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  2. The precise prediction of transcription factor binding sites (TFBSs) is pivotal for unraveling the gene regulatory networks underlying biological processes. While numerous tools have emerged for in silico TFBS...

    Authors: Dinithi V. Wanniarachchi, Sameera Viswakula and Anushka M. Wickramasuriya
    Citation: BMC Bioinformatics 2024 25:371
    Content type: Research Published on:

  3. Insertions and deletions (indels) play a significant role in genome evolution across species. Realistic modelling of indel evolution is challenging and is still an open research question. Several attempts have...

    Authors: Gholamhossein Jowkar, Jūlija Pečerska, Manuel Gil and Maria Anisimova
    Citation: BMC Bioinformatics 2024 25:370
    Content type: Research Published on:

  4. Jointly analyzing multiple phenotype/traits may increase power in genetic association studies by aggregating weak genetic effects. The chance that at least one phenotype is missing increases exponentially as t...

    Authors: Jianjun Zhang, Jane Zizhen Zhao, Samantha Gonzales, Xuexia Wang and Qiuying Sha
    Citation: BMC Bioinformatics 2024 25:369
    Content type: Research Published on:

  5. Antimicrobial peptides (AMPs) are a promising class of antimicrobial drugs due to their broad-spectrum activity against microorganisms. However, their clinical application is limited by their potential to caus...

    Authors: Ibrahim Abdelbaky, Mohamed Elhakeem, Hilal Tayara, Elsayed Badr and Mustafa Abdul Salam
    Citation: BMC Bioinformatics 2024 25:368
    Content type: Research Published on:

  6. Genomic sequence similarity comparison is a crucial research area in bioinformatics. Multiple Sequence Alignment (MSA) is the basic technique used to identify regions of similarity between sequences, although ...

    Authors: Nasma Boumajdi, Houda Bendani, Lahcen Belyamani and Azeddine Ibrahimi
    Citation: BMC Bioinformatics 2024 25:367
    Content type: Software Published on:

  7. The preservation of soil health is a critical challenge in the 21st century due to its significant impact on agriculture, human health, and biodiversity. We provide one of the first comprehensive investigation...

    Authors: Rosa Aghdam, Xudong Tang, Shan Shan, Richard Lankau and Claudia Solís-Lemus
    Citation: BMC Bioinformatics 2024 25:366
    Content type: Research Published on:

  8. Plasmids play a major role in the transfer of antimicrobial resistance (AMR) genes among bacteria via horizontal gene transfer. The identification of plasmids in short-read assemblies is a challenging problem ...

    Authors: Aniket Mane, Haley Sanderson, Aaron P. White, Rahat Zaheer, Robert Beiko and Cédric Chauve
    Citation: BMC Bioinformatics 2024 25:365
    Content type: Research Published on:

  9. The integration of multi-omics data through deep learning has greatly improved cancer subtype classification, particularly in feature learning and multi-omics data integration. However, key challenges remain i...

    Authors: Lei Cheng, Qian Huang, Zhengqun Zhu, Yanan Li, Shuguang Ge, Longzhen Zhang and Ping Gong
    Citation: BMC Bioinformatics 2024 25:364
    Content type: Research Published on:

  10. Over the last decade the drop in short-read sequencing costs has allowed experimental techniques utilizing sequencing to address specific biological questions to proliferate, oftentimes outpacing standardized ...

    Authors: Quinlan Furumo and Michelle M. Meyer
    Citation: BMC Bioinformatics 2024 25:363
    Content type: Software Published on:

  11. Advances in transcriptional profiling methods have enabled the discovery of molecular subtypes within and across traditional tissue-based cancer classifications. Such molecular subgroups hold potential for imp...

    Authors: Aideen McCabe, Gerard P. Quinn, Suneil Jain, Micheál Ó Dálaigh, Kellie Dean, Ross G. Murphy and Simon S. McDade
    Citation: BMC Bioinformatics 2024 25:362
    Content type: Software Published on:

  12. Identification of drug–target interactions is an indispensable part of drug discovery. While conventional shallow machine learning and recent deep learning methods based on chemogenomic properties of drugs and...

