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  1. Stochastic optical reconstruction microscopy (STORM), a super-resolution microscopy technique based on single-molecule localizations, has become popular to characterize sub-diffraction limit targets. However, ...

    Authors: Øystein Øvrebø, Miina Ojansivu, Kimmo Kartasalo, Hanna M. G. Barriga, Petter Ranefall, Margaret N. Holme and Molly M. Stevens
    Citation: BMC Bioinformatics 2023 24:237
  2. Biotite is a program library for sequence and structural bioinformatics written for the Python programming language. It implements widely used computational methods into a consistent and accessible package. Th...

    Authors: Patrick Kunzmann, Tom David Müller, Maximilian Greil, Jan Hendrik Krumbach, Jacob Marcel Anter, Daniel Bauer, Faisal Islam and Kay Hamacher
    Citation: BMC Bioinformatics 2023 24:236
  3. Identifying the locations of gene breakpoints between species of different taxonomic groups can provide useful insights into the underlying evolutionary processes. Given the exact locations of their genes, the...

    Authors: Lisa Fiedler, Matthias Bernt, Martin Middendorf and Peter F. Stadler
    Citation: BMC Bioinformatics 2023 24:235
  4. Long non-coding RNA (lncRNA) closely associates with numerous biological processes, and with many diseases. Therefore, lncRNA-disease association prediction helps obtain relevant biological information and und...

    Authors: Hua Zhong, Jing Luo, Lin Tang, Shicheng Liao, Zhonghao Lu, Guoliang Lin, Robert W. Murphy and Lin Liu
    Citation: BMC Bioinformatics 2023 24:234
  5. Recent epidemic outbreaks such as the SARS-CoV-2 pandemic and the mpox outbreak in 2022 have demonstrated the value of genomic sequencing data for tracking the origin and spread of pathogens. Laboratories arou...

    Authors: Chaoran Chen, Alexander Taepper, Fabian Engelniederhammer, Jonas Kellerer, Cornelius Roemer and Tanja Stadler
    Citation: BMC Bioinformatics 2023 24:232
  6. When it was first introduced in 2000, reverse vaccinology was defined as an in silico approach that begins with the pathogen's genomic sequence. It concludes with a list of potential proteins with a possible, ...

    Authors: Giulia Russo, Elena Crispino, Avisa Maleki, Valentina Di Salvatore, Filippo Stanco and Francesco Pappalardo
    Citation: BMC Bioinformatics 2023 24:231
  7. Clinical studies have shown that miRNAs are closely related to human health. The study of potential associations between miRNAs and diseases will contribute to a profound understanding of the mechanism of dise...

    Authors: Min Chen, Yingwei Deng, Zejun Li, Yifan Ye and Ziyi He
    Citation: BMC Bioinformatics 2023 24:229
  8. Comutation plot is a widely used visualization method to deliver a global view of the mutation landscape of large-scale genomic studies. Current tools for creating comutation plot are either offline packages t...

    Authors: Qiaonan Duan, Weiyi Wang, Feiling Feng, Xiaoqing Jiang, Hao Chen, Dadong Zhang and Tongyi Zhang
    Citation: BMC Bioinformatics 2023 24:226
  9. N6-methyladenosine (m6A) modification is involved in tumorigenesis and progression as well as closely correlated with stem cell differentiation and pluripotency. Moreover, tumor progression includes the acquis...

    Authors: Guihua Tang, Jianqiao Peng, Longwei Huo and Wen Yin
    Citation: BMC Bioinformatics 2023 24:225
  10. As genome sequencing becomes better integrated into scientific research, government policy, and personalized medicine, the primary challenge for researchers is shifting from generating raw data to analyzing th...

    Authors: Kyle A. O’Connell, Zelaikha B. Yosufzai, Ross A. Campbell, Collin J. Lobb, Haley T. Engelken, Laura M. Gorrell, Thad B. Carlson, Josh J. Catana, Dina Mikdadi, Vivien R. Bonazzi and Juergen A. Klenk
    Citation: BMC Bioinformatics 2023 24:221
  11. CRISPR/Cas is an efficient genome editing system that has been widely used for functional genetic studies and exhibits high potential in biomedical translational applications. Indel analysis has thus become on...

    Authors: Huancheng Fu, Ce Shan, Fanchen Kang, Ling Yu, Zhonghan Li and Yike Yin
    Citation: BMC Bioinformatics 2023 24:219
  12. Hepatocellular carcinoma (HCC) is the fifth most frequently diagnosed malignancy and the third leading cause of cancer death globally. T cells are significantly correlated with the progression, therapy and pro...

    Authors: Xu Chen, Chuang Peng, Yu Chen, Bai Ding, Sulai Liu, Yinghui Song, Yuhang Li, Bo Sun and Ranzhiqiang Yang
    Citation: BMC Bioinformatics 2023 24:216
  13. There is a pressing need for improved methods to identify effective therapeutics for diseases. Many computational approaches have been developed to repurpose existing drugs to meet this need. However, these to...

