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  1. Recent development of single cell sequencing technologies has made it possible to identify genes with different expression (DE) levels at the cell type level between different groups of samples. In this articl...

    Authors: Hongyu Li, Biqing Zhu, Zhichao Xu, Taylor Adams, Naftali Kaminski and Hongyu Zhao

    Citation: BMC Bioinformatics 2021 22:524

    Content type: Research

    Published on:

  2. In the process of designing drugs and proteins, it is crucial to recognize hot regions in protein–protein interactions. Each hot region of protein–protein interaction is composed of at least three hot spots, w...

    Authors: Jing Hu, Longwei Zhou, Bo Li, Xiaolong Zhang and Nansheng Chen

    Citation: BMC Bioinformatics 2021 22(Suppl 3):522

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  3. Liver cancer is a common malignant tumor in China, with high mortality. Its occurrence and development were thoroughly studied by high-throughput expression microarray, which produced abundant data on gene exp...

    Authors: Ye-Cheng Wang, Zhen-Bo Tian and Xu-Qing Tang

    Citation: BMC Bioinformatics 2021 22(Suppl 3):521

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 3

  4. Genetic information is becoming more readily available and is increasingly being used to predict patient cancer types as well as their subtypes. Most classification methods thus far utilize somatic mutations a...

    Authors: Zexian Zeng, Chengsheng Mao, Andy Vo, Xiaoyu Li, Janna Ore Nugent, Seema A. Khan, Susan E. Clare and Yuan Luo

    Citation: BMC Bioinformatics 2021 22(Suppl 4):491

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 4

  5. Gene co-expression networks are widely studied in the biomedical field, with algorithms such as WGCNA and lmQCM having been developed to detect co-expressed modules. However, these algorithms have limitations ...

    Authors: Yusong Liu, Xiufen Ye, Christina Y. Yu, Wei Shao, Jie Hou, Weixing Feng, Jie Zhang and Kun Huang

    Citation: BMC Bioinformatics 2021 22(Suppl 4):111

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 4

  6. Several computational tools for predicting protein Ubiquitylation and SUMOylation sites have been proposed to study their regulatory roles in gene location, gene expression, and genome replication. However, ex...

    Authors: Fei He, Jingyi Li, Rui Wang, Xiaowei Zhao and Ye Han

    Citation: BMC Bioinformatics 2021 22:519

    Content type: Methodology article

    Published on:

  7. Current alignment tools typically lack an explicit model of indel evolution, leading to artificially short inferred alignments (i.e., over-alignment) due to inconsistencies between the indel history and the ph...

    Authors: Massimo Maiolo, Lorenzo Gatti, Diego Frei, Tiziano Leidi, Manuel Gil and Maria Anisimova

    Citation: BMC Bioinformatics 2021 22:518

    Content type: Software

    Published on:

  8. Protein subcellular localization prediction plays an important role in biology research. Since traditional methods are laborious and time-consuming, many machine learning-based prediction methods have been pro...

    Authors: Zhijun Liao, Gaofeng Pan, Chao Sun and Jijun Tang

    Citation: BMC Bioinformatics 2021 22(Suppl 10):515

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  9. Systems-level analyses, such as differential gene expression analysis, co-expression analysis, and metabolic pathway reconstruction, depend on the accuracy of the transcriptome. Multiple tools exist to perform...

    Authors: Adam Voshall, Sairam Behera, Xiangjun Li, Xiao-Hong Yu, Kushagra Kapil, Jitender S. Deogun, John Shanklin, Edgar B. Cahoon and Etsuko N. Moriyama

    Citation: BMC Bioinformatics 2021 22:513

    Content type: Methodology article

    Published on:

  10. The Living Evidence Map Project at the Norwegian Institute of Public Health (NIPH) gives an updated overview of research results and publications. As part of NIPH’s mandate to inform evidence-based infection p...

    Authors: Thomas B. Røst, Laura Slaughter, Øystein Nytrø, Ashley E. Muller and Gunn E. Vist

    Citation: BMC Bioinformatics 2021 22(Suppl 11):496

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 11

  11. Concept recognition is a term that corresponds to the two sequential steps of named entity recognition and named entity normalization, and plays an essential role in the field of bioinformatics. However, the c...

    Authors: Kwangmin Kim and Doheon Lee

    Citation: BMC Bioinformatics 2021 22(Suppl 11):337

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 11

  12. Extraction of adverse drug events from biomedical literature and other textual data is an important component to monitor drug-safety and this has attracted attention of many researchers in healthcare. Existing...

