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  1. Metabolic syndrome (MetS) is a cluster of metabolic abnormalities (including obesity, insulin resistance, hypertension, and dyslipidemia), which can be used to identify at-risk populations for diabetes and car...

    Authors: Sahar Mohseni-Takalloo, Hadis Mohseni, Hassan Mozaffari-Khosravi, Masoud Mirzaei and Mahdieh Hosseinzadeh
    Citation: BMC Bioinformatics 2024 25:18
  2. The integration of biology, computer science, and statistics has given rise to the interdisciplinary field of bioinformatics, which aims to decode biological intricacies. It produces extensive and diverse feat...

    Authors: Ali Hakem Alsaeedi, Haider Hameed R. Al-Mahmood, Zainab Fahad Alnaseri, Mohammad R. Aziz, Dhiah Al-Shammary, Ayman Ibaida and Khandakar Ahmed
    Citation: BMC Bioinformatics 2024 25:12
  3. Machine learning (ML) has a rich history in structural bioinformatics, and modern approaches, such as deep learning, are revolutionizing our knowledge of the subtle relationships between biomolecular sequence,...

    Authors: Eli J. Draizen, John Readey, Cameron Mura and Philip E. Bourne
    Citation: BMC Bioinformatics 2024 25:11
  4. Highly multiplexed imaging enables single-cell-resolved detection of numerous biological molecules in their spatial tissue context. Interactive visualization of multiplexed imaging data is crucial at any step ...

    Authors: Lasse Meyer, Nils Eling and Bernd Bodenmiller
    Citation: BMC Bioinformatics 2024 25:9
  5. According to the expression of miRNA in pathological processes, miRNAs can be divided into oncogenes or tumor suppressors. Prediction of the regulation relations between miRNAs and small molecules (SMs) become...

    Authors: Yong-Jian Guan, Chang-Qing Yu, Li-Ping Li, Zhu-Hong You, Meng-meng Wei, Xin-Fei Wang, Chen Yang and Lu-Xiang Guo
    Citation: BMC Bioinformatics 2024 25:6
  6. A growing body of researches indicate that the disrupted expression of long non-coding RNA (lncRNA) is linked to a range of human disorders. Therefore, the effective prediction of lncRNA-disease association (L...

    Authors: Dengju Yao, Bailin Li, Xiaojuan Zhan, Xiaorong Zhan and Liyang Yu
    Citation: BMC Bioinformatics 2024 25:5
  7. Chemically induced skin sensitization, or allergic contact dermatitis, is a common occupational and public health issue. Regulatory authorities require an assessment of potential to cause skin sensitization fo...

    Authors: Kimberly T. To, Judy Strickland, Emily Reinke, Alexandre Borrel, Jim Truax, Heather Maldonado, Dave Allen and Nicole Kleinstreuer
    Citation: BMC Bioinformatics 2024 25:4
  8. Uniform random sampling of mass-balanced flux solutions offers an unbiased appraisal of the capabilities of metabolic networks. Unfortunately, it is impossible to avoid thermodynamically infeasible loops in fl...

    Authors: Pedro A. Saa, Sebastian Zapararte, Christopher C. Drovandi and Lars K. Nielsen
    Citation: BMC Bioinformatics 2024 25:3
  9. Graph embedding techniques are using deep learning algorithms in data analysis to solve problems of such as node classification, link prediction, community detection, and visualization. Although typically used...

    Authors: Edwin Alvarez-Mamani, Reinhard Dechant, César A. Beltran-Castañón and Alfredo J. Ibáñez
    Citation: BMC Bioinformatics 2024 25:1
  10. Flux Balance Analysis (FBA) is a key metabolic modeling method used to simulate cellular metabolism under steady-state conditions. Its simplicity and versatility have led to various strategies incorporating tr...

    Authors: Thummarat Paklao, Apichat Suratanee and Kitiporn Plaimas
    Citation: BMC Bioinformatics 2023 24:492
  11. The advent and continual improvement of high-throughput sequencing technologies has made immunoglobulin repertoire sequencing accessible and informative regardless of study species. However, to fully map dynam...

    Authors: Daniel Dorey-Robinson, Giuseppe Maccari and John A. Hammond
    Citation: BMC Bioinformatics 2023 24:491
  12. Clustering analysis is widely used to interpret biomedical data and uncover new knowledge and patterns. However, conventional clustering methods are not effective when dealing with sparse biomedical data. To o...

