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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 1 of 5

  1. Content type: Methodology article

    A recurrent problem in genome-scale metabolic models (GEMs) is to correctly represent lipids as biomass requirements, due to the numerous of possible combinations of individual lipid species and the correspond...

    Authors: Benjamín J. Sánchez, Feiran Li, Eduard J. Kerkhoven and Jens Nielsen

    Citation: BMC Systems Biology 2019 13:4

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  2. Content type: Methodology article

    Aggregation of high-throughput biological data using pathway-based approaches is useful to associate molecular results to functional features related to the studied phenomenon. Biological pathways communicate ...

    Authors: Guillermo de Anda-Jáuregui, Kai Guo, Brett A. McGregor, Eva L. Feldman and Junguk Hur

    Citation: BMC Systems Biology 2019 13:1

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    The Correction to this article has been published in BMC Systems Biology 2019 13:31

  3. Content type: Software

    Biological Regulatory Networks (BRNs) are responsible for developmental and maintenance related functions in organisms. These functions are implemented by the dynamics of BRNs and are sensitive to regulations ...

    Authors: Muhammad Tariq Saeed, Jamil Ahmad, Jan Baumbach, Josch Pauling, Aamir Shafi, Rehan Zafar Paracha, Asad Hayat and Amjad Ali

    Citation: BMC Systems Biology 2018 12:146

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  4. Content type: Methodology article

    Mathematical modeling is a powerful tool to analyze, and ultimately design biochemical networks. However, the estimation of the parameters that appear in biochemical models is a significant challenge. Paramete...

    Authors: Adithya Sagar, Rachel LeCover, Christine Shoemaker and Jeffrey Varner

    Citation: BMC Systems Biology 2018 12:87

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  5. Content type: Methodology article

    The dynamics of biochemical networks can be modelled by systems of ordinary differential equations. However, these networks are typically large and contain many parameters. Therefore model reduction procedures...

    Authors: Håvard G. Frøysa, Shirin Fallahi and Nello Blaser

    Citation: BMC Systems Biology 2018 12:79

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  6. Content type: Software

    One of the major challenges in traditional mathematical modeling of gene regulatory circuits is the insufficient knowledge of kinetic parameters. These parameters are often inferred from existing experimental ...

    Authors: Bin Huang, Dongya Jia, Jingchen Feng, Herbert Levine, José N. Onuchic and Mingyang Lu

    Citation: BMC Systems Biology 2018 12:74

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  7. Content type: Software

    Models of metabolism are often used in biotechnology and pharmaceutical research to identify drug targets or increase the direct production of valuable compounds. Due to the complexity of large metabolic syste...

    Authors: Robert W. Smith, Rik P. van Rosmalen, Vitor A. P. Martins dos Santos and Christian Fleck

    Citation: BMC Systems Biology 2018 12:72

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  8. Content type: Methodology article

    A novel framework is proposed to analyse metabolic fluxes in non-steady state conditions, based on the new concept of dynamic elementary mode (dynEM): an elementary mode activated partially depending on the ti...

    Authors: Abel Folch-Fortuny, Bas Teusink, Huub C.J. Hoefsloot, Age K. Smilde and Alberto Ferrer

    Citation: BMC Systems Biology 2018 12:71

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  9. Content type: Methodology article

    Understanding the dynamical behaviour of biological systems is challenged by their large number of components and interactions. While efforts have been made in this direction to reduce model complexity, they o...

    Authors: Stefano Casagranda, Suzanne Touzeau, Delphine Ropers and Jean-Luc Gouzé

    Citation: BMC Systems Biology 2018 12:68

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  10. Content type: Methodology article

    Certain biological processes, such as the development of cancer and immune activation, can be controlled by rare cellular events that are difficult to capture computationally through simulations of individual ...

    Authors: Brian C. Ross, Mayla Boguslav, Holly Weeks and James C. Costello

    Citation: BMC Systems Biology 2018 12:64

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  11. Content type: Methodology article

    Metabolic reactions are chemical transformations commonly catalyzed by enzymes. In recent years, the explosion of genomic data and individual experimental characterizations have contributed to the construction...

