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  1. Book ; Online: European E-Democracy in Practice

    Hennen, Leonhard / van Keulen, Ira / Korthagen, Iris / Aichholzer, Georg / Lindner, Ralf / Nielsen, Rasmus Øjvind

    (Studies in Digital Politics and Governance)

    2020  

    Author's details edited by Leonhard Hennen, Ira van Keulen, Iris Korthagen, Georg Aichholzer, Ralf Lindner, Rasmus Øjvind Nielsen
    Series title Studies in Digital Politics and Governance
    Keywords European Union ; Technology—Sociological aspects ; Computers ; Political communication ; Democracy ; Public policy ; Europa ; Demokratie ; Politische Beteiligung ; Computerunterstützte Kommunikation ; E-Government
    Subject Electronic Government ; eGovernment ; CMC ; Online-Kommunikation ; Computer mediated communication ; Computergestützte Kommunikation ; Computervermittelte Kommunikation ; Kommunikation ; Computerkommunikation ; Digitale Kommunikation ; CVK ; Politische Partizipation ; Politische Teilnahme ; Politische Teilhabe ; Volksherrschaft ; Demokratischer Staat ; Democracy
    Subject code 320.94
    Language English
    Size 1 Online-Ressource (XI, 359 p. 3 illus)
    Edition 1st ed. 2020
    Publisher Springer International Publishing ; Imprint: Springer
    Publishing place Cham
    Document type Book ; Online
    HBZ-ID HT020300790
    ISBN 978-3-030-27184-8 ; 9783030271831 ; 9783030271855 ; 9783030271862 ; 3-030-27184-6 ; 3030271838 ; 3030271854 ; 3030271862
    DOI 10.1007/978-3-030-27184-8
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Book ; Online: European E-Democracy in Practice

    Hennen, Leonhard / van Keulen, Ira / Korthagen, Iris / Aichholzer, Georg / Lindner, Ralf / Nielsen, Rasmus Øjvind

    2020  

    Keywords Sociology ; Politics & government ; Political science & theory ; Political structures: democracy ; Public administration ; Computer networking & communications ; Political science ; European Union ; Technology-Sociological aspects ; Computers ; Political communication ; Democracy ; Public policy
    Size 1 electronic resource (359 pages)
    Publisher Springer Nature
    Publishing place Cham
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021030405
    ISBN 978-3-030-27184-8 ; 3-030-27184-6
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  3. Book ; Online: Policy-Oriented Technology Assessment Across Europe: Expanding Capacities

    Klüver, Lars / Nielsen, Rasmus Øjvind / Jørgensen, Marie Louise

    2016  

    Author's details edited by Lars Klüver, Rasmus Øjvind Nielsen, Marie Louise Jørgensen
    Keywords Science
    Subject code 500
    Language English
    Size 1 Online-Ressource (XVI, 171 p)
    Publisher Palgrave Macmillan UK ; Imprint: Palgrave Macmillan
    Publishing place London
    Document type Book ; Online
    HBZ-ID HT019020865
    ISBN 978-1-137-56172-5 ; 9781349850952 ; 1-137-56172-6 ; 1349850950
    DOI 10.1007/978-1-137-56172-5
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  4. Book ; Online: Policy-Oriented Technology Assessment Across Europe

    Klüver, Lars / Nielsen, Rasmus Øjvind / Jørgensen, Marie Louise

    2015  

    Keywords Computing and Information Technology ; Communications and Networks ; Political Analysis Theories and Methods ; Public Administration and Policy ; Politics
    Size 1 electronic resource (171 pages)
    Publisher Palgrave Macmillan
    Document type Book ; Online
    Note English ; Open Access
    HBZ-ID HT021043848
    ISBN 9781137561725 ; 1137561726
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  5. Article ; Online: SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances.

    Hui, Sandra / Nielsen, Rasmus

    BMC bioinformatics

    2022  Volume 23, Issue 1, Page(s) 348

    Abstract: Background: Single cell whole genome tumor sequencing can yield novel insights into the evolutionary history of somatic copy number alterations. Existing single cell copy number calling methods do not explicitly model the shared evolutionary process of ... ...

