Article
Biotechnology & Applied Microbiology
Wenxiang Lu, Qin Zhou, Yi Chen
Summary: RNA sequencing is an innovative technology for studying transcriptomes, but clinical specimens face challenges due to sample degradation. This study replicated the process of RNA degradation and found that even slight levels of degradation can significant affect RNA expression.
Article
Microbiology
Lorena Azevedo de Lima, Kristina Reinmets, Lars Keld Nielsen, Esteban Marcellin, Audrey Harris, Michael Kopke, Kaspar Valgepea
Summary: RNA sequencing (RNA-seq) is a widely used technique for transcriptome analysis, but the choice of library preparation kits can significantly impact the results. Different commercial products show significant differences in rRNA removal, strand specificity, and transcript abundance distribution. Selecting appropriate sample processing workflows and products is crucial for RNA-seq studies.
MICROBIOLOGY SPECTRUM
(2022)
Article
Genetics & Heredity
Michael Schwabe, Sven Griep, Henrike Schmidtberg, Rudy Plarre, Alexander Goesmann, Andreas Vilcinskas, Heiko Vogel, Karina Brinkrolf
Summary: The clothes moth Tineola bisselliella is capable of digesting keratin, and the analysis of its gut transcriptome reveals various enzymes involved in keratin digestion. Additionally, the unstable intestinal microbiome of T. bisselliella larvae may play a role in keratin digestion.
Review
Environmental Sciences
Tessa M. Page, Jonathan W. Lawley
Summary: As we enter the United Nations Decade of Ocean Science for Sustainable Development, efforts to reverse ocean health decline are urgent. Transcriptomic technologies are playing an increasingly important role in marine ecology research, providing researchers with valuable tools to understand genetic variation, cellular processes, and pathways.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biology
Roberto Vera Alvarez, Lorinc Pongor, Leonardo Marino-Ramirez, David Landsman
Summary: PM4NGS is a project management framework for NGS data analysis, providing a standard organizational structure, bioinformatics tool management, and data analysis pipelines. It is easy to install and use on personal computers and laptops, aiming to bridge the gap between researchers in experimental laboratories and data analysis workflows.
Article
Biochemistry & Molecular Biology
Desalegn D. Serba, Xiaoxi Meng, James Schnable, Elfadil Bashir, J. P. Michaud, P. V. Vara Prasad, Ramasamy Perumal
Summary: The study used RNA-Seq technology to analyze the effects of sugarcane aphid on moderately resistant and susceptible genotypes, revealing transcriptome differences between the two genotypes at multiple time points after infestation by SCA. The resistant genotype exhibited differential expression of several gene clusters during SCA infestation, while the susceptible genotype showed a series of down-regulated genes on the basis of the resistant genotype.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Christos Tzaferis, Evangelos Karatzas, Fotis A. Baltoumas, Georgios A. Pavlopoulos, George Kollias, Dimitris Konstantopoulos
Summary: Analysis and interpretation of high-throughput transcriptional and chromatin accessibility data at single-cell resolution remain challenges in the biomedical field. SCALA is a bioinformatics tool for analyzing and visualizing single-cell RNA sequencing and Assay for Transposase-Accessible Chromatin using sequencing data-sets. It offers independent or integrative analysis options and various analysis modules to aid biomedical researchers in exploring, analyzing, and visualizing their data without coding experience.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Nutrition & Dietetics
Hun Hwan Kim, Sang Eun Ha, Min Yeong Park, Se Hyo Jeong, Pritam Bhagwan Bhosale, Abuyaseer Abusaliya, Chung Kil Won, Jeong Doo Heo, Meejung Ahn, Je Kyung Seong, Hyun Wook Kim, Gon Sup Kim
Summary: Using RNA sequencing, this study identified KYNA as a potential therapeutic target for gastric cancer. KYNA treatment inhibited cancer cell growth and proliferation, while inducing cell death. This research can provide valuable insights for the development of drugs targeting gastric cancer.
