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  1. Horizontal Gene Transfer (HGT) refers to the transfer of genetic materials between organisms through mechanisms other than parent-offspring inheritance. HGTs may affect human health through a large number of m...

    Authors: Chen Li, Yiqi Jiang and Shuaicheng Li

    Citation: BMC Bioinformatics 2019 20(Suppl 23):702

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  2. The main research topic in this paper is how to compare multiple biological experiments using transcriptome data, where each experiment is measured and designed to compare control and treated samples. Comparis...

    Authors: Benjamin Hur, Dongwon Kang, Sangseon Lee, Ji Hwan Moon, Gung Lee and Sun Kim

    Citation: BMC Bioinformatics 2019 20(Suppl 23):667

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  3. With recent advances in high-throughput technologies, matrix factorization techniques are increasingly being utilized for mapping quantitative omics profiling matrix data into low-dimensional embedding space, in ...

    Authors: Lingxi Chen, Jiao Xu and Shuai Cheng Li

    Citation: BMC Bioinformatics 2019 20(Suppl 23):648

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  4. Current technologies for understanding the transcriptional reprogramming in cells include the transcription factor (TF) chromatin immunoprecipitation (ChIP) experiments and the TF knockout experiments. The ChI...

    Authors: Tzu-Hsien Yang

    Citation: BMC Bioinformatics 2019 20(Suppl 23):630

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

  5. Studying multiple microRNAs (miRNAs) synergism in gene regulation could help to understand the regulatory mechanisms of complicated human diseases caused by miRNAs. Several existing methods have been presented...

    Authors: Junpeng Zhang, Vu Viet Hoang Pham, Lin Liu, Taosheng Xu, Buu Truong, Jiuyong Li, Nini Rao and Thuc Duy Le

    Citation: BMC Bioinformatics 2019 20(Suppl 23):613

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 23

    The Correction to this article has been published in BMC Bioinformatics 2020 21:32

  6. Genomic prediction is an advanced method for estimating genetic values, which has been widely accepted for genetic evaluation in animal and disease-risk prediction in human. It estimates genetic values with ge...

    Authors: Dan Jiang, Cong Xin, Jinhua Ye, Yingbo Yuan and Ming Fang

    Citation: BMC Bioinformatics 2019 20:731

    Content type: Software

    Published on:

  7. Differences in cell-type composition across subjects and conditions often carry biological significance. Recent advancements in single cell sequencing technologies enable cell-types to be identified at the sin...

    Authors: Yue Cao, Yingxin Lin, John T. Ormerod, Pengyi Yang, Jean Y.H. Yang and Kitty K. Lo

    Citation: BMC Bioinformatics 2019 20(Suppl 19):721

    Content type: Research

    Published on:

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

  8. Group B streptococcus (GBS) is an important pathogen that is responsible for invasive infections, including sepsis and meningitis. GBS serotyping is an essential means for the investigation of possible infecti...

    Authors: Hsin-Yao Wang, Wen-Chi Li, Kai-Yao Huang, Chia-Ru Chung, Jorng-Tzong Horng, Jen-Fu Hsu, Jang-Jih Lu and Tzong-Yi Lee

    Citation: BMC Bioinformatics 2019 20(Suppl 19):703

    Content type: Research

    Published on:

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

  9. Protein structural class predicting is a heavily researched subject in bioinformatics that plays a vital role in protein functional analysis, protein folding recognition, rational drug design and other related...

    Authors: Shunfang Wang and Xiaoheng Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 25):701

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  10. Membrane proteins play an important role in the life activities of organisms. Knowing membrane protein types provides clues for understanding the structure and function of proteins. Though various computationa...

    Authors: Lei Guo, Shunfang Wang, Mingyuan Li and Zicheng Cao

    Citation: BMC Bioinformatics 2019 20(Suppl 25):700

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  11. The recognition of protein interaction sites is of great significance in many biological processes, signaling pathways and drug designs. However, most sites on protein sequences cannot be defined as interface ...

    Authors: Ye Wang, Changqing Mei, Yuming Zhou, Yan Wang, Chunhou Zheng, Xiao Zhen, Yan Xiong, Peng Chen, Jun Zhang and Bing Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 25):699

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  12. Alternative splicing allows the pre-mRNAs of a gene to be spliced into various mRNAs, which greatly increases the diversity of proteins. High-throughput sequencing of mRNAs has revolutionized our ability for t...

