Skip to main content

Advertisement

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.

Page 1 of 9

  1. The recent advances in human disease network have provided insights into establishing the relationships between the genotypes and phenotypes of diseases. In spite of the great progress, it yet remains as only a m...

    Authors: Yonghyun Nam, Dong-gi Lee, Sunjoo Bang, Ju Han Kim, Jae-Hoon Kim and Hyunjung Shin

    Citation: BMC Bioinformatics 2019 20:576

    Content type: Methodology article

    Published on:

  2. Biologically data-driven networks have become powerful analytical tools that handle massive, heterogeneous datasets generated from biomedical fields. Protein-protein interaction networks can identify the most ...

    Authors: Milagros Marín, Francisco J. Esteban, Hilario Ramírez-Rodrigo, Eduardo Ros and María José Sáez-Lara

    Citation: BMC Bioinformatics 2019 20:565

    Content type: Methodology article

    Published on:

  3. An increasing number of biological and clinical evidences have indicated that the microorganisms significantly get involved in the pathological mechanism of extensive varieties of complex human diseases. Infer...

    Authors: Yahui Long and Jiawei Luo

    Citation: BMC Bioinformatics 2019 20:541

    Content type: Research Article

    Published on:

  4. At the molecular level, nonlinear networks of heterogeneous molecules control many biological processes, so that systems biology provides a valuable approach in this field, building on the integration of exper...

    Authors: S. Ha, E. Dimitrova, S. Hoops, D. Altarawy, M. Ansariola, D. Deb, J. Glazebrook, R. Hillmer, H. Shahin, F. Katagiri, J. McDowell, M. Megraw, J. Setubal, B. M. Tyler and R. Laubenbacher

    Citation: BMC Bioinformatics 2019 20:508

    Content type: Software

    Published on:

  5. Metabolic networks reflect the relationships between metabolites (biomolecules) and the enzymes (proteins), and are of particular interest since they describe all chemical reactions of an organism. The metabol...

    Authors: Adèle Weber Zendrera, Nataliya Sokolovska and Hédi A. Soula

    Citation: BMC Bioinformatics 2019 20:499

    Content type: Research Article

    Published on:

  6. Determining the association between tumor sample and the gene is demanding because it requires a high cost for conducting genetic experiments. Thus, the discovered association between tumor sample and gene fur...

    Authors: Mohan Timilsina, Haixuan Yang, Ratnesh Sahay and Dietrich Rebholz-Schuhmann

    Citation: BMC Bioinformatics 2019 20:462

    Content type: Research Article

    Published on:

  7. Protein interaction databases often provide confidence scores for each recorded interaction based on the available experimental evidence. Protein interaction networks (PINs) are then built by thresholding on t...

    Authors: Lyuba V. Bozhilova, Alan V. Whitmore, Jonny Wray, Gesine Reinert and Charlotte M. Deane

    Citation: BMC Bioinformatics 2019 20:446

    Content type: Research article

    Published on:

  8. Mining epistatic loci which affects specific phenotypic traits is an important research issue in the field of biology. Bayesian network (BN) is a graphical model which can express the relationship between gene...

    Authors: Yang Guo, Zhiman Zhong, Chen Yang, Jiangfeng Hu, Yaling Jiang, Zizhen Liang, Hui Gao and Jianxiao Liu

    Citation: BMC Bioinformatics 2019 20:444

    Content type: Methodology article

    Published on:

  9. Batch effects were not accounted for in most of the studies of computational drug repositioning based on gene expression signatures. It is unknown how batch effect removal methods impact the results of signatu...

    Authors: Wei Zhou, Karel K. M. Koudijs and Stefan Böhringer

    Citation: BMC Bioinformatics 2019 20:437

    Content type: Methodology article

    Published on:

  10. Gene and protein interaction data are often represented as interaction networks, where nodes stand for genes or gene products and each edge stands for a relationship between a pair of gene nodes. Commonly, tha...

    Authors: Joëlle Barido-Sottani, Samuel D. Chapman, Evsey Kosman and Arcady R. Mushegian

    Citation: BMC Bioinformatics 2019 20:435

    Content type: Research article

    Published on:

  11. Cartilage damage is a crucial feature involved in several pathological conditions characterized by joint disorders, such as osteoarthritis and rheumatoid arthritis. Accumulated evidences showed that Wnt/β-cate...

