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  1. Predicting drug-target interactions (DTIs) plays a pivotal role in accelerating drug repositioning by prioritizing candidate drugs and reducing experimental costs. Despite advancements in deep learning, severa...

    Authors: Shujuan Cao, Binying Cai, Zhejian Qiu, Tiantian Chang, Qiqige Wuyun and Fang-Xiang Wu
    Citation: BMC Bioinformatics 2025 26:275
    Content type: Research Published on:

  2. Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of inte...

    Authors: Shuo Shuo Liu, Shikun Wang, Yuxuan Chen, Anil K. Rustgi, Ming Yuan and Jianhua Hu
    Citation: BMC Bioinformatics 2025 26:274
    Content type: Research Published on:

  3. Identifying potential associations among food, gut microbiota and disease is fundamental for elucidating interaction mechanisms and advancing personalized healthy dietary strategies. While computational method...

    Authors: Jianqiang Hu, Mingyi Hu, Yangxiang Wu, Songyao Mu, Dahao Huang, Baolong Wang, Yuchen Gao, Shixin Gu and Jinlin Zhu
    Citation: BMC Bioinformatics 2025 26:273
    Content type: Research Published on:

  4. Understanding how the molecules in our bodyrespond to the co-occurrence of two diseases in an individual (comorbidity) could lead tomechanistic insights into novel treatments for comorbid conditions. Studies h...

    Authors: Nilesh Subramanian, Philge Philip, Anuradha Rajamanickam, Nathella Pavan Kumar, Subash Babu and Manikandan Narayanan
    Citation: BMC Bioinformatics 2025 26:272
    Content type: Research Published on:

  5. Multimodal learning for classification tasks has recently gained significant attention in bioinformatics. Current approaches primarily concentrate on devising efficient deep learning architectures to capture f...

    Authors: Duoyi Zhang, Md Abul Bashar, Richi Nayak and Leila Cuttle
    Citation: BMC Bioinformatics 2025 26:271
    Content type: Research Published on:

  6. Small nucleolar RNAs (snoRNAs), a class of non-coding RNAs broadly distributed in eukaryotes, are emerging as pivotal regulators in the field of epigenomics. In addition to guiding 2’-O-methylation and pseudou...

    Authors: Xinqing Jiang, Xiaojun Chen, Lifeng Xu, Feng Zhang, Jiawei Chen and Wenqian Zhang
    Citation: BMC Bioinformatics 2025 26:270
    Content type: Research Published on:

  7. In bottom-up proteomics using data-independent acquisition mass spectrometry (DIA-MS), quantitative measurements are obtained following multiple steps of protein fragmentation and ionization, which introduces ...

    Authors: Namgil Lee, Hojin Yoo, Juhyoung Kim and Heejung Yang
    Citation: BMC Bioinformatics 2025 26:269
    Content type: Research Published on:

  9. Sentence-transformers is a library that provides easy methods for generating embeddings for sentences, paragraphs, and images. Sentiment analysis, retrieval, and clustering are among the applications made poss...

    Authors: Mpho Mokoatle, Vukosi Marivate, Darlington Mapiye, Riana Bornman and Vanessa M. Hayes
    Citation: BMC Bioinformatics 2025 26:267
    Content type: Research Published on:

  11. Using cultivars based on a single, partly heterozygous, genotype is one of the bases of agriculture, frequently used in seed-propagated species such as vegetables and field crops (F1 hybrid varieties), and in ...

    Authors: Konstantinos G. Alexiou, Iban Eduardo and Pere Arús
    Citation: BMC Bioinformatics 2025 26:265
    Content type: Software Published on:

  12. In several contexts involving large collections of sets of biological sequences, a relevant problem is that of selecting significant groups of k-mers that characterize one set with regards to the others in the...

    Authors: Ylenia Galluzzo, Raffaele Giancarlo, Simona E. Rombo and Filippo Utro
    Citation: BMC Bioinformatics 2025 26:264
    Content type: Software Published on:

  13. Vasculogenic mimicry (VM) is the phenomenon whereby non-vascular tumor cells develop vascular-like structures. VM is linked to more aggressive tumor phenotypes including higher rates of metastasis and invasion...

    Authors: Stephen P. G. Moore, Anqi Zou, Xinyu Zhang, Olivia Chika Jonathan, Deborah Lang and Chao Zhang
    Citation: BMC Bioinformatics 2025 26:263
    Content type: Software Published on:

  14. An important challenge in flow cytometry (FCM) data analysis is making comparisons of corresponding cell populations across multiple FCM samples. An interesting solution is creating a statistical mixture model...

