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  1. Research Article

    A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study

    Mathematical models are used to gain an integrative understanding of biochemical processes and networks. Commonly the models are based on deterministic ordinary differential equations. When molecular counts ar...

    Luis U. Aguilera, Christoph Zimmer and Ursula Kummer

    BMC Systems Biology 2017 11:26

    Published on: 20 February 2017

  2. Research Article

    Making life difficult for Clostridium difficile: augmenting the pathogen’s metabolic model with transcriptomic and codon usage data for better therapeutic target characterization

    Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better under...

    Sara Saheb Kashaf, Claudio Angione and Pietro Lió

    BMC Systems Biology 2017 11:25

    Published on: 16 February 2017

  3. Research

    Gene regulatory network underlying the immortalization of epithelial cells

    Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell–state tran...

    Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García and Elena R. Alvarez-Buylla

    BMC Systems Biology 2017 11:24

    Published on: 16 February 2017

  4. Methodology Article

    A combined model reduction algorithm for controlled biochemical systems

    Systems Biology continues to produce increasingly large models of complex biochemical reaction networks. In applications requiring, for example, parameter estimation, the use of agent-based modelling approache...

    Thomas J. Snowden, Piet H. van der Graaf and Marcus J. Tindall

    BMC Systems Biology 2017 11:17

    Published on: 13 February 2017

  5. Research article

    Markov State Models of gene regulatory networks

    Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understan...

    Brian K. Chu, Margaret J. Tse, Royce R. Sato and Elizabeth L. Read

    BMC Systems Biology 2017 11:14

    Published on: 6 February 2017

  6. Research

    Theoretical model of mitotic spindle microtubule growth for FRAP curve interpretation

    Spindle FRAP curves depend on the kinetic parameters of microtubule polymerization and depolymerization. The empirical FRAP curve proposed earlier permits determination of only one such dynamic parameter, comm...

    Leonid V. Omelyanchuk and Alina F. Munzarova

    BMC Systems Biology 2017 11(Suppl 1):378

    Published on: 24 February 2017

    This article is part of a Supplement: Volume 11 Supplement 1

  7. Research

    Understanding key features of bacterial restriction-modification systems through quantitative modeling

    Restriction-modification (R-M) systems are rudimentary bacterial immune systems. The main components include restriction enzyme (R), which cuts specific unmethylated DNA sequences, and the methyltransferase (M...

    Andjela Rodic, Bojana Blagojevic, Evgeny Zdobnov, Magdalena Djordjevic and Marko Djordjevic

    BMC Systems Biology 2017 11(Suppl 1):377

    Published on: 24 February 2017

    This article is part of a Supplement: Volume 11 Supplement 1

  8. Review

    Computational modeling of the cell-autonomous mammalian circadian oscillator

    This review summarizes various mathematical models of cell-autonomous mammalian circadian clock. We present the basics necessary for understanding of the cell-autonomous mammalian circadian oscillator, modern ...

    Olga A. Podkolodnaya, Natalya N. Tverdokhleb and Nikolay L. Podkolodnyy

    BMC Systems Biology 2017 11(Suppl 1):379

    Published on: 24 February 2017

    This article is part of a Supplement: Volume 11 Supplement 1

  9. Research Article

    Sampling-based Bayesian approaches reveal the importance of quasi-bistable behavior in cellular decision processes on the example of the MAPK signaling pathway in PC-12 cell lines

    Positive and negative feedback loops are ubiquitous motifs in biochemical signaling pathways. The mitogen-activated protein kinase (MAPK) pathway module is part of many distinct signaling networks and comprise...

    Antje Jensch, Caterina Thomaseth and Nicole E. Radde

    BMC Systems Biology 2017 11:11

    Published on: 25 January 2017

  10. Software

    JuPOETs: a constrained multiobjective optimization approach to estimate biochemical model ensembles in the Julia programming language

    Ensemble modeling is a promising approach for obtaining robust predictions and coarse grained population behavior in deterministic mathematical models. Ensemble approaches address model uncertainty by using pa...

    David M. Bassen, Michael Vilkhovoy, Mason Minot, Jonathan T. Butcher and Jeffrey D. Varner

    BMC Systems Biology 2017 11:10

    Published on: 25 January 2017

  11. Research article

    The use of genome-scale metabolic network reconstruction to predict fluxes and equilibrium composition of N-fixing versus C-fixing cells in a diazotrophic cyanobacterium, Trichodesmium erythraeum

    Computational, genome based predictions of organism phenotypes has enhanced the ability to investigate the biological phenomena that help organisms survive and respond to their environments. In this study, we ...

    Joseph J. Gardner and Nanette R. Boyle

    BMC Systems Biology 2017 11:4

    Published on: 19 January 2017

  12. Research article

    Coordinated regulation of acid resistance in Escherichia coli

    Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remo...

