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  1. For gene-gene interaction analysis, the multifactor dimensionality reduction (MDR) method has been widely employed to reduce multi-levels of gene-gene interactions into high- or low-risk groups using a binary ...

    Authors: Jung Wun Lee and Seungyeoun Lee

    Citation: BioData Mining 2021 14:17

    Content type: Methodology

    Published on:

  2. In genome-wide association studies the extent and impact of confounding due to population structure have been well recognized. Inadequate handling of such confounding is likely to lead to spurious associations...

    Authors: Fentaw Abegaz, François Van Lishout, Jestinah M. Mahachie John, Kridsadakorn Chiachoompu, Archana Bhardwaj, Diane Duroux, Elena S. Gusareva, Zhi Wei, Hakon Hakonarson and Kristel Van Steen

    Citation: BioData Mining 2021 14:16

    Content type: Methodology

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  3. Evaluating binary classifications is a pivotal task in statistics and machine learning, because it can influence decisions in multiple areas, including for example prognosis or therapies of patients in critica...

    Authors: Davide Chicco, Niklas Tötsch and Giuseppe Jurman

    Citation: BioData Mining 2021 14:13

    Content type: Methodology

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  4. Screening for suicidal ideation in high-risk groups such as U.S. veterans is crucial for early detection and suicide prevention. Currently, screening is based on clinical interviews or self-report measures. Bo...

    Authors: Anas Belouali, Samir Gupta, Vaibhav Sourirajan, Jiawei Yu, Nathaniel Allen, Adil Alaoui, Mary Ann Dutton and Matthew J. Reinhard

    Citation: BioData Mining 2021 14:11

    Content type: Research

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  5. Here we present a web interface that implements a comprehensive mechanistic model of the SARS-CoV-2 disease map. In this framework, the detailed activity of the human signaling circuits related to the viral in...

    Authors: Kinza Rian, Marina Esteban-Medina, Marta R. Hidalgo, Cankut Çubuk, Matias M. Falco, Carlos Loucera, Devrim Gunyel, Marek Ostaszewski, María Peña-Chilet and Joaquín Dopazo

    Citation: BioData Mining 2021 14:5

    Content type: Short report

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  6. Prediction of novel Drug–Target interactions (DTIs) plays an important role in discovering new drug candidates and finding new proteins to target. In consideration of the time-consuming and expensive of experi...

    Authors: Ji-Yong An, Fan-Rong Meng and Zi-Ji Yan

    Citation: BioData Mining 2021 14:3

    Content type: Research

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  7. Colon cancer is occurring at an increasing rate and ginger (Zingiber officinale), as a commonly used herbal medicine, has been suggested as a potential agent for colon cancer. This study was aimed to identify the...

    Authors: Meng-Meng Zhang, Dan Wang, Feng Lu, Rong Zhao, Xun Ye, Lin He, Li Ai and Chun-Jie Wu

    Citation: BioData Mining 2021 14:1

    Content type: Research

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  8. Accurate identification of acute ischemic stroke (AIS) patient cohorts is essential for a wide range of clinical investigations. Automated phenotyping methods that leverage electronic health records (EHRs) rep...

    Authors: Phyllis M. Thangaraj, Benjamin R. Kummer, Tal Lorberbaum, Mitchell S. V. Elkind and Nicholas P. Tatonetti

    Citation: BioData Mining 2020 13:21

    Content type: Research

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  9. Determining binding affinity in protein-protein interactions is important in the discovery and design of novel therapeutics and mutagenesis studies. Determination of binding affinity of proteins in the formati...

    Authors: Wajid Arshad Abbasi, Adiba Yaseen, Fahad Ul Hassan, Saiqa Andleeb and Fayyaz Ul Amir Afsar Minhas

    Citation: BioData Mining 2020 13:20

    Content type: Research

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  10. COVID-19 has caused a global pandemic, and there is no wonder drug for epidemic control at present. However, many clinical practices have shown that traditional Chinese medicine has played an important role in...

    Authors: Kai Gao, Yan-Ping Song and Anna Song

    Citation: BioData Mining 2020 13:19

    Content type: Research

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  11. Chinese medicine Xuebijing (XBJ) has proven to be effective in the treatment of mild coronavirus disease 2019 (COVID-19) cases. But the bioactive compounds and potential mechanisms of XBJ for COVID-19 preventi...

    Authors: Wen-jiang Zheng, Qian Yan, Yong-shi Ni, Shao-feng Zhan, Liu-liu Yang, Hong-fa Zhuang, Xiao-hong Liu and Yong Jiang

    Citation: BioData Mining 2020 13:17

    Content type: Research

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  12. Throughout their lifespans, humans continually interact with the microbial world, including those organisms which live in and on the human body. Research in this domain has revealed the extensive links between...

