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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. 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
    Content type: Software Published on:

  3. 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
    Content type: Methodology article Published on:

  5. 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
    Content type: Software Published on:

  6. 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
    Content type: Methodology article Published on:

  7. 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
    Content type: Methodology article Published on:

  8. 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
    Content type: Research Article Published on:

  9. 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
    Content type: Research Article Published on:

  10. 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
    Content type: Methodology Article Published on:

  12. 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
    Content type: Research Article Published on:

  13. 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
    Content type: Methodology Article Published on:

  14. 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
    Content type: Software Published on:

  16. 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
    Content type: Research Article Published on:

  17. 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
    Content type: Software Published on:

  18. 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
    Content type: Methodology article Published on:

  19. 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
    Content type: Research Article Published on:

  21. 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
    Content type: Research Article Published on:

  22. 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
    Content type: Research Article Published on:

  23. 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
    Content type: Research Article Published on:

  24. 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
    Content type: Methodology Article Published on:

  25. 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
    Content type: Research article Published on:

  26. 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
    Content type: Software Published on:

  27. 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
    Content type: Methodology Article Published on:

  28. 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
    Content type: Research Article Published on:

  32. Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biologica...

    Authors: David Murrugarra, Alan Veliz-Cuba, Boris Aguilar and Reinhard Laubenbacher
    Citation: BMC Systems Biology 2016 10:94
    Content type: Research Article Published on:

  33. 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 ...

    Authors: Edwin F. Juarez, Roy Lau, Samuel H. Friedman, Ahmadreza Ghaffarizadeh, Edmond Jonckheere, David B. Agus, Shannon M. Mumenthaler and Paul Macklin
    Citation: BMC Systems Biology 2016 10:92
    Content type: Software Published on:

  34. The estimation of intracellular flux through traditional metabolic flux analysis (MFA) using an overdetermined system of equations is a well established practice in metabolic engineering. Despite the continued...

    Authors: Stanislav Sokolenko, Marco Quattrociocchi and Marc G. Aucoin
    Citation: BMC Systems Biology 2016 10:91
    Content type: Methodology Article Published on:

  35. Chronic wounds are often colonized by consortia comprised of different bacterial species growing as biofilms on a complex mixture of wound exudate. Bacteria growing in biofilms exhibit phenotypes distinct from...

    Authors: Poonam Phalak, Jin Chen, Ross P. Carlson and Michael A. Henson
    Citation: BMC Systems Biology 2016 10:90
    Content type: Research article Published on:

  37. 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
    Content type: Software Published on:

  38. 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
    Content type: Methodology Article Published on:

  39. 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
    Content type: Methodology Article Published on:

  40. 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
    Content type: Software Published on:

  41. 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
    Content type: Database Published on:

  42. 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
    Content type: Research Article Published on:

  44. 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
    Content type: Methodology Article Published on:

  45. 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
    Content type: Research Article Published on:

  46. 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
    Content type: Methodology Article Published on:

  48. 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
    Content type: Research article Published on:

  49. 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
    Content type: Methodology Article Published on:

  50. 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
    Content type: Research Article Published on:

BMC Systems Biology

ISSN: 1752-0509

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