| | Other Issues: previous | next | latest | archiveCorrespondence On gene dosage balance in protein complexes: a comment on Semple JI, Vavouri T, Lehner B. A simple principle concerning the robustness of protein complex activity to changes in gene expression. Reiner A Veitia PMCID: PMC2646697 A framework for evolutionary systems biology Laurence Loewe PMCID: PMC2663779 Methodology Articles Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms Jan Baumbach, Sven Rahmann, and Andreas Tauch PMCID: PMC2653031 Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation Christian L Barrett, Markus J Herrgard, and Bernhard Palsson PMCID: PMC2667477 Version control of pathway models using XML patches Peter Saffrey and Richard Orton PMCID: PMC2674044 Research Articles Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance Özgür Sahin, Holger Fröhlich, Christian Löbke, Ulrike Korf, Sara Burmester, Meher Majety, Jens Mattern, Ingo Schupp, Claudine Chaouiya, Denis Thieffry, Annemarie Poustka, Stefan Wiemann, Tim Beissbarth, and Dorit Arlt PMCID: PMC2652436 Dynamic simulations on the mitochondrial fatty acid Beta-oxidation network Robert Modre-Osprian, Ingrid Osprian, Bernhard Tilg, Günter Schreier, Klaus M Weinberger, and Armin Graber PMCID: PMC2633313 Efficiency of complex production in changing environment Shai Carmi, Erez Y Levanon, and Eli Eisenberg PMCID: PMC2647903 Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii Nanette R Boyle and John A Morgan PMCID: PMC2628641 Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies Andreas Dräger, Marcel Kronfeld, Michael J Ziller, Jochen Supper, Hannes Planatscher, Jørgen B Magnus, Marco Oldiges, Oliver Kohlbacher, and Andreas Zell PMCID: PMC2661887 Analytical approximations for the amplitude and period of a relaxation oscillator Carmen Kut, Vahid Golkhou, and Joel S Bader PMCID: PMC2657111 Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae Tobias S Christensen, Ana Paula Oliveira, and Jens Nielsen PMCID: PMC2661888 Information theoretical quantification of cooperativity in signalling complexes Tom Lenaerts, Jesper Ferkinghoff-Borg, Joost Schymkowitz, and Frederic Rousseau PMCID: PMC2637831 A Drosophila systems model of pentylenetetrazole induced locomotor plasticity responsive to antiepileptic drugs Farhan Mohammad, Priyanka Singh, and Abhay Sharma PMCID: PMC2657775 Bifurcation analysis informs Bayesian inference in the Hes1 feedback loop Catherine F Higham PMCID: PMC2669796 Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting Amina A Qutub and Aleksander S Popel PMCID: PMC2672076 Coordinations between gene modules control the operation of plant amino acid metabolic networks Hadar Less and Gad Galili PMCID: PMC2646696 Genome-scale constraint-based modeling of Geobacter metallireducens Jun Sun, Bahareh Sayyar, Jessica E Butler, Priti Pharkya, Tom R Fahland, Iman Famili, Christophe H Schilling, Derek R Lovley, and Radhakrishnan Mahadevan PMCID: PMC2640342 Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3 Donatella Cimini, Kiran R Patil, Chiara Schiraldi, and Jens Nielsen PMCID: PMC2661886 mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle Nicola Soranzo, Mattia Zampieri, Lorenzo Farina, and Claudio Altafini PMCID: PMC2677395 A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation Reza Mobini, Bengt A Andersson, Jonas Erjefält, Mirjana Hahn-Zoric, Michael A Langston, Andy D Perkins, Lars Olaf Cardell, and Mikael Benson PMCID: PMC2653464 Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation Albert C Huang, Limei Hu, Stuart A Kauffman, Wei Zhang, and Ilya Shmulevich PMCID: PMC2652435 Protein evolution on a human signaling network Qinghua Cui, Enrico O Purisima, and Edwin Wang PMCID: PMC2649034 Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart Fan Wu and Daniel A Beard PMCID: PMC2667476 Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway Yukuto Sato, Yasuyuki Hashiguchi, and Mutsumi Nishida PMCID: PMC2653465 A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola Gavin H Thomas, Jeremy Zucker, Sandy J Macdonald, Anatoly Sorokin, Igor Goryanin, and Angela E Douglas PMCID: PMC2649895 Efficient, sparse biological network determination Elias August and Antonis Papachristodoulou PMCID: PMC2671484 Protein-protein interaction as a predictor of subcellular location Chang Jin Shin, Simon Wong, Melissa J Davis, and Mark A Ragan PMCID: PMC2663780 Simple molecular networks that respond optimally to time-periodic stimulation Axel Cournac and Jacques-Alexandre Sepulchre PMCID: PMC2666635 Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo Jesse J Smith, Renée Deehan Kenney, David J Gagne, Brian P Frushour, William Ladd, Heidi L Galonek, Kristine Israelian, Jeffrey Song, Giedre Razvadauskaite, Amy V Lynch, David P Carney, Robin J Johnson, Siva Lavu, Andre Iffland, Peter J Elliott, Philip D Lambert, Keith O Elliston, Michael R Jirousek, Jill C Milne, and Olivier Boss PMCID: PMC2660283 Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks Wen-hsien Lin, Wei-chung Liu, and Ming-jing Hwang PMCID: PMC2663781 Reconstruction of metabolic pathways for the cattle genome Seongwon Seo and Harris A Lewin PMCID: PMC2669051 Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction Anu Raghunathan, Jennifer Reed, Sookil Shin, Bernhard Palsson, and Simon Daefler PMCID: PMC2678070 Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway Maria Luisa Guerriero, Anna Dudka, Nicholas Underhill-Day, John K Heath, and Corrado Priami PMCID: PMC2678071 Software SNAVI: Desktop application for analysis and visualization of large-scale signaling networks Avi Ma'ayan, Sherry L Jenkins, Ryan L Webb, Seth I Berger, Sudarshan P Purushothaman, Noura S Abul-Husn, Jeremy M Posner, Tony Flores, and Ravi Iyengar PMCID: PMC2637233 FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data Jussi Paananen and Garry Wong PMCID: PMC2651117 |
