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  1. Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of ...

    Authors: Marco Antonio Tangaro, Pietro Mandreoli, Matteo Chiara, Giacinto Donvito, Marica Antonacci, Antonio Parisi, Angelica Bianco, Angelo Romano, Daniela Manila Bianchi, Davide Cangelosi, Paolo Uva, Ivan Molineris, Vladimir Nosi, Raffaele A. Calogero, Luca Alessandri, Elena Pedrini…
    Citation: BMC Bioinformatics 2021 22(Suppl 15):544
    Content type: Software Published on:

    This article is part of a Supplement: Volume 22 Supplement 15

  2. Clinical diagnostics of whole-exome and whole-genome sequencing data requires geneticists to consider thousands of genetic variants for each patient. Various variant prioritization methods have been developed ...

    Authors: Andreas Ruscheinski, Anna Lena Reimler, Roland Ewald and Adelinde M. Uhrmacher
    Citation: BMC Bioinformatics 2021 22:543
    Content type: Software Published on:

  3. Accurate prediction of protein–ligand binding affinity is important for lowering the overall cost of drug discovery in structure-based drug design. For accurate predictions, many classical scoring functions an...

    Authors: Sangmin Seo, Jonghwan Choi, Sanghyun Park and Jaegyoon Ahn
    Citation: BMC Bioinformatics 2021 22:542
    Content type: Research Published on:

  4. Accurate segmentation and recognition algorithm of lung nodules has great important value of reference for early diagnosis of lung cancer. An algorithm is proposed for 3D CT sequence images in this paper based...

    Authors: Hui Yu, Jinqiu Li, Lixin Zhang, Yuzhen Cao, Xuyao Yu and Jinglai Sun
    Citation: BMC Bioinformatics 2021 22(Suppl 5):314
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  5. A thermal face recognition under different conditions is proposed in this article. The novelty of the proposed method is applying temperature information in the recognition of thermal face. The physiological i...

    Authors: Shinfeng D. Lin, Luming Chen and Wensheng Chen
    Citation: BMC Bioinformatics 2021 22(Suppl 5):313
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  6. The prevalence of chronic disease is growing in aging societies, and artificial-intelligence–assisted interpretation of macular degeneration images is a topic that merits research. This study proposes a residu...

    Authors: Wen-Hsien Ho, Tian-Hsiang Huang, Po-Yuan Yang, Jyh-Horng Chou, Hong-Siang Huang, Li-Chung Chi, Fu-I Chou and Jinn-Tsong Tsai
    Citation: BMC Bioinformatics 2021 22(Suppl 5):148
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  7. To classify chest computed tomography (CT) images as positive or negative for coronavirus disease 2019 (COVID-19) quickly and accurately, researchers attempted to develop effective models by using medical images.

    Authors: Yao-Mei Chen, Yenming J. Chen, Wen-Hsien Ho and Jinn-Tsong Tsai
    Citation: BMC Bioinformatics 2021 22(Suppl 5):147
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  8. To diagnose key pathologies of age-related macular degeneration (AMD) and diabetic macular edema (DME) quickly and accurately, researchers attempted to develop effective artificial intelligence methods by usin...

    Authors: Yao-Mei Chen, Wei-Tai Huang, Wen-Hsien Ho and Jinn-Tsong Tsai
    Citation: BMC Bioinformatics 2021 22(Suppl 5):99
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  9. Differentiating and counting various types of white blood cells (WBC) in bone marrow smears allows the detection of infection, anemia, and leukemia or analysis of a process of treatment. However, manually loca...

    Authors: Da Wang, Maxwell Hwang, Wei-Cheng Jiang, Kefeng Ding, Hsiao Chien Chang and Kao-Shing Hwang
    Citation: BMC Bioinformatics 2021 22(Suppl 5):94
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  12. Acute myeloid leukemia (AML) is a heterogeneous cancer of the blood, though specific recurring cytogenetic abnormalities in AML are strongly associated with attaining complete response after induction chemothe...

