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Smiljanic, Jelena; Edler, Daniel; Rosvall, Martin Mapping flows on sparse networks with missing links Journal Article Phys. Rev. E, 102 , pp. 012302, 2020. Wickman, Jonas; Dieckmann, Ulf; Hui, Cang; Brännström, Åke How geographic productivity patterns affect food-web evolution Journal Article J. Theor. Biol., 506 , pp. 110374, 2020, ([DOI:hrefhttps://dx.doi.org/10.1016/j.jtbi.2020.11037410.1016/j.jtbi.2020.110374] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/3263438632634386]). BibTeX | Tags: Öhlund, Gunnar; Bodin, Mats; Nilsson, Karin A; Öhlund, Sven‐Ola; Mobley, Kenyon B; Hudson, Alan G; Peedu, Mikael; Brännström, Åke; Bartels, Pia; Præbel, Kim; Hein, Catherine L; Johansson, Petter; Englund, Göran Ecological speciation in European whitefish is driven by a large-gaped predator Journal Article Evol Lett, 4 (3), pp. 243–256, 2020, ([PubMed Central:hrefhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293097PMC7293097] [DOI:hrefhttps://dx.doi.org/10.1002/evl3.16710.1002/evl3.167] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/2665578226655782]). BibTeX | Tags: Uszko, Wojciech; Diehl, Sebastian; Wickman, Jonas Fitting functional response surfaces to data: a best practice guide Journal Article Ecosphere, 11 (4), pp. e03051, 2020. Abstract | Links | BibTeX | Tags: data transformation, functional response, heteroscedasticity, Hill exponent, ingestion rate, parameter correlation, parameter estimation, prey density, temperature, type III Holmberg, Martin Pandemier och Epidemier - ett tvärvetenskapligt perspektiv Book 1, 2020, ISBN: 9789144135359. BibTeX | Tags: Bota, Andras; Holmberg, Martin; Gardner, Lauren; Rosvall, Martin Socio-economic and environmental patterns behind H1N1 spreading in Sweden Journal Article medRxiv, 2020. Abstract | Links | BibTeX | Tags: Franklin, O; Harrison, S P; Dewar, R; Farrior, C E; Brännström, Åke; Dieckmann, U; Pietsch, S; Falster, D; Cramer, W; Loreau, M; Wang, H; Mäkelä, A; Rebel, K T; Meron, E; Schymanski, S J; Rovenskaya, E; Stocker, B D; Zaehle, S; Manzoni, S; van Oijen, M; Wright, I J; Ciais, P; van Bodegom, P M; Peñuelas, J; Hofhansl, F; Terrer, C; Soudzilovskaia, N A; Midgley, G; Prentice, I C Organizing principles for vegetation dynamics Journal Article Nat Plants, 6 (5), pp. 444–453, 2020, ([DOI:hrefhttps://dx.doi.org/10.1038/s41477-020-0655-x10.1038/s41477-020-0655-x] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/3239388232393882]). BibTeX | Tags: Joshi, J; Brännström, Åke; Dieckmann, U Emergence of social inequality in the spatial harvesting of renewable public goods Journal Article PLoS Comput. Biol., 16 (1), pp. e1007483, 2020, ([PubMed Central:hrefhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974303PMC6974303] [DOI:hrefhttps://dx.doi.org/10.1371/journal.pcbi.100748310.1371/journal.pcbi.1007483] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/1822176118221761]). BibTeX | Tags: Calatayud, Joaquín; Andivia, Enrique; Escuderoa, Adrián; Melián, Carlos J; Bernardo-Madrid, Rubén; Stoffel, Markus; Aponte, Cristina; Medina, Nagore G; Molina-Venegas, Rafael; Arnan, Xavier; Rosvall, Martin; Neuman, Magnus; Noriega, Jorge Ari; Alves-Martins, Fernanda; Draper, Isabel; Luzuriaga, Arantzazu; Ballesteros-Cánovas, Juan Antonio; Morales-Molino, César; Ferrandis, Pablo; Herrero, Asier; Pataro, Luciano; Juen, Leandro; Cea, Alex; Madrigal-González, Jaime Positive associations among rare species and their persistence in ecological assemblages Journal Article Nature Ecology and Evolution, 4 , pp. 40-45, 2019. Abstract | Links | BibTeX | Tags: Calatayud, Rosvall Calatayud, Joaquín; Bernardo-Madrid, Rubén; Neuman, Magnus; Rojas, Alexis; Rosvall, Martin Exploring the solution landscape enables more reliable network community detection Journal Article Phys. Rev. E, 100 , pp. 052308, 2019. Berdahl, Andrew; Brelsford, Christa; Bacco, Caterina De; Dumas, Marion; Ferdinand, Vanessa; Grochow, Joshua A; Hébert-Dufresne, Laurent; Kallus, Yoav; Kempes, Christopher P; Kolchinsky, Artemy; Larremore, Daniel B; Libby, Eric; Power, Eleanor A; Stern, Caitlin A; Tracey, Brendan D Dynamics of beneficial epidemics Journal Article Scientific Reports, 9 (1), pp. 15093, 2019, ISSN: 2045-2322. Abstract | Links | BibTeX | Tags: Hajdu, László; Bóta, András; Krész, Miklós; Khani, Alireza; Gardner, Lauren M Discovering the Hidden Community Structure of Public Transportation Networks Journal Article Networks and Spatial Economics, 2019, ISSN: 1572-9427. Abstract | Links | BibTeX | Tags: Wickman, Jonas; Diehl, Sebastian; Brännström, Åke Evolution of resource specialisation in competitive metacommunities Journal Article Ecology Letters, 0 (0), 2019. Abstract | Links | BibTeX | Tags: Adaptive dynamics, Brännström, coexistence, consumer–resource