    Authors: Wei Zhou, Xiaojuan He, Ziyi Chen, Danping Fan, Yonghua Wang, Hui Feng, Ge Zhang, Aiping Lu and Lianbo Xiao

    Citation: BMC Bioinformatics 2019 20:412

    Content type: Research article

    Published on:

  12. The studies of functions of circular RNAs (circRNAs) are heavily focused on the regulation of gene expression through interactions with multiple miRNAs. However, the number of predicted target genes is typical...

    Authors: Ya-Chi Lin, Yueh-Chun Lee, Kai-Li Chang and Kuei-Yang Hsiao

    Citation: BMC Bioinformatics 2019 20:372

    Content type: Software

    Published on:

  13. Detection of central nodes in asymmetrically directed biological networks depends on centrality metrics quantifying individual nodes’ importance in a network. In topological analyses on metabolic networks, var...

    Authors: Eun-Youn Kim, Daniel Ashlock and Sung Ho Yoon

    Citation: BMC Bioinformatics 2019 20:328

    Content type: Research article

    Published on:

  14. Host factors of influenza virus replication are often found in key topological positions within protein-protein interaction networks. This work explores how protein states can be manipulated through controllab...

    Authors: Emily E. Ackerman, John F. Alcorn, Takeshi Hase and Jason E. Shoemaker

    Citation: BMC Bioinformatics 2019 20:297

    Content type: Research article

    Published on:

  15. Biochemical networks are often described through static or time-averaged measurements of the component macromolecules. Temporal variation in these components plays an important role in both describing the dyna...

    Authors: Maryam Masnadi-Shirazi, Mano R. Maurya, Gerald Pao, Eugene Ke, Inder M. Verma and Shankar Subramaniam

    Citation: BMC Bioinformatics 2019 20:294

    Content type: Research article

    Published on:

  16. Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them have unknown function. Recent evidence has shown the importance of both lncRNAs and chromat...

    Authors: Denise Thiel, Nataša Djurdjevac Conrad, Evgenia Ntini, Ria X. Peschutter, Heike Siebert and Annalisa Marsico

    Citation: BMC Bioinformatics 2019 20:292

    Content type: Methodology article

    Published on:

  17. The complexity of representing biological systems is compounded by an ever-expanding body of knowledge emerging from multi-omics experiments. A number of pathway databases have facilitated pathway-centric appr...

    Authors: Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt and Martin Hofmann-Apitius

    Citation: BMC Bioinformatics 2019 20:243

    Content type: Software

    Published on:

  18. Characterizing the modular structure of cellular network is an important way to identify novel genes for targeted therapeutics. This is made possible by the rising of high-throughput technology. Unfortunately,...

    Authors: Lifan Liang, Vicky Chen, Kunju Zhu, Xiaonan Fan, Xinghua Lu and Songjian Lu

    Citation: BMC Bioinformatics 2019 20:225

    Content type: Methodology article

    Published on:

  19. Gene networks in living cells can change depending on various conditions such as caused by different environments, tissue types, disease states, and development stages. Identifying the differential changes in ...

    Authors: Chen Wang, Feng Gao, Georgios B. Giannakis, Gennaro D’Urso and Xiaodong Cai

    Citation: BMC Bioinformatics 2019 20:224

    Content type: Methodology article

    Published on:

  20. Over one hundred different types of post-transcriptional RNA modifications have been identified in human. Researchers discovered that RNA modifications can regulate various biological processes, and RNA methyl...

    Authors: Xiangyu Wu, Zhen Wei, Kunqi Chen, Qing Zhang, Jionglong Su, Hui Liu, Lin Zhang and Jia Meng

    Citation: BMC Bioinformatics 2019 20:223

    Content type: Research article

    Published on:

  21. Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct repr...

    Authors: Leijie Li, Dongxue Che, Xiaodan Wang, Peng Zhang, Siddiq Ur Rahman, Jianbang Zhao, Jiantao Yu, Shiheng Tao, Hui Lu and Mingzhi Liao

    Citation: BMC Bioinformatics 2019 20:111

    Content type: Software

    Published on:

  22. The identification of prognostic genes that can distinguish the prognostic risks of cancer patients remains a significant challenge. Previous works have proven that functional gene sets were more reliable for ...

