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ORCIDBMC Systems Biology, Volume 3
Volume 3, 2009
- 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, Dorit Arlt:
Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. 1 - Robert Modre-Osprian, Ingrid Osprian, Bernhard Tilg, Günter Schreier, Klaus Weinberger, Armin Graber:
Dynamic simulations on the mitochondrial fatty acid Beta-oxidation network. 2 - Shai Carmi, Erez Y. Levanon, Eli Eisenberg:
Efficiency of complex production in changing environment. 3 - Nanette R. Boyle, John A. Morgan:
Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii. 4 - Andreas Dräger, Marcel Kronfeld, Michael J. Ziller, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, Oliver Kohlbacher, Andreas Zell:
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. 5 - Carmen Kut, Vahid Golkhou, Joel S. Bader:
Analytical approximations for the amplitude and period of a relaxation oscillator. 6 - Tobias S. Christensen, Ana Oliveira, Jens Nielsen:
Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae. 7 - Jan Baumbach, Sven Rahmann, Andreas Tauch:
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms. 8 - Tom Lenaerts, Jesper Ferkinghoff-Borg, Joost Schymkowitz, Frederic Rousseau:
Information theoretical quantification of cooperativity in signalling complexes. 9 - Avi Ma'ayan, Sherry L. Jenkins, Ryan L. Webb, Seth I. Berger, Sudarshan P. Purushothaman, Noura S. Abul-Husn, Jeremy M. Posner, Tony Flores, Ravi Iyengar:
SNAVI: Desktop application for analysis and visualization of large-scale signaling networks. 10 - Farhan Mohammad, Priyanka Singh, Abhay Sharma:
A Drosophila systems model of pentylenetetrazole induced locomotor plasticity responsive to antiepileptic drugs. 11 - Catherine F. Higham:
Bifurcation analysis informs Bayesian inference in the Hes1 feedback loop. 12 - Amina A. Qutub, Aleksander S. Popel:
Elongation, proliferation & migration differentiate endothelial cell phenotypes and determine capillary sprouting. 13 - Hadar Less, Gad Galili:
Coordinations between gene modules control the operation of plant amino acid metabolic networks. 14 - Jun Sun, Bahareh Sayyar, Jessica E. Butler, Priti Pharkya, Tom Fahland, Iman Famili, Christophe H. Schilling, Derek R. Lovley, Radhakrishnan Mahadevan:
Genome-scale constraint-based modeling of Geobacter metallireducens. 15 - Reiner A. Veitia:
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. 16 - Donatella Cimini, Kiran Raosaheb Patil, Chiara Schiraldi, Jens Nielsen:
Global transcriptional response of Saccharomyces cerevisiae to the deletion of SDH3. 17 - Nicola Soranzo, Mattia Zampieri, Lorenzo Farina, Claudio Altafini:
mRNA stability and the unfolding of gene expression in the long-period yeast metabolic cycle. 18 - Reza Mobini, Bengt A. Andersson, Jonas Erjefält, Mirjana Hahn-Zoric, Michael A. Langston, Andy D. Perkins, Lars Cardell, Mikael Benson:
A module-based analytical strategy to identify novel disease-associated genes shows an inhibitory role for interleukin 7 Receptor in allergic inflammation. 19 - Albert C. Huang, Limei Hu, Stuart A. Kauffman, Wei Zhang, Ilya Shmulevich:
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. 20 - Qinghua Cui, Enrico O. Purisima, Edwin Wang:
Protein evolution on a human signaling network. 21 - Fan Wu, Daniel A. Beard:
Roles of the creatine kinase system and myoglobin in maintaining energetic state in the working heart. 22 - Yukuto Sato, Yasuyuki Hashiguchi, Mutsumi Nishida:
Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. 23 - Gavin H. Thomas, Jeremy Zucker, Sandy J. Macdonald, Anatoly A. Sorokin, Igor Goryanin, Angela E. Douglas:
A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola. 24 - Elias August, Antonis Papachristodoulou:
Efficient, sparse biological network determination. 25 - Jussi Paananen, Garry Wong:
FORG3D: Force-directed 3D graph editor for visualization of integrated genome scale data. 26 - Laurence Loewe:
A framework for evolutionary systems biology. 27 - Chang Shin, Simon Wong, Melissa J. Davis, Mark A. Ragan:
Protein-protein interaction as a predictor of subcellular location. 28 - Axel Cournac, Jacques-A. Sepulchre:
Simple molecular networks that respond optimally to time-periodic stimulation. 29 - Christian L. Barrett, Markus J. Herrgård, Bernhard Ø. Palsson:
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation. 30 - Jesse J. Smith, Renée 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, Olivier Boss:
Small molecule activators of SIRT1 replicate signaling pathways triggered by calorie restriction in vivo. 31 - Wen-hsien Lin, Wei-Chung Liu, Ming-Jing Hwang:
Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. 32 - Seongwon Seo, Harris A. Lewin:
Reconstruction of metabolic pathways for the cattle genome. 33 - Peter Saffrey, Richard Orton:
Version control of pathway models using XML patches. 34 - Frank Emmert-Streib, Matthias Dehmer:
Information processing in the transcriptional regulatory network of yeast: Functional robustness. 35 - Zoltán Dezsö, Yuri Nikolsky, Tatiana Nikolskaya, Jeremy Miller, David Cherba, Craig Webb, Andrej Bugrim:
Identifying disease-specific genes based on their topological significance in protein networks. 36 - Monica L. Mo, Bernhard Ø. Palsson, Markus J. Herrgård:
Connecting extracellular metabolomic measurements to intracellular flux states in yeast. 37 - Anu Raghunathan, Jennifer L. Reed, Sook-Il Shin, Bernhard Ø. Palsson, Simon Daefler:
Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. 38 - Hossein Zare, Dipen Sangurdekar, Poonam Srivastava, Mostafa Kaveh, Arkady B. Khodursky:
Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations. 39 - Maria Luisa Guerriero, Anna Dudka, Nicholas Underhill-Day, John K. Heath, Corrado Priami:
Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway. 40 - Teppei Shimamura, Seiya Imoto, Rui Yamaguchi, André Fujita, Masao Nagasaki, Satoru Miyano:
Recursive regularization for inferring gene networks from time-course gene expression profiles. 41 - Chen Li, Masao Nagasaki, Kazuko Ueno, Satoru Miyano:
Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. 42 - Le Lu, Jinming Li:
A combinatorial approach to determine the context-dependent role in transcriptional and posttranscriptional regulation in Arabidopsis thaliana. 43 - Neema Jamshidi, Bernhard O. Palsson:
Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes. 44 - Amitabha Nandi, Candida Vaz, Alok Bhattacharya, Ramakrishna Ramaswamy:
miRNA-regulated dynamics in circadian oscillator models. 45 - Julia M. Gohlke, Reuben Thomas, Yonqing Zhang, Michael C. Rosenstein, Allan Peter Davis, Cynthia G. Murphy, Kevin G. Becker, Carolyn J. Mattingly, Christopher J. Portier:
Genetic and environmental pathways to complex diseases. 46 - Marco Vilela, Susana Vinga, Marco Maia, Eberhard O. Voit, Jonas S. Almeida:
Identification of neutral biochemical network models from time series data. 47 - José Díaz, Elena R. Álvarez-Buylla:
Information flow during gene activation by signaling molecules: ethylene transduction in Arabidopsis cells as a study system. 48 - Tom Michoel, Riet De Smet, Anagha Joshi, Yves Van de Peer, Kathleen Marchal:
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks. 49 - Tom Quaiser, Martin Mönnigmann:
Systematic identifiability testing for unambiguous mechanistic modeling - application to JAK-STAT, MAP kinase, and NF-κB signaling pathway models. 50 - Lan K. Nguyen, Don Kulasiri:
On the functional diversity of dynamical behaviour in genetic and metabolic feedback systems. 51 - Seth B. Roberts, Jennifer L. Robichaux, Arvind K. Chavali, Patricio A. Manque, Vladimir Lee, Ana M. Lara, Jason A. Papin, Gregory A. Buck:
Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi. 52 - Björn Goemann, Edgar Wingender, Anatolij Potapov:
An approach to evaluate the topological significance of motifs and other patterns in regulatory networks. 53 - Younhee Ko, ChengXiang Zhai, Sandra L. Rodriguez-Zas:
Inference of gene pathways using mixture Bayesian networks. 54 - Jen-hwa Chu, Scott T. Weiss, Vincent J. Carey, Benjamin A. Raby:
A graphical model approach for inferring large-scale networks integrating gene expression and genetic polymorphism. 55 - Jesper Tegnér, Albert Compte, Charles Auffray, Gary An, Gunnar Cedersund, Gilles Clermont, Boris S. Gutkin, Zoltán N. Oltvai, Klaas Enno Stephan, Randy Thomas, Pablo Villoslada:
Computational disease modeling - fact or fiction? 56 - Maria A. Doyle, James I. MacRae, David P. De Souza, Eleanor C. Saunders, Malcolm J. McConville, Vladimir A. Likic:
LeishCyc: a biochemical pathways database for Leishmania major. 57 - Tomás Helikar, Jim A. Rogers:
ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists. 58 - Damion Nero, Gabriel Krouk, Daniel Tranchina, Gloria M. Coruzzi:
A system biology approach highlights a hormonal enhancer effect on regulation of genes in a nitrate responsive "biomodule". 59 - Josef Thingnes, Leiv Øyehaug, Eivind Hovig, Stig W. Omholt:
The mathematics of tanning. 60 - Xiaoning Qian, Ivan Ivanov, Noushin Ghaffari, Edward R. Dougherty:
Intervention in gene regulatory networks via greedy control policies based on long-run behavior. 61 - Patricia Buendia, Giri Narasimhan:
Serial evolutionary networks of within-patient HIV-1 sequences reveal patterns of evolution of X4 strains. 62 - Ignacio Rodriguez-Llorente, Miguel A. Caviedes, Mohammed Dary, Antonio J. Palomares, Francisco M. Cánovas, José M. Peregrín-Alvarez:
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti. 63 - John M. Frazier, Yaroslav Chushak, Brent D. Foy:
Stochastic simulation and analysis of biomolecular reaction networks. 64 - Xiongying Yuan, Changning Liu, Pengcheng Yang, Shunmin He, Qi Liao, Shuli Kang, Yi Zhao:
Clustered microRNAs' coordination in regulating protein-protein interaction network. 65 - Bor-Sen Chen, Chih-Hung Wu:
A systematic design method for robust synthetic biology to satisfy design specifications. 66 - Jochen Supper, Lucía Spangenberg, Hannes Planatscher, Andreas Dräger, Adrian Schröder, Andreas Zell:
BowTieBuilder: modeling signal transduction pathways. 67 - Melanie I. Stefan, Stuart J. Edelstein, Nicolas Le Novère:
Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. 68 - Antonio Marco, Ignacio Marín:
Interactome and Gene Ontology provide congruent yet subtly different views of a eukaryotic cell. 69 - Thomas Williamson, Jean-Marc Schwartz, Douglas B. Kell, Lubomira Stateva:
Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae. 70 - Johannes Witt, Sandra Barisic, Eva Schumann, Frank Allgöwer, Oliver Sawodny, Thomas Sauter, Dagmar Kulms:
Mechanism of PP2A-mediated IKKβ dephosphorylation: a systems biological approach. 71 - Evan Mills, Kevin Truong:
Cascading signaling pathways improve the fidelity of a stochastically and deterministically simulated molecular RS latch. 72 - Huaxia Qin, Michael W. Y. Chan, Sandya Liyanarachchi, Curtis Balch, Dustin P. Potter, Irene J. Souriraj, Alfred S. L. Cheng, Francisco J. Agosto-Perez, Elena Nikonova, Pearlly Yan, Huey-Jen Lin, Kenneth P. Nephew, Joel H. Saltz, Louise C. Showe, Tim Hui-Ming Huang, Ramana V. Davuluri:
An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules. 73 - Roland A. Pache, M. Madan Babu, Patrick Aloy:
Exploiting gene deletion fitness effects in yeast to understand the modular architecture of protein complexes under different growth conditions. 74 - Jeffrey M. Dick:
Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae. 75 - Frank Emmert-Streib, Matthias Dehmer:
Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae. 76 - Johannes Wollbold, René Huber, Dirk Pohlers, Dirk Koczan, Reinhard Guthke, Raimund W. Kinne, Ulrike Gausmann:
Adapted Boolean network models for extracellular matrix formation. 77 - Junhee Seok, Wenzhong Xiao, Lyle L. Moldawer, Ronald W. Davis, Markus W. Covert:
A dynamic network of transcription in LPS-treated human subjects. 78 - Francisco Llaneras, Antonio Sala, Jesús Picó:
A possibilistic framework for constraint-based metabolic flux analysis. 79 - Armand Bankhead, Iliana Sach, Chester Ni, Nolwenn LeMeur, Mark Kruger, Marc Ferrer, Robert Gentleman, Carol Rohl:
Knowledge based identification of essential signaling from genome-scale siRNA experiments. 80 - Alexei Vazquez:
Optimal drug combinations and minimal hitting sets. 81 - Heiko Neuweger, Marcus Persicke, Stefan P. Albaum, Thomas Bekel, Michael Dondrup, Andrea T. Hüser, Jörn Winnebald, Jessica Schneider, Jörn Kalinowski, Alexander Goesmann:
Visualizing post genomics data-sets on customized pathway maps by ProMeTra - aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. 82 - Clemens Kühn, Christoph K. Wierling, Alexander Kühn, Edda Klipp, Georgia Panopoulou, Hans Lehrach, Albert J. Poustka:
Monte Carlo analysis of an ODE Model of the Sea Urchin Endomesoderm Network. 83 - Javier Macía, Stefanie Widder, Ricard V. Solé:
Specialized or flexible feed-forward loop motifs: a question of topology. 84 - Chris J. Needham, Iain W. Manfield, Andrew J. Bulpitt, Philip M. Gilmartin, David R. Westhead:
From gene expression to gene regulatory networks in Arabidopsis thaliana. 85 - Osnat Atias, Benny Chor, Daniel A. Chamovitz:
Large-scale analysis of Arabidopsis transcription reveals a basal co-regulation network. 86 - Harald Martens, Siren R. Veflingstad, Erik Plahte, Magni Martens, Dominique Bertrand, Stig W. Omholt:
The genotype-phenotype relationship in multicellular pattern-generating models - the neglected role of pattern descriptors. 87 - Rafal Zielinski, Pawel F. Przytycki, Jie Zheng, David Zhang, Teresa M. Przytycka, Jacek Capala:
The crosstalk between EGF, IGF, and Insulin cell signaling pathways - computational and experimental analysis. 88 - Alina Crudu, Arnaud Debussche, Ovidiu Radulescu:
Hybrid stochastic simplifications for multiscale gene networks. 89 - Thomas Wilhelm:
The smallest chemical reaction system with bistability. 90 - Jacob D. Feala, Laurence Coquin, Dan Zhou, Gabriel G. Haddad, Giovanni Paternostro, Andrew D. McCulloch:
Metabolism as means for hypoxia adaptation: metabolic profiling and flux balance analysis. 91 - Xin Fang, Anders Wallqvist, Jaques Reifman:
A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis. 92 - Pierre R. Bushel, Nicholas A. Heard, Roee Gutman, Liwen Liu, Shyamal D. Peddada, Saumyadipta Pyne:
Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle. 93 - Yves Fomekong-Nanfack, Marten Postma, Jaap A. Kaandorp:
Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis. 94 - Reza Ghaemi, Jing Sun, Pablo A. Iglesias, Domitilla Del Vecchio:
A method for determining the robustness of bio-molecular oscillator models. 95 - Dan Siegal-Gaskins, Erich Grotewold, Gregory D. Smith:
The capacity for multistability in small gene regulatory networks. 96 - Nicole Philippi, Dorothee Walter, Rebekka Schlatter, Karine Ferreira, Michael Ederer, Oliver Sawodny, Jens Timmer, Christoph Borner, Thomas Dandekar:
Modeling system states in liver cells: Survival, apoptosis and their modifications in response to viral infection. 97 - Dominik M. Wittmann, Jan Krumsiek, Julio Saez-Rodriguez, Douglas A. Lauffenburger, Steffen Klamt, Fabian J. Theis:
Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. 98 - Robert W. Byrnes, Dawn Cotter, Andreia Maer, Joshua Li, David Nadeau, Shankar Subramaniam:
An editor for pathway drawing and data visualization in the Biopathways Workbench. 99 - Richard J. Orton, Michiel E. Adriaens, Amelie Gormand, Oliver E. Sturm, Walter Kolch, David R. Gilbert:
Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. 100 - Ramon Grima:
Investigating the robustness of the classical enzyme kinetic equations in small intracellular compartments. 101 - Gabriel del Rio, Dirk Koschützki, Gerardo Coello:
How to identify essential genes from molecular networks? 102 - Esa Pitkänen, Paula Jouhten, Juho Rousu:
Inferring branching pathways in genome-scale metabolic networks. 103 - Paula Jouhten, Esa Pitkänen, Tiina Pakula, Markku Saloheimo, Merja Penttilä, Hannu Maaheimo:
13C-metabolic flux ratio and novel carbon path analyses confirmed that Trichoderma reesei uses primarily the respirative pathway also on the preferred carbon source glucose. 104 - Mark A. J. Roberts, Elias August, Abdullah Hamadeh, Philip K. Maini, Patrick E. McSharry, Judith P. Armitage, Antonis Papachristodoulou:
A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroides. 105 - Pingzhao Hu, Celia M. T. Greenwood, Joseph Beyene:
Using the ratio of means as the effect size measure in combining results of microarray experiments. 106 - Nadav S. Bar, Nicole Radde:
Long-term prediction of fish growth under varying ambient temperature using a multiscale dynamic model. 107 - Carmen Pin, Matthew D. Rolfe, Marina Muñoz-Cuevas, Jay C. D. Hinton, Michael W. Peck, Nicholas J. Walton, József Baranyi:
Network analysis of the transcriptional pattern of young and old cells of Escherichia coli during lag phase. 108 - Diogo F. Veiga, Helena F. Deus, Caner Akdemir, Ana Tereza Ribeiro de Vasconcelos, Jonas S. Almeida:
DASMiner: discovering and integrating data from DAS sources. 109 - Shun-Fu Chen, Yue-Li Juang, Wei-Kang Chou, Jin-Mei Lai, Chi-Ying F. Huang, Cheng-Yan Kao, Feng-Sheng Wang:
Inferring a transcriptional regulatory network of the cytokinesis-related genes by network component analysis. 110 - Yusuke Azuma, Motonori Ota:
An evaluation of minimal cellular functions to sustain a bacterial cell. 111 - Konstantin Voevodski, Shang-Hua Teng, Yu Xia:
Spectral affinity in protein networks. 112 - Jianhua Wu, James L. Sinfield, Vicky Buchanan-Wollaston, Jianfeng Feng:
Impact of environmental inputs on reverse-engineering approach to network structures. 113 - Reed L. Taffs, John E. Aston, Kristen Brileya, Zackary Jay, Christian G. Klatt, Shawn E. McGlynn, Natasha Mallette, Scott Montross, Robin Gerlach, William P. Inskeep, David M. Ward, Ross P. Carlson:
In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. 114 - Einat Sprinzak, Shawn Cokus, Todd O. Yeates, David Eisenberg, Matteo Pellegrini:
Detecting coordinated regulation of multi-protein complexes using logic analysis of gene expression. 115 - Núria Conde-Pueyo, Andreea Munteanu, Ricard V. Solé, Carlos Rodríguez-Caso:
Human synthetic lethal inference as potential anti-cancer target gene detection. 116 - Bevan Chung, Dong-Yup Lee:
Flux-sum analysis: a metabolite-centric approach for understanding the metabolic network. 117 - Dennis Y. Q. Wang, Luca Cardelli, Andrew Phillips, Nir Piterman, Jasmin Fisher:
Computational modeling of the EGFR network elucidates control mechanisms regulating signal dynamics. 118 - Nikolaus Sonnenschein, Marc-Thorsten Hütt, Helga Stoyan, Dietrich Stoyan:
Ranges of control in the transcriptional regulation of Escherichia coli. 119 - Guido Melzer, Manely Esfandabadi, Ezequiel Franco-Lara, Christoph Wittmann:
Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties. 120 - Rishi Jain, Ranjan Srivastava:
Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli. 121 - Sean H. J. Kim, Jayanta Debnath, Keith E. Mostov, Sunwoo Park, C. Anthony Hunt:
A computational approach to resolve cell level contributions to early glandular epithelial cancer progression. 122
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