    Authors: Yiran Zhang and Kellie J. Archer
    Citation: BMC Bioinformatics 2021 22:539
    Content type: Research Published on:

  13. Numerous studies on discovering the roles of long non-coding RNAs (lncRNAs) in the occurrence, development and prognosis progresses of various human diseases have drawn substantial attentions. Since only a tin...

    Authors: Jianwei Li, Jianing Li, Mengfan Kong, Duanyang Wang, Kun Fu and Jiangcheng Shi
    Citation: BMC Bioinformatics 2021 22:538
    Content type: Research Published on:

  15. Esophageal adenocarcinoma (EAC) is an aggressive malignancy with a poor prognosis. The immune-related genes (IRGs) are crucial to immunocytes tumor infiltration. This study aimed to construct a IRG-related pre...

    Authors: Xiangxin Zhang, Liu Yang, Ming Kong, Jian Ma and Yutao Wei
    Citation: BMC Bioinformatics 2021 22:536
    Content type: Research Published on:

  17. Generating high-quality de novo genome assemblies is foundational to the genomics study of model and non-model organisms. In recent years, long-read sequencing has greatly benefited genome assembly and scaffol...

    Authors: Lauren Coombe, Janet X. Li, Theodora Lo, Johnathan Wong, Vladimir Nikolic, René L. Warren and Inanc Birol
    Citation: BMC Bioinformatics 2021 22:534
    Content type: Software Published on:

  18. Optical maps record locations of specific enzyme recognition sites within long genome fragments. This long-distance information enables aligning genome assembly contigs onto optical maps and ordering contigs i...

    Authors: Bin Huang, Guozheng Wei, Bing Wang, Fusong Ju, Yi Zhong, Zhuozheng Shi, Shiwei Sun and Dongbo Bu
    Citation: BMC Bioinformatics 2021 22:533
    Content type: Methodology article Published on:

  20. Time-lapse microscopy live-cell imaging is essential for studying the evolution of bacterial communities at single-cell resolution. It allows capturing detailed information about the morphology, gene expressio...

    Authors: Athanasios D. Balomenos, Victoria Stefanou and Elias S. Manolakos
    Citation: BMC Bioinformatics 2021 22:531
    Content type: Software Published on:

  21. Accurate copy number variant (CNV) detection is especially challenging for both targeted sequencing (TS) and whole‐exome sequencing (WES) data. To maximize the performance, the parameters of the CNV calling al...

    Authors: Rosa Barcelona-Cabeza, Walter Sanseverino and Riccardo Aiese Cigliano
    Citation: BMC Bioinformatics 2021 22:530
    Content type: Software Published on:

  22. Recently, machine learning-based ligand activity prediction methods have been greatly improved. However, if known active compounds of a target protein are unavailable, the machine learning-based method cannot ...

    Authors: Toshitaka Tanebe and Takashi Ishida
    Citation: BMC Bioinformatics 2021 22(Suppl 3):529
    Content type: Research Published on:

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

  23. Boltzmann machines are energy-based models that have been shown to provide an accurate statistical description of domains of evolutionary-related protein and RNA families. They are parametrized in terms of loc...

    Authors: Anna Paola Muntoni, Andrea Pagnani, Martin Weigt and Francesco Zamponi
    Citation: BMC Bioinformatics 2021 22:528
    Content type: Software Published on:

  24. In the pharmaceutical industry, competing for few validated drug targets there is a drive to identify new ways of therapeutic intervention. Here, we attempted to define guidelines to evaluate a target’s ‘fitne...

    Authors: Ariele Viacava Follis
    Citation: BMC Bioinformatics 2021 22:527
    Content type: Research Published on:

  25. ANAT is a Cytoscape plugin for the inference of functional protein–protein interaction networks in yeast and human. It is a flexible graphical tool for scientists to explore and elucidate the protein–protein i...

    Authors: L. F. Signorini, T. Almozlino and R. Sharan
    Citation: BMC Bioinformatics 2021 22:526
    Content type: Research Published on:

  27. 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:

  29. 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

  30. 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

  32. 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

  33. 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

  34. 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:

  35. 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:

  38. 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

  40. 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:

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  48. 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:

  49. 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:

  50. 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

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