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  1. Due to the complexity and cost of preparing histopathological slides, deep learning-based methods have been developed to generate high-quality histological images. However, existing approaches primarily focus ...

    Authors: Qifeng Liu, Tao Zhou, Chi Cheng, Jin Ma and Marzia Hoque Tania
    Citation: BMC Bioinformatics 2025 26:29
    Content type: Research Published on:

  2. Drug–drug interactions (DDIs) especially antagonistic ones present significant risks to patient safety, underscoring the urgent need for reliable prediction methods. Recently, substructure-based DDI prediction...

    Authors: Jinchen Sun and Haoran Zheng
    Citation: BMC Bioinformatics 2025 26:28
    Content type: Research Published on:

  3. Currently, synthetic genomics is a rapidly developing field. Its main tasks, such as the design of synthetic sequences and the assembly of DNA sequences from synthetic oligonucleotides, require specialized sof...

    Authors: Tatiana A. Semashko, Gleb Y. Fisunov, Georgiy Y. Shevelev and Vadim M. Govorun
    Citation: BMC Bioinformatics 2025 26:27
    Content type: Software Published on:

  5. While protein-protein docking is fundamental to our understanding of how proteins interact, scoring protein-protein complex conformations is a critical component of successful docking programs. Without accurat...

    Authors: Azam Shirali, Vitalii Stebliankin, Ukesh Karki, Jimeng Shi, Prem Chapagain and Giri Narasimhan
    Citation: BMC Bioinformatics 2025 26:25
    Content type: Research Published on:

  6. Tissue clearing combined with light-sheet microscopy is gaining popularity among neuroscientists interested in unbiased assessment of their samples in 3D volume. However, the analysis of such data remains a ch...

    Authors: Stefan Pastore, Philipp Hillenbrand, Nils Molnar, Irina Kovlyagina, Monika Chanu Chongtham, Stanislav Sys, Beat Lutz, Margarita Tevosian and Susanne Gerber
    Citation: BMC Bioinformatics 2025 26:24
    Content type: Software Published on:

  10. There is a growing interest in utilizing 3D culture models for stem cell and cancer cell research due to their closer resemblance to in vivo environments. In this study, human mesenchymal stem cells (MSCs) wer...

    Authors: Arash Shahbazpoor Shahbazi, Farzin Irandoost, Reza Mahdavian, Seyedehsamaneh Shojaeilangari, Abdollah Allahvardi and Hossein Naderi-Manesh
    Citation: BMC Bioinformatics 2025 26:20
    Content type: Research Published on:

  11. Drug response prediction is critical in precision medicine to determine the most effective and safe treatments for individual patients. Traditional prediction methods relying on demographic and genetic data of...

    Authors: Dhekra Saeed, Huanlai Xing, Barakat AlBadani, Li Feng, Raeed Al-Sabri, Monir Abdullah and Amir Rehman
    Citation: BMC Bioinformatics 2025 26:19
    Content type: Research Published on:

  13. Pacific Biosciences (PacBio) circular consensus sequencing (CCS), also known as high fidelity (HiFi) technology, has revolutionized modern genomics by producing long (10 + kb) and highly accurate reads. This i...

    Authors: Minindu Weerakoon, Sangjin Lee, Emily Mitchell and Haynes Heaton
    Citation: BMC Bioinformatics 2025 26:17
    Content type: Software Published on:

  14. In recent years, combined drug screening has played a very important role in modern drug discovery. Generally, synergistic drug combinations are crucial in treatment for many diseases. However, the toxic side ...

    Authors: Leixia Tian, Qi Wang, Zhiheng Zhou, Xiya Liu, Ming Zhang and Guiying Yan
    Citation: BMC Bioinformatics 2025 26:16
    Content type: Research Published on:

  15. All chemical forms of energy and oxygen on Earth are generated via photosynthesis where light energy is converted into redox energy by two photosystems (PS I and PS II). There is an increasing number of PS I 3...

    Authors: Lujun Luo, Tarikul I. Milon, Elijah K. Tandoh, Walter J. Galdamez, Andrei Y. Chistoserdov, Jianping Yu, Jan Kern, Yingchun Wang and Wu Xu
    Citation: BMC Bioinformatics 2025 26:15
    Content type: Research Published on:

  16. The increasing availability of sequenced genomes has enabled comparative analyses of various organisms. Numerous tools and online platforms have been developed for this purpose, facilitating the identification...

