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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. The reconstruction of protein complexes from the physical interactome of organisms serves as a building block towards understanding the higher level organization of the cell. Over the past few years, several i...

    Authors: Sriganesh Srihari, Kang Ning and Hon Wai Leong

    Citation: BMC Bioinformatics 2010 11:504

    Content type: Research article

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  2. The use of ontologies to control vocabulary and structure annotation has added value to genome-scale data, and contributed to the capture and re-use of knowledge across research domains. Gene Ontology (GO) is ...

    Authors: Melissa J Davis, Muhammad Shoaib B Sehgal and Mark A Ragan

    Citation: BMC Bioinformatics 2010 11:498

    Content type: Methodology article

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  3. An increase in work on the full text of journal articles and the growth of PubMedCentral have the opportunity to create a major paradigm shift in how biomedical text mining is done. However, until now there ha...

    Authors: K Bretonnel Cohen, Helen L Johnson, Karin Verspoor, Christophe Roeder and Lawrence E Hunter

    Citation: BMC Bioinformatics 2010 11:492

    Content type: Research article

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  4. Flux variability analysis is often used to determine robustness of metabolic models in various simulation conditions. However, its use has been somehow limited by the long computation time compared to other co...

    Authors: Steinn Gudmundsson and Ines Thiele

    Citation: BMC Bioinformatics 2010 11:489

    Content type: Software

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  5. Researchers in systems biology use network visualization to summarize the results of their analysis. Such networks often include unconnected components, which popular network alignment algorithms place arbitra...

    Authors: Miha Štajdohar, Minca Mramor, Blaž Zupan and Janez Demšar

    Citation: BMC Bioinformatics 2010 11:475

    Content type: Research article

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  6. Linking high-throughput experimental data with biological networks is a key step for understanding complex biological systems. Currently, visualization tools for large metabolic networks often result in a dens...

    Authors: Ming Jia, Suh-Yeon Choi, Dirk Reiners, Eve S Wurtele and Julie A Dickerson

    Citation: BMC Bioinformatics 2010 11:469

    Content type: Software

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  7. Discovering novel disease genes is still challenging for diseases for which no prior knowledge - such as known disease genes or disease-related pathways - is available. Performing genetic studies frequently re...

    Authors: Daniela Nitsch, Joana P Gonçalves, Fabian Ojeda, Bart de Moor and Yves Moreau

    Citation: BMC Bioinformatics 2010 11:460

    Content type: Methodology article

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  8. In high-dimensional data analysis such as differential gene expression analysis, people often use filtering methods like fold-change or variance filters in an attempt to reduce the multiple testing penalty and...

    Authors: Maarten van Iterson, Judith M Boer and Renée X Menezes

    Citation: BMC Bioinformatics 2010 11:450

    Content type: Research article

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  9. Most biomedical ontologies are represented in the OBO Flatfile Format, which is an easy-to-use graph-based ontology language. The semantics of the OBO Flatfile Format 1.2 enforces a strict predetermined interp...

    Authors: Robert Hoehndorf, Anika Oellrich, Michel Dumontier, Janet Kelso, Dietrich Rebholz-Schuhmann and Heinrich Herre

    Citation: BMC Bioinformatics 2010 11:441

    Content type: Methodology article

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  10. Modern biology uses experimental systems that involve the exploration of phenotypic variation as a result of the recombination of several genomes. Such systems are useful to investigate the functional evolutio...

    Authors: Diego H Milone, Georgina S Stegmayer, Laura Kamenetzky, Mariana López, Je Min Lee, James J Giovannoni and Fernando Carrari

    Citation: BMC Bioinformatics 2010 11:438

    Content type: Software

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  11. The study of biological systems demands computational support. If targeting a biological problem, the reuse of existing computational models can save time and effort. Deciding for potentially suitable models, ...

    Authors: Ron Henkel, Lukas Endler, Andre Peters, Nicolas Le Novère and Dagmar Waltemath

    Citation: BMC Bioinformatics 2010 11:423

    Content type: Methodology article

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  12. Epistasis is recognized as a fundamental part of the genetic architecture of individuals. Several computational approaches have been developed to model gene-gene interactions in case-control studies, however, ...

