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Items: 40

1.

Wilm's tumor 1 promotes memory flexibility.

Mariottini C, Munari L, Gunzel E, Seco JM, Tzavaras N, Hansen J, Stern SA, Gao V, Aleyasin H, Sharma A, Azeloglu EU, Hodes GE, Russo SJ, Huff V, Birtwistle MR, Blitzer RD, Alberini CM, Iyengar R.

Nat Commun. 2019 Aug 21;10(1):3756. doi: 10.1038/s41467-019-11781-x.

2.

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.

3.

Mitochondrial origins of fractional control in regulated cell death.

Santos LC, Vogel R, Chipuk JE, Birtwistle MR, Stolovitzky G, Meyer P.

Nat Commun. 2019 Mar 21;10(1):1313. doi: 10.1038/s41467-019-09275-x.

4.

Fluorescence Multiplexing with Spectral Imaging and Combinatorics.

Holzapfel HY, Stern AD, Bouhaddou M, Anglin CM, Putur D, Comer S, Birtwistle MR.

ACS Comb Sci. 2018 Nov 12;20(11):653-659. doi: 10.1021/acscombsci.8b00101. Epub 2018 Oct 30.

PMID:
30339749
5.

Validating Antibodies for Quantitative Western Blot Measurements with Microwestern Array.

Koch RJ, Barrette AM, Stern AD, Hu B, Bouhaddou M, Azeloglu EU, Iyengar R, Birtwistle MR.

Sci Rep. 2018 Jul 27;8(1):11329. doi: 10.1038/s41598-018-29436-0.

6.

A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens.

Bouhaddou M, Barrette AM, Stern AD, Koch RJ, DiStefano MS, Riesel EA, Santos LC, Tan AL, Mertz AE, Birtwistle MR.

PLoS Comput Biol. 2018 Mar 26;14(3):e1005985. doi: 10.1371/journal.pcbi.1005985. eCollection 2018 Mar. Erratum in: PLoS Comput Biol. 2018 Jul 9;14(7):e1006189.

7.

Analysis of copy number loss of the ErbB4 receptor tyrosine kinase in glioblastoma.

Jones DC, Scanteianu A, DiStefano M, Bouhaddou M, Birtwistle MR.

PLoS One. 2018 Jan 17;13(1):e0190664. doi: 10.1371/journal.pone.0190664. eCollection 2018.

8.

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.

9.

A Comparison of mRNA Sequencing with Random Primed and 3'-Directed Libraries.

Xiong Y, Soumillon M, Wu J, Hansen J, Hu B, van Hasselt JGC, Jayaraman G, Lim R, Bouhaddou M, Ornelas L, Bochicchio J, Lenaeus L, Stocksdale J, Shim J, Gomez E, Sareen D, Svendsen C, Thompson LM, Mahajan M, Iyengar R, Sobie EA, Azeloglu EU, Birtwistle MR.

Sci Rep. 2017 Nov 7;7(1):14626. doi: 10.1038/s41598-017-14892-x.

10.

Mechanistic Systems Modeling to Improve Understanding and Prediction of Cardiotoxicity Caused by Targeted Cancer Therapeutics.

Shim JV, Chun B, van Hasselt JGC, Birtwistle MR, Saucerman JJ, Sobie EA.

Front Physiol. 2017 Sep 8;8:651. doi: 10.3389/fphys.2017.00651. eCollection 2017.

11.

Integrating Transcriptomic Data with Mechanistic Systems Pharmacology Models for Virtual Drug Combination Trials.

Barrette AM, Bouhaddou M, Birtwistle MR.

ACS Chem Neurosci. 2018 Jan 17;9(1):118-129. doi: 10.1021/acschemneuro.7b00197. Epub 2017 Oct 6.

12.

Drug response consistency in CCLE and CGP.

Bouhaddou M, DiStefano MS, Riesel EA, Carrasco E, Holzapfel HY, Jones DC, Smith GR, Stern AD, Somani SS, Thompson TV, Birtwistle MR.

Nature. 2016 Nov 30;540(7631):E9-E10. doi: 10.1038/nature20580. No abstract available.

13.

Cell size assays for mass cytometry.

Stern AD, Rahman AH, Birtwistle MR.

