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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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

  10. 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
  11. 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

  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. Prediction of drug–target interaction (DTI) is an essential step for drug discovery and drug reposition. Traditional methods are mostly time-consuming and labor-intensive, and deep learning-based methods addre...

    Authors: Ying Qian, Xinyi Li, Jian Wu and Qian Zhang
    Citation: BMC Bioinformatics 2023 24:323
  32. The impact of a perturbation, over-expression, or repression of a key node on an organism, can be modelled based on a regulatory and/or metabolic network. Integration of these two networks could improve our gl...

    Authors: Sophie Le Bars, Mathieu Bolteau, Jérémie Bourdon and Carito Guziolowski
    Citation: BMC Bioinformatics 2023 24(Suppl 1):321

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

  33. Quantitative analysis of neurite growth and morphology is essential for understanding the determinants of neural development and regeneration, however, it is complicated by the labor-intensive process of measu...

    Authors: Joseph T. Vecchi, Sean Mullan, Josue A. Lopez, Madeline Rhomberg, Annamarie Yamamoto, Annabelle Hallam, Amy Lee, Milan Sonka and Marlan R. Hansen
    Citation: BMC Bioinformatics 2023 24:320
  34. Single-cell RNA sequencing (scRNA-seq) technology has enabled assessment of transcriptome-wide changes at single-cell resolution. Due to the heterogeneity in environmental exposure and genetic background acros...

    Authors: Yunqing Liu, Jiayi Zhao, Taylor S. Adams, Ningya Wang, Jonas C. Schupp, Weimiao Wu, John E. McDonough, Geoffrey L. Chupp, Naftali Kaminski, Zuoheng Wang and Xiting Yan
    Citation: BMC Bioinformatics 2023 24:318
  35. Transposable elements (TEs) are short, mobile DNA elements that are known to play important roles in the genomes of many eukaryotic species. The identification and categorization of these elements is a critica...

    Authors: Shelvasha Burkes-Patton, Elizabeth A. Cooper and Jessica Schlueter
    Citation: BMC Bioinformatics 2023 24:317
  36. Biologists are faced with an ever-changing array of complex software tools with steep learning curves, often run on High Performance Computing platforms. To resolve the tradeoff between analytical sophisticati...

    Authors: Graham Alvare, Abiel Roche-Lima and Brian Fristensky
    Citation: BMC Bioinformatics 2023 24:316

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