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  1. The matched case–control design, up until recently mostly pertinent to epidemiological studies, is becoming customary in biomedical applications as well. For instance, in omics studies, it is quite common to c...

    Authors: Vera Djordjilović, Erica Ponzi, Therese Haugdahl Nøst and Magne Thoresen
    Citation: BMC Bioinformatics 2024 25:226
    Content type: Software Published on:

  2. Large Language Models (LLMs) like Generative Pre-trained Transformer (GPT) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI are increasingly recognized for their potential in the field of chem...

    Authors: Shaghayegh Sadeghi, Alan Bui, Ali Forooghi, Jianguo Lu and Alioune Ngom
    Citation: BMC Bioinformatics 2024 25:225
    Content type: Research Published on:

  5. Pan-virus detection, and virome investigation in general, can be challenging, mainly due to the lack of universally conserved genetic elements in viruses. Metagenomic next-generation sequencing can offer a pro...

    Authors: Worakorn Phumiphanjarphak and Pakorn Aiewsakun
    Citation: BMC Bioinformatics 2024 25:222
    Content type: Software Published on:

  6. Extracellular vesicle-derived (EV)-miRNAs have potential to serve as biomarkers for the diagnosis of various diseases. miRNA microarrays are widely used to quantify circulating EV-miRNA levels, and the preproc...

    Authors: Yuto Takemoto, Daisuke Ito, Shota Komori, Yoshiyuki Kishimoto, Shinichiro Yamada, Atsushi Hashizume, Masahisa Katsuno and Masahiro Nakatochi
    Citation: BMC Bioinformatics 2024 25:221
    Content type: Research Published on:

  7. Multi-omics sequencing is poised to revolutionize clinical care in the coming decade. However, there is a lack of effective and interpretable genome-wide modeling methods for the rational selection of patients...

    Authors: Sanghoon Lee, Min Sun, Yiheng Hu, Yue Wang, Md N. Islam, David Goerlitz, Peter C. Lucas, Adrian V. Lee, Sandra M. Swain, Gong Tang and Xiao-Song Wang
    Citation: BMC Bioinformatics 2024 25:220
    Content type: Software Published on:

  8. With the surge in genomic data driven by advancements in sequencing technologies, the demand for efficient bioinformatics tools for sequence analysis has become paramount. BLAST-like alignment tool (BLAT), a s...

    Authors: Yangyang Li and Rendong Yang
    Citation: BMC Bioinformatics 2024 25:219
    Content type: Software Published on:

  9. Compared to traditional supervised machine learning approaches employing fully labeled samples, positive-unlabeled (PU) learning techniques aim to classify “unlabeled” samples based on a smaller proportion of ...

    Authors: Shiwei Xu and Margaret E. Ackerman
    Citation: BMC Bioinformatics 2024 25:218
    Content type: Research Published on:

  10. Tandem repeats are specific sequences in genomic DNA repeated in tandem that are present in all organisms. Among the subcategories of TRs we have Satellite repeats, that is divided into macrosatellites, minisa...

    Authors: Carlos Willian Dias Dantas, Sebastião Rodrigues da Costa Neto, Sandy Ingrid Aguiar Alves, Kenny da Costa Pinheiro, Edian Franklin Franco De Los Santos and Rommel Thiago Jucá Ramos
    Citation: BMC Bioinformatics 2024 25:217
    Content type: Software Published on:

  12. There exists a critical transition or tipping point during the complex biological process. Such critical transition is usually accompanied by the catastrophic consequences. Therefore, hunting for the tipping p...

    Authors: Jing Ren, Peiluan Li and Jinling Yan
    Citation: BMC Bioinformatics 2024 25:215
    Content type: Research Published on:

  13. The exploration of gene-disease associations is crucial for understanding the mechanisms underlying disease onset and progression, with significant implications for prevention and treatment strategies. Advance...

    Authors: Xianghu Jia, Weiwen Luo, Jiaqi Li, Jieqi Xing, Hongjie Sun, Shunyao Wu and Xiaoquan Su
    Citation: BMC Bioinformatics 2024 25:214
    Content type: Research Published on:

  15. A vital step in analyzing single-cell data is ascertaining which cell types are present in a dataset, and at what abundance. In many diseases, the proportions of varying cell types can have important implicati...

    Authors: Courtney Schiebout and H. Robert Frost
    Citation: BMC Bioinformatics 2024 25:212
    Content type: Research Published on:

  17. In the realm of biomedical research, the growing volume, diversity and quantity of data has escalated the demand for statistical analysis as it is indispensable for synthesizing, interpreting, and publishing d...

