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  1. Article ; Online: Sequence data: expand comprehensive access.

    Roberts, Richard J

    Nature

    2021  Volume 591, Issue 7849, Page(s) 202

    Language English
    Publishing date 2021-02-22
    Publishing country England
    Document type Historical Article ; Letter
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-021-00575-1
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  2. Article: A Survey of Archaeal Restriction-Modification Systems.

    Anton, Brian P / Roberts, Richard J

    Microorganisms

    2023  Volume 11, Issue 10

    Abstract: When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the ... ...

    Abstract When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known about the genes and activities present in the 519 completely sequenced archaeal genomes currently deposited there. For 49 (9.4%) of these genomes, we also have methylome data from Single-Molecule Real-Time (SMRT) sequencing that reveal the target recognition sites of the active m
    Language English
    Publishing date 2023-09-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms11102424
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  3. Article ; Online: The impact of COVID-19 on sustainable development.

    Primorac, Dragan / Roberts, Richard J

    Croatian medical journal

    2021  Volume 63, Issue 3, Page(s) 213–220

    MeSH term(s) COVID-19 ; Humans ; SARS-CoV-2 ; Sustainable Development
    Language English
    Publishing date 2021-08-02
    Publishing country Croatia
    Document type Journal Article
    ZDB-ID 1157623-6
    ISSN 1332-8166 ; 0353-9504
    ISSN (online) 1332-8166
    ISSN 0353-9504
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  4. Article ; Online: Beyond Restriction Modification: Epigenomic Roles of DNA Methylation in Prokaryotes.

    Anton, Brian P / Roberts, Richard J

    Annual review of microbiology

    2021  Volume 75, Page(s) 129–149

    Abstract: The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional roles of DNA methylation in these organisms. Methyltransferases (MTases), the enzymes ... ...

    Abstract The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional roles of DNA methylation in these organisms. Methyltransferases (MTases), the enzymes responsible for DNA methylation, are exchanged between prokaryotes through horizontal gene transfer and can function either as part of restriction-modification systems or in apparent isolation as single (orphan) genes. The patterns of DNA methylation they confer on the host chromosome can have significant effects on gene expression, DNA replication, and other cellular processes. Some processes require very stable patterns of methylation, resulting in conservation of persistent MTases in a particular lineage. Other processes require patterns that are more dynamic yet more predictable than what is afforded by horizontal gene transfer and gene loss, resulting in phase-variable or recombination-driven MTase alleles. In this review, we discuss what is currently known about the functions of DNA methylation in prokaryotes in light of these evolutionary patterns.
    MeSH term(s) DNA Methylation ; DNA Restriction-Modification Enzymes/genetics ; DNA Restriction-Modification Enzymes/metabolism ; Epigenomics ; Methyltransferases/genetics ; Methyltransferases/metabolism ; Prokaryotic Cells/metabolism
    Chemical Substances DNA Restriction-Modification Enzymes ; Methyltransferases (EC 2.1.1.-)
    Language English
    Publishing date 2021-07-27
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 207931-8
    ISSN 1545-3251 ; 0066-4227
    ISSN (online) 1545-3251
    ISSN 0066-4227
    DOI 10.1146/annurev-micro-040521-035040
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  5. Article ; Online: Bibliometrics: An obituary for the impact factor.

    Roberts, Richard J

    Nature

    2017  Volume 546, Issue 7660, Page(s) 600

    Language English
    Publishing date 2017--28
    Publishing country England
    Document type Journal Article
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/546600e
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  6. Article ; Online: We need to keep a reproducible trace of facts, predictions, and hypotheses from gene to function in the era of big data.

    Kasif, Simon / Roberts, Richard J

    PLoS biology

    2020  Volume 18, Issue 11, Page(s) e3000999

    Abstract: How do we scale biological science to the demand of next generation biology and medicine to keep track of the facts, predictions, and hypotheses? These days, enormous amounts of DNA sequence and other omics data are generated. Since these data contain ... ...

    Abstract How do we scale biological science to the demand of next generation biology and medicine to keep track of the facts, predictions, and hypotheses? These days, enormous amounts of DNA sequence and other omics data are generated. Since these data contain the blueprint for life, it is imperative that we interpret it accurately. The abundance of DNA is only one part of the challenge. Artificial Intelligence (AI) and network methods routinely build on large screens, single cell technologies, proteomics, and other modalities to infer or predict biological functions and phenotypes associated with proteins, pathways, and organisms. As a first step, how do we systematically trace the provenance of knowledge from experimental ground truth to gene function predictions and annotations? Here, we review the main challenges in tracking the evolution of biological knowledge and propose several specific solutions to provenance and computational tracing of evidence in functional linkage networks.
    MeSH term(s) Algorithms ; Artificial Intelligence ; Big Data ; Computational Biology ; Gene Regulatory Networks ; Genetic Linkage ; Genomics/statistics & numerical data ; High-Throughput Nucleotide Sequencing ; Humans ; Models, Genetic ; Proteomics/statistics & numerical data ; Synthetic Biology ; Systems Biology
    Language English
    Publishing date 2020-11-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2126776-5
    ISSN 1545-7885 ; 1544-9173
    ISSN (online) 1545-7885
    ISSN 1544-9173
    DOI 10.1371/journal.pbio.3000999
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  7. Article ; Online: The Nobel Laureates' campaign supporting GMOs

    Roberts, Richard J.

