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  1. Authors: Garth L. Kong, Thai T. Nguyen, Wesley K. Rosales, Anjali D. Panikar, John H. W. Cheney, Theresa A. Lusardi, William M. Yashar, Brittany M. Curtiss, Sarah A. Carratt, Theodore P. Braun and Julia E. Maxson
    Citation: BMC Bioinformatics 2025 26:244
    Content type: Correction Published on:

    The original article was published in BMC Bioinformatics 2024 25:142

  4. Cophylogeny reconciliation is a powerful method for analyzing host-symbiont coevolution. The cophylogeny problem consists of mapping the phylogenetic tree of the symbionts into the one of the hosts, including ...

    Authors: Maurizio Patrignani, Giordano Dionisi, Blerina Sinaimeri and Tiziana Calamoneri
    Citation: BMC Bioinformatics 2025 26:241
    Content type: Software Published on:

  5. The study of control mechanisms of biological systems allows for interesting applications in bioengineering and medicine, for instance in cell reprogramming or drug target identification. A control strategy of...

    Authors: Laura Cifuentes-Fontanals, Elisa Tonello and Heike Siebert
    Citation: BMC Bioinformatics 2025 24(Suppl 1):494
    Content type: Research Published on:

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

  7. Cancer is a complex disease influenced by numerous concurrent genetic factors that result in diverse tumor microenvironments (TMEs) across different cancer types. Large-scale genomic projects, such as The Cancer ...

    Authors: Alessia Petescia, Gerardo Benevento, Anna Falanga, Alessandro Macaro, Delfina Malandrino, Alberto Montefusco, Rosalinda Sorrentino and Rocco Zaccagnino
    Citation: BMC Bioinformatics 2025 26:239
    Content type: Research Published on:

  9. Prior results for tRNA and 5S rRNA demonstrated that secondary structure prediction accuracy can be significantly improved by modifying the parameters in the multibranch loop entropic penalty function. However...

    Authors: Svetlana Poznanović, Owen Cardwell and Christine Heitsch
    Citation: BMC Bioinformatics 2025 26:237
    Content type: Research Published on:

  10. Small RNAs, such as microRNAs (miRNAs), are candidates for mediating communication between the host and its microbiota, regulating bacterial gene expression and influencing microbiome functions and dynamics. H...

    Authors: Jennifer Jessica Bruscadin, Tainã Figueiredo Cardoso, Liliane Costa Conteville, Juliana Virginio da Silva, Adriana Mércia Guaratini Ibelli, Gabriel Alexander Colmenarez Pena, Thanny Porto, Priscila Silva Neubern de Oliveira, Bruno Gabriel Nascimento Andrade, Adhemar Zerlotini and Luciana Correia de Almeida Regitano
    Citation: BMC Bioinformatics 2025 26:236
    Content type: Software Published on:

  11. The high error rate associated with Oxford Nanopore sequencing technology adversely affects demultiplexing. To improve demultiplexing and reduce unclassified reads from nanopore sequencing data, we developed Myst...

    Authors: Abdolrahman Khezri, Sverre Branders, Anurag Basavaraj Bellankimath, Jawad Ali, Crystal Chapagain, Fatemeh Asadi, Manfred G. Grabherr and Rafi Ahmad
    Citation: BMC Bioinformatics 2025 26:235
    Content type: Software Published on:

  12. Peptides have emerged as promising therapeutic agents for drug development against cancer, immune disorders, hypertension, and microbial infections. Peptide drugs have the advantage of high selectivity, low pr...

    Authors: Sih-Han Chen, Jen-Chieh Yu, Yi-Hsiang Lin, Shao-Chun Kuo, Kuan Ni and Ching-Tai Chen
    Citation: BMC Bioinformatics 2025 26:234
    Content type: Research Published on:

  13. The progression of cancer is driven by the accumulation of mutations in driver genes. Many researches promote to identify cancer driver genes. However, most of them ignore the high-order features in the network.

    Authors: Pi-Jing Wei, Jingxin Zhou, Rui-Fen Cao, Yun Ding, Zhenyu Yue and Chun-Hou Zheng
    Citation: BMC Bioinformatics 2025 26:233
    Content type: Research Published on:

  14. Longitudinal studies often require flexible methodologies for predicting response trajectories based on time-dependent and time-independent covariates. To address the complexities of longitudinal data, this st...

    Authors: Mohammad Sadegh Loeloe, Seyyed Mohammad Tabatabaei, Reyhane Sefidkar, Amir Houshang Mehrparvar and Sara Jambarsang
    Citation: BMC Bioinformatics 2025 26:232
    Content type: Research Published on:

  15. The human microbiome plays a crucial role in regulating the efficacy and toxicity of drugs as well as in developing the drugs. Therefore, predicting the drug-related microbes is beneficial for analyzing the fu...

