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  1. High-throughput sequencing is a powerful tool that is extensively applied in biological studies. However, sequencers may produce low-quality bases, leading to ambiguous bases, ‘N’s. PCR duplicates introduced i...

    Authors: Jianqiao Hu, Sai Luo, Ming Tian and Adam Yongxin Ye
    Citation: BMC Bioinformatics 2024 25:154
    Content type: Software Published on:

  2. With the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic classification by using alignment-based approaches to reduce the impact of...

    Authors: Rafael Peres da Silva, Chayaporn Suphavilai and Niranjan Nagarajan
    Citation: BMC Bioinformatics 2024 25(Suppl 1):153
    Content type: Research Published on:

    This article is part of a Supplement: Volume 25 Supplement 1

  3. Text summarization is a challenging problem in Natural Language Processing, which involves condensing the content of textual documents without losing their overall meaning and information content, In the domai...

    Authors: Mahira Kirmani, Gagandeep Kour, Mudasir Mohd, Nasrullah Sheikh, Dawood Ashraf Khan, Zahid Maqbool, Mohsin Altaf Wani and Abid Hussain Wani
    Citation: BMC Bioinformatics 2024 25:152
    Content type: Research Published on:

  4. Genomes are inherently inhomogeneous, with features such as base composition, recombination, gene density, and gene expression varying along chromosomes. Evolutionary, biological, and biomedical analyses aim t...

    Authors: Claus Vogl, Mariia Karapetiants, Burçin Yıldırım, Hrönn Kjartansdóttir, Carolin Kosiol, Juraj Bergman, Michal Majka and Lynette Caitlin Mikula
    Citation: BMC Bioinformatics 2024 25:151
    Content type: Research Published on:

  5. The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its go...

    Authors: Caleb K. Kibet, Jean-Baka Domelevo Entfellner, Daudi Jjingo, Etienne Pierre de Villiers, Santie de Villiers, Karen Wambui, Sam Kinyanjui and Daniel Masiga
    Citation: BMC Bioinformatics 2024 25:150
    Content type: Research Published on:

  7. Protein toxins are defense mechanisms and adaptations found in various organisms and microorganisms, and their use in scientific research as therapeutic candidates is gaining relevance due to their effectivene...

    Authors: Jorge F. Beltrán, Lisandra Herrera-Belén, Fernanda Parraguez-Contreras, Jorge G. Farías, Jorge Machuca-Sepúlveda and Stefania Short
    Citation: BMC Bioinformatics 2024 25:148
    Content type: Software Published on:

  10. Drug targets in living beings perform pivotal roles in the discovery of potential drugs. Conventional wet-lab characterization of drug targets is although accurate but generally expensive, slow, and resource i...

    Authors: Muhammad Arif, Ge Fang, Ali Ghulam, Saleh Musleh and Tanvir Alam
    Citation: BMC Bioinformatics 2024 25:145
    Content type: Research Published on:

  13. The rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These assays profile multiple modalities in the same cell and can often yield...

    Authors: Garth L. Kong, Thai T. Nguyen, Wesley K. Rosales, Anjali D. Panikar, John H. W. Cheney, Theresa A. Lusardi, William M. Yashar, Brittany M. Curtiss, Sarah A. Carratt, Theodore P. Braun and Julia E. Maxson
    Citation: BMC Bioinformatics 2024 25:142
    Content type: Software Published on:

  15. Drug combination therapy is generally more effective than monotherapy in the field of cancer treatment. However, screening for effective synergistic combinations from a wide range of drug combinations is parti...

    Authors: Yunyun Dong, Yunqing Chang, Yuxiang Wang, Qixuan Han, Xiaoyuan Wen, Ziting Yang, Yan Zhang, Yan Qiang, Kun Wu, Xiaole Fan and Xiaoqiang Ren
    Citation: BMC Bioinformatics 2024 25:140
    Content type: Research Published on:

  16. MicroRNA (miRNA) has been shown to play a key role in the occurrence and progression of diseases, making uncovering miRNA-disease associations vital for disease prevention and therapy. However, traditional lab...