interactions, Diehl, ESS, spatial models, Wickman Libby, Eric Modularity of the life cycle Journal Article Nature Ecology & Evolution, 3 (8), pp. 1142-1143, 2019, ISSN: 2397-334X. Abstract | Links | BibTeX | Tags: Lee, Sang Hoon; Kim, Yeonghoon; Lee, Sungmin; Durang, Xavier; Stenberg, Per; Jeon, Jae-Hyung; Lizana, Ludvig Mapping the spectrum of 3D communities in human chromosome conformation capture data Journal Article Scientific Reports, 9 , 2019. Abstract | Links | BibTeX | Tags: Lizana Durang, Xavier; Lee, Sungmin; Lizana, Ludvig; Jeon, Jae-Hyung First-passage statistics under stochastic resetting in bounded domains Journal Article Journal of Physics A: Mathematical and Theoretical, 52 (22), pp. 224001, 2019. Abstract | Links | BibTeX | Tags: Lambiotte, Renaud; Rosvall, Martin; Scholtes, Ingo From networks to optimal higher-order models of complex systems Journal Article Nature Physics, 15 (4), pp. 313-320, 2019, ISSN: 1745-2481. Abstract | Links | BibTeX | Tags: Sobhy, Haitham; Kumar, Rajendra; Lewerentz, Jacob; Lizana, Ludvig; Stenberg, Per Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins Journal Article Scientific Reports, 9 , 2019. Abstract | Links | BibTeX | Tags: Lizana Kumar, Rajendra; Lizana, Ludvig; Stenberg, Per Genomic 3D compartments emerge from unfolding mitotic chromosomes Journal Article Chromosoma, 128 , pp. 15-20, 2019, ISSN: 1432-0886. Abstract | Links | BibTeX | Tags: Lizana Lundström, Niklas LP; Loeuille, Nicolas; Meng, Xinzhu; Bodin, Mats; Brännström, Åke Meeting yield and conservation objectives by balancing harvesting of juveniles and adults Journal Article arXiv preprint arXiv:1712.10184, 2019. BibTeX | Tags:
title = {Mapping flows on sparse networks with missing links},
author = {Jelena Smiljanic and Daniel Edler and Martin Rosvall},
url = {https://link.aps.org/doi/10.1103/PhysRevE.102.012302},
doi = {10.1103/PhysRevE.102.012302},
year = {2020},
date = {2020-07-01},
journal = {Phys. Rev. E},
volume = {102},
pages = {012302},
publisher = {American Physical Society},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {How geographic productivity patterns affect food-web evolution},
author = {Jonas Wickman and Ulf Dieckmann and Cang Hui and Åke Brännström},
year = {2020},
date = {2020-07-01},
journal = {J. Theor. Biol.},
volume = {506},
pages = {110374},
note = {[DOI:hrefhttps://dx.doi.org/10.1016/j.jtbi.2020.11037410.1016/j.jtbi.2020.110374] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/3263438632634386]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Ecological speciation in European whitefish is driven by a large-gaped predator},
author = {Gunnar Öhlund and Mats Bodin and Karin A. Nilsson and Sven‐Ola Öhlund and Kenyon B. Mobley and Alan G. Hudson and Mikael Peedu and Åke Brännström and Pia Bartels and Kim Præbel and Catherine L. Hein and Petter Johansson and Göran Englund},
year = {2020},
date = {2020-06-01},
journal = {Evol Lett},
volume = {4},
number = {3},
pages = {243--256},
note = {[PubMed Central:hrefhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293097PMC7293097] [DOI:hrefhttps://dx.doi.org/10.1002/evl3.16710.1002/evl3.167] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/2665578226655782]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Fitting functional response surfaces to data: a best practice guide},
author = {Wojciech Uszko and Sebastian Diehl and Jonas Wickman},
url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.3051},
doi = {10.1002/ecs2.3051},
year = {2020},
date = {2020-01-01},
journal = {Ecosphere},
volume = {11},
number = {4},
pages = {e03051},
abstract = {Abstract Describing how resource consumption rates depend on resource density, conventionally termed “functional responses,” is crucial to understanding the population dynamics of trophically interacting organisms. Yet, accurately determining the functional response for any given pair of predator and prey remains a challenge. Moreover, functional responses are potentially complex surfaces in multidimensional space, where resource density is only one of several factors determining consumption rates. We explored how three sources of error can be addressed in the design and statistical analysis of functional response experiments: ill-chosen spacing of prey densities, heteroscedastic variance in consumption rates, and non-independence of parameters of the function describing prey consumption in relation to prey density and additional environmental factors. We generated extensive, virtual data sets that simulated feeding experiments in which both prey density and environmental temperature were varied, and for which the true, deterministic functional response surface was known and realistic variance had been added. We compared eight different methods of functional response fitting, one of which stood out as best