    Authors: Ping Xuan, Rui Wang, Jing Gu, Hui Cui and Tiangang Zhang
    Citation: BMC Bioinformatics 2025 26:231
    Content type: Research Published on:

  16. The advancement of technology and continuous glucose monitoring (CGM) systems has introduced several computational and technical challenges for clinicians and researchers. The growing volume of CGM data necess...

    Authors: Pablo Peiro-Corbacho, Francisco J. Lara-Abelenda, David Chushig-Muzo, Ana M. Wägner, Conceição Granja and Cristina Soguero-Ruiz
    Citation: BMC Bioinformatics 2025 26:230
    Content type: Software Published on:

  17. Copy number variation (CNV) analyses—often inferred from DNA-methylation data—depict alterations of DNA quantities across chromosomes and have improved tumour diagnostics and classification. For the analyses o...

    Authors: Antonia Gocke, Yannis Schumann, Jelena Navolić, Shweta Godbole, Melanie Schoof, Matthias Dottermusch and Julia E. Neumann
    Citation: BMC Bioinformatics 2025 26:229
    Content type: Software Published on:

  18. Bivariate monotonic classifiers (BMCs) are based on pairs of input features. Like many other models used for machine learning, they can capture nonlinear patterns in high-dimensional data. At the same time, th...

    Authors: Océane Fourquet, Martin S. Krejca, Carola Doerr and Benno Schwikowski
    Citation: BMC Bioinformatics 2025 26:228
    Content type: Research Published on:

  19. The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies– a challenging task if close reference sequences are not available...

    Authors: Fabian Kolesch, Marco Sohn, Andreas Rempel, Pia Hippel and Roland Wittler
    Citation: BMC Bioinformatics 2025 26:227
    Content type: Software Published on:

  21. Knowledge discovery in scientific literature is hindered by the increasing volume of publications and the scarcity of extensive annotated data. To tackle the challenge of information overload, it is essential ...

    Authors: Christos Theodoropoulos, Andrei Catalin Coman, James Henderson and Marie-Francine Moens
    Citation: BMC Bioinformatics 2025 26:225
    Content type: Research Published on:

  22. Antimicrobial resistance (AMR) is one of the most concerning modern threats as it places a greater burden on health systems than HIV and malaria combined. Current surveillance strategies for tracking antimicro...

    Authors: Tiago Cabral Borelli, Alexandre Rossi Paschoal and Ricardo Roberto da Silva
    Citation: BMC Bioinformatics 2025 26:224
    Content type: Research Published on:

  27. Gene-Set Analysis (GSA) is commonly used to analyze high-throughput experiments. However, GSA cannot readily disentangle clusters or pathways due to redundancies in upstream knowledge bases, which hinders comp...

    Authors: Asier Ortega-Legarreta, Alberto Maillo, Daniel Mouzo, Ana Rosa López-Pérez, Lara Kular, Majid Pahlevan Kakhki, Maja Jagodic, Jesper Tegner, Vincenzo Lagani, Ewoud Ewing and David Gomez-Cabrero
    Citation: BMC Bioinformatics 2025 26:219
    Content type: Software Published on:

  29. In the genome analysis workflow, Genome Analysis Toolkit (GATK) HaplotypeCaller is a widely used variant calling tool designed to accurately identify single nucleotide polymorphisms (SNPs) and insertions/delet...

    Authors: Xiangxing Lai, Minguang Xiao, Lingling Weng and Zhiguang Chen
    Citation: BMC Bioinformatics 2025 26:217
    Content type: Research Published on:

  30. Accurate identification of translation initiation sites is essential for the proper translation of mRNA into functional proteins. In eukaryotes, the choice of the translation initiation site is influenced by m...

    Authors: Line Sandvad Nielsen, Anders Gorm Pedersen, Ole Winther and Henrik Nielsen
    Citation: BMC Bioinformatics 2025 26:216
    Content type: Software Published on:

  31. Human Leukocyte Antigens (HLA) play central roles in histocompatibility and immune system functions, including antigen presentation. Accurate typing of Class I and II HLA genes is crucial for transplant tissue...

    Authors: Rachel Bowen-James, Weilin Wu, Marie Wong-Erasmus, Julian M. W. Quinn, Chelsea Mayoh and Mark J. Cowley
    Citation: BMC Bioinformatics 2025 26:215
    Content type: Software Published on:

  34. Estimating the time since HIV infection (TSI) at population level is essential for tracking changes in the global HIV epidemic. Most methods for determining TSI give a binary classification of infections as re...