    Authors: Philip Rutten, Tim R. Mocking, Jacqueline Cloos, Wessel N. van Wieringen and Costa Bachas
    Citation: BMC Bioinformatics 2025 26:262
    Content type: Research Published on:

  15. Virtual Screening (VS) has become an essential tool in drug discovery, enabling the rapid and cost-effective identification of potential bioactive molecules. Among recent advancements, Graph Neural Networks (G...

    Authors: Salvatore Contino, Paolo Sortino, Maria Rita Gulotta, Ugo Perricone and Roberto Pirrone
    Citation: BMC Bioinformatics 2025 26:261
    Content type: Research Published on:

  17. Multimodal visualizations are essential for identifying and interpreting complex relationships in diverse, high-dimensional biological datasets. However, existing visualization tools often lack native capabili...

    Authors: Foziya Ahmed Mohammed, El Hadj Malick Fall, Kula Kekeba Tune, Rasha Hammamieh, Marti Jett and Seid Muhie
    Citation: BMC Bioinformatics 2025 26:259
    Content type: Research Published on:

  18. The sequences and structures of the 5′ mRNA regions in prokaryotes significantly impact transcript stability and translation efficiency at the post-transcriptional level. However, the structure–function relati...

    Authors: Zihe Wang, Zilun Mei, Xiaogang Wang, Jinpeng Zhang, Zhenghong Xu, Fei Liu and Xiaojuan Zhang
    Citation: BMC Bioinformatics 2025 26:258
    Content type: Research Published on:

  19. Allele-specific expression (ASE) analyses from RNA-Seq data provide quantitative insights into genomic imprinting and the genetic variants that affect transcription. Robust ASE analysis requires the integratio...

    Authors: Weisheng Wu, Kerby Shedden, Claudius Vincenz, Chris Gates and Beverly Strassmann
    Citation: BMC Bioinformatics 2025 26:257
    Content type: Research Published on:

  22. Vasculature is an essential part of all tissues and organs and is involved in a wide range of different diseases. However, available software for blood vessel image analysis is often limited: Some only process...

    Authors: Magdalena Schüttler, Leyla Doğan, Jana Kirchner, Süleyman Ergün, Philipp Wörsdörfer and Sabine C. Fischer
    Citation: BMC Bioinformatics 2025 26:254
    Content type: Software Published on:

  23. In this paper, we introduce an image analysis approach for spatiotemporal segmentation, quantification, and visualization of movement or contraction patterns in 2D+t and 3D+t microscopy recordings of biologica...

    Authors: Marc Pereyra, Mariia Golden, Zoë Lange, Artemiy Golden, Frederic Strobl, Ernst H. K. Stelzer and Franziska Matthäus
    Citation: BMC Bioinformatics 2025 26:253
    Content type: Research Published on:

  24. Pattern matching is a fundamental challenge in bioinformatics, especially in the fields of genomics, transcriptomics and proteomics. Efficient indexing structures, such as suffix arrays, are critical for searc...

    Authors: Simon Van de Vyver, Tibo Vande Moortele, Peter Dawyndt, Bart Mesuere and Pieter Verschaffelt
    Citation: BMC Bioinformatics 2025 26:252
    Content type: Research Published on:

  28. The barriers to effective data analysis are sometimes insurmountable. Concerns ranging from privacy, security, and complexity can prevent researchers from using existing data analysis tools.

    Authors: Giada Lalli, James Collier, Yves Moreau and Daniele Raimondi
    Citation: BMC Bioinformatics 2025 26:248
    Content type: Software Published on:

  30. Although Sanger sequencing remains widely used in human genetic disease diagnosis and livestock breeding, software packages for analyzing such data have seen little innovation over time. Determining the genoty...

    Authors: Jinpeng Wang, Shuo Sun, Yaran Zhang, Ning Huang, Chunhong Yang, Yaping Gao, Xiuge Wang, Zhihua Ju, Qiang Jiang, Yao Xiao, Xiaochao Wei, Wenhao Liu and Jinming Huang
    Citation: BMC Bioinformatics 2025 26:246
    Content type: Software Published on:

  31. De novo genome assembly poses challenges when dealing with highly degraded DNA samples or ultrashort sequencing reads. Probabilistic approaches have been offered to enhance the algorithms, though existing methods...

    Authors: Patrick Pflughaupt and Aleksandr B. Sahakyan
    Citation: BMC Bioinformatics 2025 26:245
    Content type: Research Published on:

  32. 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

  35. 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:

  36. 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

  38. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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