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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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

  15. 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
  16. 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
  17. 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

  18. 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
  19. 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
  20. 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
  21. 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

  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. Drug repurposing is an exciting field of research toward recognizing a new FDA-approved drug target for the treatment of a specific disease. It has received extensive attention regarding the tedious, time-cons...

    Authors: Ramin Amiri, Jafar Razmara, Sepideh Parvizpour and Habib Izadkhah
    Citation: BMC Bioinformatics 2023 24:442
  32. Correlation metrics are widely utilized in genomics analysis and often implemented with little regard to assumptions of normality, homoscedasticity, and independence of values. This is especially true when com...

    Authors: Cullen Roth, Vrinda Venu, Vanessa Job, Nicholas Lubbers, Karissa Y. Sanbonmatsu, Christina R. Steadman and Shawn R. Starkenburg
    Citation: BMC Bioinformatics 2023 24:441
  33. Single-cell RNA sequencing (scRNA-seq) is a powerful tool for investigating cell abundance changes during tissue regeneration and remodeling processes. Differential cell abundance supports the initial clusteri...

    Authors: Juan Domingo, Oleksandra Kutsyr-Kolesnyk, Teresa Leon, Raul Perez-Moraga, Guillermo Ayala and Beatriz Roson
    Citation: BMC Bioinformatics 2023 24:440
  34. Cancer is a collection of diseases caused by the deregulation of cell processes, which is triggered by somatic mutations. The search for patterns in somatic mutations, known as mutational signatures, is a grow...

    Authors: Rodrigo D. Drummond, Alexandre Defelicibus, Mathilde Meyenberg, Renan Valieris, Emmanuel Dias-Neto, Rafael A. Rosales and Israel Tojal da Silva
    Citation: BMC Bioinformatics 2023 24:439
  35. Use of alternative non-Saccharomyces yeasts in wine and beer brewing has gained more attention the recent years. This is both due to the desire to obtain a wider variety of flavours in the product and to reduce t...

    Authors: Jakob P. Pettersen, Sandra Castillo, Paula Jouhten and Eivind Almaas
    Citation: BMC Bioinformatics 2023 24:438
  36. Biclustering of biologically meaningful binary information is essential in many applications related to drug discovery, like protein–protein interactions and gene expressions. However, for robust performance i...

    Authors: Brijesh K. Sriwastava, Anup Kumar Halder, Subhadip Basu and Tapabrata Chakraborti
    Citation: BMC Bioinformatics 2023 24:435
  37. Determining a protein’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estima...

    Authors: Orly Avraham, Tomer Tsaban, Ziv Ben-Aharon, Linoy Tsaban and Ora Schueler-Furman
    Citation: BMC Bioinformatics 2023 24:433
  38. Deep generative models naturally become nonlinear dimension reduction tools to visualize large-scale datasets such as single-cell RNA sequencing datasets for revealing latent grouping patterns or identifying o...

    Authors: Gwangwoo Kim and Hyonho Chun
    Citation: BMC Bioinformatics 2023 24:432
  39. Liquid chromatography–mass spectrometry is widely used in untargeted metabolomics for composition profiling. In multi-run analysis scenarios, features of each run are aligned into consensus features by feature...

    Authors: Ruimin Wang, Miaoshan Lu, Shaowei An, Jinyin Wang and Changbin Yu
    Citation: BMC Bioinformatics 2023 24:431

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