performing. We subsequently tested several conclusions from the simulation study against experimental data of zooplankton feeding on algae across a broad range of temperatures. We summarize our main findings in three best practice guidelines for the experimental estimation of functional response surfaces, of which the second is the most important: (1) space prey densities logarithmically, starting from very low densities; (2) log-transform prey consumption data prior to fitting; and (3) fit a multivariate functional response surface to all data (including all prey densities and other factors, in our case temperature) in a single step. We also observed that functional response surfaces were fitted more accurately and precisely than their component parameters. The latter occurred because parameter estimates were non-independent, which is an inevitable feature of fitting complex nonlinear functions to data: A given response surface can often be described with near-equal accuracy by multiple parameter combinations. We therefore conclude that fitted functional response models perform better at optimizing the fit of the overall response surface than at determining how component parameters, such as the attack rate or handling time, depend on environmental factors such as temperature.},
keywords = {data transformation, functional response, heteroscedasticity, Hill exponent, ingestion rate, parameter correlation, parameter estimation, prey density, temperature, type III},
pubstate = {published},
tppubtype = {article}
}
title = {Pandemier och Epidemier - ett tvärvetenskapligt perspektiv},
author = {Martin Holmberg},
isbn = {9789144135359},
year = {2020},
date = {2020-01-01},
pages = {155},
edition = {1},
institution = {Umeå University, Department of culture and media studies},
keywords = {},
pubstate = {published},
tppubtype = {book}
}
title = {Socio-economic and environmental patterns behind H1N1 spreading in Sweden},
author = {Andras Bota and Martin Holmberg and Lauren Gardner and Martin Rosvall},
url = {https://www.medrxiv.org/content/early/2020/04/24/2020.03.18.20038349},
doi = {10.1101/2020.03.18.20038349},
year = {2020},
date = {2020-01-01},
journal = {medRxiv},
publisher = {Cold Spring Harbor Laboratory Press},
abstract = {The first influenza pandemic in our century started in 2009, spreading from Mexico to the rest of the world, infecting a noticeable fraction of the world population. The outbreak reached Europe in late April, and eventually, almost all countries had confirmed H1N1 cases. On 6 May, Swedish authorities reported the first confirmed influenza case. By the time the pandemic ended, more than 10 thousand people were infected in the country. In this paper, we aim to discover critical socio-economic, travel, and environmental factors contributing to the spreading of H1N1 in Sweden covering six years between 2009 and 2015, focusing on the onset and 2. the peak of the epidemic phase in each municipality. We apply the Generalized Inverse Infection Method (GIIM) to identify these factors. GIIM represents an epidemic spreading process on a network of nodes corresponding to geographical objects, connected by links indicating travel routes, and transmission probabilities assigned to the links guiding the infection process. The GIIM method uses observations on a real-life outbreak as a training dataset to estimate these probabilities and construct a simulated outbreak matching the training data as close as possible. Our results show that the influenza outbreaks considered in this study are mainly driven by the largest population centers in the country. Also, changes in temperature have a noticeable effect. Other socio-economic factors contribute only moderately to the epidemic peak and have a negligible effect on the epidemic onset. We also demonstrate that by training our model on the 2009 outbreak, we can predict the timing of the epidemic onset in the following five seasons with good accuracy. The model proposed in this paper provides a real-time decision support tool advising on resource allocation and surveillance. Furthermore, while this study only considers H1N1 outbreaks, the model can be adapted to other influenza strains or diseases with a similar transmission mechanism.Competing Interest StatementThe authors have declared no competing interest.Funding StatementAndras Bota was supported by the Olle Engkvist Byggmästare Foundation. Martin Rosvall was supported by the Swedish Research Council, grant 2016-00796.Author DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesData available on request from the authors},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Organizing principles for vegetation dynamics},
