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  1. Identifying drug–target interactions (DTIs) plays a key role in drug development. Traditional wet experiments to identify DTIs are costly and time consuming. Effective computational methods to predict DTIs are...

    Authors: Junjun Zhang and Minzhu Xie
    Citation: BMC Bioinformatics 2023 24:375
  2. The relationship between the sequence of a protein, its structure, and the resulting connection between its structure and function, is a foundational principle in biological science. Only recently has the comp...

    Authors: F. Adriaan Lategan, Caroline Schreiber and Hugh G. Patterton
    Citation: BMC Bioinformatics 2023 24:373
  3. The rising risk of diabetes, particularly in emerging countries, highlights the importance of early detection. Manual prediction can be a challenging task, leading to the need for automatic approaches. The maj...

    Authors: Kiran Kumar Patro, Jaya Prakash Allam, Umamaheswararao Sanapala, Chaitanya Kumar Marpu, Nagwan Abdel Samee, Maali Alabdulhafith and Pawel Plawiak
    Citation: BMC Bioinformatics 2023 24:372
  4. Shotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases,...

    Authors: Ignas Rumbavicius, Trine B. Rounge and Torbjørn Rognes
    Citation: BMC Bioinformatics 2023 24:371
  5. Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequenci...

    Authors: Eric Kofman, Brian Yee, Hugo C. Medina-Munoz and Gene W. Yeo
    Citation: BMC Bioinformatics 2023 24:370
  6. Liquid biopsy is a minimally-invasive method of sampling bodily fluids, capable of revealing evidence of cancer. The distribution of cell-free DNA (cfDNA) fragment lengths has been shown to differ between heal...

    Authors: Mathias Cardner, Francesco Marass, Erika Gedvilaite, Julie L. Yang, Dana W. Y. Tsui and Niko Beerenwinkel
    Citation: BMC Bioinformatics 2023 24:368
  7. Obtaining accurate drug–target binding affinity (DTA) information is significant for drug discovery and drug repositioning. Although some methods have been proposed for predicting DTA, the features of proteins...

    Authors: Haixia Zhai, Hongli Hou, Junwei Luo, Xiaoyan Liu, Zhengjiang Wu and Junfeng Wang
    Citation: BMC Bioinformatics 2023 24:367
  8. We consider the problem of finding an accurate representation of neuron shapes, extracting sub-cellular features, and classifying neurons based on neuron shapes. In neuroscience research, the skeleton represen...

    Authors: Jiaxiang Jiang, Michael Goebel, Cezar Borba, William Smith and B. S. Manjunath
    Citation: BMC Bioinformatics 2023 24:366
  9. Echocardiographic interpretation during the prenatal or postnatal period is important for diagnosing cardiac septal abnormalities. However, manual interpretation can be time consuming and subject to human erro...

    Authors: Siti Nurmaini, Ade Iriani Sapitri, Bambang Tutuko, Muhammad Naufal Rachmatullah, Dian Palupi Rini, Annisa Darmawahyuni, Firdaus Firdaus, Satria Mandala, Ria Nova and Nuswil Bernolian
    Citation: BMC Bioinformatics 2023 24:365
  10. The central biological clock governs numerous facets of mammalian physiology, including sleep, metabolism, and immune system regulation. Understanding gene regulatory relationships is crucial for unravelling t...

    Authors: Shuwen Hu, Yi Jing, Tao Li, You-Gan Wang, Zhenyu Liu, Jing Gao and Yu-Chu Tian
    Citation: BMC Bioinformatics 2023 24:362
  11. Membrane proteins are critical mediators for tumor progression and present enormous therapeutic potentials. Although gene profiling can identify their cancer-specific signatures, systematic correlations betwee...

    Authors: Lina Ma, Sitao Zhang, Qi Liang, Wenting Huang, Hui Wang, Emily Pan, Ping Xu, Shuguang Zhang, Fei Tao, Jin Tang and Rui Qing
    Citation: BMC Bioinformatics 2023 24:360
  12. Helicobacter pylori is a prominent causative agent of gastric ulceration, gastric adenocarcinoma and gastric lymphoma and have been categorised as a group 1 carcinogen by WHO. The treatment of H. pylori with prot...

    Authors: Anand K. Keshri, Rimanpreet Kaur, Suraj S. Rawat, Naina Arora, Rajan K. Pandey, Bajarang V. Kumbhar, Amit Mishra, Shweta Tripathi and Amit Prasad
    Citation: BMC Bioinformatics 2023 24:358
  13. Tyrosinase is an enzyme involved in melanin production in the skin. Several hyperpigmentation disorders involve the overproduction of melanin and instability of tyrosinase activity resulting in darker, discolo...

