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  • Oxford University Press (OUP)  (82)
  • 2020-2024  (82)
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  • Oxford University Press (OUP)  (82)
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  • 2020-2024  (82)
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  • 1
    Online Resource
    Online Resource
    Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023
    Oxford University Press (OUP) ; 2023
    In:  Nucleic Acids Research Vol. 51, No. D1 ( 2023-01-06), p. D18-D28
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 51, No. D1 ( 2023-01-06), p. D18-D28
    Abstract: The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global academic and industrial communities. With the explosive accumulation of multi-omics data generated at an unprecedented rate, CNCB-NGDC constantly expands and updates core database resources by big data archive, integrative analysis and value-added curation. In the past year, efforts have been devoted to integrating multiple omics data, synthesizing the growing knowledge, developing new resources and upgrading a set of major resources. Particularly, several database resources are newly developed for infectious diseases and microbiology (MPoxVR, KGCoV, ProPan), cancer-trait association (ASCancer Atlas, TWAS Atlas, Brain Catalog, CCAS) as well as tropical plants (TCOD). Importantly, given the global health threat caused by monkeypox virus and SARS-CoV-2, CNCB-NGDC has newly constructed the monkeypox virus resource, along with frequent updates of SARS-CoV-2 genome sequences, variants as well as haplotypes. All the resources and services are publicly accessible at https://ngdc.cncb.ac.cn.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkac1073
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 2
    Online Resource
    Online Resource
    Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022
    Oxford University Press (OUP) ; 2022
    In:  Nucleic Acids Research Vol. 50, No. D1 ( 2022-01-07), p. D27-D38
    Details
    In: Nucleic Acids Research, Oxford University Press (OUP), Vol. 50, No. D1 ( 2022-01-07), p. D27-D38
    Abstract: The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), provides a family of database resources to support global research in both academia and industry. With the explosively accumulated multi-omics data at ever-faster rates, CNCB-NGDC is constantly scaling up and updating its core database resources through big data archive, curation, integration and analysis. In the past year, efforts have been made to synthesize the growing data and knowledge, particularly in single-cell omics and precision medicine research, and a series of resources have been newly developed, updated and enhanced. Moreover, CNCB-NGDC has continued to daily update SARS-CoV-2 genome sequences, variants, haplotypes and literature. Particularly, OpenLB, an open library of bioscience, has been established by providing easy and open access to a substantial number of abstract texts from PubMed, bioRxiv and medRxiv. In addition, Database Commons is significantly updated by cataloguing a full list of global databases, and BLAST tools are newly deployed to provide online sequence search services. All these resources along with their services are publicly accessible at https://ngdc.cncb.ac.cn.
    Type of Medium: Online Resource
    ISSN: 0305-1048 , 1362-4962
    URL: Article
    DOI: 10.1093/nar/gkab951
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1472175-2
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Transcriptomic and genetic approaches reveal an essential role of the NAC transcription factor SlNAP1 in the growth and defense response of tomato
    Oxford University Press (OUP) ; 2020
    In:  Horticulture Research Vol. 7, No. 1 ( 2020-12)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 7, No. 1 ( 2020-12)
    Abstract: With global climate change, plants are frequently being exposed to various stresses, such as pathogen attack, drought, and extreme temperatures. Transcription factors (TFs) play crucial roles in numerous plant biological processes; however, the functions of many tomato ( Solanum lycopersicum L.) TFs that regulate plant responses to multiple stresses are largely unknown. Here, using an RNA-seq approach, we identified SlNAP1 , a NAC TF-encoding gene, which was strongly induced by various stresses. By generating SlNAP1 transgenic lines and evaluating their responses to biotic and abiotic stresses in tomato, we found that SlNAP1 -overexpressing plants showed significantly enhanced defense against two widespread bacterial diseases, leaf speck disease, caused by Pseudomonas syringae pv. tomato ( Pst ) DC3000, and root-borne bacterial wilt disease, caused by Ralstonia solanacearum . In addition, SlNAP1 overexpression dramatically improved drought tolerance in tomato. Although the SlNAP1 -overexpressing plants were shorter than the wild-type plants during the early vegetative stage, eventually, their fruit yield increased by 10.7%. Analysis of different hormone contents revealed a reduced level of physiologically active gibberellins (GAs) and an increased level of salicylic acid (SA) and abscisic acid (ABA) in the SlNAP1 -overexpressing plants. Moreover, EMSAs and ChIP-qPCR assays showed that SlNAP1 directly activated the transcription of multiple genes involved in GA deactivation and both SA and ABA biosynthesis. Our findings reveal that SlNAP1 is a positive regulator of the tomato defense response against multiple stresses and thus may be a potential breeding target for improving crop yield and stress resistance.
