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Items: 1 to 50 of 55

1.

A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines.

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.

Cell Syst. 2019 Jul 24;9(1):35-48.e5. doi: 10.1016/j.cels.2019.06.005. Epub 2019 Jul 10.

2.

Enabling drug discovery for the PARP protein family through the detection of mono-ADP-ribosylation.

Lu AZ, Abo R, Ren Y, Gui B, Mo JR, Blackwell D, Wigle T, Keilhack H, Niepel M.

Biochem Pharmacol. 2019 Sep;167:97-106. doi: 10.1016/j.bcp.2019.05.007. Epub 2019 May 7.

3.

Tensor clustering with algebraic constraints gives interpretable groups of crosstalk mechanisms in breast cancer.

Seigal A, Beguerisse-Díaz M, Schoeberl B, Niepel M, Harrington HA.

J R Soc Interface. 2019 Feb 28;16(151):20180661. doi: 10.1098/rsif.2018.0661.

4.

Polyelectrolyte multilayers of poly (l-lysine) and hyaluronic acid on nanostructured surfaces affect stem cell response.

Niepel MS, Ekambaram BK, Schmelzer CEH, Groth T.

Nanoscale. 2019 Feb 7;11(6):2878-2891. doi: 10.1039/c8nr05529g.

PMID:
30688341
5.

Cross-linking multilayers of poly-l-lysine and hyaluronic acid: Effect on mesenchymal stem cell behavior.

Niepel MS, Almouhanna F, Ekambaram BK, Menzel M, Heilmann A, Groth T.

Int J Artif Organs. 2018 Apr;41(4):223-235. doi: 10.1177/0391398817752598. Epub 2018 Mar 12.

PMID:
29528795
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

Effects of Diode Laser, Gaseous Ozone, and Medical Dressings on Enterococcus faecalis Biofilms in the Root Canal Ex Vivo.

Bitter K, Vlassakidis A, Niepel M, Hoedke D, Schulze J, Neumann K, Moter A, Noetzel J.

Biomed Res Int. 2017;2017:6321850. doi: 10.1155/2017/6321850. Epub 2017 Apr 10.

14.

Comparative Study of Osteogenic Activity of Multilayers Made of Synthetic and Biogenic Polyelectrolytes.

Guduru D, Niepel MS, Gonzalez-Garcia C, Salmeron-Sanchez M, Groth T.

Macromol Biosci. 2017 Aug;17(8). doi: 10.1002/mabi.201700078. Epub 2017 May 26.

PMID:
28547877
15.

Effect of Polyelectrolyte Multilayers Assembled on Ordered Nanostructures on Adhesion of Human Fibroblasts.

Niepel MS, Mano JF, Groth T.

ACS Appl Mater Interfaces. 2016 Sep 28;8(38):25142-51. doi: 10.1021/acsami.6b09349. Epub 2016 Sep 15.

PMID:
27603547
16.

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.

17.

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.

18.

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.

19.

Effect of Immobilized Thiolated Glycosaminoglycans on Fibronectin Adsorption and Behavior of Fibroblasts.

Köwitsch A, Niepel MS, Michanetzis GP, Missirlis YF, Groth T.

Macromol Biosci. 2016 Mar;16(3):381-94. doi: 10.1002/mabi.201500276. Epub 2015 Nov 30.

PMID:
26618787
20.

Reducing the inflammatory responses of biomaterials by surface modification with glycosaminoglycan multilayers.

Zhou G, Niepel MS, Saretia S, Groth T.

J Biomed Mater Res A. 2016 Feb;104(2):493-502. doi: 10.1002/jbm.a.35587. Epub 2015 Oct 29.

PMID:
26458275
21.

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.

22.

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.

23.

Hepatic nuclear corepressor 1 regulates cholesterol absorption through a TRβ1-governed pathway.

Astapova I, Ramadoss P, Costa-e-Sousa RH, Ye F, Holtz KA, Li Y, Niepel MW, Cohen DE, Hollenberg AN.

