| | Other Issues: previous | next | latest | archiveCommentaries Biomolecular network querying: a promising approach in systems biology Shihua Zhang, Xiang-Sun Zhang, and Luonan Chen BMC Syst Biol. 2008; 2: 5. Published online 2008 January 18. doi: 10.1186/1752-0509-2-5.PMCID: PMC2245906 Optimization in computational systems biology Julio R Banga BMC Syst Biol. 2008; 2: 47. Published online 2008 May 28. doi: 10.1186/1752-0509-2-47.PMCID: PMC2435524 Short time-series microarray analysis: Methods and challenges Xuewei Wang, Ming Wu, Zheng Li, and Christina Chan BMC Syst Biol. 2008; 2: 58. Published online 2008 July 7. doi: 10.1186/1752-0509-2-58.PMCID: PMC2474593 Methodology Articles Equilibrium model selection: dTTP induced R1 dimerization Tomas Radivoyevitch BMC Syst Biol. 2008; 2: 15. Published online 2008 February 4. doi: 10.1186/1752-0509-2-15.PMCID: PMC2268910 OptCircuit: An optimization based method for computational design of genetic circuits Madhukar S Dasika and Costas D Maranas BMC Syst Biol. 2008; 2: 24. Published online 2008 March 3. doi: 10.1186/1752-0509-2-24.PMCID: PMC2324073 Extracting expression modules from perturbational gene expression compendia Steven Maere, Patrick Van Dijck, and Martin Kuiper BMC Syst Biol. 2008; 2: 33. Published online 2008 April 10. doi: 10.1186/1752-0509-2-33.PMCID: PMC2386865 Using genetic markers to orient the edges in quantitative trait networks: The NEO software Jason E Aten, Tova F Fuller, Aldons J Lusis, and Steve Horvath BMC Syst Biol. 2008; 2: 34. Published online 2008 April 15. doi: 10.1186/1752-0509-2-34.PMCID: PMC2387136 Exploiting the pathway structure of metabolism to reveal high-order epistasis Marcin Imielinski and Calin Belta BMC Syst Biol. 2008; 2: 40. Published online 2008 April 30. doi: 10.1186/1752-0509-2-40.PMCID: PMC2390508 A Dominated Coupling From The Past algorithm for the stochastic simulation of networks of biochemical reactions Martin Hemberg and Mauricio Barahona BMC Syst Biol. 2008; 2: 42. Published online 2008 May 8. doi: 10.1186/1752-0509-2-42.PMCID: PMC2529164 Exhaustive identification of steady state cycles in large stoichiometric networks Jeremiah Wright and Andreas Wagner BMC Syst Biol. 2008; 2: 61. Published online 2008 July 11. doi: 10.1186/1752-0509-2-61.PMCID: PMC2478680 Multiway modeling and analysis in stem cell systems biology Bülent Yener, Evrim Acar, Pheadra Aguis, Kristin Bennett, Scott L Vandenberg, and George E Plopper BMC Syst Biol. 2008; 2: 63. Published online 2008 July 14. doi: 10.1186/1752-0509-2-63.PMCID: PMC2527292 Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data Zuyi Huang, Fatih Senocak, Arul Jayaraman, and Juergen Hahn BMC Syst Biol. 2008; 2: 64. Published online 2008 July 17. doi: 10.1186/1752-0509-2-64.PMCID: PMC2491602 Machine learning based analyses on metabolic networks supports high-throughput knockout screens Kitiporn Plaimas, Jan-Phillip Mallm, Marcus Oswald, Fabian Svara, Victor Sourjik, Roland Eils, and Rainer König BMC Syst Biol. 2008; 2: 67. Published online 2008 July 24. doi: 10.1186/1752-0509-2-67.PMCID: PMC2526078 Modeling cellular deformations using the level set formalism Liu Yang, Janet C Effler, Brett L Kutscher, Sarah E Sullivan, Douglas N Robinson, and Pablo A Iglesias BMC Syst Biol. 2008; 2: 68. Published online 2008 July 24. doi: 10.1186/1752-0509-2-68.PMCID: PMC2535594 Exact model reduction of combinatorial reaction networks Holger Conzelmann, Dirk Fey, and Ernst D