Article
Biochemical Research Methods
Xiaoshuai Zhang, Lixin Wang, Hucheng Liu, Xiaofeng Zhang, Bo Liu, Yadong Wang, Junyi Li
Summary: Protein is essential in living organisms and understanding its function is crucial for drug discovery and disease treatment. In this article, the authors propose the Prot2GO model, which integrates protein sequence and PPI network data to predict protein functions. The model achieves state-of-the-art performance on multiple metrics.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Bishnu Sarker, Navya Khare, Marie-Dominique Devignes, Sabeur Aridhi
Summary: This paper introduces the GrAPFI-GO method, which enhances the automatic annotation performance of protein functions by integrating semantic similarity and hierarchical relations between GO terms in a graph. Experimental results suggest that the proposed semantic hierarchical post-processing potentially improves the performance of GrAPFI-GO and other annotation tools as well.
BMC BIOINFORMATICS
(2022)
Article
Plant Sciences
Emily B. B. Sessa, Rishi R. R. Masalia, Nils Arrigo, Michael S. S. Barker, Jessie A. A. Pelosi
Summary: The article introduces a pipeline called GOgetter, which is a fast and easy-to-implement tool for obtaining, summarizing, and visualizing GO slim categories associated with a set of genes.
APPLICATIONS IN PLANT SCIENCES
(2023)
Article
Computer Science, Software Engineering
T. Harbig, M. Witte Paz, K. Nieselt
Summary: Analysis pipelines in genomics, transcriptomics, and proteomics often produce lists of genes that overlap only partially or not at all and are too large for manual comparison. This paper presents GO-Compass, a visual analytics tool that reduces the redundancy and improves interpretability of gene lists by using semantic similarity. GO-Compass offers interactive visualizations, such as hierarchical clustering, treemaps, heatmaps, and bar charts, to facilitate the comparison of GO terms and gene information.
COMPUTER GRAPHICS FORUM
(2023)
Article
Microbiology
Daniel Peterson, Tang Li, Ana M. Calvo, Yanbin Yin
Summary: The study provides new insights into phytopathogenicity in Ascomycota through comparative genomics, revealing that group-specific orthogroups have more enriched functional terms and certain functional terms show higher significance and occurrence in these orthogroups. The analysis also suggests that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than unique genes in each genome.
Article
Entomology
Surya Saha, Amanda M. Cooksey, Anna K. Childers, Monica F. Poelchau, Fiona M. McCarthy
Summary: This article presents a fast workflow for functional annotation of whole proteomes to generate Gene Ontology and pathways information, with applications to diverse arthropod genomes and comparisons to reference genomes. The performance of the predictions remains consistent across various arthropod genomes with different assembly and annotation qualities.
Article
Computer Science, Interdisciplinary Applications
Cheng Chen, Lingyun Luo, Chunlei Zheng, Pingjian Ding, Huan Liu, Hanyu Luo
Summary: This study proposes a machine-learning-based framework for auditing gene ontology by predicting and validating the relationships between concepts. By uncovering potential errors through predicting and validating the relationships in the gene ontology, this approach can help improve the quality and accuracy of the ontology.
JOURNAL OF BIOMEDICAL INFORMATICS
(2023)
Article
Biochemical Research Methods
Kokulapalan Wimalanathan, Carolyn J. Lawrence-Dill
Summary: The GOMAP pipeline is a high-throughput genome-scale GO annotation tool optimized for plants, with containerization increasing portability and reproducibility. Testing on multiple maize genomes showed that GOMAP expands the number of annotated genes and improves the quality of annotations per gene.
Article
Biochemical Research Methods
Annika L. Gable, Damian Szklarczyk, David Lyon, Joao F. Matias Rodrigues, Christian von Mering
Summary: A knowledge-based grouping of genes into pathways or functional units is crucial for understanding cellular complexity. This study evaluates and compares existing and novel functional classification systems in terms of their discovery power and generality in gene set enrichment testing. The results show structural and performance differences between classification systems, with well-established, hierarchically organized pathway annotation systems performing best overall. On the other hand, recent unsupervised annotation systems excel in understudied areas and organisms, detecting more specific pathways.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Wang Kang, Tong Jin, Tao Zhang, Shuai Ma, Haoteng Yan, Zunpeng Liu, Zhejun Ji, Yusheng Cai, Si Wang, Moshi Song, Jie Ren, Baoyang Hu, Qi Zhou, Weiqi Zhang, Jing Qu, Yiming Bao, Guang-Hui Liu
Summary: Regeneration plays a crucial role in biological development and damage repair, but its capacity declines with age. There is currently a lack of comprehensive database to collect and standardize the abundant data generated in regeneration research.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Mathematical & Computational Biology
Baiyang Feng, Jing Gao
Summary: This study utilized text mining tools to extract relevant entities and association relationships from a large number of anthrax biomedical literature, and constructed an anthrax knowledge graph. An interactive visualized knowledge portal was developed based on the knowledge graph. The portal provides rich and authentic knowledge in various forms, facilitating efficient research.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Biochemical Research Methods
Evangelos Karatzas, Fotis A. Baltoumas, Eleni Aplakidou, Panagiota Kontou, Panos Stathopoulos, Leonidas Stefanis, Pantelis G. Bagos, Georgios A. Pavlopoulos
Summary: This article introduces Flame (v2.0), a web tool that combines and visualizes results from popular functional enrichment applications. Flame utilizes aGOtool, g: Profiler, WebGestalt, and Enrichr pipelines to present their outputs separately or in combination. It offers interactive plots for intuitive representations and easier interpretation.