    Abstract Background: Single cell whole genome tumor sequencing can yield novel insights into the evolutionary history of somatic copy number alterations. Existing single cell copy number calling methods do not explicitly model the shared evolutionary process of multiple cells, and generally analyze cells independently. Additionally, existing methods for estimating tumor cell phylogenies using copy number profiles are sensitive to profile estimation errors.
    Results: We present SCONCE2, a method for jointly calling copy number alterations and estimating pairwise distances for single cell sequencing data. Using simulations, we show that SCONCE2 has higher accuracy in copy number calling and phylogeny estimation than competing methods. We apply SCONCE2 to previously published single cell sequencing data to illustrate the utility of the method.
    Conclusions: SCONCE2 jointly estimates copy number profiles and a distance metric for inferring tumor phylogenies in single cell whole genome tumor sequencing across multiple cells, enabling deeper understandings of tumor evolution.
    MeSH term(s) DNA Copy Number Variations ; Humans ; Neoplasms/genetics ; Neoplasms/pathology ; Phylogeny ; Polymorphism, Single Nucleotide
    Language English
    Publishing date 2022-08-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-022-04890-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Covariance of pairwise differences on a multi-species coalescent tree and implications for

    Guerra, Geno / Nielsen, Rasmus

    Philosophical transactions of the Royal Society of London. Series B, Biological sciences

    2022  Volume 377, Issue 1852, Page(s) 20200415

    Abstract: The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. Its theoretical properties have been heavily studied but there are still aspects of the MSC that are largely unknown, ... ...

    Abstract The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. Its theoretical properties have been heavily studied but there are still aspects of the MSC that are largely unknown, including the covariances in pairwise coalescence times, which are fundamental for understanding the properties of statistics that combine data from multiple species, such as the fixation index (
    MeSH term(s) Gene Flow ; Genetics, Population ; Humans ; Models, Genetic ; Phylogeny ; Population Density
    Language English
    Publishing date 2022-04-18
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 208382-6
    ISSN 1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
    ISSN (online) 1471-2970
    ISSN 0080-4622 ; 0264-3839 ; 0962-8436
    DOI 10.1098/rstb.2020.0415
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: SCONCE: a method for profiling copy number alterations in cancer evolution using single-cell whole genome sequencing.

    Hui, Sandra / Nielsen, Rasmus

    Bioinformatics (Oxford, England)

    2022  Volume 38, Issue 7, Page(s) 1801–1808

    Abstract: Motivation: Copy number alterations (CNAs) are a significant driver in cancer growth and development, but remain poorly characterized on the single cell level. Although genome evolution in cancer cells is Markovian through evolutionary time, CNAs are ... ...

    Abstract Motivation: Copy number alterations (CNAs) are a significant driver in cancer growth and development, but remain poorly characterized on the single cell level. Although genome evolution in cancer cells is Markovian through evolutionary time, CNAs are not Markovian along the genome. However, existing methods call copy number profiles with Hidden Markov Models or change point detection algorithms based on changes in observed read depth, corrected by genome content and do not account for the stochastic evolutionary process.
    Results: We present a theoretical framework to use tumor evolutionary history to accurately call CNAs in a principled manner. To model the tumor evolutionary process and account for technical noise from low coverage single-cell whole genome sequencing data, we developed SCONCE, a method based on a Hidden Markov Model to analyze read depth data from tumor cells using matched normal cells as negative controls. Using a combination of public data sets and simulations, we show SCONCE accurately decodes copy number profiles, and provides a useful tool for understanding tumor evolution.
    Availabilityand implementation: SCONCE is implemented in C++11 and is freely available from https://github.com/NielsenBerkeleyLab/sconce.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Humans ; DNA Copy Number Variations ; Whole Genome Sequencing ; Neoplasms/genetics ; Algorithms ; Genome ; High-Throughput Nucleotide Sequencing ; Software
    Language English
    Publishing date 2022-01-25
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btac041
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: The evolutionary dynamics of local adaptations under genetic rescue is determined by mutational load and polygenicity.

    Zhang, Yulin / Stern, Aaron J / Nielsen, Rasmus

    The Journal of heredity

    2023  

    Abstract: Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that is studied and deployed with ... ...