    Authors: Xiaomeng Zhang, Hongtao Zhang, Zhihao Wang, Xiaofei Ma, Jiancheng Luo and Yingying Zhu
    Citation: BMC Bioinformatics 2023 24:490
  13. Plate design is a necessary and time-consuming operation for GC/LC-MS-based sample preparation. The implementation of the inter-batch balancing algorithm and the intra-batch randomization algorithm can have a ...

    Authors: Miaoshan Lu, Hengxuan Jiang, Ruimin Wang, Shaowei An, Jiawei Wang and Changbin Yu
    Citation: BMC Bioinformatics 2023 24:489
  14. The pharmaceutical field faces a significant challenge in validating drug target interactions (DTIs) due to the time and cost involved, leading to only a fraction being experimentally verified. To expedite dru...

    Authors: Warith Eddine Djeddi, Khalil Hermi, Sadok Ben Yahia and Gayo Diallo
    Citation: BMC Bioinformatics 2023 24:488
  15. Automatic and accurate extraction of diverse biomedical relations from literature is a crucial component of bio-medical text mining. Currently, stacking various classification networks on pre-trained language ...

    Authors: Xiangwen Zheng, Xuanze Wang, Xiaowei Luo, Fan Tong and Dongsheng Zhao
    Citation: BMC Bioinformatics 2023 24:486
  16. Numerous tools exist for biological sequence comparisons and search. One case of particular interest for immunologists is finding matches for linear peptide T cell epitopes, typically between 8 and 15 residues...

    Authors: Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Koşaloğlu-Yalçın, Alessandro Sette, Morten Nielsen, Jason A. Greenbaum and Bjoern Peters
    Citation: BMC Bioinformatics 2023 24:485
  17. This paper presents novel datasets providing numerical representations of ICD-10-CM codes by generating description embeddings using a large language model followed by a dimension reduction via autoencoder. Th...

    Authors: Michael J. Kane, Casey King, Denise Esserman, Nancy K. Latham, Erich J. Greene and David A. Ganz
    Citation: BMC Bioinformatics 2023 24:482
  18. The rapid emergence of single-cell RNA-seq (scRNA-seq) data presents remarkable opportunities for broad investigations through integration analyses. However, most integration models are black boxes that lack i...

    Authors: Zhen-Hao Guo, Yan Wu, Siguo Wang, Qinhu Zhang, Jin-Ming Shi, Yan-Bin Wang and Zhan-Heng Chen
    Citation: BMC Bioinformatics 2023 24:481
  19. Cancer prediction in the early stage is a topic of major interest in medicine since it allows accurate and efficient actions for successful medical treatments of cancer. Mostly cancer datasets contain various ...

    Authors: Rajul Mahto, Saboor Uddin Ahmed, Rizwan ur Rahman, Rabia Musheer Aziz, Priyanka Roy, Saurav Mallik, Aimin Li and Mohd Asif Shah
    Citation: BMC Bioinformatics 2023 24:479
  20. With more clinical trials are offering optional participation in the collection of bio-specimens for biobanking comes the increasing complexity of requirements of informed consent forms. The aim of this study ...

    Authors: Meng Zhang, Madhuri Sankaranarayanapillai, Jingcheng Du, Yang Xiang, Frank J. Manion, Marcelline R. Harris, Cooper Stansbury, Huy Anh Pham and Cui Tao
    Citation: BMC Bioinformatics 2023 24(Suppl 3):477

    This article is part of a Supplement: Volume 24 Supplement 3

  21. The increasing body of research has consistently demonstrated the intricate correlation between the human microbiome and human well-being. Microbes can impact the efficacy and toxicity of drugs through various...

    Authors: Shanghui Lu, Yong Liang, Le Li, Rui Miao, Shuilin Liao, Yongfu Zou, Chengjun Yang and Dong Ouyang
    Citation: BMC Bioinformatics 2023 24:476
  22. The standardization of biological data using unique identifiers is vital for seamless data integration, comprehensive interpretation, and reproducibility of research findings, contributing to advancements in b...

    Authors: Min Hyung Cho, Kwang-Hwi Cho and Kyoung Tai No
    Citation: BMC Bioinformatics 2023 24:475
  23. With new advances in next generation sequencing (NGS) technology at reduced costs, research on bacterial genomes in the environment has become affordable. Compared to traditional methods, NGS provides high-thr...

