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  1. As one of the fundamental problems in bioinformatics, the double digest problem (DDP) focuses on reordering genetic fragments in a proper sequence. Although many algorithms for dealing with the DDP problem wer...

    Authors: Jingwen Suo, Lize Gu, Xingyu Yan, Sijia Yang, Xiaoya Hu and Licheng Wang
    Citation: BMC Bioinformatics 2023 24:34
  2. Whole genome bisulfite sequencing (WGBS), possesses the aptitude to dissect methylation status at the nucleotide-level resolution of 5-methylcytosine (5-mC) on a genome-wide scale. It is a powerful technique f...

    Authors: Qun-ting Lin, Wei Yang, Xin Zhang, Qi-gang Li, Yong-feng Liu, Qin Yan and Lei Sun
    Citation: BMC Bioinformatics 2023 24:33
  3. In the global effort to discover biomarkers for cancer prognosis, prediction tools have become essential resources. TCR (T cell receptor) repertoires contain important features that differentiate healthy contr...

    Authors: Dhiego Souto Andrade, Patrick Terrematte, César Rennó-Costa, Alona Zilberberg and Sol Efroni
    Citation: BMC Bioinformatics 2023 24:32
  4. Nanopore sequencing allows selective sequencing, the ability to programmatically reject unwanted reads in a sample. Selective sequencing has many present and future applications in genomics research and the cl...

    Authors: Anjana Senanayake, Hasindu Gamaarachchi, Damayanthi Herath and Roshan Ragel
    Citation: BMC Bioinformatics 2023 24:31
  5. The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spati...

    Authors: Frédéric Pont, Juan Pablo Cerapio, Pauline Gravelle, Laetitia Ligat, Carine Valle, Emeline Sarot, Marion Perrier, Frédéric Lopez, Camille Laurent, Jean Jacques Fournié and Marie Tosolini
    Citation: BMC Bioinformatics 2023 24:30
  6. Rhodopsin is a seven-transmembrane protein covalently linked with retinal chromophore that absorbs photons for energy conversion and intracellular signaling in eukaryotes, bacteria, and archaea. Haloarchaeal r...

    Authors: Muthu Krishnan Selvaraj, Anamika Thakur, Manoj Kumar, Anil Kumar Pinnaka, Chander Raman Suri, Busi Siddhardha and Senthil Prasad Elumalai
    Citation: BMC Bioinformatics 2023 24:29
  7. In individuals or animals suffering from genetic or acquired diseases, it is important to identify which clinical or phenotypic variables can be used to discriminate between disease and non-disease states, the...

    Authors: Maria del Mar Muñiz Moreno, Claire Gavériaux-Ruff and Yann Herault
    Citation: BMC Bioinformatics 2023 24:28
  8. Circular RNAs (circRNAs) are a class of covalenty closed non-coding RNAs that have garnered increased attention from the research community due to their stability, tissue-specific expression and role as transc...

    Authors: Barry Digby, Stephen P. Finn and Pilib Ó Broin
    Citation: BMC Bioinformatics 2023 24:27
  9. Grouping samples with low prevalence of positives into pools and testing these pools can achieve considerable savings in testing resources compared with individual testing in the context of COVID-19. We review...

    Authors: David Brust and Johannes J. Brust
    Citation: BMC Bioinformatics 2023 24:26
  10. Bacteriocins are defined as thermolabile peptides produced by bacteria with biological activity against taxonomically related species. These antimicrobial peptides have a wide application including disease tre...

    Authors: Sávio S. Costa, Gislenne da Silva Moia, Artur Silva, Rafael A. Baraúna and Adonney Allan de Oliveira Veras
    Citation: BMC Bioinformatics 2023 24:24
  11. Recent population studies are ever growing in number of samples to investigate the diversity of a population or species. These studies reveal new polymorphism that lead to important insights into the mechanism...

    Authors: Luis F. Paulin, Muthuswamy Raveendran, R. Alan Harris, Jeffrey Rogers, Arndt von Haeseler and Fritz J. Sedlazeck
    Citation: BMC Bioinformatics 2023 24:23
  12. Microbial communities are known to be closely related to many diseases, such as obesity and HIV, and it is of interest to identify differentially abundant microbial species between two or more environments. Si...

    Authors: Hoseung Song, Wodan Ling, Ni Zhao, Anna M. Plantinga, Courtney A. Broedlow, Nichole R. Klatt, Tiffany Hensley-McBain and Michael C. Wu
    Citation: BMC Bioinformatics 2023 24:22
  13. N4-methylcytosine (4mC) is an important epigenetic mechanism, which regulates many cellular processes such as cell differentiation and gene expression. The knowledge about the 4mC sites is a key foundation to ...

