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Article ; Online: CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species.

Chiang, Tai-Wei / Mai, Te-Lun / Chuang, Trees-Juen

2022 Volume 23, Issue 1, Page(s) 164

Abstract: Background: Circular RNAs (circRNAs) are a class of non-coding RNAs formed by pre-mRNA back-splicing, which are widely expressed in animal/plant cells and often play an important role in regulating microRNA (miRNA) activities. While numerous databases ... ...

Abstract	Background: Circular RNAs (circRNAs) are a class of non-coding RNAs formed by pre-mRNA back-splicing, which are widely expressed in animal/plant cells and often play an important role in regulating microRNA (miRNA) activities. While numerous databases have collected a large amount of predicted circRNA candidates and provided the corresponding circRNA-regulated interactions, a stand-alone package for constructing circRNA-miRNA-mRNA interactions based on user-identified circRNAs across species is lacking. Results: We present CircMiMi (circRNA-miRNA-mRNA interactions), a modular, Python-based software to identify circRNA-miRNA-mRNA interactions across 18 species (including 16 animals and 2 plants) with the given coordinates of circRNA junctions. The CircMiMi-constructed circRNA-miRNA-mRNA interactions are derived from circRNA-miRNA and miRNA-mRNA axes with the support of computational predictions and/or experimental data. CircMiMi also allows users to examine alignment ambiguity of back-splice junctions for checking circRNA reliability and examine reverse complementary sequences residing in the sequences flanking the circularized exons for investigating circRNA formation. We further employ CircMiMi to identify circRNA-miRNA-mRNA interactions based on the circRNAs collected in NeuroCirc, a large-scale database of circRNAs in the human brain. We construct circRNA-miRNA-mRNA interactions comprising differentially expressed circRNAs, and miRNAs in autism spectrum disorder (ASD) and cross-species analyze the relevance of the targets to ASD. We thus provide a rich set of ASD-associated circRNA-miRNA-mRNA axes and a useful starting point for investigation of regulatory mechanisms in ASD pathophysiology. Conclusions: CircMiMi allows users to identify circRNA-mediated interactions in multiple species, shedding light on regulatory roles of circRNAs. The software package and web interface are freely available at https://github.com/TreesLab/CircMiMi and http://circmimi.genomics.sinica.edu.tw/ , respectively.
MeSH term(s)	Animals ; Autism Spectrum Disorder ; Gene Regulatory Networks ; MicroRNAs/genetics ; RNA, Circular ; RNA, Messenger/genetics ; Reproducibility of Results ; Software
Chemical Substances	MicroRNAs ; RNA, Circular ; RNA, Messenger
Language	English
Publishing date	2022-05-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2041484-5
ISSN	1471-2105 ; 1471-2105
ISSN (online)	1471-2105
ISSN	1471-2105
DOI	10.1186/s12859-022-04692-0
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Article ; Online: A-to-I RNA editing contributes to the persistence of predicted damaging mutations in populations.

Mai, Te-Lun / Chuang, Trees-Juen

Genome research

2019 Volume 29, Issue 11, Page(s) 1766–1776

Abstract: Adenosine-to-inosine (A-to-I) RNA editing is a very common co-/posttranscriptional modification that can lead to A-to-G changes at the RNA level and compensate for G-to-A genomic changes to a certain extent. It has been shown that each healthy individual ...