    Authors: Phasit Charoenkwan, Sasikarn Kongsompong, Nalini Schaduangrat, Pramote Chumnanpuen and Watshara Shoombuatong
    Citation: BMC Bioinformatics 2023 24:356
  14. Genome-wide association studies (GWAS) have identified hundreds of genetic loci associated with kidney function. By combining these findings with post-GWAS information (e.g., statistical fine-mapping to identi...

    Authors: Kira J. Stanzick, Klaus J. Stark, Mathias Gorski, Johannes Schödel, René Krüger, Florian Kronenberg, Richard Warth, Iris M. Heid and Thomas W. Winkler
    Citation: BMC Bioinformatics 2023 24:355
  15. Plummeting DNA sequencing cost in recent years has enabled genome sequencing projects to scale up by several orders of magnitude, which is transforming genomics into a highly data-intensive field of research. ...

    Authors: Amira Al-Aamri, Syafiq Kamarul Azman, Gihan Daw Elbait, Habiba Alsafar and Andreas Henschel
    Citation: BMC Bioinformatics 2023 24:354
  16. We published a paper in BMC Bioinformatics comprehensively evaluating the performance of structural variation (SV) calling with long-read SV detection methods based on simulated error-prone long-read data unde...

    Authors: Tao Jiang, Shiqi Liu and Hongzhe Guo
    Citation: BMC Bioinformatics 2023 24:352

    The original article was published in BMC Bioinformatics 2023 24:350

  17. Cross-linking mass spectrometry (XL-MS) is a powerful technique for detecting protein–protein interactions (PPIs) and modeling protein structures in a high-throughput manner. In XL-MS experiments, proteins are...

    Authors: Chen Zhou, Shuaijian Dai, Shengzhi Lai, Yuanqiao Lin, Xuechen Zhang, Ning Li and Weichuan Yu
    Citation: BMC Bioinformatics 2023 24:351
  18. A recent paper by Jiang et al. in BMC Bioinformatics presented guidelines on long-read sequencing settings for structural variation (SV) calling, and benchmarked the performance of various SV calling tools, inclu...

    Authors: Cheng Yong Tham and Touati Benoukraf
    Citation: BMC Bioinformatics 2023 24:350

    The Matters Arising to this article has been published in BMC Bioinformatics 2023 24:352

  19. Quantifying cell-type abundance in bulk tissue RNA-sequencing enables researchers to better understand complex systems. Newer deconvolution methodologies, such as MuSiC, use cell-type signatures derived from s...

    Authors: Nicholas K. O’Neill, Thor D. Stein, Junming Hu, Habbiburr Rehman, Joshua D. Campbell, Masanao Yajima, Xiaoling Zhang and Lindsay A. Farrer
    Citation: BMC Bioinformatics 2023 24:349
  20. Body composition (BC) is an important factor in determining the risk of type 2-diabetes and cardiovascular disease. Computed tomography (CT) is a useful imaging technique for studying BC, however manual segmen...

    Authors: Nouman Ahmad, Robin Strand, Björn Sparresäter, Sambit Tarai, Elin Lundström, Göran Bergström, Håkan Ahlström and Joel Kullberg
    Citation: BMC Bioinformatics 2023 24:346
  21. Understanding gene expression processes necessitates the accurate classification and identification of transcription factors, which is supported by high-throughput sequencing technologies. However, these techn...

    Authors: Jidong Zhang, Bo Liu, Jiahui Wu, Zhihan Wang and Jianqiang Li
    Citation: BMC Bioinformatics 2023 24:345
  22. Understanding the Mechanism of Action (MoA) of a compound is an often challenging but equally crucial aspect of drug discovery that can help improve both its efficacy and safety. Computational methods to aid M...

    Authors: Layla Hosseini-Gerami, Rosa Hernansaiz Ballesteros, Anika Liu, Howard Broughton, David Andrew Collier and Andreas Bender
    Citation: BMC Bioinformatics 2023 24:344
  23. Genome-wide association studies (GWASes) aim to identify single nucleotide polymorphisms (SNPs) associated with a given phenotype. A common approach for the analysis of GWAS is single marker analysis (SMA) bas...

    Authors: Shuangshuang Xu, Jacob Williams and Marco A. R. Ferreira
    Citation: BMC Bioinformatics 2023 24:343
  24. Mitochondria are the cell organelles that produce most of the chemical energy required to power the cell's biochemical reactions. Despite being a part of a eukaryotic host cell, the mitochondria contain a sepa...

    Authors: Nirmal Singh Mahar, Rohit Satyam, Durai Sundar and Ishaan Gupta
    Citation: BMC Bioinformatics 2023 24:341
  25. Bisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generat...

    Authors: Nicholas J. Eagles, Richard Wilton, Andrew E. Jaffe and Leonardo Collado-Torres
    Citation: BMC Bioinformatics 2023 24:340
  26. The human gut microbiome (HGM), consisting of trillions of microorganisms, is crucial to human health. Adverse drug use is one of the most important causes of HGM disorder. Thus, it is necessary to identify dr...