author = {O Franklin and S P Harrison and R Dewar and C E Farrior and Åke Brännström and U Dieckmann and S Pietsch and D Falster and W Cramer and M Loreau and H Wang and A Mäkelä and K T Rebel and E Meron and S J Schymanski and E Rovenskaya and B D Stocker and S Zaehle and S Manzoni and M van Oijen and I J Wright and P Ciais and P M van Bodegom and J Peñuelas and F Hofhansl and C Terrer and N A Soudzilovskaia and G Midgley and I C Prentice},
year = {2020},
date = {2020-01-01},
journal = {Nat Plants},
volume = {6},
number = {5},
pages = {444--453},
note = {[DOI:hrefhttps://dx.doi.org/10.1038/s41477-020-0655-x10.1038/s41477-020-0655-x] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/3239388232393882]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Emergence of social inequality in the spatial harvesting of renewable public goods},
author = {J Joshi and Åke Brännström and U Dieckmann},
year = {2020},
date = {2020-01-01},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {1},
pages = {e1007483},
note = {[PubMed Central:hrefhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974303PMC6974303] [DOI:hrefhttps://dx.doi.org/10.1371/journal.pcbi.100748310.1371/journal.pcbi.1007483] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/1822176118221761]},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Positive associations among rare species and their persistence in ecological assemblages},
author = {Joaquín Calatayud and Enrique Andivia and Adrián Escuderoa and Carlos J. Melián and Rubén Bernardo-Madrid and Markus Stoffel and Cristina Aponte and Nagore G. Medina and Rafael Molina-Venegas and Xavier Arnan and Martin Rosvall and Magnus Neuman and Jorge Ari Noriega and Fernanda Alves-Martins and Isabel Draper and Arantzazu Luzuriaga and Juan Antonio Ballesteros-Cánovas and César Morales-Molino and Pablo Ferrandis and Asier Herrero and Luciano Pataro and Leandro Juen and Alex Cea and Jaime Madrigal-González },
doi = {10.1038/s41559-019-1053-5},
year = {2019},
date = {2019-12-16},
journal = {Nature Ecology and Evolution},
volume = {4},
pages = {40-45},
abstract = {According to the competitive exclusion principle, species with low competitive abilities should be excluded by more efficient competitors; yet, they generally remain as rare species. Here, we describe the positive and negative spatial association networks of 326 disparate assemblages, showing a general organization pattern that simultaneously supports the primacy of competition and the persistence of rare species. Abundant species monopolize negative associations in about 90% of the assemblages. On the other hand, rare species are mostly involved in positive associations, forming small network modules. Simulations suggest that positive interactions among rare species and microhabitat preferences are the most probable mechanisms underpinning this pattern and rare species persistence. The consistent results across taxa and geography suggest a general explanation for the maintenance of biodiversity in competitive environments.},
keywords = {Calatayud, Rosvall},
pubstate = {published},
tppubtype = {article}
}
title = {Exploring the solution landscape enables more reliable network community detection},
author = {Joaquín Calatayud and Rubén Bernardo-Madrid and Magnus Neuman and Alexis Rojas and Martin Rosvall},
url = {https://link.aps.org/doi/10.1103/PhysRevE.100.052308},
doi = {10.1103/PhysRevE.100.052308},
year = {2019},
date = {2019-11-01},
journal = {Phys. Rev. E},
volume = {100},
pages = {052308},
publisher = {American Physical Society},
keywords = {Rojas},
pubstate = {published},
tppubtype = {article}
}
title = {Dynamics of beneficial epidemics},
author = {Andrew Berdahl and Christa Brelsford and Caterina De Bacco and Marion Dumas and Vanessa Ferdinand and Joshua A Grochow and Laurent Hébert-Dufresne and Yoav Kallus and Christopher P Kempes and Artemy Kolchinsky and Daniel B Larremore and Eric Libby and Eleanor A Power and Caitlin A Stern and Brendan D Tracey},
url = {https://doi.org/10.1038/s41598-019-50039-w},
doi = {10.1038/s41598-019-50039-w},
issn = {2045-2322},
year = {2019},
date = {2019-10-22},
journal = {Scientific Reports},
volume = {9},
number = {1},
pages = {15093},