    Authors: Harshit Jain, Nishant Raj and Suyash Mishra

    Citation: BMC Bioinformatics 2021 22(Suppl 11):330

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 11

  13. Paralogs formed through gene duplication and isoforms formed through alternative splicing have been important processes for increasing protein diversity and maintaining cellular homeostasis. Despite their reco...

    Authors: Jooseong Oh, Sung-Gwon Lee and Chungoo Park

    Citation: BMC Bioinformatics 2021 22(Suppl 11):311

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 11

  14. Lately, high-throughput RNA sequencing has been extensively used to elucidate the transcriptome landscape and dynamics of cell types of different species. In particular, for most non-model organisms lacking co...

    Authors: Sung-Gwon Lee, Dokyun Na and Chungoo Park

    Citation: BMC Bioinformatics 2021 22(Suppl 11):310

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 11

  15. Optimization of DNA and protein sequences based on Machine Learning models is becoming a powerful tool for molecular design. Activation maximization offers a simple design strategy for differentiable models: o...

    Authors: Johannes Linder and Georg Seelig

    Citation: BMC Bioinformatics 2021 22:510

    Content type: Methodology article

    Published on:

  16. Sequencing partial 16S rRNA genes is a cost effective method for quantifying the microbial composition of an environment, such as the human gut. However, downstream analysis relies on binning reads into microb...

    Authors: Brianna S. Chrisman, Kelley M. Paskov, Nate Stockham, Jae-Yoon Jung, Maya Varma, Peter Y. Washington, Christine Tataru, Shoko Iwai, Todd Z. DeSantis, Maude David and Dennis P. Wall

    Citation: BMC Bioinformatics 2021 22:509

    Content type: Methodology article

    Published on:

  17. The 10th and 9th revisions of the International Statistical Classification of Diseases and Related Health Problems (ICD10 and ICD9) have been adopted worldwide as a well-recognized norm to share codes for dise...

    Authors: Ling Wan, Justin Song, Virginia He, Jennifer Roman, Grace Whah, Suyuan Peng, Luxia Zhang and Yongqun He

    Citation: BMC Bioinformatics 2021 22(Suppl 6):508

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 6

  18. Ubiquitylation is an important post-translational modification of proteins that not only plays a central role in cellular coding, but is also closely associated with the development of a variety of diseases. T...

    Authors: Mengqi Luo, Zhongyan Li, Shangfu Li and Tzong-Yi Lee

    Citation: BMC Bioinformatics 2021 22:507

    Content type: Research

    Published on:

  19. Glycan-related genes play a fundamental role in various processes for energy acquisition and homeostasis maintenance while adapting to the environment in which the organism exists; however, their role in the m...

    Authors: Hayato Takihara, Nobuaki Miura, Kiyoko F. Aoki-Kinoshita and Shujiro Okuda

    Citation: BMC Bioinformatics 2021 22:505

    Content type: Research

    Published on:

  20. The functions of RNA molecules are mainly determined by their secondary structures. These functions can also be predicted using bioinformatic tools that enable the alignment of multiple RNAs to determine funct...

    Authors: Tomasz Woźniak, Małgorzata Sajek, Jadwiga Jaruzelska and Marcin Piotr Sajek

    Citation: BMC Bioinformatics 2021 22:504

    Content type: Software

    Published on:

  21. Piwi-interacting RNAs (piRNAs) are the small non-coding RNAs (ncRNAs) that silence genomic transposable elements. And researchers found out that piRNA also regulates various endogenous transcripts. However, th...

    Authors: Tzu-Hsien Yang, Sheng-Cian Shiue, Kuan-Yu Chen, Yan-Yuan Tseng and Wei-Sheng Wu

    Citation: BMC Bioinformatics 2021 22:503

    Content type: Methodology article

    Published on:

  22. Identifying human protein-phenotype relationships has attracted researchers in bioinformatics and biomedical natural language processing due to its importance in uncovering rare and complex diseases. Since exp...

    Authors: Morteza Pourreza Shahri and Indika Kahanda

    Citation: BMC Bioinformatics 2021 22:500

    Content type: Methodology article

    Published on:

  23. Identifying gene interactions is a topic of great importance in genomics, and approaches based on network models provide a powerful tool for studying these. Assuming a Gaussian graphical model, a gene associat...

    Authors: Camilla Lingjærde, Tonje G. Lien, Ørnulf Borgan, Helga Bergholtz and Ingrid K. Glad

    Citation: BMC Bioinformatics 2021 22:498

    Content type: Methodology article

    Published on:

  24. The study of drug–target interactions (DTIs) affinity plays an important role in safety assessment and pharmacology. Currently, quantitative structure–activity relationship (QSAR) and molecular docking (MD) ar...

