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  1. Content type: Research article

    Modern plant taxonomy reflects phylogenetic relationships among taxa based on proposed morphological and genetic similarities. However, taxonomical relation is not necessarily reflected by close overall resemb...

    Authors: Marco Seeland, Michael Rzanny, David Boho, Jana Wäldchen and Patrick Mäder

    Citation: BMC Bioinformatics 2019 20:4

    Published on:

  2. Content type: Software

    Non-co-linear (NCL) transcripts consist of exonic sequences that are topologically inconsistent with the reference genome in an intragenic fashion (circular or intragenic trans-spliced RNAs) or in an intergenic f...

    Authors: Chia-Ying Chen and Trees-Juen Chuang

    Citation: BMC Bioinformatics 2019 20:3

    Published on:

  3. Content type: Research

    Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major ap...

    Authors: Yingying Wang, Hongyan Wu and Yunpeng Cai

    Citation: BMC Bioinformatics 2018 19(Suppl 19):529

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  4. Content type: Research

    The detection and interpretation of CNVs are of clinical importance in genetic testing. Several databases and web services are already being used by clinical geneticists to interpret the medical relevance of i...

    Authors: Xi Yang, Zhuo Song, Chengkun Wu, Wei Wang, Gen Li, Wei Zhang, Lingqian Wu and Kai Lu

    Citation: BMC Bioinformatics 2018 19(Suppl 19):528

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  5. Content type: Research

    Cyclic peptide-based drug discovery is attracting increasing interest owing to its potential to avoid target protein depletion. In drug discovery, it is important to maintain the biostability of a drug within ...

    Authors: Takashi Tajimi, Naoki Wakui, Keisuke Yanagisawa, Yasushi Yoshikawa, Masahito Ohue and Yutaka Akiyama

    Citation: BMC Bioinformatics 2018 19(Suppl 19):527

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  6. Content type: Research

    Previous studies have suggested deep learning to be a highly effective approach for screening lead compounds for new drugs. Several deep learning models have been developed by addressing the use of various kin...

    Authors: Maya Hirohara, Yutaka Saito, Yuki Koda, Kengo Sato and Yasubumi Sakakibara

    Citation: BMC Bioinformatics 2018 19(Suppl 19):526

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  7. Content type: Research

    Identifying protein-protein interactions (PPIs) is of paramount importance for understanding cellular processes. Machine learning-based approaches have been developed to predict PPIs, but the effectiveness of ...

    Authors: Long Zhang, Guoxian Yu, Maozu Guo and Jun Wang

    Citation: BMC Bioinformatics 2018 19(Suppl 19):525

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  8. Content type: Research

    N6-methyladensine (m6A) is a common and abundant RNA methylation modification found in various species. As a type of post-transcriptional methylation, m6A plays an important role in diverse RNA activities such...

    Authors: Yiqian Zhang and Michiaki Hamada

    Citation: BMC Bioinformatics 2018 19(Suppl 19):524

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  9. Content type: Research

    The default mode network (DMN) in resting state has been increasingly used in disease diagnosis since it was found in 2001. Prior work has mainly focused on extracting a single DMN with various techniques. How...

    Authors: Shengbing Pei, Jihong Guan and Shuigeng Zhou

    Citation: BMC Bioinformatics 2018 19(Suppl 19):523

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  10. Content type: Research

    Identifying specific residues for protein-DNA interactions are of considerable importance to better recognize the binding mechanism of protein-DNA complexes. Despite the fact that many computational DNA-bindin...

    Authors: Lei Deng, Juan Pan, Xiaojie Xu, Wenyi Yang, Chuyao Liu and Hui Liu

    Citation: BMC Bioinformatics 2018 19(Suppl 19):522

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  11. Content type: Research

    Distinction between pre-microRNAs (precursor microRNAs) and length-similar pseudo pre-microRNAs can reveal more about the regulatory mechanism of RNA biological processes. Machine learning techniques have been...

    Authors: Yuanlin Ma, Zuguo Yu, Guosheng Han, Jinyan Li and Vo Anh

    Citation: BMC Bioinformatics 2018 19(Suppl 19):521

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  12. Content type: Research

    Many evidences have demonstrated that circRNAs (circular RNA) play important roles in controlling gene expression of human, mouse and nematode. More importantly, circRNAs are also involved in many diseases thr...

