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  1. 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

  2. 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

  3. 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
  4. 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
  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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
  13. 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
  14. 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

  15. 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

  16. 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

  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. Accurately predicting drug-target binding affinity (DTA) in silico plays an important role in drug discovery. Most of the computational methods developed for predicting DTA use machine learning models, especia...

    Authors: Shaofu Lin, Chengyu Shi and Jianhui Chen
    Citation: BMC Bioinformatics 2022 23:367
  27. In various fields, searching for the Longest Common Subsequences (LCS) of Multiple (i.e., three or more) sequences (MLCS) is a classic but difficult problem to solve. The primary bottleneck in this problem is ...

    Authors: Changyong Yu, Pengxi Lin, Yuhai Zhao, Tianmei Ren and Guoren Wang
    Citation: BMC Bioinformatics 2022 23:366
  28. Pathogenic mutations in genes that control chromatin function have been implicated in rare genetic syndromes. These chromatin modifiers exhibit extraordinary diversity in the scale of the epigenetic changes th...

    Authors: Leroy Bondhus, Angela Wei and Valerie A. Arboleda
    Citation: BMC Bioinformatics 2022 23:364
  29. Presently, there is a wide variety of classification methods and deep neural network approaches in bioinformatics. Deep neural networks have proven their effectiveness for classification tasks, and have outper...

    Authors: David Chardin, Cyprien Gille, Thierry Pourcher, Olivier Humbert and Michel Barlaud
    Citation: BMC Bioinformatics 2022 23:361
  30. Despite recent advances in cellular cryo-electron tomography (CET), developing automated tools for macromolecule identification in submolecular resolution remains challenging due to the lack of annotated data ...

    Authors: Noushin Hajarolasvadi, Vikram Sunkara, Sagar Khavnekar, Florian Beck, Robert Brandt and Daniel Baum
    Citation: BMC Bioinformatics 2022 23:360
  31. Multilocus analysis on a set of single nucleotide polymorphisms (SNPs) pre-assigned within a gene constitutes a valuable complement to single-marker analysis by aggregating data on complex traits in a biologic...

    Authors: Zhonghe Shao, Ting Wang, Jiahao Qiao, Yuchen Zhang, Shuiping Huang and Ping Zeng
    Citation: BMC Bioinformatics 2022 23:359
  32. Fractional vegetation coverage (FVC) is a crucial parameter in determining vegetation structure. Automatic measurement of FVC using digital images captured by mobile smart devices is a potential direction for ...

    Authors: Chuangye Song, Jiawen Sang, Lin Zhang, Huiming Liu, Dongxiu Wu, Weiying Yuan and Chong Huang
    Citation: BMC Bioinformatics 2022 23:358

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