    Authors: Jin Zhao, Haodi Feng, Daming Zhu, Chi Zhang and Ying Xu

    Citation: BMC Bioinformatics 2019 20(Suppl 25):698

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  13. Along with the development of precision medicine, individual heterogeneity is attracting more and more attentions in clinical research and application. Although the biomolecular reaction seems to be some vario...

    Authors: Shaoyan Sun, Xiangtian Yu, Fengnan Sun, Ying Tang, Juan Zhao and Tao Zeng

    Citation: BMC Bioinformatics 2019 20(Suppl 25):697

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  14. Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity is the most basic component of a scoring function and plays an important role ...

    Authors: Yumeng Yan and Sheng-You Huang

    Citation: BMC Bioinformatics 2019 20(Suppl 25):696

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  15. Imbalanced datasets are commonly encountered in bioinformatics classification problems, that is, the number of negative samples is much larger than that of positive samples. Particularly, the data imbalance ph...

    Authors: Yongqing Zhang, Shaojie Qiao, Rongzhao Lu, Nan Han, Dingxiang Liu and Jiliu Zhou

    Citation: BMC Bioinformatics 2019 20(Suppl 25):695

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  16. The interactions among proteins act as crucial roles in most cellular processes. Despite enormous effort put for identifying protein-protein interactions (PPIs) from a large number of organisms, existing first...

    Authors: Zhengwei Li, Ru Nie, Zhuhong You, Chen Cao and Jiashu Li

    Citation: BMC Bioinformatics 2019 20(Suppl 25):694

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  17. Glaucoma is an irreversible eye disease caused by the optic nerve injury. Therefore, it usually changes the structure of the optic nerve head (ONH). Clinically, ONH assessment based on fundus image is one of t...

    Authors: Beiji Zou, Changlong Chen, Rongchang Zhao, Pingbo Ouyang, Chengzhang Zhu, Qilin Chen and Xuanchu Duan

    Citation: BMC Bioinformatics 2019 20(Suppl 25):693

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  18. The Copy Number Alterations (CNAs) are discovered to be tightly associated with cancers, so accurately detecting them is one of the most important tasks in the cancer genomics. A series of CNAs detection metho...

    Authors: Fei Luo

    Citation: BMC Bioinformatics 2019 20(Suppl 25):692

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  19. The association between BIN1 rs744373 variant and Alzheimer’s disease (AD) had been identified by genome-wide association studies (GWASs) as well as candidate gene studies in Caucasian populations. But in East...

    Authors: Zhifa Han, Tao Wang, Rui Tian, Wenyang Zhou, Pingping Wang, Peng Ren, Jian Zong, Yang Hu, Shuilin Jin and Qinghua Jiang

    Citation: BMC Bioinformatics 2019 20(Suppl 25):691

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  20. 2′-O-methylation (2′-O-me or Nm) is a post-transcriptional RNA methylation modified at 2′-hydroxy, which is common in mRNAs and various non-coding RNAs. Previous studies revealed the significance of Nm in mult...

    Authors: Yiran Zhou, Qinghua Cui and Yuan Zhou

    Citation: BMC Bioinformatics 2019 20(Suppl 25):690

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  21. Accurate identification of potential interactions between drugs and protein targets is a critical step to accelerate drug discovery. Despite many relative experimental researches have been done in the past dec...

    Authors: ShanShan Hu, Chenglin Zhang, Peng Chen, Pengying Gu, Jun Zhang and Bing Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 25):689

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  22. The occurrence of cotton pests and diseases has always been an important factor affecting the total cotton production. Cotton has a great dependence on environmental factors during its growth, especially clima...

    Authors: Qingxin Xiao, Weilu Li, Yuanzhong Kai, Peng Chen, Jun Zhang and Bing Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 25):688

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  23. Bamboo is a very important forest resource. However, the prolonged vegetative stages and uncertainty of flowering brings difficulties in bamboo flowers sampling. Until now, the flowering mechanism of bamboo is...

    Authors: Yulian Jiao, Qiutao Hu, Yan Zhu, Longfei Zhu, Tengfei Ma, Haiyong Zeng, Qiaolu Zang, Xuan Li and Xinchun Lin

    Citation: BMC Bioinformatics 2019 20(Suppl 25):687

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  24. Predicting miRNA-disease associations (MDAs) is time-consuming and expensive. It is imminent to improve the accuracy of prediction results. So it is crucial to develop a novel computing technology to predict n...

    Authors: Zhen Cui, Jin-Xing Liu, Ying-Lian Gao, Chun-Hou Zheng and Juan Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 25):686

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  25. Protein structure prediction has always been an important issue in bioinformatics. Prediction of the two-dimensional structure of proteins based on the hydrophobic polarity model is a typical non-deterministic...

