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  1. Accurate identification of protein complexes in protein-protein interaction (PPI) networks is crucial for understanding the principles of cellular organization. Most computational methods ignore the fact that ...

    Authors: Rongquan Wang, Caixia Wang and Huimin Ma
    Citation: BMC Bioinformatics 2022 23:414

    The Correction to this article has been published in BMC Bioinformatics 2022 23:494

  2. Biological age (BA) has been recognized as a more accurate indicator of aging than chronological age (CA). However, the current limitations include: insufficient attention to the incompleteness of medical data...

    Authors: Qing Yang, Sunan Gao, Junfen Lin, Ke Lyu, Zexu Wu, Yuhao Chen, Yinwei Qiu, Yanrong Zhao, Wei Wang, Tianxiang Lin, Huiyun Pan and Ming Chen
    Citation: BMC Bioinformatics 2022 23:411
  3. We used a hybrid machine learning systems (HMLS) strategy that includes the extensive search for the discovery of the most optimal HMLSs, including feature selection algorithms, a feature extraction algorithm,...

    Authors: Eskandar Taghizadeh, Sahel Heydarheydari, Alihossein Saberi, Shabnam JafarpoorNesheli and Seyed Masoud Rezaeijo
    Citation: BMC Bioinformatics 2022 23:410
  4. Artificial intelligence (AI) and machine learning (ML) have resulted in significant enthusiasm for their promise in healthcare. Despite this, prospective randomized controlled trials and successful clinical im...

    Authors: Julian C. Hong, Neville C. W. Eclov, Sarah J. Stephens, Yvonne M. Mowery and Manisha Palta
    Citation: BMC Bioinformatics 2022 23(Suppl 12):408

    This article is part of a Supplement: Volume 23 Supplement 12

  5. To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leverag...

    Authors: Yi Nian, Xinyue Hu, Rui Zhang, Jingna Feng, Jingcheng Du, Fang Li, Larry Bu, Yuji Zhang, Yong Chen and Cui Tao
    Citation: BMC Bioinformatics 2022 23(Suppl 6):407

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

  6. Oxidative stress plays an important role in the progression of various types of tumors. However, its role in esophageal squamous cell carcinoma (ESCC) has seldom been explored. This study aimed to discover pro...

    Authors: Wei Liu, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng and Yi-Yan Lei
    Citation: BMC Bioinformatics 2022 23:406
  7. Identifying protein complexes from protein-protein interaction network is one of significant tasks in the postgenome era. Protein complexes, none of which exceeds 10 in size play an irreplaceable role in life ...

    Authors: Jiaqing Lyu, Zhen Yao, Bing Liang, Yiwei Liu and Yijia Zhang
    Citation: BMC Bioinformatics 2022 23:405
  8. Bioinformatics has gained much attention as a fast growing interdisciplinary field. Several attempts have been conducted to explore the field of bioinformatics by bibliometric analysis, however, such works did...

    Authors: Jiaqi Wang, Zeyu Li and Jiawan Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 8):404

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

  9. Microbes are associated with many human diseases and influence drug efficacy. Small-molecule drugs may revolutionize biomedicine by fine-tuning the microbiota on the basis of individual patient microbiome sign...

    Authors: Qiao Liu, Bohyun Lee and Lei Xie
    Citation: BMC Bioinformatics 2022 23(Suppl 3):403

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

  10. In Alzheimer’s Diseases (AD) research, multimodal imaging analysis can unveil complementary information from multiple imaging modalities and further our understanding of the disease. One application is to disc...

    Authors: Yixue Feng, Mansu Kim, Xiaohui Yao, Kefei Liu, Qi Long and Li Shen
    Citation: BMC Bioinformatics 2022 23(Suppl 3):402

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

  11. Population variant analysis is of great importance for gathering insights into the links between human genotype and phenotype. The 1000 Genomes Project established a valuable reference for human genetic variat...

    Authors: Tommaso Alfonsi, Anna Bernasconi, Arif Canakoglu and Marco Masseroli
    Citation: BMC Bioinformatics 2022 23:401
  12. Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate disc...

    Authors: E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki…
    Citation: BMC Bioinformatics 2022 23:400
  13. Twitter is a popular social networking site where short messages or “tweets” of users have been used extensively for research purposes. However, not much research has been done in mining the medical profession...