    Type of Medium: Online Resource
    ISSN: 2662-6810 , 2052-7276
    URL: Article
    DOI: 10.1038/s41438-020-00442-6
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2781828-7
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  • 4
    Online Resource
    Online Resource
    An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer’s disease
    Oxford University Press (OUP) ; 2022
    In:  Briefings in Bioinformatics Vol. 23, No. 1 ( 2022-01-17)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 23, No. 1 ( 2022-01-17)
    Abstract: Alzheimer’s disease (AD) has a strong genetic predisposition. However, its risk genes remain incompletely identified. We developed an Alzheimer’s brain gene network-based approach to predict AD-associated genes by leveraging the functional pattern of known AD-associated genes. Our constructed network outperformed existing networks in predicting AD genes. We then systematically validated the predictions using independent genetic, transcriptomic, proteomic data, neuropathological and clinical data. First, top-ranked genes were enriched in AD-associated pathways. Second, using external gene expression data from the Mount Sinai Brain Bank study, we found that the top-ranked genes were significantly associated with neuropathological and clinical traits, including the Consortium to Establish a Registry for Alzheimer’s Disease score, Braak stage score and clinical dementia rating. The analysis of Alzheimer’s brain single-cell RNA-seq data revealed cell-type-specific association of predicted genes with early pathology of AD. Third, by interrogating proteomic data in the Religious Orders Study and Memory and Aging Project and Baltimore Longitudinal Study of Aging studies, we observed a significant association of protein expression level with cognitive function and AD clinical severity. The network, method and predictions could become a valuable resource to advance the identification of risk genes for AD.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbab522
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry
    Oxford University Press (OUP) ; 2023
    In:  Horticulture Research Vol. 10, No. 1 ( 2023-01-04)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 10, No. 1 ( 2023-01-04)
    Abstract: Cultivated strawberry (Fragaria × ananassa), a perennial herb belonging to the family Rosaceae, is a complex octoploid with high heterozygosity at most loci. However, there is no research on the haplotype of the octoploid strawberry genome. Here we aimed to obtain a high-quality genome of the cultivated strawberry cultivar, “Yanli”, using single molecule real-time sequencing and high-throughput chromosome conformation capture technology. The “Yanli” genome was 823 Mb in size, with a long terminal repeat assembly index of 14.99. The genome was phased into two haplotypes, Hap1 (825 Mb with contig N50 of 26.70 Mb) and Hap2 (808 Mb with contig N50 of 27.51 Mb). Using the combination of Hap1 and Hap2, we obtained for the first time a haplotype-resolved genome with 56 chromosomes for the cultivated octoploid strawberry. We identified a ~ 10 Mb inversion and translocation on chromosome 2-1. 104 957 and 102 356 protein-coding genes were annotated in Hap1 and Hap2, respectively. Analysis of the genes related to the anthocyanin biosynthesis pathway revealed the structural diversity and complexity in the expression of the alleles in the octoploid F. × ananassa genome. In summary, we obtained a high-quality haplotype-resolved genome assembly of F. × ananassa, which will provide the foundation for investigating gene function and evolution of the genome of cultivated octoploid strawberry.
    Type of Medium: Online Resource
    ISSN: 2052-7276
    URL: Article
    DOI: 10.1093/hr/uhad002
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2781828-7
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  • 6
    Online Resource
    Online Resource
    Bacterial communities are more sensitive to ocean acidification than fungal communities in estuarine sediments
    Oxford University Press (OUP) ; 2021
    In:  FEMS Microbiology Ecology Vol. 97, No. 5 ( 2021-04-13)
    Details
    In: FEMS Microbiology Ecology, Oxford University Press (OUP), Vol. 97, No. 5 ( 2021-04-13)
    Abstract: Ocean acidification (OA) in estuaries is becoming a global concern, and may affect microbial characteristics in estuarine sediments. Bacterial communities in response to acidification in this habitat have been well discussed; however, knowledge about how fungal communities respond to OA remains poorly understood. Here, we explored the effects of acidification on bacterial and fungal activities, structures and functions in estuarine sediments during a 50-day incubation experiment. Under acidified conditions, activities of three extracellular enzymes related to nutrient cycling were inhibited and basal respiration rates were decreased. Acidification significantly altered bacterial communities and their interactions, while weak alkalization had a minor impact on fungal communities. We distinguished pH-sensitive/tolerant bacteria and fungi in estuarine sediments, and found that only pH-sensitive/tolerant bacteria had strong correlations with sediment basal respiration activity. FUNGuild analysis indicated that animal pathogen abundances in sediment were greatly increased by acidification, while plant pathogens were unaffected. High-throughput quantitative PCR-based SmartChip analysis suggested that the nutrient cycling-related multifunctionality of sediments was reduced under acidified conditions. Most functional genes associated with nutrient cycling were identified in bacterial communities and their relative abundances were decreased by acidification. These new findings highlight that acidification in estuarine regions affects bacterial and fungal communities differently, increases potential pathogens and disrupts bacteria-mediated nutrient cycling.
