Skip to main content

Articles

Page 5 of 248

  1. 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
    Content type: Software Published on:

  2. 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
    Content type: Research Published on:

  4. 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
    Content type: Research Published on:

  5. 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
    Content type: Software Published on:

  8. 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
    Content type: Database Published on:

  9. 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
    Content type: Research Published on:

  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
    Content type: Research Published on:

  13. 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
    Content type: Research Published on:

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

  14. 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
    Content type: Research Published on:

  15. 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
    Content type: Research Published on:

  16. 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
    Content type: Database Published on:

  17. 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
    Content type: Research Published on:

  20. 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
    Content type: Software Published on:

  21. 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
    Content type: Software Published on:

  22. 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
    Content type: Software Published on:

  23. 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
    Content type: Research Published on:

  25. 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
    Content type: Research Published on:

  27. 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
    Content type: Database Published on:

  28. 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
    Content type: Research Published on:

  29. 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
    Content type: Research Published on:

  30. 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
    Content type: Research Published on:

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

  31. 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
    Content type: Software Published on:

  32. 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
    Content type: Research Published on:

  33. 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
    Content type: Software Published on:

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

  34. 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
    Content type: Research Published on:

  35. 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
    Content type: Research Published on:

  36. 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
    Content type: Software Published on:

  37. 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
    Content type: Software Published on:

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

  38. 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
    Content type: Research Published on:

  39. 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
    Content type: Software Published on:

  40. 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
    Content type: Research Published on:

  41. 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
    Content type: Research Published on:

  42. 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
    Content type: Research Published on:

  43. 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
    Content type: Research Published on:

  44. 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
    Content type: Software Published on:

  45. 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
    Content type: Software Published on:

  46. 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
    Content type: Research Published on:

  48. 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
    Content type: Research Published on:

  49. 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
    Content type: Research Published on:

  50. 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
    Content type: Software Published on:

Featured videos

View featured videos from across the BMC-series journals

Submit manuscript

Annual Journal Metrics

  • 2022 Citation Impact
    3.0 - 2-year Impact Factor
    4.3 - 5-year Impact Factor
    0.938 - SNIP (Source Normalized Impact per Paper)
    1.100 - SJR (SCImago Journal Rank)

    2023 Speed
    19 days submission to first editorial decision for all manuscripts (Median)
    146 days submission to accept (Median)

    2023 Usage
    5,987,678 downloads
    4,858 Altmetric mentions 

Follow

Sign up for article alerts and news from this journal

BMC Bioinformatics

ISSN: 1471-2105

Contact us