Gilles BMC Syst Biol. 2008; 2: 78. Published online 2008 August 28. doi: 10.1186/1752-0509-2-78.PMCID: PMC2570670 Network evaluation from the consistency of the graph structure with the measured data Shigeru Saito, Sachiyo Aburatani, and Katsuhisa Horimoto BMC Syst Biol. 2008; 2: 84. Published online 2008 October 1. doi: 10.1186/1752-0509-2-84.PMCID: PMC2566979 Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome Angela P Presson, Eric M Sobel, Jeanette C Papp, Charlyn J Suarez, Toni Whistler, Mangalathu S Rajeevan, Suzanne D Vernon, and Steve Horvath BMC Syst Biol. 2008; 2: 95. Published online 2008 November 6. doi: 10.1186/1752-0509-2-95.PMCID: PMC2625353 Research Articles A simple principle concerning the robustness of protein complex activity to changes in gene expression Jennifer I Semple, Tanya Vavouri, and Ben Lehner BMC Syst Biol. 2008; 2: 1. Published online 2008 January 2. doi: 10.1186/1752-0509-2-1.PMCID: PMC2242779 Linking the ovarian cancer transcriptome and immunome Ronald Rapberger, Paul Perco, Cornelia Sax, Thomas Pangerl, Christian Siehs, Dietmar Pils, Andreas Bernthaler, Arno Lukas, Bernd Mayer, and Michael Krainer BMC Syst Biol. 2008; 2: 2. Published online 2008 January 3. doi: 10.1186/1752-0509-2-2.PMCID: PMC2265674 Annotating novel genes by integrating synthetic lethals and genomic information Daniel Schöner, Markus Kalisch, Christian Leisner, Lukas Meier, Marc Sohrmann, Mahamadou Faty, Yves Barral, Matthias Peter, Wilhelm Gruissem, and Peter Bühlmann BMC Syst Biol. 2008; 2: 3. Published online 2008 January 14. doi: 10.1186/1752-0509-2-3.PMCID: PMC2258006 Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction Raimo Franke, Melanie Müller, Nicole Wundrack, Ernst-Dieter Gilles, Steffen Klamt, Thilo Kähne, and Michael Naumann BMC Syst Biol. 2008; 2: 4. Published online 2008 January 14. doi: 10.1186/1752-0509-2-4.PMCID: PMC2254585 Strong negative self regulation of Prokaryotic transcription factors increases the intrinsic noise of protein expression Dov J Stekel and Dafyd J Jenkins BMC Syst Biol. 2008; 2: 6. Published online 2008 January 18. doi: 10.1186/1752-0509-2-6.PMCID: PMC2263017 Impact of the solvent capacity constraint on E. coli metabolism Alexei Vazquez, Qasim K Beg, Marcio A deMenezes, Jason Ernst, Ziv Bar-Joseph, Albert-László Barabási, László G Boros, and Zoltán N Oltvai BMC Syst Biol. 2008; 2: 7. Published online 2008 January 23. doi: 10.1186/1752-0509-2-7.PMCID: PMC2270259 Regulatory network reconstruction using an integral additive model with flexible kernel functions Eugene Novikov and Emmanuel Barillot BMC Syst Biol. 2008; 2: 8. Published online 2008 January 24. doi: 10.1186/1752-0509-2-8.PMCID: PMC2248159 Dynamical pathway analysis Hao Xiong and Yoonsuck Choe BMC Syst Biol. 2008; 2: 9. Published online 2008 January 27. doi: 10.1186/1752-0509-2-9.PMCID: PMC2268661 Identification of gene interactions associated with disease from gene expression data using synergy networks John Watkinson, Xiaodong Wang, Tian Zheng, and Dimitris Anastassiou BMC Syst Biol. 2008; 2: 10. Published online 2008 January 30. doi: 10.1186/1752-0509-2-10.PMCID: PMC2258206 Evidence of probabilistic behaviour in protein interaction networks Joseph Ivanic, Anders Wallqvist, and Jaques Reifman BMC Syst Biol. 2008; 2: 11. Published online 2008 January 31. doi: 10.1186/1752-0509-2-11.PMCID: PMC2267158 On cycles in the transcription network of Saccharomyces cerevisiae Jieun Jeong and Piotr