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  1. Graph embedding techniques are using deep learning algorithms in data analysis to solve problems of such as node classification, link prediction, community detection, and visualization. Although typically used...

    Authors: Edwin Alvarez-Mamani, Reinhard Dechant, César A. Beltran-Castañón and Alfredo J. Ibáñez
    Citation: BMC Bioinformatics 2024 25:1
  2. Flux Balance Analysis (FBA) is a key metabolic modeling method used to simulate cellular metabolism under steady-state conditions. Its simplicity and versatility have led to various strategies incorporating tr...

    Authors: Thummarat Paklao, Apichat Suratanee and Kitiporn Plaimas
    Citation: BMC Bioinformatics 2023 24:492
  3. The advent and continual improvement of high-throughput sequencing technologies has made immunoglobulin repertoire sequencing accessible and informative regardless of study species. However, to fully map dynam...

    Authors: Daniel Dorey-Robinson, Giuseppe Maccari and John A. Hammond
    Citation: BMC Bioinformatics 2023 24:491
  4. Clustering analysis is widely used to interpret biomedical data and uncover new knowledge and patterns. However, conventional clustering methods are not effective when dealing with sparse biomedical data. To o...

    Authors: Xiaomeng Zhang, Hongtao Zhang, Zhihao Wang, Xiaofei Ma, Jiancheng Luo and Yingying Zhu
    Citation: BMC Bioinformatics 2023 24:490
  5. Plate design is a necessary and time-consuming operation for GC/LC-MS-based sample preparation. The implementation of the inter-batch balancing algorithm and the intra-batch randomization algorithm can have a ...

    Authors: Miaoshan Lu, Hengxuan Jiang, Ruimin Wang, Shaowei An, Jiawei Wang and Changbin Yu
    Citation: BMC Bioinformatics 2023 24:489
  6. The pharmaceutical field faces a significant challenge in validating drug target interactions (DTIs) due to the time and cost involved, leading to only a fraction being experimentally verified. To expedite dru...

    Authors: Warith Eddine Djeddi, Khalil Hermi, Sadok Ben Yahia and Gayo Diallo
    Citation: BMC Bioinformatics 2023 24:488
  7. Automatic and accurate extraction of diverse biomedical relations from literature is a crucial component of bio-medical text mining. Currently, stacking various classification networks on pre-trained language ...

    Authors: Xiangwen Zheng, Xuanze Wang, Xiaowei Luo, Fan Tong and Dongsheng Zhao
    Citation: BMC Bioinformatics 2023 24:486
  8. Numerous tools exist for biological sequence comparisons and search. One case of particular interest for immunologists is finding matches for linear peptide T cell epitopes, typically between 8 and 15 residues...

    Authors: Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Koşaloğlu-Yalçın, Alessandro Sette, Morten Nielsen, Jason A. Greenbaum and Bjoern Peters
    Citation: BMC Bioinformatics 2023 24:485
  9. This paper presents novel datasets providing numerical representations of ICD-10-CM codes by generating description embeddings using a large language model followed by a dimension reduction via autoencoder. Th...

    Authors: Michael J. Kane, Casey King, Denise Esserman, Nancy K. Latham, Erich J. Greene and David A. Ganz
    Citation: BMC Bioinformatics 2023 24:482
  10. The rapid emergence of single-cell RNA-seq (scRNA-seq) data presents remarkable opportunities for broad investigations through integration analyses. However, most integration models are black boxes that lack i...

    Authors: Zhen-Hao Guo, Yan Wu, Siguo Wang, Qinhu Zhang, Jin-Ming Shi, Yan-Bin Wang and Zhan-Heng Chen
    Citation: BMC Bioinformatics 2023 24:481
  11. Cancer prediction in the early stage is a topic of major interest in medicine since it allows accurate and efficient actions for successful medical treatments of cancer. Mostly cancer datasets contain various ...

