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  1. Inference of Gene Regulatory Networks (GRNs) is a difficult and long-standing question in Systems Biology. Numerous approaches have been proposed with the latest methods exploring the richness of single-cell d...

    Authors: Matteo Bouvier, Souad Zreika, Elodie Vallin, Camille Fourneaux, Sandrine Gonin-Giraud, Arnaud Bonnaffoux and Olivier Gandrillon
    Citation: BMC Bioinformatics 2024 25:245
    Content type: Research Published on:

  3. The growing number of portable consumer-grade electroencephalography (EEG) wearables offers potential to track brain activity and neurological disease in real-world environments. However, accompanying open sof...

    Authors: Richard James Sugden, Ingrid Campbell, Viet-Linh Luke Pham-Kim-Nghiem-Phu, Randa Higazy, Eliza Dent, Kim Edelstein, Alberto Leon and Phedias Diamandis
    Citation: BMC Bioinformatics 2024 25:243
    Content type: Software Published on:

  5. 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
    Content type: Research Published on:

  6. 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
    Content type: Research Published on:

  8. 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
    Content type: Research Published on:

  9. 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
    Content type: Research Published on:

  10. 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
    Content type: Research Published on:

  12. 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
    Content type: Research Published on:

  15. 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
    Content type: Research Published on:

  17. 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
    Content type: Research Published on:

  18. 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
    Content type: Software Published on:

  20. 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:

  21. 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:

  24. 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:

  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  31. 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:

  32. 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:

  34. 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:

  36. 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:

  39. 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:

  41. 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:

  44. 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:

  45. 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:

  46. 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:

  47. 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:

  48. 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:

  49. 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:

  50. 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:

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