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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 3 of 5

  1. Mathematical modeling is often used to formalize hypotheses on how a biochemical network operates by discriminating between competing models. Bayesian model selection offers a way to determine the amount of ev...

    Authors: Joep Vanlier, Christian A Tiemann, Peter AJ Hilbers and Natal AW van Riel
    Citation: BMC Systems Biology 2014 8:20
    Content type: Methodology article Published on:

  4. When studying metabolism at the organ level, a major challenge is to understand the matter exchanges between the input and output components of the system. For example, in nutrition, biochemical models have be...

    Authors: Oumarou Abdou-Arbi, Sophie Lemosquet, Jaap Van Milgen, Anne Siegel and Jérémie Bourdon
    Citation: BMC Systems Biology 2014 8:8
    Content type: Methodology article Published on:

  5. Genome-wide microarrays have been useful for predicting chemical-genetic interactions at the gene level. However, interpreting genome-wide microarray results can be overwhelming due to the vast output of gene ...

    Authors: Lisa M Christadore, Lisa Pham, Eric D Kolaczyk and Scott E Schaus
    Citation: BMC Systems Biology 2014 8:7
    Content type: Methodology article Published on:

  7. A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to add...

    Authors: Austin WT Chiang, Wei-Chung Liu, Pep Charusanti and Ming-Jing Hwang
    Citation: BMC Systems Biology 2014 8:4
    Content type: Research article Published on:

  8. During embryogenesis, signaling molecules produced by one cell population direct gene regulatory changes in neighboring cells and influence their developmental fates and spatial organization. One of the earlie...

    Authors: Zhenzhen Zheng, Scott Christley, William T Chiu, Ira L Blitz, Xiaohui Xie, Ken WY Cho and Qing Nie
    Citation: BMC Systems Biology 2014 8:3
    Content type: Methodology article Published on:

  10. Cellular differentiation and reprogramming are processes that are carefully orchestrated by the activation and repression of specific sets of genes. An increasing amount of experimental results show that despi...

    Authors: Isaac Crespo, Thanneer M Perumal, Wiktor Jurkowski and Antonio del Sol
    Citation: BMC Systems Biology 2013 7:140
    Content type: Methodology article Published on:

  11. Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not re...

    Authors: Claudine Chaouiya, Duncan Bérenguier, Sarah M Keating, Aurélien Naldi, Martijn P van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T Monteiro, Axel von Kamp…
    Citation: BMC Systems Biology 2013 7:135
    Content type: Methodology article Published on:

  12. The study of cellular metabolism in the context of high-throughput -omics data has allowed us to decipher novel mechanisms of importance in biotechnology and health. To continue with this progress, it is essen...

    Authors: Jon Pey, Kaspar Valgepea, Angel Rubio, John E Beasley and Francisco J Planes
    Citation: BMC Systems Biology 2013 7:134
    Content type: Methodology article Published on:

  13. Chemical reaction networks provide an abstraction scheme for a broad range of models in biology and ecology. The two common means for simulating these networks are the deterministic and the stochastic approach...

    Authors: Ozan Kahramanoğulları and James F Lynch
    Citation: BMC Systems Biology 2013 7:133
    Content type: Methodology article Published on:

  15. Stoichiometric models provide a structural framework for analyzing steady-state cellular behavior. Models are developed either through augmentations of existing models or more recently through automatic recons...

    Authors: Mona Yousofshahi, Ehsan Ullah, Russell Stern and Soha Hassoun
    Citation: BMC Systems Biology 2013 7:129
    Content type: Methodology article Published on:

  16. Constraint-based analyses of metabolic networks are widely used to simulate the properties of genome-scale metabolic networks. Publicly available implementations tend to be slow, impeding large scale analyses ...

    Authors: Gabriel Gelius-Dietrich, Abdelmoneim Amer Desouki, Claus Jonathan Fritzemeier and Martin J Lercher
    Citation: BMC Systems Biology 2013 7:125
    Content type: Software Published on:

  18. Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature...

    Authors: Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka…
    Citation: BMC Systems Biology 2013 7:116
    Content type: Research article Published on:

  19. The Systems Biology Graphical Notation (SBGN) provides standard graphical languages for representing cellular processes, interactions, and biological networks. SBGN consists of three languages: Process Descrip...