J Clin Invest. 2014 May;124(5):1976-86. doi: 10.1172/JCI73419. Epub 2014 Apr 8.

24.

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.

25.

The nuclear basket proteins Mlp1p and Mlp2p are part of a dynamic interactome including Esc1p and the proteasome.

Niepel M, Molloy KR, Williams R, Farr JC, Meinema AC, Vecchietti N, Cristea IM, Chait BT, Rout MP, Strambio-De-Castillia C.

Mol Biol Cell. 2013 Dec;24(24):3920-38. doi: 10.1091/mbc.E13-07-0412. Epub 2013 Oct 23.

26.

Nanoscaled surface patterns influence adhesion and growth of human dermal fibroblasts.

Niepel MS, Fuhrmann B, Leipner HS, Groth T.

Langmuir. 2013 Oct 29;29(43):13278-90. doi: 10.1021/la402705r. Epub 2013 Oct 18.

PMID:
24090166
27.

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.

28.

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.

29.

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.

30.

Enantiopure chiral poly(glycerol methacrylate) self-assembled monolayers knock down protein adsorption and cell adhesion.

Li Z, Köwitsch A, Zhou G, Groth T, Fuhrmann B, Niepel M, Amado E, Kressler J.

Adv Healthc Mater. 2013 Oct;2(10):1377-87. doi: 10.1002/adhm.201200402. Epub 2013 Mar 25.

PMID:
23526806
31.

Targeted deletion of fibrinogen like protein 1 reveals a novel role in energy substrate utilization.

Demchev V, Malana G, Vangala D, Stoll J, Desai A, Kang HW, Li Y, Nayeb-Hashemi H, Niepel M, Cohen DE, Ukomadu C.

PLoS One. 2013;8(3):e58084. doi: 10.1371/journal.pone.0058084. Epub 2013 Mar 6.

32.

Characterization of Torin2, an ATP-competitive inhibitor of mTOR, ATM, and ATR.

Liu Q, Xu C, Kirubakaran S, Zhang X, Hur W, Liu Y, Kwiatkowski NP, Wang J, Westover KD, Gao P, Ercan D, Niepel M, Thoreen CC, Kang SA, Patricelli MP, Wang Y, Tupper T, Altabef A, Kawamura H, Held KD, Chou DM, Elledge SJ, Janne PA, Wong KK, Sabatini DM, Gray NS.

Cancer Res. 2013 Apr 15;73(8):2574-86. doi: 10.1158/0008-5472.CAN-12-1702. Epub 2013 Feb 22.

33.

Targeted deletion of thioesterase superfamily member 1 promotes energy expenditure and protects against obesity and insulin resistance.

Zhang Y, Li Y, Niepel MW, Kawano Y, Han S, Liu S, Marsili A, Larsen PR, Lee CH, Cohen DE.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5417-22. doi: 10.1073/pnas.1116011109. Epub 2012 Mar 16.

34.

Thioesterase superfamily member 2/acyl-CoA thioesterase 13 (Them2/Acot13) regulates hepatic lipid and glucose metabolism.

Kang HW, Niepel MW, Han S, Kawano Y, Cohen DE.

FASEB J. 2012 May;26(5):2209-21. doi: 10.1096/fj.11-202853. Epub 2012 Feb 17.

35.

Discovery of potent and selective covalent inhibitors of JNK.

Zhang T, Inesta-Vaquera F, Niepel M, Zhang J, Ficarro SB, Machleidt T, Xie T, Marto JA, Kim N, Sim T, Laughlin JD, Park H, LoGrasso PV, Patricelli M, Nomanbhoy TK, Sorger PK, Alessi DR, Gray NS.

Chem Biol. 2012 Jan 27;19(1):140-54. doi: 10.1016/j.chembiol.2011.11.010.

36.

Kinome-wide selectivity profiling of ATP-competitive mammalian target of rapamycin (mTOR) inhibitors and characterization of their binding kinetics.

