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Machine learning for computational and systems biology

Section Editor: Professor Jean-Philippe Vert

As part of the launch of the journal section "Machine Learning and Artificial Intelligence in Bioinformatics", BMC Bioinformatics is excited to present a collection of papers included as part of the thematic series Machine learning for computational and systems biology.  

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Papers included in this collection will appear below as they are published.

  1. The interactions of proteins are determined by their sequences and affect the regulation of the cell cycle, signal transduction and metabolism, which is of extraordinary significance to modern proteomics resea...

    Authors: Yang Wang, Zhanchao Li, Yanfei Zhang, Yingjun Ma, Qixing Huang, Xingyu Chen, Zong Dai and Xiaoyong Zou

    Citation: BMC Bioinformatics 2021 22:184

    Content type: Research article

    Published on:

  2. Accumulating evidence has demonstrated that long non-coding RNAs (lncRNAs) are closely associated with human diseases, and it is useful for the diagnosis and treatment of diseases to get the relationships betw...

    Authors: Yubin Xiao, Zheng Xiao, Xiang Feng, Zhiping Chen, Linai Kuang and Lei Wang

    Citation: BMC Bioinformatics 2020 21:555

    Content type: Methodology article

    Published on:

  3. Elucidation of interactive relation between chemicals and genes is of key relevance not only for discovering new drug leads in drug development but also for repositioning existing drugs to novel therapeutic ta...

    Authors: Wei Wang, Xi Yang, Chengkun Wu and Canqun Yang

    Citation: BMC Bioinformatics 2020 21:544

    Content type: Methodology article

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  4. Circular RNAs (circRNAs) are special noncoding RNA molecules with closed loop structures. Compared with the traditional linear RNA, circRNA is more stable and not easily degraded. Many studies have shown that ...

    Authors: Lei Deng, Wei Lin, Jiacheng Wang and Jingpu Zhang

    Citation: BMC Bioinformatics 2020 21:519

    Content type: Research article

    Published on:

  5. An enzyme activity is influenced by the external environment. It is important to have an enzyme remain high activity in a specific condition. A usual way is to first determine the optimal condition of an enzym...

    Authors: Xiangjun Li, Zhixin Dou, Yuqing Sun, Lushan Wang, Bin Gong and Lin Wan

    Citation: BMC Bioinformatics 2020 21:512

    Content type: Methodology article

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  6. MicroRNAs (miRNAs) are non-coding RNAs with regulatory functions. Many studies have shown that miRNAs are closely associated with human diseases. Among the methods to explore the relationship between the miRNA...

    Authors: Tian-Ru Wu, Meng-Meng Yin, Cui-Na Jiao, Ying-Lian Gao, Xiang-Zhen Kong and Jin-Xing Liu

    Citation: BMC Bioinformatics 2020 21:454

    Content type: Methodology article

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  7. The treatment of complex diseases by taking multiple drugs becomes increasingly popular. However, drug-drug interactions (DDIs) may give rise to the risk of unanticipated adverse effects and even unknown toxic...

    Authors: Yue-Hua Feng, Shao-Wu Zhang and Jian-Yu Shi

    Citation: BMC Bioinformatics 2020 21:419

    Content type: Methodology article

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  8. The interactions between proteins and aptamers are prevalent in organisms and play an important role in various life activities. Thanks to the rapid accumulation of protein-aptamer interaction data, it is nece...

    Authors: Jianwei Li, Xiaoyu Ma, Xichuan Li and Junhua Gu

    Citation: BMC Bioinformatics 2020 21:236

    Content type: Methodology article

    Published on:

  9. In addition to causing the pandemic influenza outbreaks of 1918 and 2009, subtype H1N1 influenza A viruses (IAVs) have caused seasonal epidemics since 1977. Antigenic property of influenza viruses are determin...

    Authors: Lei Li, Deborah Chang, Lei Han, Xiaojian Zhang, Joseph Zaia and Xiu-Feng Wan

    Citation: BMC Bioinformatics 2020 21:182

    Content type: Methodology article

    Published on:

  10. Recent years have witnessed an increasing interest in multi-omics data, because these data allow for better understanding complex diseases such as cancer on a molecular system level. In addition, multi-omics d...

