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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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

  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. Although gene expression data play significant roles in biological and medical studies, their applications are hampered due to the difficulty and high expenses of gathering them through biological experiments....

    Authors: Rongyuan Li, Jingli Wu, Gaoshi Li, Jiafei Liu, Junbo Xuan and Qi Zhu
    Citation: BMC Bioinformatics 2023 24:427
  32. Computational methods of predicting protein stability changes upon missense mutations are invaluable tools in high-throughput studies involving a large number of protein variants. However, they are limited by ...

    Authors: Yesol Sapozhnikov, Jagdish Suresh Patel, F. Marty Ytreberg and Craig R. Miller
    Citation: BMC Bioinformatics 2023 24:426
  33. Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical As...

    Authors: Irena Roterman, Katarzyna Stapor and Leszek Konieczny
    Citation: BMC Bioinformatics 2023 24:425
  34. The causes of many complex human diseases are still largely unknown. Genetics plays an important role in uncovering the molecular mechanisms of complex human diseases. A key step to characterize the genetics o...

    Authors: Yixin Zhang, Wei Liu and Weiliang Qiu
    Citation: BMC Bioinformatics 2023 24:423
  35. Single-stranded nucleic acids (ssNAs) have important biological roles and a high biotechnological potential linked to their ability to bind to numerous molecular targets. This depends on the different spatial ...

    Authors: Thomas Binet, Séverine Padiolleau-Lefèvre, Stéphane Octave, Bérangère Avalle and Irene Maffucci
    Citation: BMC Bioinformatics 2023 24:422
  36. In proteomics, the interpretation of mass spectra representing peptides carrying multiple complex modifications remains challenging, as it is difficult to strike a balance between reasonable execution time, a ...

    Authors: Grégoire Prunier, Mehdi Cherkaoui, Albane Lysiak, Olivier Langella, Mélisande Blein-Nicolas, Virginie Lollier, Emile Benoist, Géraldine Jean, Guillaume Fertin, Hélène Rogniaux and Dominique Tessier
    Citation: BMC Bioinformatics 2023 24:421
  37. The aqueous environment directs the protein folding process towards the generation of micelle-type structures, which results in the exposure of hydrophilic residues on the surface (polarity) and the concentrat...

    Authors: Irena Roterman, Katarzyna Stapor and Leszek Konieczny
    Citation: BMC Bioinformatics 2023 24:418

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