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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. Modelling discrete-time cause-specific hazards in the presence of competing events and non-proportional hazards is a challenging task in many domains. Survival analysis in longitudinal cohorts often requires s...

    Authors: Matthieu Oliver, Nicolas Allou, Marjolaine Devineau, Jèrôme Allyn and Cyril Ferdynus
    Citation: BMC Bioinformatics 2024 25:175
  23. Principal component analysis (PCA) is an important and widely used unsupervised learning method that determines population structure based on genetic variation. Genome sequencing of thousands of individuals us...

    Authors: Weiming He, Lian Xu, JingXian Wang, Zhen Yue, Yi Jing, Shuaishuai Tai, Jian Yang and Xiaodong Fang
    Citation: BMC Bioinformatics 2024 25:173
  24. Deep neural networks (DNNs) have the potential to revolutionize our understanding and treatment of genetic diseases. An inherent limitation of deep neural networks, however, is their high demand for data durin...

    Authors: Hyunjung Lee, Utku Ozbulak, Homin Park, Stephen Depuydt, Wesley De Neve and Joris Vankerschaver
    Citation: BMC Bioinformatics 2024 25:170
  25. Numerous transcriptomic-based models have been developed to predict or understand the fundamental mechanisms driving biological phenotypes. However, few models have successfully transitioned into clinical prac...

    Authors: S. R. Oshternian, S. Loipfinger, A. Bhattacharya and R. S. N. Fehrmann
    Citation: BMC Bioinformatics 2024 25:167
  26. The Biology System Description Language (BiSDL) is an accessible, easy-to-use computational language for multicellular synthetic biology. It allows synthetic biologists to represent spatiality and multi-level ...

    Authors: Leonardo Giannantoni, Roberta Bardini, Alessandro Savino and Stefano Di Carlo
    Citation: BMC Bioinformatics 2024 25:166
  27. The annotation of protein sequences in public databases has long posed a challenge in molecular biology. This issue is particularly acute for viral proteins, which demonstrate limited homology to known protein...

    Authors: William L. Harrigan, Barbra D. Ferrell, K. Eric Wommack, Shawn W. Polson, Zachary D. Schreiber and Mahdi Belcaid
    Citation: BMC Bioinformatics 2024 25:165
  28. Multimodal integration combines information from different sources or modalities to gain a more comprehensive understanding of a phenomenon. The challenges in multi-omics data analysis lie in the complexity, h...

    Authors: Yufang Liu, Yongkai Chen, Haoran Lu, Wenxuan Zhong, Guo-Cheng Yuan and Ping Ma
    Citation: BMC Bioinformatics 2024 25:164

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