Berman BMC Syst Biol. 2008; 2: 12. Published online 2008 January 31. doi: 10.1186/1752-0509-2-12.PMCID: PMC2275720 Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae Lev Guzmán-Vargas and Moisés Santillán BMC Syst Biol. 2008; 2: 13. Published online 2008 January 31. doi: 10.1186/1752-0509-2-13.PMCID: PMC2268659 Three factors underlying incorrect in silico predictions of essential metabolic genes Scott A Becker and Bernhard O Palsson BMC Syst Biol. 2008; 2: 14. Published online 2008 February 4. doi: 10.1186/1752-0509-2-14.PMCID: PMC2248557 Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants David J Weston, Lee E Gunter, Alistair Rogers, and Stan D Wullschleger BMC Syst Biol. 2008; 2: 16. Published online 2008 February 4. doi: 10.1186/1752-0509-2-16.PMCID: PMC2277374 Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks Ana Paula Oliveira, Kiran Raosaheb Patil, and Jens Nielsen BMC Syst Biol. 2008; 2: 17. Published online 2008 February 8. doi: 10.1186/1752-0509-2-17.PMCID: PMC2268660 Dissecting the logical types of network control in gene expression profiles Carsten Marr, Marcel Geertz, Marc-Thorsten Hütt, and Georgi Muskhelishvili BMC Syst Biol. 2008; 2: 18. Published online 2008 February 19. doi: 10.1186/1752-0509-2-18.PMCID: PMC2263018 Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility Divyaswetha Peddinti, Bindu Nanduri, Abdullah Kaya, Jean M Feugang, Shane C Burgess, and Erdogan Memili BMC Syst Biol. 2008; 2: 19. Published online 2008 February 22. doi: 10.1186/1752-0509-2-19.PMCID: PMC2291030 Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis Anne Goelzer, Fadia Bekkal Brikci, Isabelle Martin-Verstraete, Philippe Noirot, Philippe Bessières, Stéphane Aymerich, and Vincent Fromion BMC Syst Biol. 2008; 2: 20. Published online 2008 February 26. doi: 10.1186/1752-0509-2-20.PMCID: PMC2311275 The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response Areejit Samal and Sanjay Jain BMC Syst Biol. 2008; 2: 21. Published online 2008 February 29. doi: 10.1186/1752-0509-2-21.PMCID: PMC2322946 Global parameter search reveals design principles of the mammalian circadian clock James CW Locke, Pål O Westermark, Achim Kramer, and Hanspeter Herzel BMC Syst Biol. 2008; 2: 22. Published online 2008 February 29. doi: 10.1186/1752-0509-2-22.PMCID: PMC2277373 One hub-one process: a tool based view on regulatory network topology Jacob Bock Axelsen, Sebastian Bernhardsson, and Kim Sneppen BMC Syst Biol. 2008; 2: 25. Published online 2008 March 4. doi: 10.1186/1752-0509-2-25.PMCID: PMC2292138 Hybrid optimization method with general switching strategy for parameter estimation Eva Balsa-Canto, Martin Peifer, Julio R Banga, Jens Timmer, and Christian Fleck BMC Syst Biol. 2008; 2: 26. Published online 2008 March 24. doi: 10.1186/1752-0509-2-26.PMCID: PMC2373877 A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency Patrick Amar, Guillaume Legent, Michel Thellier, Camille Ripoll, Gilles Bernot, Thomas Nystrom, Milton H Saier, Jr, and Vic Norris BMC Syst Biol. 2008; 2: 27. Published online 2008 March 25. doi: 10.1186/1752-0509-2-27.PMCID: PMC2322945 The dynamics and efficacy of antiviral RNA silencing: A model study Marian AC Groenenboom and Paulien Hogeweg BMC Syst Biol. 2008; 2: 28. Published online 2008 March 26. doi: 10.1186/1752-0509-2-28.PMCID: PMC2373878 Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification Tae Hoon Yang, Oliver Frick, and Elmar Heinzle BMC Syst Biol. 2008; 