    Authors: Torsten Vogt, Tobias Czauderna and Falk Schreiber
    Citation: BMC Systems Biology 2013 7:115
    Content type: Methodology article Published on:

  20. Metabolic reconstruction is the computational-based process that aims to elucidate the network of metabolites interconnected through reactions catalyzed by activities assigned to one or more genes. Reconstruct...

    Authors: Miguel Ponce-de-León, Francisco Montero and Juli Peretó
    Citation: BMC Systems Biology 2013 7:114
    Content type: Research article Published on:

  23. Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular ...

    Authors: Inna Kuperstein, David PA Cohen, Stuart Pook, Eric Viara, Laurence Calzone, Emmanuel Barillot and Andrei Zinovyev
    Citation: BMC Systems Biology 2013 7:100
    Content type: Software Published on:

  24. Understanding the process of amino acid fermentation as a comprehensive system is a challenging task. Previously, we developed a literature-based dynamic simulation model, which included transcriptional regula...

    Authors: Yousuke Nishio, Soichi Ogishima, Masao Ichikawa, Yohei Yamada, Yoshihiro Usuda, Tadashi Masuda and Hiroshi Tanaka
    Citation: BMC Systems Biology 2013 7:92
    Content type: Research article Published on:

  26. There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute...

    Authors: Sarp A Coskun, A Ercument Cicek, Nicola Lai, Ranjan K Dash, Z Meral Ozsoyoglu and Gultekin Ozsoyoglu
    Citation: BMC Systems Biology 2013 7:88
    Content type: Software Published on:

  27. Despite clinical research and development in the last decades, infectious diseases remain a top global problem in public health today, being responsible for millions of morbidities and mortalities each year. T...

    Authors: Yu-Chao Wang, Che Lin, Ming-Ta Chuang, Wen-Ping Hsieh, Chung-Yu Lan, Yung-Jen Chuang and Bor-Sen Chen
    Citation: BMC Systems Biology 2013 7:79
    Content type: Research article Published on:

  28. Analysis of genome-wide data is often carried out using standard methods such as differential expression analysis, clustering analysis and heatmaps. Beyond that, differential correlation analysis was suggested...

    Authors: Michael Bockmayr, Frederick Klauschen, Balazs Györffy, Carsten Denkert and Jan Budczies
    Citation: BMC Systems Biology 2013 7:78
    Content type: Research article Published on:

  29. Model development is a key task in systems biology, which typically starts from an initial model candidate and, involving an iterative cycle of hypotheses-driven model modifications, leads to new experimentati...

    Authors: Maria Rodriguez-Fernandez, Markus Rehberg, Andreas Kremling and Julio R Banga
    Citation: BMC Systems Biology 2013 7:76
    Content type: Methodology article Published on:

  30. COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. Due to the successes with metabolism, there is a...

    Authors: Ali Ebrahim, Joshua A Lerman, Bernhard O Palsson and Daniel R Hyduke
    Citation: BMC Systems Biology 2013 7:74
    Content type: Software Published on:

  31. The data-driven inference of intracellular networks is one of the key challenges of computational and systems biology. As suggested by recent works, a simple yet effective approach for reconstructing regulator...

    Authors: Andrea Pinna, Sandra Heise, Robert J Flassig, Alberto de la Fuente and Steffen Klamt
    Citation: BMC Systems Biology 2013 7:73
    Content type: Methodology article Published on:

  35. Integrative and comparative analyses of multiple transcriptomics, proteomics and metabolomics datasets require an intensive knowledge of tools and background concepts. Thus, it is challenging for users to perf...

    Authors: Tien-Chueh Kuo, Tze-Feng Tian and Yufeng Jane Tseng
    Citation: BMC Systems Biology 2013 7:64
    Content type: Software Published on:

  37. The study of metabolism has attracted much attention during the last years due to its relevance in various diseases. The advance in metabolomics platforms allows us to detect an increasing number of metabolite...

