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  1. Existing computational methods for studying miRNA regulation are mostly based on bulk miRNA and mRNA expression data. However, bulk data only allows the analysis of miRNA regulation regarding a group of cells,...

    Authors: Junpeng Zhang, Lin Liu, Taosheng Xu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao and Thuc Duy Le

    Citation: BMC Bioinformatics 2021 22:578

    Content type: Research

    Published on:

  3. Deep learning is an active bioinformatics artificial intelligence field that is useful in solving many biological problems, including predicting altered epigenetics such as DNA methylation regions. Deep learni...

    Authors: Pegah Mavaie, Lawrence Holder, Daniel Beck and Michael K. Skinner

    Citation: BMC Bioinformatics 2021 22:575

    Content type: Research

    Published on:

  4. Several computational methods have been developed that integrate transcriptomics data with genome-scale metabolic reconstructions to increase accuracy of inferences of intracellular metabolic flux distribution...

    Authors: Neeraj Sinha, Evert M. van Schothorst, Guido J. E. J. Hooiveld, Jaap Keijer, Vitor A. P. Martins dos Santos and Maria Suarez-Diez

    Citation: BMC Bioinformatics 2021 22:574

    Content type: Research

    Published on:

  5. With the rapid development of various advanced biotechnologies, researchers in related fields have realized that microRNAs (miRNAs) play critical roles in many serious human diseases. However, experimental ide...

    Authors: Feng Zhou, Meng-Meng Yin, Cui-Na Jiao, Zhen Cui, Jing-Xiu Zhao and Jin-Xing Liu

    Citation: BMC Bioinformatics 2021 22:573

    Content type: Methodology article

    Published on:

  6. Viral infections are causing significant morbidity and mortality worldwide. Understanding the interaction patterns between a particular virus and human proteins plays a crucial role in unveiling the underlying...

    Authors: Thi Ngan Dong, Graham Brogden, Gisa Gerold and Megha Khosla

    Citation: BMC Bioinformatics 2021 22:572

    Content type: Methodology article

    Published on:

  7. In-depth analysis of regulation networks of genes aberrantly expressed in cancer is essential for better understanding tumors and identifying key genes that could be therapeutically targeted.

    Authors: Chiara Regondi, Maddalena Fratelli, Giovanna Damia, Federica Guffanti, Monica Ganzinelli, Matteo Matteucci and Marco Masseroli

    Citation: BMC Bioinformatics 2021 22:571

    Content type: Methodology article

    Published on:

  9. Efficient and effective genome scaffolding tools are still in high demand for generating reference-quality assemblies. While long read data itself is unlikely to create a chromosome-scale assembly for most euk...

    Authors: Dengfeng Guan, Shane A. McCarthy, Zemin Ning, Guohua Wang, Yadong Wang and Richard Durbin

    Citation: BMC Bioinformatics 2021 22:569

    Content type: Software

    Published on:

    The Correction to this article has been published in BMC Bioinformatics 2021 22:612

  10. Long noncoding RNAs (lncRNAs) have dense linkages with a plethora of important cellular activities. lncRNAs exert functions by linking with corresponding RNA-binding proteins. Since experimental techniques to ...

    Authors: Liqian Zhou, Qi Duan, Xiongfei Tian, He Xu, Jianxin Tang and Lihong Peng

    Citation: BMC Bioinformatics 2021 22:568

    Content type: Research

    Published on:

  12. BRAKER is a suite of automatic pipelines, BRAKER1 and BRAKER2, for the accurate annotation of protein-coding genes in eukaryotic genomes. Each pipeline trains statistical models of protein-coding genes based o...

    Authors: Lars Gabriel, Katharina J. Hoff, Tomáš Brůna, Mark Borodovsky and Mario Stanke

    Citation: BMC Bioinformatics 2021 22:566

    Content type: Software

    Published on:

  14. For differential abundance analysis, zero-inflated generalized linear models, typically zero-inflated NB models, have been increasingly used to model microbiome and other sequencing count data. A common assump...

    Authors: Wei Bai, Mei Dong, Longhai Li, Cindy Feng and Wei Xu

    Citation: BMC Bioinformatics 2021 22:564

    Content type: Research

    Published on:

  15. Liver cancer (Hepatocellular carcinoma; HCC) prevalence is increasing and with poor clinical outcome expected it means greater understanding of HCC aetiology is urgently required. This study explored a deep le...

