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Networks analysis

Section edited by Jean-Philippe Vert

This section incorporates all aspects of network analysis including but not limited to: methods for predicting, analyzing and visualizing networks, and applications to systems biology.

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  1. Sparse Gaussian graphical models are popular for inferring biological networks, such as gene regulatory networks. In this paper, we investigate the consistency of these models across different data platforms, ...

    Authors: Veronica Vinciotti, Ernst C. Wit, Rick Jansen, Eco J. C. N. de Geus, Brenda W. J. H. Penninx, Dorret I. Boomsma and Peter A. C. ’t Hoen

    Citation: BMC Bioinformatics 2016 17:254

    Content type: Methodology Article

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  2. Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth...

    Authors: Luciano Fernandez-Ricaud, Olga Kourtchenko, Martin Zackrisson, Jonas Warringer and Anders Blomberg

    Citation: BMC Bioinformatics 2016 17:249

    Content type: Software

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  3. The targeting of disease-related proteins is important for drug discovery, and yet target-based discovery has not been fruitful. Contextualizing overall biological processes is critical to formulating successf...

    Authors: Naiem T. Issa, Jordan Kruger, Henri Wathieu, Rajarajan Raja, Stephen W. Byers and Sivanesan Dakshanamurthy

    Citation: BMC Bioinformatics 2016 17:202

    Content type: Research article

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  4. We have previously presented a formal language for describing population dynamics based on environment-dependent Stochastic Tree Grammars (eSTG). The language captures in broad terms the effect of the changing...

    Authors: Adam Spiro and Ehud Shapiro

    Citation: BMC Bioinformatics 2016 17:187

    Content type: Software

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    The Erratum to this article has been published in BMC Bioinformatics 2016 17:303

  5. Recently, high-throughput experimental techniques have generated a large amount of protein-protein interaction (PPI) data which can construct large complex PPI networks for numerous organisms. System biology a...

    Authors: Yijia Zhang, Hongfei Lin, Zhihao Yang and Jian Wang

    Citation: BMC Bioinformatics 2016 17:186

    Content type: Research article

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  6. Network visualization and analysis tools aid in better understanding of complex biological systems. Furthermore, to understand the differences in behaviour of system(s) under various environmental conditions (...

    Authors: Bhusan K. Kuntal, Anirban Dutta and Sharmila S. Mande

    Citation: BMC Bioinformatics 2016 17:185

    Content type: Software

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    The Correction to this article has been published in BMC Bioinformatics 2019 20:600

  7. Biological research increasingly relies on network models to study complex phenomena. Signal Transduction Pathways are molecular circuits that model how cells receive, process, and respond to information from ...

    Authors: Gianfranco Politano, Francesca Orso, Monica Raimo, Alfredo Benso, Alessandro Savino, Daniela Taverna and Stefano Di Carlo

    Citation: BMC Bioinformatics 2016 17:157

    Content type: Software

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  8. Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However, they have been developed...

    Authors: Nicolas Rodriguez, Jean-Baptiste Pettit, Piero Dalle Pezze, Lu Li, Arnaud Henry, Martijn P. van Iersel, Gael Jalowicki, Martina Kutmon, Kedar N. Natarajan, David Tolnay, Melanie I. Stefan, Chris T. Evelo and Nicolas Le Novère

    Citation: BMC Bioinformatics 2016 17:154

    Content type: Software

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  9. Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available...

    Authors: Sapna Kumari, Wenping Deng, Chathura Gunasekara, Vincent Chiang, Huann-sheng Chen, Hao Ma, Xin Davis and Hairong Wei

    Citation: BMC Bioinformatics 2016 17:132

    Content type: Methodology article

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  10. It is generally acknowledged that a functional understanding of a biological system can only be obtained by an understanding of the collective of molecular interactions in form of biological networks. Protein ...

    Authors: Shailesh Tripathi, Salissou Moutari, Matthias Dehmer and Frank Emmert-Streib

    Citation: BMC Bioinformatics 2016 17:129

    Content type: Research Article

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  11. Networks or graphs play an important role in the biological sciences. Protein interaction networks and metabolic networks support the understanding of basic cellular mechanisms. In the human brain, networks of...