    Authors: Kazi Zainab, Gautam Srivastava and Vijay Mago
    Citation: BMC Bioinformatics 2022 22(Suppl 10):630

    This article is part of a Supplement: Volume 22 Supplement 10

  14. Protein histidine phosphorylation (pHis) plays critical roles in prokaryotic signal transduction pathways and various eukaryotic cellular processes. It is estimated to account for 6–10% of the phosphoproteome,...

    Authors: Jian Zhao, Minhui Zhuang, Jingjing Liu, Meng Zhang, Cong Zeng, Bin Jiang, Jing Wu and Xiaofeng Song
    Citation: BMC Bioinformatics 2022 23(Suppl 3):399

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

  15. Brain volume has been widely studied in the neuroimaging field, since it is an important and heritable trait associated with brain development, aging and various neurological and psychiatric disorders. Genome-...

    Authors: Hung Mai, Jingxuan Bao, Paul M. Thompson, Dokyoon Kim and Li Shen
    Citation: BMC Bioinformatics 2022 23(Suppl 3):398

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

  16. Advances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to dat...

    Authors: Nathan Ranno and Dong Si
    Citation: BMC Bioinformatics 2022 23(Suppl 3):397

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

  17. The eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3′-untranslated region (3′-UTR) of mRNA produces transcri...

    Authors: Naima Ahmed Fahmi, Khandakar Tanvir Ahmed, Jae-Woong Chang, Heba Nassereddeen, Deliang Fan, Jeongsik Yong and Wei Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 3):396

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

  18. Making clear what kinds of metabolic pathways a drug compound involves in can help researchers understand how the drug is absorbed, distributed, metabolized, and excreted. The characteristics of a compound suc...

    Authors: Zhihui Yang, Juan Liu, Hayat Ali Shah and Jing Feng
    Citation: BMC Bioinformatics 2022 23(Suppl 5):329

    This article is part of a Supplement: Volume 23 Supplement 5

  19. Microarrays can perform large scale studies of differential expressed gene (DEGs) and even single nucleotide polymorphisms (SNPs), thereby screening thousands of genes for single experiment simultaneously. How...

    Authors: Giuseppe Agapito, Marianna Milano and Mario Cannataro
    Citation: BMC Bioinformatics 2022 23(Suppl 6):393

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

  20. Collagen VI family (COL6A) is a major member of extracellular matrix protein. There is accumulating evidence that COL6A is involved in tumorigenesis and tumor progression. In this study, we performed a systema...

    Authors: Xiang Li, Zeng Li, Shanzhi Gu and Xinhan Zhao
    Citation: BMC Bioinformatics 2022 23:390
  21. The recent global focus on big data in medicine has been associated with the rise of artificial intelligence (AI) in diagnosis and decision-making following recent advances in computer technology. Up to now, A...

    Authors: Xiaoxia Wen, Ping Leng, Jiasi Wang, Guishu Yang, Ruiling Zu, Xiaojiong Jia, Kaijiong Zhang, Birga Anteneh Mengesha, Jian Huang, Dongsheng Wang and Huaichao Luo
    Citation: BMC Bioinformatics 2022 23:387
  22. Public Data Commons (PDC) have been highlighted in the scientific literature for their capacity to collect and harmonize big data. On the other hand, local data commons (LDC), located within an institution or ...

    Authors: Jong Cheol Jeong, Isaac Hands, Jill M. Kolesar, Mahadev Rao, Bront Davis, York Dobyns, Joseph Hurt-Mueller, Justin Levens, Jenny Gregory, John Williams, Lisa Witt, Eun Mi Kim, Carlee Burton, Amir A. Elbiheary, Mingguang Chang and Eric B. Durbin
    Citation: BMC Bioinformatics 2022 23(Suppl 12):386

    This article is part of a Supplement: Volume 23 Supplement 12

  23. The placental barrier protects the fetus from exposure to some toxicants and is vital for drug development and risk assessment of environmental chemicals. However, in vivo experiments for assessing the placent...

