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Items: 12

1.

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
2.

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.

3.

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.

4.

A Quantitative Approach to Screen for Nephrotoxic Compounds In Vitro.

Adler M, Ramm S, Hafner M, Muhlich JL, Gottwald EM, Weber E, Jaklic A, Ajay AK, Svoboda D, Auerbach S, Kelly EJ, Himmelfarb J, Vaidya VS.

J Am Soc Nephrol. 2016 Apr;27(4):1015-28. doi: 10.1681/ASN.2015010060. Epub 2015 Aug 10.

5.

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.

6.

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.

7.

Metadata Standard and Data Exchange Specifications to Describe, Model, and Integrate Complex and Diverse High-Throughput Screening Data from the Library of Integrated Network-based Cellular Signatures (LINCS).

Vempati UD, Chung C, Mader C, Koleti A, Datar N, Vidović D, Wrobel D, Erickson S, Muhlich JL, Berriz G, Benes CH, Subramanian A, Pillai A, Shamu CE, Schürer SC.

J Biomol Screen. 2014 Jun;19(5):803-16. doi: 10.1177/1087057114522514. Epub 2014 Feb 11.

PMID:
24518066
8.

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.

9.

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.

10.

Adaptive informatics for multifactorial and high-content biological data.

Millard BL, Niepel M, Menden MP, Muhlich JL, Sorger PK.

Nat Methods. 2011 Jun;8(6):487-93. doi: 10.1038/nmeth.1600. Epub 2011 Apr 24.

11.

Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities.

Tolopko AN, Sullivan JP, Erickson SD, Wrobel D, Chiang SL, Rudnicki K, Rudnicki S, Nale J, Selfors LM, Greenhouse D, Muhlich JL, Shamu CE.

BMC Bioinformatics. 2010 May 18;11:260. doi: 10.1186/1471-2105-11-260.

12.

Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/insulin-induced signaling.

Aldridge BB, Saez-Rodriguez J, Muhlich JL, Sorger PK, Lauffenburger DA.

PLoS Comput Biol. 2009 Apr;5(4):e1000340. doi: 10.1371/journal.pcbi.1000340. Epub 2009 Apr 3.

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