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ORCIDBMC 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, Hisao Moriya:
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, Pep Charusanti, Ming-Jing Hwang:
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, Junaid Gamieldien, Eric C. Mwambene:
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, Anne Siegel, Jérémie Bourdon:
Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. 8 - Carlos Espinosa-Soto, Richard G. H. Immink, Gerco C. Angenent, Elena R. Álvarez-Buylla, Stefan de Folter:
Tetramer formation in Arabidopsis MADS domain proteins: analysis of a protein-protein interaction network. 9 - Aaron Ingham, Simone A. Osborne, Moira Menzies, Suzie Briscoe, Wei Chen, Kritaya Kongsuwan, Antonio Reverter, Angela Jeanes, Brian P. Dalrymple, Gene Wijffels, Robert A. Seymour, Nicholas J. Hudson:
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, Deepak Chandran, Kyung Hyuk Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer, Erhan Bilal, Herbert M. Sauro, Gustavo Stolovitzky, Julio Saez-Rodriguez:
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, Jeffrey J. P. Tsai:
A model comparison study of the flowering time regulatory network in Arabidopsis. 15 - Erno Lindfors, Paula Jouhten, Merja Oja, Eija Rintala, Matej Oresic, Merja Penttilä:
Integration of transcription and flux data reveals molecular paths associated with differences in oxygen-dependent phenotypes of Saccharomyces cerevisiae. 16 - Gabriel N. Teku, Csaba P. Ortutay, Mauno Vihinen:
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, Stefan Grünewald, Yifei Xu, Xiu-Feng Wan:
Quartet-based methods to reconstruct phylogenetic networks. 21 - Georg R. Walther, Matthew Hartley, Maya Mincheva:
GraTeLPy: graph-theoretic linear stability analysis. 22 - Andrew E. Blanchard, Venhar Celik, Ting Lu:
Extinction, coexistence, and localized patterns of a bacterial population with contact-dependent inhibition. 23 - Edgar D. Coelho, Joel Arrais, Sérgio Matos, Carlos Pereira, Nuno Rosa, Maria José Correia, Marlene Barros, José Luís Oliveira:
Computational prediction of the human-microbial oral interactome. 24 - Yun-Bo Zhao, J. Krishnan:
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, James Hernandez, James D. Cavalcoli, Kenneth J. Pienta, Richard C. McEachin:
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, Michel Le Borgne, Nathalie Théret:
An integrative modeling framework reveals plasticity of TGF-β signaling. 30 - Wai Ong, Trang T. Vu, Klaus N. Lovendahl, Jenna M. Llull, Margrethe H. Serres, Margaret F. Romine, Jennifer L. Reed:
Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. 31 - Pierre Blavy, Florence Gondret, Sandrine Lagarrigue, Jaap Van Milgen, Anne Siegel:
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, Gargi Datta, Gregory P. Cosgrove, Michael Strong:
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, Abdul Salam Jarrah, Luis David García-Puente, John McGee, Reinhard C. Laubenbacher:
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, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau:
A web server for protein-protein interaction network querying. 40 - Ibrahim E. El-Semman, Fredrik H. Karlsson, Saeed Shoaie, Intawat Nookaew, Taysir Hassan A. Soliman, Jens Nielsen:
Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction. 41 - Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer:
Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. 42 - Berta Verd, Anton Crombach, Johannes Jaeger:
Classification of transient behaviours in a time-dependent toggle switch model. 43 - Chin Wee Tan, Bruce S. Gardiner, Yumiko Hirokawa, David W. Smith, Antony W. Burgess:
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, Peter Strålfors, Gunnar Cedersund:
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, Olivier C. Martin, Andreas Wagner:
Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms. 48 - Jürgen Dönitz, Edgar Wingender:
EndoNet: an information resource about the intercellular signaling network. 49 - Averina Nicolae, Judith Wahrheit, Janina Bahnemann, An-Ping Zeng, Elmar Heinzle:
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, Arjan van der Schaft, Karen van Eunen, Barbara M. Bakker, Bayu Jayawardhana:
A model reduction method for biochemical reaction networks. 52 - Colin Campbell, Réka Albert:
Stabilization of perturbed Boolean network attractors through compensatory interactions. 53 - Eleftherios Ouzounoglou, Dimitrios Kalamatianos, Evangelia Emmanouilidou, Maria Xilouri, Leonidas Stefanis, Kostas Vekrellis, Elias S. Manolakos:
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, Bert Smeets, Kurt Hoffmann, Wolfgang Wagner, Martin Zenke, Ralf Weiskirchen, Holger Fröhlich:
TGF-beta stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level. 55 - Rosario M. Piro, Stefan Wiesberg, Gunnar Schramm, Nico Rebel, Marcus Oswald, Roland Eils, Gerhard Reinelt, Rainer König:
Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. 56 - Feng-Jen Tseng, Wei-Tso Chia, Jia-Fwu Shyu, Guo-Hau Gou, Huey-Kang Sytwu, Ching-Wu Hsia, Min-Jen Tseng, Ru-Yu Pan:
Interactomics profiling of the negative regulatory function of carbon monoxide on RANKL-treated RAW 264.7 cells during osteoclastogenesis. 57 - Ricardo Alberich, Mercè Llabrés, David Sánchez, Marta Simeoni, Marc Tuduri:
MP-Align: alignment of metabolic pathways. 58 - Kristin Tøndel, Steven A. Niederer, Sander Land, Nicolas Smith:
Insight into model mechanisms through automatic parameter fitting: a new methodological framework for model development. 59 - Peican Zhu, Jinghang Liang, Jie Han:
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, Andreas Wagner:
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, Kelly J. Sutton, Bindi S. Brook, Dann G. Mallet, Daniel P. Simpson, Roger G. Rank:
STI-GMaS: an open-source environment for simulation of sexually-transmitted infections. 66 - Magdalena San Román, Héctor Cancela, Luis Acerenza:
Source and regulation of flux variability in Escherichia coli. 67 - Emad Fadhal, Eric C. Mwambene, Junaid Gamieldien:
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, Martin Meier-Schellersheim:
NetworkViewer: visualizing biochemical reaction networks with embedded rendering of molecular interaction rules. 70 - Tamás Székely, Kevin Burrage, Konstantinos C. Zygalakis, Manuel Barrio:
Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch-Stoer extrapolation method. 71 - Jean-Eudes J. Dazard, Yana Sandlers, Stephanie K. Doerner, Nathan A. Berger, Henri Brunengraber:
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, Andrew P. Hodges, Giovanni Paternostro, Carlo Piermarocchi:
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, Ulrike Korf, Tim Beißbarth:
Boolean ErbB network reconstructions and perturbation simulations reveal individual drug response in different breast cancer cell lines. 75 - Jérémy Hamon, Paul Jennings, Frédéric Y. Bois:
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, Shankar Subramaniam:
Information theoretic approach to complex biological network reconstruction: application to cytokine release in RAW 264.7 macrophages. 77 - Jen-hwa Chu, Craig P. Hersh, Peter J. Castaldi, Michael H. Cho, Benjamin A. Raby, Nan M. Laird, Russell Bowler, Stephen I. Rennard, Joseph Loscalzo, John Quackenbush, Edwin K. Silverman:
Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD. 78 - Daniel S. Weaver, Ingrid M. Keseler, Amanda Mackie, Ian T. Paulsen, Peter D. Karp:
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, Lorenzo Farina:
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, André Veríssimo, Susana Vinga:
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, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, Yue Joseph Wang:
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. 87 - Orit Lavi, Jeff Skinner, Michael M. Gottesman:
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, Serpil Eraslan, Kazim Yalçin Arga, Ebru Oner, Betül Kirdar:
A system based network approach to ethanol tolerance in Saccharomyces cerevisiae. 90 - Sarala M. Wimalaratne, Pierre Grenon, Henning Hermjakob, Nicolas Le Novère, Camille Laibe:
BioModels linked dataset. 91 - Naomi Kochi, Tomás Helikar, Laura Allen, Jim A. Rogers, Zhenyuan Wang, Mihaela Teodora Matache:
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, Lars Keld Nielsen:
A depth-first search algorithm to compute elementary flux modes by linear programming. 94 - Brenden K. Petersen, Glen E. P. Ropella, C. Anthony Hunt:
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, Andrea Acquaviva, Chris H. Wiggins, Veronique Frattini, Anna Lasorella, Antonio Iavarone, Giorgio Inghirami, Raul Rabadan:
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, Josch Pauling, Richa Batra, Eudes Barbosa, Alexander Junge, Anne Christensen, Vasco Ariston de Carvalho Azevedo, Henrik J. Ditzel, Jan Baumbach:
KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape. 99 - Nikolaos A. Papanikolaou, Andrej Tillinger, Xiaoping Liu, Athanasios G. Papavassiliou, Esther L. Sabban:
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, Sachin Sharma, Parul Tripathi, Simarjeet Negi, Kamiya Tikoo, Dhiraj Kumar, Kanury Rao, Samrat Chatterjee:
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, Claudia Matschegewski, J. Barbara Nebe, Susanne Stählke, Adelinde M. Uhrmacher:
Membrane related dynamics and the formation of actin in cells growing on micro-topographies: a spatial computational model. 106 - Min Wu, Chee Keong Kwoh, Xiaoli Li, Jie Zheng:
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, Marijana Radonjic:
Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters. 108 - Shirley Guzmán, Silvia Marin, Anibal Miranda, Vitaly A. Selivanov, Josep J. Centelles, Romain Harmancey, Fatima Smih, Annie Turkieh, Yves Durocher, Antonio Zorzano, Philippe Rouet, Marta Cascante:
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, Bernhard O. Palsson, Adam M. Feist:
Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale. 110 - Jesse C. J. van Dam, Peter J. Schaap, Vítor A. P. Martins dos Santos, María Suárez-Diez:
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, Julio R. Banga:
Multicriteria global optimization for biocircuit design. 113 - Irene Otero-Muras, Pencho Yordanov, Jörg Stelling:
A method for inverse bifurcation of biochemical switches: inferring parameters from dose response curves. 114 - Jesse R. Walsh, Taner Z. Sen, Julie A. Dickerson:
A computational platform to maintain and migrate manual functional annotations for BioCyc databases. 115 - Che Lin, Chin-Nan Lin, Yu-Chao Wang, Fang-Yu Liu, Yung-Jen Chuang, Chung-Yu Lan, Wen-Ping Hsieh, Bor-Sen Chen:
The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach. 116