    2018  

    Abstract: More than 800 million people suffer from hunger in the world. Using modern plant breeding methods to generate so-called GMOs (Genetically Modified Organisms), agricultural scientists have shown that crop yields and nutritional quality can be greatly ... ...

    Abstract More than 800 million people suffer from hunger in the world. Using modern plant breeding methods to generate so-called GMOs (Genetically Modified Organisms), agricultural scientists have shown that crop yields and nutritional quality can be greatly improved. Many GMO varieties have been specifically developed with the aim of being resistant to pests, tolerant to drought and containing beneficial nutrients. This leads to a reduction in the use of insecticides in water and on land. If anything, the GMO varieties are safer than traditionally bred varieties because they are made in a very precise manner. However, the scientific evidence on this issue is being ignored by the Green Parties such as Greenpeace who continue to deny the science and mislead the public. 129 Nobel Laureates have joined in a campaign to convince the Green Parties and the public that they should support the use of GMOs, especially for the sake of the developing world.
    Keywords ddc:650 ; GMO ; Hunger ; Nutrition ; Crop ; Pest ; Food ; Precision agriculture
    Language English
    Publisher Amsterdam: Elsevier
    Publishing country de
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Ten simple rules to win a Nobel Prize.

    Roberts, Richard J

    PLoS computational biology

    2015  Volume 11, Issue 4, Page(s) e1004084

    MeSH term(s) Algorithms ; Employment/organization & administration ; Laboratories/organization & administration ; Nobel Prize ; Research/organization & administration ; Science/organization & administration
    Language English
    Publishing date 2015-04
    Publishing country United States
    Document type Editorial
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1004084
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  9. Article ; Online: REBASE: a database for DNA restriction and modification: enzymes, genes and genomes.

    Roberts, Richard J / Vincze, Tamas / Posfai, Janos / Macelis, Dana

    Nucleic acids research

    2022  Volume 51, Issue D1, Page(s) D629–D630

    Abstract: REBASE is a comprehensive and extensively curated database of information about the components of restriction-modification (RM) systems. It is fully referenced and provides information about the recognition and cleavage sites for both restriction enzymes ...

    Abstract REBASE is a comprehensive and extensively curated database of information about the components of restriction-modification (RM) systems. It is fully referenced and provides information about the recognition and cleavage sites for both restriction enzymes and DNA methyltransferases together with their commercial availability, methylation sensitivity, crystal and sequence data. All completely sequenced genomes and select shotgun sequences are analyzed for RM system components. When PacBio sequence data is available, the recognition sequences of many DNA methyltransferases (MTases) can be determined. This has led to an explosive growth in the number of well-characterized MTases in REBASE. The contents of REBASE may be browsed from the web rebase.neb.com and selected compilations can be downloaded by FTP (ftp.neb.com). Monthly updates are also available via email.
    MeSH term(s) Databases, Factual ; DNA Restriction Enzymes/metabolism ; DNA Modification Methylases/metabolism ; DNA Methylation ; DNA/genetics ; DNA Restriction-Modification Enzymes/genetics
    Chemical Substances DNA Restriction Enzymes (EC 3.1.21.-) ; DNA Modification Methylases (EC 2.1.1.-) ; DNA (9007-49-2) ; DNA Restriction-Modification Enzymes
    Language English
    Publishing date 2022-10-31
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkac975
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  10. Article: Complete genome assembly and methylome dissection of

    Fomenkov, Alexey / Weigele, Peter / McClung, Colleen / Madinger, Casey / Roberts, Richard J

    Frontiers in microbiology

    2023  Volume 14, Page(s) 1112734

    Abstract: Although restriction-modification systems are found in both Eubacterial and Archaeal kingdoms, comparatively less is known about patterns of DNA methylation and genome defense systems in archaea. Here we report the complete closed genome sequence and ... ...

    Abstract Although restriction-modification systems are found in both Eubacterial and Archaeal kingdoms, comparatively less is known about patterns of DNA methylation and genome defense systems in archaea. Here we report the complete closed genome sequence and methylome analysis of
    Language English
    Publishing date 2023-04-05
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2023.1112734
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