    Authors: Peijie Zheng, Guiyang Zhang, Yuewu Liu and Guohua Huang
    Citation: BMC Bioinformatics 2023 24:21
  14. Emerging evidences show that Piwi-interacting RNAs (piRNAs) play a pivotal role in numerous complex human diseases. Identifying potential piRNA-disease associations (PDAs) is crucial for understanding disease ...

    Authors: Ping Zhang, Weicheng Sun, Dengguo Wei, Guodong Li, Jinsheng Xu, Zhuhong You, Bowei Zhao and Li Li
    Citation: BMC Bioinformatics 2023 24:18
  15. Colorectal cancer (CRC) is the third most common cancer and the second most deathly worldwide. It is a very heterogeneous disease that can develop via distinct pathways where metastasis is the primary cause of...

    Authors: Carolina Peixoto, Marta B. Lopes, Marta Martins, Sandra Casimiro, Daniel Sobral, Ana Rita Grosso, Catarina Abreu, Daniela Macedo, Ana Lúcia Costa, Helena Pais, Cecília Alvim, André Mansinho, Pedro Filipe, Pedro Marques da Costa, Afonso Fernandes, Paula Borralho…
    Citation: BMC Bioinformatics 2023 24:17
  16. Correctly identifying the driver genes that promote cell growth can significantly assist drug design, cancer diagnosis and treatment. The recent large-scale cancer genomics projects have revealed multi-omics d...

    Authors: Wei Peng, Rong Wu, Wei Dai and Ning Yu
    Citation: BMC Bioinformatics 2023 24:16
  17. Elucidating the Transcription Factors (TFs) that drive the gene expression changes in a given experiment is a common question asked by researchers. The existing methods rely on the predicted Transcription Fact...

    Authors: Maciej Migdał, Takahiro Arakawa, Satoshi Takizawa, Masaaki Furuno, Harukazu Suzuki, Erik Arner, Cecilia Lanny Winata and Bogumił Kaczkowski
    Citation: BMC Bioinformatics 2023 24:14
  18. Constructing molecular interaction networks from microarray data and then identifying disease module biomarkers can provide insight into the underlying pathogenic mechanisms of non-small cell lung cancer. A pr...

    Authors: Junliang Shang, Xuhui Zhu, Yan Sun, Feng Li, Xiangzhen Kong and Jin-Xing Liu
    Citation: BMC Bioinformatics 2023 24:13
  19. Gallbladder carcinoma (GBC), an aggressive malignant tumor of the biliary system, is characterized by high cellular heterogeneity and poor prognosis. Fewer data have been reported in GBC than other common canc...

    Authors: Li Guo, Yangyang Xiang, Yuyang Dou, Zibo Yin, Xinru Xu, Lihua Tang, Jiafeng Yu, Jun Wang and Tingming Liang
    Citation: BMC Bioinformatics 2023 24:12
  20. Old mosquitoes are more likely to transmit malaria than young ones. Therefore, accurate prediction of mosquito population age can drastically improve the evaluation of mosquito-targeted interventions. However,...

    Authors: Emmanuel P. Mwanga, Doreen J. Siria, Joshua Mitton, Issa H. Mshani, Mario González-Jiménez, Prashanth Selvaraj, Klaas Wynne, Francesco Baldini, Fredros O. Okumu and Simon A. Babayan
    Citation: BMC Bioinformatics 2023 24:11
  21. When developing models for clinical information retrieval and decision support systems, the discrete outcomes required for training are often missing. These labels need to be extracted from free text in electr...

    Authors: Bram van Es, Leon C. Reteig, Sander C. Tan, Marijn Schraagen, Myrthe M. Hemker, Sebastiaan R. S. Arends, Miguel A. R. Rios and Saskia Haitjema
    Citation: BMC Bioinformatics 2023 24:10
  22. Feature selection is often used to identify the important features in a dataset but can produce unstable results when applied to high-dimensional data. The stability of feature selection can be improved with t...

    Authors: Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty and Arcot Sowmya
    Citation: BMC Bioinformatics 2023 24:9
  23. Being among the most common malignancies worldwide, hepatocellular carcinoma (HCC) accounting for the third cause of cancer mortality. The regulation of cell death is the most crucial step in tumor progression...

    Authors: Chunhua Liu, Simin Wu, Liying Lai, Jinyu Liu, Zhaofu Guo, Zegen Ye and Xiang Chen
    Citation: BMC Bioinformatics 2023 24:4
  24. Gene-based association tests provide a useful alternative and complement to the usual single marker association tests, especially in genome-wide association studies (GWAS). The way of weighting for variants in...

    Authors: Jianjun Zhang, Xiaoyu Liang, Samantha Gonzales, Jianguo Liu, Xiaoyi Raymond Gao and Xuexia Wang
    Citation: BMC Bioinformatics 2023 24:2
  25. Prostate cancer is a major health concern in aging men. Paralleling an aging society, prostate cancer prevalence increases emphasizing the need for efficient diagnostic algorithms.