    Authors: Gabriele Moro, Rossano Atzeni, Ali Al-Subhi and Maria Giovanna Marche
    Citation: BMC Bioinformatics 2025 26:14
    Content type: Software Published on:

  17. MicroRNAs (miRNAs) are pivotal in the initiation and progression of complex human diseases and have been identified as targets for small molecule (SM) drugs. However, the expensive and time-intensive character...

    Authors: Jianwei Li, Xukun Zhang, Bing Li, Ziyu Li and Zhenzhen Chen
    Citation: BMC Bioinformatics 2025 26:13
    Content type: Research Published on:

  18. Genomic surveillance is extensively used for tracking public health outbreaks and healthcare-associated pathogens. Despite advancements in bioinformatics pipelines, there are still significant challenges in te...

    Authors: Timo Saratto, Kerkko Visuri, Jonatan Lehtinen, Irene Ortega-Sanz, Jacob L. Steenwyk and Samuel Sihvonen
    Citation: BMC Bioinformatics 2025 26:12
    Content type: Software Published on:

  19. Drug-target interactions (DTIs) are pivotal in drug discovery and development, and their accurate identification can significantly expedite the process. Numerous DTI prediction methods have emerged, yet many f...

    Authors: Guang Yang, Yinbo Liu, Sijian Wen, Wenxi Chen, Xiaolei Zhu and Yongmei Wang
    Citation: BMC Bioinformatics 2025 26:11
    Content type: Research Published on:

  20. Antimicrobial peptides (AMPs) have been widely recognized as a promising solution to combat antimicrobial resistance of microorganisms due to the increasing abuse of antibiotics in medicine and agriculture aro...

    Authors: Zixin Chen, Chengming Ji, Wenwen Xu, Jianfeng Gao, Ji Huang, Huanliang Xu, Guoliang Qian and Junxian Huang
    Citation: BMC Bioinformatics 2025 26:10
    Content type: Research Published on:

  21. Deep learning (DL) has set new standards in cancer diagnosis, significantly enhancing the accuracy of automated classification of whole slide images (WSIs) derived from biopsied tissue samples. To enable DL mo...

    Authors: Olga Fourkioti, Matt De Vries, Reed Naidoo and Chris Bakal
    Citation: BMC Bioinformatics 2025 26:9
    Content type: Research Published on:

  22. Interpreting biological system changes requires interpreting vast amounts of multi-omics data. While user-friendly tools exist for single-omics analysis, integrating multiple omics still requires bioinformatic...

    Authors: Cristian Iperi, Álvaro Fernández-Ochoa, Guillermo Barturen, Jacques-Olivier Pers, Nathan Foulquier, Eleonore Bettacchioli, Marta Alarcón-Riquelme, Divi Cornec, Anne Bordron and Christophe Jamin
    Citation: BMC Bioinformatics 2025 26:8
    Content type: Software Published on:

  23. Natural language processing (NLP) enables the extraction of information embedded within unstructured texts, such as clinical case reports and trial eligibility criteria. By identifying relevant medical concept...

    Authors: Leonardo Campillos-Llanos, Ana Valverde-Mateos and Adrián Capllonch-Carrión
    Citation: BMC Bioinformatics 2025 26:7
    Content type: Software Published on:

  25. The process of new drug development is complex, whereas drug-disease association (DDA) prediction aims to identify new therapeutic uses for existing medications. However, existing graph contrastive learning ap...

    Authors: Xianfang Tang, Yawen Hou, Yajie Meng, Zhaojing Wang, Changcheng Lu, Juan Lv, Xinrong Hu, Junlin Xu and Jialiang Yang
    Citation: BMC Bioinformatics 2025 26:5
    Content type: Research Published on:

  26. In cell line perturbation experiments, a collection of cells is perturbed with external agents and responses such as protein expression measured. Due to cost constraints, only a small fraction of all possible ...

    Authors: James P. Long, Yumeng Yang, Shohei Shimizu, Thong Pham and Kim-Anh Do
    Citation: BMC Bioinformatics 2025 26:4
    Content type: Research Published on:

  27. Accurate taxonomic classification in genome databases is essential for reliable biological research and effective data sharing. Mislabeling or inaccuracies in genome annotations can lead to incorrect scientifi...

    Authors: Mohamed Elmanzalawi, Takatomo Fujisawa, Hiroshi Mori, Yasukazu Nakamura and Yasuhiro Tanizawa
    Citation: BMC Bioinformatics 2025 26:3
    Content type: Software Published on:

  31. Cancer classification has consistently been a challenging problem, with the main difficulties being high-dimensional data and the collection of patient samples. Concretely, obtaining patient samples is a costl...

