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Items: 1 to 50 of 52

1.

Lack of evidence for substrate channeling or flux between wildtype and mutant isocitrate dehydrogenase to produce the oncometabolite 2-hydroxyglutarate.

Dexter JP, Ward PS, Dasgupta T, Hosios AM, Gunawardena J, Vander Heiden MG.

J Biol Chem. 2018 Oct 31. pii: jbc.RA118.004278. doi: 10.1074/jbc.RA118.004278. [Epub ahead of print]

2.

Structural conditions on complex networks for the Michaelis-Menten input-output response.

Wong F, Dutta A, Chowdhury D, Gunawardena J.

Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):9738-9743. doi: 10.1073/pnas.1808053115. Epub 2018 Sep 7.

PMID:
30194237
3.

Heavy metals transport pathways: The importance of atmospheric pollution contributing to stormwater pollution.

Liu A, Ma Y, Gunawardena JMA, Egodawatta P, Ayoko GA, Goonetilleke A.

Ecotoxicol Environ Saf. 2018 Nov 30;164:696-703. doi: 10.1016/j.ecoenv.2018.08.072. Epub 2018 Aug 29.

PMID:
30172206
4.

Energy-speed-accuracy relation in complex networks for biological discrimination.

Wong F, Amir A, Gunawardena J.

Phys Rev E. 2018 Jul;98(1-1):012420. doi: 10.1103/PhysRevE.98.012420.

PMID:
30110782
5.

Model discrimination for Ca2+ -dependent regulation of myosin light chain kinase in smooth muscle contraction.

Dexter JP, Biddle JW, Gunawardena J.

FEBS Lett. 2018 Aug;592(16):2811-2821. doi: 10.1002/1873-3468.13207. Epub 2018 Aug 13.

PMID:
30066333
6.

Estimating the Distribution of Protein Post-Translational Modification States by Mass Spectrometry.

Compton PD, Kelleher NL, Gunawardena J.

J Proteome Res. 2018 Aug 3;17(8):2727-2734. doi: 10.1021/acs.jproteome.8b00150. Epub 2018 Jul 10.

PMID:
29945451
7.

How many human proteoforms are there?

Aebersold R, Agar JN, Amster IJ, Baker MS, Bertozzi CR, Boja ES, Costello CE, Cravatt BF, Fenselau C, Garcia BA, Ge Y, Gunawardena J, Hendrickson RC, Hergenrother PJ, Huber CG, Ivanov AR, Jensen ON, Jewett MC, Kelleher NL, Kiessling LL, Krogan NJ, Larsen MR, Loo JA, Ogorzalek Loo RR, Lundberg E, MacCoss MJ, Mallick P, Mootha VK, Mrksich M, Muir TW, Patrie SM, Pesavento JJ, Pitteri SJ, Rodriguez H, Saghatelian A, Sandoval W, Schlüter H, Sechi S, Slavoff SA, Smith LM, Snyder MP, Thomas PM, Uhlén M, Van Eyk JE, Vidal M, Walt DR, White FM, Williams ER, Wohlschlager T, Wysocki VH, Yates NA, Young NL, Zhang B.

Nat Chem Biol. 2018 Feb 14;14(3):206-214. doi: 10.1038/nchembio.2576.

PMID:
29443976
8.

Transcription factors, coregulators, and epigenetic marks are linearly correlated and highly redundant.

Ahsendorf T, Müller FJ, Topkar V, Gunawardena J, Eils R.

PLoS One. 2017 Dec 7;12(12):e0186324. doi: 10.1371/journal.pone.0186324. eCollection 2017.

9.

The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell.

Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM Jr, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P.

Curr Biol. 2017 Feb 20;27(4):569-575. doi: 10.1016/j.cub.2016.12.057. Epub 2017 Feb 9.

10.
11.

Information Integration and Energy Expenditure in Gene Regulation.

Estrada J, Wong F, DePace A, Gunawardena J.

Cell. 2016 Jun 30;166(1):234-44. doi: 10.1016/j.cell.2016.06.012.

12.

Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling.

Estrada J, Andrew N, Gibson D, Chang F, Gnad F, Gunawardena J.

PLoS Comput Biol. 2016 Jul 1;12(7):e1004995. doi: 10.1371/journal.pcbi.1004995. eCollection 2016 Jul.

13.

Taxonomy of factors which influence heavy metal build-up on urban road surfaces.

Liu A, Gunawardana C, Gunawardena J, Egodawatta P, Ayoko GA, Goonetilleke A.

J Hazard Mater. 2016 Jun 5;310:20-9. doi: 10.1016/j.jhazmat.2016.02.026. Epub 2016 Feb 11.

PMID:
26897571
14.

Characterization of Neuronal Tau Protein as a Target of Extracellular Signal-regulated Kinase.

Qi H, Prabakaran S, Cantrelle FX, Chambraud B, Gunawardena J, Lippens G, Landrieu I.