Review
Biochemistry & Molecular Biology
Sushma Naithani, Cecilia H. Deng, Sunil Kumar Sahu, Pankaj Jaiswal
Summary: The development of pan-genomics enables the identification and introduction of lost genes and alleles in crops, which can improve crop yield and resistance. This offers new avenues for targeted breeding and helps mitigate the impact of global climate change.
Article
Multidisciplinary Sciences
Jacob L. Steenwyk, Megan A. Phillips, Feng Yang, Swapneeta S. Date, Todd R. Graham, Judith Berman, Chris Todd Hittinger, Antonis Rokas
Summary: The evolutionary rates of functionally related genes are often correlated. A gene coevolution network was established by studying orthologous gene pairs of budding yeast species. The network modules provide insights into cellular and genomic structure and function. Analysis of deletion mutant data reveals that the neighborhood and connectivity of orthologous genes affect fitness in diverse environments.
Article
Genetics & Heredity
Guilherme Augusto Maia, Vilmar Benetti Filho, Eric Kazuo Kawagoe, Tatiany Aparecida Teixeira Soratto, Renato Simoes Moreira, Edmundo Carlos Grisard, Glauber Wagner
Summary: Assignment of gene function is crucial in genomics, but manual annotation is no longer feasible due to the increasing amounts of data. An integrated pipeline called AnnotaPipeline is introduced here, which uses experimental data to validate in silico predictions of gene function. The pipeline integrates different software and data types to annotate and validate predicted features in genomic sequences.
FRONTIERS IN GENETICS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Jinjun Chen, Hui-Lin Pan
JOURNAL OF NEUROCHEMISTRY
(2017)
Article
Plant Sciences
Lan Yang, Juan Tang, Jin-Jun Chen, Ai-Yun Peng, Qi-Ming Wang, Li-Qun Rao, Hua Yang, Xian-Wen Zhang, Huan-Zhi Yang, Chen Zhang, Guo-Ping Peng
JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH
(2019)
Article
Cell Biology
Jinjun Chen, Lingyong Li, Shao-Rui Chen, Hong Chen, Jing-Dun Xie, Rita E. Sirrieh, David M. MacLean, Yuhao Zhang, Meng-Hua Zhou, Vasanthi Jayaraman, Hui-Lin Pan
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Biochemistry & Molecular Biology
J. Chen, M. Deng, Q. He, E. Meng, L. Jiang, Z. Liao, M. Rong, S. Liang
CELLULAR AND MOLECULAR LIFE SCIENCES
(2008)
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Biochemistry & Molecular Biology
Liping Jiang, Dongyi Zhang, Yongqun Zhang, Li Peng, Jinjun Chen, Songping Liang
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS
(2010)
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Biotechnology & Applied Microbiology
Qingyang Liu, Tiehan Zhang, Nan Song, Qian Li, Zhi Wang, Xuewen Zhang, Xiangyang Lu, Jun Fang, Jinjun Chen
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2014)
Article
Biochemistry & Molecular Biology
Fang Qu, Qingwang Chen, Yiying Ding, Zihao Liu, Yan Zhao, Xuewen Zhang, Zikui Liu, Jinjun Chen
MOLECULAR BIOLOGY REPORTS
(2018)
Article
Biochemistry & Molecular Biology
Liping Jiang, Jinjun Chen, Li Peng, Yongqun Zhang, Xia Xiong, Songping Liang
Article
Biochemistry & Molecular Biology
Jinjun Chen, Yongqun Zhang, Mingqiang Rong, Liqun Zhao, Liping Jiang, Dongyi Zhang, Meichi Wang, Yucheng Mao, Songping Liang
Article
Biochemistry & Molecular Biology
Liping Jiang, Li Peng, Yongqun Zhang, Jinjun Chen, Dongyi Zhang, Songping Liang
Article
Multidisciplinary Sciences
Jianguo Zeng, Yisong Liu, Wei Liu, Xiubing Liu, Fuqing Liu, Peng Huang, Pengcheng Zhu, Jinjun Chen, Mingming Shi, Fang Guo, Pi Cheng, Jing Zeng, Yifang Liao, Jing Gong, Hong-Mei Zhang, Depeng Wang, An-Yuan Guo, Xingyao Xiong
Article
Zoology
Yongqun Zhang, Jinjun Chen, Xing Tang, Fan Wang, Liping Jiang, Xia Xiong, Meichi Wang, Mingqiang Rong, Zhonghua Liu, Songping Liang
Article
Oncology
Zhe Cao, Ping Wu, Min Su, Hongyan Ling, Ramina Khoshaba, Chenfei Huang, Han Gao, Yan Zhao, Jinjun Chen, Qianjin Liao, Deliang Cao, Junfei Jin, Xuewen Zhang
Article
Biotechnology & Applied Microbiology
Qingyang Liu, Keren Long, Fangjia Lu, Jinjun Chen
BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY
(2017)
Article
Pharmacology & Pharmacy
Li Li, De-Pei Li, Shao-Rui Chen, Jinjun Chen, Hongzhen Hu, Hui-Lin Pan
MOLECULAR PHARMACOLOGY
(2014)
Article
Pharmacology & Pharmacy
Mohammadhossein Movassaghghazani, Nazanin Shabansalmani
Summary: The study revealed high levels of AFM1 in both breast milk and powdered milk samples in Tehran, with some samples exceeding the established limits. Therefore, monitoring and regulating toxin levels in these products is crucial for maternal and infant health.
Article
Pharmacology & Pharmacy
Defeng Wen, Wantong Han, Quan Chen, Guanhui Qi, Mengling Gao, Pu Guo, Yu Liu, Zhongyuan Wu, Shulin Fu, Qirong Lu, Yinsheng Qiu
Summary: Luteolin can inhibit FB1-induced intestinal inflammatory injury by inhibiting the activation of NF-kappa B and ERK signaling pathways, according to network pharmacology and in vitro experiments.
