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Biochemistry & Molecular Biology
Lingyu Qiu, Chen Liang, Yidong Zheng, Huayu Kang, Aiyue Chen, Chunlin Chen, Xinlong Wang, Jielin Yang, Qiongfang Fang, Xinjie Hui, Yueming Hu, Zewei Chen, Ou Sha, Wei-Guo Zhu, Yejun Wang
Summary: This research systematically investigates stable expressed genes (SEGs) in humans at the single-cell level and observes their specificity in development, tissue, and cell types. The study identifies a list of 408 spatial-temporal SEGs and finds development-specific SEGs as well as tissue-specific SEGs with immune and RNA splicing functions. The research also explores the application of SEGs in cell decomposition and accurately predicts the proportions of major immune cells in peripheral blood samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Zelin Liu, Huiru Ding, Jianqi She, Chunhua Chen, Weiguang Zhang, Ence Yang
Summary: The study presents a software program DEBKS that efficiently and accurately detects differential back-splicing (BS) events in circular RNAs (circRNAs). This software is important for identifying differential BS events in circRNAs.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biotechnology & Applied Microbiology
Yong Liu, Jing Huang, Rajan Pandey, Pengyuan Liu, Bhavika Therani, Qiongzi Qiu, Sridhar Rao, Aron M. Geurts, Allen W. Cowley Jr, Andrew S. Greene, Mingyu Liang
Summary: This study found that in order to accurately identify differentially expressed genes (DEGs) with various characteristics in single-cell clusters, there need to be at least 2000 cells. However, for the majority of DEGs with extremely small p values or transcript abundance greater than a few hundred transcripts per million in bulk RNA-seq analysis, clusters with as few as 50-100 cells may be sufficient.
Article
Biochemistry & Molecular Biology
Dong Liu, Zhenzhen Hong, Lang Gui, Li Zhao, Yude Wang, Shengming Sun, Mingyou Li
Summary: In this study, PacBio RNA-seq was utilized to analyze the full-length transcriptomes of the brains and thoracic ganglia of Macrobrachium rosenbergii. The results revealed sexual dimorphism in the growth of this aquaculture prawn. Genes associated with protein processing pathways were also identified, and their regulation by multiple LncRNAs in different organs and sexes of the prawn was observed. These findings provide new theories and insights for studying the nervous system, sexual control, and growth dimorphism.
Article
Biotechnology & Applied Microbiology
Yao Dai, Yumeng Cao, Jens Kohler, Aiping Lu, Shaohua Xu, Haiyun Wang
Summary: This study identified OAZ1 and hsa-miR-6835-3p as the most reliable individual reference genes for mRNA and miRNA quantification in cancer exosomes. A combination of reference genes - OAZ1/SERF2/MPP1 for mRNA and hsa-miR-6835-3p/hsa-miR-4468-3p for miRNA analyses is recommended for superior accuracy.
Article
Biochemistry & Molecular Biology
Yu Zhang, Feng Zhang, Zekun Wang, Siyi Wu, Weidong Tian
Summary: scMAGIC is a method that uses well-annotated single-cell RNA sequencing data as a reference to assist in the classification of query data. It introduces a second round of reference-based classification to eliminate batch effects and performs well, especially when the query dataset is not completely covered by the reference dataset. Additionally, scMAGIC can also annotate query cells with high accuracy using an atlas dataset as a reference.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Musu Yuan, Liang Chen, Minghua Deng
Summary: The research introduces a robust deep learning-based single-cell Multiple Reference Annotator that effectively transfers knowledge from multiple insufficient reference datasets to unlabeled target data, while also removing batch effects.
Article
Plant Sciences
Sau-Shan Cheng, Yee-Shan Ku, Ming-Yan Cheung, Hon-Ming Lam
Summary: This study reports stable reference genes for gene expression studies in Arabidopsis thaliana. Using mass spectrometry-based analysis and validation with RT-qPCR, the results demonstrate the stability of these genes' expression during infection and stress treatments.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity Law, Sean Davis, Vincent Carey, Martin Morgan, Ralf Zimmer, Levi Waldron
Summary: Researchers developed a framework for assessing enrichment methods based on defined criteria, evaluated 10 major enrichment methods using a curated compendium of expression datasets, and provided practical recommendations for efficient interpretation of results when applying these methods.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agriculture, Dairy & Animal Science
Junxiao Ren, Quanlin Li, Qinghe Zhang, Michael Clinton, Congjiao Sun, Ning Yang
Summary: This study systematically identified lincRNAs in developing chicken embryos using Iso-Seq and RNA-Seq techniques, discovering a set of novel lincRNAs that share many characteristics with mammalian lincRNAs. The functional studies associated individual lincRNAs with specific GO functions, and a gene co-expression network analysis revealed stage-specific associations with genes involved in hematopoiesis and lipid metabolism. This research will serve as a valuable resource for studying lincRNA functions in the future.
Article
Cell & Tissue Engineering
Jonas Simon Fleck, Fatima Sanchis-Calleja, Zhisong He, Malgorzata Santel, Michael James Boyle, J. Gray Camp, Barbara Treutlein
Summary: Complex 3D models resembling brain structures generated from human stem cells provide exciting possibilities for studying brain development, disease, and evolution. However, understanding the heterogeneity observed within and between individual organoids remains a major challenge. Researchers have developed a computational tool (VoxHunt) to assess brain organoid patterning, developmental state, and cell identity through comparisons to spatial and single-cell transcriptome reference datasets.