abstract = {Pathogens can spread epidemically through populations. Beneficial contagions, such as viruses that enhance host survival or technological innovations that improve quality of life, also have the potential to spread epidemically. How do the dynamics of beneficial biological and social epidemics differ from those of detrimental epidemics? We investigate this question using a breadth-first modeling approach involving three distinct theoretical models. First, in the context of population genetics, we show that a horizontally-transmissible element that increases fitness, such as viral DNA, spreads superexponentially through a population, more quickly than a beneficial mutation. Second, in the context of behavioral epidemiology, we show that infections that cause increased connectivity lead to superexponential fixation in the population. Third, in the context of dynamic social networks, we find that preferences for increased global infection accelerate spread and produce superexponential fixation, but preferences for local assortativity halt epidemics by disconnecting the infected from the susceptible. We conclude that the dynamics of beneficial biological and social epidemics are characterized by the rapid spread of beneficial elements, which is facilitated in biological systems by horizontal transmission and in social systems by active spreading behavior of infected individuals.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Discovering the Hidden Community Structure of Public Transportation Networks},
author = {László Hajdu and András Bóta and Miklós Krész and Alireza Khani and Lauren M Gardner},
url = {https://doi.org/10.1007/s11067-019-09476-3},
doi = {10.1007/s11067-019-09476-3},
issn = {1572-9427},
year = {2019},
date = {2019-08-20},
journal = {Networks and Spatial Economics},
abstract = {Advances in public transit modeling and smart card technologies can reveal detailed contact patterns of passengers. A natural way to represent such contact patterns is in the form of networks. In this paper we utilize known contact patterns from a public transit assignment model in a major metropolitan city, and propose the development of two novel network structures, each of which elucidate certain aspects of passenger travel behavior. We first propose the development of a transfer network, which can reveal passenger groups that travel together on a given day. Second, we propose the development of a community network, which is derived from the transfer network, and captures the similarity of travel patterns among passengers. We then explore the application of each of these network structures to identify the most frequently used travel paths, i.e., routes and transfers, in the public transit system, and model epidemic spreading risk among passengers of a public transit network, respectively. In the latter our conclusions reinforce previous observations, that routes crossing or connecting to the city center in the morning and afternoon peak hours are the most ``dangerous'' during an outbreak.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Evolution of resource specialisation in competitive metacommunities},
author = {Jonas Wickman and Sebastian Diehl and Åke Brännström},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13338},
doi = {10.1111/ele.13338},
year = {2019},
date = {2019-08-07},
journal = {Ecology Letters},
volume = {0},
number = {0},
abstract = {Abstract Spatial environmental heterogeneity coupled with dispersal can promote ecological persistence of diverse metacommunities. Does this premise hold when metacommunities evolve? Using a two-resource competition model, we studied the evolution of resource-uptake specialisation as a function of resource type (substitutable to essential) and shape of the trade-off between resource uptake affinities (generalist- to specialist-favouring). In spatially homogeneous environments, evolutionarily stable coexistence of consumers is only possible for sufficiently substitutable resources and specialist-favouring trade-offs. Remarkably, these same conditions yield comparatively low diversity in heterogeneous environments, because they promote sympatric evolution of two opposite resource specialists that, together, monopolise the two resources everywhere. Consumer diversity is instead maximised for intermediate trade-offs and clearly substitutable or clearly essential resources, where evolved metacommunities are characterised by contrasting selection regimes. Taken together, our results present new insights into resource-competition-mediated evolutionarily stable diversity in homogeneous and heterogeneous environments, which should be applicable to a wide range of systems.},
keywords = {Adaptive dynamics, Brännström, coexistence, consumer–resource interactions, Diehl, ESS, spatial models, Wickman},
pubstate = {published},
tppubtype = {article}
}
title = {Modularity of the life cycle},
author = {Eric Libby},
url = {https://doi.org/10.1038/s41559-019-0956-5},
doi = {10.1038/s41559-019-0956-5},
issn = {2397-334X},
year = {2019},
date = {2019-08-01},
journal = {Nature Ecology & Evolution},
volume = {3},
number = {8},
pages = {1142-1143},
abstract = {Life stages in Bacillus subtilis are controlled by regulatory blocks that can be kept or lost across species in response to selection in different environments.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Mapping the spectrum of 3D communities in human chromosome conformation capture data},