    Authors: Alice R. Owens, Caitríona E. McInerney, Kevin M. Prise, Darragh G. McArt and Anna Jurek-Loughrey

    Citation: BMC Bioinformatics 2021 22:563

    Content type: Methodology article

    Published on:

  16. The gain or loss of large chromosomal regions or even whole chromosomes is termed as genomic scarring and can be observed as copy number variations resulting from the failure of DNA damage repair.

    Authors: Dongju Chen, Minghui Shao, Pei Meng, Chunli Wang, Qi Li, Yuhang Cai, Chengcheng Song, Xi Wang and Taiping Shi

    Citation: BMC Bioinformatics 2021 22:562

    Content type: Research

    Published on:

  17. Ab initio prediction of splice sites is an essential step in eukaryotic genome annotation. Recent predictors have exploited Deep Learning algorithms and reliable gene structures from model organisms. However, ...

    Authors: Nicolas Scalzitti, Arnaud Kress, Romain Orhand, Thomas Weber, Luc Moulinier, Anne Jeannin-Girardon, Pierre Collet, Olivier Poch and Julie D. Thompson

    Citation: BMC Bioinformatics 2021 22:561

    Content type: Software

    Published on:

  20. The ability to rapidly adapt to adverse environmental conditions represents the key of success of many pathogens and, in particular, of Mycobacterium tuberculosis. Upon exposition to heat shock, antibiotics or ot...

    Authors: Irene Zorzan, Simone Del Favero, Alberto Giaretta, Riccardo Manganelli, Barbara Di Camillo and Luca Schenato

    Citation: BMC Bioinformatics 2021 22:558

    Content type: Research

    Published on:

  21. The research landscape of single-cell and single-nuclei RNA-sequencing is evolving rapidly. In particular, the area for the detection of rare cells was highly facilitated by this technology. However, an automa...

    Authors: Saptarshi Bej, Anne-Marie Galow, Robert David, Markus Wolfien and Olaf Wolkenhauer

    Citation: BMC Bioinformatics 2021 22:557

    Content type: Research

    Published on:

  22. Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, sc...

    Authors: W. J. Pereira, F. M. Almeida, D. Conde, K. M. Balmant, P. M. Triozzi, H. W. Schmidt, C. Dervinis, G. J. Pappas Jr and M. Kirst

    Citation: BMC Bioinformatics 2021 22:556

    Content type: Software

    Published on:

  23. Wet-lab experiments for identification of interactions between drugs and target proteins are time-consuming, costly and labor-intensive. The use of computational prediction of drug–target interactions (DTIs), ...

    Authors: Ali Ghanbari Sorkhi, Zahra Abbasi, Majid Iranpour Mobarakeh and Jamshid Pirgazi

    Citation: BMC Bioinformatics 2021 22:555

    Content type: Methodology article

    Published on:

  24. Protein-RNA interactions play key roles in many processes regulating gene expression. To understand the underlying binding preference, ultraviolet cross-linking and immunoprecipitation (CLIP)-based methods hav...

    Authors: Shitao Zhao and Michiaki Hamada

    Citation: BMC Bioinformatics 2021 22:554

    Content type: Research

    Published on:

  25. Wearable devices enable monitoring and measurement of physiological parameters over a 24-h period, and some of which exhibit circadian rhythm characteristics. However, the currently available R package cosinor co...

    Authors: Ruixue Hou, Lewis E. Tomalin and Mayte Suárez-Fariñas

    Citation: BMC Bioinformatics 2021 22:553

    Content type: Software

    Published on:

  26. With the rapid development of long-read sequencing technologies, it is possible to reveal the full spectrum of genetic structural variation (SV). However, the expensive cost, finite read length and high sequen...

    Authors: Tao Jiang, Shiqi Liu, Shuqi Cao, Yadong Liu, Zhe Cui, Yadong Wang and Hongzhe Guo

    Citation: BMC Bioinformatics 2021 22:552

    Content type: Research article

    Published on:

  28. The aim of the present paper is to construct an emulator of a complex biological system simulator using a machine learning approach. More specifically, the simulator is a patient-specific model that integrates...

    Authors: Paola Stolfi and Filippo Castiglione

    Citation: BMC Bioinformatics 2021 22(Suppl 14):483

    Content type: Research

    Published on:

    This article is part of a Supplement: Volume 22 Supplement 14

  29. Ancestry estimation of skulls is under a wide range of applications in forensic science, anthropology, and facial reconstruction. This study aims to avoid defects in traditional skull ancestry estimation metho...