    Authors: Yauheniya Zhdanovich, Jörg Ackermann, Peter J. Wild, Jens Köllermann, Katrin Bankov, Claudia Döring, Nadine Flinner, Henning Reis, Mike Wenzel, Benedikt Höh, Philipp Mandel, Thomas J. Vogl, Patrick Harter, Katharina Filipski, Ina Koch and Simon Bernatz
    Citation: BMC Bioinformatics 2023 24:1
  26. Gene set enrichment analysis (detecting phenotypic terms that emerge as significant in a set of genes) plays an important role in bioinformatics focused on diseases of genetic basis. To facilitate phenotype-or...

    Authors: Alejandro Cisterna, Aurora González-Vidal, Daniel Ruiz, Jordi Ortiz, Alicia Gómez-Pascual, Zhongbo Chen, Mike Nalls, Faraz Faghri, John Hardy, Irene Díez, Paolo Maietta, Sara Álvarez, Mina Ryten and Juan A. Botía
    Citation: BMC Bioinformatics 2022 23:567
  27. Escherichia coli Nissle 1917 (EcN) is a probiotic bacterium used to treat various gastrointestinal diseases. EcN is increasingly being used as a chassis for the engineering of advanced microbiome therapeutics. To...

    Authors: Max van ‘t Hof, Omkar S. Mohite, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson and Morten O. A. Sommer
    Citation: BMC Bioinformatics 2022 23:566
  28. There is evidence that DNA breathing (spontaneous opening of the DNA strands) plays a relevant role in the interactions of DNA with other molecules, and in particular in the transcription process. Therefore, h...

    Authors: José Antonio Barbero-Aparicio, Santiago Cuesta-Lopez, César Ignacio García-Osorio, Javier Pérez-Rodríguez and Nicolás García-Pedrajas
    Citation: BMC Bioinformatics 2022 23:565
  29. Identifying drug–target interactions (DTIs) plays a key role in drug development. Traditional wet experiments to identify DTIs are expensive and time consuming. Effective computational methods to predict DTIs ...

    Authors: Junjun Zhang and Minzhu Xie
    Citation: BMC Bioinformatics 2022 23:564
  30. Lung adenocarcinoma (LUAD) is the most common malignant tumor that seriously affects human health. Previous studies have indicated that abnormal levels of glycosylation promote progression and poor prognosis o...

    Authors: Jin-xiao Liang, Qian Chen, Wei Gao, Da Chen, Xin-yu Qian, Jin-qiao Bi, Xing-chen Lin, Bing-bing Han and Jin-shi Liu
    Citation: BMC Bioinformatics 2022 23:562
  31. Drug–drug interactions (DDIs) occur when two or more drugs are taken simultaneously or successively. Early detection of adverse drug interactions can be essential in preventing medical errors and reducing heal...

    Authors: Dingkai Huang, Hongjian He, Jiaming Ouyang, Chang Zhao, Xin Dong and Jiang Xie
    Citation: BMC Bioinformatics 2022 23:561
  32. RNA secondary structure has broad impact on the fate of RNA metabolism. The reduced stability of secondary structures near the translation initiation site/start codon of the coding region promotes the efficie...

    Authors: Jianan Lin, Yang Chen, Yuping Zhang, Haifan Lin and Zhengqing Ouyang
    Citation: BMC Bioinformatics 2022 23(Suppl 3):559

    This article is part of a Supplement: Volume 23 Supplement 3

  33. In order to detect threats to public health and to be well-prepared for endemic and pandemic illness outbreaks, countries usually rely on event-based surveillance (EBS) and indicator-based surveillance systems...

    Authors: Antonella Dellanzo, Viviana Cotik, Daniel Yunior Lozano Barriga, Jonathan Jimmy Mollapaza Apaza, Daniel Palomino, Fernando Schiaffino, Alexander Yanque Aliaga and José Ochoa-Luna
    Citation: BMC Bioinformatics 2022 23:558
  34. Over the last few years, dozens of healthcare surveys have shown a shortage of doctors and an alarming doctor-population ratio. With the motivation of assisting doctors and utilizing their time efficiently, au...

    Authors: Abhisek Tiwari, Tulika Saha, Sriparna Saha, Pushpak Bhattacharyya, Shemim Begum, Minakshi Dhar and Sarbajeet Tiwari
    Citation: BMC Bioinformatics 2022 23:556
  35. Flux balance analysis (FBA) is an optimization based approach to find the optimal steady state of a metabolic network, commonly of microorganisms such as yeast strains and Escherichia coli. However, the resulting...

    Authors: Dustin Kenefake, Erick Armingol, Nathan E. Lewis and Efstratios N. Pistikopoulos
    Citation: BMC Bioinformatics 2022 23:550

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