author = {Sang Hoon Lee and Yeonghoon Kim and Sungmin Lee and Xavier Durang and Per Stenberg and Jae-Hyung Jeon and Ludvig Lizana},
doi = {https://doi.org/10.1038/s41598-019-42212-y},
year = {2019},
date = {2019-05-02},
journal = {Scientific Reports},
volume = {9},
abstract = {Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is able to detect the pairwise physical contacts of all chromosomal loci. The Hi-C data shows that chromosomes are composed of 3D compartments that range over a variety of scales. However, it is challenging to systematically detect these cross-scale structures. Most studies have therefore designed methods for specific scales to study foremost topologically associated domains (TADs) and A/B compartments. To go beyond this limitation, we tailor a network community detection method that finds communities in compact fractal globule polymer systems. Our method allows us to continuously scan through all scales with a single resolution parameter. We found: (i) polymer segments belonging to the same 3D community do not have to be in consecutive order along the polymer chain. In other words, several TADs may belong to the same 3D community. (ii) CTCF proteins---a loop-stabilizing protein that is ascribed a big role in TAD formation---are correlated well with community borders only at one level of organization. (iii) TADs and A/B compartments are traditionally treated as two weakly related 3D structures and detected with different algorithms. With our method, we detect both by simply adjusting the resolution parameter. We therefore argue that they represent two specific levels of a continuous spectrum 3D communities, rather than seeing them as different structural entities.},
keywords = {Lizana},
pubstate = {published},
tppubtype = {article}
}
title = {First-passage statistics under stochastic resetting in bounded domains},
author = {Xavier Durang and Sungmin Lee and Ludvig Lizana and Jae-Hyung Jeon},
url = {https://doi.org/10.1088%2F1751-8121%2Fab15f5},
doi = {10.1088/1751-8121/ab15f5},
year = {2019},
date = {2019-04-01},
journal = {Journal of Physics A: Mathematical and Theoretical},
volume = {52},
number = {22},
pages = {224001},
publisher = {IOP Publishing},
abstract = {We investigate the first-passage problem where a diffusive searcher stochastically resets to a fixed position at a constant rate in a bounded domain. We put forward an analytical framework for this problem where the resetting rate r, the resetting position x
r
, the initial position x
0, the domain size L, and the particle’s diffusion constant D are independent variables. From this we obtain analytical expressions for the mean-first passage time, survival probability and the first-passage time density in Laplace space in terms of the above independent variables, and closed forms in time-domain expression in some cases. For the first-passage time distributions their full-time profiles in time-domain are numerically obtained and validated by Monte Carlo simulations. We show that for the general resetting condition the first-passage process has rich nontrivial features as it combines effects from resetting and the finiteness of the domain. A phase diagram showing the regions for resetting-enhanced and -suppressed first-passages is obtained analytically. Counter-intuitively, resetting facilitates the first-passage event even if the particle resets to a position that is further away from the target than where it started. Finally, we show that averaging over resetting positions, resetting never helps the search compared to a random search, unless the resetting position is displaced from the initial position.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
r
, the initial position x
0, the domain size L, and the particle’s diffusion constant D are independent variables. From this we obtain analytical expressions for the mean-first passage time, survival probability and the first-passage time density in Laplace space in terms of the above independent variables, and closed forms in time-domain expression in some cases. For the first-passage time distributions their full-time profiles in time-domain are numerically obtained and validated by Monte Carlo simulations. We show that for the general resetting condition the first-passage process has rich nontrivial features as it combines effects from resetting and the finiteness of the domain. A phase diagram showing the regions for resetting-enhanced and -suppressed first-passages is obtained analytically. Counter-intuitively, resetting facilitates the first-passage event even if the particle resets to a position that is further away from the target than where it started. Finally, we show that averaging over resetting positions, resetting never helps the search compared to a random search, unless the resetting position is displaced from the initial position.
