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BMC Systems Biology, Volume 9
Volume 9, 2015
- Chao Ye
, Nan Xu
Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina. 1 - A. K. M. Azad, Alfons Lawen
Prediction of signaling cross-talks contributing to acquired drug resistance in breast cancer cells by Bayesian statistical modeling. 2 - Takahide Ota, Masayo Maeda, Mayumi Okamoto, Masaaki Tatsuka:
Positive regulation of Rho GTPase activity by RhoGDIs as a result of their direct interaction with GAPs. 3 - Wenjuan Mo, Chao Tong, Yan Zhang, Hong Lu:
microRNAs' differential regulations mediate the progress of Human Papillomavirus (HPV)-induced Cervical Intraepithelial Neoplasia (CIN). 4 - Gautham Vivek Sridharan, Ehsan Ullah, Soha Hassoun, Kyongbum Lee
Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity. 5 - Stina K. Lien, Sebastian Niedenführ, Håvard Sletta
Fluxome study of Pseudomonas fluorescens reveals major reorganisation of carbon flux through central metabolic pathways in response to inactivation of the anti-sigma factor MucA. 6 - Tim Sands:
Annual acknowledgement of reviewers. 7 - Alejandro Fernández Villaverde
BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. 8 - Patrick Weber, Mariana Hornjik, Monilola A. Olayioye, Angelika Hausser
A computational model of PKD and CERT interactions at the trans-Golgi network of mammalian cells. 9 - Anna Zhukova, David James Sherman
Mimoza: web-based semantic zooming and navigation in metabolic networks. 10 - Li-Ying Wang, Jun Liu, Yuan Li, Bing Li, Yingying Zhang, Zhi-Wei Jing, Ya-Nan Yu, Hai-Xia Li, Shan-Shan Guo, Yi-Jun Zhao, Zhong Wang, Yongyan Wang:
Time-dependent variation of pathways and networks in a 24-hour window after cerebral ischemia-reperfusion injury. 11 - Avichai Tendler, Avraham E. Mayo
Evolutionary tradeoffs, Pareto optimality and the morphology of ammonite shells. 12 - Traci L. Marin, Brendan Gongol, Marcy Martin
Identification of AMP-activated protein kinase targets by a consensus sequence search of the proteome. 13 - Takanori Hasegawa, Tomoya Mori, Rui Yamaguchi, Teppei Shimamura
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. 14 - John A. Cole, Lars Kohler, Jamila Hedhli, Zaida Luthey-Schulten
Spatially-resolved metabolic cooperativity within dense bacterial colonies. 15 - Lifang Huang, Zhanjiang Yuan, Peijiang Liu, Tianshou Zhou:
Effects of promoter leakage on dynamics of gene expression. 16 - Joseph P. Dexter, Ping Xu, Jeremy Gunawardena, Megan N. McClean
Robust network structure of the Sln1-Ypd1-Ssk1 three-component phospho-relay prevents unintended activation of the HOG MAPK pathway in Saccharomyces cerevisiae. 17 - André Schultz, Amina A. Qutub
Predicting internal cell fluxes at sub-optimal growth. 18 - Madison Brandon, Brad Howard, Christopher Lawrence, Reinhard C. Laubenbacher
Iron acquisition and oxidative stress response in aspergillus fumigatus. 19 - Jose Davila-Velderrain
Reshaping the epigenetic landscape during early flower development: induction of attractor transitions by relative differences in gene decay rates. 20 - Ricardo de Matos Simoes
Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data. 21 - Elisenda Feliu
Finding the positive feedback loops underlying multi-stationarity. 22 - Ali Sharifi-Zarchi
Increased robustness of early embryogenesis through collective decision-making by key transcription factors. 23 - Jakob Wieczorek, Rahuman S. Malik-Sheriff
Uncovering distinct protein-network topologies in heterogeneous cell populations. 24 - Cielito Reyes-Gibby, Christine Yuan, Jian Wang, Sai-Ching Yeung
Gene network analysis shows immune-signaling and ERK1/2 as novel genetic markers for multiple addiction phenotypes: alcohol, smoking and opioid addiction. 25 - Zichen Wang
Dynamics of the discovery process of protein-protein interactions from low content studies. 26 - Qing Wang, David J. Klinke II
CD8 + T cell response to adenovirusvaccination and subsequent suppression of tumor growth: modeling, simulation and analysis. 27 - Clémence Chamard-Jovenin, Alain Jung
From ERα66 to ERα36: a generic method for validating a prognosis marker of breast tumor progression. 28 - Ye Chen, Cheng Lv
Distinguishing the rates of gene activation from phenotypic variations. 29 - Devin H. Currie, Babu Raman, Christopher M. Gowen, Timothy J. Tschaplinski