    Type of Medium: Online Resource
    ISSN: 1574-6941
    URL: Article
    DOI: 10.1093/femsec/fiab058
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2021
    detail.hit.zdb_id: 1501712-6
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  • 7
    Online Resource
    Online Resource
    Significance of differential expression profiles of ABC transporters in azole susceptibility between Cryptococcus gattii VGI and VGII strains
    Oxford University Press (OUP) ; 2022
    In:  Medical Mycology Vol. 60, No. 7 ( 2022-07-08)
    Details
    In: Medical Mycology, Oxford University Press (OUP), Vol. 60, No. 7 ( 2022-07-08)
    Abstract: Azoles were used as the primary antifungal agents to treat the Cryptococcus gattii infection. Evidence showed that subtypes of C. gattii respond differently to azoles, but the mechanism is largely elusive. In this study, we aimed to find the mechanisms of differences in azole drug susceptibility in different subtypes of C. gattii. Eight clinical strains of C. gattii were collected for molecular typing, multilocus sequence typing (MLST) analysis, and antifungal susceptibility testing. Based on drug susceptibility differences, the RNA sequencing data were analyzed to find candidate azole drug susceptibility genes, and qPCR validation was performed. Five VGI subtypes and three VGII subtypes were identified among the eight strains of C. gattii. The clinical isolates showed high genetic diversity, and seven sequence types (STs) were identified. The geometric mean (GM) of minimum inhibitory concentration (MIC) for fluconazole, voriconazole, and itraconazole of VGI subtype was significantly lower than that of VGII subtype, and genes related to transporter activities were differentially expressed between VGI and VGII strains. The results of the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the DEGs (differential expressed genes) were found to be enriched in multiple ABC transporters. We further performed qPCR to quantify the expression level of seven ABC transporters. We found that ABC transporters ATM1, MDR1, PDR5, PDR5-3, and PXA2 were expressed significantly higher in VGII strains than in VGI strains. Our work revealed four novel ABC transporters, ATM1, PDR5, PDR5-3, and PXA2, promising candidate targets regulating azole susceptibility in C. gattii strains. Lay Summary Azoles were used as the primary antifungal agents for treating Cryptococuss gattii infection. Since subtypes of C. gattii respond differently to azoles. We analyzed mRNA expression profiles of different subtypes and identified four ABC transporters that could be potential genes regulating azole sensitivity.
    Type of Medium: Online Resource
    ISSN: 1369-3786 , 1460-2709
    URL: Article
    DOI: 10.1093/mmy/myac035
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2020733-5
    SSG: 12
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  • 8
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    Online Resource
    Nitrite- and N2O-reducing bacteria respond differently to ecological factors in saline lakes
    Oxford University Press (OUP) ; 2022
    In:  FEMS Microbiology Ecology Vol. 98, No. 2 ( 2022-03-08)
    Details
    In: FEMS Microbiology Ecology, Oxford University Press (OUP), Vol. 98, No. 2 ( 2022-03-08)
    Abstract: The distribution of nitrite- and N2O-reducing bacteria is key to potential N2O emission from lakes. However, such information in highland saline lakes remains unknown. Here, we investigated the abundance and community composition of nitrite- and N2O-reducing bacteria in the sediments of six saline lakes on the Qing-Tibetan Plateau. The studied lakes covered a wide range of salinity (1.0–340.0 g/L). Results showed that in the studied saline lake sediments, nitrite-reducing bacteria were significantly more abundant than N2O-reducing bacteria, and their abundances ranged 7.14 × 103–8.26 × 108 and 1.18 × 106–6.51 × 107 copies per gram sediment (dry weight), respectively. Nitrite-reducing bacteria were mainly affiliated with α-, β- and γ-Proteobacteria, with β- and α-Proteobacteria being dominant in low- and high-salinity lakes, respectively; N2O-reducing bacterial communities mainly consisted of Proteobacteria (α-, β-, γ- and δ-subgroups), Bacteroidetes, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes and Balneolaeota, with Proteobacteria and Bacteroidetes/Verrucomicrobia dominating in low- and high-salinity lakes, respectively. The nitrite- and N2O-reducing bacterial communities showed distinct responses to ecological factors, and they were mainly regulated by mineralogical and physicochemical factors, respectively. In response to salinity change, the community composition of nitrite-reducing bacteria was more stable than that of N2O-reducing bacteria. These findings suggest that nitrite- and N2O-reducing bacteria may prefer niches with different salinity.