    Authors: Rajul Mahto, Saboor Uddin Ahmed, Rizwan ur Rahman, Rabia Musheer Aziz, Priyanka Roy, Saurav Mallik, Aimin Li and Mohd Asif Shah
    Citation: BMC Bioinformatics 2023 24:479
  12. With more clinical trials are offering optional participation in the collection of bio-specimens for biobanking comes the increasing complexity of requirements of informed consent forms. The aim of this study ...

    Authors: Meng Zhang, Madhuri Sankaranarayanapillai, Jingcheng Du, Yang Xiang, Frank J. Manion, Marcelline R. Harris, Cooper Stansbury, Huy Anh Pham and Cui Tao
    Citation: BMC Bioinformatics 2023 24(Suppl 3):477

    This article is part of a Supplement: Volume 24 Supplement 3

  13. The increasing body of research has consistently demonstrated the intricate correlation between the human microbiome and human well-being. Microbes can impact the efficacy and toxicity of drugs through various...

    Authors: Shanghui Lu, Yong Liang, Le Li, Rui Miao, Shuilin Liao, Yongfu Zou, Chengjun Yang and Dong Ouyang
    Citation: BMC Bioinformatics 2023 24:476
  14. The standardization of biological data using unique identifiers is vital for seamless data integration, comprehensive interpretation, and reproducibility of research findings, contributing to advancements in b...

    Authors: Min Hyung Cho, Kwang-Hwi Cho and Kyoung Tai No
    Citation: BMC Bioinformatics 2023 24:475
  15. With new advances in next generation sequencing (NGS) technology at reduced costs, research on bacterial genomes in the environment has become affordable. Compared to traditional methods, NGS provides high-thr...

    Authors: Amrita Chattopadhyay, Chien-Yueh Lee, Ya-Chin Lee, Chiang-Lin Liu, Hsin-Kuang Chen, Yung-Hua Li, Liang-Chuan Lai, Mong-Hsun Tsai, Yen-Hsuan Ni, Han-Mo Chiu, Tzu-Pin Lu and Eric Y. Chuang
    Citation: BMC Bioinformatics 2023 24:474
  16. Sequenced Protein–Protein Interaction (PPI) prediction represents a pivotal area of study in biology, playing a crucial role in elucidating the mechanistic underpinnings of diseases and facilitating the design...

    Authors: Jiahui Wu, Bo Liu, Jidong Zhang, Zhihan Wang and Jianqiang Li
    Citation: BMC Bioinformatics 2023 24:473
  17. Detection of exotic plant pathogens and preventing their entry and establishment are critical for the protection of agricultural systems while securing the global trading of agricultural commodities. High-thro...

    Authors: Xiaojun Hu, Oscar P. Hurtado-Gonzales, Bishwo N. Adhikari, Ronald D. French-Monar, Martha Malapi, Joseph A. Foster and Clint D. McFarland
    Citation: BMC Bioinformatics 2023 24:470
  18. The success of AlphaFold2 in reliable protein three-dimensional (3D) structure prediction, assists the move of structural biology toward studies of protein dynamics and mutational impact on structure and function...

    Authors: Konstantin Weissenow and Burkhard Rost
    Citation: BMC Bioinformatics 2023 24:469
  19. Multiplex PCR amplifies numerous targets in a single tube reaction and is essential in molecular biology and clinical diagnostics. One of its most important applications is in the targeted sequencing of pathog...

    Authors: Jason D. Limberis and John Z. Metcalfe
    Citation: BMC Bioinformatics 2023 24:468
  20. With the COVID-19 outbreak, an increasing number of individuals are concerned about their health, particularly their immune status. However, as of now, there is no available algorithm that effectively assesses...

    Authors: Min Zhang, Chengkui Zhao, Qi Cheng, Jiayu Xu, Nan Xu, Lei Yu and Weixing Feng
    Citation: BMC Bioinformatics 2023 24:467
  21. Hierarchical classification offers a more specific categorization of data and breaks down large classification problems into subproblems, providing improved prediction accuracy and predictive power for undefin...

