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  1. RNA secondary structure is very important for deciphering cell’s activity and disease occurrence. The first method which was used by the academics to predict this structure is biological experiment, But this m...

    Authors: Yinchao Fei, Hao Zhang, Yili Wang, Zhen Liu and Yuanning Liu
    Citation: BMC Bioinformatics 2022 23:354
  2. Integration of multi-omics data can provide a more complex view of the biological system consisting of different interconnected molecular components, the crucial aspect for developing novel personalised therapeut...

    Authors: Anna Pačínková and Vlad Popovici
    Citation: BMC Bioinformatics 2022 23:351

    The Correction to this article has been published in BMC Bioinformatics 2022 23:376

  3. Cuproptosis induction represents a promising alternative for immunotherapies and targeted therapies in breast cancer. This study aimed to investigate the prognostic and biological significance of cuproptosis-r...

    Authors: Linrong Li, Lin Li and Qiang Sun
    Citation: BMC Bioinformatics 2022 23:350
  4. Amino acid property-aware phylogenetic analysis (APPA) refers to the phylogenetic analysis method based on amino acid property encoding, which is used for understanding and inferring evolutionary relationships...

    Authors: Wei Li, Lina Yang, Yu Qiu, Yujian Yuan, Xichun Li and Zuqiang Meng
    Citation: BMC Bioinformatics 2022 23:347
  5. G-protein coupled receptors (GPCRs) sense and transmit extracellular signals into the intracellular machinery by regulating G proteins. GPCR malfunctions are associated with a variety of signaling-related dise...

    Authors: Jooseong Oh, Hyi-thaek Ceong, Dokyun Na and Chungoo Park
    Citation: BMC Bioinformatics 2022 23(Suppl 9):346

    This article is part of a Supplement: Volume 23 Supplement 9

  6. Due to its key role in various biological processes, RNA secondary structures have always been the focus of in-depth analyses, with great efforts from mathematicians and biologists, to find a suitable abstract...

    Authors: Daniele Marchei and Emanuela Merelli
    Citation: BMC Bioinformatics 2022 23(Suppl 6):345

    This article is part of a Supplement: Volume 23 Supplement 6

  7. A recurring problem in image segmentation is a lack of labelled data. This problem is especially acute in the segmentation of lung computed tomography (CT) of patients with Coronavirus Disease 2019 (COVID-19)....

    Authors: Judah Zammit, Daryl L. X. Fung, Qian Liu, Carson Kai-Sang Leung and Pingzhao Hu
    Citation: BMC Bioinformatics 2022 23(Suppl 7):343

    This article is part of a Supplement: Volume 23 Supplement 7

  8. Gene regulatory networks have garnered a large amount of attention to understand disease mechanisms caused by complex molecular network interactions. These networks have been applied to predict specific clinic...

    Authors: Heewon Park, Seiya Imoto and Satoru Miyano
    Citation: BMC Bioinformatics 2022 23:342
  9. Cancer is a heterogeneous disease in which tumor genes cooperate as well as adapt and evolve to the changing conditions for individual patients. It is a meaningful task to discover the personalized cancer driv...

    Authors: Shao-Wu Zhang, Zhen-Nan Wang, Yan Li and Wei-Feng Guo
    Citation: BMC Bioinformatics 2022 23:341
  10. Cells progressing from an early state to a developed state give rise to lineages in cell differentiation. Knowledge of these lineages is central to developmental biology. Each biological lineage corresponds to...

    Authors: Lovemore Tenha and Mingzhou Song
    Citation: BMC Bioinformatics 2022 23(Suppl 8):340

    This article is part of a Supplement: Volume 23 Supplement 8

  11. Essential proteins are indispensable to the development and survival of cells. The identification of essential proteins not only is helpful for the understanding of the minimal requirements for cell survival, ...

    Authors: Weixia Xu, Yunfeng Dong, Jihong Guan and Shuigeng Zhou
    Citation: BMC Bioinformatics 2022 23(Suppl 8):339

    This article is part of a Supplement: Volume 23 Supplement 8

  12. Extraction of drug drug interactions from biomedical literature and other textual data is an important component to monitor drug-safety and this has attracted attention of many researchers in healthcare. Exist...