    Authors: Tanguy Pace-Loscos, Jocelyn Gal, Sara Contu, Renaud Schiappa, Emmanuel Chamorey and Dorian Culié
    Citation: BMC Bioinformatics 2024 25:210
    Content type: Software Published on:

  20. Gene families are groups of homologous genes that often have similar biological functions. These families are formed by gene duplication events throughout evolution, resulting in multiple copies of an ancestra...

    Authors: Laila Viana Almeida, João Luís Reis-Cunha and Daniella C. Bartholomeu
    Citation: BMC Bioinformatics 2024 25:207
    Content type: Software Published on:

  22. Although RNA-seq data are traditionally used for quantifying gene expression levels, the same data could be useful in an integrated approach to compute genetic distances as well. Challenges to using mRNA seque...

    Authors: Andrew C. Tapia, Jerzy W. Jaromczyk, Neil Moore and Christopher L. Schardl
    Citation: BMC Bioinformatics 2024 25:205
    Content type: Research Published on:

  25. In systems biology, an organism is viewed as a system of interconnected molecular entities. To understand the functioning of organisms it is essential to integrate information about the variations in the conce...

    Authors: Georgios Bartzis, Carel F. W. Peeters, Wilco Ligterink and Fred A. Van Eeuwijk
    Citation: BMC Bioinformatics 2024 25:202
    Content type: Research Published on:

  26. Cancers are spatially heterogenous, thus their clonal evolution, especially following anti-cancer treatments, depends on where the mutated cells are located within the tumor tissue. For example, cells exposed ...

    Authors: Anjun Hu, Awino Maureiq E. Ojwang’, Kayode D. Olumoyin and Katarzyna A. Rejniak
    Citation: BMC Bioinformatics 2024 25:201
    Content type: Software Published on:

  27. The initial version of SEDA assists life science researchers without programming skills with the preparation of DNA and protein sequence FASTA files for multiple bioinformatics applications. However, the initi...

    Authors: Miguel Reboiro-Jato, Daniel Pérez-Rodríguez, Miguel José Da Silva, David Vila-Fernández, Cristina P. Vieira, Jorge Vieira and Hugo López-Fernández
    Citation: BMC Bioinformatics 2024 25:200
    Content type: Software Published on:

  28. Computational models in systems biology are becoming more important with the advancement of experimental techniques to query the mechanistic details responsible for leading to phenotypes of interest. In partic...

    Authors: Adam Šmelko, Miroslav Kratochvíl, Emmanuel Barillot and Vincent Noël
    Citation: BMC Bioinformatics 2024 25:199
    Content type: Software Published on:

  29. Single-cell transcriptome sequencing (scRNA-Seq) has allowed new types of investigations at unprecedented levels of resolution. Among the primary goals of scRNA-Seq is the classification of cells into distinct...

    Authors: Hector Roux de Bézieux, Kelly Street, Stephan Fischer, Koen Van den Berge, Rebecca Chance, Davide Risso, Jesse Gillis, John Ngai, Elizabeth Purdom and Sandrine Dudoit
    Citation: BMC Bioinformatics 2024 25:198
    Content type: Research Published on:

  30. CAR-T cell therapy represents a novel approach for the treatment of hematologic malignancies and solid tumors. However, its implementation is accompanied by the emergence of potentially life-threatening advers...

    Authors: Zhenyu Wei, Chengkui Zhao, Min Zhang, Jiayu Xu, Nan Xu, Shiwei Wu, Xiaohui Xin, Lei Yu and Weixing Feng
    Citation: BMC Bioinformatics 2024 25:197
    Content type: Research Published on:

  31. The identification of drug side effects plays a critical role in drug repositioning and drug screening. While clinical experiments yield accurate and reliable information about drug-related side effects, they ...

    Authors: Wuyong Liu, Jingyu Zhang, Guanyu Qiao, Jilong Bian, Benzhi Dong and Yang Li
    Citation: BMC Bioinformatics 2024 25:196
    Content type: Research Published on:

  32. 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
    Content type: Research Published on:

  34. 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
    Content type: Software Published on:

  38. 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
    Content type: Software Published on:

  39. 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
    Content type: Research Published on:

  42. 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
    Content type: Research Published on:

  46. 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
    Content type: Research Published on:

  47. 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
    Content type: Software Published on:

  48. 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
    Content type: Software Published on:

  49. 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
    Content type: Research Published on:

  50. 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
    Content type: Research Published on:

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