    Authors: Lin Pengyue, Xia Siyuan, Jiang Yi, Yang Wen, Liu Xiaoning, Geng Guohua and Wang Shixiong

    Citation: BMC Bioinformatics 2021 22:550

    Content type: Research

    Published on:

  30. Antimicrobial peptides are promising tools to fight against ever-growing antibiotic resistance. However, despite many advantages, their toxicity to mammalian cells is a critical obstacle in clinical applicatio...

    Authors: Hossein Khabbaz, Mohammad Hossein Karimi-Jafari, Ali Akbar Saboury and Bagher BabaAli

    Citation: BMC Bioinformatics 2021 22:549

    Content type: Research

    Published on:

  31. Discerning genes crucial to antimicrobial resistance (AMR) mechanisms is becoming more and more important to accurately and swiftly identify AMR pathogenic strains. Pangenome-wide association studies (e.g. Sco...

    Authors: Hsuan-Lin Her, Po-Ting Lin and Yu-Wei Wu

    Citation: BMC Bioinformatics 2021 22:548

    Content type: Research

    Published on:

  33. Host population structure is a key determinant of pathogen and infectious disease transmission patterns. Pathogen phylogenetic trees are useful tools to reveal the population structure underlying an epidemic. ...

    Authors: Hassan W. Kayondo, Alfred Ssekagiri, Grace Nabakooza, Nicholas Bbosa, Deogratius Ssemwanga, Pontiano Kaleebu, Samuel Mwalili, John M. Mango, Andrew J. Leigh Brown, Roberto A. Saenz, Ronald Galiwango and John M. Kitayimbwa

    Citation: BMC Bioinformatics 2021 22:546

    Content type: Research article

    Published on:

  34. Amyloids are insoluble fibrillar aggregates that are highly associated with complex human diseases, such as Alzheimer’s disease, Parkinson’s disease, and type II diabetes. Recently, many studies reported that ...

    Authors: Zhixia Teng, Zitong Zhang, Zhen Tian, Yanjuan Li and Guohua Wang

    Citation: BMC Bioinformatics 2021 22:545

    Content type: Research

    Published on:

  35. 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

  36. 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:

  37. 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:

  38. 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

  39. 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

  40. 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

  41. 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

  42. Dengue epidemics is affected by vector-human interactive dynamics. Infectious disease prevention and control emphasize the timing intervention at the right diffusion phase. In such a way, control measures can ...

    Authors: Chien-Hung Lee, Ko Chang, Yao-Mei Chen, Jinn-Tsong Tsai, Yenming J. Chen and Wen-Hsien Ho

    Citation: BMC Bioinformatics 2021 22(Suppl 5):118

    Content type: Research

    Published on:

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

  43. 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

  44. 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

  45. Atrial fibrillation is a paroxysmal heart disease without any obvious symptoms for most people during the onset. The electrocardiogram (ECG) at the time other than the onset of this disease is not significantl...

    Authors: Cai Wu, Maxwell Hwang, Tian-Hsiang Huang, Yen-Ming J. Chen, Yiu-Jen Chang, Tsung-Han Ho, Jian Huang, Kao-Shing Hwang and Wen-Hsien Ho

    Citation: BMC Bioinformatics 2021 22(Suppl 5):93

    Content type: Research

    Published on:

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

  46. Heart sound measurement is crucial for analyzing and diagnosing patients with heart diseases. This study employed phonocardiogram signals as the input signal for heart disease analysis due to the accessibility...

    Authors: Wen-Hsien Ho, Tian-Hsiang Huang, Po-Yuan Yang, Jyh-Horng Chou, Jin-Yi Qu, Po-Chih Chang, Fu-I. Chou and Jinn-Tsong Tsai

    Citation: BMC Bioinformatics 2021 22(Suppl 5):92

    Content type: Research

    Published on:

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

  47. Doctors can detect symptoms of diabetic retinopathy (DR) early by using retinal ophthalmoscopy, and they can improve diagnostic efficiency with the assistance of deep learning to select treatments and support ...

    Authors: Ping-Nan Chen, Chia-Chiang Lee, Chang-Min Liang, Shu-I Pao, Ke-Hao Huang and Ke-Feng Lin

    Citation: BMC Bioinformatics 2021 22(Suppl 5):84

    Content type: Research

    Published on:

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

  50. 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:

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