Abstract	Adenosine-to-inosine (A-to-I) RNA editing is a very common co-/posttranscriptional modification that can lead to A-to-G changes at the RNA level and compensate for G-to-A genomic changes to a certain extent. It has been shown that each healthy individual can carry dozens of missense variants predicted to be severely deleterious. Why strongly detrimental variants are preserved in a population and not eliminated by negative natural selection remains mostly unclear. Here, we ask if RNA editing correlates with the burden of deleterious A/G polymorphisms in a population. Integrating genome and transcriptome sequencing data from 447 human lymphoblastoid cell lines, we show that nonsynonymous editing activities (prevalence/level) are negatively correlated with the deleteriousness of A-to-G genomic changes and positively correlated with that of G-to-A genomic changes within the population. We find a significantly negative correlation between nonsynonymous editing activities and allele frequency of A within the population. This negative editing-allele frequency correlation is particularly strong when editing sites are located in highly important genes/loci. Examinations of deleterious missense variants from the 1000 Genomes Project further show a significantly higher proportion of rare missense mutations for G-to-A changes than for other types of changes. The proportion for G-to-A changes increases with increasing deleterious effects of the changes. Moreover, the deleteriousness of G-to-A changes is significantly positively correlated with the percentage of editing enzyme binding motifs at the variants. Overall, we show that nonsynonymous editing is associated with the increased burden of G-to-A missense mutations in healthy individuals, expanding RNA editing in pathogenomics studies.
MeSH term(s)	Adenosine/genetics ; Gene Frequency ; Humans ; Inosine/genetics ; Mutation, Missense ; RNA/genetics ; RNA Editing
Chemical Substances	Inosine (5A614L51CT) ; RNA (63231-63-0) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2019-09-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1284872-4
ISSN	1549-5469 ; 1088-9051 ; 1054-9803
ISSN (online)	1549-5469
ISSN	1088-9051 ; 1054-9803
DOI	10.1101/gr.246033.118
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Article ; Online: Trans-genetic effects of circular RNA expression quantitative trait loci and potential causal mechanisms in autism.

Mai, Te-Lun / Chen, Chia-Ying / Chen, Yu-Chen / Chiang, Tai-Wei / Chuang, Trees-Juen

Molecular psychiatry

2022 Volume 27, Issue 11, Page(s) 4695–4706

Abstract: Genetic risk variants and transcriptional expression changes in autism spectrum disorder (ASD) were widely investigated, but their causal relationship remains largely unknown. Circular RNAs (circRNAs) are abundant in brain and often serve as upstream ... ...

Abstract	Genetic risk variants and transcriptional expression changes in autism spectrum disorder (ASD) were widely investigated, but their causal relationship remains largely unknown. Circular RNAs (circRNAs) are abundant in brain and often serve as upstream regulators of mRNAs. By integrating RNA-sequencing with genotype data from autistic brains, we assessed expression quantitative trait loci of circRNAs (circQTLs) that cis-regulated expression of nearby circRNAs and trans-regulated expression of distant genes (trans-eGenes) simultaneously. We thus identified 3619 circQTLs that were also trans-eQTLs and constructed 19,804 circQTL-circRNA-trans-eGene regulatory axes. We conducted two different types of approaches, mediation and partial correlation tests (MPT), to determine the axes with mediation effects of circQTLs on trans-eGene expression through circRNA expression. We showed that the mediation effects of the circQTLs (trans-eQTLs) on circRNA expression were positively correlated with the magnitude of circRNA-trans-eGene correlation of expression profile. The positive correlation became more significant after adjustment for the circQTLs. Of the 19,804 axes, 8103 passed MPT. Meanwhile, we performed causal inference test (CIT) and identified 2070 circQTL-trans-eGene-ASD diagnosis propagation paths. We showed that the CIT-passing genes were significantly enriched for ASD risk genes, genes encoding postsynaptic density proteins, and other ASD-relevant genes, supporting the relevance of the CIT-passing genes to ASD pathophysiology. Integration of MPT- and CIT-passing axes further constructed 352 circQTL-circRNA-trans-eGene-ASD diagnosis propagation paths, wherein the circRNA-trans-eGene axes may act as causal mediators for the circQTL-ASD diagnosis associations. These analyses were also successfully applied to an independent dataset from schizophrenia brains. Collectively, this study provided the first framework for systematically investigating trans-genetic effects of circQTLs and inferring the corresponding causal relations in diseases. The identified circQTL-circRNA-trans-eGene regulatory interactions, particularly the internal modules that were previously implicated in the examined disorders, also provided a helpful dataset for further investigating causative biology and cryptic regulatory mechanisms underlying the neuropsychiatric diseases.
MeSH term(s)	Humans ; RNA, Circular/genetics ; Autism Spectrum Disorder/genetics ; Quantitative Trait Loci/genetics ; RNA, Messenger/genetics ; Sequence Analysis, RNA ; MicroRNAs/genetics ; Gene Expression Profiling ; Gene Regulatory Networks ; RNA/genetics
Chemical Substances	RNA, Circular ; RNA, Messenger ; MicroRNAs ; RNA (63231-63-0)
Language	English
Publishing date	2022-08-12
Publishing country	England
Document type	Journal Article
ZDB-ID	1330655-8
ISSN	1476-5578 ; 1359-4184
ISSN (online)	1476-5578
ISSN	1359-4184
DOI	10.1038/s41380-022-01714-4
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Article ; Online: Multipathway regulation induced by 4-(phenylsulfonyl)morpholine derivatives against triple-negative breast cancer.