    Authors: Jon Pey, Luis Tobalina, Joaquín Prada J de Cisneros and Francisco J Planes
    Citation: BMC Systems Biology 2013 7:62
    Content type: Methodology article Published on:

  38. Recent advancements in genetics and proteomics have led to the acquisition of large quantitative data sets. However, the use of these data to reverse engineer biochemical networks has remained a challenging pr...

    Authors: Tapesh Santra, Walter Kolch and Boris N Kholodenko
    Citation: BMC Systems Biology 2013 7:57
    Content type: Methodology article Published on:

  39. With the increasing availability of high dimensional time course data for metabolites, genes, and fluxes, the mathematical description of dynamical systems has become an essential aspect of research in systems...

    Authors: Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell and Andreas Dräger
    Citation: BMC Systems Biology 2013 7:55
    Content type: Methodology article Published on:

  40. Parameter estimation from experimental data is critical for mathematical modeling of protein regulatory networks. For realistic networks with dozens of species and reactions, parameter estimation is an especia...

    Authors: Cihan Oguz, Teeraphan Laomettachit, Katherine C Chen, Layne T Watson, William T Baumann and John J Tyson
    Citation: BMC Systems Biology 2013 7:53
    Content type: Research article Published on:

  41. The metabolic network of H. sapiens and many other organisms is described in multiple pathway databases. The level of agreement between these descriptions, however, has proven to be low. We can use these differen...

    Authors: Miranda D Stobbe, Morris A Swertz, Ines Thiele, Trebor Rengaw, Antoine HC van Kampen and Perry D Moerland
    Citation: BMC Systems Biology 2013 7:50
    Content type: Research article Published on:

  44. Systems Biology develops computational models in order to understand biological phenomena. The increasing number and complexity of such “bio-models” necessitate computer support for the overall modelling task....

    Authors: Christian Knüpfer, Clemens Beckstein, Peter Dittrich and Nicolas Le Novère
    Citation: BMC Systems Biology 2013 7:43
    Content type: Methodology article Published on:

  45. Identifying protein complexes from protein-protein interaction network is fundamental for understanding the mechanism of cellular component and protein function. At present, many methods to identify protein co...

    Authors: Jianxin Wang, Xiaoqing Peng, Qianghua Xiao, Min Li and Yi Pan
    Citation: BMC Systems Biology 2013 7:28
    Content type: Methodology article Published on:

  46. With the continued proliferation of high-throughput biological experiments, there is a pressing need for tools to integrate the data produced in ways that produce biologically meaningful conclusions. Many micr...

    Authors: William A Bryant, Michael JE Sternberg and John W Pinney
    Citation: BMC Systems Biology 2013 7:26
    Content type: Methodology article Published on:

  47. Most tumors are the result of accumulated genomic alterations in somatic cells. The emerging spectrum of alterations in tumors is complex and the identification of relevant genes and pathways remains a challen...

    Authors: Vladimir Trifonov, Laura Pasqualucci, Riccardo Dalla Favera and Raul Rabadan
    Citation: BMC Systems Biology 2013 7:25
    Content type: Methodology article Published on:

  48. Elucidation of the direct/indirect protein interactions and gene associations is required to fully understand the workings of the cell. This can be achieved through the use of both low- and high-throughput bio...

    Authors: Fatemeh Vafaee, Daniela Rosu, Fiona Broackes-Carter and Igor Jurisica
    Citation: BMC Systems Biology 2013 7:22
    Content type: Methodology article Published on:

  49. The models in this article generalize current models for both correlation networks and multigraph networks. Correlation networks are widely applied in genomics research. In contrast to general networks, it is ...

    Authors: John Michael Ranola, Peter Langfelder, Kenneth Lange and Steve Horvath
    Citation: BMC Systems Biology 2013 7:21
    Content type: Methodology article Published on:

  50. Public repositories of biological pathways and networks have greatly expanded in recent years. Such databases contain many pathways that facilitate the analysis of high-throughput experimental work and the for...

    Authors: Eric Bonnet, Laurence Calzone, Daniel Rovera, Gautier Stoll, Emmanuel Barillot and Andrei Zinovyev
    Citation: BMC Systems Biology 2013 7:18
    Content type: Software Published on:

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