    Authors: Jie Zhou, Weston D. Viles, Boran Lu, Zhigang Li, Juliette C. Madan, Margaret R. Karagas, Jiang Gui and Anne G. Hoen

    Citation: BioData Mining 2020 13:16

    Content type: Methodology

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  13. Chinese medicine Toujie Quwen granule (TJQW) has proven to be effective in the treatment of mild coronavirus disease 2019 (COVID-19) cases by relieving symptoms, slowing the progression of the disease, and boo...

    Authors: Ying Huang, Wen-jiang Zheng, Yong-shi Ni, Mian-sha Li, Jian-kun Chen, Xiao-hong Liu, Xing-hua Tan and Ji-qiang Li

    Citation: BioData Mining 2020 13:15

    Content type: Research

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  14. Various combinations of ultrasonographic (US) characteristics are increasingly utilized to classify thyroid nodules. But they lack theories, and heavily depend on radiologists’ experience, and cannot correctly...

    Authors: Dan Chen, Jun Hu, Mei Zhu, Niansheng Tang, Yang Yang and Yuran Feng

    Citation: BioData Mining 2020 13:14

    Content type: Research

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  15. Identification of non-trivial and meaningful patterns in omics data is one of the most important biological tasks. The patterns help to better understand biological systems and interpret experimental outcomes....

    Authors: František Malinka, Filip železný and Jiří Kléma

    Citation: BioData Mining 2020 13:13

    Content type: Research

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  16. Osteoarthritis is a disabling disease, which seriously affects the quality of life of patients. Increasing evidence has indicated that Chinese herbal medicine including Eucommia ulmoides (EU) and Radix Achyranthi...

    Authors: Gong-hui Jian, Bing-zhu Su, Wen-jia Zhou and Hui Xiong

    Citation: BioData Mining 2020 13:12

    Content type: Research

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  17. Non-alcoholic fatty liver (NAFLD) is a chronic disease worldwide, which poses a huge threat to human health. Xiaochaihu decoction is a well-known traditional Chinese medicine prescription. It has been proven e...

    Authors: Qichao Hu, Shizhang Wei, Jianxia Wen, Wenwen Zhang, Yinxiao Jiang, Caiyan Qu, Junbao Xiang, Yanling Zhao, Xi Peng and Xiao Ma

    Citation: BioData Mining 2020 13:11

    Content type: Research

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  18. Heart disease is the leading cause of death worldwide. Knowing a gene expression signature in heart disease can lead to the development of more efficient diagnosis and treatments that may prevent premature dea...

    Authors: Olga Fajarda, Sara Duarte-Pereira, Raquel M. Silva and José Luís Oliveira

    Citation: BioData Mining 2020 13:8

    Content type: Research

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  19. Asthma is one of the leading chronic illnesses among children in the United States. Asthma prevalence is higher among African Americans (11.2%) compared to European Americans (7.7%). Bronchodilator medications...

    Authors: J. Magaña, M. G. Contreras, K. L. Keys, O. Risse-Adams, P. C. Goddard, A. M. Zeiger, A. C. Y. Mak, J. R. Elhawary, L. A. Samedy-Bates, E. Lee, N. Thakur, D. Hu, C. Eng, S. Salazar, S. Huntsman, T. Hu…

    Citation: BioData Mining 2020 13:7

    Content type: Research

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  20. Mapping disease-associated genetic variants to complex disease pathophysiology is a major challenge in translating findings from genome-wide association studies into novel therapeutic opportunities. The diffic...

    Authors: Hao-Chih Lee, Osamu Ichikawa, Benjamin S. Glicksberg, Aparna A. Divaraniya, Christine E. Becker, Pankaj Agarwal and Joel T. Dudley

    Citation: BioData Mining 2020 13:6

    Content type: Methodology

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  21. The use of graph theory models is widespread in biological pathway analyses as it is often desired to evaluate the position of genes and proteins in their interaction networks of the biological systems. In thi...

    Authors: Pourya Naderi Yeganeh, Chrsitine Richardson, Erik Saule, Ann Loraine and M. Taghi Mostafavi

    Citation: BioData Mining 2020 13:5

    Content type: Research

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  22. The coronavirus disease 2019 (COVID-19) pandemic has had a significant impact on population health and wellbeing. Biomedical informatics is central to COVID-19 research efforts and for the delivery of healthca...

    Authors: Jason H. Moore, Ian Barnett, Mary Regina Boland, Yong Chen, George Demiris, Graciela Gonzalez-Hernandez, Daniel S. Herman, Blanca E. Himes, Rebecca A. Hubbard, Dokyoon Kim, Jeffrey S. Morris, Danielle L. Mowery, Marylyn D. Ritchie, Li Shen, Ryan Urbanowicz and John H. Holmes

    Citation: BioData Mining 2020 13:3

    Content type: Editorial

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  23. As the pathological mechanisms of AD are complex, increasing evidence have demonstrated Chinese Medicine with multi-ingredients and multi-targets may be more suitable for the treatment of diseases with complex...