    Authors: Yanling Liu, Ruiyan Zhang, Xiaojing Dong, Hong Yang, Jing Li, Hongyan Cao, Jing Tian and Yanbo Zhang
    Citation: BMC Bioinformatics 2024 25:139
    Content type: Research Published on:

  17. Even though high-throughput transcriptome sequencing is routinely performed in many laboratories, computational analysis of such data remains a cumbersome process often executed manually, hence error-prone and...

    Authors: Patrick Blumenkamp, Max Pfister, Sonja Diedrich, Karina Brinkrolf, Sebastian Jaenicke and Alexander Goesmann
    Citation: BMC Bioinformatics 2024 25:138
    Content type: Software Published on:

  19. Cross-platform normalization seeks to minimize technological bias between microarray and RNAseq whole-transcriptome data. Incorporating multiple gene expression platforms permits external validation of experim...

    Authors: Daniel Skubleny, Sunita Ghosh, Jennifer Spratlin, Daniel E. Schiller and Gina R. Rayat
    Citation: BMC Bioinformatics 2024 25:136
    Content type: Research Published on:

  21. Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few open-source option...

    Authors: James M. Dolezal, Sara Kochanny, Emma Dyer, Siddhi Ramesh, Andrew Srisuwananukorn, Matteo Sacco, Frederick M. Howard, Anran Li, Prajval Mohan and Alexander T. Pearson
    Citation: BMC Bioinformatics 2024 25:134
    Content type: Software Published on:

  22. Cancer is one of the leading causes of deaths worldwide. Survival analysis and prediction of cancer patients is of great significance for their precision medicine. The robustness and interpretability of the su...

    Authors: Shuo Wang, Yuanning Liu, Hao Zhang and Zhen Liu
    Citation: BMC Bioinformatics 2024 25:133
    Content type: Research Published on:

  24. The global spread of the SARS-CoV-2 pandemic, originating in Wuhan, China, has had profound consequences on both health and the economy. Traditional alignment-based phylogenetic tree methods for tracking epide...

    Authors: Ahmed M. A. Elsherbini, Amr Hassan Elkholy, Youssef M. Fadel, Gleb Goussarov, Ahmed Mohamed Elshal, Mohamed El-Hadidi and Mohamed Mysara
    Citation: BMC Bioinformatics 2024 25:131
    Content type: Research Published on:

  25. Recent improvements in sequencing technologies enabled detailed profiling of genomic features. These technologies mostly rely on short reads which are merged and compared to reference genome for variant identi...

    Authors: Mehmet Arif Ergun, Omer Cinal, Berkant Bakışlı, Abdullah Asım Emül and Mehmet Baysan
    Citation: BMC Bioinformatics 2024 25:130
    Content type: Software Published on:

  26. The RNA-Recognition motif (RRM) is a protein domain that binds single-stranded RNA (ssRNA) and is present in as much as 2% of the human genome. Despite this important role in biology, RRM-ssRNA interactions ar...

    Authors: Anna Kravchenko, Sjoerd Jacob de Vries, Malika Smaïl-Tabbone and Isaure Chauvot de Beauchene
    Citation: BMC Bioinformatics 2024 25:129
    Content type: Research Published on:

  27. Discovery biological motifs plays a fundamental role in understanding regulatory mechanisms. Computationally, they can be efficiently represented as kmers, making the counting of these elements a critical aspect ...

    Authors: Jader M. Caldonazzo Garbelini, Danilo S. Sanches and Aurora T. Ramirez Pozo
    Citation: BMC Bioinformatics 2024 25:128
    Content type: Software Published on:

  29. Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an importan...

    Authors: Jasper van Bemmelen, Davida S. Smyth and Jasmijn A. Baaijens
    Citation: BMC Bioinformatics 2024 25:126
    Content type: Research Published on:

  30. In the battle of the host against lentiviral pathogenesis, the immune response is crucial. However, several questions remain unanswered about the interaction with different viruses and their influence on disea...