    Authors: Biao Duan, Jing Peng and Yi Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 7):338

    This article is part of a Supplement: Volume 23 Supplement 7

  13. Single-cell RNA sequencing (scRNA-seq) technologies offer unique opportunities for exploring heterogeneous cell populations. However, in-depth single-cell transcriptomic characterization of complex tissues oft...

    Authors: Mariia Bilous, Loc Tran, Chiara Cianciaruso, Aurélie Gabriel, Hugo Michel, Santiago J. Carmona, Mikael J. Pittet and David Gfeller
    Citation: BMC Bioinformatics 2022 23:336
  14. Image segmentation in fluorescence microscopy is often based on spectral separation of fluorescent probes (color-based segmentation) or on significant intensity differences in individual image regions (intensi...

    Authors: Daniel Wüstner
    Citation: BMC Bioinformatics 2022 23:334
  15. Influenza A viruses (IAV) exhibit vast genetic mutability and have great zoonotic potential to infect avian and mammalian hosts and are known to be responsible for a number of pandemics. A key computational is...

    Authors: Yixiang Zhang, Kent M. Eskridge, Shunpu Zhang and Guoqing Lu
    Citation: BMC Bioinformatics 2022 23:333
  16. Several types of RNA in the cell are usually involved in biological processes with multiple functions. Coding RNAs code for proteins while non-coding RNAs regulate gene expression. Some single-strand RNAs can ...

    Authors: Morteza Kouhsar, Esra Kashaninia, Behnam Mardani and Hamid R. Rabiee
    Citation: BMC Bioinformatics 2022 23:331
  17. Biological data suffers from noise that is inherent in the measurements. This is particularly true for time-series gene expression measurements. Nevertheless, in order to to explore cellular dynamics, scientis...

    Authors: Nadav Bar, Bahareh Nikparvar, Naresh Doni Jayavelu and Fabienne Krystin Roessler
    Citation: BMC Bioinformatics 2022 23:330
  18. The treatment and prognosis of lung adenocarcinoma (LUAD) remains a challenge. The study aimed to conduct a systematic analysis of the predictive capacity of N6-methyladenosine (m6A)-related long non-coding RN...

    Authors: Chen Gao, Ning Kong, Fan Zhang, Liuzhi Zhou, Maosheng Xu and Linyu Wu
    Citation: BMC Bioinformatics 2022 23:327
  19. The malaria risk prediction is currently limited to using advanced statistical methods, such as time series and cluster analysis on epidemiological data. Nevertheless, machine learning models have been explore...

    Authors: Kah Yee Tai, Jasbir Dhaliwal and KokSheik Wong
    Citation: BMC Bioinformatics 2022 23:325
  20. Applying directed acyclic graph (DAG) models to proteogenomic data has been shown effective for detecting causal biomarkers of complex diseases. However, there remain unsolved challenges in DAG learning to joi...

    Authors: Shrabanti Chowdhury, Ru Wang, Qing Yu, Catherine J. Huntoon, Larry M. Karnitz, Scott H. Kaufmann, Steven P. Gygi, Michael J. Birrer, Amanda G. Paulovich, Jie Peng and Pei Wang
    Citation: BMC Bioinformatics 2022 23:321
  21. Visceral Leishmaniasis (VL) is a fatal vector-borne parasitic disorder occurring mainly in tropical and subtropical regions. VL falls under the category of neglected tropical diseases with growing drug resista...

    Authors: Subhadip Saha, Shubham Vashishtha, Bishwajit Kundu and Monidipa Ghosh
    Citation: BMC Bioinformatics 2022 23:319
  22. Essential Proteins are demonstrated to exert vital functions on cellular processes and are indispensable for the survival and reproduction of the organism. Traditional centrality methods perform poorly on comp...