Article
Microbiology
Juliet F. Nilsson, Lucas G. Castellani, Walter O. Draghi, Ezequiel G. Mogro, Daniel Wibberg, Anika Winkler, L. H. Hansen, Andreas Schluter, Alfred Puhler, Jorn Kalinowski, Gonzalo A. Torres Tejerizo, Mariano Pistorio
Summary: Acidic environments and improper agricultural management can lead to soil acidification globally, impacting the interaction between plants and rhizobia. Research on Rhizobium favelukesii revealed that under acidic conditions, 60% of genes were underexpressed. Transcriptome sequencing identified mechanisms including changes in energy metabolism and protein turnover, as well as GABA and histidine metabolism, contributing to acid tolerance in the bacteria.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Biochemical Research Methods
Fei Wu, Yao-Zhong Liu, Binhua Ling
Summary: A software pipeline called MTD was developed to comprehensively analyze and correlate host and meta-transcriptome information, providing insights into the interaction between microbiome and host transcriptome. MTD is a convenient tool that offers valuable genomics insights for researchers.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Genetics & Heredity
Giulia Carangelo, Alberto Magi, Roberto Semeraro
Summary: Single cell RNA sequencing (scRNA-seq) is a common and powerful technology in biomedical research, allowing for the analysis of the entire transcriptome of individual cells and revealing the heterogeneity of complex clinical samples. With advancements in technology and computation, scRNA-seq has become an important tool in biomedical research.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Juan-Carlos A. Padilla, Seda Barutcu, Ludovic Malet, Gabrielle Deschamps-Francoeur, Virginie Calderon, Eunjeong Kwon, Eric Lecuyer
Summary: This study provides novel insights into the compositional diversity of poly-A transcript isoforms enriched within EVs and highlights the potential usefulness of nanopore sequencing in interrogating secreted RNA transcriptomes.
Article
Ecology
Bing Zhang, Xinyu Li, Yusuo Jiang, Jinjia Liu, Jiangchao Zhang, Weihua Ma
Summary: High temperature affects behavior, physiology, survival, and gene expression in honeybees. This study compared the gene expression profiles of adult worker bees at 25 and 45 degrees C and identified 277 differentially expressed genes (DEGs). The DEGs were enriched for protein folding, unfold protein binding, heme binding, protein processing in endoplasmic reticulum, and longevity regulating pathway. Moreover, the expression patterns of some DEGs were found to be higher in the thorax, suggesting its importance in the response to heat stress. This study provides valuable insights into heat resistance-related genes.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2023)
Article
Biochemical Research Methods
Panagiotis Moulos
Summary: This article introduces a software package called recoup, which can visualize genomic coverage profiles generated from Next Generation Sequencing data quickly, flexibly, comprehensively, while also considering ease of use and reusability.
BMC BIOINFORMATICS
(2021)
Article
Dermatology
Angelique N. Voorberg, Hanna Niehues, Jart A. F. Oosterhaven, Geertruida L. E. Romeijn, Ivonne M. J. J. Vlijmen-Willems, Piet E. J. Erp, Thomas H. A. Ederveen, Patrick L. J. M. Zeeuwen, Marie L. A. Schuttelaar
Summary: Hand eczema is a common inflammatory skin condition of the hands with unknown pathogenesis. Through RNA-sequencing analysis, this study found significantly elevated expression of genes/proteins related to keratinocyte host defense and inflammation in lesional skin of patients with vesicular hand eczema.
EXPERIMENTAL DERMATOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chan Jiao, Lin Li, Pei Zhang, Li Zhang, Ke Li, Riqun Fang, Lei Yuan, Kaixuan Shi, Linan Pan, Qiannan Guo, Xiao Gao, Geng Chen, Shichen Xu, Qingwei Wang, Di Zuo, Wei Wu, Shanlou Qiao, Xiaoshuang Wang, Robb Moses, Jianru Xiao, Lei Li, Yongyan Dang, Xiaotao Li
CELL DEATH AND DIFFERENTIATION
(2020)
Article
Biochemistry & Molecular Biology
Lu Tong, Shihui Shen, Quan Huang, Junjiang Fu, Tianzhen Wang, Linian Pan, Pei Zhang, Geng Chen, Tingmei Huang, Ke Li, Qingwu Liu, Shaofang Xie, Xiao Yang, Robb E. Moses, Xiaotao Li, Lei Li