title = {From networks to optimal higher-order models of complex systems},
author = {Renaud Lambiotte and Martin Rosvall and Ingo Scholtes},
url = {https://doi.org/10.1038/s41567-019-0459-y},
doi = {10.1038/s41567-019-0459-y},
issn = {1745-2481},
year = {2019},
date = {2019-04-01},
journal = {Nature Physics},
volume = {15},
number = {4},
pages = {313-320},
abstract = {Rich data are revealing that complex dependencies between the nodes of a network may not be captured by models based on pairwise interactions. Higher-order network models go beyond these limitations, offering new perspectives for understanding complex systems.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
title = {Highly interacting regions of the human genome are enriched with enhancers and bound by DNA repair proteins},
author = {Haitham Sobhy and Rajendra Kumar and Jacob Lewerentz and Ludvig Lizana and Per Stenberg},
url = {https://www.nature.com/articles/s41598-019-40770-9},
doi = {https://doi.org/10.1038/s41598-019-40770-9},
year = {2019},
date = {2019-03-14},
journal = {Scientific Reports},
volume = {9},
abstract = {In specific cases, chromatin clearly forms long-range loops that place distant regulatory elements in close proximity to transcription start sites, but we have limited understanding of many loops identified by Chromosome Conformation Capture (such as Hi-C) analyses. In efforts to elucidate their characteristics and functions, we have identified highly interacting regions (HIRs) using intra-chromosomal Hi-C datasets with a new computational method based on looking at the eigenvector that corresponds to the smallest eigenvalue (here unity). Analysis of these regions using ENCODE data shows that they are in general enriched in bound factors involved in DNA damage repair and have actively transcribed genes. However, both highly transcribed regions as well as transcriptionally inactive regions can form HIRs. The results also indicate that enhancers and super-enhancers in particular form long-range interactions within the same chromosome. The accumulation of DNA repair factors in most identified HIRs suggests that protection from DNA damage in these regions is essential for avoidance of detrimental rearrangements.},
keywords = {Lizana},
pubstate = {published},
tppubtype = {article}
}
title = {Genomic 3D compartments emerge from unfolding mitotic chromosomes},
author = {Rajendra Kumar and Ludvig Lizana and Per Stenberg},
url = {https://doi.org/10.1007/s00412-018-0684-7},
doi = {10.1007/s00412-018-0684-7},
issn = {1432-0886},
year = {2019},
date = {2019-03-01},
journal = {Chromosoma},
volume = {128},
pages = {15-20},
abstract = {The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription, chromatin modifications and protein binding. However, these compartments do not exist during cell division when the DNA is condensed, and it is unclear how and when they emerge. In this paper, we focus on the early stages after cell division as the chromosomes start to decondense. We use a simple polymer model to understand the types of 3D structures that emerge from local unfolding of a compact initial state. From simulations, we recover 3D compartments, such as TADs and A/B compartments that are consistently detected in chromosome capture experiments across cell types and organisms. This suggests that the large-scale 3D organisation is a result of an inflation process.},
keywords = {Lizana},
pubstate = {published},
tppubtype = {article}
}
title = {Meeting yield and conservation objectives by balancing harvesting of juveniles and adults},
author = {Niklas LP Lundström and Nicolas Loeuille and Xinzhu Meng and Mats Bodin and Åke Brännström},
year = {2019},
date = {2019-02-25},
journal = {arXiv preprint arXiv:1712.10184},
keywords = {},
pubstate = {published},
tppubtype = {article}
}