    Authors: Youpeng Yang, Qiuhong Zeng, Gaotong Liu, Shiyao Zheng, Tianyang Luo, Yibin Guo, Jia Tang and Yi Huang
    Citation: BMC Bioinformatics 2023 24:465
  22. Single-cell sequencing has shed light on previously inaccessible biological questions from different fields of research, including organism development, immune function, and disease progression. The number of ...

    Authors: Kun Wang, Xiao Zhang, Hansen Cheng, Wenhao Ma, Guangchao Bao, Liting Dong, Yixiong Gou, Jian Yang and Haoyang Cai
    Citation: BMC Bioinformatics 2023 24:463
  23. Synonymous mutations, which change the DNA sequence but not the encoded protein sequence, can affect protein structure and function, mRNA maturation, and mRNA half-lives. The possibility that synonymous mutati...

    Authors: Yiyun Rao, Nabeel Ahmed, Justin Pritchard and Edward P. O’Brien
    Citation: BMC Bioinformatics 2023 24:462
  24. Basecalling long DNA sequences is a crucial step in nanopore-based DNA sequencing protocols. In recent years, the CTC-RNN model has become the leading basecalling model, supplanting preceding hidden Markov mod...

    Authors: Xuechun Xu, Nayanika Bhalla, Patrik Ståhl and Joakim Jaldén
    Citation: BMC Bioinformatics 2023 24:461
  25. Synthetic biologists use and combine diverse biological parts to build systems such as genetic circuits that perform desirable functions in, for example, biomedical or industrial applications. Computer-aided d...

    Authors: Baptiste Turpin, Eline Y. Bijman, Hans-Michael Kaltenbach and Jörg Stelling
    Citation: BMC Bioinformatics 2023 24(Suppl 1):460

    This article is part of a Supplement: Volume 24 Supplement 1

  26. Variability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat and ComBat-Seq are among the most widely used tools for correcting those technical...

    Authors: Abdelkader Behdenna, Maximilien Colange, Julien Haziza, Aryo Gema, Guillaume Appé, Chloé-Agathe Azencott and Akpéli Nordor
    Citation: BMC Bioinformatics 2023 24:459
  27. Intense sun exposure is a major risk factor for the development of melanoma, an abnormal proliferation of skin cells. Yet, this more prevalent type of skin cancer can also develop in less-exposed areas, such a...

    Authors: P. Kavitha, G. Ayyappan, Prabhu Jayagopal, Sandeep Kumar Mathivanan, Saurav Mallik, Amal Al-Rasheed, Mohammed S. Alqahtani and Ben Othman Soufiene
    Citation: BMC Bioinformatics 2023 24:458
  28. Biclustering is increasingly used in biomedical data analysis, recommendation tasks, and text mining domains, with hundreds of biclustering algorithms proposed. When assessing the performance of these algorith...

    Authors: Eduardo N. Castanho, João P. Lobo, Rui Henriques and Sara C. Madeira
    Citation: BMC Bioinformatics 2023 24:457

    The Correction to this article has been published in BMC Bioinformatics 2024 25:16

  29. Protein–protein interactions (PPIs) are crucial in various biological functions and cellular processes. Thus, many computational approaches have been proposed to predict PPI sites. Although significant progres...

    Authors: Hanhan Cong, Hong Liu, Yi Cao, Cheng Liang and Yuehui Chen
    Citation: BMC Bioinformatics 2023 24:456
  30. The escalation of viruses over the past decade has highlighted the need to determine their respective hosts, particularly for emerging ones that pose a potential menace to the welfare of both human and animal ...

    Authors: Zhaoyan Ming, Xiangjun Chen, Shunlong Wang, Hong Liu, Zhiming Yuan, Minghui Wu and Han Xia
    Citation: BMC Bioinformatics 2023 24:455
  31. Genomic sequencing reads compressors are essential for balancing high-throughput sequencing short reads generation speed, large-scale genomic data sharing, and infrastructure storage expenditure. However, most...

    Authors: Hui Sun, Yingfeng Zheng, Haonan Xie, Huidong Ma, Xiaoguang Liu and Gang Wang
    Citation: BMC Bioinformatics 2023 24:454
  32. Genomic insights in settings where tumour sample sizes are limited to just hundreds or even tens of cells hold great clinical potential, but also present significant technical challenges. We previously develop...

