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ORCIDBMC Systems Biology, Volume 2
Volume 2, 2008
- Jennifer I. Semple
, Tanya Vavouri, Ben Lehner:
A simple principle concerning the robustness of protein complex activity to changes in gene expression. 1 - Ronald Rapberger, Paul Perco, Cornelia Sax, Thomas Pangerl, Christian Siehs, Dietmar Pils, Andreas Bernthaler, Arno Lukas, Bernd Mayer, Michael Krainer:
Linking the ovarian cancer transcriptome and immunome. 2 - Daniel Schöner, Markus Kalisch, Christian Leisner, Lukas Meier, Marc Sohrmann, Mahamadou Faty, Yves Barral, Matthias Peter, Wilhelm Gruissem, Peter Bühlmann:
Annotating novel genes by integrating synthetic lethals and genomic information. 3 - Raimo Franke, Melanie Müller, Nicole Wundrack, Ernst Dieter Gilles, Steffen Klamt, Thilo Kähne, Michael Naumann:
Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. 4 - Shihua Zhang, Xiang-Sun Zhang, Luonan Chen:
Biomolecular network querying: a promising approach in systems biology. 5 - Dov J. Stekel, Dafyd J. Jenkins:
Strong negative self regulation of Prokaryotic transcription factors increases the intrinsic noise of protein expression. 6 - Alexei Vázquez, Qasim K. Beg, Marcio A. de Menezes, Jason Ernst, Ziv Bar-Joseph, Albert-László Barabási, László G. Boros, Zoltán N. Oltvai:
Impact of the solvent capacity constraint on E. coli metabolism. 7 - Eugene Novikov, Emmanuel Barillot:
Regulatory network reconstruction using an integral additive model with flexible kernel functions. 8 - Hao Xiong, Yoonsuck Choe:
Dynamical pathway analysis. 9 - John Watkinson, Xiaodong Wang, Tian Zheng, Dimitris Anastassiou:
Identification of gene interactions associated with disease from gene expression data using synergy networks. 10 - Joseph Ivanic, Anders Wallqvist, Jaques Reifman:
Evidence of probabilistic behaviour in protein interaction networks. 11 - Jieun K. Jeong, Piotr Berman:
On cycles in the transcription network of Saccharomyces cerevisiae. 12 - Lev Guzmán-Vargas, Moisés Santillán:
Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae. 13 - Scott A. Becker, Bernhard O. Palsson:
Three factors underlying incorrect in silico predictions of essential metabolic genes. 14 - Tomas Radivoyevitch:
Equilibrium model selection: dTTP induced R1 dimerization. 15 - David J. Weston, Lee E. Gunter, Alistair Rogers, Stan D. Wullschleger:
Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants. 16 - Ana Oliveira, Kiran Raosaheb Patil, Jens Nielsen:
Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks. 17 - Carsten Marr, Marcel Geertz, Marc-Thorsten Hütt, Georgi Muskhelishvili:
Dissecting the logical types of network control in gene expression profiles. 18 - Divyaswetha Peddinti, Bindu Nanduri, Abdullah Kaya, Jean M. Feugang, Shane C. Burgess, Erdogan Memili:
Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility. 19 - Anne Goelzer, Fadia Bekkal-Brikci, Isabelle Martin-Verstraete, Philippe Noirot, Philippe Bessières, Stéphane Aymerich, Vincent Fromion:
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis. 20 - Areejit Samal, Sanjay Jain:
The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response. 21 - James C. W. Locke, Pål O. Westermark, Achim Kramer, Hanspeter Herzel:
Global parameter search reveals design principles of the mammalian circadian clock. 22 - Mingwu Zhang, Qi Ouyang, Alan Stephenson, Michael D. Kane, David E. Salt, Sunil Prabhakar, John Burgner, Charles R. Buck, Xiang Zhang:
Interactive analysis of systems biology molecular expression data. 23 - Madhukar S. Dasika, Costas D. Maranas:
OptCircuit: An optimization based method for computational design of genetic circuits. 24 - Jacob Axelsen, Sebastian Bernhardsson, Kim Sneppen:
One hub-one process: a tool based view on regulatory network topology. 25 - Eva Balsa-Canto, Martin Peifer, Julio R. Banga, Jens Timmer, Christian Fleck:
Hybrid optimization method with general switching strategy for parameter estimation. 26 - Patrick Amar, Guillaume Legent, Michel Thellier, Camille Ripoll, Gilles Bernot, Thomas Nyström, Milton H. Saier Jr., Vic Norris:
A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency. 27 - Marian Groenenboom, Paulien Hogeweg:
The dynamics and efficacy of antiviral RNA silencing: A model study. 28 - Tae Hoon Yang, Oliver Frick, Elmar Heinzle:
Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification. 29 - Youfang Cao, Jie Liang:
Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability. 30 - Karen E. Thum, Michael J. Shin, Rodrigo A. Gutiérrez, Indrani Mukherjee, Manpreet S. Katari, Damion Nero, Dennis E. Shasha, Gloria M. Coruzzi:
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis. 31 - Hannah Schmidt-Glenewinkel, Ivayla Vacheva, Daniela Hoeller, Ivan Dikic, Roland Eils:
An ultrasensitive sorting mechanism for EGF Receptor Endocytosis. 32 - Steven Maere, Patrick Van Dijck, Martin Kuiper:
Extracting expression modules from perturbational gene expression compendia. 33 - Jason E. Aten, Tova Fuller, Aldons J. Lusis, Steve Horvath:
Using genetic markers to orient the edges in quantitative trait networks: The NEO software. 34 - Marco Vilela, I-Chun Chou, Susana Vinga, Ana Tereza Ribeiro de Vasconcelos, Eberhard O. Voit, Jonas S. Almeida:
Parameter optimization in S-system models. 35 - Sobia Raza, Kevin A. Robertson, Paul A. Lacaze, David Page, Anton J. Enright, Peter Ghazal, Tom C. Freeman:
A logic-based diagram of signalling pathways central to macrophage activation. 36 - Christoph Kaleta, Florian Centler, Pietro Speroni di Fenizio, Peter Dittrich:
Phenotype prediction in regulated metabolic networks. 37 - Julio Vera, Julie Bachmann, Andrea C. Pfeifer, Verena Becker, Jose A. Hormiga, Néstor Torres Darias, Jens Timmer, Ursula Klingmüller, Olaf Wolkenhauer:
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway. 38 - Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, Andreas Zell:
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks. 39 - Marcin Imielinski, Calin Belta:
Exploiting the pathway structure of metabolism to reveal high-order epistasis. 40 - Jiao Zhao, Douglas Ridgway, Gordon Broderick, Andriy Kovalenko, Michael J. Ellison:
Extraction of elementary rate constants from global network analysis of E. coli central metabolism. 41 - Martin Hemberg, Mauricio Barahona:
A Dominated Coupling From The Past algorithm for the stochastic simulation of networks of biochemical reactions. 42 - Markus Koschorreck, Ernst Dieter Gilles:
Mathematical modeling and analysis of insulin clearance in vivo. 43 - William J. Heuett, Daniel A. Beard, Hong Qian:
Linear analysis near a steady-state of biochemical networks: control analysis, correlation metrics and circuit theory. 44 - Anaïs Baudot, Jean-Baptiste Angelelli, Alain Guénoche, Bernard Jacq, Christine Brun:
Defining a Modular Signalling Network from the Fly Interactome. 45 - Susanne Reymann, Jürgen Borlak:
Transcription profiling of lung adenocarcinomas of c-myc-transgenic mice: Identification of the c-myc regulatory gene network. 46 - Julio R. Banga:
Optimization in computational systems biology. 47 - Najl V. Valeyev, Declan G. Bates, Pat Heslop-Harrison, Ian Postlethwaite, Nikolay V. Kotov:
Elucidating the mechanisms of cooperative calcium-calmodulin interactions: a structural systems biology approach. 48 - Xiaodong Huang, Jean Y. J. Wang, Xin Lu:
Systems analysis of quantitative shRNA-library screens identifies regulators of cell adhesion. 49 - David Deutscher, Isaac Meilijson, Stefan Schuster, Eytan Ruppin:
Can single knockouts accurately single out gene functions? 50 - Shigeru Sato, Masanori Arita, Tomoyoshi Soga, Takaaki Nishioka, Masaru Tomita:
Time-resolved metabolomics reveals metabolic modulation in rice foliage. 51 - Joaquín Goñi, Francisco José Esteban, Nieves Vélez de Mendizábal, Jorge Sepulcre, Sergio Ardanza-Trevijano, Ion Agirrezabal, Pablo Villoslada:
A computational analysis of protein-protein interaction networks in neurodegenerative diseases. 52 - Masao Nagasaki, Ayumu Saito, Chen Li, Euna Jeong, Satoru Miyano:
Systematic reconstruction of TRANSPATH data into Cell System Markup Language. 53 - Linqi Zhou, Xiaotu Ma, Fengzhu Sun:
The effects of protein interactions, gene essentiality and regulatory regions on expression variation. 54 - Jeremiah Wright, Andreas Wagner:
The Systems Biology Research Tool: evolvable open-source software. 55 - Liang-Hui Chu, Bor-Sen Chen:
Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets. 56 - Amira Djebbari, John Quackenbush:
Seeded Bayesian Networks: Constructing genetic networks from microarray data. 57 - Xuewei Wang, Ming Wu, Zheng Li, Christina Chan:
Short time-series microarray analysis: Methods and challenges. 58 - João M. L. Dias, Adrian Oehmen, Luísa S. Serafim, Paulo C. Lemos, Maria A. M. Reis, Rui Oliveira:
Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures. 59 - Paula Jouhten, Eija Rintala, Anne Huuskonen, Anu Tamminen, Mervi Toivari, Marilyn Wiebe, Laura Ruohonen, Merja Penttilä, Hannu Maaheimo:
Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A. 60 - Jeremiah Wright, Andreas Wagner:
Exhaustive identification of steady state cycles in large stoichiometric networks. 61 - Julius H. Jackson, Thomas M. Schmidt, Patricia A. Herring:
A systems approach to model natural variation in reactive properties of bacterial ribosomes. 62 - Bülent Yener, Evrim Acar, Phaedra Agius, Kristin P. Bennett, Scott L. Vandenberg, George E. Plopper:
Multiway modeling and analysis in stem cell systems biology. 63 - Zuyi Huang, Fatih Senocak, Arul Jayaraman, Juergen Hahn:
Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data. 64 - Rajat K. De, Mouli Das, Subhasis Mukhopadhyay:
Incorporation of enzyme concentrations into FBA and identification of optimal metabolic pathways. 65 - Laurier Boulianne, Sevin Al Assaad, Michel Dumontier, Warren J. Gross:
GridCell: a stochastic particle-based biological system simulator. 66 - Kitiporn Plaimas, Jan-Phillip Mallm, Marcus Oswald, Fabian Svara, Victor Sourjik, Roland Eils, Rainer König:
Machine learning based analyses on metabolic networks supports high-throughput knockout screens. 67 - Liu Yang, Janet C. Effler, Brett L. Kutscher, Sarah E. Sullivan, Douglas N. Robinson, Pablo A. Iglesias:
Modeling cellular deformations using the level set formalism. 68 - Oranit Dror, Dina Schneidman-Duhovny, Alexandra Shulman-Peleg, Ruth Nussinov, Haim J. Wolfson, Roded Sharan:
Structural similarity of genetically interacting proteins. 69 - Chin-Rang Yang:
An enzyme-centric approach for modelling non-linear biological complexity. 70 - Intawat Nookaew, Michael C. Jewett, Asawin Meechai, Chinae Thammarongtham, Kobkul Laoteng, Supapon Cheevadhanarak, Jens Nielsen, Sakarindr Bhumiratana:
The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. 71 - Wei Jiang, Xia Li, Shaoqi Rao, Lihong Wang, Lei Du, Chuanxing Li, Chao Wu, Hongzhi Wang, Yadong Wang, Baofeng Yang:
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. 72 - Arun Siddharth Konagurthu, Arthur M. Lesk:
On the origin of distribution patterns of motifs in biological networks. 73 - Armen Kherlopian, Ting Song, Qi Duan, Matthew A. Neimark, Ming Jack Po, John K. Gohagan, Andrew F. Laine:
A review of imaging techniques for systems biology. 74 - Carole J. Proctor, Douglas A. Gray:
Explaining oscillations and variability in the p53-Mdm2 system. 75 - Derek A. Ruths, Luay Nakhleh, Prahlad T. Ram:
Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle. 76 - Marianne O. Stefanini, Florence T. H. Wu, Feilim Mac Gabhann, Aleksander S. Popel:
A compartment model of VEGF distribution in blood, healthy and diseased tissues. 77 - Holger Conzelmann, Dirk Fey, Ernst Dieter Gilles:
Exact model reduction of combinatorial reaction networks. 78 - Juan Nogales, Bernhard Ø. Palsson, Ines Thiele:
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. 79 - Michael Hsing, Kendall G. Byler, Artem Cherkasov:
The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks. 80 - Carsten O. Daub, Erik L. L. Sonnhammer:
Employing conservation of co-expression to improve functional inference. 81 - Kazuhiro Takemoto, Tatsuya Akutsu:
Origin of structural difference in metabolic networks with respect to temperature. 82 - Maksat Ashyraliyev, Johannes Jaeger, Joke G. Blom:
Parameter estimation and determinability analysis applied to Drosophila gap gene circuits. 83 - Shigeru Saito, Sachiyo Aburatani, Katsuhisa Horimoto:
Network evaluation from the consistency of the graph structure with the measured data. 84 - Maxime Durot, François Le Fèvre, Véronique de Berardinis, Annett Kreimeyer, David Vallenet, Cyril Combe, Serge Smidtas, Marcel Salanoubat, Jean Weissenbach, Vincent Schächter:
Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data. 85 - Ovidiu Radulescu, Alexander N. Gorban, Andrei Yu. Zinovyev, Alain Lilienbaum:
Robust simplifications of multiscale biochemical networks. 86 - Tobias von der Haar:
A quantitative estimation of the global translational activity in logarithmically growing yeast cells. 87 - Ashley J. Waardenberg, Antonio Reverter, Christine A. Wells, Brian P. Dalrymple:
Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle. 88 - Jiangjun Cui, Jaap A. Kaandorp, Catherine M. Lloyd:
Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli. 89 - Michal Kolár, Michael Lässig, Johannes Berg:
From protein interactions to functional annotation: graph alignment in Herpes. 90 - Markus Koschorreck, Ernst Dieter Gilles:
ALC: automated reduction of rule-based models. 91 - Julio Vera, Thomas Millat, Walter Kolch, Olaf Wolkenhauer:
Dynamics of receptor and protein transducer homodimerisation. 92 - Ioannis A. Maraziotis, Konstantina Dimitrakopoulou, Anastasios Bezerianos:
An in silico method for detecting overlapping functional modules from composite biological networks. 93 - Cheol-Min Ghim, Eivind Almaas:
Genetic noise control via protein oligomerization. 94 - Angela P. Presson, Eric M. Sobel, Jeanette C. Papp, Charlyn J. Suarez, Toni Whistler, Mangalathu S. Rajeevan, Suzanne D. Vernon, Steve Horvath:
Integrated Weighted Gene Co-expression Network Analysis with an Application to Chronic Fatigue Syndrome. 95 - I. King Jordan, Lee S. Katz, Dee R. Denver, J. Todd Streelman:
Natural selection governs local, but not global, evolutionary gene coexpression networks in Caenorhabditis elegans. 96 - Vinay Prasad, Kareenhalli V. Venkatesh:
Stochastic analysis of the GAL genetic switch in Saccharomyces cerevisiae: Modeling and experiments reveal hierarchy in glucose repression. 97 - Mariana Benítez, Carlos Espinosa-Soto, Pablo Padilla-Longoria, Elena R. Álvarez-Buylla:
Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model. 98 - Gwenael Kervizic, Laurent Corcos:
Dynamical modeling of the cholesterol regulatory pathway with Boolean networks. 99 - Pawel Durek, Dirk Walther:
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. 100 - Christopher R. Bauer, Andrew M. Epstein, Sarah J. Sweeney, Daniela C. Zarnescu, Giovanni Bosco:
Genetic and systems level analysis of Drosophila sticky/citron kinase and dFmr1 mutants reveals common regulation of genetic networks. 101 - Dawn C. Walker, Nikolaos T. Georgopoulos, Jennifer Southgate:
From pathway to population - a multiscale model of juxtacrine EGFR-MAPK signalling. 102 - Bor-Sen Chen, Yu-Te Chang:
A systematic molecular circuit design method for gene networks under biochemical time delays and molecular noises. 103 - Georgios A. Pavlopoulos, Seán I. O'Donoghue, Venkata P. Satagopam, Theodoros G. Soldatos, Evangelos Pafilis, Reinhard Schneider:
Arena3D: visualization of biological networks in 3D. 104 - Marian Groenenboom, Paulien Hogeweg:
RNA silencing can explain chlorotic infection patterns on plant leaves. 105 - André Fujita, Luciana Rodrigues Gomes, João Ricardo Sato, Rui Yamaguchi, Carlos E. Thomaz, Mari Cleide Sogayar, Satoru Miyano:
Multivariate gene expression analysis reveals functional connectivity changes between normal/tumoral prostates. 106 - Mark Kühnel, Luis S. Mayorga, Thomas Dandekar, Juilee Thakar, Roland Schwarz, Elsa Anes, Gareth Griffiths, Jens G. Reich:
Modelling phagosomal lipid networks that regulate actin assembly. 107 - Jason W. Locasale:
Signal duration and the time scale dependence of signal integration in biochemical pathways. 108 - Karthik Raman, Kalidas Yeturu, Nagasuma R. Chandra:
targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. 109 - Jesse Engelberg, Glen E. P. Ropella, C. Anthony Hunt:
Essential operating principles for tumor spheroid growth. 110 - Yunlei Li, Dick de Ridder, Marco J. L. de Groot, Marcel J. T. Reinders:
Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. 111
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