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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.

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  2. The study of cancer therapy is a key issue in the field of oncology research and the development of target therapies is one of the main problems currently under investigation. This is particularly relevant in ...

    Authors: Fortunato Bianconi, Elisa Baldelli, Vienna Luovini, Emanuel F. Petricoin, Lucio Crinò and Paolo Valigi

    Citation: BMC Systems Biology 2015 9:70

    Content type: Methodology Article

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    The Erratum to this article has been published in BMC Systems Biology 2016 10:24

  3. The size and complexity of published biochemical network reconstructions are steadily increasing, expanding the potential scale of derived computational models. However, the construction of large biochemical n...

    Authors: Andreas Dräger, Daniel C Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O Palsson and Andreas Zell

    Citation: BMC Systems Biology 2015 9:68

    Content type: Software

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  4. The chemical master equation is the fundamental equation of stochastic chemical kinetics. This differential-difference equation describes temporal evolution of the probability density function for states of a ...

    Authors: Ivan Kryven, Susanna Röblitz and Christof Schütte

    Citation: BMC Systems Biology 2015 9:67

    Content type: Research Article

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  5. High-throughput assays such as mass spectrometry have opened up the possibility for large-scale in vivo measurements of the metabolome. This data could potentially be used to estimate kinetic parameters for many ...

    Authors: Weiruo Zhang, Ritesh Kolte and David L Dill

    Citation: BMC Systems Biology 2015 9:66

    Content type: Methodology Article

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  7. Development of human cancer can proceed through the accumulation of different genetic changes affecting the structure and function of the genome. Combined analyses of molecular data at multiple levels, such as...

    Authors: Claudia Cava, Gloria Bertoli and Isabella Castiglioni

    Citation: BMC Systems Biology 2015 9:62

    Content type: Review

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  8. Joint modeling and analysis of phenotypic, genotypic and transcriptomic data have the potential to uncover the genetic control of gene activity and phenotypic variation, as well as shed light on the manner and...

    Authors: Francisco Peñagaricano, Bruno D. Valente, Juan P. Steibel, Ronald O. Bates, Catherine W. Ernst, Hasan Khatib and Guilherme JM Rosa

    Citation: BMC Systems Biology 2015 9:58

    Content type: Research article

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  10. Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistic insights into biological functions. Currently, it is possible to visualize high-thro...

    Authors: Urszula Czerwinska, Laurence Calzone, Emmanuel Barillot and Andrei Zinovyev

    Citation: BMC Systems Biology 2015 9:46

    Content type: Software

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  11. Over the past years, tremendous efforts have been made to elucidate the molecular basis of the initiation and progression of ovarian cancer. However, most existing studies have been focused on individual genes...

    Authors: Qingyang Zhang, Joanna E Burdette and Ji-Ping Wang

    Citation: BMC Systems Biology 2014 8:1338

    Content type: Methodology Article

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  12. Clinical trials are the main method for evaluating safety and efficacy of medical interventions and have produced many advances in improving human health. The Women’s Health Initiative overturned a half-centur...

    Authors: Yuanyuan Cui, Brendan Murphy, Anastasia Gentilcore, Yugal Sharma, Lori M Minasian, Barnett S Kramer, Paul M Coates, John K Gohagan, Juergen Klenk and Bruce Tidor

    Citation: BMC Systems Biology 2014 8:9000

    Content type: Methodology article

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  13. Metabolic reactions have been extensively studied and compiled over the last century. These have provided a theoretical base to implement models, simulations of which are used to identify drug targets and opti...

    Authors: Pankaj Narang, Shawez Khan, Anmol Jaywant Hemrom and Andrew Michael Lynn

    Citation: BMC Systems Biology 2014 8:130

    Content type: Software

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  15. Flux analysis methods lie at the core of Metabolic Engineering (ME), providing methods for phenotype simulation that allow the determination of flux distributions under different conditions. Although many cons...

    Authors: Rafael Carreira, Pedro Evangelista, Paulo Maia, Paulo Vilaça, Marcellinus Pont, Jean-François Tomb, Isabel Rocha and Miguel Rocha

    Citation: BMC Systems Biology 2014 8:123

    Content type: Software

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  17. Dynamical models used in systems biology involve unknown kinetic parameters. Setting these parameters is a bottleneck in many modeling projects. This motivates the estimation of these parameters from empirical...

