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  1. Article ; Online: Diversity and ecotones in a model ecosystems of sessile species.

    Hofer, Markus / Sneppen, Kim

    Physical review. E

    2024  Volume 109, Issue 2-1, Page(s) 24309

    Abstract: Sessile species compete for space and accessible light, with directed interactions evident in one species overgrowing another and with multispecies systems characterized by nontransitive relationships. Such patterns are observed in coral reefs or lichens ...

    Abstract Sessile species compete for space and accessible light, with directed interactions evident in one species overgrowing another and with multispecies systems characterized by nontransitive relationships. Such patterns are observed in coral reefs or lichens on rock surfaces. Open systems with episodic invasions of such species have been predicted to exhibit a stable high-diversity state when the interaction probability is below a certain critical threshold. Here, we explore this metastable high-diversity state and find that the diversity in the high-diversity state scales with the square root of the system area. When introducing two different environments, we predict a hugely increased diversity along mutual environment border. Further, the presence of spatially segregated environments is predicted to allow for increased robustness of the high-diversity state.
    Language English
    Publishing date 2024-03-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2844562-4
    ISSN 2470-0053 ; 2470-0045
    ISSN (online) 2470-0053
    ISSN 2470-0045
    DOI 10.1103/PhysRevE.109.024309
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  2. Article ; Online: The counterintuitive implications of superspreading diseases.

    Nielsen, Bjarke Frost / Sneppen, Kim / Simonsen, Lone

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 6954

    Language English
    Publishing date 2023-10-31
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-42612-9
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  3. Article ; Online: Models of life: epigenetics, diversity and cycles.

    Sneppen, Kim

    Reports on progress in physics. Physical Society (Great Britain)

    2017  Volume 80, Issue 4, Page(s) 42601

    Abstract: This review emphasizes aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model ...

    Abstract This review emphasizes aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model approaches to diversity and to punctuated equilibrium in evolution. Two outstanding features are repeatedly described. One is the minimal number of rules to sustain specific states of complex systems for a long time. The other is the collapse of such states and the subsequent dynamical cycle of situations that restitute the system to a potentially new metastable state.
    MeSH term(s) Animals ; Bacteria/genetics ; Bacteria/metabolism ; Bacteriophage lambda/genetics ; Bacteriophage lambda/metabolism ; Biodiversity ; Biological Evolution ; Epigenesis, Genetic ; Humans ; Models, Biological ; Population Dynamics
    Language English
    Publishing date 2017-01-20
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 205657-4
    ISSN 1361-6633 ; 0034-4885
    ISSN (online) 1361-6633
    ISSN 0034-4885
    DOI 10.1088/1361-6633/aa5aeb
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    In stock of ZB MED Bonn / Germany

    Z 52/38: Show issues

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  4. Article ; Online: Superspreading quantified from bursty epidemic trajectories.

    Kirkegaard, Julius B / Sneppen, Kim

    Scientific reports

    2021  Volume 11, Issue 1, Page(s) 24124

    Abstract: The quantification of spreading heterogeneity in the COVID-19 epidemic is crucial as it affects the choice of efficient mitigating strategies irrespective of whether its origin is biological or social. We present a method to deduce temporal and ... ...

    Abstract The quantification of spreading heterogeneity in the COVID-19 epidemic is crucial as it affects the choice of efficient mitigating strategies irrespective of whether its origin is biological or social. We present a method to deduce temporal and individual variations in the basic reproduction number directly from epidemic trajectories at a community level. Using epidemic data from the 98 districts in Denmark we estimate an overdispersion factor k for COVID-19 to be about 0.11 (95% confidence interval 0.08-0.18), implying that 10 % of the infected cause between 70 % and 87 % of all infections.
    MeSH term(s) Algorithms ; Basic Reproduction Number/statistics & numerical data ; COVID-19/epidemiology ; COVID-19/transmission ; COVID-19/virology ; Denmark/epidemiology ; Epidemics/prevention & control ; Geography ; Humans ; Models, Theoretical ; SARS-CoV-2/isolation & purification ; SARS-CoV-2/physiology
    Language English
    Publishing date 2021-12-16
    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/s41598-021-03126-w
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  5. Article ; Online: SARS-CoV-2 superspreading in cities vs the countryside.