    Authors: Xian-rui Wang, Ting-ting Cao, Cong Min Jia, Xue-mei Tian and Yun Wang

    Citation: BMC Bioinformatics 2021 22:497

    Content type: Research article

    Published on:

  25. Circular RNA (circRNA) is an emerging class of RNA molecules attracting researchers due to its potential for serving as markers for diagnosis, prognosis, or therapeutic targets of cancer, cardiovascular, and a...

    Authors: Dat Thanh Nguyen, Quang Thinh Trac, Thi-Hau Nguyen, Ha-Nam Nguyen, Nir Ohad, Yudi Pawitan and Trung Nghia Vu

    Citation: BMC Bioinformatics 2021 22:495

    Content type: Research

    Published on:

  26. This work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein follo...

    Authors: Teng-Ruei Chen, Yen-Cheng Lin, Yu-Wei Huang, Chih-Chieh Chen and Wei-Cheng Lo

    Citation: BMC Bioinformatics 2021 22(Suppl 10):494

    Content type: Methodology

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 10

  27. Taxonomic classification of genetic markers for microbiome analysis is affected by the numerous choices made from sample preparation to bioinformatics analysis. Paired-end read merging is routinely used to cap...

    Authors: Daniel P. Dacey and Frédéric J. J. Chain

    Citation: BMC Bioinformatics 2021 22:493

    Content type: Research article

    Published on:

  28. Data visualization, especially the genome track plots, is crucial for genomics researchers to discover patterns in large-scale sequencing dataset. Although existing tools works well for producing a normal view...

    Authors: Weize Xu, Quan Zhong, Da Lin, Ya Zuo, Jinxia Dai, Guoliang Li and Gang Cao

    Citation: BMC Bioinformatics 2021 22:489

    Content type: Software

    Published on:

  29. Population genetic studies of humans make increasing use of high-throughput sequencing in order to capture diversity in an unbiased way. There is an abundance of sequencing technologies, bioinformatic tools an...

    Authors: Gwenna Breton, Anna C. V. Johansson, Per Sjödin, Carina M. Schlebusch and Mattias Jakobsson

    Citation: BMC Bioinformatics 2021 22:488

    Content type: Research article

    Published on:

  30. Alignment-free methods are a popular approach for comparing biological sequences, including complete genomes. The methods range from probability distributions of sequence composition to first and higher-order ...

    Authors: Joel Gustafsson, Peter Norberg, Jan R. Qvick-Wester and Alexander Schliep

    Citation: BMC Bioinformatics 2021 22:487

    Content type: Software

    Published on:

  31. Protein protein interactions (PPIs) are essential to most of the biological processes. The prediction of PPIs is beneficial to the understanding of protein functions and thus is helpful to pathological analysi...

    Authors: Weixia Xu, Yangyun Gao, Yang Wang and Jihong Guan

    Citation: BMC Bioinformatics 2021 22(Suppl 6):485

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 6

  32. Traditional methods for single-variant genome-wide association study (GWAS) incur a substantial multiple-testing burden because of the need to test for associations with a vast number of single-nucleotide poly...

    Authors: William R. P. Denault, Håkon K. Gjessing, Julius Juodakis, Bo Jacobsson and Astanand Jugessur

    Citation: BMC Bioinformatics 2021 22:484

    Content type: Methodology article

    Published on:

  33. Identifying interaction effects between genes is one of the main tasks of genome-wide association studies aiming to shed light on the biological mechanisms underlying complex diseases. Multifactor dimensionali...

    Authors: Mira Park, Hoe-Bin Jeong, Jong-Hyun Lee and Taesung Park

    Citation: BMC Bioinformatics 2021 22:480

    Content type: Research

    Published on:

  34. Long noncoding RNAs (lncRNAs) play important roles in various biological and pathological processes. Discovery of lncRNA–protein interactions (LPIs) contributes to understand the biological functions and mecha...

    Authors: Liqian Zhou, Zhao Wang, Xiongfei Tian and Lihong Peng

    Citation: BMC Bioinformatics 2021 22:479

    Content type: Research

    Published on:

  35. Deep learning methods are a proven commodity in many fields and endeavors. One of these endeavors is predicting the presence of adverse drug–drug interactions (DDIs). The models generated can predict, with rea...

    Authors: Rogia Kpanou, Mazid Abiodoun Osseni, Prudencio Tossou, Francois Laviolette and Jacques Corbeil

    Citation: BMC Bioinformatics 2021 22:477

    Content type: Research

    Published on:

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