    Authors: Amrita Chattopadhyay, Chien-Yueh Lee, Ya-Chin Lee, Chiang-Lin Liu, Hsin-Kuang Chen, Yung-Hua Li, Liang-Chuan Lai, Mong-Hsun Tsai, Yen-Hsuan Ni, Han-Mo Chiu, Tzu-Pin Lu and Eric Y. Chuang
    Citation: BMC Bioinformatics 2023 24:474
  24. Sequenced Protein–Protein Interaction (PPI) prediction represents a pivotal area of study in biology, playing a crucial role in elucidating the mechanistic underpinnings of diseases and facilitating the design...

    Authors: Jiahui Wu, Bo Liu, Jidong Zhang, Zhihan Wang and Jianqiang Li
    Citation: BMC Bioinformatics 2023 24:473
  25. Detection of exotic plant pathogens and preventing their entry and establishment are critical for the protection of agricultural systems while securing the global trading of agricultural commodities. High-thro...

    Authors: Xiaojun Hu, Oscar P. Hurtado-Gonzales, Bishwo N. Adhikari, Ronald D. French-Monar, Martha Malapi, Joseph A. Foster and Clint D. McFarland
    Citation: BMC Bioinformatics 2023 24:470
  26. The success of AlphaFold2 in reliable protein three-dimensional (3D) structure prediction, assists the move of structural biology toward studies of protein dynamics and mutational impact on structure and function...

    Authors: Konstantin Weissenow and Burkhard Rost
    Citation: BMC Bioinformatics 2023 24:469
  27. Multiplex PCR amplifies numerous targets in a single tube reaction and is essential in molecular biology and clinical diagnostics. One of its most important applications is in the targeted sequencing of pathog...

    Authors: Jason D. Limberis and John Z. Metcalfe
    Citation: BMC Bioinformatics 2023 24:468
  28. With the COVID-19 outbreak, an increasing number of individuals are concerned about their health, particularly their immune status. However, as of now, there is no available algorithm that effectively assesses...

    Authors: Min Zhang, Chengkui Zhao, Qi Cheng, Jiayu Xu, Nan Xu, Lei Yu and Weixing Feng
    Citation: BMC Bioinformatics 2023 24:467
  29. Hierarchical classification offers a more specific categorization of data and breaks down large classification problems into subproblems, providing improved prediction accuracy and predictive power for undefin...

    Authors: Youpeng Yang, Qiuhong Zeng, Gaotong Liu, Shiyao Zheng, Tianyang Luo, Yibin Guo, Jia Tang and Yi Huang
    Citation: BMC Bioinformatics 2023 24:465
  30. Single-cell sequencing has shed light on previously inaccessible biological questions from different fields of research, including organism development, immune function, and disease progression. The number of ...

    Authors: Kun Wang, Xiao Zhang, Hansen Cheng, Wenhao Ma, Guangchao Bao, Liting Dong, Yixiong Gou, Jian Yang and Haoyang Cai
    Citation: BMC Bioinformatics 2023 24:463
  31. Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutati...

    Authors: Yiyun Rao, Nabeel Ahmed, Justin Pritchard and Edward P. O’Brien
    Citation: BMC Bioinformatics 2023 24:462
  32. Basecalling long DNA sequences is a crucial step in nanopore-based DNA sequencing protocols. In recent years, the CTC-RNN model has become the leading basecalling model, supplanting preceding hidden Markov mod...

    Authors: Xuechun Xu, Nayanika Bhalla, Patrik Ståhl and Joakim Jaldén
    Citation: BMC Bioinformatics 2023 24:461
  33. Synthetic biologists use and combine diverse biological parts to build systems such as genetic circuits that perform desirable functions in, for example, biomedical or industrial applications. Computer-aided d...

    Authors: Baptiste Turpin, Eline Y. Bijman, Hans-Michael Kaltenbach and Jörg Stelling
    Citation: BMC Bioinformatics 2023 24(Suppl 1):460

    This article is part of a Supplement: Volume 24 Supplement 1

  34. Variability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat and ComBat-Seq are among the most widely used tools for correcting those technical...

    Authors: Abdelkader Behdenna, Maximilien Colange, Julien Haziza, Aryo Gema, Guillaume Appé, Chloé-Agathe Azencott and Akpéli Nordor
    Citation: BMC Bioinformatics 2023 24:459
  35. Biclustering is increasingly used in biomedical data analysis, recommendation tasks, and text mining domains, with hundreds of biclustering algorithms proposed. When assessing the performance of these algorith...

    Authors: Eduardo N. Castanho, João P. Lobo, Rui Henriques and Sara C. Madeira
    Citation: BMC Bioinformatics 2023 24:457

    The Correction to this article has been published in BMC Bioinformatics 2024 25:16

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