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  1. 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
  2. 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
  3. 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

  4. 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

  5. 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

  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. Alzheimer’s disease affects profoundly the quality of human behavior and cognition. The very broad distribution of its severity across various human subjects requires the quantitative diagnose of Alzheimer’s d...

    Authors: Sangyeol Kim, Seongjun Park and Iksoo Chang
    Citation: BMC Bioinformatics 2022 23:357
  23. 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
  24. Gene expression analysis can provide useful information for analyzing complex biological mechanisms. However, many reported findings are unrepeatable due to small sample sizes relative to a large number of gen...

    Authors: Hai-Hui Huang, Hao Rao, Rui Miao and Yong Liang
    Citation: BMC Bioinformatics 2022 23(Suppl 10):353

    This article is part of a Supplement: Volume 23 Supplement 10

  25. 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

  26. 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
  27. 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
  28. 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

  29. 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

  30. 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

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