| | Other Issues: previous | next | latest | archiveCommentaries Biomolecular network querying: a promising approach in systems biology Shihua Zhang, Xiang-Sun Zhang, and Luonan Chen PMCID: PMC2245906 Optimization in computational systems biology Julio R Banga PMCID: PMC2435524 Short time-series microarray analysis: Methods and challenges Xuewei Wang, Ming Wu, Zheng Li, and Christina Chan PMCID: PMC2474593 Methodology Articles Equilibrium model selection: dTTP induced R1 dimerization Tomas Radivoyevitch PMCID: PMC2268910 OptCircuit: An optimization based method for computational design of genetic circuits Madhukar S Dasika and Costas D Maranas PMCID: PMC2324073 Extracting expression modules from perturbational gene expression compendia Steven Maere, Patrick Van Dijck, and Martin Kuiper 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 PMCID: PMC2387136 Exploiting the pathway structure of metabolism to reveal high-order epistasis Marcin Imielinski and Calin Belta PMCID: PMC2390508 A Dominated Coupling From The Past algorithm for the stochastic simulation of networks of biochemical reactions Martin Hemberg and Mauricio Barahona PMCID: PMC2529164 Exhaustive identification of steady state cycles in large stoichiometric networks Jeremiah Wright and Andreas Wagner 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 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 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 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 PMCID: PMC2535594 Exact model reduction of combinatorial reaction networks Holger Conzelmann, Dirk Fey, and Ernst D Gilles PMCID: PMC2570670 Network evaluation from the consistency of the graph structure with the measured data Shigeru Saito, Sachiyo Aburatani, and Katsuhisa Horimoto PMCID: PMC2566979 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 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 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 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 PMCID: PMC2254585 Strong negative self regulation of Prokaryotic transcription factors increases the intrinsic noise of protein expression Dov J Stekel and Dafyd J Jenkins 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 PMCID: PMC2270259 Regulatory network reconstruction using an integral additive model with flexible kernel functions Eugene Novikov and Emmanuel Barillot PMCID: PMC2248159 Dynamical pathway analysis Hao Xiong and Yoonsuck Choe 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 PMCID: PMC2258206 Evidence of probabilistic behaviour in protein interaction networks Joseph Ivanic, Anders Wallqvist, and Jaques Reifman PMCID: PMC2267158 On cycles in the transcription network of Saccharomyces cerevisiae Jieun Jeong and Piotr Berman PMCID: PMC2275720 Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae Lev Guzmán-Vargas and Moisés Santillán PMCID: PMC2268659 Three factors underlying incorrect in silico predictions of essential metabolic genes Scott A Becker and Bernhard O Palsson 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 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 PMCID: PMC2268660 Dissecting the logical types of network control in gene expression profiles Carsten Marr, Marcel Geertz, Marc-Thorsten Hütt, and Georgi Muskhelishvili 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 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 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 PMCID: PMC2322946 Global parameter search reveals design principles of the mammalian circadian clock James CW Locke, Pål O Westermark, Achim Kramer, and Hanspeter Herzel PMCID: PMC2277373 One hub-one process: a tool based view on regulatory network topology Jacob Bock Axelsen, Sebastian Bernhardsson, and Kim Sneppen 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 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 PMCID: PMC2322945 The dynamics and efficacy of antiviral RNA silencing: A model study Marian AC Groenenboom and Paulien Hogeweg PMCID: PMC2373878 Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification Tae Hoon Yang, Oliver Frick, and Elmar Heinzle 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 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 PMCID: PMC2335094 An ultrasensitive sorting mechanism for EGF Receptor Endocytosis Hannah Schmidt-Glenewinkel, Ivayla Vacheva, Daniela Hoeller, Ivan Dikic, and Roland Eils 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 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 PMCID: PMC2383880 Phenotype prediction in regulated metabolic networks Christoph Kaleta, Florian Centler, Pietro Speroni di Fenizio, and Peter Dittrich 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 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 PMCID: PMC2396597 