    Authors: Raquel L. Costa, Luiz Gadelha, Mirela D’arc, Marcelo Ribeiro-Alves, David L. Robertson, Jean-Marc Schwartz, Marcelo A. Soares and Fábio Porto
    Citation: BMC Bioinformatics 2024 25:125
    Content type: Database Published on:

  31. Next-generation sequencing (NGS) technologies offer fast and inexpensive identification of DNA sequences. Somatic sequencing is among the primary applications of NGS, where acquired (non-inherited) variants ar...

    Authors: Yunus Emre Cebeci, Rumeysa Aslihan Erturk, Mehmet Arif Ergun and Mehmet Baysan
    Citation: BMC Bioinformatics 2024 25:124
    Content type: Research Published on:

  36. High-dimensional omics data are increasingly utilized in clinical and public health research for disease risk prediction. Many previous sparse methods have been proposed that using prior knowledge, e.g., biolo...

    Authors: Junjie Shen, Shuo Wang, Yongfei Dong, Hao Sun, Xichao Wang and Zaixiang Tang
    Citation: BMC Bioinformatics 2024 25:119
    Content type: Research Published on:

  37. Bacteria in the human body, particularly in the large intestine, are known to be associated with various diseases. To identify disease-associated bacteria (markers), a typical method is to statistically compar...

    Authors: Shota Nose, Hirotsugu Shiroma, Takuji Yamada and Yushi Uno
    Citation: BMC Bioinformatics 2024 25:118
    Content type: Research Published on:

  41. Neuroscience research in Drosophila is benefiting from large-scale connectomics efforts using electron microscopy (EM) to reveal all the neurons in a brain and their connections. To exploit this knowledge base, r...

    Authors: Jody Clements, Cristian Goina, Philip M. Hubbard, Takashi Kawase, Donald J. Olbris, Hideo Otsuna, Robert Svirskas and Konrad Rokicki
    Citation: BMC Bioinformatics 2024 25:114
    Content type: Software Published on:

  45. The analysis of large and complex biological datasets in bioinformatics poses a significant challenge to achieving reproducible research outcomes due to inconsistencies and the lack of standardization in the a...

    Authors: Simone Alessandri, Maria L. Ratto, Sergio Rabellino, Gabriele Piacenti, Sandro Gepiro Contaldo, Simone Pernice, Marco Beccuti, Raffaele A. Calogero and Luca Alessandri
    Citation: BMC Bioinformatics 2024 25:110
    Content type: Software Published on:

  47. RNA-protein interaction (RPI) is crucial to the life processes of diverse organisms. Various researchers have identified RPI through long-term and high-cost biological experiments. Although numerous machine le...

    Authors: Ying Liang, XingRui Yin, YangSen Zhang, You Guo and YingLong Wang
    Citation: BMC Bioinformatics 2024 25:108
    Content type: Research Published on:

  48. As noncommunicable diseases (NCDs) pose a significant global health burden, identifying effective diagnostic and predictive markers for these diseases is of paramount importance. Epigenetic modifications, such...

    Authors: Steven Gore, Bailey Meche, Danyang Shao, Benjamin Ginnett, Kelly Zhou and Rajeev K. Azad
    Citation: BMC Bioinformatics 2024 25:107
    Content type: Research Published on:

  49. Predicting protein–protein interactions (PPIs) from sequence data is a key challenge in computational biology. While various computational methods have been proposed, the utilization of sequence embeddings fro...

    Authors: Thanh Hai Dang and Tien Anh Vu
    Citation: BMC Bioinformatics 2024 25:106
    Content type: Research Published on:

  50. The prediction of cancer drug response is a challenging subject in modern personalized cancer therapy due to the uncertainty of drug efficacy and the heterogeneity of patients. It has been shown that the chara...

    Authors: Chuanqi Lao, Pengfei Zheng, Hongyang Chen, Qiao Liu, Feng An and Zhao Li
    Citation: BMC Bioinformatics 2024 25:105
    Content type: Research Published on:

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