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. 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. PMID: 29954318 Abstract

BACKGROUND: For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other […]

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. Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases. Cell Syst. 2018 May 31; PMID: 29886111 Abstract

Extracellular growth factors signal to transcription factors via a limited number of cytoplasmic kinase cascades. It […]

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. A High Content Screen in Macrophages Identifies Small Molecule Modulators of STING-IRF3 and NFkB Signaling. ACS Chem Biol. 2018 Mar 19; PMID: 29553248 Abstract

We screened a library of bioactive small molecules for activators and […]

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. Inflammatory but not mitogenic contexts prime synovial fibroblasts for compensatory signaling responses to p38 inhibition. Sci Signal. 2018 Mar 6;11(520). PMID: 29511118 Abstract

Rheumatoid arthritis (RA) is a chronic inflammatory disorder that causes joint pain, swelling, and loss of function. Development of effective new drugs […]

Multiplexed Immunofluorescence Reveals Potential PD-1/PD-L1 Pathway Vulnerabilities in Craniopharyngioma

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-oncology. 2018 Mar 2; PMID: 29509940 Abstract

Background: Craniopharyngiomas are neoplasms of the sellar/parasellar region that are classified into adamantinomatous (ACP) and […]

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 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 Abstract […]

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

Palmer AC, Sorger PK. Combination Cancer Therapy Can Confer Benefit via Patient-to-Patient Variability without Drug Additivity or Synergy. Cell. 2017 Dec 14;171(7):1678–1691.e13. PMID: 29245013 Abstract

Combination cancer therapies aim to improve the probability and magnitude of therapeutic responses and reduce the likelihood of acquired resistance in an individual patient. However, drugs are tested in clinical […]

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 […]

From Word Models to Executable Models of Signaling Networks Using Automated Assembly

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. 2017 Nov 24;13(11):954. PMID: 29175850 Abstract

Word models (natural language descriptions of molecular mechanisms) are a common currency in spoken and written communication in biomedicine but are of […]

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. Quantification of sensitivity and resistance of breast cancer cell lines to anti-cancer drugs using GR metrics. Sci Data. 2017 Nov 7;4:170166. PMCID: PMC5674849 Abstract

Traditional means for scoring the effects of anti-cancer drugs on the growth and survival of […]