Liu Q, Kirubakaran S, Hur W, Niepel M, Westover K, Thoreen CC, Wang J, Ni J, Patricelli MP, Vogel K, Riddle S, Waller DL, Traynor R, Sanda T, Zhao Z, Kang SA, Zhao J, Look AT, Sorger PK, Sabatini DM, Gray NS.

J Biol Chem. 2012 Mar 23;287(13):9742-52. doi: 10.1074/jbc.M111.304485. Epub 2012 Jan 5.

37.

Nanostructured material surfaces--preparation, effect on cellular behavior, and potential biomedical applications: a review.

Guduru D, Niepel M, Vogel J, Groth T.

Int J Artif Organs. 2011 Oct;34(10):963-85. doi: 10.5301/IJAO.5000012. Review.

PMID:
22161281
38.

A cell cycle phosphoproteome of the yeast centrosome.

Keck JM, Jones MH, Wong CC, Binkley J, Chen D, Jaspersen SL, Holinger EP, Xu T, Niepel M, Rout MP, Vogel J, Sidow A, Yates JR 3rd, Winey M.

Science. 2011 Jun 24;332(6037):1557-61. doi: 10.1126/science.1205193.

39.

Genetic ablation or chemical inhibition of phosphatidylcholine transfer protein attenuates diet-induced hepatic glucose production.

Shishova EY, Stoll JM, Ersoy BA, Shrestha S, Scapa EF, Li Y, Niepel MW, Su Y, Jelicks LA, Stahl GL, Glicksman MA, Gutierrez-Juarez R, Cuny GD, Cohen DE.

Hepatology. 2011 Aug;54(2):664-74. doi: 10.1002/hep.24393. Epub 2011 Jun 23.

40.

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.

41.

Controlling fibroblast adhesion with pH modified polyelectrolyte multilayers.

Niepel MS, Peschel D, Groth T.

Int J Artif Organs. 2011 Feb;34(2):185-91.

PMID:
21374559
42.

Classic and contemporary approaches to modeling biochemical reactions.

Chen WW, Niepel M, Sorger PK.

Genes Dev. 2010 Sep 1;24(17):1861-75. doi: 10.1101/gad.1945410. Review.

43.

The nuclear pore complex: bridging nuclear transport and gene regulation.

Strambio-De-Castillia C, Niepel M, Rout MP.

Nat Rev Mol Cell Biol. 2010 Jul;11(7):490-501. doi: 10.1038/nrm2928. Review.

PMID:
20571586
44.

Dissecting variability in responses to cancer chemotherapy through systems pharmacology.

Yang R, Niepel M, Mitchison TK, Sorger PK.

Clin Pharmacol Ther. 2010 Jul;88(1):34-8. doi: 10.1038/clpt.2010.96. Epub 2010 Jun 2. Review.

45.

Non-genetic cell-to-cell variability and the consequences for pharmacology.

Niepel M, Spencer SL, Sorger PK.

Curr Opin Chem Biol. 2009 Dec;13(5-6):556-61. doi: 10.1016/j.cbpa.2009.09.015. Epub 2009 Oct 14. Review.

46.

pH-dependent modulation of fibroblast adhesion on multilayers composed of poly(ethylene imine) and heparin.

Niepel MS, Peschel D, Sisquella X, Planell JA, Groth T.

Biomaterials. 2009 Oct;30(28):4939-47. doi: 10.1016/j.biomaterials.2009.06.014. Epub 2009 Jul 1.

PMID:
19573910
47.

Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data.

Chen WW, Schoeberl B, Jasper PJ, Niepel M, Nielsen UB, Lauffenburger DA, Sorger PK.

Mol Syst Biol. 2009;5:239. doi: 10.1038/msb.2008.74. Epub 2009 Jan 20.

48.

The nuclear pore complex-associated protein, Mlp2p, binds to the yeast spindle pole body and promotes its efficient assembly.

Niepel M, Strambio-de-Castillia C, Fasolo J, Chait BT, Rout MP.

J Cell Biol. 2005 Jul 18;170(2):225-35.

49.
50.

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