    Authors: Amina Lemsara, Salima Ouadfel and Holger Fröhlich

    Citation: BMC Bioinformatics 2020 21:146

    Content type: Methodology article

    Published on:

  11. Accumulated evidence shows that the abnormal regulation of long non-coding RNA (lncRNA) is associated with various human diseases. Accurately identifying disease-associated lncRNAs is helpful to study the mech...

    Authors: Dengju Yao, Xiaojuan Zhan, Xiaorong Zhan, Chee Keong Kwoh, Peng Li and Jinke Wang

    Citation: BMC Bioinformatics 2020 21:126

    Content type: Methodology article

    Published on:

  12. Both intra- and inter-sentential semantic relations in biomedical texts provide valuable information for biomedical research. However, most existing methods either focus on extracting intra-sentential relation...

    Authors: Zhiheng Li, Zhihao Yang, Yang Xiang, Ling Luo, Yuanyuan Sun and Hongfei Lin

    Citation: BMC Bioinformatics 2020 21:125

    Content type: Methodology article

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  13. 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

    Published on:

  14. 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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  15. Glycans are complex sugar chains, crucial to many biological processes. By participating in binding interactions with proteins, glycans often play key roles in host–pathogen interactions. The specificities of ...

    Authors: Lachlan Coff, Jeffrey Chan, Paul A. Ramsland and Andrew J. Guy

    Citation: BMC Bioinformatics 2020 21:42

    Content type: Methodology Article

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  16. 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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  17. Late-Onset Alzheimer’s Disease (LOAD) is a leading form of dementia. There is no effective cure for LOAD, leaving the treatment efforts to depend on preventive cognitive therapies, which stand to benefit from ...

    Authors: Javier De Velasco Oriol, Edgar E. Vallejo, Karol Estrada, José Gerardo Taméz Peña and The Alzheimer’s Disease Neuroimaging Initiative

    Citation: BMC Bioinformatics 2019 20:709

    Content type: Research Article

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  18. Next generation sequencing instruments are providing new opportunities for comprehensive analyses of cancer genomes. The increasing availability of tumor data allows to research the complexity of cancer diseas...

    Authors: Martin Palazzo, Pierre Beauseroy and Patricio Yankilevich

    Citation: BMC Bioinformatics 2019 20:655

    Content type: Methodology Article

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  19. In recent years, lncRNAs (long-non-coding RNAs) have been proved to be closely related to the occurrence and development of many serious diseases that are seriously harmful to human health. However, most of th...

    Authors: Jiechen Li, Xueyong Li, Xiang Feng, Bing Wang, Bihai Zhao and Lei Wang

    Citation: BMC Bioinformatics 2019 20:626

    Content type: Research article

    Published on:

  20. Recurrent neural network(RNN) is a good way to process sequential data, but the capability of RNN to compute long sequence data is inefficient. As a variant of RNN, long short term memory(LSTM) solved the prob...

    Authors: Jiale Liu and Xinqi Gong

    Citation: BMC Bioinformatics 2019 20:609

    Content type: Methodology Article

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  21. 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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  22. Recent advances in high-volume sequencing technology and mining of genomes from metagenomic samples call for rapid and reliable genome quality evaluation. The current release of the PATRIC database contains ov...

    Authors: Bruce Parrello, Rory Butler, Philippe Chlenski, Robert Olson, Jamie Overbeek, Gordon D. Pusch, Veronika Vonstein and Ross Overbeek

    Citation: BMC Bioinformatics 2019 20:486

    Content type: Database

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  23. Host immune response is coordinated by a variety of different specialized cell types that vary in time and location. While host immune response can be studied using conventional low-dimensional approaches, adv...

    Authors: Arezo Torang, Paraag Gupta and David J. Klinke II

    Citation: BMC Bioinformatics 2019 20:433

    Content type: Research article

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  24. 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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  25. Modern genomic and proteomic profiling methods produce large amounts of data from tissue and blood-based samples that are of potential utility for improving patient care. However, the design of precision medic...

    Authors: Joanna Roder, Carlos Oliveira, Lelia Net, Maxim Tsypin, Benjamin Linstid and Heinrich Roder

    Citation: BMC Bioinformatics 2019 20:325

    Content type: Methodology article

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