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Recent Advances in Network-based Methods for Disease Gene Prediction [article]

Sezin Kircali Ata, Min Wu, Yuan Fang, Le Ou-Yang, Chee Keong Kwoh, Xiao-Li Li
2020 arXiv   pre-print
In this survey, we aim to provide a comprehensive and an up-to-date review of network-based methods for disease gene prediction. We also conduct an empirical analysis on 14 state-of-the-art methods.  ...  Since molecular networks are able to capture complex interplay among molecules in diseases, they become one of the most extensively used data for disease-gene association prediction.  ...  Then, we introduce various network-based diseasegene prediction methods in details in Section 'Network-based Methods for Disease Gene Prediction'.  ... 
arXiv:2007.10848v1 fatcat:zhrspbsj6zfpfhwa42mzjp4lvy

Advanced Systems Biology Methods in Drug Discovery and Translational Biomedicine

Jun Zou, Ming-Wu Zheng, Gen Li, Zhi-Guang Su
2013 BioMed Research International  
gene prediction.  ...  In addition, important advances in drug discovery, to which systems biology makes significant contributions, are discussed, including drug-target networks, prediction of drug-target interactions, investigation  ...  This new method is based on the observation that similar drugs are indicated for similar diseases and utilizes the chemical similarity of drugs and disease-disease similarity measures for the prediction  ... 
doi:10.1155/2013/742835 pmid:24171171 pmcid:PMC3792523 fatcat:nhsv3ig7vzgspjhnzkaj3pwypm

The Impact of Network Medicine in Gastroenterology and Hepatology

György Baffy
2013 Clinical Gastroenterology and Hepatology  
Figure 2 . 2 Network-based discovery of gene-disease associations in complex disease A.  ...  Technological primer: Systems biology strategies for finding gene-disease associations Big data science: Cataloging the parts A number of recent advances in biomedical technologies began to tackle complexity  ... 
doi:10.1016/j.cgh.2013.07.033 pmid:23932906 fatcat:emuddivujvbbdbf7pbun5n64ze

A General Computational Framework for Prediction of Disease-associated Non-coding RNAs

Duc-Hau Le
2019 VNU Journal of Science Computer Science and Communication Engineering  
To date, many computational methods have been also proposed for prediction of disease-associated miRNAs and lncRNAs, and recently comprehensively reviewed.  ...  Therefore, in this study, we propose a general computational framework for prediction of disease-associated ncRNAs.  ...  Acknowledgements Funding: This research is funded by Vietnam National Foundation for Science and Technology Development (NAFOSTED) under grant number 102.01-2017.14.  ... 
doi:10.25073/2588-1086/vnucsce.224 fatcat:6ivojgsgh5bonkasyseodx34fm

Drug Repurposing Using Biological Networks

Francisco Javier Somolinos, Carlos León, Sara Guerrero-Aspizua
2021 Processes  
The goal of this review is to show the usefulness of these computational methods to predict associations and to find candidate drugs for repositioning in new indications of certain diseases.  ...  This allows the use of computational methods and models based on biological networks to develop new possibilities for drug repurposing.  ...  In recent years, network-based methods have become a major strategy for drug repositioning [4, 9] .  ... 
doi:10.3390/pr9061057 fatcat:wrdrh3hi65gszjec2prg6pixn4

Biomolecular Networks for Complex Diseases

Fang-Xiang Wu, Jianxin Wang, Min Li, Haiying Wang
2018 Complexity  
In the paper "DriverFinder: A Gene Length-Based Network Method to Identify Cancer Driver Genes," P.-J.  ...  In the paper "SDTRLS: Predicting Drug-Target Interactions for Complex Diseases Based on Chemical Substructures," C.  ...  In summary, this focus issue has reported the recent progress in the studies of biomolecular networks for complex diseases.  ... 
doi:10.1155/2018/4210160 fatcat:2boeaxsahbdkjekgwpkv23r4be

The Emerging Paradigm of Network Medicine in the Study of Human Disease

S. Y. Chan, J. Loscalzo
2012 Circulation Research  
This review introduces the fundamental concepts of network medicine and explores the feasibility and potential impact of network-based methods for predicting individual manifestations of human disease  ...  As methodologies evolve, network medicine has the potential to capture the molecular complexity of human disease while offering computational methods to discern how such complexity controls disease manifestations  ...  Acknowledgments We thank Stephanie Tribuna for expert administrative assistance and Sol Chan for assistance with figures.  ... 
doi:10.1161/circresaha.111.258541 pmid:22821909 pmcid:PMC3425394 fatcat:m4zwmfv42vejrpd3kkbpx2k4h4

Computational Systems Biology

Xing-Ming Zhao, Weidong Tian, Rui Jiang, Jun Wan
2013 The Scientific World Journal  
In this special issue, we reported the recent progress made in developing new computational methodologies to analyze the genomics data, construct gene networks, and identify disease genes.  ...  In recent years, the advance of next-generation sequencing (NGS) technology makes it more easier for researchers to access and analyze genetics data and has influential effects on the biomedical research  ...  Acknowledgments We would like to thank all reviewers for their invaluable contributions to the peer review process which have made this special issue possible.  ... 
doi:10.1155/2013/350358 pmid:23576901 pmcid:PMC3612478 fatcat:2y33vzm44vcrpb6puwiunlwt7e