    Authors: Joel Nulsen, Nosheen Hussain, Aws Al-Deka, Jason Yap, Khalil Uddin, Christopher Yau and Ahmed Ashour Ahmed
    Citation: BMC Bioinformatics 2023 24:453

    The Correction to this article has been published in BMC Bioinformatics 2024 25:20

  33. The identification of essential proteins is of great significance in biology and pathology. However, protein–protein interaction (PPI) data obtained through high-throughput technology include a high number of ...

    Authors: He Zhao, Guixia Liu and Xintian Cao
    Citation: BMC Bioinformatics 2023 24:452
  34. As an important task in bioinformatics, clustering analysis plays a critical role in understanding the functional mechanisms of many complex biological systems, which can be modeled as biological networks. The...

    Authors: Dong-Xu Li, Peng Zhou, Bo-Wei Zhao, Xiao-Rui Su, Guo-Dong Li, Jun Zhang, Peng-Wei Hu and Lun Hu
    Citation: BMC Bioinformatics 2023 24:451
  35. Acute myeloid leukaemia (AML) is characterised by the malignant accumulation of myeloid progenitors with a high recurrence rate after chemotherapy. Blasts (leukaemia cells) exhibit a complete myeloid different...

    Authors: Nan Shao, Chenshuo Ren, Tianyuan Hu, Dianbing Wang, Xiaofan Zhu, Min Li, Tao Cheng, Yingchi Zhang and Xian-En Zhang
    Citation: BMC Bioinformatics 2023 24:450
  36. Protein ubiquitination is a critical post-translational modification (PTMs) involved in numerous cellular processes. Identifying ubiquitination sites (Ubi-sites) on proteins offers valuable insights into their...

    Authors: Mahdi Pourmirzaei, Shahin Ramazi, Farzaneh Esmaili, Seyedehsamaneh Shojaeilangari and Abdollah Allahvardi
    Citation: BMC Bioinformatics 2023 24:449
  37. The discovery of anticancer drug combinations is a crucial work of anticancer treatment. In recent years, pre-screening drug combinations with synergistic effects in a large-scale search space adopting computa...

    Authors: Danyi Chen, Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Qi Liu and Qin Liu
    Citation: BMC Bioinformatics 2023 24:448
  38. Aptamers, which are biomaterials comprised of single-stranded DNA/RNA that form tertiary structures, have significant potential as next-generation materials, particularly for drug discovery. The systematic evo...

    Authors: Incheol Shin, Keumseok Kang, Juseong Kim, Sanghun Sel, Jeonghoon Choi, Jae-Wook Lee, Ho Young Kang and Giltae Song
    Citation: BMC Bioinformatics 2023 24:447
  39. Galaxy is a web-based open-source platform for scientific analyses. Researchers use thousands of high-quality tools and workflows for their respective analyses in Galaxy. Tool recommender system predicts a col...

    Authors: Anup Kumar, Björn Grüning and Rolf Backofen
    Citation: BMC Bioinformatics 2023 24:446
  40. Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which is one of the main obstacles for the development of effective cancer treatments. Such t...

    Authors: Valentina Nale, Alice Chiodi, Noemi Di Nanni, Ingrid Cifola, Marco Moscatelli, Cinzia Cocola, Matteo Gnocchi, Eleonora Piscitelli, Ada Sula, Ileana Zucchi, Rolland Reinbold, Luciano Milanesi, Alessandra Mezzelani, Paride Pelucchi and Ettore Mosca
    Citation: BMC Bioinformatics 2023 24:445
  41. For ligand binding prediction, it is crucial for molecular docking programs to integrate template-based modeling with a precise scoring function. Here, we proposed the CoDock-Ligand docking method that combine...

    Authors: Mingwei Pang, Wangqiu He, Xufeng Lu, Yuting She, Liangxu Xie, Ren Kong and Shan Chang
    Citation: BMC Bioinformatics 2023 24:444

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