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Machine Learning and Artificial Intelligence in Bioinformatics

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  1. Feature selection in class-imbalance learning has gained increasing attention in recent years due to the massive growth of high-dimensional class-imbalanced data across many scientific fields. In addition to r...

    Authors: Guang-Hui Fu, Yuan-Jiao Wu, Min-Jie Zong and Jianxin Pan

    Citation: BMC Bioinformatics 2020 21:121

    Content type: Research Article

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  2. The ability to confidently predict health outcomes from gene expression would catalyze a revolution in molecular diagnostics. Yet, the goal of developing actionable, robust, and reproducible predictive signatu...

    Authors: Aaron M. Smith, Jonathan R. Walsh, John Long, Craig B. Davis, Peter Henstock, Martin R. Hodge, Mateusz Maciejewski, Xinmeng Jasmine Mu, Stephen Ra, Shanrong Zhao, Daniel Ziemek and Charles K. Fisher

    Citation: BMC Bioinformatics 2020 21:119

    Content type: Research Article

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  3. MicroRNA (miRNA) regulation is associated with several diseases, including neurodegenerative diseases. Several approaches can be used for modeling miRNA regulation. However, their precision may be limited for ...

    Authors: Lucile Mégret, Satish Sasidharan Nair, Julia Dancourt, Jeff Aaronson, Jim Rosinski and Christian Neri

    Citation: BMC Bioinformatics 2020 21:75

    Content type: Research article

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  4. The study of functional associations between ncRNAs and human diseases is a pivotal task of modern research to develop new and more effective therapeutic approaches. Nevertheless, it is not a trivial task sinc...

    Authors: Emanuele Pio Barracchia, Gianvito Pio, Domenica D’Elia and Michelangelo Ceci

    Citation: BMC Bioinformatics 2020 21:70

    Content type: Methodology Article

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  5. Genome-wide association studies (GWAS) provide a powerful means to identify associations between genetic variants and phenotypes. However, GWAS techniques for detecting epistasis, the interactions between gene...

    Authors: Yu-Chuan Chang, June-Tai Wu, Ming-Yi Hong, Yi-An Tung, Ping-Han Hsieh, Sook Wah Yee, Kathleen M. Giacomini, Yen-Jen Oyang and Chien-Yu Chen

    Citation: BMC Bioinformatics 2020 21:68

    Content type: Software

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  6. Single-cell RNA sequencing (scRNA-seq) is an emerging technology that can assess the function of an individual cell and cell-to-cell variability at the single cell level in an unbiased manner. Dimensionality r...

    Authors: Eugene Lin, Sudipto Mukherjee and Sreeram Kannan

    Citation: BMC Bioinformatics 2020 21:64

    Content type: Methodology article

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  7. Feature selection is a crucial step in machine learning analysis. Currently, many feature selection approaches do not ensure satisfying results, in terms of accuracy and computational time, when the amount of ...

    Authors: Mattia Chiesa, Giada Maioli, Gualtiero I. Colombo and Luca Piacentini

    Citation: BMC Bioinformatics 2020 21:54

    Content type: Software

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  8. Various methods for differential expression analysis have been widely used to identify features which best distinguish between different categories of samples. Multiple hypothesis testing may leave out explana...

    Authors: Xudong Zhao, Qing Jiao, Hangyu Li, Yiming Wu, Hanxu Wang, Shan Huang and Guohua Wang

    Citation: BMC Bioinformatics 2020 21:43

    Content type: Software

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  9. Automated biomedical named entity recognition and normalization serves as the basis for many downstream applications in information management. However, this task is challenging due to name variations and enti...

    Authors: Huiwei Zhou, Shixian Ning, Zhe Liu, Chengkun Lang, Zhuang Liu and Bizun Lei

    Citation: BMC Bioinformatics 2020 21:35

    Content type: Research article

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  10. MicroRNAs (miRNAs) play important roles in a variety of biological processes by regulating gene expression at the post-transcriptional level. So, the discovery of new miRNAs has become a popular task in biolog...

