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  1. The computation of a similarity measure for genomic data is a standard tool in computational genetics. The principal components of such matrices are routinely used to correct for biases due to confounding by p...

    Authors: Georg Hahn, Sharon M. Lutz, Julian Hecker, Dmitry Prokopenko, Michael H. Cho, Edwin K. Silverman, Scott T. Weiss and Christoph Lange
    Citation: BMC Bioinformatics 2024 25:43
  2. The clustering of immune repertoire data is challenging due to the computational cost associated with a very large number of pairwise sequence comparisons. To overcome this limitation, we developed Anchor Clus...

    Authors: Haiyang Chang, Daniel A. Ashlock, Steffen P. Graether and Stefan M. Keller
    Citation: BMC Bioinformatics 2024 25:42
  3. With the development of single-cell technology, many cell traits can be measured. Furthermore, the multi-omics profiling technology could jointly measure two or more traits in a single cell simultaneously. In ...

    Authors: Lifei Wang, Rui Nie, Xuexia Miao, Yankai Cai, Anqi Wang, Hanwen Zhang, Jiang Zhang and Jun Cai
    Citation: BMC Bioinformatics 2024 25:41
  4. 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
  5. 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
  6. 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
  7. Given a genome-scale metabolic model (GEM) of a microorganism and criteria for optimization, flux balance analysis (FBA) predicts the optimal growth rate and its corresponding flux distribution for a specific ...

    Authors: Clémence Joseph, Haris Zafeiropoulos, Kristel Bernaerts and Karoline Faust
    Citation: BMC Bioinformatics 2024 25:36
  8. Natural proteins occupy a small portion of the protein sequence space, whereas artificial proteins can explore a wider range of possibilities within the sequence space. However, specific requirements may not b...

    Authors: Xiaoping Min, Chongzhou Yang, Jun Xie, Yang Huang, Nan Liu, Xiaocheng Jin, Tianshu Wang, Zhibo Kong, Xiaoli Lu, Shengxiang Ge, Jun Zhang and Ningshao Xia
    Citation: BMC Bioinformatics 2024 25:35
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. 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

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