scholarly journals Prediction of microRNA-disease associations based on distance correlation set

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Haochen Zhao ◽  
Linai Kuang ◽  
Lei Wang ◽  
Pengyao Ping ◽  
Zhanwei Xuan ◽  
...  
2018 ◽  
Vol 2018 ◽  
pp. 1-12 ◽  
Author(s):  
Haochen Zhao ◽  
Linai Kuang ◽  
Lei Wang ◽  
Zhanwei Xuan

Recently, accumulating laboratorial studies have indicated that plenty of long noncoding RNAs (lncRNAs) play important roles in various biological processes and are associated with many complex human diseases. Therefore, developing powerful computational models to predict correlation between lncRNAs and diseases based on heterogeneous biological datasets will be important. However, there are few approaches to calculating and analyzing lncRNA-disease associations on the basis of information about miRNAs. In this article, a new computational method based on distance correlation set is developed to predict lncRNA-disease associations (DCSLDA). Comparing with existing state-of-the-art methods, we found that the major novelty of DCSLDA lies in the introduction of lncRNA-miRNA-disease network and distance correlation set; thus DCSLDA can be applied to predict potential lncRNA-disease associations without requiring any known disease-lncRNA associations. Simulation results show that DCSLDA can significantly improve previous existing models with reliable AUC of 0.8517 in the leave-one-out cross-validation. Furthermore, while implementing DCSLDA to prioritize candidate lncRNAs for three important cancers, in the first 0.5% of forecast results, 17 predicted associations are verified by other independent studies and biological experimental studies. Hence, it is anticipated that DCSLDA could be a great addition to the biomedical research field.


2020 ◽  
Vol 21 (11) ◽  
pp. 1078-1084
Author(s):  
Ruizhi Fan ◽  
Chenhua Dong ◽  
Hu Song ◽  
Yixin Xu ◽  
Linsen Shi ◽  
...  

: Recently, an increasing number of biological and clinical reports have demonstrated that imbalance of microbial community has the ability to play important roles among several complex diseases concerning human health. Having a good knowledge of discovering potential of microbe-disease relationships, which provides the ability to having a better understanding of some issues, including disease pathology, further boosts disease diagnostics and prognostics, has been taken into account. Nevertheless, a few computational approaches can meet the need of huge scale of microbe-disease association discovery. In this work, we proposed the EHAI model, which is Enhanced Human microbe- disease Association Identification. EHAI employed the microbe-disease associations, and then Gaussian interaction profile kernel similarity has been utilized to enhance the basic microbe-disease association. Actually, some known microbe-disease associations and a large amount of associations are still unavailable among the datasets. The ‘super-microbe’ and ‘super-disease’ were employed to enhance the model. Computational results demonstrated that such super-classes have the ability to be helpful to the performance of EHAI. Therefore, it is anticipated that EHAI can be treated as an important biological tool in this field.


2019 ◽  
Vol 19 (4) ◽  
pp. 232-241 ◽  
Author(s):  
Xuegong Chen ◽  
Wanwan Shi ◽  
Lei Deng

Background: Accumulating experimental studies have indicated that disease comorbidity causes additional pain to patients and leads to the failure of standard treatments compared to patients who have a single disease. Therefore, accurate prediction of potential comorbidity is essential to design more efficient treatment strategies. However, only a few disease comorbidities have been discovered in the clinic. Objective: In this work, we propose PCHS, an effective computational method for predicting disease comorbidity. Materials and Methods: We utilized the HeteSim measure to calculate the relatedness score for different disease pairs in the global heterogeneous network, which integrates six networks based on biological information, including disease-disease associations, drug-drug interactions, protein-protein interactions and associations among them. We built the prediction model using the Support Vector Machine (SVM) based on the HeteSim scores. Results and Conclusion: The results showed that PCHS performed significantly better than previous state-of-the-art approaches and achieved an AUC score of 0.90 in 10-fold cross-validation. Furthermore, some of our predictions have been verified in literatures, indicating the effectiveness of our method.


2019 ◽  
Vol 70 (11) ◽  
pp. 2396-2402
Author(s):  
Kristin N Nelson ◽  
Samuel M Jenness ◽  
Barun Mathema ◽  
Benjamin A Lopman ◽  
Sara C Auld ◽  
...  

Abstract Background Tuberculosis (TB) is the leading infectious cause of death globally, and drug-resistant TB strains pose a serious threat to controlling the global TB epidemic. The clinical features, locations, and social factors driving transmission in settings with high incidences of drug-resistant TB are poorly understood. Methods We measured a network of genomic links using Mycobacterium tuberculosis whole-genome sequences. Results Patients with 2–3 months of cough or who spent time in urban locations were more likely to be linked in the network, while patients with sputum smear–positive disease were less likely to be linked than those with smear-negative disease. Associations persisted using different thresholds to define genomic links and irrespective of assumptions about the direction of transmission. Conclusions Identifying factors that lead to many transmissions, including contact with urban areas, can suggest settings instrumental in transmission and indicate optimal locations and groups to target with interventions.


2021 ◽  
Vol 14 (3) ◽  
pp. e240576
Author(s):  
Bilal Athar Jalil ◽  
Mohsin Ijaz ◽  
Amir Maqbul Khan ◽  
Thomas Glenn Ledbetter

COVID-19 has now emerged from a respiratory illness to a systemic viral illness with multisystem involvement. There is still a lot to learn about this illness as new disease associations with COVID-19 emerge consistently. We present a unique case of a neurological manifestation of a patient with structural brain disease who was COVID-19 positive and developed mental status changes, new-onset seizures and findings suggestive of viral meningitis on lumbar puncture. We also review the literature and discuss our case in the context of the other cases reported. We highlight the value of considering seizures and encephalopathy as one of the presenting features of COVID-19 disease.


2020 ◽  
Vol 22 (Supplement_1) ◽  
pp. S1-S3
Author(s):  
Cassandra A Stanton ◽  
Robert Tarran ◽  
Robin Mermelstein

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