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  1. Drug–drug interactions (DDI) are prevalent in combination therapy, necessitating the importance of identifying and predicting potential DDI. While various artificial intelligence methods can predict and identi...

    Authors: Jing Zhu, Chao Che, Hao Jiang, Jian Xu, Jiajun Yin and Zhaoqian Zhong
    Citation: BMC Bioinformatics 2024 25:39
  2. Previously, many methods have been used to predict the incidence trends of infectious diseases. There are numerous methods for predicting the incidence trends of infectious diseases, and they have exhibited va...

    Authors: Tianhua Yao, Xicheng Chen, Haojia Wang, Chengcheng Gao, Jia Chen, Dali Yi, Zeliang Wei, Ning Yao, Yang Li, Dong Yi and Yazhou Wu
    Citation: BMC Bioinformatics 2024 25:38
  3. DNA methylation is a major epigenetic modification involved in many physiological processes. Normal methylation patterns are disrupted in many diseases and methylation-based biomarkers have shown promise in se...

    Authors: Naghme Nazer, Mohammad Hossein Sepehri, Hoda Mohammadzade and Mahya Mehrmohamadi
    Citation: BMC Bioinformatics 2024 25:37
  4. Driver genes play a vital role in the development of cancer. Identifying driver genes is critical for diagnosing and understanding cancer. However, challenges remain in identifying personalized driver genes du...

    Authors: Yiran Huang, Fuhao Chen, Hongtao Sun and Cheng Zhong
    Citation: BMC Bioinformatics 2024 25:34
  5. Breast cancer remains a major public health challenge worldwide. The identification of accurate biomarkers is critical for the early detection and effective treatment of breast cancer. This study utilizes an i...

    Authors: Morteza Rakhshaninejad, Mohammad Fathian, Reza Shirkoohi, Farnaz Barzinpour and Amir H. Gandomi
    Citation: BMC Bioinformatics 2024 25:33
  6. Epi-transcriptome regulation through post-transcriptional RNA modifications is essential for all RNA types. Precise recognition of RNA modifications is critical for understanding their functions and regulatory...

    Authors: Honglei Wang, Tao Huang, Dong Wang, Wenliang Zeng, Yanjing Sun and Lin Zhang
    Citation: BMC Bioinformatics 2024 25:32
  7. Within the frame of their genetic capacity, organisms are able to modify their molecular state to cope with changing environmental conditions or induced genetic disposition. As high throughput methods are beco...

    Authors: Benedikt Venn, Thomas Leifeld, Ping Zhang and Timo Mühlhaus
    Citation: BMC Bioinformatics 2024 25:30
  8. The impairment of sperm maturation is one of the major pathogenic factors in male subfertility, a serious medical and social problem affecting millions of global couples. Regrettably, the existing research on ...

    Authors: Yifan Li, Qianying Li, Lvying Wu, Haiyan Wang, Hui Shi, Chenhui Yang, Yiqun Gu, Jianyuan Li and Zhiliang Ji
    Citation: BMC Bioinformatics 2024 25:29
  9. COVID-19 is a disease that caused a contagious respiratory ailment that killed and infected hundreds of millions. It is necessary to develop a computer-based tool that is fast, precise, and inexpensive to dete...

    Authors: Rukundo Prince, Zhendong Niu, Zahid Younas Khan, Masabo Emmanuel and Niyishaka Patrick
    Citation: BMC Bioinformatics 2024 25:28
  10. In recent years, human microbiome studies have received increasing attention as this field is considered a potential source for clinical applications. With the advancements in omics technologies and AI, resear...

    Authors: David Rojas-Velazquez, Sarah Kidwai, Aletta D. Kraneveld, Alberto Tonda, Daniel Oberski, Johan Garssen and Alejandro Lopez-Rincon
    Citation: BMC Bioinformatics 2024 25:26
  11. With the growing number of single-cell datasets collected under more complex experimental conditions, there is an opportunity to leverage single-cell variability to reveal deeper insights into how cells respon...

    Authors: Jamshaid A. Shahir, Natalie Stanley and Jeremy E. Purvis
    Citation: BMC Bioinformatics 2024 25:25
  12. Meta-analysis is a statistical method that combines the results of multiple studies to increase statistical power. When multiple studies participating in a meta-analysis utilize the same public dataset as cont...

    Authors: Emma E. Kim, Chloe Soohyun Jang, Hakin Kim and Buhm Han
    Citation: BMC Bioinformatics 2024 25:24
  13. With the exponential growth of high-throughput technologies, multiple pathway analysis methods have been proposed to estimate pathway activities from gene expression profiles. These pathway activity inference ...

    Authors: Tay Xin Hui, Shahreen Kasim, Izzatdin Abdul Aziz, Mohd Farhan Md Fudzee, Nazleeni Samiha Haron, Tole Sutikno, Rohayanti Hassan, Hairulnizam Mahdin and Seah Choon Sen
    Citation: BMC Bioinformatics 2024 25:23
  14. MiRNAs are involved in the occurrence and development of many diseases. Extensive literature studies have demonstrated that miRNA-disease associations are stratified and encompass ~ 20% causal associations. Co...

    Authors: Yu Han, Qiong Zhou, Leibo Liu, Jianwei Li and Yuan Zhou
    Citation: BMC Bioinformatics 2024 25:22
  15. 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
  16. Long reads have gained popularity in the analysis of metagenomics data. Therefore, we comprehensively assessed metagenomics classification tools on the species taxonomic level. We analysed kmer-based tools, ma...

    Authors: Josip Marić, Krešimir Križanović, Sylvain Riondet, Niranjan Nagarajan and Mile Šikić
    Citation: BMC Bioinformatics 2024 25:15
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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

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