    Authors: Yuanyuan Zhang, Yingdong Wang, Chaoyong Wu, Lingmin Zhan, Aoyi Wang, Caiping Cheng, Jinzhong Zhao, Wuxia Zhang, Jianxin Chen and Peng Li
    Citation: BMC Bioinformatics 2024 25:361
    Content type: Research Published on:

  13. RNA 5-methyluridine (m5U) modifications play a crucial role in biological processes, making their accurate identification a key focus in computational biology. This paper introduces Deep-m5U, a robust predicto...

    Authors: Sumaiya Noor, Afshan Naseem, Hamid Hussain Awan, Wasiq Aslam, Salman Khan, Salman A. AlQahtani and Nijad Ahmad
    Citation: BMC Bioinformatics 2024 25:360
    Content type: Research Published on:

  14. The rewiring of molecular interactions in various conditions leads to distinct phenotypic outcomes. Differential network analysis (DINA) is dedicated to exploring these rewirings within gene and protein netwo...

    Authors: Pietro Hiram Guzzi, Arkaprava Roy, Marianna Milano and Pierangelo Veltri
    Citation: BMC Bioinformatics 2024 25:359
    Content type: Research Published on:

  15. Graphical representations are useful to model complex data in general and biological interactions in particular. Our main motivation is the comparison of metabolic networks in the wider context of developing n...

    Authors: Ariane Marandon, Tabea Rebafka, Nataliya Sokolovska and Hédi Soula
    Citation: BMC Bioinformatics 2024 25:358
    Content type: Research Published on:

  16. Rare copy number variants (CNVs) significantly influence the human genome and may contribute to disease susceptibility. High-throughput SNP genotyping platforms provide data that can be used for CNV detection,...

    Authors: Haydee Artaza, Ksenia Lavrichenko, Anette S. B. Wolff, Ellen C. Røyrvik, Marc Vaudel and Stefan Johansson
    Citation: BMC Bioinformatics 2024 25:357
    Content type: Software Published on:

  19. In unforeseen situations, such as nuclear power plant’s or civilian radiation accidents, there is a need for effective and computationally inexpensive methods to determine the expression level of a selected ge...

    Authors: Tomasz Strzoda, Lourdes Cruz-Garcia, Mustafa Najim, Christophe Badie and Joanna Polanska
    Citation: BMC Bioinformatics 2024 25:354
    Content type: Research Published on:

  20. The explosive growth of next-generation sequencing data has resulted in ultra-large-scale datasets and significant computational challenges. As the cost of next-generation sequencing (NGS) has decreased, the a...

    Authors: Gunhwan Ko, Pan-Gyu Kim, Byung-Ha Yoon, JaeHee Kim, Wangho Song, IkSu Byeon, JongCheol Yoon, Byungwook Lee and Young-Kuk Kim
    Citation: BMC Bioinformatics 2024 25:353
    Content type: Software Published on:

  22. Viral proteins that evade the host’s innate immune response play a crucial role in pathogenesis, significantly impacting viral infections and potential therapeutic strategies. Identifying these proteins throug...

    Authors: Jorge F. Beltrán, Lisandra Herrera Belén, Alejandro J. Yáñez and Luis Jimenez
    Citation: BMC Bioinformatics 2024 25:351
    Content type: Research Published on:

  23.  Stochastic models are commonly employed in the system and synthetic biology to study the effects of stochastic fluctuations emanating from reactions involving species with low copy-numbers. Many important mod...

    Authors: Martin Helfrich, Roman Andriushchenko, Milan Češka, Jan Křetínský, Štefan Martiček and David Šafránek
    Citation: BMC Bioinformatics 2024 25:350
    Content type: Research Published on:

  24. Proteins interact with each other in complex ways to perform significant biological functions. These interactions, known as protein–protein interactions (PPIs), can be depicted as a graph where proteins are no...