Mathematical modeling and analysis of insulin clearance in vivo Markus Koschorreck and Ernst Dieter Gilles 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 PMCID: PMC2435235 Defining a Modular Signalling Network from the Fly Interactome Anaïs Baudot, Jean-Baptiste Angelelli, Alain Guénoche, Bernard Jacq, and Christine Brun 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 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 PMCID: PMC2435525 Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion XiaoDong Huang, Jean YJ Wang, and Xin Lu PMCID: PMC2441606 Can single knockouts accurately single out gene functions? David Deutscher, Isaac Meilijson, Stefan Schuster, and Eytan Ruppin PMCID: PMC2443110 Time-resolved metabolomics reveals metabolic modulation in rice foliage Shigeru Sato, Masanori Arita, Tomoyoshi Soga, Takaaki Nishioka, and Masaru Tomita 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 PMCID: PMC2443111 Systematic reconstruction of TRANSPATH data into Cell System Markup Language Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, and Satoru Miyano PMCID: PMC2474843 The effects of protein interactions, gene essentiality and regulatory regions on expression variation Linqi Zhou, Xiaotu Ma, and Fengzhu Sun PMCID: PMC2474594 Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets Liang-Hui Chu and Bor-Sen Chen PMCID: PMC2488323 Seeded Bayesian Networks: Constructing genetic networks from microarray data Amira Djebbari and John Quackenbush 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 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 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 PMCID: PMC2488324 Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways Rajat K De, Mouli Das, and Subhasis Mukhopadhyay PMCID: PMC2533768 Structural similarity of genetically interacting proteins Oranit Dror, Dina Schneidman-Duhovny, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J Wolfson, and Roded Sharan 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 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 PMCID: PMC2535780 On the origin of distribution patterns of motifs in biological networks Arun S Konagurthu and Arthur M Lesk PMCID: PMC2538512 Explaining oscillations and variability in the p53-Mdm2 system Carole J Proctor and Douglas A Gray 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 PMCID: PMC2562372 A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory Juan Nogales, Bernhard Ø Palsson, and Ines Thiele 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 PMCID: PMC2553323 Employing conservation of co-expression to improve functional inference Carsten O Daub and Erik LL Sonnhammer PMCID: PMC2561017 Origin of structural difference in metabolic networks with respect to temperature Kazuhiro Takemoto and Tatsuya Akutsu PMCID: PMC2564917 Parameter estimation and determinability analysis applied to Drosophila gap gene circuits Maksat Ashyraliyev, Johannes Jaeger, and Joke G Blom 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 PMCID: PMC2606687 A quantitative estimation of the global translational activity in logarithmically growing yeast cells Tobias von der Haar 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 PMCID: PMC2596796 Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli Jiangjun Cui, Jaap A Kaandorp, and Catherine M Lloyd PMCID: PMC2611976 From protein interactions to functional annotation: graph alignment in Herpes Michal Kolář, Michael Lässig, and Johannes Berg PMCID: PMC2607256 An in silico method for detecting overlapping functional modules from composite biological networks Ioannis A Maraziotis, Konstantina Dimitrakopoulou, and Anastasios Bezerianos PMCID: PMC2600641 Genetic noise control via protein oligomerization Cheol-Min Ghim and Eivind Almaas 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 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 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 PMCID: PMC2600786 Dynamical modeling of the cholesterol regulatory pathway with Boolean networks Gwenael Kervizic and Laurent Corcos PMCID: PMC2612667 The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles Pawel Durek and Dirk Walther 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 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 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 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 PMCID: PMC2412839 The Systems Biology Research Tool: evolvable open-source software Jeremiah Wright and Andreas Wagner PMCID: PMC2446383 GridCell: a stochastic particle-based biological system simulator Laurier Boulianne, Sevin Al Assaad, Michel Dumontier, and Warren J Gross PMCID: PMC2517591 Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle Derek Ruths, Luay Nakhleh, and Prahlad T Ram PMCID: PMC2527501 |