2: 29. Published online 2008 March 26. doi: 10.1186/1752-0509-2-29.PMCID: PMC2333969 Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability Youfang Cao and Jie Liang BMC Syst Biol. 2008; 2: 30. Published online 2008 March 29. doi: 10.1186/1752-0509-2-30.PMCID: PMC2375859 An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis Karen E Thum, Michael J Shin, Rodrigo A Gutiérrez, Indrani Mukherjee, Manpreet S Katari, Damion Nero, Dennis Shasha, and Gloria M Coruzzi BMC Syst Biol. 2008; 2: 31. Published online 2008 April 4. doi: 10.1186/1752-0509-2-31.PMCID: PMC2335094 An ultrasensitive sorting mechanism for EGF Receptor Endocytosis Hannah Schmidt-Glenewinkel, Ivayla Vacheva, Daniela Hoeller, Ivan Dikic, and Roland Eils BMC Syst Biol. 2008; 2: 32. Published online 2008 April 7. doi: 10.1186/1752-0509-2-32.PMCID: PMC2377235 Parameter optimization in S-system models Marco Vilela, I-Chun Chou, Susana Vinga, Ana Tereza R Vasconcelos, Eberhard O Voit, and Jonas S Almeida BMC Syst Biol. 2008; 2: 35. Published online 2008 April 16. doi: 10.1186/1752-0509-2-35.PMCID: PMC2333970 A logic-based diagram of signalling pathways central to macrophage activation Sobia Raza, Kevin A Robertson, Paul A Lacaze, David Page, Anton J Enright, Peter Ghazal, and Tom C Freeman BMC Syst Biol. 2008; 2: 36. Published online 2008 April 23. doi: 10.1186/1752-0509-2-36.PMCID: PMC2383880 Phenotype prediction in regulated metabolic networks Christoph Kaleta, Florian Centler, Pietro Speroni di Fenizio, and Peter Dittrich BMC Syst Biol. 2008; 2: 37. Published online 2008 April 25. doi: 10.1186/1752-0509-2-37.PMCID: PMC2443871 A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway Julio Vera, Julie Bachmann, Andrea C Pfeifer, Verena Becker, Jose A Hormiga, Nestor V Torres Darias, Jens Timmer, Ursula Klingmüller, and Olaf Wolkenhauer BMC Syst Biol. 2008; 2: 38. Published online 2008 April 25. doi: 10.1186/1752-0509-2-38.PMCID: PMC2386439 Extraction of elementary rate constants from global network analysis of E. coli central metabolism Jiao Zhao, Douglas Ridgway, Gordon Broderick, Andriy Kovalenko, and Michael Ellison BMC Syst Biol. 2008; 2: 41. Published online 2008 May 7. doi: 10.1186/1752-0509-2-41.PMCID: PMC2396597 Mathematical modeling and analysis of insulin clearance in vivo Markus Koschorreck and Ernst Dieter Gilles BMC Syst Biol. 2008; 2: 43. Published online 2008 May 13. doi: 10.1186/1752-0509-2-43.PMCID: PMC2430945 Linear analysis near a steady-state of biochemical networks: Control analysis, correlation metrics and circuit theory William J Heuett, Daniel A Beard, and Hong Qian BMC Syst Biol. 2008; 2: 44. Published online 2008 May 15. doi: 10.1186/1752-0509-2-44.PMCID: PMC2435235 Defining a Modular Signalling Network from the Fly Interactome Anaïs Baudot, Jean-Baptiste Angelelli, Alain Guénoche, Bernard Jacq, and Christine Brun BMC Syst Biol. 2008; 2: 45. Published online 2008 May 19. doi: 10.1186/1752-0509-2-45.PMCID: PMC2405789 Transcription profiling of lung adenocarcinomas of c-myc-transgenic mice: Identification of the c-myc regulatory gene network Susanne Reymann and Jürgen Borlak BMC Syst Biol. 2008; 2: 46. Published online 2008 May 22. doi: 10.1186/1752-0509-2-46.PMCID: PMC2430022 Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach Najl V Valeyev, Declan G Bates, Pat Heslop-Harrison, Ian Postlethwaite, and Nikolay V Kotov BMC Syst Biol. 2008; 2: 48. Published online 2008 June 2. doi: 10.1186/1752-0509-2-48.PMCID: PMC2435525 Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion XiaoDong Huang, Jean YJ Wang, and Xin Lu BMC Syst Biol. 2008; 2: 49. Published online 2008 June 13. doi: 10.1186/1752-0509-2-49.PMCID: PMC2441606 Can single knockouts accurately single out gene functions? David Deutscher, Isaac Meilijson, Stefan Schuster, and Eytan Ruppin BMC Syst Biol. 2008; 2: 50. Published online 2008 June 18. doi: 10.1186/1752-0509-2-50.PMCID: PMC2443110 Time-resolved metabolomics reveals metabolic modulation in rice foliage Shigeru Sato, Masanori Arita, Tomoyoshi Soga, Takaaki Nishioka, and Masaru Tomita BMC Syst Biol. 2008; 2: 51. Published online 2008 June 18. doi: 10.1186/1752-0509-2-51.PMCID: PMC2442833 A computational analysis of protein-protein interaction networks in neurodegenerative diseases Joaquín Goñi, Francisco J Esteban, Nieves Vélez de Mendizábal, Jorge Sepulcre, Sergio Ardanza-Trevijano, Ion Agirrezabal, and Pablo Villoslada BMC Syst Biol. 2008; 2: 52. Published online 2008 June 20. doi: 10.1186/1752-0509-2-52.PMCID: PMC2443111 Systematic reconstruction of TRANSPATH data into Cell System Markup Language Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, and Satoru Miyano BMC Syst Biol. 2008; 2: 53. Published online 2008 June 23. doi: 10.1186/1752-0509-2-53.PMCID: PMC2474843 The effects of protein interactions, gene essentiality and regulatory regions on expression variation Linqi Zhou, Xiaotu Ma, and Fengzhu Sun BMC Syst Biol. 2008; 2: 54. Published online 2008 June 26. doi: 10.1186/1752-0509-2-54.PMCID: PMC2474594 Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets Liang-Hui Chu and Bor-Sen Chen BMC Syst Biol. 2008; 2: 56. Published online 2008 June 30. doi: 10.1186/1752-0509-2-56.PMCID: PMC2488323 Seeded Bayesian Networks: Constructing genetic networks from microarray data Amira Djebbari and John Quackenbush BMC Syst Biol. 2008; 2: 57. Published online 2008 July 4. doi: 10.1186/1752-0509-2-57.PMCID: PMC2474592 Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures João ML Dias, Adrian Oehmen, Luísa S Serafim, Paulo C Lemos, Maria AM Reis, and Rui Oliveira BMC Syst Biol. 2008; 2: 59. Published online 2008 July 8. doi: 10.1186/1752-0509-2-59.PMCID: PMC2483998 Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A Paula Jouhten, Eija Rintala, Anne Huuskonen, Anu Tamminen, Mervi Toivari, Marilyn Wiebe, Laura Ruohonen, Merja Penttilä, and Hannu Maaheimo BMC Syst Biol. 2008; 2: 60. Published online 2008 July 9. doi: 10.1186/1752-0509-2-60.PMCID: PMC2507709 A systems approach to model natural variation in reactive properties of bacterial ribosomes Julius H Jackson, Thomas M Schmidt, and Patricia A Herring BMC Syst Biol. 2008; 2: 62. Published online 2008 July 13. doi: 10.1186/1752-0509-2-62.PMCID: PMC2488324 Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways Rajat K De, Mouli Das, and Subhasis Mukhopadhyay BMC Syst Biol. 2008; 2: 65. Published online 2008 July 18. doi: 10.1186/1752-0509-2-65.PMCID: PMC2533768 Structural similarity of genetically interacting proteins Oranit Dror, Dina Schneidman-Duhovny, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J Wolfson, and Roded Sharan BMC Syst Biol. 2008; 2: 69. Published online 2008 July 31. doi: 10.1186/1752-0509-2-69.PMCID: PMC2525628 The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism Intawat Nookaew, Michael C Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, and Sakarindr Bhumiratana BMC Syst Biol. 2008; 