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  1. High-throughput sequencing enables the analysis of the composition of numerous biological systems, such as microbial communities. The identification of dependencies within these systems requires the analysis a...

    Authors: Sebastian Racedo, Ivan Portnoy, Jorge I. Vélez, Homero San-Juan-Vergara, Marco Sanjuan and Eduardo Zurek
    Citation: BioData Mining 2021 14:31
  2. Hepatocellular carcinoma (HCC) is a disease with a high incidence and a poor prognosis. Growing amounts of evidence have shown that the immune system plays a critical role in the biological processes of HCC su...

    Authors: Qian Yan, Wenjiang Zheng, Boqing Wang, Baoqian Ye, Huiyan Luo, Xinqian Yang, Ping Zhang and Xiongwen Wang
    Citation: BioData Mining 2021 14:29
  3. Machine learning approaches for predicting disease risk from high-dimensional whole genome sequence (WGS) data often result in unstable models that can be difficult to interpret, limiting the identification of...

    Authors: Maya Varma, Kelley M. Paskov, Brianna S. Chrisman, Min Woo Sun, Jae-Yoon Jung, Nate T. Stockham, Peter Y. Washington and Dennis P. Wall
    Citation: BioData Mining 2021 14:28
  4. As next-generation sequencing technologies make their way into the clinic, knowledge of their error rates is essential if they are to be used to guide patient care. However, sequencing platforms and variant-ca...

    Authors: Kelley Paskov, Jae-Yoon Jung, Brianna Chrisman, Nate T. Stockham, Peter Washington, Maya Varma, Min Woo Sun and Dennis P. Wall
    Citation: BioData Mining 2021 14:27
  5. As per the 2017 WHO fact sheet, Coronary Artery Disease (CAD) is the primary cause of death in the world, and accounts for 31% of total fatalities. The unprecedented 17.6 million deaths caused by CAD in 2016 u...

    Authors: Seema Singh Saharan, Pankaj Nagar, Kate Townsend Creasy, Eveline O. Stock, James Feng, Mary J. Malloy and John P. Kane
    Citation: BioData Mining 2021 14:26
  6. Longitudinal gene expression analysis and survival modeling have been proved to add valuable biological and clinical knowledge. This study proposes a novel framework to discover gene signatures and patterns in...

    Authors: Cláudia S. Constantino, Alexandra M. Carvalho and Susana Vinga
    Citation: BioData Mining 2021 14:25
  7. Aortic dissection (AD) is one of the most catastrophic aortic diseases associated with a high mortality rate. In contrast to the advances in most cardiovascular diseases, both the incidence and in-hospital mor...

    Authors: Peng Qiu, Yixuan Li, Kai Liu, Jinbao Qin, Kaichuang Ye, Tao Chen and Xinwu Lu
    Citation: BioData Mining 2021 14:24
  8. Acute heart failure (AHF) is associated with significant morbidity and mortality. Effective patient risk stratification is essential to guiding hospitalization decisions and the clinical management of AHF. Cli...

    Authors: Ashwath Radhachandran, Anurag Garikipati, Nicole S. Zelin, Emily Pellegrini, Sina Ghandian, Jacob Calvert, Jana Hoffman, Qingqing Mao and Ritankar Das
    Citation: BioData Mining 2021 14:23
  9. The evolutionary dynamics of SARS-CoV-2 have been carefully monitored since the COVID-19 pandemic began in December 2019. However, analysis has focused primarily on single nucleotide polymorphisms and largely ...

    Authors: Brianna Sierra Chrisman, Kelley Paskov, Nate. Stockham, Kevin Tabatabaei, Jae-Yoon Jung, Peter Washington, Maya Varma, Min Woo Sun, Sepideh Maleki and Dennis P. Wall
    Citation: BioData Mining 2021 14:20
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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

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