    Authors: Hongjie Wu, Ru Yang, Qiming Fu, Jianping Chen, Weizhong Lu and Haiou Li

    Citation: BMC Bioinformatics 2019 20(Suppl 25):685

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  26. RNA secondary structure prediction is an important issue in structural bioinformatics, and RNA pseudoknotted secondary structure prediction represents an NP-hard problem. Recently, many different machine-learn...

    Authors: Weizhong Lu, Ye Tang, Hongjie Wu, Hongmei Huang, Qiming Fu, Jing Qiu and Haiou Li

    Citation: BMC Bioinformatics 2019 20(Suppl 25):684

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  27. In ab initio protein-structure predictions, a large set of structural decoys are often generated, with the requirement to select best five or three candidates from the decoys. The clustered central structures ...

    Authors: Hongjie Wu, Hongmei Huang, Weizhong Lu, Qiming Fu, Yijie Ding, Jing Qiu and Haiou Li

    Citation: BMC Bioinformatics 2019 20(Suppl 25):683

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  28. Protein complexes are the cornerstones of many biological processes and gather them to form various types of molecular machinery that perform a vast array of biological functions. In fact, a protein may belong...

    Authors: Jie Zhao and Xiujuan Lei

    Citation: BMC Bioinformatics 2019 20(Suppl 25):682

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  29. Cost-sensitive algorithm is an effective strategy to solve imbalanced classification problem. However, the misclassification costs are usually determined empirically based on user expertise, which leads to uns...

    Authors: Huijuan Lu, Yige Xu, Minchao Ye, Ke Yan, Zhigang Gao and Qun Jin

    Citation: BMC Bioinformatics 2019 20(Suppl 25):681

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 25

  30. Protein comparative analysis and similarity searches play essential roles in structural bioinformatics. A couple of algorithms for protein structure alignments have been developed in recent years. However, fac...

    Authors: Lei Deng, Guolun Zhong, Chenzhe Liu, Judong Luo and Hui Liu

    Citation: BMC Bioinformatics 2019 20(Suppl 19):662

    Content type: Methodology

    Published on:

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

  31. Drug-drug interactions (DDIs) are a major concern in patients’ medication. It’s unfeasible to identify all potential DDIs using experimental methods which are time-consuming and expensive. Computational method...

    Authors: Yi Zheng, Hui Peng, Xiaocai Zhang, Zhixun Zhao, Xiaoying Gao and Jinyan Li

    Citation: BMC Bioinformatics 2019 20(Suppl 19):661

    Content type: Research

    Published on:

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

  32. Single-cell RNA-sequencing (scRNA-seq) is a transformative technology, allowing global transcriptomes of individual cells to be profiled with high accuracy. An essential task in scRNA-seq data analysis is the ...

    Authors: Thomas A. Geddes, Taiyun Kim, Lihao Nan, James G. Burchfield, Jean Y. H. Yang, Dacheng Tao and Pengyi Yang

    Citation: BMC Bioinformatics 2019 20(Suppl 19):660

    Content type: Research

    Published on:

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

  33. Accurate classification of diffuse gliomas, the most common tumors of the central nervous system in adults, is important for appropriate treatment. However, detection of isocitrate dehydrogenase (IDH) mutation an...

    Authors: Sean Chun-Chang Chen, Chung-Ming Lo, Shih-Hua Wang and Emily Chia-Yu Su

    Citation: BMC Bioinformatics 2019 20(Suppl 19):659

    Content type: Research

    Published on:

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

  34. Studying structural and functional morphology of small organisms such as monogenean, is difficult due to the lack of visualization in three dimensions. One possible way to resolve this visualization issue is t...

    Authors: Bee Guan Teo and Sarinder Kaur Dhillon

    Citation: BMC Bioinformatics 2019 20(Suppl 19):658

    Content type: Research

    Published on:

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

  35. Synthetic lethality has attracted a lot of attentions in cancer therapeutics due to its utility in identifying new anticancer drug targets. Identifying synthetic lethal (SL) interactions is the key step toward...

    Authors: Jiang Huang, Min Wu, Fan Lu, Le Ou-Yang and Zexuan Zhu

    Citation: BMC Bioinformatics 2019 20(Suppl 19):657

    Content type: Research

    Published on:

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

  36. A survey of presences and absences of specific species across multiple biogeographic units (or bioregions) are used in a broad area of biological studies from ecology to microbiology. Using binary presence-abs...

