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  1. Pathogenic infections pose a significant threat to global health, affecting millions of people every year and presenting substantial challenges to healthcare systems worldwide. Efficient and timely testing pla...

    Authors: Ananthan Nambiar, Chao Pan, Vishal Rana, Mahdi Cheraghchi, João Ribeiro, Sergei Maslov and Olgica Milenkovic
    Citation: BMC Bioinformatics 2024 25:195
  2. We have developed AMRViz, a toolkit for analyzing, visualizing, and managing bacterial genomics samples. The toolkit is bundled with the current best practice analysis pipeline allowing researchers to perform ...

    Authors: Duc Quang Le, Son Hoang Nguyen, Tam Thi Nguyen, Canh Hao Nguyen, Tho Huu Ho, Nam S. Vo, Trang Nguyen, Hoang Anh Nguyen and Minh Duc Cao
    Citation: BMC Bioinformatics 2024 25:193
  3. The selection of primer pairs in sequencing-based research can greatly influence the results, highlighting the need for a tool capable of analysing their performance in-silico prior to the sequencing process. We ...

    Authors: Lara Vázquez-González, Alba Regueira-Iglesias, Carlos Balsa-Castro, Nicolás Vila-Blanco, Inmaculada Tomás and María J. Carreira
    Citation: BMC Bioinformatics 2024 25:189
  4. Microbiome dysbiosis has recently been associated with different diseases and disorders. In this context, machine learning (ML) approaches can be useful either to identify new patterns or learn predictive mode...

    Authors: Andrea Simeon, Miloš Radovanović, Tatjana Lončar-Turukalo, Michelangelo Ceci, Sanja Brdar and Gianvito Pio
    Citation: BMC Bioinformatics 2024 25:188
  5. Surveillance for genetic variation of microbial pathogens, both within and among species, plays an important role in informing research, diagnostic, prevention, and treatment activities for disease control. Ho...

    Authors: Aaron Boussina, Lennart Langouche, Augustine C. Obirieze, Mridu Sinha, Hannah Mack, William Leineweber, April Aralar, David T. Pride, Todd P. Coleman and Stephanie I. Fraley
    Citation: BMC Bioinformatics 2024 25:185
  6. RNA sequencing combined with machine learning techniques has provided a modern approach to the molecular classification of cancer. Class predictors, reflecting the disease class, can be constructed for known t...

    Authors: Richard Van, Daniel Alvarez, Travis Mize, Sravani Gannavarapu, Lohitha Chintham Reddy, Fatma Nasoz and Mira V. Han
    Citation: BMC Bioinformatics 2024 25:181
  7. High-throughput sequencing (HTS) has become the gold standard approach for variant analysis in cancer research. However, somatic variants may occur at low fractions due to contamination from normal cells or tu...

    Authors: Aldo Sergi, Luca Beltrame, Sergio Marchini and Marco Masseroli
    Citation: BMC Bioinformatics 2024 25:180
  8. As genomic studies continue to implicate non-coding sequences in disease, testing the roles of these variants requires insights into the cell type(s) in which they are likely to be mediating their effects. Pri...

    Authors: Samuel Rosean, Eric A. Sosa, Dónal O’Shea, Srilakshmi M. Raj, Cathal Seoighe and John M. Greally
    Citation: BMC Bioinformatics 2024 25:179
  9. In low-middle income countries, healthcare providers primarily use paper health records for capturing data. Paper health records are utilized predominately due to the prohibitive cost of acquisition and mainte...

    Authors: Ryan D. Folks, Bhiken I. Naik, Donald E. Brown and Marcel E. Durieux
    Citation: BMC Bioinformatics 2024 25:178
  10. Protein residue–residue distance maps are used for remote homology detection, protein information estimation, and protein structure research. However, existing prediction approaches are time-consuming, and hun...

    Authors: Jiajian Huang, Jinpeng Li, Qinchang Chen, Xia Wang, Guangyong Chen and Jin Tang
    Citation: BMC Bioinformatics 2024 25:176
  11. Modelling discrete-time cause-specific hazards in the presence of competing events and non-proportional hazards is a challenging task in many domains. Survival analysis in longitudinal cohorts often requires s...

    Authors: Matthieu Oliver, Nicolas Allou, Marjolaine Devineau, Jèrôme Allyn and Cyril Ferdynus
    Citation: BMC Bioinformatics 2024 25:175
  12. Principal component analysis (PCA) is an important and widely used unsupervised learning method that determines population structure based on genetic variation. Genome sequencing of thousands of individuals us...

    Authors: Weiming He, Lian Xu, JingXian Wang, Zhen Yue, Yi Jing, Shuaishuai Tai, Jian Yang and Xiaodong Fang
    Citation: BMC Bioinformatics 2024 25:173
  13. Deep neural networks (DNNs) have the potential to revolutionize our understanding and treatment of genetic diseases. An inherent limitation of deep neural networks, however, is their high demand for data durin...

