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  1. Mining the vast pool of biomedical literature to extract accurate responses and relevant references is challenging due to the domain's interdisciplinary nature, specialized jargon, and continuous evolution. Ea...

    Authors: Wasim Aftab, Zivkos Apostolou, Karim Bouazoune and Tobias Straub
    Citation: BMC Bioinformatics 2024 25:281
    Content type: Research Published on:

  2. Over the past two decades, scientists have increasingly realized the importance of the three-dimensional (3D) genome organization in regulating cellular activity. Hi-C and related experiments yield 2D contact ...

    Authors: Chrisostomos Drogaris, Yanlin Zhang, Eric Zhang, Elena Nazarova, Roman Sarrazin-Gendron, Sélik Wilhelm-Landry, Yan Cyr, Jacek Majewski, Mathieu Blanchette and Jérôme Waldispühl
    Citation: BMC Bioinformatics 2024 25:277
    Content type: Software Published on:

  3. Sparse multiple canonical correlation network analysis (SmCCNet) is a machine learning technique for integrating omics data along with a variable of interest (e.g., phenotype of complex disease), and reconstru...

    Authors: Weixuan Liu, Thao Vu, Iain R. Konigsberg, Katherine A. Pratte, Yonghua Zhuang and Katerina J. Kechris
    Citation: BMC Bioinformatics 2024 25:276
    Content type: Software Published on:

  4. The rise of network pharmacology has led to the widespread use of network-based computational methods in predicting drug target interaction (DTI). However, existing DTI prediction models typically rely on a li...

    Authors: Beiyi Zhang, Dongjiang Niu, Lianwei Zhang, Qiang Zhang and Zhen Li
    Citation: BMC Bioinformatics 2024 25:275
    Content type: Research Published on:

  7. The availability of transcriptomic data for species without a reference genome enables the construction of de novo transcriptome assemblies as alternative reference resources from RNA-Seq data. A transcriptome...

    Authors: Lorenzo Arcioni, Manuel Arcieri, Jessica Di Martino, Franco Liberati, Paolo Bottoni and Tiziana Castrignanò
    Citation: BMC Bioinformatics 2024 25:272
    Content type: Research Published on:

  9. In the present work, we aimed at modeling a relaxation experiment which consists in selecting a subfraction of a cell population and observing the speed at which the entire initial distribution for a given mar...

    Authors: Maxime Estavoyer, Marion Dufeu, Grégoire Ranson, Sylvain Lefort, Thibault Voeltzel, Véronique Maguer-Satta, Olivier Gandrillon and Thomas Lepoutre
    Citation: BMC Bioinformatics 2024 25:270
    Content type: Research Published on:

  14. Survival analysis has been used to characterize the time-to-event data. In medical studies, a typical application is to analyze the survival time of specific cancers by using high-dimensional gene expressions....

    Authors: Li-Pang Chen and Hsiao-Ting Huang
    Citation: BMC Bioinformatics 2024 25:265
    Content type: Software Published on:

  15. Circular RNA (CircRNA)–microRNA (miRNA) interaction (CMI) is an important model for the regulation of biological processes by non-coding RNA (ncRNA), which provides a new perspective for the study of human com...

    Authors: Xin-Fei Wang, Chang-Qing Yu, Zhu-Hong You, Yan Wang, Lan Huang, Yan Qiao, Lei Wang and Zheng-Wei Li
    Citation: BMC Bioinformatics 2024 25:264
    Content type: Research Published on:

  17. In complex agricultural environments, the presence of shadows, leaf debris, and uneven illumination can hinder the performance of leaf segmentation models for cucumber disease detection. This is further exacer...

    Authors: Jie Yang, Jiya Tian, Jinchao Miao and Yunsheng Chen
    Citation: BMC Bioinformatics 2024 25:262
    Content type: Research Published on:

  19. Quantitative measurement of RNA expression levels through RNA-Seq is an ideal replacement for conventional cancer diagnosis via microscope examination. Currently, cancer-related RNA-Seq studies focus on two as...

    Authors: Xing Zhao, Zigui Chen, Huating Wang and Hao Sun
    Citation: BMC Bioinformatics 2024 25:260
    Content type: Research Published on:

  20. Effective identification of differentially expressed genes (DEGs) has been challenging for single-cell RNA sequencing (scRNA-seq) profiles. Many existing algorithms have high false positive rates (FPRs) and of...

    Authors: Jing Yan, Qiuhong Zeng and Xianlong Wang
    Citation: BMC Bioinformatics 2024 25:259
    Content type: Software Published on:

  22. The recent advances in high-throughput single-cell sequencing have created an urgent demand for computational models which can address the high complexity of single-cell multiomics data. Meticulous single-cell...

    Authors: Yunhee Jeong, Jonathan Ronen, Wolfgang Kopp, Pavlo Lutsik and Altuna Akalin
    Citation: BMC Bioinformatics 2024 25:257
    Content type: Software Published on:

  23. Antioxidant proteins are involved in several biological processes and can protect DNA and cells from the damage of free radicals. These proteins regulate the body's oxidative stress and perform a significant r...

    Authors: Gul Rukh, Shahid Akbar, Gauhar Rehman, Fawaz Khaled Alarfaj and Quan Zou
    Citation: BMC Bioinformatics 2024 25:256
    Content type: Research Published on:

  27. Proteins play a pivotal role in the diverse array of biological processes, making the precise prediction of protein–protein interaction (PPI) sites critical to numerous disciplines including biology, medicine ...

    Authors: Zijian Feng, Weihong Huang, Haohao Li, Hancan Zhu, Yanlei Kang and Zhong Li
    Citation: BMC Bioinformatics 2024 25:252
    Content type: Research Published on:

  29. The potential benefits of drug combination synergy in cancer medicine are significant, yet the risks must be carefully managed due to the possibility of increased toxicity. Although artificial intelligence app...

    Authors: Yi-Ching Tang, Rongbin Li, Jing Tang, W. Jim Zheng and Xiaoqian Jiang
    Citation: BMC Bioinformatics 2024 25:250
    Content type: Research Published on:

  31. Normalization is a crucial step in the analysis of single-cell RNA-sequencing (scRNA-seq) counts data. Its principal objectives are reduction of systematic biases primarily introduced through technical sources...

    Authors: Amartya Singh and Hossein Khiabanian
    Citation: BMC Bioinformatics 2024 25:248
    Content type: Research Published on:

  34. 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:

  36. 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:

  38. 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:

  39. 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:

  41. 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: Egor Guguchkin, Artem Kasianov, Maksim Belenikin, Gaukhar Zobkova, Ekaterina Kosova, Vsevolod Makeev and Evgeny Karpulevich
    Citation: BMC Bioinformatics 2024 25:238
    Content type: Research Published on:

    The Correction to this article has been published in BMC Bioinformatics 2024 25:268

  42. 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:

  43. 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:

  45. 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:

  48. 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:

  49. 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:

  50. 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:

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