Parameter estimation of qualitative biological regulatory networks on high performance computing hardware
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Volume 12, issue 1, December 2018
57 articles in this issue
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Mechanistic insight into activation of MAPK signaling by pro-angiogenic factors
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Qualitative modelling of the interplay of inflammatory status and butyrate in the human gut: a hypotheses about robust bi-stability
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Reframing gene essentiality in terms of adaptive flexibility
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Retraction Note: detangling PPI networks to uncover functionally meaningful clusters
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Metabolic modeling and response surface analysis of an Escherichia coli strain engineered for shikimic acid production
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The anticancer mechanism investigation of Tanshinone IIA by pharmacological clustering in protein network
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Sex differences in hepatic one-carbon metabolism
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Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin
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Dynamic Optimization with Particle Swarms (DOPS): a meta-heuristic for parameter estimation in biochemical models
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Cellular network modeling and single cell gene expression analysis reveals novel hepatic stellate cell phenotypes controlling liver regeneration dynamics
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Multi-component gene network design as a survival strategy in diverse environments
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Escher-FBA: a web application for interactive flux balance analysis
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The synthetic histone-binding regulator protein PcTF activates interferon genes in breast cancer cells
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An ensemble of mathematical models showing diauxic growth behaviour
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Statistical relationship between metabolic decomposition and chemical uptake predicts bioconcentration factor data for diverse chemical exposures
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A systematic survey of centrality measures for protein-protein interaction networks
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Extracting proteins involved in disease progression using temporally connected networks
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A quantitative systems pharmacology (QSP) model for Pneumocystis treatment in mice
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High-fidelity discrete modeling of the HPA axis: a study of regulatory plasticity in biology
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Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity
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RACIPE: a computational tool for modeling gene regulatory circuits using randomization
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DMPy: a Python package for automated mathematical model construction of large-scale metabolic systems
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Dynamic elementary mode modelling of non-steady state flux data
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Single molecules can operate as primitive biological sensors, switches and oscillators
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Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss
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Principal process analysis of biological models
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Landscape reveals critical network structures for sharpening gene expression boundaries
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Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa
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A method for efficient Bayesian optimization of self-assembly systems from scattering data
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Simulating heterogeneous populations using Boolean models
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Identification of reaction organization patterns that naturally cluster enzymatic transformations
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NUP155 insufficiency recalibrates a pluripotent transcriptome with network remodeling of a cardiogenic signaling module
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Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z
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A computational framework for complex disease stratification from multiple large-scale datasets
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SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data
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A powerful nonparametric method for detecting differentially co-expressed genes: distance correlation screening and edge-count test
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Evolution of computational models in BioModels Database and the Physiome Model Repository
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Putative human sperm Interactome: a networks study
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The innate immune response to ischemic injury: a multiscale modeling perspective
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The phenotype control kernel of a biomolecular regulatory network
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Identification of new progestogen-associated networks in mammalian ovulation using bioinformatics
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Mathematical modelling of interacting mechanisms for hypoxia mediated cell cycle commitment for mesenchymal stromal cells
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Three-dimensional experiments and individual based simulations show that cell proliferation drives melanoma nest formation in human skin tissue
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Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma
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Systems biology as an emerging paradigm in transfusion medicine
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Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy
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