2: 71. Published online 2008 August 7. doi: 10.1186/1752-0509-2-71.PMCID: PMC2542360 Constructing disease-specific gene networks using pair-wise relevance metric: Application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements Wei Jiang, Xia Li, Shaoqi Rao, Lihong Wang, Lei Du, Chuanxing Li, Chao Wu, Hongzhi Wang, Yadong Wang, and Baofeng Yang BMC Syst Biol. 2008; 2: 72. Published online 2008 August 10. doi: 10.1186/1752-0509-2-72.PMCID: PMC2535780 On the origin of distribution patterns of motifs in biological networks Arun S Konagurthu and Arthur M Lesk BMC Syst Biol. 2008; 2: 73. Published online 2008 August 12. doi: 10.1186/1752-0509-2-73.PMCID: PMC2538512 Explaining oscillations and variability in the p53-Mdm2 system Carole J Proctor and Douglas A Gray BMC Syst Biol. 2008; 2: 75. Published online 2008 August 18. doi: 10.1186/1752-0509-2-75.PMCID: PMC2553322 A compartment model of VEGF distribution in blood, healthy and diseased tissues Marianne O Stefanini, Florence TH Wu, Feilim Mac Gabhann, and Aleksander S Popel BMC Syst Biol. 2008; 2: 77. Published online 2008 August 19. doi: 10.1186/1752-0509-2-77.PMCID: PMC2562372 A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory Juan Nogales, Bernhard Ø Palsson, and Ines Thiele BMC Syst Biol. 2008; 2: 79. Published online 2008 September 16. doi: 10.1186/1752-0509-2-79.PMCID: PMC2569920 The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks Michael Hsing, Kendall Grant Byler, and Artem Cherkasov BMC Syst Biol. 2008; 2: 80. Published online 2008 September 16. doi: 10.1186/1752-0509-2-80.PMCID: PMC2553323 Employing conservation of co-expression to improve functional inference Carsten O Daub and Erik LL Sonnhammer BMC Syst Biol. 2008; 2: 81. Published online 2008 September 22. doi: 10.1186/1752-0509-2-81.PMCID: PMC2561017 Origin of structural difference in metabolic networks with respect to temperature Kazuhiro Takemoto and Tatsuya Akutsu BMC Syst Biol. 2008; 2: 82. Published online 2008 September 22. doi: 10.1186/1752-0509-2-82.PMCID: PMC2564917 Parameter estimation and determinability analysis applied to Drosophila gap gene circuits Maksat Ashyraliyev, Johannes Jaeger, and Joke G Blom BMC Syst Biol. 2008; 2: 83. Published online 2008 September 25. doi: 10.1186/1752-0509-2-83.PMCID: PMC2586632 Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data Maxime Durot, François Le Fèvre, Véronique de Berardinis, Annett Kreimeyer, David Vallenet, Cyril Combe, Serge Smidtas, Marcel Salanoubat, Jean Weissenbach, and Vincent Schachter BMC Syst Biol. 2008; 2: 85. Published online 2008 October 7. doi: 10.1186/1752-0509-2-85.PMCID: PMC2606687 A quantitative estimation of the global translational activity in logarithmically growing yeast cells Tobias von der Haar BMC Syst Biol. 2008; 2: 87. Published online 2008 October 16. doi: 10.1186/1752-0509-2-87.PMCID: PMC2590609 Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle Ashley J Waardenberg, Antonio Reverter, Christine A Wells, and Brian P Dalrymple BMC Syst Biol. 2008; 2: 88. Published online 2008 October 22. doi: 10.1186/1752-0509-2-88.PMCID: PMC2596796 Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli Jiangjun Cui, Jaap A Kaandorp, and Catherine M Lloyd BMC Syst Biol. 2008; 2: 89. Published online 2008 October 24. doi: 10.1186/1752-0509-2-89.PMCID: PMC2611976 From protein interactions to functional annotation: graph alignment in Herpes Michal Kolář, Michael Lässig, and Johannes Berg