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  1. 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
    Content type: Research Published on:

  4. 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
    Content type: Research Published on:

  5. 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
    Content type: Research Published on:

  6. 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
    Content type: Research Published on:

  8. 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
    Content type: Software Published on:

  9. 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
    Content type: Research Published on:

  10. 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
    Content type: Database Published on:

  11. 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
    Content type: Research Published on:

  12. 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
    Content type: Research Published on:

  13. 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
    Content type: Research Published on:

  17. Single-cell omics technology is rapidly developing to measure the epigenome, genome, and transcriptome across a range of cell types. However, it is still challenging to integrate omics data from different moda...

    Authors: Chaozhong Liu, Linhua Wang and Zhandong Liu
    Citation: BMC Bioinformatics 2023 24:5
    Content type: Research Article Published on:

    The Correction to this article has been published in BMC Bioinformatics 2023 24:123

  18. 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
    Content type: Research Published on:

  20. 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
    Content type: Research Published on:

  21. 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
    Content type: Research Published on:

  22. 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
    Content type: Software Published on:

  23. 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
    Content type: Research Published on:

  24. 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
    Content type: Research Published on:

  25. 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
    Content type: Research Published on:

  27. 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
    Content type: Research Published on:

  28. 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
    Content type: Research Published on:

  30. 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
    Content type: Research Published on:

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

  31. 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
    Content type: Research Published on:

  33. 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
    Content type: Research Published on:

  37. Medication recommendation based on electronic medical record (EMR) is a research hot spot in smart healthcare. For developing computational medication recommendation methods based on EMR, an important challeng...

    Authors: Shaofu Lin, Mengzhen Wang, Chengyu Shi, Zhe Xu, Lihong Chen, Qingcai Gao and Jianhui Chen
    Citation: BMC Bioinformatics 2022 23:552
    Content type: Research Published on:

  38. The genomes of SARS-CoV-2 are classified into variants, some of which are monitored as variants of concern (e.g. the Delta variant B.1.617.2 or Omicron variant B.1.1.529). Proportions of these variants circula...

    Authors: Askar Gafurov, Andrej Baláž, Fabian Amman, Kristína Boršová, Viktória Čabanová, Boris Klempa, Andreas Bergthaler, Tomáš Vinař and Broňa Brejová
    Citation: BMC Bioinformatics 2022 23:551
    Content type: Research Published on:

  39. 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
    Content type: Research Published on:

  42. As of June 2022, the GISAID database contains more than 11 million SARS-CoV-2 genomes, including several thousand nucleotide sequences for the most common variants such as delta or omicron. These SARS-CoV-2 st...

    Authors: Georg Hahn, Sanghun Lee, Dmitry Prokopenko, Jonathan Abraham, Tanya Novak, Julian Hecker, Michael Cho, Surender Khurana, Lindsey R. Baden, Adrienne G. Randolph, Scott T. Weiss and Christoph Lange
    Citation: BMC Bioinformatics 2022 23:547
    Content type: Research Published on:

  43. The human protein atlas (HPA) is an online database containing large sets of protein expression data in normal and cancerous tissues in image form from immunohistochemically (IHC) stained tissue microarrays. I...

    Authors: Benedek Bozoky, Laszlo Szekely, Ingemar Ernberg and Andrii Savchenko
    Citation: BMC Bioinformatics 2022 23:546
    Content type: Software Published on:

  45. The Basic Local Alignment Search Tool (BLAST) is a suite of commonly used algorithms for identifying matches between biological sequences. The user supplies a database file and query file of sequences for BLAS...

    Authors: Trinity Cheng, Pei-Ju Chin, Kenny Cha, Nicholas Petrick and Mike Mikailov
    Citation: BMC Bioinformatics 2022 23:544
    Content type: Research Published on:

  46. Compound–protein interaction site and binding affinity predictions are crucial for drug discovery and drug design. In recent years, many deep learning-based methods have been proposed for predications related ...

    Authors: Jialin Wu, Zhe Liu, Xiaofeng Yang and Zhanglin Lin
    Citation: BMC Bioinformatics 2022 23:543
    Content type: Research Published on:

  47. During atherosclerosis, the narrowing of the arterial lumen is observed through the accumulation of bio compounds and the formation of plaque within artery walls. A non-linear optical imaging modality (NLOM), ...

    Authors: Natasha N. Kunchur and Leila B. Mostaço-Guidolin
    Citation: BMC Bioinformatics 2022 23:542
    Content type: Research Published on:

  48. Brain tumor segmentation plays a significant role in clinical treatment and surgical planning. Recently, several deep convolutional networks have been proposed for brain tumor segmentation and have achieved im...

    Authors: Yuhu Wang, Yuzhen Cao, Jinqiu Li, Hongtao Wu, Shuo Wang, Xinming Dong and Hui Yu
    Citation: BMC Bioinformatics 2022 22(Suppl 5):636
    Content type: Research Published on:

    This article is part of a Supplement: Volume 22 Supplement 5

  49. Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics ana...

    Authors: Daniel M. Portik, C. Titus Brown and N. Tessa Pierce-Ward
    Citation: BMC Bioinformatics 2022 23:541
    Content type: Research Published on:

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