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.

Previous Page Page 1 of 10 Next Page
  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. 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

  3. 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

  4. 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

  5. Research Article

    SParSE++: improved event-based stochastic parameter search

    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 ...

    Min K. Roh and Bernie J. Daigle

    BMC Systems Biology 2016 10:109

    Published on: 25 November 2016

  6. Methodology Article

    Unearthing the transition rates between photoreceptor conformers

    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. ...

    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

    BMC Systems Biology 2016 10:110

    Published on: 25 November 2016

  7. Software

    BCM: toolkit for Bayesian analysis of Computational Models using samplers

    Computational models in biology are characterized by a large degree of uncertainty. This uncertainty can be analyzed with Bayesian statistics, however, the sampling algorithms that are frequently used for calc...

    Bram Thijssen, Tjeerd M. H. Dijkstra, Tom Heskes and Lodewyk F. A. Wessels

    BMC Systems Biology 2016 10:100

    Published on: 21 October 2016

  8. Software

    Quantifying differences in cell line population dynamics using CellPD

    The increased availability of high-throughput datasets has revealed a need for reproducible and accessible analyses which can quantitatively relate molecular changes to phenotypic behavior. Existing tools for ...

    Edwin F. Juarez, Roy Lau, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Edmond Jonckheere, David B. Agus, Shannon M. Mumenthaler and Paul Macklin

    BMC Systems Biology 2016 10:92

    Published on: 21 September 2016

  9. Research Article

    Dynamic optimization of biological networks under parametric uncertainty

    Micro-organisms play an important role in various industrial sectors (including biochemical, food and pharmaceutical industries). A profound insight in the biochemical reactions inside micro-organisms enables ...

    Philippe Nimmegeers, Dries Telen, Filip Logist and Jan Van Impe

    BMC Systems Biology 2016 10:86

    Published on: 31 August 2016

  10. Software

    Cross-species Conservation of context-specific networks

    Many large data compendia on context-specific high-throughput genomic and regulatory data have been made available by international research consortia such as ENCODE, TCGA, and Epigenomics Roadmap. The use of ...

    Robert Pesch and Ralf Zimmer

    BMC Systems Biology 2016 10:76

    Published on: 17 August 2016

  11. Methodology Article

    Robust sparse canonical correlation analysis

    Canonical correlation analysis (CCA) is a multivariate statistical method which describes the associations between two sets of variables. The objective is to find linear combinations of the variables in each d...

    Ines Wilms and Christophe Croux

    BMC Systems Biology 2016 10:72

    Published on: 11 August 2016

  12. Methodology Article

    Modelling with ANIMO: between fuzzy logic and differential equations

    Computational support is essential in order to reason on the dynamics of biological systems. We have developed the software tool ANIMO (Analysis of Networks with Interactive MOdeling) to provide such computati...

    Stefano Schivo, Jetse Scholma, Paul E. van der Vet, Marcel Karperien, Janine N. Post, Jaco van de Pol and Rom Langerak

    BMC Systems Biology 2016 10:56

    Published on: 27 July 2016

Previous Page Page 1 of 10 Next Page

Can't find what you are looking for?

Articles for this section are still being added to this new-look site. In the meantime you can still view this section on our old site.