    Authors: Cheng Yan, Jianxin Wang and Fang-Xiang Wu

    Citation: BMC Bioinformatics 2018 19(Suppl 19):520

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  13. Content type: Research

    Establishing the relationship between microbiota and specific diseases is important but requires appropriate statistical methodology. A specialized feature of microbiome count data is the presence of a large n...

    Authors: Ko Abe, Masaaki Hirayama, Kinji Ohno and Teppei Shimamura

    Citation: BMC Bioinformatics 2018 19(Suppl 19):519

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  14. Content type: Research

    Estimating heterogeneous treatment effect is a fundamental problem in biological and medical applications. Recently, several recursive partitioning methods have been proposed to identify the subgroups that res...

    Authors: Weijia Zhang, Thuc Duy Le, Lin Liu and Jiuyong Li

    Citation: BMC Bioinformatics 2018 19(Suppl 19):518

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  15. Content type: Research

    Early and accurate identification of potential adverse drug reactions (ADRs) for combined medication is vital for public health. Existing methods either rely on expensive wet-lab experiments or detecting exist...

    Authors: Yi Zheng, Hui Peng, Xiaocai Zhang, Zhixun Zhao, Jie Yin and Jinyan Li

    Citation: BMC Bioinformatics 2018 19(Suppl 19):517

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  16. Content type: Methodology

    Finding peptides with high binding affinity to Class I major histocompatibility complex (MHC-I) attracts intensive research, and it serves a crucial part of developing a better vaccine for precision medicine. ...

    Authors: Zhoujian Xiao, Yuwei Zhang, Runsheng Yu, Yin Chen, Xiaosen Jiang, Ziwei Wang and Shuaicheng Li

    Citation: BMC Bioinformatics 2018 19(Suppl 19):516

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  17. Content type: Research

    Type 2 diabetes (T2D) is one of the most common chronic diseases. Studies on T2D are mainly built upon bulk-cell data analysis, which measures the average gene expression levels for a population of cells and c...

    Authors: Lichun Ma and Jie Zheng

    Citation: BMC Bioinformatics 2018 19(Suppl 19):515

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  18. Content type: Software

    miRBase is the primary repository for published miRNA sequence and annotation data, and serves as the “go-to” place for miRNA research. However, the definition and annotation of miRNAs have been changed signif...

    Authors: Taosheng Xu, Ning Su, Lin Liu, Junpeng Zhang, Hongqiang Wang, Weijia Zhang, Jie Gui, Kui Yu, Jiuyong Li and Thuc Duy Le

    Citation: BMC Bioinformatics 2018 19(Suppl 19):514

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 19

  19. Content type: Software

    Direct-coupling analysis (DCA) is a method for protein contact prediction from sequence information alone. Its underlying principle is parameter estimation for a Hamiltonian interaction function stemming from ...

    Authors: Michael Schmidt and Kay Hamacher

    Citation: BMC Bioinformatics 2018 19:546

    Published on:

  20. Content type: Methodology article

    Accurate gene regulatory networks can be used to explain the emergence of different phenotypes, disease mechanisms, and other biological functions. Many methods have been proposed to infer networks from gene e...

    Authors: Phan Nguyen and Rosemary Braun

    Citation: BMC Bioinformatics 2018 19:545

    Published on:

  21. Content type: Research

    A range of rare and common genetic variants have been discovered to be potentially associated with mental diseases, but many more have not been uncovered. Powerful integrative methods are needed to systematica...

    Authors: Atlas Khan, Qian Liu and Kai Wang

    Citation: BMC Bioinformatics 2018 19(Suppl 17):501

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  22. Content type: Research

    Systems approaches in studying disease relationship have wide applications in biomedical discovery, such as disease mechanism understanding and drug discovery. The FDA Adverse Event Reporting System (FAERS) co...

    Authors: Chunlei Zheng and Rong Xu

    Citation: BMC Bioinformatics 2018 19(Suppl 17):500

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  23. Content type: Research

    Electronic Medical Record (EMR) comprises patients’ medical information gathered by medical stuff for providing better health care. Named Entity Recognition (NER) is a sub-field of information extraction aimed...

    Authors: Shanta Chowdhury, Xishuang Dong, Lijun Qian, Xiangfang Li, Yi Guan, Jinfeng Yang and Qiubin Yu

    Citation: BMC Bioinformatics 2018 19(Suppl 17):499

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  24. Content type: Research

    Identifying local recurrences in breast cancer from patient data sets is important for clinical research and practice. Developing a model using natural language processing and machine learning to identify loca...