    Authors: Klaus Hahn, Peter R. Massopust and Sergei Prigarin

    Citation: BMC Bioinformatics 2016 17:87

    Content type: Methodology Article

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  12. Complex disease is largely determined by a number of biomolecules interwoven into networks, rather than a single biomolecule. A key but inadequately addressed issue is how to test possible differences of the n...

    Authors: Jiadong Ji, Zhongshang Yuan, Xiaoshuai Zhang and Fuzhong Xue

    Citation: BMC Bioinformatics 2016 17:86

    Content type: Methodology article

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  13. Dynamical models of gene regulatory networks (GRNs) are highly effective in describing complex biological phenomena and processes, such as cell differentiation and cancer development. Yet, the topological and ...

    Authors: Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri and Marco Antoniotti

    Citation: BMC Bioinformatics 2016 17:64

    Content type: Software

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  14. Inflammatory bowel disease (IBD) consists of two main disease-subtypes, Crohn’s disease (CD) and ulcerative colitis (UC); these subtypes share overlapping genetic and clinical features. Genome-wide microarray ...

    Authors: Daniele Muraro and Alison Simmons

    Citation: BMC Bioinformatics 2016 17:42

    Content type: Research Article

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  15. Gene co-expression evidenced as a response to environmental changes has shown that transcriptional activity is coordinated, which pinpoints the role of transcriptional regulatory networks (TRNs). Nevertheless,...

    Authors: Vicente Acuña, Andrés Aravena, Carito Guziolowski, Damien Eveillard, Anne Siegel and Alejandro Maass

    Citation: BMC Bioinformatics 2016 17:35

    Content type: Research Article

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  16. Differential networks have recently been introduced as a powerful way to study the dynamic rewiring capabilities of an interactome in response to changing environmental conditions or stimuli. Currently, such d...

    Authors: Sofie Van Landeghem, Thomas Van Parys, Marieke Dubois, Dirk Inzé and Yves Van de Peer

    Citation: BMC Bioinformatics 2016 17:18

    Content type: Research Article

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  17. Advances in high throughput technologies and growth of biomedical knowledge have contributed to an exponential increase in associative data. These data can be represented in the form of complex networks of bio...

    Authors: Ákos Tényi, Pedro de Atauri, David Gomez-Cabrero, Isaac Cano, Kim Clarke, Francesco Falciani, Marta Cascante, Josep Roca and Dieter Maier

    Citation: BMC Bioinformatics 2016 17:17

    Content type: Methodology article

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  18. Inferring gene regulatory network (GRN) has been an important topic in Bioinformatics. Many computational methods infer the GRN from high-throughput expression data. Due to the presence of time delays in the r...

    Authors: Leung-Yau Lo, Man-Leung Wong, Kin-Hong Lee and Kwong-Sak Leung

    Citation: BMC Bioinformatics 2015 16:395

    Content type: Research Article

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  19. Inferring gene networks from high-throughput data constitutes an important step in the discovery of relevant regulatory relationships in organism cells. Despite the large number of available Gene Regulatory Ne...

    Authors: Aurélie Pirayre, Camille Couprie, Frédérique Bidard, Laurent Duval and Jean-Christophe Pesquet

    Citation: BMC Bioinformatics 2015 16:368

    Content type: Research Article

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  20. Network component analysis (NCA) became a popular tool to understand complex regulatory networks. The method uses high-throughput gene expression data and a priori topology to reconstruct transcription factor ...

    Authors: Naresh Doni Jayavelu, Lasse S. Aasgaard and Nadav Bar

    Citation: BMC Bioinformatics 2015 16:366

    Content type: Methodology Article

    Published on:

  21. Enrichment analysis is a popular approach to identify pathways or sets of genes which are significantly enriched in the context of differentially expressed genes. The traditional gene set enrichment approach c...

    Authors: Michaela Bayerlová, Klaus Jung, Frank Kramer, Florian Klemm, Annalen Bleckmann and Tim Beißbarth

    Citation: BMC Bioinformatics 2015 16:334

    Content type: Research article

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  22. In the field of network science, exploring principal and crucial modules or communities is critical in the deduction of relationships and organization of complex networks. This approach expands an arena, and t...