    Authors: Edouard Pauwels, Christian Lajaunie and Jean-Philippe Vert

    Citation: BMC Systems Biology 2014 8:102

    Content type: Methodology Article

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  18. Within cells, stimuli are transduced into cell responses by complex networks of biochemical reactions. In many cell decision processes the underlying networks behave as bistable switches, converting graded sti...

    Authors: Irene Otero-Muras, Pencho Yordanov and Joerg Stelling

    Citation: BMC Systems Biology 2014 8:114

    Content type: Methodology Article

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  20. With recent increase in affordability and accessibility of high-performance computing (HPC), the use of large stochastic models has become increasingly popular for its ability to accurately mimic the behavior ...

    Authors: Min K Roh and Philip Eckhoff

    Citation: BMC Systems Biology 2014 8:126

    Content type: Research article

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  21. Understanding the aspects of the cell functionality that account for disease or drug action mechanisms is one of the main challenges in the analysis of genomic data and is on the basis of the future implementa...

    Authors: Patricia Sebastian-Leon, Enrique Vidal, Pablo Minguez, Ana Conesa, Sonia Tarazona, Alicia Amadoz, Carmen Armero, Francisco Salavert, Antonio Vidal-Puig, David Montaner and Joaquín Dopazo

    Citation: BMC Systems Biology 2014 8:121

    Content type: Methodology article

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  23. Different methods have been developed to infer regulatory networks from heterogeneous omics datasets and to construct co-expression networks. Each algorithm produces different networks and efforts have been de...

    Authors: Jesse CJ van Dam, Peter J Schaap, Vitor AP Martins dos Santos and María Suárez-Diez

    Citation: BMC Systems Biology 2014 8:111

    Content type: Methodology article

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  24. The regulatory mechanism of recombination is one of the most fundamental problems in genomics, with wide applications in genome wide association studies (GWAS), birth-defect diseases, molecular evolution, canc...

    Authors: Min Wu, Chee-Keong Kwoh, Xiaoli Li and Jie Zheng

    Citation: BMC Systems Biology 2014 8:107

    Content type: Methodology Article

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  25. Over the last decade network enrichment analysis has become popular in computational systems biology to elucidate aberrant network modules. Traditionally, these approaches focus on combining gene expression da...

    Authors: Nicolas Alcaraz, Josch Pauling, Richa Batra, Eudes Barbosa, Alexander Junge, Anne GL Christensen, Vasco Azevedo, Henrik J Ditzel and Jan Baumbach

    Citation: BMC Systems Biology 2014 8:99

    Content type: Software

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  26. Currently, most biomedical models exist in isolation. It is often difficult to reuse or integrate models or their components, in part because they are not modular. Modular components allow the modeler to think...

    Authors: Brenden K Petersen, Glen EP Ropella and C Anthony Hunt

    Citation: BMC Systems Biology 2014 8:95

    Content type: Methodology article

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  27. BioModels Database is a reference repository of mathematical models used in biology. Models are stored as SBML files on a file system and metadata is provided in a relational database. Models can be retrieved ...

    Authors: Sarala M Wimalaratne, Pierre Grenon, Henning Hermjakob, Nicolas Le Novère and Camille Laibe

    Citation: BMC Systems Biology 2014 8:91

    Content type: Methodology article

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  31. Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are conte...

    Authors: Ye Tian, Bai Zhang, Eric P Hoffman, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M Herrington and Yue Wang

    Citation: BMC Systems Biology 2014 8:87

    Content type: Methodology article

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  32. Many kinase inhibitors have been approved as cancer therapies. Recently, libraries of kinase inhibitors have been extensively profiled, thus providing a map of the strength of action of each compound on a larg...

    Authors: Trish P Tran, Edison Ong, Andrew P Hodges, Giovanni Paternostro and Carlo Piermarocchi

    Citation: BMC Systems Biology 2014 8:74

    Content type: Methodology article

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  33. Biochemical systems with relatively low numbers of components must be simulated stochastically in order to capture their inherent noise. Although there has recently been considerable work on discrete stochasti...

    Authors: Tamás Székely Jr., Kevin Burrage, Konstantinos C Zygalakis and Manuel Barrio

    Citation: BMC Systems Biology 2014 8:71

    Content type: Methodology article

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  34. Network representations of cell-biological signaling processes frequently contain large numbers of interacting molecular and multi-molecular components that can exist in, and switch between, multiple biochemic...

    Authors: Hsueh-Chien Cheng, Bastian R Angermann, Fengkai Zhang and Martin Meier-Schellersheim

    Citation: BMC Systems Biology 2014 8:70

    Content type: Software

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  35. Sexually-transmitted pathogens often have severe reproductive health implications if treatment is delayed or absent, especially in females. The complex processes of disease progression, namely replication and ...