    Authors: Hajer Akid, Kirsley Chennen, Gabriel Frey, Julie Thompson, Mounir Ben Ayed and Nicolas Lachiche
    Citation: BMC Bioinformatics 2024 25:349
    Content type: Research Published on:

  26. The increasing antimicrobial resistance caused by the improper use of antibiotics poses a significant challenge to humanity. Rapid and accurate identification of microbial species in clinical settings is cruci...

    Authors: Bowen Yan, Lin Zeng, Yanyi Lu, Min Li, Weiping Lu, Bangfu Zhou and Qinghua He
    Citation: BMC Bioinformatics 2024 25:347
    Content type: Research Published on:

  28. The prediction of protein–protein interaction sites plays a crucial role in biochemical processes. Investigating the interaction between viruses and receptor proteins through biological techniques aids in unde...

    Authors: Shuang Wang, Kaiyu Dong, Dingming Liang, Yunjing Zhang, Xue Li and Tao Song
    Citation: BMC Bioinformatics 2024 25:345
    Content type: Research Published on:

  29. The construction of a pangenome graph is a fundamental task in pangenomics. A natural theoretical question is how to formalize the computational problem of building an optimal pangenome graph, making explicit ...

    Authors: Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova and Luca Denti
    Citation: BMC Bioinformatics 2024 25:344
    Content type: Research Published on:

  30. G-protein coupled receptors (GPCRs), the largest family of membrane proteins in human body, involve a great variety of biological processes and thus have become highly valuable drug targets. By binding with li...

    Authors: Fan Liu, Han Zhou, Xiaonong Li, Liangliang Zhou, Chungong Yu, Haicang Zhang, Dongbo Bu and Xinmiao Liang
    Citation: BMC Bioinformatics 2024 25:343
    Content type: Database Published on:

  32. The study focuses on enhancing the effectiveness of precision agriculture through the application of deep learning technologies. Precision agriculture, which aims to optimize farming practices by monitoring an...

    Authors: J. Logeshwaran, Durgesh Srivastava, K. Sree Kumar, M. Jenolin Rex, Amal Al-Rasheed, Masresha Getahun and Ben Othman Soufiene
    Citation: BMC Bioinformatics 2024 25:341
    Content type: Research Published on:

  33. Deep learning-based drug-target affinity (DTA) prediction methods have shown impressive performance, despite a high number of training parameters relative to the available data. Previous studies have highlight...

    Authors: Hyojin Son, Sechan Lee, Jaeuk Kim, Haangik Park, Myeong-Ha Hwang and Gwan-Su Yi
    Citation: BMC Bioinformatics 2024 25:340
    Content type: Research Published on:

  35. Protein kinases are a diverse superfamily of proteins common to organisms across the tree of life that are typically involved in signal transduction, allowing organisms to sense and respond to biotic or abioti...

    Authors: Elisabeth Hellec, Flavia Nunes, Charlotte Corporeau and Alexandre Cormier
    Citation: BMC Bioinformatics 2024 25:338
    Content type: Software Published on:

  36. E. coli chemotactic motion in the presence of a chemonutrient field can be studied using wet laboratory experiments or macroscale-level partial differential equations (PDEs) (among others). Bridging experimental ...

    Authors: Yorgos M. Psarellis, Seungjoon Lee, Tapomoy Bhattacharjee, Sujit S. Datta, Juan M. Bello-Rivas and Ioannis G. Kevrekidis
    Citation: BMC Bioinformatics 2024 25:337
    Content type: Research Published on:

  37. Background: As noncoding RNAs, circular RNAs (circRNAs) can act as microRNA (miRNA) sponges due to their abundant miRNA binding sites, allowing them to regulate gene expression and influence disease developmen...

    Authors: Anhui Yin, Lei Chen, Bo Zhou and Yu-Dong Cai
    Citation: BMC Bioinformatics 2024 25:336
    Content type: Research Published on:

  38. Conventional differential gene expression analysis pipelines for non-model organisms require computationally expensive transcriptome assembly. We recently proposed an alternative strategy of directly aligning ...