    Authors: Xiong-Hui Zhou, Xin-Yi Chu, Gang Xue, Jiang-Hui Xiong and Hong-Yu Zhang

    Citation: BMC Bioinformatics 2019 20:85

    Content type: Research article

    Published on:

  23. Biomarker discovery studies have been moving the focus from a single target gene to a set of target genes. However, the number of target genes in a drug should be minimum to avoid drug side-effect or toxicity....

    Authors: Sunjoo Bang, Sangjoon Son, Sooyoung Kim and Hyunjung Shin

    Citation: BMC Bioinformatics 2019 20:74

    Content type: Methodology article

    Published on:

  24. Reconstruction of protein-protein interaction networks (PPIN) has been riddled with controversy for decades. Particularly, false-negative and -positive interactions make this progress even more complicated. Al...

    Authors: Minoo Ashtiani, Payman Nickchi, Soheil Jahangiri-Tazehkand, Abdollah Safari, Mehdi Mirzaie and Mohieddin Jafari

    Citation: BMC Bioinformatics 2019 20:73

    Content type: Software

    Published on:

  25. Clustering molecular network is a typical method in system biology, which is effective in predicting protein complexes or functional modules. However, few studies have realized that biological molecules are sp...

    Authors: Lixin Cheng, Pengfei Liu, Dong Wang and Kwong-Sak Leung

    Citation: BMC Bioinformatics 2019 20:23

    Content type: Methodology article

    Published on:

  26. In systems biology, there is an acute need for integrative approaches in heterogeneous network mining in order to exploit the continuous flux of genomic data. Simultaneous analysis of the metabolic pathways an...

    Authors: Alexandra Zaharia, Bernard Labedan, Christine Froidevaux and Alain Denise

    Citation: BMC Bioinformatics 2019 20:19

    Content type: Methodology article

    Published on:

  27. Reverse engineering approaches to infer gene regulatory networks using computational methods are of great importance to annotate gene functionality and identify hub genes. Although various statistical algorith...

    Authors: Minzhe Zhang, Qiwei Li, Donghyeon Yu, Bo Yao, Wei Guo, Yang Xie and Guanghua Xiao

    Citation: BMC Bioinformatics 2019 20:12

    Content type: Software

    Published on:

  28. Predicting drug-disease interactions (DDIs) is time-consuming and expensive. Improving the accuracy of prediction results is necessary, and it is crucial to develop a novel computing technology to predict new ...

    Authors: Zhen Cui, Ying-Lian Gao, Jin-Xing Liu, Juan Wang, Junliang Shang and Ling-Yun Dai

    Citation: BMC Bioinformatics 2019 20:5

    Content type: Methodology article

    Published on:

  29. Accurate gene regulatory networks can be used to explain the emergence of different phenotypes, disease mechanisms, and other biological functions. Many methods have been proposed to infer networks from gene e...

    Authors: Phan Nguyen and Rosemary Braun

    Citation: BMC Bioinformatics 2018 19:545

    Content type: Methodology article

    Published on:

  30. Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidence...

    Authors: Bo Xu, Kun Li, Wei Zheng, Xiaoxia Liu, Yijia Zhang, Zhehuan Zhao and Zengyou He

    Citation: BMC Bioinformatics 2018 19:535

    Content type: Research article

    Published on:

  31. Network analyses, such as of gene co-expression networks, metabolic networks and ecological networks have become a central approach for the systems-level study of biological data. Several software packages exi...

    Authors: Deisy Morselli Gysi, Andre Voigt, Tiago de Miranda Fragoso, Eivind Almaas and Katja Nowick

    Citation: BMC Bioinformatics 2018 19:392

    Content type: Software

    Published on:

2018 Journal Metrics

  • Citation Impact
    2.511 - 2-year Impact Factor
    2.970 - 5-year Impact Factor
    0.855 - Source Normalized Impact per Paper (SNIP)
    1.374 - SCImago Journal Rank (SJR)

    Usage 
    4,129,368 downloads

    Social Media Impact
    4446 mentions

Advertisement