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Genome-wide inferring gene–phenotype relationship by walking on the heterogeneous network

Yongjin Li, Jagdish C. Patra
2010 Computer applications in the biosciences : CABIOS  
These candidate genes need to be further investigated to identify disease-causing genes.  ...  These algorithms typically prioritize candidate genes based on their similarity to known disease genes. Though these methods perform well, they still have some limitations.  ... 
doi:10.1093/bioinformatics/btq108 pmid:20215462 fatcat:qpeqz2ow6zfyddw774pvbxbmum

Genome-wide network-based pathway analysis of CSF t-tau/Aβ1-42 ratio in the ADNI cohort

Wang Cong, Xianglian Meng, Jin Li, Qiushi Zhang, Feng Chen, Wenjie Liu, Ying Wang, Sipu Cheng, Xiaohui Yao, Jingwen Yan, Sungeun Kim, Andrew J. Saykin (+2 others)
2017 BMC Genomics  
The influence of genetic variation on these CSF biomarkers has been investigated in candidate or genome-wide association studies (GWAS).  ...  as Alzheimer's disease, colorectal cancer, gliomas, renal cell carcinoma, Huntington's disease, and others.  ...  Acknowledgements Alzheimer's Disease Neuroimaging Initiative Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database (  ... 
doi:10.1186/s12864-017-3798-z pmid:28558704 pmcid:PMC5450240 fatcat:ispbmmcqsneg3lsxev3j3kcodu

Drug Repurposing for Alzheimer's Disease Based on Protein-Protein Interaction Network

Negar Sadat Soleimani Zakeri, Saeid Pashazadeh, Habib MotieGhader, Vida Demarin
2021 BioMed Research International  
This study proposes a method to extract substantial gene complexes and then introduces potential drugs in Alzheimer's disease.  ...  To this end, a protein-protein interaction (PPI) network was utilized to extract five meaningful gene complexes functionally interconnected.  ...  The extracted network is then clustered by the EAGLE algorithm, one of the algorithms in the ClusterViz application [14] .  ... 
doi:10.1155/2021/1280237 pmid:34692825 pmcid:PMC8531773 fatcat:owxb567ql5g3bjujp4x67xk75m

A Network-Based Perspective in Alzheimer's Disease: Current State and an Integrative Framework

2018 IEEE journal of biomedical and health informatics  
In this work, we review current state-of-the-art, focusing on network-based biomarkers at molecular and brain functional connectivity levels.  ...  A major rise in the prevalence and impact of Alzheimer's disease (AD) is projected in the coming decades, resulting from increasing life expectancy, thus leading to substantially increased healthcare costs  ...  Similarly in [34] , a network-based approach to identify novel AD-related genes was described using an integration of PPI and a list of AD-genes along with a strategy that combines local and global network  ... 
doi:10.1109/jbhi.2018.2863202 pmid:30080151 fatcat:vtub3nvgpvbflersyeaciftoxy

Drug Repurposing Using Biological Networks

Francisco Javier Somolinos, Carlos León, Sara Guerrero-Aspizua
2021 Processes  
This allows the use of computational methods and models based on biological networks to develop new possibilities for drug repurposing.  ...  Drug repurposing is based on the fact that one drug can act on multiple targets or that two diseases can have molecular similarities, among others.  ...  (b) Network proximity between drug targets and HCoV-associated proteins. (c,d) Gene set enrichment analysis to validate the network-based prediction. (e) Drug combinations using network-based method.  ... 
doi:10.3390/pr9061057 fatcat:wrdrh3hi65gszjec2prg6pixn4

Knowledge-Based Neuroendocrine Immunomodulation (NIM) Molecular Network Construction and Its Application

