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  1. Using next-generation sequencing technologies, scientists can sequence complex microbial communities directly from the environment. Significant insights into the structure, diversity, and ecology of microbial ...

    Authors: Amin Darabi, Sayeh Sobhani, Rosa Aghdam and Changiz Eslahchi
    Citation: BMC Bioinformatics 2024 25:241
  2. Identification of human leukocyte antigen (HLA) types from DNA-sequenced human samples is important in organ transplantation and cancer immunotherapy and remains a challenging task considering sequence homolog...

    Authors: Hamdiye Uzuner, Annette Paschen, Dirk Schadendorf and Johannes Köster
    Citation: BMC Bioinformatics 2024 25:240
  3. Alignment of reads to a reference genome sequence is one of the key steps in the analysis of human whole-genome sequencing data obtained through Next-generation sequencing (NGS) technologies. The quality of th...

    Authors: Guguchkin Egor, Kasianov Artem, Belenikin Maksim, Zobkova Gaukhar, Kosova Ekaterina, Makeev Vsevolod and Karpulevich Evgeny
    Citation: BMC Bioinformatics 2024 25:238
  4. With the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error level and structure, the analysis of such data demands some database of...

    Authors: Melcy Philip, Knut Rudi, Ida Ormaasen, Inga Leena Angell, Ragnhild Pettersen, Nigel B. Keeley and Lars-Gustav Snipen
    Citation: BMC Bioinformatics 2024 25:237
  5. Homologous recombination deficiency (HRD) stands as a clinical indicator for discerning responsive outcomes to platinum-based chemotherapy and poly ADP-ribose polymerase (PARP) inhibitors. One of the conventio...

    Authors: Jae Jun Lee, Hyun Ju Kang, Donghyo Kim, Si On Lim, Stephanie S. Kim, Gahyun Kim, Sanguk Kim, Jin-Ku Lee and Jinho Kim
    Citation: BMC Bioinformatics 2024 25:236
  6. The growing abundance of in vitro omics data, coupled with the necessity to reduce animal testing in the safety assessment of chemical compounds and even eliminate it in the evaluation of cosmetics, highlights...

    Authors: Louison Fresnais, Olivier Perin, Anne Riu, Romain Grall, Alban Ott, Bernard Fromenty, Jean-Clément Gallardo, Maximilian Stingl, Clément Frainay, Fabien Jourdan and Nathalie Poupin
    Citation: BMC Bioinformatics 2024 25:234
  7. In this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral sequences among other subtypes of the coronaviridae fa...

    Authors: Karolayne S. Azevedo, Luísa C. de Souza, Maria G. F. Coutinho, Raquel de M. Barbosa and Marcelo A. C. Fernandes
    Citation: BMC Bioinformatics 2024 25:231
  8. Adeno-associated viruses 2 (AAV2) are minute viruses renowned for their capacity to infect human cells and akin organisms. They have recently emerged as prominent candidates in the field of gene therapy, prima...

    Authors: Matteo De Leonardis, Jorge Fernandez-de-Cossio-Diaz, Guido Uguzzoni and Andrea Pagnani
    Citation: BMC Bioinformatics 2024 25:229
  9. Fungi play a key role in several important ecological functions, ranging from organic matter decomposition to symbiotic associations with plants. Moreover, fungi naturally inhabit the human body and can be ben...

    Authors: Fábio M. Miranda, Vasco C. Azevedo, Rommel J. Ramos, Bernhard Y. Renard and Vitor C. Piro
    Citation: BMC Bioinformatics 2024 25:228
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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

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