    Authors: Mohieddin Jafari, Mehdi Mirzaie and Mehdi Sadeghi

    Citation: BMC Bioinformatics 2015 16:319

    Content type: Research article

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  23. In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproduc...

    Authors: Pau Bellot, Catharina Olsen, Philippe Salembier, Albert Oliveras-Vergés and Patrick E. Meyer

    Citation: BMC Bioinformatics 2015 16:312

    Content type: Software

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  24. The inference of complex networks from data is a challenging problem in biological sciences, as well as in a wide range of disciplines such as chemistry, technology, economics, or sociology. The quantity and q...

    Authors: Abel Folch-Fortuny, Alejandro F. Villaverde, Alberto Ferrer and Julio R. Banga

    Citation: BMC Bioinformatics 2015 16:283

    Content type: Methodology Article

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  25. The cascade computer model (CCM) was designed as a machine-learning feature platform for prediction of drug diffusivity from the mucoadhesive formulations. Three basic models (the statistical regression model,...

    Authors: Yugyung Lee, Alok Khemka, Gayathri Acharya, Namita Giri and Chi H. Lee

    Citation: BMC Bioinformatics 2015 16:263

    Content type: Research article

    Published on:

  26. The concept of Petri nets (PN) is widely used in systems biology and allows modeling of complex biochemical systems like metabolic systems, signal transduction pathways, and gene expression networks. In partic...

    Authors: Pavel Balazki, Klaus Lindauer, Jens Einloft, Jörg Ackermann and Ina Koch

    Citation: BMC Bioinformatics 2015 16:215

    Content type: Software

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    The Erratum to this article has been published in BMC Bioinformatics 2015 16:371

  27. Tandem repetition of structural motifs in proteins is frequently observed across all forms of life. Topology of repeating unit and its frequency of occurrence are associated to a wide range of structural and f...

    Authors: Broto Chakrabarty and Nita Parekh

    Citation: BMC Bioinformatics 2014 15:6599

    Content type: Methodology article

    Published on:

  28. With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, ...

    Authors: Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez, Herbert M Sauro, Martin Scharm, Stian Soiland-Reyes, Dagmar Waltemath…

    Citation: BMC Bioinformatics 2014 15:369

    Content type: Software

    Published on:

  29. Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods.

    Authors: Andrew Schoenrock, Bahram Samanfar, Sylvain Pitre, Mohsen Hooshyar, Ke Jin, Charles A Phillips, Hui Wang, Sadhna Phanse, Katayoun Omidi, Yuan Gui, Md Alamgir, Alex Wong, Fredrik Barrenäs, Mohan Babu, Mikael Benson, Michael A Langston…

    Citation: BMC Bioinformatics 2014 15:383

    Content type: Research article

    Published on:

  30. Predication of gene regularity network (GRN) from expression data is a challenging task. There are many methods that have been developed to address this challenge ranging from supervised to unsupervised method...

    Authors: Zeeshan Gillani, Muhammad Sajid Hamid Akash, MD Matiur Rahaman and Ming Chen

    Citation: BMC Bioinformatics 2014 15:395

    Content type: Research article

    Published on:

  31. Respiratory epithelial cells are the primary target of influenza virus infection in human. However, the molecular mechanisms of airway epithelial cell responses to viral infection are not fully understood. Rev...

    Authors: Zhi-Ping Liu, Hulin Wu, Jian Zhu and Hongyu Miao

    Citation: BMC Bioinformatics 2014 15:336

    Content type: Methodology article

    Published on:

  32. Proteins dynamically interact with each other to perform their biological functions. The dynamic operations of protein interaction networks (PPI) are also reflected in the dynamic formations of protein complex...

    Authors: Le Ou-Yang, Dao-Qing Dai, Xiao-Li Li, Min Wu, Xiao-Fei Zhang and Peng Yang

    Citation: BMC Bioinformatics 2014 15:335

    Content type: Research article

    Published on:

  33. Metabolic networks are represented by the set of metabolic pathways. Metabolic pathways are a series of biochemical reactions, in which the product (output) from one reaction serves as the substrate (input) to...

    Authors: Abiel Roche-Lima, Michael Domaratzki and Brian Fristensky

    Citation: BMC Bioinformatics 2014 15:318

    Content type: Research article

    Published on:

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