    Eilersen, Andreas / Sneppen, Kim

    APMIS : acta pathologica, microbiologica, et immunologica Scandinavica

    2021  Volume 129, Issue 7, Page(s) 401–407

    Abstract: The first wave of the COVID-19 pandemic was characterized by an initial rapid rise in new cases followed by a peak and a more erratic behaviour that varies between regions. This is not easy to reproduce with traditional SIR models, which predict a more ... ...

    Abstract The first wave of the COVID-19 pandemic was characterized by an initial rapid rise in new cases followed by a peak and a more erratic behaviour that varies between regions. This is not easy to reproduce with traditional SIR models, which predict a more symmetric epidemic. Here, we argue that superspreaders and population heterogeneity would predict such behaviour even in the absence of restrictions on social life. We present an agent-based lattice model of a disease spreading in a heterogeneous population. We predict that an epidemic driven by superspreaders will spread rapidly in cities, but not in the countryside where the sparse population limits the maximal number of secondary infections. This suggests that mitigation strategies should include restrictions on venues where people meet a large number of strangers. Furthermore, mitigating the epidemic in cities and in the countryside may require different levels of restrictions.
    MeSH term(s) COVID-19/epidemiology ; COVID-19/transmission ; Cities ; Humans ; SARS-CoV-2
    Language English
    Publishing date 2021-02-23
    Publishing country Denmark
    Document type Journal Article
    ZDB-ID 93340-5
    ISSN 1600-0463 ; 0903-4641
    ISSN (online) 1600-0463
    ISSN 0903-4641
    DOI 10.1111/apm.13120
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    In stock of ZB MED Cologne/Königswinter

    Ud II Zs.73: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
    ab Jg. 2022: Lesesaal (EG)

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  6. Article ; Online: Protection of bacteriophage-sensitive

    Brown, Stanley / Mitarai, Namiko / Sneppen, Kim

    Proceedings of the National Academy of Sciences of the United States of America

    2022  Volume 119, Issue 14, Page(s) e2106005119

    Abstract: SignificanceSome viruses that infect bacteria, temperate bacteriophages, can confer immunity to infection by the same virus. Here we ... ...

    Abstract SignificanceSome viruses that infect bacteria, temperate bacteriophages, can confer immunity to infection by the same virus. Here we report
    MeSH term(s) Bacteriophage lambda/genetics ; Bacteriophages ; Escherichia coli/metabolism
    Language English
    Publishing date 2022-03-28
    Publishing country United States
    Document type Journal Article
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2106005119
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1148: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Jg. 1995 - 2021: Lesesall (1.OG)
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  7. Article ; Online: The counterintuitive implications of superspreading diseases

    Bjarke Frost Nielsen / Kim Sneppen / Lone Simonsen

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Volume 3

    Abstract: Superspreading is known to have played an important role in the transmission dynamics of SARS-CoV-2. In this Comment, the authors discuss how knowledge of the extent and cause of superspreading is important for designing appropriate control measures for ... ...

    Abstract Superspreading is known to have played an important role in the transmission dynamics of SARS-CoV-2. In this Comment, the authors discuss how knowledge of the extent and cause of superspreading is important for designing appropriate control measures for emerging infectious diseases.
    Keywords Science ; Q
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
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  8. Article ; Online: Epigenetic switching with asymmetric bridging interactions.

    Skjegstad, Lars Erik J / Nickels, Jan Fabio / Sneppen, Kim / Kirkegaard, Julius B

    Biophysical journal

    2023  Volume 122, Issue 12, Page(s) 2421–2429

    Abstract: Gene expression states are often stably sustained in cis despite massively disruptive events like DNA replication. This is achieved by on-going enzymatic activity that maintains parts of the DNA in either heterochromatic (packed) or euchromatic (free) ... ...