    Authors: Lorenzo Beretta, Alessandro Santaniello, Piet LCM van Riel, Marieke JH Coenen and Raffaella Scorza

    Citation: BMC Bioinformatics 2010 11:416

    Content type: Research article

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  13. At present, the organization of system modules is typically limited to either a multilevel hierarchy that describes the "vertical" relationships between modules at different levels (e.g., module A at level two...

    Authors: Chia-Ying Cheng and Yuh-Jyh Hu

    Citation: BMC Bioinformatics 2010 11:411

    Content type: Research article

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  14. Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious d...

    Authors: Miguel García-Remesal, Alejandro Cuevas, Victoria López-Alonso, Guillermo López-Campos, Guillermo de la Calle, Diana de la Iglesia, David Pérez-Rey, José Crespo, Fernando Martín-Sánchez and Víctor Maojo

    Citation: BMC Bioinformatics 2010 11:410

    Content type: Methodology article

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  15. Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regi...

    Authors: Lina Chen, Hong Wang, Liangcai Zhang, Wan Li, Qian Wang, Yukui Shang, Yuehan He, Weiming He, Xu Li, Jingxie Tai and Xia Li

    Citation: BMC Bioinformatics 2010 11:392

    Content type: Research article

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  16. The development of high-throughput laboratory techniques created a demand for computer-assisted result analysis tools. Many of these techniques return lists of genes whose interpretation requires finding relev...

    Authors: Joel P Arrais, João Fernandes, João Pereira and José Luís Oliveira

    Citation: BMC Bioinformatics 2010 11:389

    Content type: Software

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  17. Sub-cellular structures interact in numerous direct and indirect ways in order to fulfill cellular functions. While direct molecular interactions crucially depend on spatial proximity, other interactions typicall...

    Authors: Jo A Helmuth, Grégory Paul and Ivo F Sbalzarini

    Citation: BMC Bioinformatics 2010 11:372

    Content type: Research article

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  18. Environmental sequence datasets are increasing at an exponential rate; however, the vast majority of them lack appropriate descriptors like sampling location, time and depth/altitude: generally referred to as ...

    Authors: Wolfgang Hankeln, Pier Luigi Buttigieg, Dennis Fink, Renzo Kottmann, Pelin Yilmaz and Frank Oliver Glöckner

    Citation: BMC Bioinformatics 2010 11:358

    Content type: Software

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  19. Many high-throughput genomic experiments, such as Synthetic Genetic Array and yeast two-hybrid, use colony growth on solid media as a screen metric. These experiments routinely generate over 100,000 data point...

    Authors: John C Dittmar, Robert JD Reid and Rodney Rothstein

    Citation: BMC Bioinformatics 2010 11:353

    Content type: Software

    Published on:

  20. Cell volume determination plays a pivotal role in the investigation of the biophysical mechanisms underlying various cellular processes. Whereas light microscopy in principle enables one to obtain three dimens...

    Authors: Patrick Happel, Kerstin Möller, Ralf Kunz and Irmgard D Dietzel

    Citation: BMC Bioinformatics 2010 11:323

    Content type: Methodology article

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  21. The omics fields promise to revolutionize our understanding of biology and biomedicine. However, their potential is compromised by the challenge to analyze the huge datasets produced. Analysis of omics data is...

    Authors: Martin Eklund, Ola Spjuth and Jarl ES Wikberg

    Citation: BMC Bioinformatics 2010 11:282

    Content type: Methodology article

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  22. Shared-usage high throughput screening (HTS) facilities are becoming more common in academe as large-scale small molecule and genome-scale RNAi screening strategies are adopted for basic research purposes. The...

    Authors: Andrew N Tolopko, John P Sullivan, Sean D Erickson, David Wrobel, Su L Chiang, Katrina Rudnicki, Stewart Rudnicki, Jennifer Nale, Laura M Selfors, Dara Greenhouse, Jeremy L Muhlich and Caroline E Shamu

    Citation: BMC Bioinformatics 2010 11:260

    Content type: Software

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    3.213 - 5-year Impact Factor
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