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  1. Article ; Online: Human genetics seen through an evolutionary lens.

    Ponting, Chris P

    Cell genomics

    2023  Volume 3, Issue 5, Page(s) 100323

    Abstract: Most DNA bases crucial for species perpetuation are marked by a dearth of sequence change among species related over long evolutionary time. Recently, Christmas et al. ...

    Abstract Most DNA bases crucial for species perpetuation are marked by a dearth of sequence change among species related over long evolutionary time. Recently, Christmas et al.
    Language English
    Publishing date 2023-05-10
    Publishing country United States
    Document type News
    ISSN 2666-979X
    ISSN (online) 2666-979X
    DOI 10.1016/j.xgen.2023.100323
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Big knowledge from big data in functional genomics.

    Ponting, Chris P

    Emerging topics in life sciences

    2021  Volume 1, Issue 3, Page(s) 245–248

    Abstract: With so much genomics data being produced, it might be wise to pause and consider what purpose this data can or should serve. Some improve annotations, others predict molecular interactions, but few add directly to existing knowledge. This is because ... ...

    Abstract With so much genomics data being produced, it might be wise to pause and consider what purpose this data can or should serve. Some improve annotations, others predict molecular interactions, but few add directly to existing knowledge. This is because sequence annotations do not always implicate function, and molecular interactions are often irrelevant to a cell's or organism's survival or propagation. Merely correlative relationships found in big data fail to provide answers to the Why questions of human biology. Instead, those answers are expected from methods that causally link DNA changes to downstream effects without being confounded by reverse causation. These approaches require the controlled measurement of the consequences of DNA variants, for example, either those introduced in single cells using CRISPR/Cas9 genome editing or that are already present across the human population. Inferred causal relationships between genetic variation and cellular phenotypes or disease show promise to rapidly grow and underpin our knowledge base.
    Language English
    Publishing date 2021-01-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 2882721-1
    ISSN 2397-8554 ; 2397-8554 ; 2397-8562
    ISSN (online) 2397-8554
    ISSN 2397-8554 ; 2397-8562
    DOI 10.1042/ETLS20170129
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Genetics Needs Non-geneticists.

    Ponting, Chris P

    Trends in genetics : TIG

    2020  Volume 36, Issue 9, Page(s) 629–630

    Abstract: Answering genetics' big data questions often needs an interdisciplinary team whose members freely share their diverse expertise in analysis, statistics, and computation. Sharing requires mutual trust and open acknowledgement of strengths and weaknesses, ... ...

    Abstract Answering genetics' big data questions often needs an interdisciplinary team whose members freely share their diverse expertise in analysis, statistics, and computation. Sharing requires mutual trust and open acknowledgement of strengths and weaknesses, including those of established geneticists. Only then will newcomers to genetics contribute far beyond their entry-level expectations.
    MeSH term(s) Computational Biology/statistics & numerical data ; Cooperative Behavior ; Genetics/education ; Genetics/standards ; Humans ; Information Services/statistics & numerical data ; Translational Research, Biomedical
    Language English
    Publishing date 2020-07-24
    Publishing country England
    Document type Journal Article
    ZDB-ID 619240-3
    ISSN 1362-4555 ; 0168-9525 ; 0168-9479
    ISSN (online) 1362-4555
    ISSN 0168-9525 ; 0168-9479
    DOI 10.1016/j.tig.2020.06.015
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2272: Show issues Location:
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  4. Article ; Online: Genome-Wide Analysis of Human Long Noncoding RNAs: A Provocative Review.

    Ponting, Chris P / Haerty, Wilfried

    Annual review of genomics and human genetics

    2022  Volume 23, Page(s) 153–172

    Abstract: Do long noncoding RNAs (lncRNAs) contribute little or substantively to human biology? To address how lncRNA loci and their transcripts, structures, interactions, and functions contribute to human traits and disease, we adopt a genome-wide perspective. We ...

    Abstract Do long noncoding RNAs (lncRNAs) contribute little or substantively to human biology? To address how lncRNA loci and their transcripts, structures, interactions, and functions contribute to human traits and disease, we adopt a genome-wide perspective. We intend to provoke alternative interpretation of questionable evidence and thorough inquiry into unsubstantiated claims. We discuss pitfalls of lncRNA experimental and computational methods as well as opposing interpretations of their results. The majority of evidence, we argue, indicates that most lncRNA transcript models reflect transcriptional noise or provide minor regulatory roles, leaving relatively few human lncRNAs that contribute centrally to human development, physiology, or behavior. These important few tend to be spliced and better conserved but lack a simple syntax relating sequence to structure and mechanism, and so resist simple categorization. This genome-wide view should help investigators prioritize individual lncRNAs based on their likely contribution to human biology.
    MeSH term(s) Genome ; Humans ; RNA, Long Noncoding/genetics
    Chemical Substances RNA, Long Noncoding
    Language English
    Publishing date 2022-04-08
    Publishing country United States
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2037670-4
    ISSN 1545-293X ; 1527-8204
    ISSN (online) 1545-293X
    ISSN 1527-8204
    DOI 10.1146/annurev-genom-112921-123710
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    In stock of ZB MED Cologne/Königswinter

    Se 2016: Show issues Location:
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  5. Article ; Online: The Human Cell Atlas: making 'cell space' for disease.

