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Methods, software and technology

Section edited by Nitin Baliga and Pedro Mendes

This section covers the development and refinement of novel computational, statistical and experimental methods for the analysis of biological systems.

Page 2 of 11
  1. Content type: Research Article

    In quantitative biology, mathematical models are used to describe and analyze biological processes. The parameters of these models are usually unknown and need to be estimated from experimental data using stat...

    Authors: Benjamin Ballnus, Sabine Hug, Kathrin Hatz, Linus Görlitz, Jan Hasenauer and Fabian J. Theis

    Citation: BMC Systems Biology 2017 11:63

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  2. Content type: Methodology Article

    Co-expression has been widely used to identify novel regulatory relationships using high throughput measurements, such as microarray and RNA-seq data. Evaluation studies on co-expression network analysis metho...

    Authors: Wenbin Guo, Cristiane P. G. Calixto, Nikoleta Tzioutziou, Ping Lin, Robbie Waugh, John W. S. Brown and Runxuan Zhang

    Citation: BMC Systems Biology 2017 11:62

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  3. Content type: Software

    Finding gene-disease and disease-disease associations play important roles in the biomedical area and many prioritization methods have been proposed for this goal. Among them, approaches based on a heterogeneo...

    Authors: Duc-Hau Le and Van-Huy Pham

    Citation: BMC Systems Biology 2017 11:61

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  4. Content type: Methodology Article

    Kinetic models of biochemical systems usually consist of ordinary differential equations that have many unknown parameters. Some of these parameters are often practically unidentifiable, that is, their values ...

    Authors: Attila Gábor, Alejandro F. Villaverde and Julio R. Banga

    Citation: BMC Systems Biology 2017 11:54

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  5. Content type: Methodology Article

    With the advance of experimental techniques such as time-lapse fluorescence microscopy, the availability of single-cell trajectory data has vastly increased, and so has the demand for computational methods sui...

    Authors: Irena Kuzmanovska, Andreas Milias-Argeitis, Jan Mikelson, Christoph Zechner and Mustafa Khammash

    Citation: BMC Systems Biology 2017 11:52

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  6. Content type: Research Article

    Transforming growth factor β (TGF-β) signalling regulates the development of embryos and tissue homeostasis in adults. In conjunction with other oncogenic changes, long-term perturbation of TGF-β signalling is as...

    Authors: Shabnam Khatibi, Hong-Jian Zhu, John Wagner, Chin Wee Tan, Jonathan H. Manton and Antony W. Burgess

    Citation: BMC Systems Biology 2017 11:48

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  7. Content type: Software

    Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of cluste...

    Authors: Juan A. Botía, Jana Vandrovcova, Paola Forabosco, Sebastian Guelfi, Karishma D’Sa, John Hardy, Cathryn M. Lewis, Mina Ryten and Michael E. Weale

    Citation: BMC Systems Biology 2017 11:47

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  8. Content type: Research Article

    Early afterdepolarizations (EADs) are pathological voltage oscillations during the repolarization phase of cardiac action potentials (APs). EADs are caused by drugs, oxidative stress or ion channel disease, an...

    Authors: Philipp Kügler, M.A.K. Bulelzai and André H. Erhardt

    Citation: BMC Systems Biology 2017 11:42

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  9. Content type: Methodology article

    Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited ...

    Authors: Athanasios D. Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P. Tampakaki, Konstantinos P. Koutsoumanis and Elias S. Manolakos

    Citation: BMC Systems Biology 2017 11:43

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  10. Content type: Research Article

    Parameter optimisation is a critical step in the construction of computational biology models. In eye movement research, computational models are increasingly important to understanding the mechanistic basis o...

    Authors: Eleftherios Avramidis and Ozgur E. Akman

    Citation: BMC Systems Biology 2017 11:40

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  11. Content type: Research Article

    Parameter estimation in systems biology is typically done by enforcing experimental observations through an objective function as the parameter space of a model is explored by numerical simulations. Past studi...

    Authors: Cihan Oguz, Layne T. Watson, William T. Baumann and John J. Tyson

    Citation: BMC Systems Biology 2017 11:30

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  12. Content type: Research Article

    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...

    Authors: Luis U. Aguilera, Christoph Zimmer and Ursula Kummer

    Citation: BMC Systems Biology 2017 11:26

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  13. Content type: Methodology Article

    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...

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

    Citation: BMC Systems Biology 2017 11:17

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  14. Content type: Research article

    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...

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

    Citation: BMC Systems Biology 2017 11:14

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  15. Content type: Software

    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...

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

    Citation: BMC Systems Biology 2017 11:10

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  16. Content type: Methodology Article

    Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. ...

    Authors: Robert W. Smith, Britta Helwig, Adrie H. Westphal, Eran Pel, Maximilian Hörner, Hannes M. Beyer, Sophia L. Samodelov, Wilfried Weber, Matias D. Zurbriggen, Jan Willem Borst and Christian Fleck

    Citation: BMC Systems Biology 2016 10:110

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  17. Content type: Research Article

    Despite the increasing availability of high performance computing capabilities, analysis and characterization of stochastic biochemical systems remain a computational challenge. To address this challenge, the ...

    Authors: Min K. Roh and Bernie J. Daigle Jr.

    Citation: BMC Systems Biology 2016 10:109

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Page 2 of 11

2016 Journal Metrics

  • Citation Impact
    2.303 - 2-year Impact Factor
    2.526 - 5-year Impact Factor
    0.735 - Source Normalized Impact per Paper (SNIP)
    1.144 - SCImago Journal Rank (SJR)

    1233 Usage Factor

    Social Media Impact
    134 mentions