    Authors: Xueming Zheng, Xingli Fu, Kaicheng Wang and Meng Wang

    Citation: BMC Bioinformatics 2020 21:17

    Content type: Methodology article

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  11. With the global spread of multidrug resistance in pathogenic microbes, infectious diseases emerge as a key public health concern of the recent time. Identification of host genes associated with infectious dise...

    Authors: Ranjan Kumar Barman, Anirban Mukhopadhyay, Ujjwal Maulik and Santasabuj Das

    Citation: BMC Bioinformatics 2019 20:736

    Content type: Research article

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  12. Predicting protein function and structure from sequence is one important challenge for computational biology. For 26 years, most state-of-the-art approaches combined machine learning and evolutionary informati...

    Authors: Michael Heinzinger, Ahmed Elnaggar, Yu Wang, Christian Dallago, Dmitrii Nechaev, Florian Matthes and Burkhard Rost

    Citation: BMC Bioinformatics 2019 20:723

    Content type: Research article

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  13. In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence...

    Authors: Louis Ranjard, Thomas K. F. Wong and Allen G. Rodrigo

    Citation: BMC Bioinformatics 2019 20:654

    Content type: Research Article

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    The Correction to this article has been published in BMC Bioinformatics 2020 21:24

  14. Computational compound repositioning has the potential for identifying new uses for existing drugs, and new algorithms and data source aggregation strategies provide ever-improving results via in silico metric...

    Authors: Michael Mayers, Tong Shu Li, Núria Queralt-Rosinach and Andrew I. Su

    Citation: BMC Bioinformatics 2019 20:653

    Content type: Research article

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  15. The Bacteria Biotope (BB) task is a biomedical relation extraction (RE) that aims to study the interaction between bacteria and their locations. This task is considered to pertain to fundamental knowledge in a...

    Authors: Amarin Jettakul, Duangdao Wichadakul and Peerapon Vateekul

    Citation: BMC Bioinformatics 2019 20:627

    Content type: Research Article

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  16. Microarray datasets consist of complex and high-dimensional samples and genes, and generally the number of samples is much smaller than the number of genes. Due to this data imbalance, gene selection is a dema...

    Authors: Russul Alanni, Jingyu Hou, Hasseeb Azzawi and Yong Xiang

    Citation: BMC Bioinformatics 2019 20:608

    Content type: Research article

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  17. De novo drug discovery is a time-consuming and expensive process. Nowadays, drug repositioning is utilized as a common strategy to discover a new drug indication for existing drugs. This strategy is mostly use...

    Authors: Mahroo Moridi, Marzieh Ghadirinia, Ali Sharifi-Zarchi and Fatemeh Zare-Mirakabad

    Citation: BMC Bioinformatics 2019 20:577

    Content type: Research article

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  18. Cancer subtype classification attains the great importance for accurate diagnosis and personalized treatment of cancer. Latest developments in high-throughput sequencing technologies have rapidly produced mult...

    Authors: Jing Xu, Peng Wu, Yuehui Chen, Qingfang Meng, Hussain Dawood and Hassan Dawood

    Citation: BMC Bioinformatics 2019 20:527

    Content type: Methodology Article

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  19. Network inference is crucial for biomedicine and systems biology. Biological entities and their associations are often modeled as interaction networks. Examples include drug protein interaction or gene regulat...

    Authors: Konstantinos Pliakos and Celine Vens

    Citation: BMC Bioinformatics 2019 20:525

    Content type: Research Article

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  20. Protein subcellular localization plays a crucial role in understanding cell function. Proteins need to be in the right place at the right time, and combine with the corresponding molecules to fulfill their fun...

    Authors: Fan Yang, Yang Liu, Yanbin Wang, Zhijian Yin and Zhen Yang

    Citation: BMC Bioinformatics 2019 20:522

    Content type: Research article

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  21. Quantitative structure-activity relationship (QSAR) is a computational modeling method for revealing relationships between structural properties of chemical compounds and biological activities. QSAR modeling i...

    Authors: Sunyoung Kwon, Ho Bae, Jeonghee Jo and Sungroh Yoon

    Citation: BMC Bioinformatics 2019 20:521

    Content type: Methodology Article

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  22. When applying genomic medicine to a rare disease patient, the primary goal is to identify one or more genomic variants that may explain the patient’s phenotypes. Typically, this is done through annotation, fil...