    Abstract Inbred populations often suffer from increased mutational load and reduced fitness due to lower efficacy of purifying selection in groups with small effective population sizes. Genetic rescue (GR) is a conservation tool that is studied and deployed with the aim of increasing the fitness of such inbred populations by assisted migration of individuals from closely related outbred populations. The success of GR depends on several factors--such as their demographic history and distribution of dominance effects of mutations--that may vary across populations. While we understand the impact of these factors on the dynamics of GR, their impact on local adaptations remains unclear. To this end, we conduct a population genetics simulation study to evaluate the impact of trait complexity (Mendelian vs. polygenic), dominance effects, and demographic history on the efficacy of GR. We find that the impact on local adaptations depends highly on the mutational load at the time of GR, which is in turn shaped dynamically by interactions between demographic history and dominance effects of deleterious variation. Over time local adaptations are generally restored post-GR, though in the short term they are often compromised in the process of purging deleterious variation. We also show that while local adaptations are almost always fully restored, the degree to which ancestral genetic variation affecting the trait is replaced by donor variation can vary drastically and is especially high for complex traits. Our results provide insights on the impact of GR on trait evolution and considerations for the practical implementation of GR.
    Language English
    Publishing date 2023-12-26
    Publishing country United States
    Document type Journal Article
    ZDB-ID 3044-2
    ISSN 1465-7333 ; 0022-1503
    ISSN (online) 1465-7333
    ISSN 0022-1503
    DOI 10.1093/jhered/esad079
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: An upstream-downstream externality related to water quality: The case of the Porong River in Indonesia

    Jensen, Frank / Hukom, Venticia / Nielsen, Rasmus / Nielsen, Max

    Aquaculture Economics & Management. 2023 July 3, v. 27, no. 3 p.405-440

    2023  

    Abstract: In this paper, we discuss an upstream-downstream externality related to water quality (the level of ammonia) in a river by distinguishing between a non-cooperative and cooperative case. As empirical case, we use the Porong River, which is located in the ... ...

    Abstract In this paper, we discuss an upstream-downstream externality related to water quality (the level of ammonia) in a river by distinguishing between a non-cooperative and cooperative case. As empirical case, we use the Porong River, which is located in the East Java province of Indonesia. In this river, aquaculture farmers are located downstream while the industrial firms are placed upstream. In both the non-cooperative and cooperative case, we find that the optimal profit by a polyculture is higher than the optimal profit for an industrial firm, and this result is robust to variations in relevant parameter values. Furthermore, by comparing the non-cooperative and cooperative cases, we find that the optimal gain of moving to joint management is reasonably high, and when varying relevant parameter values, this gain remains almost unchanged.
    Keywords administrative management ; ammonia ; aquaculture ; economics ; rivers ; water quality ; Indonesia ; River sharing ; non-cooperative case ; cooperative case ; D24 ; C71 ; C72 ; D62 ; Q25
    Language English
    Dates of publication 2023-0703
    Size p. 405-440.
    Publishing place Taylor & Francis
    Document type Article ; Online
    ZDB-ID 2009823-6
    ISSN 1551-8663 ; 1365-7313 ; 1365-7305
    ISSN (online) 1551-8663 ; 1365-7313
    ISSN 1365-7305
    DOI 10.1080/13657305.2022.2137263
    Database NAL-Catalogue (AGRICOLA)

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  10. Article ; Online: AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees.

    Pipes, Lenore / Nielsen, Rasmus

    Bioinformatics (Oxford, England)

    2021  Volume 38, Issue 3, Page(s) 663–670

    Abstract: Motivation: Clustering is a fundamental task in the analysis of nucleotide sequences. Despite the exponential increase in the size of sequence databases of homologous genes, few methods exist to cluster divergent sequences. Traditional clustering ... ...

    Abstract Motivation: Clustering is a fundamental task in the analysis of nucleotide sequences. Despite the exponential increase in the size of sequence databases of homologous genes, few methods exist to cluster divergent sequences. Traditional clustering methods have mostly focused on optimizing high speed clustering of highly similar sequences. We develop a phylogenetic clustering method which infers ancestral sequences for a set of initial clusters and then uses a greedy algorithm to cluster sequences.
    Results: We describe a clustering program AncestralClust, which is developed for clustering divergent sequences. We compare this method with other state-of-the-art clustering methods using datasets of homologous sequences from different species. We show that, in divergent datasets, AncestralClust has higher accuracy and more even cluster sizes than current popular methods.
    Availability and implementation: AncestralClust is an Open Source program available at https://github.com/lpipes/ancestralclust.
    Supplementary information: Supplementary data are available at Bioinformatics online.
    MeSH term(s) Software ; Phylogeny ; Base Sequence ; Algorithms ; Cluster Analysis
    Language English
    Publishing date 2021-08-11
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btab723
    Database MEDical Literature Analysis and Retrieval System OnLINE

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