    Authors: Martin R Nelson, Kelly J Sutton, Bindi S Brook, Dann G Mallet, Daniel P Simpson and Roger G Rank

    Citation: BMC Systems Biology 2014 8:66

    Content type: Software

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  36. Kinetic models can present mechanistic descriptions of molecular processes within a cell. They can be used to predict the dynamics of metabolite production, signal transduction or transcription of genes. Altho...

    Authors: Dicle Hasdemir, Huub CJ Hoefsloot, Johan A Westerhuis and Age K Smilde

    Citation: BMC Systems Biology 2014 8:61

    Content type: Research article

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  37. Comparing the metabolic pathways of different species is useful for understanding metabolic functions and can help in studying diseases and engineering drugs. Several comparison techniques for metabolic pathwa...

    Authors: Ricardo Alberich, Mercè Llabrés, David Sánchez, Marta Simeoni and Marc Tuduri

    Citation: BMC Systems Biology 2014 8:58

    Content type: Research article

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  38. Common approaches to pathway analysis treat pathways merely as lists of genes disregarding their topological structures, that is, ignoring the genes' interactions on which a pathway's cellular function depends...

    Authors: Rosario M Piro, Stefan Wiesberg, Gunnar Schramm, Nico Rebel, Marcus Oswald, Roland Eils, Gerhard Reinelt and Rainer König

    Citation: BMC Systems Biology 2014 8:56

    Content type: Software

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  40. In this paper we propose a model reduction method for biochemical reaction networks governed by a variety of reversible and irreversible enzyme kinetic rate laws, including reversible Michaelis-Menten and Hill...

    Authors: Shodhan Rao, Arjan van der Schaft, Karen van Eunen, Barbara M Bakker and Bayu Jayawardhana

    Citation: BMC Systems Biology 2014 8:52

    Content type: Methodology article

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  41. Genome-wide time-series data provide a rich set of information for discovering gene regulatory relationships. As genome-wide data for mammalian systems are being generated, it is critical to develop network in...

    Authors: William Chad Young, Adrian E Raftery and Ka Yee Yeung

    Citation: BMC Systems Biology 2014 8:47

    Content type: Methodology article

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  43. Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system’s set of defining differential equations. Traditionally, this would be don...

    Authors: Kaier Wang, Moira L Steyn-Ross, D Alistair Steyn-Ross, Marcus T Wilson, Jamie W Sleigh and Yoichi Shiraishi

    Citation: BMC Systems Biology 2014 8:45

    Content type: Methodology article

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  44. Building models of molecular regulatory networks is challenging not just because of the intrinsic difficulty of describing complex biological processes. Writing a model is a creative effort that calls for more...

    Authors: Alida Palmisano, Stefan Hoops, Layne T Watson, Thomas C Jones Jr, John J Tyson and Clifford A Shaffer

    Citation: BMC Systems Biology 2014 8:42

    Content type: Software

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  46. The inference of gene regulatory networks (GRNs) from experimental observations is at the heart of systems biology. This includes the inference of both the network topology and its dynamics. While there are ma...

    Authors: Paola Vera-Licona, Abdul Jarrah, Luis David Garcia-Puente, John McGee and Reinhard Laubenbacher

    Citation: BMC Systems Biology 2014 8:37

    Content type: Research article

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  47. Characterization of unknown proteins through computational approaches is one of the most challenging problems in silico biology, which has attracted world-wide interests and great efforts. There have been some...

    Authors: Wei Peng, Jianxin Wang, Juan Cai, Lu Chen, Min Li and Fang-Xiang Wu

    Citation: BMC Systems Biology 2014 8:35

    Content type: Methodology article

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  48. Most of the existing methods to analyze high-throughput data are based on gene ontology principles, providing information on the main functions and biological processes. However, these methods do not indicate ...

    Authors: Pierre Blavy, Florence Gondret, Sandrine Lagarrigue, Jaap van Milgen and Anne Siegel

    Citation: BMC Systems Biology 2014 8:32

    Content type: Methodology article

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  50. A biochemical mechanism with mass action kinetics can be represented as a directed bipartite graph (bipartite digraph), and modeled by a system of differential equations. If the differential equations (DE) mod...

    Authors: Georg R Walther, Matthew Hartley and Maya Mincheva

    Citation: BMC Systems Biology 2014 8:22

    Content type: Software

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BMC Systems Biology

ISSN: 1752-0509

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