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BMC Systems Biology, Volume 8
Volume 8, 2014
- Gundián M. de Hijas-Liste, Edda Klipp, Eva Balsa-Canto
, Julio R. Banga
Global dynamic optimization approach to predict activation in metabolic pathways. 1 - Masataka Sasabe, Sayumi Shintani, Reiko Kintaka, Kazunari Kaizu, Koji Makanae
Evaluation of the lower protein limit in the budding yeast Saccharomyces cerevisiae using TIPI-gTOW. 2 - Zhenzhen Zheng, Scott Christley, William T. Chiu, Ira L. Blitz, Xiaohui Xie, Ken W. Y. Cho, Qing Nie:
Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. 3 - Austin W. T. Chiang, Wei-Chung Liu
Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters. 4 - Wei-Po Lee, Yu-Ting Hsiao, Wei-Che Hwang:
Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment. 5 - Emad Fadhal
Protein interaction networks as metric spaces: a novel perspective on distribution of hubs. 6 - Lisa M. Christadore, Lisa Pham, Eric D. Kolaczyk, Scott E. Schaus:
Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets. 7 - Oumarou Abdou-Arbi, Sophie Lemosquet, Jaap Van Milgen
Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. 8 - Carlos Espinosa-Soto
Tetramer formation in Arabidopsis MADS domain proteins: analysis of a protein-protein interaction network. 9 - Aaron Ingham
RNF14 is a regulator of mitochondrial and immune function in muscle. 10 - Timothy R. Sands:
Annual Acknowledgement of Reviewers. 11 - Nadia M. Penrod, Jason H. Moore
Influence networks based on coexpression improve drug target discovery for the development of novel cancer therapeutics. 12 - Pablo Meyer, Thomas Cokelaer
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. 13 - Wei Zhu, Yi-Ping Phoebe Chen
Computational developments in microRNA-regulated protein-protein interactions. 14 - Charles C. N. Wang, Pei-Chun Chang, Ka-Lok Ng, Chun-Ming Chang, Phillip C.-Y. Sheu
A model comparison study of the flowering time regulatory network in Arabidopsis. 15 - Erno Lindfors
Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae. 16 - Gabriel N. Teku
Identification of core T cell network based on immunome interactome. 17 - Ferdi L. Hellweger, Neil D. Fredrick, John A. Berges
Age-correlated stress resistance improves fitness of yeast: support from agent-based simulations. 18 - Zijun Luo, Robert Azencott, Yi Zhao:
Modeling miRNA-mRNA interactions: fitting chemical kinetics equations to microarray data. 19 - Joep Vanlier, Christian A. Tiemann, Peter A. J. Hilbers, Natal A. W. van Riel
Optimal experiment design for model selection in biochemical networks. 20 - Jialiang Yang
Quartet-based methods to reconstruct phylogenetic networks. 21 - Georg R. Walther, Matthew Hartley
GraTeLPy: graph-theoretic linear stability analysis. 22 - Andrew E. Blanchard, Venhar Celik
Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition. 23 - Edgar D. Coelho, Joel Arrais
Computational prediction of the human-microbial oral interactome. 24 - Yun-Bo Zhao
mRNA translation and protein synthesis: an analysis of different modelling methodologies and a new PBN based approach. 25 - Shubhada R. Hegde, Khushbu Pal, Shekhar C. Mande:
Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions. 26 - Ala Trusina
Stress induced telomere shortening: longer life with less mutations? 27 - Sudhakar Jonnalagadda, Rajagopalan Srinivasan:
An efficient graph theory based method to identify every minimal reaction set in a metabolic network. 28 - Hernan Roca, Manjusha Pande, Jeffrey S. Huo
A bioinformatics approach reveals novel interactions of the OVOL transcription factors in the regulation of epithelial - mesenchymal cell reprogramming and cancer progression. 29 - Geoffroy Andrieux
An integrative modeling framework reveals plasticity of TGF-β signaling. 30 - Wai Ong, Trang T. Vu, Klaus N. Lovendahl
Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. 31 - Pierre Blavy, Florence Gondret
Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism. 32 - Amanda M. Lanza, Kathleen A. Curran, Lindsey G. Rey, Hal S. Alper:
A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae. 33 - Benjamin Garcia
Network and matrix analysis of the respiratory disease interactome. 34 - Wei Peng, Jianxin Wang, Juan Cai, Lu Chen, Min Li, Fang-Xiang Wu