    Authors: Qiaosheng Zhang, Yalong Wei, Jie Hou, Hongpeng Li and Zhaoman Zhong
    Citation: BMC Bioinformatics 2024 25:392
    Content type: Research Published on:

  32. As a heterogeneous disease, prostate cancer (PCa) exhibits diverse clinical and biological features, which pose significant challenges for early diagnosis and treatment. Metabolomics offers promising new appro...

    Authors: Liqiang Sun, Xiaojing Fan, Yunwei Zhao, Qi Zhang and Mingyang Jiang
    Citation: BMC Bioinformatics 2024 25:391
    Content type: Research Published on:

  34. Accurate prediction of copy number variations (CNVs) from targeted capture next-generation sequencing (NGS) data relies on effective normalization of read coverage profiles. The normalization process is partic...

    Authors: Zoltán Maróti, Peter Juma Ochieng, József Dombi, Miklós Krész and Tibor Kalmár
    Citation: BMC Bioinformatics 2024 25:389
    Content type: Research Published on:

  35. Time-series scRNA-seq data have opened a door to elucidate cell differentiation, and in this context, the optimal transport theory has been attracting much attention. However, there remain critical issues in i...

    Authors: Toshiaki Yachimura, Hanbo Wang, Yusuke Imoto, Momoko Yoshida, Sohei Tasaki, Yoji Kojima, Yukihiro Yabuta, Mitinori Saitou and Yasuaki Hiraoka
    Citation: BMC Bioinformatics 2024 25:388
    Content type: Research Published on:

  39. The bacterium Vibrio cholerae causes diarrheal illness and can acquire genetic material leading to multiple drug resistance (MDR). Rapid detection of resistance-conferring mobile genetic elements helps avoid the ...

    Authors: Daniel Antonio Negrón, Shipra Trivedi, Nicholas Tolli, David Ashford, Gabrielle Melton, Stephanie Guertin, Katharine Jennings, Bryan D. Necciai, Shanmuga Sozhamannan and Bradley W. Abramson
    Citation: BMC Bioinformatics 2024 25:384
    Content type: Research Published on:

  40. Metabolomics is a high-throughput technology that measures small molecule metabolites in cells, tissues or biofluids. Analysis of metabolomics data is a multi-step process that involves data processing, qualit...

    Authors: Christopher Patsalis, Gayatri Iyer, Marci Brandenburg, Alla Karnovsky and George Michailidis
    Citation: BMC Bioinformatics 2024 25:383
    Content type: Software Published on:

  41. Using information measures to infer biological regulatory networks can capture nonlinear relationships between variables. However, it is computationally challenging, and there is a lack of convenient tools.

    Authors: Chu Pan and Yanlin Chen
    Citation: BMC Bioinformatics 2024 25:382
    Content type: Software Published on:

  44. Recent developments in spatially resolved transcriptomics (SRT) enable the characterization of spatial structures for different tissues. Many decomposition methods have been proposed to depict the cellular dis...

    Authors: Zhongning Jiang, Wei Huang, Raymond H. W. Lam and Wei Zhang
    Citation: BMC Bioinformatics 2024 25:379
    Content type: Research Published on:

  45. Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screeni...

    Authors: Andrea Conte, Nicola Gulmini, Francesco Costa, Matteo Cartura, Felix Bröhl, Francesco Patanè and Francesco Filippini
    Citation: BMC Bioinformatics 2024 25:378
    Content type: Software Published on:

  47. Methods to call, analyze and visualize copy number variations (CNVs) from massive parallel sequencing data have been widely adopted in clinical practice and genetic research. To enable a streamlined analysis o...

    Authors: Jeremias Krause, Carlos Classen, Daniela Dey, Eva Lausberg, Luise Kessler, Thomas Eggermann, Ingo Kurth, Matthias Begemann and Florian Kraft
    Citation: BMC Bioinformatics 2024 25:376
    Content type: Software Published on:

  50. Phenotypic data comparison is essential for disease association studies, patient stratification, and genotype–phenotype correlation analysis. To support these efforts, the Global Alliance for Genomics and Heal...

    Authors: Ivo C. Leist, María Rivas-Torrubia, Marta E. Alarcón-Riquelme, Guillermo Barturen, PRECISESADS Clinical Consortium, Ivo G. Gut and Manuel Rueda
    Citation: BMC Bioinformatics 2024 25:373
    Content type: Software Published on:

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