Yang, Fan-Wei / Mai, Te-Lun / Lin, Ying-Chung Jimmy / Chen, Yu-Chen / Kuo, Shang-Che / Lin, Chia-Ming / Lee, Meng-Hsuan / Su, Jung-Chen

Archiv der Pharmazie

2024 Volume 357, Issue 5, Page(s) e2300435

Abstract: Phenotypic drug discovery (PDD) is an effective drug discovery approach by observation of therapeutic effects on disease phenotypes, especially in complex disease systems. Triple-negative breast cancer (TNBC) is composed of several complex disease ... ...

Abstract	Phenotypic drug discovery (PDD) is an effective drug discovery approach by observation of therapeutic effects on disease phenotypes, especially in complex disease systems. Triple-negative breast cancer (TNBC) is composed of several complex disease features, including high tumor heterogeneity, high invasive and metastatic potential, and a lack of effective therapeutic targets. Therefore, identifying effective and novel agents through PDD is a current trend in TNBC drug development. In this study, 23 novel small molecules were synthesized using 4-(phenylsulfonyl)morpholine as a pharmacophore. Among these derivatives, GL24 (4m) exhibited the lowest half-maximal inhibitory concentration value (0.90 µM) in MDA-MB-231 cells. To investigate the tumor-suppressive mechanisms of GL24, transcriptomic analyses were used to detect the perturbation for gene expression upon GL24 treatment. Followed by gene ontology (GO) analysis, gene set enrichment analysis (GSEA), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, multiple ER stress-dependent tumor suppressive signals were identified, such as unfolded protein response (UPR), p53 pathway, G2/M checkpoint, and E2F targets. Most of the identified pathways triggered by GL24 eventually led to cell-cycle arrest and then to apoptosis. In summary, we developed a novel 4-(phenylsulfonyl)morpholine derivative GL24 with a strong potential for inhibiting TNBC cell growth through ER stress-dependent tumor suppressive signals.
MeSH term(s)	Triple Negative Breast Neoplasms/pathology ; Triple Negative Breast Neoplasms/drug therapy ; Humans ; Morpholines/pharmacology ; Morpholines/chemical synthesis ; Morpholines/chemistry ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/chemical synthesis ; Antineoplastic Agents/chemistry ; Female ; Cell Proliferation/drug effects ; Cell Line, Tumor ; Structure-Activity Relationship ; Apoptosis/drug effects ; Drug Screening Assays, Antitumor ; Dose-Response Relationship, Drug ; Gene Expression Regulation, Neoplastic/drug effects ; Molecular Structure
Chemical Substances	Morpholines ; Antineoplastic Agents
Language	English
Publishing date	2024-02-05
Publishing country	Germany
Document type	Journal Article
ZDB-ID	6381-2
ISSN	1521-4184 ; 0365-6233 ; 1437-1014
ISSN (online)	1521-4184
ISSN	0365-6233 ; 1437-1014
DOI	10.1002/ardp.202300435
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Article: Synchronization and Inter-Layer Interactions of Noise-Driven Neural Networks.

Yuniati, Anis / Mai, Te-Lun / Chen, Chi-Ming

Frontiers in computational neuroscience

2017 Volume 11, Page(s) 2

Abstract: In this study, we used the Hodgkin-Huxley (HH) model of neurons to investigate the phase diagram of a developing single-layer neural network and that of a network consisting of two weakly coupled neural layers. These networks are noise driven and learn ... ...

Abstract	In this study, we used the Hodgkin-Huxley (HH) model of neurons to investigate the phase diagram of a developing single-layer neural network and that of a network consisting of two weakly coupled neural layers. These networks are noise driven and learn through the spike-timing-dependent plasticity (STDP) or the inverse STDP rules. We described how these networks transited from a non-synchronous background activity state (BAS) to a synchronous firing state (SFS) by varying the network connectivity and the learning efficacy. In particular, we studied the interaction between a SFS layer and a BAS layer, and investigated how synchronous firing dynamics was induced in the BAS layer. We further investigated the effect of the inter-layer interaction on a BAS to SFS repair mechanism by considering three types of neuron positioning (random, grid, and lognormal distributions) and two types of inter-layer connections (random and preferential connections). Among these scenarios, we concluded that the repair mechanism has the largest effect for a network with the lognormal neuron positioning and the preferential inter-layer connections.
Language	English
Publishing date	2017-01-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452964-3
ISSN	1662-5188
ISSN	1662-5188
DOI	10.3389/fncom.2017.00002
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Article ; Online: Visualizing the GPCR Network: Classification and Evolution.