    Authors: Carlos Vazquez-Hernandez, Antonio Loza, Esteban Peguero-Sanchez, Lorenzo Segovia and Rosa-Maria Gutierrez-Rios

    Citation: BMC Systems Biology 2018 12:63

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  12. Content type: Software

    Reconstruction of executable mechanistic models from single-cell gene expression data represents a powerful approach to understanding developmental and disease processes. New ambitious efforts like the Human C...

    Authors: Steven Woodhouse, Nir Piterman, Christoph M. Wintersteiger, Berthold Göttgens and Jasmin Fisher

    Citation: BMC Systems Biology 2018 12:59

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  13. Content type: Research article

    Melanoma can be diagnosed by identifying nests of cells on the skin surface. Understanding the processes that drive nest formation is important as these processes could be potential targets for new cancer drug...

    Authors: Parvathi Haridas, Alexander P. Browning, Jacqui A. McGovern, D. L. Sean McElwain and Matthew J. Simpson

    Citation: BMC Systems Biology 2018 12:34

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  14. Content type: Software

    We propose OptPipe - a Pipeline for Optimizing Metabolic Engineering Targets, based on a consensus approach. The method generates consensus hypotheses for metabolic engineering applications by combining severa...

    Authors: András Hartmann, Ana Vila-Santa, Nicolai Kallscheuer, Michael Vogt, Alice Julien-Laferrière, Marie-France Sagot, Jan Marienhagen and Susana Vinga

    Citation: BMC Systems Biology 2017 11:143

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  15. Content type: Research Article

    Specific cellular states are often associated with distinct gene expression patterns. These states are plastic, changing during development, or in the transition from health to disease. One relatively simple e...

    Authors: Daniel Schlauch, Kimberly Glass, Craig P. Hersh, Edwin K. Silverman and John Quackenbush

    Citation: BMC Systems Biology 2017 11:139

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  16. Content type: Methodology Article

    Glioblastoma multiforme (GBM) is a devastating brain cancer for which there is no known cure. Its malignancy is due to rapid cell division along with high motility and invasiveness of cells into the brain tiss...

    Authors: Justin Caccavale, David Fiumara, Michael Stapf, Liedeke Sweitzer, Hannah J. Anderson, Jonathan Gorky, Prasad Dhurjati and Deni S. Galileo

    Citation: BMC Systems Biology 2017 11:124

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  17. Content type: Research Article

    The complexity of metabolic networks can make the origin and impact of changes in central metabolism occurring during diseases difficult to understand. Computer simulations can help unravel this complexity, an...

    Authors: Anthony C. Smith, Filmon Eyassu, Jean-Pierre Mazat and Alan J. Robinson

    Citation: BMC Systems Biology 2017 11:114

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  18. Content type: Research Article

    Translating in vitro results to clinical tests is a major challenge in systems biology. Here we present a new Multi-Task learning framework which integrates thousands of cell line expression experiments to rec...

    Authors: Matthew Ruffalo, Petar Stojanov, Venkata Krishna Pillutla, Rohan Varma and Ziv Bar-Joseph

    Citation: BMC Systems Biology 2017 11:96

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  19. Content type: Methodology Article

    High-throughput assays are widely used in biological research to select potential targets. One single high-throughput experiment can efficiently study a large number of candidates simultaneously, but is subjec...

    Authors: Wenfei Zhang, Ying Liu, Mindy Zhang, Cheng Zhu and Yuefeng Lu

    Citation: BMC Systems Biology 2017 11:73

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  20. Content type: Research Article

    Large sets of protein-protein interaction data coming either from biological experiments or predictive methods are available and can be combined to construct networks from which information about various cell ...

    Authors: Annie Glatigny, Philippe Gambette, Alexa Bourand-Plantefol, Geneviève Dujardin and Marie-Hélène Mucchielli-Giorgi

    Citation: BMC Systems Biology 2017 11:67

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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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2017 Journal Metrics

  • Citation Impact
    2.05 - 2-year Impact Factor
    2.505 - 5-year Impact Factor
    0.689 - Source Normalized Impact per Paper (SNIP)
    1.109 - SCImago Journal Rank (SJR)


    Social Media Impact
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