    Authors: Belinda B. Garana, James H. Joly, Alireza Delfarah, Hyunjun Hong and Nicholas A. Graham
    Citation: BMC Bioinformatics 2023 24:215
  14. Boolean Networks (BNs) are a popular dynamical model in biology where the state of each component is represented by a variable taking binary values that express, for instance, activation/deactivation or high/l...

    Authors: Georgios A. Argyris, Alberto Lluch Lafuente, Mirco Tribastone, Max Tschaikowski and Andrea Vandin
    Citation: BMC Bioinformatics 2023 24(Suppl 1):212

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

  15. The microbiome plays a key role in the health of the human body. Interest often lies in finding features of the microbiome, alongside other covariates, which are associated with a phenotype of interest. One im...

    Authors: Darren A. V. Scott, Ernest Benavente, Julian Libiseller-Egger, Dmitry Fedorov, Jody Phelan, Elena Ilina, Polina Tikhonova, Alexander Kudryavstev, Julia Galeeva, Taane Clark and Alex Lewin
    Citation: BMC Bioinformatics 2023 24:210
  16. Cluster and transmission analysis utilising pairwise SNP distance are increasingly used in genomic epidemiological studies. However, current methods are often challenging to install and use, and lack interacti...

    Authors: Budi Permana, Scott A. Beatson and Brian M. Forde
    Citation: BMC Bioinformatics 2023 24:209
  17. Better understanding the transcriptomic response produced by a compound perturbing its targets can shed light on the underlying biological processes regulated by the compound. However, establishing the relatio...

    Authors: Chloe Engler Hart, Daniel Ence, David Healey and Daniel Domingo-Fernández
    Citation: BMC Bioinformatics 2023 24:207
  18. In the sporadic form of amyotrophic lateral sclerosis (ALS), the pathogenicity of rare variants in the causative genes characterizing the familial form remains largely unknown. To predict the pathogenicity of ...

    Authors: Yuya Hatano, Tomohiko Ishihara and Osamu Onodera
    Citation: BMC Bioinformatics 2023 24:206
  19. Circular RNAs (circRNAs) are covalently closed-loop RNAs with critical regulatory roles in cells. Tens of thousands of circRNAs have been unveiled due to the recent advances in high throughput RNA sequencing t...

    Authors: Fedor Sharko, Golam Rbbani, Prabhugouda Siriyappagouder, Joost A. M. Raeymaekers, Jorge Galindo-Villegas, Artem Nedoluzhko and Jorge M. O. Fernandes
    Citation: BMC Bioinformatics 2023 24:205
  20. In the ten years since the initial publication of the RenSeq protocol, the method has proved to be a powerful tool for studying disease resistance in plants and providing target genes for breeding programmes. ...

    Authors: Thomas M. Adams, Moray Smith, Yuhan Wang, Lynn H. Brown, Micha M. Bayer and Ingo Hein
    Citation: BMC Bioinformatics 2023 24:204
  21. A major current focus in the analysis of protein–protein interaction (PPI) data is how to identify essential proteins. As massive PPI data are available, this warrants the design of efficient computing methods...

    Authors: Peiqiang Liu, Chang Liu, Yanyan Mao, Junhong Guo, Fanshu Liu, Wangmin Cai and Feng Zhao
    Citation: BMC Bioinformatics 2023 24:203
  22. Cysteine-dense peptides (CDPs) are an attractive pharmaceutical scaffold that display extreme biochemical properties, low immunogenicity, and the ability to bind targets with high affinity and selectivity. Whi...

    Authors: Sébastien Ouellet, Larissa Ferguson, Angus Z. Lau and Tony K. Y. Lim
    Citation: BMC Bioinformatics 2023 24:200
  23. There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transpa...

    Authors: Magdalena Wysocka, Oskar Wysocki, Marie Zufferey, Dónal Landers and André Freitas
    Citation: BMC Bioinformatics 2023 24:198
  24. Large-scale population variant data is often used to filter and aid interpretation of variant calls in a single sample. These approaches do not incorporate population information directly into the process of v...

    Authors: Nae-Chyun Chen, Alexey Kolesnikov, Sidharth Goel, Taedong Yun, Pi-Chuan Chang and Andrew Carroll
    Citation: BMC Bioinformatics 2023 24:197
  25. Atherosclerosis is the common pathological basis for many cardiovascular and cerebrovascular diseases. The purpose of this study is to identify the diagnostic biomarkers related to atherosclerosis through mach...

    Authors: Li Rao, Bo Peng and Tao Li
    Citation: BMC Bioinformatics 2023 24:196
  26. Genome-wide association studies (GWAS) seek to identify single nucleotide polymorphisms (SNPs) that cause observed phenotypes. However, with highly correlated SNPs, correlated observations, and the number of S...

    Authors: Jacob Williams, Shuangshuang Xu and Marco A. R. Ferreira
    Citation: BMC Bioinformatics 2023 24:194
  27. In a previous paper, we classified populated HLA class I alleles into supertypes and subtypes based on the similarity of 3D landscape of peptide binding grooves, using newly defined structure distance metric a...

    Authors: Yue Shen, Jerry M. Parks and Jeremy C. Smith
    Citation: BMC Bioinformatics 2023 24:189

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