    Authors: Hyunjung Lee, Utku Ozbulak, Homin Park, Stephen Depuydt, Wesley De Neve and Joris Vankerschaver
    Citation: BMC Bioinformatics 2024 25:170
  14. Numerous transcriptomic-based models have been developed to predict or understand the fundamental mechanisms driving biological phenotypes. However, few models have successfully transitioned into clinical prac...

    Authors: S. R. Oshternian, S. Loipfinger, A. Bhattacharya and R. S. N. Fehrmann
    Citation: BMC Bioinformatics 2024 25:167
  15. The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level ...

    Authors: Leonardo Giannantoni, Roberta Bardini, Alessandro Savino and Stefano Di Carlo
    Citation: BMC Bioinformatics 2024 25:166
  16. The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known protein...

    Authors: William L. Harrigan, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson, Zachary D. Schreiber and Mahdi Belcaid
    Citation: BMC Bioinformatics 2024 25:165
  17. Multimodal integration combines information from different sources or modalities to gain a more comprehensive understanding of a phenomenon. The challenges in multi-omics data analysis lie in the complexity, h...

    Authors: Yufang Liu, Yongkai Chen, Haoran Lu, Wenxuan Zhong, Guo-Cheng Yuan and Ping Ma
    Citation: BMC Bioinformatics 2024 25:164
  18. The results of high-throughput biology (‘omic’) experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as o...

    Authors: Terrence R. Ernst, John D. Blischak, Paul Nordlund, Joe Dalen, Justin Moore, Akshay Bhamidipati, Pankaj Dwivedi, Joe LoGrasso, Marco Rocha Curado and Brett Warren Engelmann
    Citation: BMC Bioinformatics 2024 25:162
  19. The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different...

    Authors: Luan Pinto Rabelo, Davidson Sodré, Rodrigo Petry Corrêa de Sousa, Luciana Watanabe, Grazielle Gomes, Iracilda Sampaio and Marcelo Vallinoto
    Citation: BMC Bioinformatics 2024 25:160
  20. Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites (TFBSs) and their pivotal roles in gene...

    Authors: Xiaotian Wu, Wenju Hou, Ziqi Zhao, Lan Huang, Nan Sheng, Qixing Yang, Shuangquan Zhang and Yan Wang
    Citation: BMC Bioinformatics 2024 25:158
  21. Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning, and design, as well as for understanding the functions of target. Alt...

    Authors: Xin Zeng, Guang-Peng Su, Shu-Juan Li, Shuang-Qing Lv, Meng-Liang Wen and Yi Li
    Citation: BMC Bioinformatics 2024 25:156
  22. Classification of binary data arises naturally in many clinical applications, such as patient risk stratification through ICD codes. One of the key practical challenges in data classification using machine lea...

    Authors: Moein E. Samadi, Hedieh Mirzaieazar, Alexander Mitsos and Andreas Schuppert
    Citation: BMC Bioinformatics 2024 25:155
  23. High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, ‘N’s. PCR duplicates introduced i...

    Authors: Jianqiao Hu, Sai Luo, Ming Tian and Adam Yongxin Ye
    Citation: BMC Bioinformatics 2024 25:154
  24. With the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic classification by using alignment-based approaches to reduce the impact of...

    Authors: Rafael Peres da Silva, Chayaporn Suphavilai and Niranjan Nagarajan
    Citation: BMC Bioinformatics 2024 25(Suppl 1):153

    This article is part of a Supplement: Volume 25 Supplement 1

  25. Text summarization is a challenging problem in Natural Language Processing, which involves condensing the content of textual documents without losing their overall meaning and information content, In the domai...

    Authors: Mahira Kirmani, Gagandeep Kour, Mudasir Mohd, Nasrullah Sheikh, Dawood Ashraf Khan, Zahid Maqbool, Mohsin Altaf Wani and Abid Hussain Wani
    Citation: BMC Bioinformatics 2024 25:152
  26. Genomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and gene expression varying along chromosomes. Evolutionary, biological, and biomedical analyses aim t...

    Authors: Claus Vogl, Mariia Karapetiants, Burçin Yıldırım, Hrönn Kjartansdóttir, Carolin Kosiol, Juraj Bergman, Michal Majka and Lynette Caitlin Mikula
    Citation: BMC Bioinformatics 2024 25:151
  27. The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its go...

    Authors: Caleb K. Kibet, Jean-Baka Domelevo Entfellner, Daudi Jjingo, Etienne Pierre de Villiers, Santie de Villiers, Karen Wambui, Sam Kinyanjui and Daniel Masiga
    Citation: BMC Bioinformatics 2024 25:150
  28. Protein toxins are defense mechanisms and adaptations found in various organisms and microorganisms, and their use in scientific research as therapeutic candidates is gaining relevance due to their effectivene...

    Authors: Jorge F. Beltrán, Lisandra Herrera-Belén, Fernanda Parraguez-Contreras, Jorge G. Farías, Jorge Machuca-Sepúlveda and Stefania Short
    Citation: BMC Bioinformatics 2024 25:148

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