    Type of Medium: Online Resource
    ISSN: 1574-6941
    URL: Article
    DOI: 10.1093/femsec/fiac007
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1501712-6
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  • 9
    Online Resource
    Online Resource
    NASMDR: a framework for miRNA-drug resistance prediction using efficient neural architecture search and graph isomorphism networks
    Oxford University Press (OUP) ; 2022
    In:  Briefings in Bioinformatics Vol. 23, No. 5 ( 2022-09-20)
    Details
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 23, No. 5 ( 2022-09-20)
    Abstract: As a frontier field of individualized therapy, microRNA (miRNA) pharmacogenomics facilitates the understanding of different individual responses to certain drugs and provides a reasonable reference for clinical treatment. However, the known drug resistance-associated miRNAs are not yet sufficient to support precision medicine. Although existing methods are effective, they all focus on modelling miRNA-drug resistance interaction graphs, making their performance bounded by the interaction density. In this study, we propose a framework for miRNA-drug resistance prediction through efficient neural architecture search and graph isomorphism networks (NASMDR). NASMDR uses attribute information instead of the commonly used interactive graph information. In the cross-validation experiment, the proposed framework can achieve an AUC of 0.9468 on the ncDR dataset, which is 2.29% higher than the state-of-the-art method. In addition, we propose a novel sequence characterization approach, k-mer Sparse Nonnegative Matrix Factorization (KSNMF). The results show that NASMDR provides novel insights for integrating efficient neural architecture search and graph isomorphic networks into a unified framework to predict drug resistance-related miRNAs. The codes for NASMDR are available at https://github.com/kaizheng-academic/NASMDR.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    URL: Article
    DOI: 10.1093/bib/bbac338
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 10
    Online Resource
    Online Resource
    An efficient algebraic multi-resolution sampling approach to 3-D magnetotelluric modelling
    Oxford University Press (OUP) ; 2023
    In:  Geophysical Journal International Vol. 235, No. 1 ( 2023-05-27), p. 166-177
    Details
    In: Geophysical Journal International, Oxford University Press (OUP), Vol. 235, No. 1 ( 2023-05-27), p. 166-177
    Abstract: Since electromagnetic (EM) fields diffuse more smoothly to greater depth, it physically makes sense to apply fine discretization to model structure at near surface with an increasingly coarser grid both in horizontal and vertical directions as the depth increases for the numerical solution of EM fields. For finite-difference magnetotelluric (MT) forward modelling on regular staggered grids, this can lead to difficulties in discretizing the curl–curl equation governing the EM diffusion in the earth at regions, where the grid resolution changes. In this paper, we propose an efficient algebraic multi-resolution sampling (MRS) method for MT forward modelling. In this method, we do not require the generation of physical subgrids and merely subsample the field components. The coefficient matrix for the subsampled components can be obtained by matrix multiplication based on the initial linear system of equations and field interpolation. To guarantee divergence-free current during the iterative solution process at low frequencies, which is considered crucial for the development of efficient iterative solvers, our forward modelling is based a regularization equation obtained by augmenting the curl–curl equation with an equivalent scaled grad–div operator for electrical fields (explicitly enforcing the divergence-free condition). The correctness of our algebraic MRS algorithm is examined based on a layered model. Its stability and efficiency is exploited by comparing our results with the forward modelling on unsampled staggered grids for the Dublin Test Model 1 (DTM1) and a complex model with realistic topography, indicating a time reduction of about 42–82 per cent.
    Type of Medium: Online Resource
    ISSN: 0956-540X , 1365-246X
    URL: Article
    DOI: 10.1093/gji/ggad207
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 3042-9
    detail.hit.zdb_id: 2006420-2
    detail.hit.zdb_id: 1002799-3
    SSG: 16,13
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