Improving protein function prediction using domain and protein complexes in PPI networks. 35 - Christopher G. Hill, Lilya V. Matyunina, L. DeEtte Walker, Benedict B. Benigno, John F. McDonald:
Transcriptional override: a regulatory network model of indirect responses to modulations in microRNA expression. 36 - Paola Vera-Licona
An Algebra-Based Method for Inferring Gene Regulatory Networks. 37 - Emma Kate Mullen, Mark Daley, Alanna Gabrielle Backx, Graham James Thompson:
Gene co-citation networks associated with worker sterility in honey bees. 38 - Tong Hao, Zheng Zeng, Bin Wang, Yichen Zhang, Yichen Liu, Xuyun Geng, Jinsheng Sun:
The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis. 39 - Mohammed El-Kebir
A web server for protein-protein interaction network querying. 40 - Ibrahim E. El-Semman
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. 41 - Alida Palmisano
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. 42 - Berta Verd
Classification of transient behaviours in a time-dependent toggle switch model. 43 - Chin Wee Tan
Analysis of Wnt signaling β-catenin spatial dynamics in HEK293T cells. 44 - Kaier Wang, Moira L. Steyn-Ross, D. A. Steyn-Ross, Marcus T. Wilson, Jamie W. Sleigh, Yoichi Shiraishi:
Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK. 45 - Rikard Johansson
Combining test statistics and models in bootstrapped model rejection: it is a balancing act. 46 - William Chad Young, Adrian E. Raftery, Ka Yee Yeung
Fast Bayesian inference for gene regulatory networks using ScanBMA. 47 - Aditya Barve, Sayed-Rzgar Hosseini
Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms. 48 - Jürgen Dönitz
EndoNet: an information resource about the intercellular signaling network. 49 - Averina Nicolae, Judith Wahrheit, Janina Bahnemann
Non-stationary 13C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation. 50 - Xueming Liu, Linqiang Pan
Detection of driver metabolites in the human liver metabolic network using structural controllability analysis. 51 - Shodhan Rao
A model reduction method for biochemical reaction networks. 52 - Colin Campbell
Stabilization of perturbed Boolean network attractors through compensatory interactions. 53 - Eleftherios Ouzounoglou
In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis. 54 - Khalid Abnaof, Nikhil Mallela, Gudrun Walenda, Steffen Meurer, Kristin Seré, Qiong Lin
TGF-beta stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level. 55 - Rosario M. Piro
Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. 56 - Feng-Jen Tseng, Wei-Tso Chia
Interactomics profiling of the negative regulatory function of carbon monoxide on RANKL-treated RAW 264.7 cells during osteoclastogenesis. 57 - Ricardo Alberich
MP-Align: alignment of metabolic pathways. 58 - Kristin Tøndel, Steven A. Niederer
Insight into model mechanisms through automatic parameter fitting: a new methodological framework for model development. 59 - Peican Zhu
Gene perturbation and intervention in context-sensitive stochastic Boolean networks. 60 - Dicle Hasdemir, Huub C. J. Hoefsloot, Johan A. Westerhuis, Age K. Smilde
How informative is your kinetic model?: using resampling methods for model invalidation. 61 - Kathryn Dempsey, Hesham H. Ali:
Identifying aging-related genes in mouse hippocampus using gateway nodes. 62 - Chia-Hua Chuang, Chun-Liang Lin:
Synthesizing genetic sequential logic circuit with clock pulse generator. 63 - Joshua L. Payne
Latent phenotypes pervade gene regulatory circuits. 64 - Laura Caberlotto, Thanh-Phuong Nguyen:
A systems biology investigation of neurodegenerative dementia reveals a pivotal role of autophagy. 65 - Martin R. Nelson
STI-GMaS: an open-source environment for simulation of sexually-transmitted infections. 66 - Magdalena San Román
Source and regulation of flux variability in Escherichia coli. 67 - Emad Fadhal
Modelling human protein interaction networks as metric spaces has potential in disease research and drug target discovery. 68 - Ruijie Song, Ping Liu, Murat Acar:
Network-dosage compensation topologies as recurrent network motifs in natural gene networks. 69 - Hsueh-Chien Cheng, Bastian Robert Angermann, Fengkai Zhang
NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules. 70 - Tamás Székely
Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch-Stoer extrapolation method. 71 - Jean-Eudes J. Dazard