    Ponting, Chris P

    Disease models & mechanisms

    2019  Volume 12, Issue 2

    Abstract: A single change in DNA, RNA, proteins or cellular images can be useful as a biomarker of disease onset or progression. With high-throughput molecular phenotyping of single cells, it is now conceivable that the molecular changes occurring across thousands, ...

    Abstract A single change in DNA, RNA, proteins or cellular images can be useful as a biomarker of disease onset or progression. With high-throughput molecular phenotyping of single cells, it is now conceivable that the molecular changes occurring across thousands, or tens of thousands, of individual cells could additionally be considered as a disease biomarker. Transition to a disease state would then be reflected by the shifts in cell numbers and locations across a multidimensional space that is defined by the molecular content of cells. Realising this ambition requires a robust formulation of such a multidimensional 'cell space'
    MeSH term(s) Cells/pathology ; Disease/genetics ; Genetic Variation ; Humans
    Language English
    Publishing date 2019-02-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2451104-3
    ISSN 1754-8411 ; 1754-8403
    ISSN (online) 1754-8411
    ISSN 1754-8403
    DOI 10.1242/dmm.037622
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Biological function in the twilight zone of sequence conservation.

    Ponting, Chris P

    BMC biology

    2017  Volume 15, Issue 1, Page(s) 71

    Abstract: Strong DNA conservation among divergent species is an indicator of enduring functionality. With weaker sequence conservation we enter a vast 'twilight zone' in which sequence subject to transient or lower constraint cannot be distinguished easily from ... ...

    Abstract Strong DNA conservation among divergent species is an indicator of enduring functionality. With weaker sequence conservation we enter a vast 'twilight zone' in which sequence subject to transient or lower constraint cannot be distinguished easily from neutrally evolving, non-functional sequence. Twilight zone functional sequence is illuminated instead by principles of selective constraint and positive selection using genomic data acquired from within a species' population. Application of these principles reveals that despite being biochemically active, most twilight zone sequence is not functional.
    MeSH term(s) Amino Acid Sequence ; Conserved Sequence ; Evolution, Molecular ; Sequence Analysis, Protein
    Language English
    Publishing date 2017-08-16
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2133020-7
    ISSN 1741-7007 ; 1741-7007
    ISSN (online) 1741-7007
    ISSN 1741-7007
    DOI 10.1186/s12915-017-0411-5
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  7. Article ; Online: OAF: a new member of the BRICHOS family.

    Sanchez-Pulido, Luis / Ponting, Chris P

    Bioinformatics advances

    2022  Volume 2, Issue 1, Page(s) vbac087

    Abstract: Summary: The 10 known BRICHOS domain-containing proteins in humans have been linked to an unusually long list of pathologies, including cancer, obesity and two amyloid-like diseases. BRICHOS domains themselves have been described as intramolecular ... ...

    Abstract Summary: The 10 known BRICHOS domain-containing proteins in humans have been linked to an unusually long list of pathologies, including cancer, obesity and two amyloid-like diseases. BRICHOS domains themselves have been described as intramolecular chaperones that act to prevent amyloid-like aggregation of their proteins' mature polypeptides. Using structural comparison of coevolution-based AlphaFold models and sequence conservation, we identified the Out at First (OAF) protein as a new member of the BRICHOS family in humans. OAF is an experimentally uncharacterized protein that has been proposed as a candidate biomarker for clinical management of coronavirus disease 2019 infections. Our analysis revealed how structural comparison of AlphaFold models can discover remote homology relationships and lead to a better understanding of BRICHOS domain molecular mechanism.
    Supplementary information: Supplementary data are available at
    Language English
    Publishing date 2022-11-24
    Publishing country England
    Document type Journal Article
    ISSN 2635-0041
    ISSN (online) 2635-0041
    DOI 10.1093/bioadv/vbac087
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  8. Article ; Online: The genetics of ME: A commentary on Hajdarevic et al.