Hu, Geng-Ming / Mai, Te-Lun / Chen, Chi-Ming

Scientific reports

2017 Volume 7, Issue 1, Page(s) 15495

Abstract: In this study, we delineate an unsupervised clustering algorithm, minimum span clustering (MSC), and apply it to detect G-protein coupled receptor (GPCR) sequences and to study the GPCR network using a base dataset of 2770 GPCR and 652 non-GPCR sequences. ...

Abstract	In this study, we delineate an unsupervised clustering algorithm, minimum span clustering (MSC), and apply it to detect G-protein coupled receptor (GPCR) sequences and to study the GPCR network using a base dataset of 2770 GPCR and 652 non-GPCR sequences. High detection accuracy can be achieved with a proper dataset. The clustering results of GPCRs derived from MSC show a strong correlation between their sequences and functions. By comparing our level 1 MSC results with the GPCRdb classification, the consistency is 87.9% for the fourth level of GPCRdb, 89.2% for the third level, 98.4% for the second level, and 100% for the top level (the lowest resolution level of GPCRdb). The MSC results of GPCRs can be well explained by estimating the selective pressure of GPCRs, as exemplified by investigating the largest two subfamilies, peptide receptors (PRs) and olfactory receptors (ORs), in class A GPCRs. PRs are decomposed into three groups due to a positive selective pressure, whilst ORs remain as a single group due to a negative selective pressure. Finally, we construct and compare phylogenetic trees using distance-based and character-based methods, a combination of which could convey more comprehensive information about the evolution of GPCRs.
MeSH term(s)	Algorithms ; Amino Acid Sequence/genetics ; Cluster Analysis ; Databases, Protein ; Datasets as Topic ; Evolution, Molecular ; Molecular Sequence Annotation ; Phylogeny ; Receptors, G-Protein-Coupled/chemistry ; Receptors, G-Protein-Coupled/classification ; Receptors, G-Protein-Coupled/genetics ; Sequence Alignment ; Sequence Analysis, Protein
Chemical Substances	Receptors, G-Protein-Coupled
Language	English
Publishing date	2017-11-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-017-15707-9
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Article ; Online: Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions.

Mai, Te-Lun / Hu, Geng-Ming / Chen, Chi-Ming

Journal of proteome research

2016 Volume 15, Issue 7, Page(s) 2123–2131

Abstract: Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this ... ...

Abstract	Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence-structure-function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard's similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence-structure-function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences.
MeSH term(s)	Amino Acid Sequence ; Cluster Analysis ; Enzymes/classification ; Evolution, Molecular ; Protein Conformation ; Protein Interaction Maps ; Structure-Activity Relationship
Chemical Substances	Enzymes
Language	English
Publishing date	2016-07-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.5b01031
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Article ; Online: Clustering and visualizing similarity networks of membrane proteins.

Hu, Geng-Ming / Mai, Te-Lun / Chen, Chi-Ming

Proteins

2015 Volume 83, Issue 8, Page(s) 1450–1461

Abstract: We proposed a fast and unsupervised clustering method, minimum span clustering (MSC), for analyzing the sequence-structure-function relationship of biological networks, and demonstrated its validity in clustering the sequence/structure similarity ... ...

Abstract	We proposed a fast and unsupervised clustering method, minimum span clustering (MSC), for analyzing the sequence-structure-function relationship of biological networks, and demonstrated its validity in clustering the sequence/structure similarity networks (SSN) of 682 membrane protein (MP) chains. The MSC clustering of MPs based on their sequence information was found to be consistent with their tertiary structures and functions. For the largest seven clusters predicted by MSC, the consistency in chain function within the same cluster is found to be 100%. From analyzing the edge distribution of SSN for MPs, we found a characteristic threshold distance for the boundary between clusters, over which SSN of MPs could be properly clustered by an unsupervised sparsification of the network distance matrix. The clustering results of MPs from both MSC and the unsupervised sparsification methods are consistent with each other, and have high intracluster similarity and low intercluster similarity in sequence, structure, and function. Our study showed a strong sequence-structure-function relationship of MPs. We discussed evidence of convergent evolution of MPs and suggested applications in finding structural similarities and predicting biological functions of MP chains based on their sequence information.
MeSH term(s)	Algorithms ; Cluster Analysis ; Computational Biology/methods ; Databases, Protein ; Markov Chains ; Membrane Proteins/chemistry ; Membrane Proteins/classification ; Membrane Proteins/physiology ; Sequence Homology, Amino Acid
Chemical Substances	Membrane Proteins
Language	English
Publishing date	2015-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.24832
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Article: Visualizing and Clustering Protein Similarity Networks: Sequences, Structures, and Functions

