Skip to content


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 5

  1. Content type: Software

    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 ...

    Authors: Robert Pesch and Ralf Zimmer

    Citation: BMC Systems Biology 2016 10:76

    Published on:

  2. Content type: Methodology Article

    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...

    Authors: Ines Wilms and Christophe Croux

    Citation: BMC Systems Biology 2016 10:72

    Published on:

  3. Content type: Methodology Article

    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...

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

    Citation: BMC Systems Biology 2016 10:56

    Published on:

  4. Content type: Software

    Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, par...

    Authors: Yeimy Morales, Gabriel Bosque, Josep Vehí, Jesús Picó and Francisco Llaneras

    Citation: BMC Systems Biology 2016 10:46

    Published on:

  5. Content type: Database

    Disease similarity study provides new insights into disease taxonomy, pathogenesis, which plays a guiding role in diagnosis and treatment. The early studies were limited to estimate disease similarities based ...

    Authors: Jing Yang, Su-Juan Wu, Shao-You Yang, Jia-Wei Peng, Shi-Nuo Wang, Fu-Yan Wang, Yu-Xing Song, Ting Qi, Yi-Xue Li and Yuan-Yuan Li

    Citation: BMC Systems Biology 2016 10:36

    Published on:

  6. Content type: Research Article

    Invasive aspergillosis is a severe infection of immunocompromised hosts, caused by the inhalation of the spores of the ubiquitous environmental molds of the Aspergillus genus. The innate immune response in this i...

    Authors: Matthew Oremland, Kathryn R. Michels, Alexandra M. Bettina, Chris Lawrence, Borna Mehrad and Reinhard Laubenbacher

    Citation: BMC Systems Biology 2016 10:34

    Published on:

  7. Content type: Methodology Article

    Systems Biology has motivated dynamic models of important intracellular processes at the pathway level, for example, in signal transduction and cell cycle control. To answer important biomedical questions, how...

    Authors: Katrin Kolczyk and Carsten Conradi

    Citation: BMC Systems Biology 2016 10:28

    Published on:

  8. Content type: Research Article

    In planarian flatworms, the mechanisms underlying the activity of collectively pluripotent adult stem cells (neoblasts) and their descendants can now be studied from the level of the individual gene to the ent...

    Authors: Marc Mangel, Michael B. Bonsall and Aziz Aboobaker

    Citation: BMC Systems Biology 2016 10:17

    Published on:

  9. Content type: Methodology Article

    High throughput technologies have been used to profile genes in multiple different dimensions, such as genetic variation, copy number, gene and protein expression, epigenetics, metabolomics. Computational anal...

    Authors: Ana B. Pavel, Dmitriy Sonkin and Anupama Reddy

    Citation: BMC Systems Biology 2016 10:16

    Published on:

  10. Content type: Research article

    Contamination of the environment with bioactive chemicals has emerged as a potential public health risk. These substances that may cause distress or disease in humans can be found in air, water and food suppli...

    Authors: Mona Yousofshahi, Sara Manteiga, Charmian Wu, Kyongbum Lee and Soha Hassoun

    Citation: BMC Systems Biology 2015 9:94

    Published on:

  11. Content type: Methodology Article

    Reconstructing gene regulatory networks (GRNs) from expression data is a challenging task that has become essential to the understanding of complex regulatory mechanisms in cells. The major issues are the usua...

    Authors: Mahsa Ghanbari, Julia Lasserre and Martin Vingron

    Citation: BMC Systems Biology 2015 9:84

    Published on:

  12. Content type: Research Article

    The differentiation of naive CD 4+ helper T (Th) cells into effector Th17 cells is steered by extracellular cytokines that activate and control the lineage specific transcriptional program. While the inducing cyt...

    Authors: Jukka Intosalmi, Helena Ahlfors, Sini Rautio, Henrik Mannerstöm, Zhi Jane Chen, Riitta Lahesmaa, Brigitta Stockinger and Harri Lähdesmäki

    Citation: BMC Systems Biology 2015 9:81

    Published on:

  13. Content type: Methodology Article

    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

    Published on:

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

  14. Content type: Software

    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

    Published on:

  15. Content type: Research Article

    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

    Published on:

  16. Content type: Methodology Article

    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

    Published on:

  17. Content type: Review

    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

    Published on:

  18. Content type: Research article

    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

    Published on:

  19. Content type: Software

    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

    Published on:

  20. Content type: Methodology Article

    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

    Published on:

  21. Content type: Methodology article

    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

    Published on:

  22. Content type: Software

    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

    Published on:

  23. Content type: Software

    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

    Published on:

  24. Content type: Methodology Article

    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

    Published on:

  25. Content type: Methodology Article

    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

    Published on:

  26. Content type: Research article

    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

    Published on:

  27. Content type: Methodology article

    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

    Published on:

  28. Content type: Methodology article

    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

    Published on:

  29. Content type: Methodology Article

    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

    Published on:

  30. Content type: Software

    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

    Published on:

  31. Content type: Methodology article

    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

    Published on:

  32. Content type: Methodology article

    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

    Published on:

  33. Content type: Methodology article

    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

    Published on:

  34. Content type: Methodology article

    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

    Published on:

  35. Content type: Methodology article

    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

    Published on:

  36. Content type: Software

    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

    Published on:

  37. Content type: Software

    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

    Published on:

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
    523 mentions