Cytometry A. 2017 Jan;91(1):14-24. doi: 10.1002/cyto.a.23000. Epub 2016 Oct 21.

14.

Current Proteomic Methods to Investigate the Dynamics of Histone Turnover in the Central Nervous System.

Farrelly LA, Dill BD, Molina H, Birtwistle MR, Maze I.

Methods Enzymol. 2016;574:331-354. doi: 10.1016/bs.mie.2016.01.013. Epub 2016 Feb 16.

15.

A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data.

Smith GR, Birtwistle MR.

PLoS One. 2016 Jun 21;11(6):e0157828. doi: 10.1371/journal.pone.0157828. eCollection 2016.

16.

Creating Complex Fluorophore Spectra on Antibodies Through Combinatorial Labeling.

Holzapfel HY, Birtwistle MR.

Transl Sci. 2016 Mar;2(3). pii: e03. Epub 2016 Mar 31.

17.

Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches.

Byrne KM, Monsefi N, Dawson JC, Degasperi A, Bukowski-Wills JC, Volinsky N, Dobrzyński M, Birtwistle MR, Tsyganov MA, Kiyatkin A, Kida K, Finch AJ, Carragher NO, Kolch W, Nguyen LK, von Kriegsheim A, Kholodenko BN.

Cell Syst. 2016 Jan 27;2(1):38-48. doi: 10.1016/j.cels.2016.01.003. Epub 2016 Jan 27.

18.

CNS Anticancer Drug Discovery and Development Conference White Paper.

Levin VA, Tonge PJ, Gallo JM, Birtwistle MR, Dar AC, Iavarone A, Paddison PJ, Heffron TP, Elmquist WF, Lachowicz JE, Johnson TW, White FM, Sul J, Smith QR, Shen W, Sarkaria JN, Samala R, Wen PY, Berry DA, Petter RC.

Neuro Oncol. 2015 Nov;17 Suppl 6:vi1-26. doi: 10.1093/neuonc/nov169.

19.
20.

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity.

Maze I, Wenderski W, Noh KM, Bagot RC, Tzavaras N, Purushothaman I, Elsässer SJ, Guo Y, Ionete C, Hurd YL, Tamminga CA, Halene T, Farrelly L, Soshnev AA, Wen D, Rafii S, Birtwistle MR, Akbarian S, Buchholz BA, Blitzer RD, Nestler EJ, Yuan ZF, Garcia BA, Shen L, Molina H, Allis CD.

Neuron. 2015 Jul 1;87(1):77-94. doi: 10.1016/j.neuron.2015.06.014.

21.

Network pharmacodynamic models for customized cancer therapy.

Gallo JM, Birtwistle MR.

Wiley Interdiscip Rev Syst Biol Med. 2015 Jul-Aug;7(4):243-51. doi: 10.1002/wsbm.1300. Epub 2015 Apr 24.

22.

Silence on the relevant literature and errors in implementation.

Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN.

Nat Biotechnol. 2015 Apr;33(4):336-9. doi: 10.1038/nbt.3185. No abstract available.

PMID:
25850052
23.

Analytical reduction of combinatorial complexity arising from multiple protein modification sites.

Birtwistle MR.

J R Soc Interface. 2015 Feb 6;12(103). pii: 20141215. doi: 10.1098/rsif.2014.1215.

24.

Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses.

Dobrzyński M, Nguyen LK, Birtwistle MR, von Kriegsheim A, Blanco Fernández A, Cheong A, Kolch W, Kholodenko BN.

J R Soc Interface. 2014 Sep 6;11(98):20140383. doi: 10.1098/rsif.2014.0383.

25.

Transcriptomes and shRNA suppressors in a TP53 allele-specific model of early-onset colon cancer in African Americans.

Weige CC, Birtwistle MR, Mallick H, Yi N, Berrong Z, Cloessner E, Duff K, Tidwell J, Clendenning M, Wilkerson B, Farrell C, Bunz F, Ji H, Shtutman M, Creek KE, Banister CE, Buckhaults PJ.

Mol Cancer Res. 2014 Jul;12(7):1029-41. doi: 10.1158/1541-7786.MCR-13-0286-T. Epub 2014 Apr 17.

26.

Dimerization-based control of cooperativity.

Bouhaddou M, Birtwistle MR.

