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  1. Book ; Online: From Genes to Species: Novel Insights from Metagenomics

    Sleator, Roy D. / Culligan, Eamonn P.

    2016  

    Abstract: The majority of microbes in many environments are considered "as yet uncultured" and were traditionally considered inaccessible for study through the microbiological gold standard of pure culture. The emergence of metagenomic approaches has allowed ... ...

    Abstract The majority of microbes in many environments are considered "as yet uncultured" and were traditionally considered inaccessible for study through the microbiological gold standard of pure culture. The emergence of metagenomic approaches has allowed researchers to access and study these microbes in a culture-independent manner through DNA sequencing and functional expression of metagenomic DNA in a heterologous host. Metagenomics has revealed an extraordinary degree of diversity and novelty, not only among microbial communities themselves, but also within the genomes of these microbes. This Research Topic aims to showcase the utility of metagenomics to gain insights on the microbial and genomic diversity in different environments by revealing the breadth of novelty that was in the past, largely untapped
    Keywords Science (General) ; Microbiology
    Size 1 electronic resource (229 p.)
    Publisher Frontiers Media SA
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT020090692
    ISBN 9782889199754 ; 2889199754
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Unravelling the genetic basis of Schizophrenia.

    Casey, Clara / Fullard, John F / Sleator, Roy D

    Gene

    2024  Volume 902, Page(s) 148198

    Abstract: Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant ... ...

    Abstract Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale 'omics' studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain. Herein, we provide a brief overview of some of the key omics methods currently being used in SCZ research, including RNA-seq, the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and high-throughput chromosome conformation capture (3C) approaches (e.g., Hi-C), as well as single-cell/nuclei iterations of these methods. We also discuss how these techniques are being employed to further our understanding of the genetic basis of SCZ, and to identify associated molecular pathways, biomarkers, and candidate drug targets.
    MeSH term(s) Animals ; Humans ; Schizophrenia/genetics ; Chromatin/genetics ; Chromatin/metabolism ; Chromatin Immunoprecipitation Sequencing ; Brain/metabolism ; High-Throughput Nucleotide Sequencing
    Chemical Substances Chromatin
    Language English
    Publishing date 2024-01-22
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2024.148198
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: An Alternative Viewpoint-Comment on Prescott and Bland

    Sleator, Roy D

    International journal of environmental research and public health

    2020  Volume 17, Issue 14

    Abstract: I would like to commend Prescott and Bland [ ... ]. ...

    Abstract I would like to commend Prescott and Bland [...].
    MeSH term(s) Extinction, Biological ; Planets ; Public Health ; Spacecraft
    Language English
    Publishing date 2020-07-11
    Publishing country Switzerland
    Document type Journal Article ; Comment
    ISSN 1660-4601
    ISSN (online) 1660-4601
    DOI 10.3390/ijerph17145004
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: So long, farewell, Auf Wiedersehen, Adieu….

    Sleator, Roy D

    Bioengineered

    2017  Volume 9, Issue 1, Page(s) 1

    Language English
    Publishing date 2017-11-30
    Publishing country United States
    Document type Editorial
    ISSN 2165-5987
    ISSN (online) 2165-5987
    DOI 10.1080/21655979.2017.1404788
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The roles of code in biology.

    Lawlor, Brendan / Sleator, Roy D

    Science progress

    2021  Volume 104, Issue 2, Page(s) 368504211010570

    Abstract: The way in which computer code is perceived and used in biological research has been a source of some controversy and confusion, and has resulted in sub-optimal outcomes related to reproducibility, scalability and productivity. We suggest that the ... ...

    Abstract The way in which computer code is perceived and used in biological research has been a source of some controversy and confusion, and has resulted in sub-optimal outcomes related to reproducibility, scalability and productivity. We suggest that the confusion is due in part to a misunderstanding of the function of code when applied to the life sciences. Code has many roles, and in this paper we present a three-dimensional taxonomy to classify those roles and map them specifically to the life sciences. We identify a "sweet spot" in the taxonomy-a convergence where bioinformaticians should concentrate their efforts in order to derive the most value from the time they spend using code. We suggest the use of the "inverse Conway maneuver" to shape a research team so as to allow dedicated software engineers to interface with researchers working in this "sweet spot." We conclude that in order to address current issues in the use of software in life science research such as reproducibility and scalability, the field must reevaluate its relationship with software engineering, and adapt its research structures to overcome current issues in bioinformatics such as reproducibility, scalability and productivity.
    MeSH term(s) Biological Science Disciplines ; Computational Biology/methods ; Reproducibility of Results ; Software
    Language English
    Publishing date 2021-04-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 128412-5
    ISSN 2047-7163 ; 0036-8504 ; 0302-1785
    ISSN (online) 2047-7163
    ISSN 0036-8504 ; 0302-1785
    DOI 10.1177/00368504211010570
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: An Alternative Viewpoint—Comment on Prescott and Bland Int. J. Environ. Res. Public Health 2020, 17 , 1407