Metabolomics of Apc Min/+ mice genetically susceptible to intestinal cancer. 72 - Lifang Liu, Amir Feizi, Tobias Österlund, Carsten Hjort, Jens Nielsen
Genome-scale analysis of the high-efficient protein secretion system of Aspergillus oryzae. 73 - Trish P. Tran, Edison Ong
Prediction of kinase inhibitor response using activity profiling, in vitro screening, and elastic net regression. 74 - Silvia von der Heyde, Christian Bender, Frauke Henjes, Johanna Sonntag
Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines. 75 - Jérémy Hamon, Paul Jennings
Systems biology modeling of omics data: effect of cyclosporine a on the Nrf2 pathway in human renal cells. 76 - Farzaneh Farhangmehr, Mano Ram Maurya, Daniel M. Tartakovsky
Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages. 77 - Jen-hwa Chu
Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD. 78 - Daniel S. Weaver, Ingrid M. Keseler, Amanda Mackie, Ian T. Paulsen
A genome-scale metabolic flux model of Escherichia coli K-12 derived from the EcoCyc database. 79 - Hnin H. Aung, Athanasios Tsoukalas, John C. Rutledge, Ilias Tagkopoulos:
A systems biology analysis of brain microvascular endothelial cell lipotoxicity. 80 - Alok Srivastava, Suraj Kumar, Ramakrishna Ramaswamy
Two-layer modular analysis of gene and protein networks in breast cancer. 81 - Xiaochuang Luo, Jingyi Gu, Rongxuan Zhu, Maoxiao Feng, Xuejiao Zhu, Yumin Li, Jia Fei:
Integrative analysis of differential miRNA and functional study of miR-21 by seed-targeting inhibition in multiple myeloma cells in response to berberine. 82 - Paola Paci, Teresa Colombo
Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer. 83 - Luca Cardelli
Morphisms of reaction networks that couple structure to function. 84 - Rafael S. Costa
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. 85 - Niti Vanee, J. Paul Brooks, Victor Spicer, Dmitriy Shamshurin, Oleg Krokhin, John A. Wilkins, Yu Deng, Stephen S. Fong:
Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca. 86 - Ye Tian, Bai Zhang, Eric P. Hoffman
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. 87 - Orit Lavi, Jeff Skinner
Network features suggest new hepatocellular carcinoma treatment strategies. 88 - Iman Habibi, Effat S. Emamian, Ali Abdi:
Quantitative analysis of intracellular communication and signaling errors in signaling networks. 89 - Ceyda Kasavi
A system based network approach to ethanol tolerance in Saccharomyces cerevisiae. 90 - Sarala M. Wimalaratne
BioModels linked dataset. 91 - Naomi Kochi, Tomás Helikar
Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions. 92 - Mikyung Lee, Zhichao Liu, Reagan Kelly, Weida Tong:
Of text and gene - using text mining methods to uncover hidden knowledge in toxicogenomics. 93 - Lake-Ee Quek
A depth-first search algorithm to compute elementary flux modes by linear programming. 94 - Brenden K. Petersen
Toward modular biological models: defining analog modules based on referent physiological mechanisms. 95 - Stéphanie Gérin, Grégory Mathy, Fabrice Franck:
Modeling the dependence of respiration and photosynthesis upon light, acetate, carbon dioxide, nitrate and ammonium in Chlamydomonas reinhardtii using design of experiments and multiple regression. 96 - Francesco Abate, Sakellarios Zairis, Elisa Ficarra
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. 97 - Dan Tian, Pamela K. Kreeger
Analysis of the quantitative balance between insulin-like growth factor (IGF)-1 ligand, receptor, and binding protein levels to predict cell sensitivity and therapeutic efficacy. 98 - Nicolas Alcaraz
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. 99 - Nikolaos A. Papanikolaou, Andrej Tillinger
A systems approach identifies co-signaling molecules of early growth response 1 transcription factor in immobilization stress. 100 - Johannes Wollbold, Robert Jaster, Sarah Müller, Katja Rateitschak, Olaf Wolkenhauer:
Anti-inflammatory effects of reactive oxygen species - a multi-valued logical model validated by formal concept analysis. 101 - Edouard Pauwels, Christian Lajaunie, Jean-Philippe Vert
A Bayesian active learning strategy for sequential experimental design in systems biology. 102:1-102:11 - Neeraj Sinha
