Article
Biochemical Research Methods
Yixuan Qiu, Jiebiao Wang, Jing Lei, Kathryn Roeder
Summary: Marker genes, primarily expressed in a single-cell type, are highly correlated in bulk data, allowing for their identification through correlation patterns. A new algorithm has been developed to detect these marker genes by combining published information and bulk transcriptome data, refining the list of known marker genes based on the correlation structure of the bulk data.
Article
Mathematical & Computational Biology
Li-Sha Pan, Zacharia Ackbarkha, Jing Zeng, Min-Li Huang, Zhen Yang, Hao Liang
Summary: This study investigated the molecular function of tumor microenvironment in uveal melanoma by analyzing RNA-sequencing data from 80 patients. A prognostic model based on four characteristic genes was constructed, showing better ability to predict survival outcomes. The risk signature based on immune index was identified as an indicator for evaluating prognosis in patients with UVM.
MATHEMATICAL BIOSCIENCES AND ENGINEERING
(2021)
Article
Cell Biology
Zhipeng Zhao, Jijun Shi, Guang Zhao, Yanjun Gao, Zhigang Jiang, Fusheng Yuan
Summary: Osteosarcoma is typically treated with chemotherapy and surgery, but its 5-year survival rate has not seen significant improvement. Due to its complex multigenomic heterogeneity and lack of universally applicable treatment targets, it is crucial to explore its genetic pathogenic factors.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Risa Karakida Kawaguchi, Ziqi Tang, Stephan Fischer, Chandana Rajesh, Rohit Tripathy, Peter K. Koo, Jesse Gillis
Summary: In this study, the use of redundant marker genes improves cell type annotation in sparse scATAC-seq data, and simple aggregation of these marker genes achieves comparable or better performance than machine-learning classifiers. This suggests the potential of marker genes for downstream applications.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Oncology
Yuanshuai Su, Chen Xue, Xinyu Gu, Wankun Wang, Yu Sun, Renfang Zhang, Lanjuan Li
Summary: This study constructed a TAM-related gene model that is associated with the prognosis and immunotherapeutic response of hepatocellular carcinoma (HCC) patients by analyzing single-cell transcriptomic data. The model can predict patient survival and response to immunotherapy, and characterize the immune landscape and tumor immune escape status.
FRONTIERS IN ONCOLOGY
(2023)
Editorial Material
Multidisciplinary Sciences
Reinhard Hohlfeld, Roland S. Liblau
Summary: The clinical variability of multiple sclerosis aligns with the diversity of four previously unidentified autoantigens.
Article
Medicine, General & Internal
Ying Li, Xin Zhao, Qiang Liu, Yujie Liu
Summary: This study developed a prognostic macrophage marker genes signature (MMGS) for breast cancer, which showed effectiveness in stratifying patients and providing reference for immunotherapy decision-making.
ANNALS OF MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Zhimin Wu, Xu Wang, Hao Liang, Fangfang Liu, Yingxuan Li, Huaxing Zhang, Chunying Wang, Qiao Wang
Summary: This study aimed to explore the significant genes of dilated cardiomyopathy (DCM) by combining public database resources and a doxorubicin-induced DCM mouse model. Through the integration of multiple microarray datasets and animal experiments, three key differential genes (BEX1, RGCC, and VSIG4) associated with DCM were identified, along with important biological processes and a signaling pathway. These findings provide valuable insights into the pathogenesis of DCM and offer potential targets for future clinical management.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Shahana Sharmin, Fatima Tuj Zohura, Md. Sajedul Islam, Anika Shimonty, Md. Abdullah-Al-Kamran Khan, Rehana Parveen, Foujia Sharmin, Chowdhury Rafiqul Ahsan, Abul Bashar Mir Md. Khademul Islam, Mahmuda Yasmin
Summary: This study investigated the mutation frequency of five different genomic regions within the top three most frequently mutated genes in Bangladeshi patients with cervical cancer. The findings show that the observed mutation frequency in our patients is higher than those reported earlier in other parts of the world, except for KRAS. The study can serve as a basis for building a mutation database for cervical cancer in Bangladesh, with potential implications for future diagnostics and personalized medicine decisions.
Article
Neurosciences
Zachary Beine, Zimei Wang, Pantelis Tsoulfas, Murray G. Blackmore
Summary: This study analyzed neurons projecting from the brain to the spinal cord in mice, identifying 14 transcriptionally distinct cell types and marker genes. The findings provide insights into the molecular characteristics and physiological functions of supraspinal cell populations.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Haftom Baraki Abraha, Jae-Won Lee, Gayeong Kim, Mokhammad Khoiron Ferdiansyah, Rathnayaka Mudiyanselage Ramesha, Kwang-Pyo Kim
Summary: In this study, the genomic diversity of 61 BSPs was analyzed, and a comprehensive classification scheme was proposed. The identification of orthologs taxonomic signature genes contributed to phage taxonomy.
Article
Biochemistry & Molecular Biology
Christopher P. Chaney, Keri A. Drake, Thomas J. Carroll
Summary: Identifying genes that reliably mark distinct cell types is crucial for using single-cell RNA sequencing to enhance our understanding of organismal biology. This study demonstrates that applying an ensemble of differential expression methods robustly identifies genes that mark clustered cells with restricted expression, as validated by antisense mRNA in situ and immunofluorescence techniques. This technique can easily be extended to incorporate additional methods, leading to further improvements in performance.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Immunology
Peiru Wei, Mingyou Dong, Yin Bi, Saiqiong Chen, Weiyu Huang, Ting Li, Bo Liu, Xiaoqian Fu, Yihua Yang
Summary: The study identified 1293 macrophage marker genes through single-cell RNA sequencing analysis, and identified seven core genes closely related to recurrent miscarriage (RM) using various algorithms. A nomogram constructed from the expression levels of these genes showed high diagnostic value for RM, suggesting potential targets for preventative treatments.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Gastroenterology & Hepatology
Josef Ecker, Elisa Benedetti, Alida S. D. Kindt, Marcus Hoering, Markus Perl, Andrea Christel Machmueller, Anna Sichler, Johannes Plagge, Yuting Wang, Sebastian Zeissig, Andrej Shevchenko, Ralph Burkhardt, Jan Krumsiek, Gerhard Liebisch, Klaus-Peter Janssen
Summary: Analysis of the CRC lipidome revealed a robust TG-species signature with prognostic potential, shedding light on the importance of lipid metabolism abnormalities in CRC.
Article
Plant Sciences
Zhijun Zhang, Bin Huang, Jialu Chen, Yang Jiao, Hui Guo, Shenkui Liu, Muthusamy Ramakrishnan, Guoning Qi
Summary: This study identified 25 JRL genes in moso bamboo and found their important roles in plant growth, development, and abiotic stress response. These genes are unequally distributed among different genome scaffolds and are more closely related to JRL genes in Brachypodium distachyon. They exhibited different expression patterns in response to stress and hormone treatments.
FRONTIERS IN PLANT SCIENCE
(2022)