    Authors: Zexian Zeng, Sasa Espino, Ankita Roy, Xiaoyu Li, Seema A. Khan, Susan E. Clare, Xia Jiang, Richard Neapolitan and Yuan Luo

    Citation: BMC Bioinformatics 2018 19(Suppl 17):498

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  25. Content type: Research

    In precision medicine, scarcity of suitable biological data often hinders the design of an appropriate predictive model. In this regard, large scale pharmacogenomics studies, like CCLE and GDSC hold the promis...

    Authors: Saugato Rahman Dhruba, Raziur Rahman, Kevin Matlock, Souparno Ghosh and Ranadip Pal

    Citation: BMC Bioinformatics 2018 19(Suppl 17):497

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  26. Content type: Research

    Hi-C data have been widely used to reconstruct chromosomal three-dimensional (3D) structures. One of the key limitations of Hi-C is the unclear relationship between spatial distance and the number of Hi-C cont...

    Authors: Tong Liu and Zheng Wang

    Citation: BMC Bioinformatics 2018 19(Suppl 17):496

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  27. Content type: Research

    Due to recent technology advancements, disease related knowledge is growing rapidly. It becomes nontrivial to go through all published literature to identify associations between human diseases and genetic, en...

    Authors: Junhui Shen, Suhas Vasaikar and Bing Zhang

    Citation: BMC Bioinformatics 2018 19(Suppl 17):495

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  28. Content type: Research

    Top-down mass spectrometry has unique advantages in identifying proteoforms with multiple post-translational modifications and/or unknown alterations. Most software tools in this area search top-down mass spec...

    Authors: Ziwei Li, Bo He, Qiang Kou, Zhe Wang, Si Wu, Yunlong Liu, Weixing Feng and Xiaowen Liu

    Citation: BMC Bioinformatics 2018 19(Suppl 17):494

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  29. Content type: Research

    In genomic studies, to investigate how the structure of a genetic network differs between two experiment conditions is a very interesting but challenging problem, especially in high-dimensional setting. Existi...

    Authors: Yong He, Jiadong Ji, Lei Xie, Xinsheng Zhang and Fuzhong Xue

    Citation: BMC Bioinformatics 2018 19(Suppl 17):493

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  30. Content type: Introduction

    The 2018 International Conference on Intelligent Biology and Medicine (ICIBM 2018) was held on June 10–12, 2018, in Los Angeles, California, USA. The conference consisted of a total of eleven scientific sessio...

    Authors: Xiaoming Liu, Lei Xie, Zhijin Wu, Kai Wang, Zhongming Zhao, Jianhua Ruan and Degui Zhi

    Citation: BMC Bioinformatics 2018 19(Suppl 17):492

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 17

  31. Content type: Research

    Adverse drug reactions (ADRs) are unintended and harmful reactions caused by normal uses of drugs. Predicting and preventing ADRs in the early stage of the drug development pipeline can help to enhance drug sa...

    Authors: Sanjoy Dey, Heng Luo, Achille Fokoue, Jianying Hu and Ping Zhang

    Citation: BMC Bioinformatics 2018 19(Suppl 21):476

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 21

  32. Content type: Research article

    The neutral theory of Motoo Kimura stipulates that evolution is mostly driven by neutral mutations. However adaptive pressure eventually leads to changes in phenotype that involve non-neutral mutations. The re...

    Authors: Reza Rezazadegan and Christian Reidys

    Citation: BMC Bioinformatics 2018 19:543

    Published on:

  33. Content type: Software

    As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase ...

    Authors: Gue-Ho Hwang, Jeongbin Park, Kayeong Lim, Sunghyun Kim, Jihyeon Yu, Eunchong Yu, Sang-Tae Kim, Roland Eils, Jin-Soo Kim and Sangsu Bae

    Citation: BMC Bioinformatics 2018 19:542

    Published on:

  34. Content type: Methodology article

    DNA methylation of CpG dinucleotides is an essential epigenetic modification that plays a key role in transcription. Widely used DNA enrichment-based methods offer high coverage for measuring methylated CpG di...