J Biol Chem. 2016 Apr 1;291(14):7742-53. doi: 10.1074/jbc.M115.700914. Epub 2016 Feb 8.

15.

Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation.

Malleshaiah M, Padi M, Rué P, Quackenbush J, Martinez-Arias A, Gunawardena J.

Cell Rep. 2016 Feb 9;14(5):1181-1194. doi: 10.1016/j.celrep.2015.12.101. Epub 2016 Jan 28.

16.

Cybernetics, Redux: An Outside-In Strategy for Unraveling Cellular Function.

Malleshaiah M, Gunawardena J.

Dev Cell. 2016 Jan 11;36(1):2-4. doi: 10.1016/j.devcel.2015.12.025.

17.

Bayesian modeling suggests that IL-12 (p40), IL-13 and MCP-1 drive murine cytokine networks in vivo.

Field SL, Dasgupta T, Cummings M, Savage RS, Adebayo J, McSara H, Gunawardena J, Orsi NM.

BMC Syst Biol. 2015 Nov 9;9:76. doi: 10.1186/s12918-015-0226-3.

18.

Invariants reveal multiple forms of robustness in bifunctional enzyme systems.

Dexter JP, Dasgupta T, Gunawardena J.

Integr Biol (Camb). 2015 Aug;7(8):883-94. doi: 10.1039/c5ib00009b. Epub 2015 May 29.

PMID:
26021467
19.
20.

A framework for modelling gene regulation which accommodates non-equilibrium mechanisms.

Ahsendorf T, Wong F, Eils R, Gunawardena J.

BMC Biol. 2014 Dec 5;12:102. doi: 10.1186/s12915-014-0102-4.

21.

Quantitative profiling of peptides from RNAs classified as noncoding.

Prabakaran S, Hemberg M, Chauhan R, Winter D, Tweedie-Cullen RY, Dittrich C, Hong E, Gunawardena J, Steen H, Kreiman G, Steen JA.

Nat Commun. 2014 Nov 18;5:5429. doi: 10.1038/ncomms6429.

22.

Beware the tail that wags the dog: informal and formal models in biology.

Gunawardena J.

Mol Biol Cell. 2014 Nov 5;25(22):3441-4. doi: 10.1091/mbc.E14-02-0717.

23.

Paradoxical results in perturbation-based signaling network reconstruction.

Prabakaran S, Gunawardena J, Sontag E.

Biophys J. 2014 Jun 17;106(12):2720-8. doi: 10.1016/j.bpj.2014.04.031.

24.

Models in biology: 'accurate descriptions of our pathetic thinking'.

Gunawardena J.

BMC Biol. 2014 Apr 30;12:29. doi: 10.1186/1741-7007-12-29.

25.

A fundamental trade-off in covalent switching and its circumvention by enzyme bifunctionality in glucose homeostasis.

Dasgupta T, Croll DH, Owen JA, Vander Heiden MG, Locasale JW, Alon U, Cantley LC, Gunawardena J.

J Biol Chem. 2014 May 9;289(19):13010-25. doi: 10.1074/jbc.M113.546515. Epub 2014 Mar 14.

26.

Mathematical relationships for metal build-up on urban road surfaces based on traffic and land use characteristics.

Gunawardena J, Ziyath AM, Egodawatta P, Ayoko GA, Goonetilleke A.

Chemosphere. 2014 Mar;99:267-71. doi: 10.1016/j.chemosphere.2013.10.068. Epub 2013 Nov 20.

PMID:
24268173
27.

Time-scale separation--Michaelis and Menten's old idea, still bearing fruit.

Gunawardena J.

FEBS J. 2014 Jan;281(2):473-88. doi: 10.1111/febs.12532. Epub 2013 Oct 17. Review.

28.

Laplacian dynamics on general graphs.

Mirzaev I, Gunawardena J.

Bull Math Biol. 2013 Nov;75(11):2118-49. doi: 10.1007/s11538-013-9884-8. Epub 2013 Sep 10.

PMID:
24018536
29.

Biology is more theoretical than physics.

Gunawardena J.

Mol Biol Cell. 2013 Jun;24(12):1827-9. doi: 10.1091/mbc.E12-03-0227.

30.

Characterisation of atmospheric deposited particles during a dust storm in urban areas of Eastern Australia.

Gunawardena J, Ziyath AM, Bostrom TE, Bekessy LK, Ayoko GA, Egodawatta P, Goonetilleke A.

Sci Total Environ. 2013 Sep 1;461-462:72-80. doi: 10.1016/j.scitotenv.2013.04.080. Epub 2013 May 25.

PMID:
23712117
31.

Tunable signal processing through modular control of transcription factor translocation.

Hao N, Budnik BA, Gunawardena J, O'Shea EK.

Science. 2013 Jan 25;339(6118):460-4. doi: 10.1126/science.1227299.

32.

Dimerization and bifunctionality confer robustness to the isocitrate dehydrogenase regulatory system in Escherichia coli.