    Authors: Binyou Wang, Jianmin Guo, Xiaofeng Liu, Yang Yu, Jianming Wu and Yiwei Wang
    Citation: BMC Bioinformatics 2023 24:338
  27. Residue Interaction Networks (RINs) map the crystallographic description of a protein into a graph, where amino acids are represented as nodes and non-covalent bonds as edges. Determination and visualization o...

    Authors: Alvise Spanò, Lorenzo Fanton, Davide Pizzolato, Jacopo Moi, Francesco Vinci, Alberto Pesce, Cedrix J. Dongmo Foumthuim, Achille Giacometti and Marta Simeoni
    Citation: BMC Bioinformatics 2023 24:336
  28. Circular RNA (CircRNA) is a type of non-coding RNAs in which both ends are covalently linked. Researchers have demonstrated that many circRNAs can act as biomarkers of diseases. However, traditional experiment...

    Authors: Shiyang Liang, Siwei Liu, Junliang Song, Qiang Lin, Shihong Zhao, Shuaixin Li, Jiahui Li, Shangsong Liang and Jingjie Wang
    Citation: BMC Bioinformatics 2023 24:335
  29. To present an approach that autonomously identifies and selects a self-selective optimal target for the purpose of enhancing learning efficiency to segment infected regions of the lung from chest computed tomo...

    Authors: Peng Du, Xiaofeng Niu, Xukun Li, Chiqing Ying, Yukun Zhou, Chang He, Shuangzhi Lv, Xiaoli Liu, Weibo Du and Wei Wu
    Citation: BMC Bioinformatics 2023 24:332
  30. Over the past several decades, metrics have been defined to assess the quality of various types of models and to compare their performance depending on their capacity to explain the variance found in real-life...

    Authors: Evgueni Jacob, Angélique Perrillat-Mercerot, Jean-Louis Palgen, Adèle L’Hostis, Nicoletta Ceres, Jean-Pierre Boissel, Jim Bosley, Claudio Monteiro and Riad Kahoul
    Citation: BMC Bioinformatics 2023 24:331
  31. The study of de novo variation is important for assessing biological characteristics of new variation and for studies related to human phenotypes. Software programs exist to call de novo variants and programs ...

    Authors: Tychele N. Turner
    Citation: BMC Bioinformatics 2023 24:330
  32. Alcohol use disorder (AUD) causes significant morbidity, mortality, and injuries. According to reports, approximately 5% of all registered deaths in Denmark could be due to AUD. The problem is compounded by th...

    Authors: Ali Ebrahimi, Uffe Kock Wiil, Ruben Baskaran, Abdolrahman Peimankar, Kjeld Andersen and Anette Søgaard Nielsen
    Citation: BMC Bioinformatics 2023 24:329
  33. Longitudinal data on key cancer outcomes for clinical research, such as response to treatment and disease progression, are not captured in standard cancer registry reporting. Manual extraction of such outcomes...

    Authors: Haitham A. Elmarakeby, Pavel S. Trukhanov, Vidal M. Arroyo, Irbaz Bin Riaz, Deborah Schrag, Eliezer M. Van Allen and Kenneth L. Kehl
    Citation: BMC Bioinformatics 2023 24:328
  34. The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data i...

    Authors: Tomáš Brůna, Heng Li, Joseph Guhlin, Daniel Honsel, Steffen Herbold, Mario Stanke, Natalia Nenasheva, Matthis Ebel, Lars Gabriel and Katharina J. Hoff
    Citation: BMC Bioinformatics 2023 24:327
  35. Here we present scSNPdemux, a sample demultiplexing pipeline for single-cell RNA sequencing data using natural genetic variations in humans. The pipeline requires alignment files from Cell Ranger (10× Genomics...

    Authors: John K. L. Wong, Lena Jassowicz, Christel Herold-Mende, Martina Seiffert, Jan-Philipp Mallm, Peter Lichter and Marc Zapatka
    Citation: BMC Bioinformatics 2023 24:326
  36. There are countless possibilities for drug combinations, which makes it expensive and time-consuming to rely solely on clinical trials to determine the effects of each possible drug combination. In order to sc...

    Authors: Jing Chen, Lianlian Wu, Kunhong Liu, Yong Xu, Song He and Xiaochen Bo
    Citation: BMC Bioinformatics 2023 24:325
  37. Understanding the impact of gene interactions on disease phenotypes is increasingly recognised as a crucial aspect of genetic disease research. This trend is reflected by the growing amount of clinical researc...

    Authors: Alexandre Renaux, Chloé Terwagne, Michael Cochez, Ilaria Tiddi, Ann Nowé and Tom Lenaerts
    Citation: BMC Bioinformatics 2023 24:324

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