    Abstract Gene expression states are often stably sustained in cis despite massively disruptive events like DNA replication. This is achieved by on-going enzymatic activity that maintains parts of the DNA in either heterochromatic (packed) or euchromatic (free) states, each of which is stabilized by both positive feedback and bridging interactions between individual nucleosomes. In contrast to condensed matter, however, the dynamics is not only governed by equilibrium binding interactions but is also mediated by enzymes that recognize and act on specific amino acid tails of the nucleosomes. The mechanical result is that some nucleosomes can bind to one another and form tightly packed polymer configurations, whereas others remain unbound and form free, noncompact polymer configurations. Here, we study the consequences of such an asymmetric interaction pattern on the dynamics of epigenetic switching. We develop a 3D polymer model and show that traits associated with epigenetic switching, such as bistability and epigenetic memory, are permitted by such a model. We find, however, that the experimentally observed burst-like nature of some epigenetic switches is difficult to reproduce by this biologically motivated interaction. Instead, the behavior seen in experiments can be explained by introducing partial confinement, which particularly affects the euchromatic regions of the chromosome.
    MeSH term(s) Nucleosomes ; DNA/metabolism ; DNA Replication ; Epigenesis, Genetic ; Polymers/metabolism
    Chemical Substances Nucleosomes ; DNA (9007-49-2) ; Polymers
    Language English
    Publishing date 2023-04-20
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 218078-9
    ISSN 1542-0086 ; 0006-3495
    ISSN (online) 1542-0086
    ISSN 0006-3495
    DOI 10.1016/j.bpj.2023.04.019
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 235: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MO 2: Show issues

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  9. Article ; Online: Spatial model of Ebola outbreaks contained by behavior change.

    Halvorsen, Gustav S / Simonsen, Lone / Sneppen, Kim

    PloS one

    2022  Volume 17, Issue 3, Page(s) e0264425

    Abstract: The West African Ebola (2014-2016) epidemic caused an estimated 11.310 deaths and massive social and economic disruption. The epidemic was comprised of many local outbreaks of varying sizes. However, often local outbreaks recede before the arrival of ... ...

    Abstract The West African Ebola (2014-2016) epidemic caused an estimated 11.310 deaths and massive social and economic disruption. The epidemic was comprised of many local outbreaks of varying sizes. However, often local outbreaks recede before the arrival of international aid or susceptible depletion. We modeled Ebola virus transmission under the effect of behavior changes acting as a local inhibitor. A spatial model is used to simulate Ebola epidemics. Our findings suggest that behavior changes can explain why local Ebola outbreaks recede before substantial international aid was mobilized during the 2014-2016 epidemic.
    MeSH term(s) Africa, Western/epidemiology ; Disease Outbreaks ; Ebolavirus ; Epidemics ; Hemorrhagic Fever, Ebola ; Humans
    Language English
    Publishing date 2022-03-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0264425
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  10. Article ; Online: From kill the winner to eliminate the winner in open phage-bacteria systems.

    Marantos, Anastasios / Mitarai, Namiko / Sneppen, Kim

    PLoS computational biology

    2022  Volume 18, Issue 8, Page(s) e1010400

    Abstract: Phages and bacteria manage to coexist and sustain ecosystems with a high diversity of strains, despite limited resources and heavy predation. This diversity can be explained by the "kill the winner" model where virulent phages predominantly prey on fast- ... ...

    Abstract Phages and bacteria manage to coexist and sustain ecosystems with a high diversity of strains, despite limited resources and heavy predation. This diversity can be explained by the "kill the winner" model where virulent phages predominantly prey on fast-growing bacteria and thereby suppress the competitive exclusion of slower-growing bacteria. Here we computationally investigate the robustness of these systems against invasions, where new phages or bacteria may interact with more than one of the resident strains. The resulting interaction networks were found to self-organize into a network with strongly interacting specialized predator-prey pairs, resembling that of the "kill the winner" model. Furthermore, the "kill the winner" dynamics is enforced with the occasional elimination of even the fastest-growing bacteria strains due to a phage infecting the fast and slow growers. The frequency of slower-growing strains was increased with the introduction of even a few non-diagonal interactions. Hence, phages capable of infecting multiple hosts play significant roles both in the evolution of the ecosystem by eliminating the winner and in supporting diversity by allowing slow growers to coexist with faster growers.
    MeSH term(s) Animals ; Bacteria ; Bacteriophages ; Ecosystem ; Predatory Behavior
    Language English
    Publishing date 2022-08-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1010400
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