    Patricia Aquino, Brent Honda, Suma Jaini, Anna Lyubetskaya, Krutika Hosur, Joanna G. Chiu, Iriny Ekladious, Dongjian Hu, Lin Jin, Marianna K. Sayeg, Arion I. Stettner, Julia Wang, Brandon G. Wong, Winnie S. Wong, Stephen L. Alexander, Cong Ba…

    BMC Systems Biology 2017 11:1

    Published on: 6 January 2017

  13. Research

    Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice

    Drought tolerance is an important trait related to growth and yield in crop. Until now, drought related research has focused on coding genes. However, non-coding RNAs also respond significantly to environmenta...

    Inuk Jung, Hongryul Ahn, Seon-Ju Shin, Jukon Kim, Hawk-Bin Kwon, Woosuk Jung and Sun Kim

    BMC Systems Biology 2016 10(Suppl 4):115

    Published on: 23 December 2016

    This article is part of a Supplement: Volume 10 Supplement 4

  14. Research

    Sig2GRN: a software tool linking signaling pathway with gene regulatory network for dynamic simulation

    Linking computational models of signaling pathways to predicted cellular responses such as gene expression regulation is a major challenge in computational systems biology. In this work, we present Sig2GRN, a ...

    Fan Zhang, Runsheng Liu and Jie Zheng

    BMC Systems Biology 2016 10(Suppl 4):123

    Published on: 23 December 2016

    This article is part of a Supplement: Volume 10 Supplement 4

  15. Research

    Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy

    It is necessary and essential to discovery protein function from the novel primary sequences. Wet lab experimental procedures are not only time-consuming, but also costly, so predicting protein structure and f...

    Quan Zou, Shixiang Wan, Ying Ju, Jijun Tang and Xiangxiang Zeng

    BMC Systems Biology 2016 10(Suppl 4):114

    Published on: 23 December 2016

    This article is part of a Supplement: Volume 10 Supplement 4

  16. Research

    Integrative analysis of methylation and transcriptional profiles to predict aging and construct aging specific cross-tissue networks

    Aging is a complex process relating multi-scale omics data. Finding key age markers in normal tissues could help to provide reliable aging predictions in human. However, predicting age based on multi-omics dat...

    Yin Wang, Tao Huang, Lu Xie and Lei Liu

    BMC Systems Biology 2016 10(Suppl 4):132

    Published on: 23 December 2016

    This article is part of a Supplement: Volume 10 Supplement 4

  17. Research

    The extraction of drug-disease correlations based on module distance in incomplete human interactome

    Extracting drug-disease correlations is crucial in unveiling disease mechanisms, as well as discovering new indications of available drugs, or drug repositioning. Both the interactome and the knowledge of dise...

    Liang Yu, Bingbo Wang, Xiaoke Ma and Lin Gao

    BMC Systems Biology 2016 10(Suppl 4):111

    Published on: 23 December 2016

    This article is part of a Supplement: Volume 10 Supplement 4

  18. Research

    Screening lifespan-extending drugs in Caenorhabditis elegans via label propagation on drug-protein networks

    One of the most challenging tasks in the exploration of anti-aging is to discover drugs that can promote longevity and delay the incidence of age-associated diseases of human. Up to date, a number of drugs, in...

    Hui Liu, Mengmeng Guo, Ting Xue, Jihong Guan, Libo Luo and Ziheng Zhuang

    BMC Systems Biology 2016 10(Suppl 4):131

    Published on: 23 December 2016

    This article is part of a Supplement: Volume 10 Supplement 4

  19. Research

    High-dimensional omics data analysis using a variable screening protocol with prior knowledge integration (SKI)

    High-throughput technology could generate thousands to millions biomarker measurements in one experiment. However, results from high throughput analysis are often barely reproducible due to small sample size. ...

    Cong Liu, Jianping Jiang, Jianlei Gu, Zhangsheng Yu, Tao Wang and Hui Lu

    BMC Systems Biology 2016 10(Suppl 4):118

    Published on: 23 December 2016

    This article is part of a Supplement: Volume 10 Supplement 4

  20. Research

    Improved protein-protein interactions prediction via weighted sparse representation model combining continuous wavelet descriptor and PseAA composition

    Protein-protein interactions (PPIs) are essential to most biological processes. Since bioscience has entered into the era of genome and proteome, there is a growing demand for the knowledge about PPI network. ...

    Yu-An Huang, Zhu-Hong You, Xing Chen and Gui-Ying Yan

    BMC Systems Biology 2016 10(Suppl 4):120

    Published on: 23 December 2016

    This article is part of a Supplement: Volume 10 Supplement 4

  21. Research

    Subtype-specific CpG island shore methylation and mutation patterns in 30 breast cancer cell lines

    Aberrant epigenetic modifications, including DNA methylation, are key regulators of gene activity in tumorigenesis. Breast cancer is a heterogeneous disease, and large-scale analyses indicate that tumor from n...

    Heejoon Chae, Sangseon Lee, Kenneth P. Nephew and Sun Kim

    BMC Systems Biology 2016 10(Suppl 4):116

    Published on: 23 December 2016

    This article is part of a Supplement: Volume 10 Supplement 4

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