    Authors: Che-Yu Chou, Pinpin Lin, Jongwoon Kim, Shan-Shan Wang, Chia-Chi Wang and Chun-Wei Tung
    Citation: BMC Bioinformatics 2022 22(Suppl 10):629

    This article is part of a Supplement: Volume 22 Supplement 10

  24. The technologies advances of single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) allowed to generate thousands of single cells in a relatively easy and economic manner and it i...

    Authors: Hongzhe Guo, Zhongbo Yang, Tao Jiang, Shiqi Liu, Yadong Wang and Zhe Cui
    Citation: BMC Bioinformatics 2022 23(Suppl 5):249

    This article is part of a Supplement: Volume 23 Supplement 5

  25. DNA methylation is an important epigenetic modification that is known to regulate gene expression. Whole-genome bisulfite sequencing (WGBS) is a powerful method for studying cytosine methylation in a whole gen...

    Authors: Heesun Kim, Mikang Sim, Nayoung Park, Kisang Kwon, Junyoung Kim and Jaebum Kim
    Citation: BMC Bioinformatics 2022 23:383
  26. Biclustering algorithm is an effective tool for processing gene expression datasets. There are two kinds of data matrices, binary data and non-binary data, which are processed by biclustering method. A binary ...

    Authors: He-Ming Chu, Jin-Xing Liu, Ke Zhang, Chun-Hou Zheng, Juan Wang and Xiang-Zhen Kong
    Citation: BMC Bioinformatics 2022 23:381
  27. Metabolomic time course analyses of biofluids are highly relevant for clinical diagnostics. However, many sampling methods suffer from unknown sample sizes, commonly known as size effects. This prevents absolu...

    Authors: Mathias Gotsmy, Julia Brunmair, Christoph Büschl, Christopher Gerner and Jürgen Zanghellini
    Citation: BMC Bioinformatics 2022 23:379
  28. The L1000 technology, a cost-effective high-throughput transcriptomics technology, has been applied to profile a collection of human cell lines for their gene expression response to > 30,000 chemical and genet...

    Authors: Minji Jeon, Zhuorui Xie, John E. Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke and Avi Ma’ayan
    Citation: BMC Bioinformatics 2022 23:374
  29. Chimeric antigen receptor T-cell (CAR-T) therapy is a new and efficient cellular immunotherapy. The therapy shows significant efficacy, but also has serious side effects, collectively known as cytokine release...

    Authors: Zhenyu Wei, Qi Cheng, Nan Xu, Chengkui Zhao, Jiayu Xu, Liqing Kang, Xiaoyan Lou, Lei Yu and Weixing Feng
    Citation: BMC Bioinformatics 2022 23:373
  30. Epigenetic modifications established in mammalian gametes are largely reprogrammed during early development, however, are partly inherited by the embryo to support its development. In this study, we examine Cp...

    Authors: Osamu Maruyama, Yinuo Li, Hiroki Narita, Hidehiro Toh, Wan Kin Au Yeung and Hiroyuki Sasaki
    Citation: BMC Bioinformatics 2022 23:371
  31. Development of new methods for analysis of protein–protein interactions (PPIs) at molecular and nanometer scales gives insights into intracellular signaling pathways and will improve understanding of protein f...

    Authors: Mayank Baranwal, Abram Magner, Jacob Saldinger, Emine S. Turali-Emre, Paolo Elvati, Shivani Kozarekar, J. Scott VanEpps, Nicholas A. Kotov, Angela Violi and Alfred O. Hero
    Citation: BMC Bioinformatics 2022 23:370
  32. Though proposing algorithmic approaches for protein domain decomposition has been of high interest, the inherent ambiguity to the problem makes it still an active area of research. Besides, accurate automated ...

    Authors: Mohammad Taheri-Ledari, Amirali Zandieh, Seyed Peyman Shariatpanahi and Changiz Eslahchi
    Citation: BMC Bioinformatics 2022 23:369
  33. Protein ligand docking is an indispensable tool for computational prediction of protein functions and screening drug candidates. Despite significant progress over the past two decades, it is still a challengin...

    Authors: Chenran Wang, Yang Chen, Yuan Zhang, Keqiao Li, Menghan Lin, Feng Pan, Wei Wu and Jinfeng Zhang
    Citation: BMC Bioinformatics 2022 23:368

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