    Authors: Jie-shu You, Chen-yue Li, Wei Chen, Xia-lin Wu, Li-jie Huang, Ren-kai Li, Fei Gao, Ming-yue Zhang, Huan-lan Liu and Wei-ling Qu

    Citation: BioData Mining 2020 13:2

    Content type: Research

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  24. The sequencing platform BGISEQ-500 is based on DNBSEQ technology and provides high throughput with low costs. This sequencer has been widely used in various areas of scientific and clinical research. A better ...

    Authors: Yanqiu Zhou, Chen Liu, Rongfang Zhou, Anzhi Lu, Biao Huang, Liling Liu, Ling Chen, Bei Luo, Jin Huang and Zhijian Tian

    Citation: BioData Mining 2019 12:21

    Content type: Research

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  25. Gerontogenes include those that modulate life expectancy in various species and may be the actual longevity genes. We believe that a long (relative to body weight) lifespan in individual rodent and primate spe...

    Authors: Lev I. Rubanov, Andrey G. Zaraisky, Gregory A. Shilovsky, Alexandr V. Seliverstov, Oleg A. Zverkov and Vassily A. Lyubetsky

    Citation: BioData Mining 2019 12:20

    Content type: Research

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  26. Incidence and mortality of lung cancer have dramatically decreased during the last decades, yet still approximately 160,000 deaths per year occurred in United States. Smoking intensity, duration, starting age,...

    Authors: Bidong Ma, Zhiyou Huang, Qian Wang, Jizhou Zhang, Bin Zhou and Jiaohong Wu

    Citation: BioData Mining 2019 12:18

    Content type: Research

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  27. The clinical outcomes of patients with resected T1-3N0–2M0 non-small cell lung cancer (NSCLC) with the same tumor-node-metastasis (TNM) stage are diverse. Although other prognostic factors and prognostic predicti...

    Authors: Yunkui Zhang, YaoChen Li, Rongsheng Zhang, Yujie Zhang and Haitao Ma

    Citation: BioData Mining 2019 12:17

    Content type: Software article

    Published on:

  28. The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontolog...

    Authors: Aurélien Brionne, Amélie Juanchich and Christelle Hennequet-Antier

    Citation: BioData Mining 2019 12:16

    Content type: Short report

    Published on:

  29. Widespread adoption of Electronic Health Records (EHR) increased the number of reported disease association studies, or Phenome-Wide Association Studies (PheWAS). Traditional PheWAS studies ignore visit type (i.e...

    Authors: Mary Regina Boland, Snigdha Alur-Gupta, Lisa Levine, Peter Gabriel and Graciela Gonzalez-Hernandez

    Citation: BioData Mining 2019 12:15

    Content type: Short report

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  30. The principal line of investigation in Genome Wide Association Studies (GWAS) is the identification of main effects, that is individual Single Nucleotide Polymorphisms (SNPs) which are associated with the trai...

    Authors: Elisabetta Manduchi, Patryk R. Orzechowski, Marylyn D. Ritchie and Jason H. Moore

    Citation: BioData Mining 2019 12:14

    Content type: Research

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  31. Fraudulent milk adulteration is a dangerous practice in the dairy industry that is harmful to consumers since milk is one of the most consumed food products. Milk quality can be assessed by Fourier Transformed...

    Authors: Habib Asseiss Neto, Wanessa L.F. Tavares, Daniela C.S.Z. Ribeiro, Ronnie C.O. Alves, Leorges M. Fonseca and Sérgio V.A. Campos

    Citation: BioData Mining 2019 12:13

    Content type: Methodology

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  32. Tremendous amount of whole-genome sequencing data have been provided by large consortium projects such as TCGA (The Cancer Genome Atlas), COSMIC and so on, which creates incredible opportunities for functional...

    Authors: Jia-Hao Bi, Yi-Fan Tong, Zhe-Wei Qiu, Xing-Feng Yang, John Minna, Adi F. Gazdar and Kai Song

    Citation: BioData Mining 2019 12:12

    Content type: Software article

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  33. In Genome-Wide Association Studies (GWAS), the concept of linkage disequilibrium is important as it allows identifying genetic markers that tag the actual causal variants. In Genome-Wide Association Interactio...

    Authors: Marc Joiret, Jestinah M. Mahachie John, Elena S. Gusareva and Kristel Van Steen

    Citation: BioData Mining 2019 12:11

    Content type: Research

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