Genome-scale resources for Thermoanaerobacterium saccharolyticum. 30 - Jovan Tanevski
Domain-specific model selection for structural identification of the Rab5-Rab7 dynamics in endocytosis. 31 - Dicle Hasdemir, Huub C. J. Hoefsloot, Age K. Smilde
Validation and selection of ODE based systems biology models: how to arrive at more reliable decisions. 32 - Katherine Wolstencroft
SEEK: a systems biology data and model management platform. 33 - Aristotelis Kittas, Amélie Barozet, Jekaterina Sereshti, Niels Grabe
CytoASP: a Cytoscape app for qualitative consistency reasoning, prediction and repair in biological networks. 34 - Manuel Garcia-Albornoz
Finding directionality and gene-disease predictions in disease associations. 35 - Randolph Faustino
Systems biology surveillance decrypts pathological transcriptome remodeling. 36 - Soudabeh Sabetian
Identification of putative drug targets for human sperm-egg interaction defect using protein network approach. 37 - Stuart T. Johnston
Estimating cell diffusivity and cell proliferation rate by interpreting IncuCyte ZOOM™ assay data using the Fisher-Kolmogorov model. 38 - Kaveh Yousef, Adam Streck, Christof Schütte, Heike Siebert
Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. 39 - Sushil Tripathi
The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. 40 - Joseph Cursons
Regulation of ERK-MAPK signaling in human epidermis. 41 - Sergio Pérez-Landero, Santiago Sandoval-Motta, Claudia Martínez-Anaya
Complex regulation of Hsf1-Skn7 activities by the catalytic subunits of PKA in Saccharomyces cerevisiae: experimental and computational evidences. 42 - Mohammad Tajparast, Dominic Frigon:
Genome-scale metabolic model of Rhodococcus jostii RHA1 (iMT1174) to study the accumulation of storage compounds during nitrogen-limited condition. 43 - Khuram Shahzad
The organization of domains in proteins obeys Menzerath-Altmann's law of language. 44 - Tomoya Mori, Max Flöttmann, Marcus Krantz
Stochastic simulation of Boolean rxncon models: towards quantitative analysis of large signaling networks. 45 - Urszula Czerwinska
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. 46 - Weronika Wronowska, Agata Charzynska
Computational modeling of sphingolipid metabolism. 47 - Philipp Erdrich, Ralf Steuer
An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. 48 - Weiwei Yin, Swetha Garimalla, Alberto Moreno
A tree-like Bayesian structure learning algorithm for small-sample datasets from complex biological model systems. 49 - Yue Deng, Lin Gao, Bingbo Wang:
Erratum to: ppiPre: predicting protein-protein interactions by combining heterogeneous features. 50 - Stanislav Sokolenko, Marc Aucoin
A correction method for systematic error in 1 H-NMR time-course data validated through stochastic cell culture simulation. 51 - Markus Karlsson
Nonlinear mixed-effects modelling for single cell estimation: when, why, and how to use it. 52 - Justin M. Fear
The wright stuff: reimagining path analysis reveals novel components of the sex determination hierarchy in drosophila melanogaster. 53 - Kun-Nan Tsai, Shu-Hsi Lin, Wei-Chung Liu
Inferring microbial interaction network from microbiome data using RMN algorithm. 54 - R. Joseph Bender, Feilim Mac Gabhann:
Dysregulation of the vascular endothelial growth factor and semaphorin ligand-receptor families in prostate cancer metastasis. 55 - Di Chen, Xi Liu, Yiping Yang, Hongjun Yang, Peng Lu:
Systematic synergy modeling: understanding drug synergy from a systems biology perspective. 56 - Christopher Garay
Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis. 57 - Francisco Peñagaricano
Exploring causal networks underlying fat deposition and muscularity in pigs through the integration of phenotypic, genotypic and transcriptomic data. 58 - Andrew E. Blanchard, Ting Lu:
Bacterial social interactions drive the emergence of differential spatial colony structures. 59 - Lydia M. Rickett, Nick Pullen, Matthew Hartley
Incorporating prior knowledge improves detection of differences in bacterial growth rate. 60 - Michael K. Strasser, Justin Feigelman, Fabian J. Theis
Inference of spatiotemporal effects on cellular state transitions from time-lapse microscopy. 61 - Claudia Cava
Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. 62 - Daniel Botman, Fredrik Jansson
Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development. 63 - Pierre Millard