    Roy D. Sleator

    International Journal of Environmental Research and Public Health, Vol 17, Iss 5004, p

    2020  Volume 5004

    Abstract: I would like to commend Prescott and Bland [.] ...

    Abstract I would like to commend Prescott and Bland [.]
    Keywords n/a ; Medicine ; R
    Language English
    Publishing date 2020-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: DIY Biology - hacking goes viral!

    Sleator, Roy D

    Science progress

    2017  Volume 99, Issue 3, Page(s) 278–281

    Abstract: The D-It-Yourself Biology (DIYBio) movement has gained significant traction in recent years ...

    Abstract The D-It-Yourself Biology (DIYBio) movement has gained significant traction in recent years; morphing from counter culture to an essential component of biology's future development.
    Language English
    Publishing date 2017-08-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 128412-5
    ISSN 0036-8504 ; 0302-1785
    ISSN 0036-8504 ; 0302-1785
    DOI 10.3184/003685016X14684989326984
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A genomic analysis of osmotolerance in Staphylococcus aureus.

    Casey, Dylan / Sleator, Roy D

    Gene

    2020  Volume 767, Page(s) 145268

    Abstract: A key phenotypic characteristic of the Gram-positive bacterial pathogen, Staphylococcus aureus, is its ability to grow in low ... ...

    Abstract A key phenotypic characteristic of the Gram-positive bacterial pathogen, Staphylococcus aureus, is its ability to grow in low a
    MeSH term(s) Bacterial Proteins/genetics ; Computer Simulation ; Genome, Bacterial/genetics ; Genomics/methods ; Methicillin-Resistant Staphylococcus aureus/genetics ; Osmoregulation/genetics ; Staphylococcal Infections/genetics ; Staphylococcus aureus/genetics
    Chemical Substances Bacterial Proteins
    Language English
    Publishing date 2020-11-03
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2020.145268
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Cryptosporidium

    O'Leary, Jennifer K / Sleator, Roy D / Lucey, Brigid

    Food and waterborne parasitology

    2021  Volume 24, Page(s) e00131

    Abstract: The protozoan ... ...

    Abstract The protozoan parasite
    Language English
    Publishing date 2021-08-20
    Publishing country Netherlands
    Document type Journal Article ; Review
    ISSN 2405-6766
    ISSN (online) 2405-6766
    DOI 10.1016/j.fawpar.2021.e00131
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: The democratization of bioinformatics: A software engineering perspective.

    Lawlor, Brendan / Sleator, Roy D

    GigaScience

    2020  Volume 9, Issue 6

    Abstract: Today, thanks to advances in cloud computing, it is possible for small teams of software developers to produce internet-scale products, a feat that was previously the preserve of large organizations. Herein, we describe how these advances in software ... ...

    Abstract Today, thanks to advances in cloud computing, it is possible for small teams of software developers to produce internet-scale products, a feat that was previously the preserve of large organizations. Herein, we describe how these advances in software engineering can be made more readily available to bioinformaticians. In the same way that cloud computing has democratized access to distributed systems engineering for generalist software engineers, access to scalable and reproducible bioinformatic engineering can be democratized for generalist bioinformaticians and biologists. We present solutions, based on our own efforts, to achieve this goal.
    MeSH term(s) Cloud Computing ; Computational Biology/methods ; Genomics/methods ; Software
    Language English
    Publishing date 2020-09-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2708999-X
    ISSN 2047-217X ; 2047-217X
    ISSN (online) 2047-217X
    ISSN 2047-217X
    DOI 10.1093/gigascience/giaa063
    Database MEDical Literature Analysis and Retrieval System OnLINE

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