Tongxing Wang, Lu Han, Xiaorui Zhang, Rongrong Wu, Xiaorui Cheng, Wenxia Zhou, Yongxiang Zhang
2018 Molecules  
To investigate the reliability of the NIM network, we used the forest algorithm to extract the NIM subnetworks for two complex diseases (rheumatoid arthritis (RA) and Alzheimer's disease (AD)) and conducted  ...  Finally, employing the forest algorithm, we identified the molecular hub playing an important role in the pathogenesis of rheumatoid arthritis (RA) and Alzheimer's disease (AD), based on the NIM molecular  ...  Then, we extracted the disease-specific NIM subnetworks from the extended network of NIM signaling molecules using the forest algorithm.  ... 
doi:10.3390/molecules23061312 pmid:29848990 fatcat:wx25lgtfqjbshj3fidy4vesnpq

Molecular Inverse Comorbidity between Alzheimer's Disease and Lung Cancer: New Insights from Matrix Factorization

Alessandro Greco, Jon Sanchez Valle, Vera Pancaldi, Anaïs Baudot, Emmanuel Barillot, Michele Caselle, Alfonso Valencia, Andrei Zinovyev, Laura Cantini
2019 International Journal of Molecular Sciences  
As a use case, we focus on the inverse comorbidity association between Alzheimer's disease (AD) and lung cancer (LC), described as a lower than expected probability of developing LC in AD patients.  ...  Here, we challenge MF in depicting the molecular bases of epidemiologically described diseasedisease (DD) relationships.  ...  Abbreviations AD Alzheimer's disease LC Lung Cancer RBH Reciprocal Best Hit DD Disease-Disease  ... 
doi:10.3390/ijms20133114 pmid:31247897 pmcid:PMC6650839 fatcat:kfoloynfhnf3zkqkdj6l6p74fq

KDiamend: a package for detecting key drivers in a molecular ecological network of disease

Mengxuan Lyu, Jiaxing Chen, Yiqi Jiang, Wei Dong, Zhou Fang, Shuaicheng Li
2018 BMC Systems Biology  
By investigating the abundance associations of species or genes, we can construct molecular ecological networks (MENs).  ...  The extracted subnetworks include InterPro matches (IPRs) concerned with immunoglobulin, Sporulation, biofilm, Flaviviruses, bacteriophage, etc., while the development of biofilms is regarded as one of  ...  We thank Tan Bowen for offering assistance during designing the algorithm and Zhao Zicheng, Xu Chang for comments that greatly improved the manuscript.  ... 
doi:10.1186/s12918-018-0531-8 pmid:29671403 pmcid:PMC5907152 fatcat:z5e5g7tpjnh5lo3h6pspprz5be

Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data

Shweta Bagewadi Kawalia, Tamara Raschka, Mufassra Naz, Ricardo de Matos Simoes, Philipp Senger, Martin Hofmann-Apitius
2017 Journal of Alzheimer's Disease  
Alzheimer's disease (AD) progressively destroys cognitive abilities in the aging population with tremendous effects on memory.  ...  Several methods to infer such networks exist, but most of them do not elaborate on context specificity and completeness of the generated networks, missing out on lesser-known candidates.  ...  Subsequently, BC3Net10 algorithm was applied only on diseased samples for AD seed genes, cf. Fig. 1 .  ... 
doi:10.3233/jad-170011 pmid:28800327 pmcid:PMC5611835 fatcat:gbicsri3pbefbizk4c2xeh6vti

Molecular Inverse Comorbidity between Alzheimer's disease and Lung Cancer: new insights from Matrix Factorization [article]

Alessandro Greco, Jon Sanchez-Valle, Vera Pancaldi, Anais Baudot, Emmanuel Barillot, Michele Caselle, Alfonso Valencia, Amdrei Zinovyev, Laura Cantini
2019 biorxiv/medrxiv   pre-print
As use case, we focus on the inverse comorbidity association between Alzheimer's disease (AD) and lung cancer (LC), described as a lower than expected probability of developing LC described in AD patients  ...  We here challenge MF in depicting the molecular bases of epidemiologically described Disease-Disease (DD) relationships.  ...  The results shown here are in part based upon data generated by the TCGA Research Network: Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.1101/643890 fatcat:v52zrqoicbaedhxehramn7sn6a