Dexter JP, Gunawardena J.

J Biol Chem. 2013 Feb 22;288(8):5770-8. doi: 10.1074/jbc.M112.339226. Epub 2012 Nov 28.

33.

Silicon dreams of cells into symbols.

Gunawardena J.

Nat Biotechnol. 2012 Sep;30(9):838-40. doi: 10.1038/nbt.2358. No abstract available.

PMID:
22965055
34.

Post-translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding.

Prabakaran S, Lippens G, Steen H, Gunawardena J.

Wiley Interdiscip Rev Syst Biol Med. 2012 Nov-Dec;4(6):565-83. doi: 10.1002/wsbm.1185. Epub 2012 Aug 15. Review.

35.

Realistic enzymology for post-translational modification: zero-order ultrasensitivity revisited.

Xu Y, Gunawardena J.

J Theor Biol. 2012 Oct 21;311:139-52. doi: 10.1016/j.jtbi.2012.07.012. Epub 2012 Jul 22.

36.

Complex-linear invariants of biochemical networks.

Karp RL, Pérez Millán M, Dasgupta T, Dickenstein A, Gunawardena J.

J Theor Biol. 2012 Oct 21;311:130-8. doi: 10.1016/j.jtbi.2012.07.004. Epub 2012 Jul 16.

PMID:
22814477
37.

A linear framework for time-scale separation in nonlinear biochemical systems.

Gunawardena J.

PLoS One. 2012;7(5):e36321. doi: 10.1371/journal.pone.0036321. Epub 2012 May 14. Erratum in: PLoS One. 2013;8(12). doi:10.1371/annotation/6830fba7-6e52-48f9-9f55-75ee37c75b5a. PLoS One. 2013;8(6). doi:10.1371/annotation/fa4c5f9f-4071-4b32-864f-b82c2e4e973b.

38.

Proteus: a web-based, context-specific modelling tool for molecular networks.

Gnad F, Estrada J, Gunawardena J.

Bioinformatics. 2012 May 1;28(9):1284-6. doi: 10.1093/bioinformatics/bts126. Epub 2012 Mar 15.

39.

Some lessons about models from Michaelis and Menten.

Gunawardena J.

Mol Biol Cell. 2012 Feb;23(4):517-9. doi: 10.1091/mbc.E11-07-0643. Erratum in: Mol Biol Cell. 2012 Jul;23(14):2819.

40.

A phosphatase threshold sets the level of Cdk1 activity in early mitosis in budding yeast.

Harvey SL, Enciso G, Dephoure N, Gygi SP, Gunawardena J, Kellogg DR.

Mol Biol Cell. 2011 Oct;22(19):3595-608. doi: 10.1091/mbc.E11-04-0340. Epub 2011 Aug 17.

41.

Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions.

Prabakaran S, Everley RA, Landrieu I, Wieruszeski JM, Lippens G, Steen H, Gunawardena J.

Mol Syst Biol. 2011 Apr 12;7:482. doi: 10.1038/msb.2011.15.

42.

PHOSIDA 2011: the posttranslational modification database.

Gnad F, Gunawardena J, Mann M.

Nucleic Acids Res. 2011 Jan;39(Database issue):D253-60. doi: 10.1093/nar/gkq1159. Epub 2010 Nov 16.

43.

Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.

Gnad F, Forner F, Zielinska DF, Birney E, Gunawardena J, Mann M.

Mol Cell Proteomics. 2010 Dec;9(12):2642-53. doi: 10.1074/mcp.M110.001594. Epub 2010 Aug 5.

44.

Systems biology. Biological systems theory.

Gunawardena J.

Science. 2010 Apr 30;328(5978):581-2. doi: 10.1126/science.1188974. No abstract available.

PMID:
20431005
45.

The rational parameterization theorem for multisite post-translational modification systems.

Thomson M, Gunawardena J.

J Theor Biol. 2009 Dec 21;261(4):626-36. doi: 10.1016/j.jtbi.2009.09.003. Epub 2009 Sep 16.

46.

Unlimited multistability in multisite phosphorylation systems.

Thomson M, Gunawardena J.

Nature. 2009 Jul 9;460(7252):274-7. doi: 10.1038/nature08102. Epub 2009 Jun 17.

47.

The geometry of multisite phosphorylation.

Manrai AK, Gunawardena J.

Biophys J. 2008 Dec 15;95(12):5533-43. doi: 10.1529/biophysj.108.140632. Epub 2008 Oct 10.

48.

Programming with models: modularity and abstraction provide powerful capabilities for systems biology.

Mallavarapu A, Thomson M, Ullian B, Gunawardena J.

J R Soc Interface. 2009 Mar 6;6(32):257-70. doi: 10.1098/rsif.2008.0205.

49.
50.

Multisite protein phosphorylation makes a good threshold but can be a poor switch.

Gunawardena J.

Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14617-22. Epub 2005 Sep 29.

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