    Authors: Yi Yue, Chen Ye, Pei-Yun Peng, Hui-Xin Zhai, Iftikhar Ahmad, Chuan Xia, Yun-Zhi Wu and You-Hua Zhang
    Citation: BMC Bioinformatics 2022 23:318
  23. ImputAccur is a software tool to measure genotype-imputation accuracy. Imputation of untyped markers is a standard approach in genome-wide association studies to close the gap between directly genotyped and other...

    Authors: Kolja A. Thormann, Viola Tozzi, Paula Starke, Heike Bickeböller, Marcus Baum and Albert Rosenberger
    Citation: BMC Bioinformatics 2022 23:316
  24. Drug–target interaction (DTI) prediction plays a crucial role in drug discovery. Although the advanced deep learning has shown promising results in predicting DTIs, it still needs improvements in two aspects: ...

    Authors: Yuni Zeng, Xiangru Chen, Dezhong Peng, Lijun Zhang and Haixiao Huang
    Citation: BMC Bioinformatics 2022 23:314
  25. DIRs are mysterious protein that have the ability to scavenge free radicals, which, are highly reactive with molecules in their vicinity. What is even more fascinating is that they carry out from these highly ...

    Authors: Merlin Bardin, Pierre Rousselot-Pailley, Thierry Tron and Viviane Robert
    Citation: BMC Bioinformatics 2022 23:313
  26. Although there have been some recent cell and animal experiments indicating that expression of the gene encoding apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B) is closely related to cancer, ...

    Authors: Jiacheng Wu, Ni Li, Linwen Zhu, Dawei Zhen, Mengqi Li, Hang Chen, Mengmeng Ye, Yiqin Wei and Guofeng Shao
    Citation: BMC Bioinformatics 2022 23:312
  27. Cervical cancer is the fourth most common cancer affecting women and is caused by human Papillomavirus (HPV) infections that are sexually transmitted. There are currently commercially available prophylactic va...

    Authors: Samira Sanami, Mahmoud Rafieian-Kopaei, Korosh Ashrafi Dehkordi, Hamidreza Pazoki-Toroudi, Fatemeh Azadegan-Dehkordi, Gholam-Reza Mobini, Morteza Alizadeh, Muhammad Sadeqi Nezhad, Maryam Ghasemi-Dehnoo and Nader Bagheri
    Citation: BMC Bioinformatics 2022 23:311
  28. Technical improvement in ATAC-seq makes it possible for high throughput profiling the chromatin states of single cells. However, data from multiple sources frequently show strong technical variations, which is...

    Authors: Li Lin and Liye Zhang
    Citation: BMC Bioinformatics 2022 23:309
  29. Heritability and genetic correlation can be estimated from genome-wide single-nucleotide polymorphism (SNP) data using various methods. We recently developed multivariate genomic-relatedness-based restricted m...

    Authors: Ronald De Vlaming, Eric A. W. Slob, Patrick J. F. Groenen and Cornelius A. Rietveld
    Citation: BMC Bioinformatics 2022 23:305
  30. Previous studies have demonstrated the value of re-analysing publicly available genetics data with recent analytical approaches. Publicly available datasets, such as the Women’s Health Initiative (WHI) offered...

    Authors: Adam N. Bennett, Jethro Rainford, Xiaotai Huang, Qian He and Kei Hang Katie Chan
    Citation: BMC Bioinformatics 2022 23:304
  31. The discovery of critical biomarkers is significant for clinical diagnosis, drug research and development. Researchers usually obtain biomarkers from microarray data, which comes from the dimensional curse. Fe...

    Authors: Weidong Xie, Wei Li, Shoujia Zhang, Linjie Wang, Jinzhu Yang and Dazhe Zhao
    Citation: BMC Bioinformatics 2022 23:303
  32. Protein complexes are essential for biologists to understand cell organization and function effectively. In recent years, predicting complexes from protein–protein interaction (PPI) networks through computatio...

    Authors: Xiaoxu Wang, Yijia Zhang, Peixuan Zhou and Xiaoxia Liu
    Citation: BMC Bioinformatics 2022 23:300

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