Network-based analysis reveals distinct association patterns in a semantic MEDLINE-based drug-disease-gene network

Yuji Zhang, Cui Tao, Guoqian Jiang, Asha A Nair, Jian Su, Christopher G Chute, Hongfang Liu
2014 Journal of Biomedical Semantics  
Results: We propose a novel network-based computational framework to identify statistically over-expressed subnetwork patterns, called network motifs, in an integrated disease-drug-gene network extracted  ...  Conclusions: We have developed a novel network-based computational approach to investigate the heterogeneous drug-gene-disease network extracted from Semantic MEDLINE.  ...  We focus on a heterogeneous drug-disease-gene network derived from Semantic MEDLINE and investigated underlying associations using network-based systems biology approaches.  ... 
doi:10.1186/2041-1480-5-33 pmid:25170419 pmcid:PMC4137727 fatcat:uggl3kazqrcubn63achjtgzqtq

Network medicine for disease module identification and drug repurposing with the NeDRex platform

Sepideh Sadegh, James Skelton, Elisa Anastasi, Judith Bernett, David B. Blumenthal, Gihanna Galindez, Marisol Salgado-Albarrán, Olga Lazareva, Keith Flanagan, Simon Cockell, Cristian Nogales, Ana I. Casas (+4 others)
2021 Nature Communications  
There is an unmet need for adaptable tools allowing biomedical researchers to employ network-based drug repurposing approaches for their individual use cases.  ...  We close this gap with NeDRex, an integrative and interactive platform for network-based drug repurposing and disease module discovery.  ...  This publication reflects only the authors' view and the European Commission is not responsible for any use that may be made of the information it contains. J. Ba  ... 
doi:10.1038/s41467-021-27138-2 pmid:34824199 pmcid:PMC8617287 fatcat:czmxg3x3cbczvaqdvixh5ptt4i

Enriching Human Interactome with Functional Mutations to Detect High-Impact Network Modules Underlying Complex Diseases

Cui, Srinivasan, Korkin
2019 Genes  
Rapid progress in high-throughput -omics technologies moves us one step closer to the datacalypse in life sciences.  ...  Specifically, our approach incorporates and propagates the functional impact of non-synonymous single nucleotide polymorphisms (nsSNPs) on PPIs to implicate the genes that are most likely influenced by  ...  Thus, the impact score combines the disease relevance and potential disruption to existing subnetwork caused by the candidate gene. II.  ... 
doi:10.3390/genes10110933 pmid:31731769 pmcid:PMC6895925 fatcat:hlfpixohdvcwxdmm3fvgwgmbfa

Analyzing the genes and pathways related to major depressive disorder via a systems biology approach

Ting Fan, Ying Hu, Juncai Xin, Mengwen Zhao, Ju Wang
2019 Brain and Behavior  
Under such situation, a systems biology approach focusing on the function correlation and interaction of the candidate genes in the context of MDD will provide useful information on exploring the molecular  ...  From the MDD-specific network, 35 novel genes potentially associated with the disease were identified.  ...  to construct and extract potential specific disease subnetworks by introducing a minimum number of genes according to the Steiner minimum tree algorithm.  ... 
doi:10.1002/brb3.1502 pmid:31875662 pmcid:PMC7010578 fatcat:idiw5a5vknhnxn2uwgdez4cpgy

BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language

Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius
2018 Database: The Journal of Biological Databases and Curation  
complex algorithmic analysis.  ...  networks.  ...  The second step in the query builder allows users to generate subnetworks based on nodes, edge annotations and references of interest by using one or several 'seeding methods'.  ... 
doi:10.1093/database/bay126 pmid:30576488 pmcid:PMC6301338 fatcat:2hikgxf7rfbxbdsx6gnnnm4kua
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