Mai, Te-Lun / Hu Geng-Ming / Chen Chi-Ming

Journal of Proteome Research. 2016 July 01, v. 15, no. 7

2016

Abstract	Research in the recent decade has demonstrated the usefulness of protein network knowledge in furthering the study of molecular evolution of proteins, understanding the robustness of cells to perturbation, and annotating new protein functions. In this study, we aimed to provide a general clustering approach to visualize the sequence–structure–function relationship of protein networks, and investigate possible causes for inconsistency in the protein classifications based on sequences, structures, and functions. Such visualization of protein networks could facilitate our understanding of the overall relationship among proteins and help researchers comprehend various protein databases. As a demonstration, we clustered 1437 enzymes by their sequences and structures using the minimum span clustering (MSC) method. The general structure of this protein network was delineated at two clustering resolutions, and the second level MSC clustering was found to be highly similar to existing enzyme classifications. The clustering of these enzymes based on sequence, structure, and function information is consistent with each other. For proteases, the Jaccard’s similarity coefficient is 0.86 between sequence and function classifications, 0.82 between sequence and structure classifications, and 0.78 between structure and function classifications. From our clustering results, we discussed possible examples of divergent evolution and convergent evolution of enzymes. Our clustering approach provides a panoramic view of the sequence–structure–function network of proteins, helps visualize the relation between related proteins intuitively, and is useful in predicting the structure and function of newly determined protein sequences.
Keywords	amino acid sequences ; convergent evolution ; databases ; divergent evolution ; prediction ; proteinases ; proteins ; proteome
Language	English
Dates of publication	2016-0701
Size	p. 2123-2131.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021%2Facs.jproteome.5b01031
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species.

Hung, Li-Yuan / Chen, Yen-Ju / Mai, Te-Lun / Chen, Chia-Ying / Yang, Min-Yu / Chiang, Tai-Wei / Wang, Yi-Da / Chuang, Trees-Juen

Genome biology and evolution

2018 Volume 10, Issue 2, Page(s) 521–537

Abstract: Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence ... ...

Abstract	Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence editing sites using clustering and conservation strategies based on RNA sequencing data alone, without using single-nucleotide polymorphism information or genome sequencing data from the same sample. We thereby unveil the first evolutionary landscape of A-to-I editing maps across 20 metazoan species (from worm to human), providing unprecedented evidence on how the editing mechanism gradually expands its territory and increases its influence along the history of evolution. Our result revealed that highly clustered and conserved editing sites tended to have a higher editing level and a higher magnitude of the ADAR motif. The ratio of the frequencies of nonsynonymous editing to that of synonymous editing remarkably increased with increasing the conservation level of A-to-I editing. These results thus suggest potentially functional benefit of highly clustered and conserved editing sites. In addition, spatiotemporal dynamics analyses reveal a conserved enrichment of editing and ADAR expression in the central nervous system throughout more than 300 Myr of divergent evolution in complex animals and the comparability of editing patterns between invertebrates and between vertebrates during development. This study provides evolutionary and dynamic aspects of A-to-I editome across metazoan species, expanding this important but understudied class of nongenomically encoded events for comprehensive characterization.
MeSH term(s)	Adenosine/genetics ; Animals ; Cluster Analysis ; Evolution, Molecular ; Humans ; Inosine/genetics ; RNA/genetics ; RNA Editing ; Sequence Analysis, RNA
Chemical Substances	Inosine (5A614L51CT) ; RNA (63231-63-0) ; Adenosine (K72T3FS567)
Language	English
Publishing date	2018-01-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1759-6653
ISSN (online)	1759-6653
DOI	10.1093/gbe/evx277
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