    Authors: Tanya Golubchik, Lucie Abeler-Dörner, Matthew Hall, Chris Wymant, David Bonsall, George Macintyre-Cockett, Laura Thomson, Jared M. Baeten, Connie L. Celum, Ronald M. Galiwango, Barry Kosloff, Mohammed Limbada, Andrew Mujugira, Nelly R. Mugo, Astrid Gall, François Blanquart…
    Citation: BMC Bioinformatics 2025 26:212
    Content type: Research Published on:

  35. The rapid expansion of next-generation sequencing (NGS) technologies has generated vast amounts of genomic data, creating a growing demand for secure, scalable, and accessible tools to support variant interpre...

    Authors: Jing Zhai, Nelly Pitteloud and Federico A. Santoni
    Citation: BMC Bioinformatics 2025 26:211
    Content type: Software Published on:

  36. Understanding and comparing three-dimensional (3D) structures of proteins can advance bioinformatics, molecular biology, and drug discovery. While 3D models offer detailed insights, comparing multiple structur...

    Authors: Tobias Olenyi, Constantin Carl, Tobias Senoner, Ivan Koludarov and Burkhard Rost
    Citation: BMC Bioinformatics 2025 26:210
    Content type: Software Published on:

  38. As a typical type of neurodegenerative disorders, Parkinson’s disease(PD) is characterized by significant clinical and progression heterogeneity. Based on gene expression data, reliable detection of PACE subty...

    Authors: Wei Zhang, Zeqi Xu, Ruochen Yu, Mingfeng Jiang and Qi Dai
    Citation: BMC Bioinformatics 2025 26:208
    Content type: Research Published on:

  39. When a single gene exhibits an insignificant association with complex disease, applying gene–gene interactions as biomarkers may achieve striking findings. However, it is still a barrier to measuring the stren...

    Authors: Chen Sun, Haiyan Chen, Jing Xu, Siyu Wei, Junxian Tao, Jiacheng Wang, Yuping Zou, Wei She, Ruilin Li, Linna Yuan, Fanwu Kong, Guoping Tang, Zhenwei Shang, Wenhua Lyu, Mingming Zhang, Hongchao Lyu…
    Citation: BMC Bioinformatics 2025 26:207
    Content type: Research Published on:

  41. Cellular development and differentiation in Eukaryotes depends upon sequential gene regulatory decisions that allow a single genome to encode many hundreds of distinct cellular phenotypes. Decisions are stored...

    Authors: Dave T. Gerrard
    Citation: BMC Bioinformatics 2025 26:205
    Content type: Software Published on:

  42. DNA data storage is an emerging technology that caught the attention of many researchers and engineers. This technology uses DNA molecules as a storage medium and thus presents an extremely dense and durable s...

    Authors: Gadi Chaykin, Omer Sabary, Nili Furman, Dvir Ben Shabat and Eitan Yaakobi
    Citation: BMC Bioinformatics 2025 26:204
    Content type: Software Published on:

  43. Drug repurposing offers a promising strategy for drug discovery. Drug repurposing involves identifying new therapeutic indications for existing, marketed drugs, thereby reducing the risks, costs, and time typi...

    Authors: Xianglong Liang, Xin Jiang and Yifang Ma
    Citation: BMC Bioinformatics 2025 26:203
    Content type: Research Published on:

  45. Rapid extraction and visualization of cell-specific gene expression is important for automatic cell type annotation, e.g. in single cell analysis. There is an emerging field in which tools such as curated data...

    Authors: Lucas Bickmann, Sarah Sandmann, Carolin Walter and Julian Varghese
    Citation: BMC Bioinformatics 2025 26:201
    Content type: Software Published on:

  47. The rapid advancement of single-cell RNA sequencing (scRNAseq) technology provides high-resolution views of transcriptomic activity within individual cells. Most routine analyses of scRNAseq data focus on indi...

    Authors: Shuyi Yang, Anderson Bussing, Giampiero Marra, Michelle L. Brinkmeier, Sally A. Camper, Shannon W. Davis and Yen-Yi Ho
    Citation: BMC Bioinformatics 2025 26:199
    Content type: Research Published on:

  49. The advent of next-generation and long-read sequencing technologies has provided an ever-increasing wealth of phylogenetic data that require specially designed algorithms to decipher the underlying evolutionar...

    Authors: Sriram Vijendran, Tavis Anderson, Alexey Markin and Oliver Eulenstein
    Citation: BMC Bioinformatics 2025 26:197
    Content type: Software Published on:

  50. A key challenge in differential abundance analysis (DAA) of microbial sequencing data is that the counts for each sample are compositional, resulting in potentially biased comparisons of the absolute abundance...

    Authors: Dylan Clark-Boucher, Brent A. Coull, Harrison T. Reeder, Fenglei Wang, Qi Sun, Jacqueline R. Starr and Kyu Ha Lee
    Citation: BMC Bioinformatics 2025 26:196
    Content type: Research Published on:

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