Article
Entomology
Kakeru Yokoi, Takuya Tsubota, Akiya Jouraku, Hideki Sezutsu, Hidemasa Bono
Summary: In this study, reference transcriptome data for the silkworm was established and detailed examination of gene expression in silkworm tissues was performed. The results contribute to understanding silkworm biology and promoting industrial applications.
Article
Biotechnology & Applied Microbiology
Huseyin Basim, Esin Basim, Huseyin Tombuloglu, Turgay Unver
Summary: The transcriptome responses of Cmm-resistant and -susceptible tomato lines were compared after inoculation with Clavibacter michiganensis subsp. michiganensis. Differentially expressed genes were identified, with susceptible lines showing more genes involved in biological processes and molecular functions, while resistant lines exhibited distinct defense response and stress-related genes upon inoculation. This study provides insights for molecular breeding studies aiming to control the pathogen in tomato.
Article
Physiology
Guo Ding, Qionghua Gao, Jun Chen, Jie Zhao, Guojie Zhang, Weiwei Liu
Summary: This study validates reliable reference genes for RT-qPCR analysis in pharaoh ants and lays the foundation for future research.
FRONTIERS IN PHYSIOLOGY
(2022)
Review
Plant Sciences
Umair Ahmed, Qi Xie, Xueping Shi, Bo Zheng
Summary: This article reviews the importance of developing appropriate reference genes (RGs) for accurately quantifying gene expression levels, and discusses the strategies and processes for developing RGs using different techniques and methods. The most commonly used RGs in horticultural plants and their development strategies are also discussed in detail. The information provided in this article will help in designing effective strategies for developing RGs in horticultural plants.
CRITICAL REVIEWS IN PLANT SCIENCES
(2022)
Article
Microbiology
Jennifer C. Clifford, Alex Buchanan, Oliver Vining, Teresa A. Kidarsa, Jeff H. Chang, Kerry L. McPhail, Joyce E. Loper
ENVIRONMENTAL MICROBIOLOGY
(2016)
Editorial Material
Microbiology
Jeff H. Chang, Javier F. Tabima
Cell Host & Microbe
(2016)
Article
Plant Sciences
Khaled H. Almabruk, Jeff H. Chang, Taifo Mahmud
JOURNAL OF NATURAL PRODUCTS
(2016)
Article
Biochemistry & Molecular Biology
Welington L. Araujo, Allison L. Creason, Emy T. Mano, Aline A. Camargo-Neves, Sonia N. Minami, Jeff H. Chang, Joyce E. Loper
MOLECULAR PLANT-MICROBE INTERACTIONS
(2016)
Article
Multidisciplinary Sciences
Xiu-Fang Xin, Kinya Nomura, Kyaw Aung, Andre C. Velasquez, Jian Yao, Freddy Boutrot, Jeff H. Chang, Cyril Zipfel, Sheng Yang He
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Plant Sciences
Masaki Shimono, Yi-Ju Lu, Katie Porter, Brian H. Kvitko, Jessica Henty-Ridilla, Allison Creason, Sheng Yang He, Jeff H. Chang, Christopher J. Staiger, Brad Day
Article
Microbiology
Qing Yan, Benjamin Philmus, Cedar Hesse, Max Kohen, Jeff H. Chang, Joyce E. Loper
FRONTIERS IN MICROBIOLOGY
(2016)
Article
Multidisciplinary Sciences
Javier F. Tabima, Sydney E. Everhart, Meredith M. Larsen, Alexandra J. Weisberg, Zhian N. Kamvar, Matthew A. Tancos, Christine D. Smart, Jeff H. Chang, Niklaus J. Grunwald
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Biochemistry & Molecular Biology
Laura M. Beaver, Rachael Kuintzle, Alex Buchanan, Michelle W. Wiley, Sarah T. Glasser, Carmen P. Wong, Gavin S. Johnson, Jeff H. Chang, Christiane V. Lohr, David E. Williams, Roderick H. Dashwood, David A. Hendrix, Emily Ho
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2017)
Article
Plant Sciences
Skylar L. Fuller, Elizabeth A. Savory, Alexandra J. Weisberg, Jessica Z. Buser, Michael I. Gordon, Melodie L. Putnam, Jeff H. Chang
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Multidisciplinary Sciences
Eric R. Moore, Briana S. Bullington, Alexandra J. Weisberg, Yuan Jiang, Jeff Chang, Kimberly H. Halsey
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Biology
Elizabeth A. Savory, Skylar L. Fuller, Alexandra J. Weisberg, William J. Thomas, Michael I. Gordon, Danielle M. Stevens, Allison L. Creason, Michael S. Belcher, Maryna Serdani, Michele S. Wiseman, Niklaus J. Grunwald, Melodie L. Putnam, Jeff H. Chang
Article
Biology
Qing Yan, Benjamin Philmus, Jeff H. Chang, Joyce E. Loper
Review
Plant Sciences
Alexandra J. Weisberg, Yu wu, Jeff H. Chang, Erh-Min Lai, Chih-Horng Kuo
Summary: Agrobacteria are feared as agricultural pathogens, causing abnormalities and economic damage to plants, but they are also revered in the laboratory for their usefulness as models and tools in biological research. This review synthesizes elegant work on agrobacterial virulence mechanisms and ecology, emphasizing their genomic and plasmid characteristics, and highlights areas for further research.
ANNUAL REVIEW OF PHYTOPATHOLOGY
(2023)
Article
Microbiology
Brett L. Mellbye, Edward W. Davis, Eva Spieck, Jeff H. Chang, Peter J. Bottomley, Luis A. Sayavedra-Soto
GENOME ANNOUNCEMENTS
(2017)