    Ponting, Chris P / McGrath, Simon J

    Brain, behavior, and immunity

    2022  Volume 104, Page(s) 181–182

    Language English
    Publishing date 2022-06-14
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 639219-2
    ISSN 1090-2139 ; 0889-1591
    ISSN (online) 1090-2139
    ISSN 0889-1591
    DOI 10.1016/j.bbi.2022.06.008
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2276: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
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    Zs.MO 327: Show issues

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  9. Article: Extending the Horizon of Homology Detection with Coevolution-based Structure Prediction

    Sanchez-Pulido, Luis / Ponting, Chris P.

    Journal of molecular biology. 2021 Oct. 01, v. 433, no. 20

    2021  

    Abstract: Traditional sequence analysis algorithms fail to identify distant homologies when they lie beyond a detection horizon. In this review, we discuss how co-evolution-based contact and distance prediction methods are pushing back this homology detection ... ...

    Abstract Traditional sequence analysis algorithms fail to identify distant homologies when they lie beyond a detection horizon. In this review, we discuss how co-evolution-based contact and distance prediction methods are pushing back this homology detection horizon, thereby yielding new functional insights and experimentally testable hypotheses. Based on correlated substitutions, these methods divine three-dimensional constraints among amino acids in protein sequences that were previously devoid of all annotated domains and repeats. The new algorithms discern hidden structure in an otherwise featureless sequence landscape. Their revelatory impact promises to be as profound as the use, by archaeologists, of ground-penetrating radar to discern long-hidden, subterranean structures. As examples of this, we describe how triplicated structures reflecting longin domains in MON1A-like proteins, or UVR-like repeats in DISC1, emerge from their predicted contact and distance maps. These methods also help to resolve structures that do not conform to a “beads-on-a-string” model of protein domains. In one such example, we describe CFAP298 whose ubiquitin-like domain was previously challenging to perceive owing to a large sequence insertion within it. More generally, the new algorithms permit an easier appreciation of domain families and folds whose evolution involved structural insertion or rearrangement. As we exemplify with α1-antitrypsin, coevolution-based predicted contacts may also yield insights into protein dynamics and conformational change. This new combination of structure prediction (using innovative co-evolution based methods) and homology inference (using more traditional sequence analysis approaches) shows great promise for bringing into view a sea of evolutionary relationships that had hitherto lain far beyond the horizon of homology detection.
    Keywords coevolution ; ground-penetrating radar ; landscapes ; models ; molecular biology ; new combination ; prediction ; sequence analysis
    Language English
    Dates of publication 2021-1001
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 80229-3
    ISSN 1089-8638 ; 0022-2836
    ISSN (online) 1089-8638
    ISSN 0022-2836
    DOI 10.1016/j.jmb.2021.167106
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  10. Article ; Online: Comparison of T-cell receptor diversity of people with myalgic encephalomyelitis versus controls.

    Dibble, Joshua J / Ferneyhough, Ben / Roddis, Matthew / Millington, Sam / Fischer, Michael D / Parkinson, Nick J / Ponting, Chris P

    BMC research notes

    2024  Volume 17, Issue 1, Page(s) 17

    Abstract: Objective: Myalgic Encephalomyelitis (ME; sometimes referred to as Chronic Fatigue Syndrome) is a chronic disease without laboratory test, detailed aetiological understanding or effective therapy. Its symptoms are diverse, but it is distinguished from ... ...

    Abstract Objective: Myalgic Encephalomyelitis (ME; sometimes referred to as Chronic Fatigue Syndrome) is a chronic disease without laboratory test, detailed aetiological understanding or effective therapy. Its symptoms are diverse, but it is distinguished from other fatiguing illnesses by the experience of post-exertional malaise, the worsening of symptoms even after minor physical or mental exertion. Its frequent onset after infection suggests autoimmune involvement or that it arises from abnormal T-cell activation.
    Results: To test this hypothesis, we sequenced the genomic loci of α/δ, β and γ T-cell receptors (TCR) from 40 human blood samples from each of four groups: severely affected people with ME; mildly or moderately affected people with ME; people diagnosed with Multiple Sclerosis, as disease controls; and, healthy controls. Seeking to automatically classify these individuals' samples by their TCR repertoires, we applied P-SVM, a machine learning method. However, despite working well on a simulated data set, this approach did not allow statistically significant partitioning of samples into the four subgroups. Our findings do not support the hypothesis that blood samples from people with ME frequently contain altered T-cell receptor diversity.
    MeSH term(s) Humans ; Fatigue Syndrome, Chronic/diagnosis ; Receptors, Antigen, T-Cell/genetics
    Chemical Substances Receptors, Antigen, T-Cell
    Language English
    Publishing date 2024-01-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 2413336-X
    ISSN 1756-0500 ; 1756-0500
    ISSN (online) 1756-0500
    ISSN 1756-0500
    DOI 10.1186/s13104-023-06616-4
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