Impact of kinetic isotope effects in isotopic studies of metabolic systems. 64 - Karol Nienaltowski, Michal Wlodarczyk, Tomasz Lipniacki
Clustering reveals limits of parameter identifiability in multi-parameter models of biochemical dynamics. 65 - Weiruo Zhang
Towards in vivo estimation of reaction kinetics using high-throughput metabolomics data: a maximum likelihood approach. 66 - Ivan Kryven
Solution of the chemical master equation by radial basis functions approximation with interface tracking. 67 - Andreas Dräger
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. 68 - Michael Reed, Mary Gamble, Megan Hall, H. Nijhout:
Mathematical analysis of the regulation of competing methyltransferases. 69 - Fortunato Bianconi
Conditional robustness analysis for fragility discovery and target identification in biochemical networks and in cancer systems biology. 70 - Daniel Cook, Babatunde A. Ogunnaike, Rajanikanth Vadigepalli
Systems analysis of non-parenchymal cell modulation of liver repair across multiple regeneration modes. 71 - Martin Kavscek
Optimization of lipid production with a genome-scale model of Yarrowia lipolytica. 72 - Meiyappan Lakshmanan
Flux-sum analysis identifies metabolite targets for strain improvement. 73 - Attila Gábor
Robust and efficient parameter estimation in dynamic models of biological systems. 74 - Christopher J. Mitchell, Derese Getnet, Min Sik Kim
A multi-omic analysis of human naïve CD4+ T cells. 75 - Sarah L. Field, Tathagata Dasgupta, Michele Cummings, Richard S. Savage
Bayesian modeling suggests that IL-12 (p40), IL-13 and MCP-1 drive murine cytokine networks in vivo. 76 - D. B. R. K. Gupta Udatha
Deciphering the signaling mechanisms of the plant cell wall degradation machinery in Aspergillus oryzae. 77 - Anuprabha Bhargava, Hanspeter Herzel, Bharath Ananthasubramaniam
Mining for novel candidate clock genes in the circadian regulatory network. 78 - Elsje Pienaar, Véronique Dartois, Jennifer J. Linderman, Denise E. Kirschner:
In silico evaluation and exploration of antibiotic tuberculosis treatment regimens. 79 - Megha Padi, John Quackenbush
Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators. 80 - Jukka Intosalmi, Helena Ahlfors
Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data. 81 - Tatsuya Ando
Differential variability and correlation of gene expression identifies key genes involved in neuronal differentiation. 82 - Kerstin Abshagen, Matthias König
Pathobiochemical signatures of cholestatic liver disease in bile duct ligated mice. 83 - Mahsa Ghanbari, Julia Lasserre, Martin Vingron:
Reconstruction of gene networks using prior knowledge. 84 - Sonja E. M. Boas, María I. Navarro Jimenez, Roeland M. H. Merks
A global sensitivity analysis approach for morphogenesis models. 85 - Sonja E. M. Boas, Roeland M. H. Merks
Tip cell overtaking occurs as a side effect of sprouting in computational models of angiogenesis. 86 - Jae Kyoung Kim
The relationship between stochastic and deterministic quasi-steady state approximations. 87 - Nima Abedpour, Markus Kollmann:
Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks. 88 - Carl D. Christensen, Jan-Hendrik S. Hofmeyr, Johann M. Rohwer
Tracing regulatory routes in metabolism using generalised supply-demand analysis. 89 - Yuya Hattori, Akinari Yokoya, Ritsuko Watanabe:
Cellular automaton-based model for radiation-induced bystander effects. 90 - Ruijie Song, Weilin Peng, Ping Liu, Murat Acar:
A cell size- and cell cycle-aware stochastic model for predicting time-dynamic gene network activity in individual cells. 91 - Pu Li
A simple method for identifying parameter correlations in partially observed linear dynamic models. 92 - Lucas Marmiesse
FlexFlux: combining metabolic flux and regulatory network analyses. 93 - Mona Yousofshahi, Sara Manteiga, Charmian Wu, Kyongbum Lee
PROXIMAL: a method for Prediction of Xenobiotic Metabolism. 94 - Alida Palmisano
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. 95 - Shahin Mohammadi
Scope and limitations of yeast as a model organism for studying human tissue-specific pathways. 96 - Katja Kolar, Hanna M. Wischhusen, Konrad Müller, Maria Karlsson, Wilfried Weber
A synthetic mammalian network to compute population borders based on engineered reciprocal cell-cell communication. 97
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