    Authors: James M. Holt, Brandon Wilk, Camille L. Birch, Donna M. Brown, Manavalan Gajapathy, Alexander C. Moss, Nadiya Sosonkina, Melissa A. Wilk, Julie A. Anderson, Jeremy M. Harris, Jacob M. Kelly, Fariba Shaterferdosian, Angelina E. Uno-Antonison, Arthur Weborg and Elizabeth A. Worthey

    Citation: BMC Bioinformatics 2019 20:496

    Content type: Research Article

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  23. The data deluge can leverage sophisticated ML techniques for functionally annotating the regulatory non-coding genome. The challenge lies in selecting the appropriate classifier for the specific functional ann...

    Authors: Chih-Hao Fang, Nawanol Theera-Ampornpunt, Michael A. Roth, Ananth Grama and Somali Chaterji

    Citation: BMC Bioinformatics 2019 20:488

    Content type: Research Article

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  24. MicroRNAs (miRNAs) are noncoding RNA molecules heavily involved in human tumors, in which few of them circulating the human body. Finding a tumor-associated signature of miRNA, that is, the minimum miRNA entit...

    Authors: Alejandro Lopez-Rincon, Marlet Martinez-Archundia, Gustavo U. Martinez-Ruiz, Alexander Schoenhuth and Alberto Tonda

    Citation: BMC Bioinformatics 2019 20:480

    Content type: Research Article

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  25. The adverse reactions that are caused by drugs are potentially life-threatening problems. Comprehensive knowledge of adverse drug reactions (ADRs) can reduce their detrimental impacts on patients. Detecting AD...

    Authors: Tongxuan Zhang, Hongfei Lin, Yuqi Ren, Liang Yang, Bo Xu, Zhihao Yang, Jian Wang and Yijia Zhang

    Citation: BMC Bioinformatics 2019 20:479

    Content type: Research Article

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  26. Binding sites are the pockets of proteins that can bind drugs; the discovery of these pockets is a critical step in drug design. With the help of computers, protein pockets prediction can save manpower and fin...

    Authors: Mingjian Jiang, Zhen Li, Yujie Bian and Zhiqiang Wei

    Citation: BMC Bioinformatics 2019 20:478

    Content type: Methodology Article

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  27. Long-chain non-coding RNA (lncRNA) is closely related to many biological activities. Since its sequence structure is similar to that of messenger RNA (mRNA), it is difficult to distinguish between the two base...

    Authors: Jianghui Wen, Yeshu Liu, Yu Shi, Haoran Huang, Bing Deng and Xinping Xiao

    Citation: BMC Bioinformatics 2019 20:469

    Content type: Methodology article

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  28. MiRNAs play significant roles in many fundamental and important biological processes, and predicting potential miRNA-disease associations makes contributions to understanding the molecular mechanism of human d...

    Authors: Yuchong Gong, Yanqing Niu, Wen Zhang and Xiaohong Li

    Citation: BMC Bioinformatics 2019 20:468

    Content type: Research article

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  29. Although many of the genic features in Mycobacterium abscessus have been fully validated, a comprehensive understanding of the regulatory elements remains lacking. Moreover, there is little understanding of how t...

    Authors: Patrick M. Staunton, Aleksandra A. Miranda-CasoLuengo, Brendan J. Loftus and Isobel Claire Gormley

    Citation: BMC Bioinformatics 2019 20:466

    Content type: Research Article

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  30. The efficient biological production of industrially and economically important compounds is a challenging problem. Brute-force determination of the optimal pathways to efficient production of a target chemical...

    Authors: Leanne S. Whitmore, Bernard Nguyen, Ali Pinar, Anthe George and Corey M. Hudson

    Citation: BMC Bioinformatics 2019 20:461

    Content type: Software

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  31. With the advent of array-based techniques to measure methylation levels in primary tumor samples, systematic investigations of methylomes have widely been performed on a large number of tumor entities. Most of...

    Authors: Pascal David Johann, Natalie Jäger, Stefan M. Pfister and Martin Sill

    Citation: BMC Bioinformatics 2019 20:428

    Content type: Methodology article

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