Mol Biosyst. 2014 Jul;10(7):1824-32. doi: 10.1039/c4mb00022f.

27.

Evaluating strategies to normalise biological replicates of Western blot data.

Degasperi A, Birtwistle MR, Volinsky N, Rauch J, Kolch W, Kholodenko BN.

PLoS One. 2014 Jan 27;9(1):e87293. doi: 10.1371/journal.pone.0087293. eCollection 2014.

28.

Mechanistic vs. Empirical network models of drug action.

Birtwistle MR, Mager DE, Gallo JM.

CPT Pharmacometrics Syst Pharmacol. 2013 Sep 6;2:e72. doi: 10.1038/psp.2013.51.

29.

A General Network Pharmacodynamic Model-Based Design Pipeline for Customized Cancer Therapy Applied to the VEGFR Pathway.

Zhang XY, Birtwistle MR, Gallo JM.

CPT Pharmacometrics Syst Pharmacol. 2014 Jan 15;3:e92. doi: 10.1038/psp.2013.65.

30.

A Comparison of Methods for RNA-Seq Differential Expression Analysis and a New Empirical Bayes Approach.

Wesolowski S, Birtwistle MR, Rempala GA.

Biosensors (Basel). 2013 Jun 28;3(3):238-58. doi: 10.3390/bios3030238. eCollection 2013 Sep.

31.

Bayesian multivariate Poisson abundance models for T-cell receptor data.

Greene J, Birtwistle MR, Ignatowicz L, Rempala GA.

J Theor Biol. 2013 Jun 7;326:1-10. doi: 10.1016/j.jtbi.2013.02.009. Epub 2013 Mar 1.

32.

Mammalian protein expression noise: scaling principles and the implications for knockdown experiments.

Birtwistle MR, von Kriegsheim A, Dobrzyński M, Kholodenko BN, Kolch W.

Mol Biosyst. 2012 Nov;8(11):3068-76. doi: 10.1039/c2mb25168j.

PMID:
22990612
33.

Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise.

Birtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzyński M, Hoek JB, Kolch W, Ogunnaike BA, Kholodenko BN.

BMC Syst Biol. 2012 Aug 24;6:109. doi: 10.1186/1752-0509-6-109.

34.

Novel somatic mutations to PI3K pathway genes in metastatic melanoma.

Shull AY, Latham-Schwark A, Ramasamy P, Leskoske K, Oroian D, Birtwistle MR, Buckhaults PJ.

PLoS One. 2012;7(8):e43369. doi: 10.1371/journal.pone.0043369. Epub 2012 Aug 17.

35.

Linear approaches to intramolecular Förster resonance energy transfer probe measurements for quantitative modeling.

Birtwistle MR, von Kriegsheim A, Kida K, Schwarz JP, Anderson KI, Kolch W.

PLoS One. 2011;6(11):e27823. doi: 10.1371/journal.pone.0027823. Epub 2011 Nov 16.

36.

Biology using engineering tools: the negative feedback amplifier.

Birtwistle MR, Kolch W.

Cell Cycle. 2011 Jul 1;10(13):2069-76. Epub 2011 Jul 1.

37.

Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics.

Nakakuki T, Birtwistle MR, Saeki Y, Yumoto N, Ide K, Nagashima T, Brusch L, Ogunnaike BA, Okada-Hatakeyama M, Kholodenko BN.

Cell. 2010 May 28;141(5):884-96. doi: 10.1016/j.cell.2010.03.054. Epub 2010 May 20.

38.

Four-dimensional dynamics of MAPK information processing systems.

Kholodenko BN, Birtwistle MR.

Wiley Interdiscip Rev Syst Biol Med. 2009 Jul-Aug;1(1):28-44. doi: 10.1002/wsbm.16. Review.

39.

Endocytosis and signalling: a meeting with mathematics.

Birtwistle MR, Kholodenko BN.

Mol Oncol. 2009 Aug;3(4):308-20. doi: 10.1016/j.molonc.2009.05.009. Epub 2009 Jun 16. Review.

40.

Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses.

Birtwistle MR, Hatakeyama M, Yumoto N, Ogunnaike BA, Hoek JB, Kholodenko BN.

Mol Syst Biol. 2007;3:144. Epub 2007 Nov 13.

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