BMC Syst Biol. 2008; 2: 90. Published online 2008 October 28. doi: 10.1186/1752-0509-2-90.PMCID: PMC2607256 An in silico method for detecting overlapping functional modules from composite biological networks Ioannis A Maraziotis, Konstantina Dimitrakopoulou, and Anastasios Bezerianos BMC Syst Biol. 2008; 2: 93. Published online 2008 November 1. doi: 10.1186/1752-0509-2-93.PMCID: PMC2600641 Genetic noise control via protein oligomerization Cheol-Min Ghim and Eivind Almaas BMC Syst Biol. 2008; 2: 94. Published online 2008 November 3. doi: 10.1186/1752-0509-2-94.PMCID: PMC2584638 Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans I King Jordan, Lee S Katz, Dee R Denver, and J Todd Streelman BMC Syst Biol. 2008; 2: 96. Published online 2008 November 13. doi: 10.1186/1752-0509-2-96.PMCID: PMC2596099 Stochastic analysis of the GAL genetic switch in Saccharomyces cerevisiae: Modeling and experiments reveal hierarchy in glucose repression Vinay Prasad and KV Venkatesh BMC Syst Biol. 2008; 2: 97. Published online 2008 November 17. doi: 10.1186/1752-0509-2-97.PMCID: PMC2614938 Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model Mariana Benítez, Carlos Espinosa-Soto, Pablo Padilla-Longoria, and Elena R Alvarez-Buylla BMC Syst Biol. 2008; 2: 98. Published online 2008 November 17. doi: 10.1186/1752-0509-2-98.PMCID: PMC2600786 Dynamical modeling of the cholesterol regulatory pathway with Boolean networks Gwenael Kervizic and Laurent Corcos BMC Syst Biol. 2008; 2: 99. Published online 2008 November 24. doi: 10.1186/1752-0509-2-99.PMCID: PMC2612667 The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles Pawel Durek and Dirk Walther BMC Syst Biol. 2008; 2: 100. Published online 2008 November 25. doi: 10.1186/1752-0509-2-100.PMCID: PMC2607255 Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks Christopher R Bauer, Andrew M Epstein, Sarah J Sweeney, Daniela C Zarnescu, and Giovanni Bosco BMC Syst Biol. 2008; 2: 101. Published online 2008 November 25. doi: 10.1186/1752-0509-2-101.PMCID: PMC2610033 Review A review of imaging techniques for systems biology Armen R Kherlopian, Ting Song, Qi Duan, Mathew A Neimark, Ming J Po, John K Gohagan, and Andrew F Laine BMC Syst Biol. 2008; 2: 74. Published online 2008 August 12. doi: 10.1186/1752-0509-2-74.PMCID: PMC2533300 Software Interactive analysis of systems biology molecular expression data Mingwu Zhang, Qi Ouyang, Alan Stephenson, Michael D Kane, David E Salt, Sunil Prabhakar, John Burgner, Charles Buck, and Xiang Zhang BMC Syst Biol. 2008; 2: 23. Published online 2008 February 29. doi: 10.1186/1752-0509-2-23.PMCID: PMC2294108 SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, and Andreas Zell BMC Syst Biol. 2008; 2: 39. Published online 2008 April 30. doi: 10.1186/1752-0509-2-39.PMCID: PMC2412839 The Systems Biology Research Tool: evolvable open-source software Jeremiah Wright and Andreas Wagner BMC Syst Biol. 2008; 2: 55. Published online 2008 June 29. doi: 10.1186/1752-0509-2-55.PMCID: PMC2446383 GridCell: a stochastic particle-based biological system simulator Laurier Boulianne, Sevin Al Assaad, Michel Dumontier, and Warren J Gross BMC Syst Biol. 2008; 2: 66. Published online 2008 July 23. doi: 10.1186/1752-0509-2-66.PMCID: PMC2517591 Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle Derek Ruths, Luay Nakhleh, and Prahlad T Ram BMC Syst Biol. 2008; 2: 76. Published online 2008 August 19. doi: 10.1186/1752-0509-2-76.PMCID: PMC2527501 |