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  1. 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
  2. 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
  3. 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

  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. Gastric cancer is the third leading cause of death from cancer worldwide and has a poor prognosis. Practical risk scores and prognostic models for gastric cancer are lacking. While immunotherapy has succeeded ...

    Authors: YaLing Liu, Dan Li, Yong Chen, YiJuan Liu, YiJuan Lin, XunRu Huang, Ting Wu, ChengDang Wang and Jian Ding
    Citation: BMC Bioinformatics 2023 24:191
  17. 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
  18. The limited knowledge of miRNA–lncRNA interactions is considered as an obstruction of revealing the regulatory mechanism. Accumulating evidence on Human diseases indicates that the modulation of gene expression h...

    Authors: Leon Wong, Lei Wang, Zhu-Hong You, Chang-An Yuan, Yu-An Huang and Mei-Yuan Cao
    Citation: BMC Bioinformatics 2023 24:188
  19. The spectrum of mutations in a collection of cancer genomes can be described by a mixture of a few mutational signatures. The mutational signatures can be found using non-negative matrix factorization (NMF). T...

    Authors: Marta Pelizzola, Ragnhild Laursen and Asger Hobolth
    Citation: BMC Bioinformatics 2023 24:187
  20. Alimentary tract malignancies (ATM) caused nearly one-third of all tumor-related death. Cuproptosis is a newly identified cell death pattern. The role of cuproptosis-associated lncRNAs in ATM is unknown.

    Authors: Yangyang Xie, Xue Song, Danwei Du, Zhongkai Ni and Hai Huang
    Citation: BMC Bioinformatics 2023 24:184
  21. Despite the availability of batch effect correcting algorithms (BECA), no comprehensive tool that combines batch correction and evaluation of the results exists for microbiome datasets. This work outlines the ...

    Authors: Michael Olbrich, Axel Künstner and Hauke Busch
    Citation: BMC Bioinformatics 2023 24:182
  22. Co-localized sets of genes that encode specialized functions are common across microbial genomes and occur in genomes of larger eukaryotes as well. Important examples include Biosynthetic Gene Clusters (BGCs) ...

    Authors: Matthias van den Belt, Cameron Gilchrist, Thomas J. Booth, Yit-Heng Chooi, Marnix H. Medema and Mohammad Alanjary
    Citation: BMC Bioinformatics 2023 24:181
  23. Large-scale multi-ethnic DNA sequencing data is increasingly available owing to decreasing cost of modern sequencing technologies. Inference of the population structure with such sequencing data is fundamental...

    Authors: Jinghan Yang, Yuyang Xu, Minhao Yao, Gao Wang and Zhonghua Liu
    Citation: BMC Bioinformatics 2023 24:180
  24. The prediction of potentially pathogenic variant combinations in patients remains a key task in the field of medical genetics for the understanding and detection of oligogenic/multilocus diseases. Models tailo...

    Authors: Nassim Versbraegen, Barbara Gravel, Charlotte Nachtegael, Alexandre Renaux, Emma Verkinderen, Ann Nowé, Tom Lenaerts and Sofia Papadimitriou
    Citation: BMC Bioinformatics 2023 24:179
  25. The field of epigenomics holds great promise in understanding and treating disease with advances in machine learning (ML) and artificial intelligence being vitally important in this pursuit. Increasingly, rese...

    Authors: Trevor Doherty, Emma Dempster, Eilis Hannon, Jonathan Mill, Richie Poulton, David Corcoran, Karen Sugden, Ben Williams, Avshalom Caspi, Terrie E. Moffitt, Sarah Jane Delany and Therese M. Murphy
    Citation: BMC Bioinformatics 2023 24:178
  26. Pyroptosis is closely related to cancer prognosis. In this study, we tried to construct an individualized prognostic risk model for hepatocellular carcinoma (HCC) based on within-sample relative expression ord...

    Authors: Tong Wu, Na Li, Fengyuan Luo, Zhihong Chen, Liyuan Ma, Tao Hu, Guini Hong and Hongdong Li
    Citation: BMC Bioinformatics 2023 24:176
  27. Complex diseases such as neurodevelopmental disorders (NDDs) exhibit multiple etiologies. The multi-etiological nature of complex-diseases emerges from distinct but functionally similar group of genes. Differe...

    Authors: Muhammad Asif, Hugo F. M. C. Martiniano, Andre Lamurias, Samina Kausar and Francisco M. Couto
    Citation: BMC Bioinformatics 2023 24:171
  28. Genome-wide tests, including genome-wide association studies (GWAS) of germ-line genetic variants, driver tests of cancer somatic mutations, and transcriptome-wide association tests of RNAseq data, carry a hig...

    Authors: Jitong Cai, Jianan Zhan, Dan E. Arking and Joel S. Bader
    Citation: BMC Bioinformatics 2023 24:170
  29. Identification of the cancer subtype plays a crucial role to provide an accurate diagnosis and proper treatment to improve the clinical outcomes of patients. Recent studies have shown that DNA methylation is o...

    Authors: Joung Min Choi, Chaelin Park and Heejoon Chae
    Citation: BMC Bioinformatics 2023 24:168

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