Editorial: Graph Embedding Methods for Multiple-Omics Data Analysis

Wei Lan, Qingfeng Chen, Yi-Ping Phoebe Chen, Wilson Wen Bin Goh
2021 Frontiers in Genetics  
Pan et al. presented an embedding-based method for predicting the subcellular localization of proteins.  ...  Recently, machine learning methods especially graph embedding have shown powerful capability in analyzing multiple-omics data.  ...  National Natural Science Foundation of China (Nos. 62072124, 61963004, and 61972185), the Natural Science Foundation of Guangxi (Nos. 2021GXNSFAA075041 and 2018GXNSFBA281193), the Science and Technology Base  ... 
doi:10.3389/fgene.2021.762274 pmid:34616440 pmcid:PMC8488216 fatcat:msr5ycebtned3hz27dieediyiu

Incorporating Machine Learning into Established Bioinformatics Frameworks

Noam Auslander, Ayal B. Gussow, Eugene V. Koonin
2021 International Journal of Molecular Sciences  
Here, we review recently developed methods that incorporate machine learning within the same framework with techniques from molecular evolution, protein structure analysis, systems biology, and disease  ...  We outline the challenges posed for machine learning, and, in particular, deep learning in biomedicine, and suggest unique opportunities for machine learning techniques integrated with established bioinformatics  ...  These methods primarily exploit recent advances in deep learning architectures to enhance the prediction of PPI networks [93] .  ... 
doi:10.3390/ijms22062903 pmid:33809353 pmcid:PMC8000113 fatcat:ssfoobbtcjhidbaffbkakqbwfe

Review of Biological Network Data and Its Applications

Donghyeon Yu, MinSoo Kim, Guanghua Xiao, Tae Hyun Hwang
2013 Genomics & Informatics  
Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization  ...  In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions.  ...  The methods are summarized in Table 3 [10, 11, 13-16, 59-83]. Table 4 . 4 Network-based disease gene prioritization methods .  ... 
doi:10.5808/gi.2013.11.4.200 pmid:24465231 pmcid:PMC3897847 fatcat:v72gan3nara6xfqwbxwwljzouq

An outlook on metabolic pathway engineering in crop plants

Jyoti Prakash Sahoo, Upasana Mohapatra, Priyadarshini Mishra
2020 Archives of Agriculture and Environmental Science  
Mathematical and statistical models to scale and map the genome for integrative metabolic pathway activity, signal transduction mechanism in the genome, gene regulation and the networks of protein-protein  ...  Recently, artificial intelligence concept and approaches are experimentally applied for efficient and accurate metabolic engineering in plants.  ...  DeepEc (Ryu et al., 2019) is another convolutional neural networks-based method with homology analysis for predicting enzyme using protein sequences as inputs.  ... 
doi:10.26832/24566632.2020.0503027 fatcat:qml5yxl54vhh3hpyqsgbboasfa

Network biology methods integrating biological data for translational science

G. Bebek, M. Koyuturk, N. D. Price, M. R. Chance
2012 Briefings in Bioinformatics  
In this review, recent advances in network biology approaches and results are identified.  ...  can be jointly analyzed to understand and predict disease phenotypes.  ...  Acknowledgements The authors would like to acknowledge James Eddy for making  ... 
doi:10.1093/bib/bbr075 pmid:22390873 pmcid:PMC3404396 fatcat:cdfuoph3o5b5bcpdkfgop4fzpy

Identification of aberrant pathways and network activities from high-throughput data

J. Wang, Y. Zhang, C. Marian, H. W. Ressom
2012 Briefings in Bioinformatics  
Many complex diseases such as cancer are associated with changes in biological pathways and molecular networks rather than being caused by single gene alterations.  ...  This review presents recent progress in using high-throughput biological assays to decipher aberrant pathways and network activities.  ...  Rhoda Perozzi for her kindness in performing a thorough review and edit. We thank the anonymous reviewers for their suggestions for improving the manuscript.  ... 
doi:10.1093/bib/bbs001 pmid:22287794 pmcid:PMC3404398 fatcat:woielqwwtbc6bhdoub3hycnu6a

A survey of current trends in computational drug repositioning

Jiao Li, Si Zheng, Bin Chen, Atul J. Butte, S. Joshua Swamidass, Zhiyong Lu
2015 Briefings in Bioinformatics  
In this review, we show recent advancements in the critical areas of computational drug repositioning from multiple aspects.  ...  Third, we discuss validation strategies for repositioning studies, including both computational and experimental methods.  ...  Acknowledgment The authors would like to thank Dr Pankaj Agarwal for his helpful discussion.  ... 
doi:10.1093/bib/bbv020 pmid:25832646 pmcid:PMC4719067 fatcat:aogwknlldvhtxfct5wwmorqtk4
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