Molecular signatures for obesity and associated disorders identified through partial least square regression models. 104 - Retraction Note: Predicting new molecular targets for rhein using network pharmacology. 105
- Arne T. Bittig
Membrane related dynamics and the formation of actin in cells growing on micro-topographies: a spatial computational model. 106 - Min Wu
Finding trans-regulatory genes and protein complexes modulating meiotic recombination hotspots of human, mouse and yeast. 107 - Thomas Kelder, Lars Verschuren, Ben van Ommen, Alain J. van Gool
Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters. 108 - Shirley Guzmán, Silvia Marin
13C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes. 109 - Joanne K. Liu, Edward J. O'Brien, Joshua A. Lerman, Karsten Zengler
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. 110 - Jesse C. J. van Dam
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis. 111 - Dora Lakatos, Emily D. Travis, Kelsey E. Pierson, Jay L. Vivian, András Czirók:
Autocrine FGF feedback can establish distinct states of Nanog expression in pluripotent stem cells: a computational analysis. 112 - Irene Otero-Muras
Multicriteria global optimization for biocircuit design. 113 - Irene Otero-Muras, Pencho Yordanov
A method for inverse bifurcation of biochemical switches: inferring parameters from dose response curves. 114 - Jesse R. Walsh
A computational platform to maintain and migrate manual functional annotations for BioCyc databases. 115 - Che Lin, Chin-Nan Lin, Yu-Chao Wang
The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach. 116 - Mathieu Larocque, Thierry Chénard, Rafael Najmanovich:
A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors. 117 - Kimberly Glass
Sexually-dimorphic targeting of functionally-related genes in COPD. 118 - Adaoha E. C. Ihekwaba
Computational modelling and analysis of the molecular network regulating sporulation initiation in Bacillus subtilis. 119 - Jaime Iranzo
Autoimmunity and tumor immunology: two facets of a probabilistic immune system. 120 - Patricia Sebastián-León
Understanding disease mechanisms with models of signaling pathway activities. 121 - Christopher L. Plaisier
Evolution of context dependent regulation by expansion of feast/famine regulatory proteins. 122 - Rafael Carreira, Pedro Evangelista, Paulo Maia, Paulo Vilaça, Marcellinus Pont, Jean-François Tomb, Isabel Rocha, Miguel Rocha:
CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data. 123 - Ovidiu Parvu
Automatic validation of computational models using pseudo-3D spatio-temporal model checking. 124 - Min K. Roh
Stochastic parameter search for events. 126 - Yang Liu, Rudiyanto Gunawan
Parameter estimation of dynamic biological network models using integrated fluxes. 127 - Svetlana Usherenko, Hilke Stibbe, Massimiliano Muscò, Lars-Oliver Essen
Photo-sensitive degron variants for tuning protein stability by light. 128 - Gabriel Bosque, Abel Folch-Fortuny
Topology analysis and visualization of Potyvirus protein-protein interaction network. 129 - Pankaj Narang, Shawez Khan
MetaNET - a web-accessible interactive platform for biological metabolic network analysis. 130 - Pablo Meyer, Guillermo A. Cecchi, Gustavo Stolovitzky:
Spatial localization of the first and last enzymes effectively connects active metabolic pathways in bacteria. 131 - Dominique Vercammen, Filip Logist
Dynamic estimation of specific fluxes in metabolic networks using non-linear dynamic optimization. 132 - Guy Aidelberg, Benjamin D. Towbin
Hierarchy of non-glucose sugars in Escherichia coli. 133 - Kathleen A. Vermeersch, Lijuan Wang, John F. McDonald, Mark P. Styczynski:
Distinct metabolic responses of an ovarian cancer stem cell line. 134 - Sibylle Schirm, Christoph Engel
Modelling chemotherapy effects on granulopoiesis. 138 - Ramkumar Hariharan, Jessica M. Hoffman, Ariel S. Thomas, Quinlyn A. Soltow, Dean P. Jones, Daniel E. L. Promislow
Invariance and plasticity in the Drosophila melanogaster metabolomic network in response to temperature. 139 - Peng Li
Insights from systems pharmacology into cardiovascular drug discovery and therapy. 141 - Yeimy Morales
Validation of an FBA model for Pichia pastoris in chemostat cultures. 142 - Qingyang Zhang, Joanna E. Burdette
Integrative network analysis of TCGA data for ovarian cancer. 1338
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