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Items: 1 to 20 of 170


Transcriptome-wide functional characterization reveals novel relationships among differentially expressed transcripts in developing soybean embryos.

Aghamirzaie D, Batra D, Heath LS, Schneider A, Grene R, Collakova E.

BMC Genomics. 2015 Nov 14;16(1):928. doi: 10.1186/s12864-015-2108-x.


Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants.

Hill CB, Czauderna T, Klapperstück M, Roessner U, Schreiber F.

Front Bioeng Biotechnol. 2015 Oct 21;3:167. doi: 10.3389/fbioe.2015.00167. eCollection 2015. Review.


Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.

Flis A, Fernández AP, Zielinski T, Mengin V, Sulpice R, Stratford K, Hume A, Pokhilko A, Southern MM, Seaton DD, McWatters HG, Stitt M, Halliday KJ, Millar AJ.

Open Biol. 2015 Oct;5(10). pii: 150042. doi: 10.1098/rsob.150042.


SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.

Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A.

BMC Syst Biol. 2015 Oct 9;9:68. doi: 10.1186/s12918-015-0212-9.


Impact of kinetic isotope effects in isotopic studies of metabolic systems.

Millard P, Portais JC, Mendes P.

BMC Syst Biol. 2015 Sep 26;9:64. doi: 10.1186/s12918-015-0213-8.


Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells.

Korkut A, Wang W, Demir E, Aksoy BA, Jing X, Molinelli EJ, Babur Ö, Bemis DL, Onur Sumer S, Solit DB, Pratilas CA, Sander C.

Elife. 2015 Aug 18;4. doi: 10.7554/eLife.04640.


Regulation of ERK-MAPK signaling in human epidermis.

Cursons J, Gao J, Hurley DG, Print CG, Dunbar PR, Jacobs MD, Crampin EJ.

BMC Syst Biol. 2015 Jul 25;9:41. doi: 10.1186/s12918-015-0187-6.


The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms.

Tripathi S, Flobak Å, Chawla K, Baudot A, Bruland T, Thommesen L, Kuiper M, Lægreid A.

BMC Syst Biol. 2015 Jul 24;9:40. doi: 10.1186/s12918-015-0181-z.


Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps.

Kuperstein I, Bonnet E, Nguyen HA, Cohen D, Viara E, Grieco L, Fourquet S, Calzone L, Russo C, Kondratova M, Dutreix M, Barillot E, Zinovyev A.

Oncogenesis. 2015 Jul 20;4:e160. doi: 10.1038/oncsis.2015.19.


Modeling for (physical) biologists: an introduction to the rule-based approach.

Chylek LA, Harris LA, Faeder JR, Hlavacek WS.

Phys Biol. 2015 Jul 16;12(4):045007. doi: 10.1088/1478-3975/12/4/045007.


Tools for visualization and analysis of molecular networks, pathways, and -omics data.

Villaveces JM, Koti P, Habermann BH.

Adv Appl Bioinform Chem. 2015 Jun 4;8:11-22. doi: 10.2147/AABC.S63534. eCollection 2015. Review.


Potential unsatisfiability of cyclic constraints on stochastic biological networks biases selection towards hierarchical architectures.

Smith C, Pechuan X, Puzio RS, Biro D, Bergman A.

J R Soc Interface. 2015 Jul 6;12(108):20150179. doi: 10.1098/rsif.2015.0179.


SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

Sari M, Bahceci I, Dogrusoz U, Sumer SO, Aksoy BA, Babur Ö, Demir E.

PLoS One. 2015 Jun 1;10(6):e0128985. doi: 10.1371/journal.pone.0128985. eCollection 2015.


Integrated Stochastic Model of DNA Damage Repair by Non-homologous End Joining and p53/p21-Mediated Early Senescence Signalling.

Dolan DW, Zupanic A, Nelson G, Hall P, Miwa S, Kirkwood TB, Shanley DP.

PLoS Comput Biol. 2015 May 28;11(5):e1004246. doi: 10.1371/journal.pcbi.1004246. eCollection 2015 May.


NaviCell Web Service for network-based data visualization.

Bonnet E, Viara E, Kuperstein I, Calzone L, Cohen DP, Barillot E, Zinovyev A.

Nucleic Acids Res. 2015 Jul 1;43(W1):W560-5. doi: 10.1093/nar/gkv450. Epub 2015 May 9.


Pathways with PathWhiz.

Pon A, Jewison T, Su Y, Liang Y, Knox C, Maciejewski A, Wilson M, Wishart DS.

Nucleic Acids Res. 2015 Jul 1;43(W1):W552-9. doi: 10.1093/nar/gkv399. Epub 2015 May 1.


Mathematical modelling of metabolic regulation in aging.

Auley MT, Mooney KM, Angell PJ, Wilkinson SJ.

Metabolites. 2015 Apr 27;5(2):232-51. doi: 10.3390/metabo5020232. Review.


Mimoza: web-based semantic zooming and navigation in metabolic networks.

Zhukova A, Sherman DJ.

BMC Syst Biol. 2015 Feb 26;9:10. doi: 10.1186/s12918-015-0151-5.


A generalised enzyme kinetic model for predicting the behaviour of complex biochemical systems.

Wong MK, Krycer JR, Burchfield JG, James DE, Kuncic Z.

FEBS Open Bio. 2015 Mar 9;5:226-39. doi: 10.1016/j.fob.2015.03.002. eCollection 2015.


Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.

Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N.

Front Bioeng Biotechnol. 2015 Feb 24;3:19. doi: 10.3389/fbioe.2015.00019. eCollection 2015. Review.

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