CELL DEATH AND DIFFERENTIATION
(2020)
Article
Biochemistry & Molecular Biology
Wubin Ding, Jiwei Chen, Guoshuang Feng, Geng Chen, Jun Wu, Yongli Guo, Xin Ni, Tieliu Shi
NUCLEIC ACIDS RESEARCH
(2020)
Article
Cell Biology
Yunjin Li, Qiyue Xu, Lu Ma, Duojiao Wu, Jie Gao, Geng Chen, Hua Li
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2020)
Article
Biochemistry & Molecular Biology
Xiangjun Ji, Peng Li, James C. Fuscoe, Geng Chen, Wenzhong Xiao, Leming Shi, Baitang Ning, Zhichao Liu, Huixiao Hong, Jun Wu, Jinghua Liu, Lei Guo, David P. Kreil, Pawel P. Labaj, Liping Zhong, Wenjun Bao, Yong Huang, Jian He, Yongxiang Zhao, Weida Tong, Tieliu Shi
NUCLEIC ACIDS RESEARCH
(2020)
Letter
Biology
Yunjin Li, Jiwei Chen, Qiyue Xu, Zebei Han, Fei Tan, Tieliu Shi, Geng Chen
SCIENCE CHINA-LIFE SCIENCES
(2021)
Article
Multidisciplinary Sciences
Xiao Gao, Qingwei Wang, Ying Wang, Jiang Liu, Shuang Liu, Jian Liu, Xingli Zhou, Li Zhou, Hui Chen, Linian Pan, Jiwei Chen, Da Wang, Qing Zhang, Shihui Shen, Yu Xiao, Zhipeng Wu, Yiyun Cheng, Geng Chen, Syeda Krubra, Jun Qin, Lan Huang, Pei Zhang, Chuangui Wang, Robb E. Moses, David M. Lonard, Bert W. O'Malley, Fuad Fares, Bianhong Zhang, Xiaotao Li, Lei Li, Jianru Xiao
NATURE COMMUNICATIONS
(2020)
Correction
Multidisciplinary Sciences
Xiao Gao, Qingwei Wang, Ying Wang, Jiang Liu, Shuang Liu, Jian Liu, Xingli Zhou, Li Zhou, Hui Chen, Linian Pan, Jiwei Chen, Da Wang, Qing Zhang, Shihui Shen, Yu Xiao, Zhipeng Wu, Yiyun Cheng, Geng Chen, Syeda Kubra, Jun Qin, Lan Huang, Pei Zhang, Chuangui Wang, Robb E. Moses, David M. Lonard, Bert W. O' Malley, Fuad Fares, Bianhong Zhang, Xiaotao Li, Lei Li, Jianru Xiao
NATURE COMMUNICATIONS
(2020)
Review
Cell Biology
Yunjin Li, Qiyue Xu, Duojiao Wu, Geng Chen
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2020)
Article
Pharmacology & Pharmacy
Fanhua Wang, Lu Ma, Yi Ding, Liang He, Mingzhi Chang, Yingquan Shan, Stefan Siwko, Geng Chen, Yuwei Liu, Yunyun Jin, Xiaochun Peng, Jian Luo
Summary: The study identified Gpr84 as the receptor for medium-chain fatty acids in chondrocytes, showing that deficiency of Gpr84 exacerbated cartilage degradation in OA pathogenesis. Activation of Gpr84 enhanced cartilage extracellular matrix generation and protected against OA degeneration, without severe cartilaginous side effects.
PHARMACOLOGICAL RESEARCH
(2021)
Editorial Material
Genetics & Heredity
Geng Chen
FRONTIERS IN GENETICS
(2021)
Review
Biochemical Research Methods
Yunjin Li, Lu Ma, Duojiao Wu, Geng Chen
Summary: Multi-omics allows for a comprehensive understanding of biological systems by integrating information flow from different omics layers, playing a significant role in systems biology and precision medicine. Single-cell technologies are valuable for studying cellular dynamics and heterogeneity, while bulk technologies are more suitable for individual or population-level investigations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Oncology
Geng Chen, Jing Zhang, Qiaoting Fu, Valerie Taly, Fei Tan
Summary: The innovation of liquid biopsy and the integration of different tumor-derived omics data hold great potential in revolutionizing cancer management by enabling early diagnosis and timely treatment. By analyzing multiple types of tumor-derived components from body fluids, such as genomics, epigenetics, fragmentomics, and proteomics, the accuracy of cancer detection and monitoring can be improved compared to analyzing single modality data alone.
BRITISH JOURNAL OF CANCER
(2023)
Correction
Oncology
Geng Chen, Jing Zhang, Qiaoting Fu, Valerie Taly, Fei Tan
BRITISH JOURNAL OF CANCER
(2023)
Article
Biochemistry & Molecular Biology
Li Fang, Yunjin Li, Lu Ma, Qiyue Xu, Fei Tan, Geng Chen
Summary: Studying gene regulatory networks is crucial for understanding disease pathogenesis, but there is a lack of comprehensive single-cell level databases. By predicting GRNs in various physiological and pathological conditions for humans and mice, the development of the freely accessible database GRNdb provides a valuable resource for the scientific community.
NUCLEIC ACIDS RESEARCH
(2021)