    Authors: Kyle Christian L. Santiago and Anish M. S. Shrestha
    Citation: BMC Bioinformatics 2024 25(Suppl 2):335
    Content type: Software Published on:

    This article is part of a Supplement: Volume 25 Supplement 2

  39. Stochastic modelling plays a crucial role in comprehending the dynamics of intracellular events in various biochemical systems, including gene-expression models. Cell-to-cell variability arises from the stocha...

    Authors: Candan Çelik, Pavol Bokes and Abhyudai Singh
    Citation: BMC Bioinformatics 2024 24(Suppl 1):493
    Content type: Research Published on:

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

  40. Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenge...

    Authors: Cezary Turek, Márton Ölbei, Tamás Stirling, Gergely Fekete, Ervin Tasnádi, Leila Gul, Balázs Bohár, Balázs Papp, Wiktor Jurkowski and Eszter Ari
    Citation: BMC Bioinformatics 2024 25:334
    Content type: Software Published on:

  42. Long non-coding RNAs (lncRNAs) can prevent, diagnose, and treat a variety of complex human diseases, and it is crucial to establish a method to efficiently predict lncRNA-disease associations.

    Authors: Bing Zhang, Haoyu Wang, Chao Ma, Hai Huang, Zhou Fang and Jiaxing Qu
    Citation: BMC Bioinformatics 2024 25:332
    Content type: Research Published on:

  43. The dilution-replicate experimental design for qPCR assays is especially efficient. It is based on multiple linear regression of multiple 3-point standard curves that are derived from the experimental samples ...

    Authors: Deyan Yordanov Yosifov, Michaela Reichenzeller, Stephan Stilgenbauer and Daniel Mertens
    Citation: BMC Bioinformatics 2024 25:331
    Content type: Software Published on:

  44. Base editing is an enhanced gene editing approach that enables the precise transformation of single nucleotides and has the potential to cure rare diseases. The design process of base editors is labour-intensi...

    Authors: Lucas Schneider and Peter Minary
    Citation: BMC Bioinformatics 2024 25:330
    Content type: Research Published on:

  45. Stroke prediction remains a critical area of research in healthcare, aiming to enhance early intervention and patient care strategies. This study investigates the efficacy of machine learning techniques, parti...

    Authors: Pritam Chakraborty, Anjan Bandyopadhyay, Preeti Padma Sahu, Aniket Burman, Saurav Mallik, Najah Alsubaie, Mohamed Abbas, Mohammed S. Alqahtani and Ben Othman Soufiene
    Citation: BMC Bioinformatics 2024 25:329
    Content type: Research Published on:

  46. The rapid advancements in deep neural network models have significantly enhanced the ability to extract features from microbial sequence data, which is critical for addressing biological challenges. However, t...

    Authors: Minghao Yang, Zehua Wang, Zizhuo Yan, Wenxiang Wang, Qian Zhu and Changlong Jin
    Citation: BMC Bioinformatics 2024 25:328
    Content type: Research Published on:

  47. Drug combination treatments have proven to be a realistic technique for treating challenging diseases such as cancer by enhancing efficacy and mitigating side effects. To achieve the therapeutic goals of these...

    Authors: Samar Monem, Aboul Ella Hassanien and Alaa H. Abdel-Hamid
    Citation: BMC Bioinformatics 2024 25:327
    Content type: Research Published on:

  48. Some transcription factors, MYC for example, bind sites of potentially methylated DNA. This may increase binding specificity as such sites are (1) highly under-represented in the genome, and (2) offer addition...

    Authors: Fei-Man Hsu and Paul Horton
    Citation: BMC Bioinformatics 2024 25(Suppl 2):326
    Content type: Research Published on:

    This article is part of a Supplement: Volume 25 Supplement 2

    The Correction to this article has been published in BMC Bioinformatics 2025 25:394

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