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  1. 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
  2. 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
  3. The results of high-throughput biology (‘omic’) experiments provide insight into biological mechanisms but can be challenging to explore, archive and share. The scale of these challenges continues to grow as o...

    Authors: Terrence R. Ernst, John D. Blischak, Paul Nordlund, Joe Dalen, Justin Moore, Akshay Bhamidipati, Pankaj Dwivedi, Joe LoGrasso, Marco Rocha Curado and Brett Warren Engelmann
    Citation: BMC Bioinformatics 2024 25:162
  4. The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different...

    Authors: Luan Pinto Rabelo, Davidson Sodré, Rodrigo Petry Corrêa de Sousa, Luciana Watanabe, Grazielle Gomes, Iracilda Sampaio and Marcelo Vallinoto
    Citation: BMC Bioinformatics 2024 25:160
  5. Motif finding in Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) data is essential to reveal the intricacies of transcription factor binding sites (TFBSs) and their pivotal roles in gene...

    Authors: Xiaotian Wu, Wenju Hou, Ziqi Zhao, Lan Huang, Nan Sheng, Qixing Yang, Shuangquan Zhang and Yan Wang
    Citation: BMC Bioinformatics 2024 25:158
  6. Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning, and design, as well as for understanding the functions of target. Alt...

    Authors: Xin Zeng, Guang-Peng Su, Shu-Juan Li, Shuang-Qing Lv, Meng-Liang Wen and Yi Li
    Citation: BMC Bioinformatics 2024 25:156
  7. Classification of binary data arises naturally in many clinical applications, such as patient risk stratification through ICD codes. One of the key practical challenges in data classification using machine lea...

    Authors: Moein E. Samadi, Hedieh Mirzaieazar, Alexander Mitsos and Andreas Schuppert
    Citation: BMC Bioinformatics 2024 25:155
  8. 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
  9. 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

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

  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. Nanobodies, also known as VHH or single-domain antibodies, are unique antibody fragments derived solely from heavy chains. They offer advantages of small molecules and conventional antibodies, making them prom...

    Authors: Shangru Li, Xiangpeng Meng, Rui Li, Bingding Huang and Xin Wang
    Citation: BMC Bioinformatics 2024 25:122

    The Correction to this article has been published in BMC Bioinformatics 2024 25:190

  30. 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
  31. 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

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