    Authors: Neo Christopher Chung, BłaŻej Miasojedow, Michał Startek and Anna Gambin

    Citation: BMC Bioinformatics 2019 20(Suppl 15):644

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  37. Super-enhancers (SEs) are clusters of transcriptional active enhancers, which dictate the expression of genes defining cell identity and play an important role in the development and progression of tumors and ...

    Authors: Hongda Bu, Jiaqi Hao, Yanglan Gan, Shuigeng Zhou and Jihong Guan

    Citation: BMC Bioinformatics 2019 20(Suppl 15):598

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  38. Traditional drug research and development is high cost, time-consuming and risky. Computationally identifying new indications for existing drugs, referred as drug repositioning, greatly reduces the cost and attra...

    Authors: Yuehui Wang, Maozu Guo, Yazhou Ren, Lianyin Jia and Guoxian Yu

    Citation: BMC Bioinformatics 2019 20(Suppl 15):547

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  39. A drug-drug interaction (DDI) is defined as a drug effect modified by another drug, which is very common in treating complex diseases such as cancer. Many studies have evidenced that some DDIs could be an incr...

    Authors: Cheng Yan, Guihua Duan, Yi Pan, Fang-Xiang Wu and Jianxin Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 15):538

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  40. Antimicrobial resistance (AMR) is a major threat to global public health because it makes standard treatments ineffective and contributes to the spread of infections. It is important to understand AMR’s biolog...

    Authors: Jinhong Shi, Yan Yan, Matthew G. Links, Longhai Li, Jo-Anne R. Dillon, Michael Horsch and Anthony Kusalik

    Citation: BMC Bioinformatics 2019 20(Suppl 15):535

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  41. Chromatin immunoprecipitation sequencing (ChIP-seq) is a technology that combines chromatin immunoprecipitation (ChIP) with next generation of sequencing technology (NGS) to analyze protein interactions with D...

    Authors: Min Li, Li Tang, Fang-Xiang Wu, Yi Pan and Jianxin Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 15):515

    Content type: Software

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  42. Cluster analysis is a core task in modern data-centric computation. Algorithmic choice is driven by factors such as data size and heterogeneity, the similarity measures employed, and the type of clusters sough...

    Authors: Yuping Lu, Charles A. Phillips and Michael A. Langston

    Citation: BMC Bioinformatics 2019 20(Suppl 15):503

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  43. The biological network is highly dynamic. Functional relations between genes can be activated or deactivated depending on the biological conditions. On the genome-scale network, subnetworks that gain or lose l...

    Authors: Jianwei Lu, Yao Lu, Yusheng Ding, Qingyang Xiao, Linqing Liu, Qingpo Cai, Yunchuan Kong, Yun Bai and Tianwei Yu

    Citation: BMC Bioinformatics 2019 20(Suppl 15):489

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  44. Protein-protein interaction plays a key role in a multitude of biological processes, such as signal transduction, de novo drug design, immune responses, and enzymatic activities. Gaining insights of various bi...

    Authors: Fei Guo, Quan Zou, Guang Yang, Dan Wang, Jijun Tang and Junhai Xu

    Citation: BMC Bioinformatics 2019 20(Suppl 15):483

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  45. Gene is a key step in genome annotation. Ab initio gene prediction enables gene annotation of new genomes regardless of availability of homologous sequences. There exist a number of ab initio gene prediction tool...

    Authors: Prapaporn Techa-Angkoon, Kevin L. Childs and Yanni Sun

    Citation: BMC Bioinformatics 2019 20(Suppl 15):482

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  46. Cognitive decline has emerged as a significant threat to both public health and personal welfare, and mild cognitive decline/impairment (MCI) can further develop into Dementia/Alzheimer’s disease. While treatm...

    Authors: Liyuan Liu, Bingchen Yu, Meng Han, Shanshan Yuan and Na Wang

    Citation: BMC Bioinformatics 2019 20(Suppl 15):481

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 15

  47. This Editorial first introduces the background of the vaccine and drug relations and how biomedical terminologies and ontologies have been used to support their studies. The history of the seven workshops, ini...

    Authors: Junguk Hur, Cui Tao and Yongqun He

    Citation: BMC Bioinformatics 2019 20(Suppl 21):705

    Content type: Introduction

    Published on:

    This article is part of a Supplement: Volume 20 Supplement 21

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2018 Journal Metrics

  • Citation Impact
    2.511 - 2-year Impact Factor
    2.970 - 5-year Impact Factor
    0.855 - Source Normalized Impact per Paper (SNIP)
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