cancer drugs.

Hafner M, Niepel M, Chung M, Sorger PK.

Nat Methods. 2016 Jun;13(6):521-7. doi: 10.1038/nmeth.3853. Epub 2016 May 2.

28.

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq.

Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CG, Kazer SW, Gaillard A, Kolb KE, Villani AC, 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.

Science. 2016 Apr 8;352(6282):189-96. doi: 10.1126/science.aad0501.

29.

L1000CDS2: LINCS L1000 characteristic direction signatures search engine.

Duan Q, Reid SP, Clark NR, Wang Z, Fernandez NF, Rouillard AD, Readhead B, Tritsch SR, Hodos R, Hafner M, Niepel M, Sorger PK, Dudley JT, Bavari S, Panchal RG, Ma'ayan A.

NPJ Syst Biol Appl. 2016;2. pii: 16015. doi: 10.1038/npjsba.2016.15. Epub 2016 Aug 4.

30.

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method.

Lin JR, Fallahi-Sichani M, Sorger PK.

Nat Commun. 2015 Sep 24;6:8390. doi: 10.1038/ncomms9390.

31.

Fractional killing arises from cell-to-cell variability in overcoming a caspase activity threshold.

Roux J, Hafner M, Bandara S, Sims JJ, Hudson H, Chai D, Sorger PK.

Mol Syst Biol. 2015 May 7;11(5):803. doi: 10.15252/msb.20145584.

32.

Surviving apoptosis: life-death signaling in single cells.

Flusberg DA, Sorger PK.

Trends Cell Biol. 2015 Aug;25(8):446-58. doi: 10.1016/j.tcb.2015.03.003. Epub 2015 Apr 25. Review.

33.

Systematic analysis of BRAF(V600E) melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis.

Fallahi-Sichani M, Moerke NJ, Niepel M, Zhang T, Gray NS, Sorger PK.

Mol Syst Biol. 2015 Mar 26;11(3):797. doi: 10.15252/msb.20145877.

34.

A noncanonical Frizzled2 pathway regulates epithelial-mesenchymal transition and metastasis.

Gujral TS, Chan M, Peshkin L, Sorger PK, Kirschner MW, MacBeath G.

Cell. 2014 Nov 6;159(4):844-56. doi: 10.1016/j.cell.2014.10.032.

35.

A multiscale statistical mechanical framework integrates biophysical and genomic data to assemble cancer networks.

AlQuraishi M, Koytiger G, Jenney A, MacBeath G, Sorger PK.

Nat Genet. 2014 Dec;46(12):1363-1371. doi: 10.1038/ng.3138. Epub 2014 Nov 2.

36.

Chromosome instability induced by Mps1 and p53 mutation generates aggressive lymphomas exhibiting aneuploidy-induced stress.

Foijer F, Xie SZ, Simon JE, Bakker PL, Conte N, Davis SH, Kregel E, Jonkers J, Bradley A, Sorger PK.

Proc Natl Acad Sci U S A. 2014 Sep 16;111(37):13427-32. doi: 10.1073/pnas.1400892111. Epub 2014 Sep 2.

37.

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.

Duan Q, Flynn C, Niepel M, Hafner M, Muhlich JL, Fernandez NF, Rouillard AD, Tan CM, Chen EY, Golub TR, Sorger PK, Subramanian A, Ma'ayan A.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W449-60. doi: 10.1093/nar/gku476. Epub 2014 Jun 6.

38.

Analysis of growth factor signaling in genetically diverse breast cancer lines.

Niepel M, Hafner M, Pace EA, Chung M, Chai DH, Zhou L, Muhlich JL, Schoeberl B, Sorger PK.

BMC Biol. 2014 Mar 21;12:20. doi: 10.1186/1741-7007-12-20.

39.

Intra- and interdimeric caspase-8 self-cleavage controls strength and timing of CD95-induced apoptosis.

Kallenberger SM, Beaudouin J, Claus J, Fischer C, Sorger PK, Legewie S, Eils R.

Sci Signal. 2014 Mar 11;7(316):ra23. doi: 10.1126/scisignal.2004738.

40.

Decision-tree based model analysis for efficient identification of parameter relations leading to different signaling states.

Koch Y, Wolf T, Sorger PK, Eils R, Brors B.

PLoS One. 2013 Dec 18;8(12):e82593. doi: 10.1371/journal.pone.0082593. eCollection 2013.

41.

Profiles of Basal and stimulated receptor signaling networks predict drug response in breast cancer lines.

Niepel M, Hafner M, Pace EA, Chung M, Chai DH, Zhou L, Schoeberl B, Sorger PK.

Sci Signal. 2013 Sep 24;6(294):ra84. doi: 10.1126/scisignal.2004379.

42.

Metrics other than potency reveal systematic variation in responses to cancer drugs.

Fallahi-Sichani M, Honarnejad S, Heiser LM, Gray JW, Sorger PK.

Nat Chem Biol. 2013 Nov;9(11):708-14. doi: 10.1038/nchembio.1337. Epub 2013 Sep 8.

43.

S. cerevisiae chromosomes biorient via gradual resolution of syntely between S phase and anaphase.

Marco E, Dorn JF, Hsu PH, Jaqaman K, Sorger PK, Danuser G.

Cell. 2013 Aug 29;154(5):1127-1139. doi: 10.1016/j.cell.2013.08.008.

44.

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE).

Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM.

Bioinformatics. 2013 Nov 1;29(21):2757-64. doi: 10.1093/bioinformatics/btt471. Epub 2013 Aug 27.

45.

Modulating cell-to-cell variability and sensitivity to death ligands by co-drugging.

Flusberg DA, Sorger PK.

Phys Biol. 2013 Jun;10(3):035002. doi: 10.1088/1478-3975/10/3/035002. Epub 2013 Jun 4.

46.

Cells surviving fractional killing by TRAIL exhibit transient but sustainable resistance and inflammatory phenotypes.

Flusberg DA, Roux J, Spencer SL, Sorger PK.

Mol Biol Cell. 2013 Jul;24(14):2186-200. doi: 10.1091/mbc.E12-10-0737. Epub 2013 May 22.

47.

Mass spectrometry based method to increase throughput for kinome analyses using ATP probes.

McAllister FE, Niepel M, Haas W, Huttlin E, Sorger PK, Gygi SP.

Anal Chem. 2013 May 7;85(9):4666-74. doi: 10.1021/ac303478g. Epub 2013 Apr 22.

48.

Programming biological models in Python using PySB.

Lopez CF, Muhlich JL, Bachman JA, Sorger PK.

Mol Syst Biol. 2013;9:646. doi: 10.1038/msb.2013.1.

49.

Properties of cell death models calibrated and compared using Bayesian approaches.

Eydgahi H, Chen WW, Muhlich JL, Vitkup D, Tsitsiklis JN, Sorger PK.

Mol Syst Biol. 2013;9:644. doi: 10.1038/msb.2012.69.

50.

Spindle checkpoint deficiency is tolerated by murine epidermal cells but not hair follicle stem cells.

Foijer F, DiTommaso T, Donati G, Hautaviita K, Xie SZ, Heath E, Smyth I, Watt FM, Sorger PK, Bradley A.

Proc Natl Acad Sci U S A. 2013 Feb 19;110(8):2928-33. doi: 10.1073/pnas.1217388110. Epub 2013 Feb 4.

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