    Authors: Jingting Xu, Shimeng Liu, Ping Yin, Serdar Bulun and Yang Dai

    Citation: BMC Bioinformatics 2018 19:540

    Published on:

  35. Content type: Software

    Pathway enrichment techniques are useful for understanding experimental metabolomics data. Their purpose is to give context to the affected metabolites in terms of the prior knowledge contained in metabolic pa...

    Authors: Sergio Picart-Armada, Francesc Fernández-Albert, Maria Vinaixa, Oscar Yanes and Alexandre Perera-Lluna

    Citation: BMC Bioinformatics 2018 19:538

    Published on:

  36. Content type: Research

    With applications in cancer, drug metabolism, and disease etiology, understanding structural variation in the human genome is critical in advancing the thrusts of individualized medicine. However, structural v...

    Authors: Zachary Stephens, Chen Wang, Ravishankar K. Iyer and Jean-Pierre Kocher

    Citation: BMC Bioinformatics 2018 19(Suppl 20):508

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  37. Content type: Research

    In biomedical information extraction, event extraction plays a crucial role. Biological events are used to describe the dynamic effects or relationships between biological entities such as proteins and genes. ...

    Authors: Yan Wang, Jian Wang, Hongfei Lin, Xiwei Tang, Shaowu Zhang and Lishuang Li

    Citation: BMC Bioinformatics 2018 19(Suppl 20):507

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  38. Content type: Research

    Atomic details of protein-DNA complexes can provide insightful information for better understanding of the function and binding specificity of DNA binding proteins. In addition to experimental methods for solv...

    Authors: Rosario I. Corona, Sanjana Sudarshan, Srinivas Aluru and Jun-tao Guo

    Citation: BMC Bioinformatics 2018 19(Suppl 20):506

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  39. Content type: Research

    The majority of cancer-related deaths are due to lung cancer, and there is a need for reliable diagnostic biomarkers to predict stages in non-small cell lung cancer cases. Recently, microRNAs were found to hav...

    Authors: Nhat Tran, Vinay Abhyankar, KyTai Nguyen, Jon Weidanz and Jean Gao

    Citation: BMC Bioinformatics 2018 19(Suppl 20):504

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  40. Content type: Research

    Biomedical semantic indexing is important for information retrieval and many other research fields in bioinformatics. It annotates biomedical citations with Medical Subject Headings. In face of unbalanced cate...

    Authors: Yongping Du, Yunpeng Pan, Chencheng Wang and Junzhong Ji

    Citation: BMC Bioinformatics 2018 19(Suppl 20):502

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 20

  41. Content type: Methodology

    Current multi-petaflop supercomputers are powerful systems, but present challenges when faced with problems requiring large machine learning workflows. Complex algorithms running at system scale, often with di...

    Authors: Justin M. Wozniak, Rajeev Jain, Prasanna Balaprakash, Jonathan Ozik, Nicholson T. Collier, John Bauer, Fangfang Xia, Thomas Brettin, Rick Stevens, Jamaludin Mohd-Yusof, Cristina Garcia Cardona, Brian Van Essen and Matthew Baughman

    Citation: BMC Bioinformatics 2018 19(Suppl 18):491

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  42. Content type: Research

    Real-time analysis of patient data during medical procedures can provide vital diagnostic feedback that significantly improves chances of success. With sensors becoming increasingly fast, frameworks such as De...

    Authors: Ahmed Sanaullah, Chen Yang, Yuri Alexeev, Kazutomo Yoshii and Martin C. Herbordt

    Citation: BMC Bioinformatics 2018 19(Suppl 18):490

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  43. Content type: Research

    Histopathology images of tumor biopsies present unique challenges for applying machine learning to the diagnosis and treatment of cancer. The pathology slides are high resolution, often exceeding 1GB, have non...

    Authors: Will Fischer, Sanketh S. Moudgalya, Judith D. Cohn, Nga T. T. Nguyen and Garrett T. Kenyon

    Citation: BMC Bioinformatics 2018 19(Suppl 18):489

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

  44. Content type: Research

    Manual extraction of information from electronic pathology (epath) reports to populate the Surveillance, Epidemiology, and End Result (SEER) database is labor intensive. Systematizing the data extraction autom...

    Authors: Nicolas Hengartner, Leticia Cuellar, Xiao-Cheng Wu, Georgia Tourassi, John Qiu, Blair Christian and Tanmoy Bhattacharya

    Citation: BMC Bioinformatics 2018 19(Suppl 18):485

    Published on:

    This article is part of a Supplement: Volume 19 Supplement 18

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