SwePub
Sök i SwePub databas

  Utökad sökning

Träfflista för sökning "WFRF:(Jakobsson Mattias) ;conttype:(scientificother)"

Sökning: WFRF:(Jakobsson Mattias) > Övrigt vetenskapligt/konstnärligt

  • Resultat 1-10 av 63
Sortera/gruppera träfflistan
   
NumreringReferensOmslagsbildHitta
1.
  •  
2.
  •  
3.
  • Ausmees, Kristiina (författare)
  • Efficient computational methods for applications in genomics
  • 2019
  • Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • During the last two decades, advances in molecular technology have facilitated the sequencing and analysis of ancient DNA recovered from archaeological finds, contributing to novel insights into human evolutionary history. As more ancient genetic information has become available, the need for specialized methods of analysis has also increased. In this thesis, we investigate statistical and computational models for analysis of genetic data, with a particular focus on the context of ancient DNA.The main focus is on imputation, or the inference of missing genotypes based on observed sequence data. We present results from a systematic evaluation of a common imputation pipeline on empirical ancient samples, and show that imputed data can constitute a realistic option for population-genetic analyses. We also discuss preliminary results from a simulation study comparing two methods of phasing and imputation, which suggest that the parametric Li and Stephens framework may be more robust to extremely low levels of sparsity than the parsimonious Browning and Browning model.An evaluation of methods to handle missing data in the application of PCA for dimensionality reduction of genotype data is also presented. We illustrate that non-overlapping sequence data can lead to artifacts in projected scores, and evaluate different methods for handling unobserved genotypes.In genomics, as in other fields of research, increasing sizes of data sets are placing larger demands on efficient data management and compute infrastructures. The last part of this thesis addresses the use of cloud resources for facilitating such analysis. We present two different cloud-based solutions, and exemplify them on applications from genomics.
  •  
4.
  • Ausmees, Kristiina (författare)
  • Methodology and Infrastructure for Statistical Computing in Genomics : Applications for Ancient DNA
  • 2022
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • This thesis concerns the development and evaluation of computational methods for analysis of genetic data. A particular focus is on ancient DNA recovered from archaeological finds, the analysis of which has contributed to novel insights into human evolutionary and demographic history, while also introducing new challenges and the demand for specialized methods.A main topic is that of imputation, or the inference of missing genotypes based on observed sequence data. We present results from a systematic evaluation of a common imputation pipeline on empirical ancient samples, and show that imputed data can constitute a realistic option for population-genetic analyses. We also develop a tool for genotype imputation that is based on the full probabilistic Li and Stephens model for haplotype frequencies and show that it can yield improved accuracy on particularly challenging data.  Another central subject in genomics and population genetics is that of data characterization methods that allow for visualization and exploratory analysis of complex information. We discuss challenges associated with performing dimensionality reduction of genetic data, demonstrating how the use of principal component analysis is sensitive to incomplete information and performing an evaluation of methods to handle unobserved genotypes. We also discuss the use of deep learning models as an alternative to traditional methods of data characterization in genomics and propose a framework based on convolutional autoencoders that we exemplify on the applications of dimensionality reduction and genetic clustering.In genomics, as in other fields of research, increasing sizes of data sets are placing larger demands on efficient data management and compute infrastructures. The final part of this thesis addresses the use of cloud resources for facilitating data analysis in scientific applications. We present two different cloud-based solutions, and exemplify them on applications from genomics.
  •  
5.
  • Björklund, Mattias, 1971- (författare)
  • Beyond Moral Teaching : Financial Literacy as Citizenship Education
  • 2021
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • This thesis explores what financial literacy is, what financial literacy becomes and what financial literacy could become within the context of a citizenship education such as the Swedish upper secondary subject of social studies.  Financial literacy does not intuitively converge with social sciences which leaves social studies teachers to both teach and realise financial literacy. Thus, teachers become co-creators of financial literacy as a school subject. This thesis explores this process via two different studies resulting in four research articles. In the first study, semi-structured interviews – analysed through PCK – are used to explore the perceptions of Swedish social studies teachers in upper secondary school regarding financial literacy teaching and learning. The findings include differences between experienced and novice teachers regarding which content knowledge and pedagogical approaches they use. However, all teachers express difficulties fitting financial literacy into social studies, mainly due to a perception of financial literacy primarily being a private matter, along with the unclear relationship between financial and societal issues. The second study is designed as a financial literacy teaching intervention. Students’ views on a financial dilemma are analysed using citizenship conceptions and threshold concepts. The findings are used to discuss design principles for financial literacy teaching. Salient conclusions in the thesis include citizenship education being able to frame financial literacy and provide epistemic features which can make financial literacy more teachable and learnable. It is hoped that the results from this thesis can inform future financial literacy teaching design as well as policy discussion related to financial literacy teaching and learning contextualised with another subject, especially citizenship education.
  •  
6.
  • Breton, Gwenna, et al. (författare)
  • Deciphering early human history using Approximate Bayesian Computation and 74 whole genomes from Central and Southern Africa
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Human evolutionary history in Africa before and after the out-of-Africa event remains largely unexplored, due to lack of genome sequence data, limited representation of populations and limitations of presently available inference methods. We generated high-coverage genomes from 49 Central African individuals, from five rainforest hunter-gatherer populations and four neighboring populations, and from 25 Khoe-San individuals, from five populations. We analyzed these genomes jointly with 104 comparative genomes from worldwide populations. We showed that rainforest hunter-gatherers and Khoe-San populations define two distinct major axes of genetic variation both at the worldwide and Sub-Saharan scales. This new data provides unprecedented resolution to unravel complex genetic differentiation among rainforest hunter-gatherer populations in particular. Using both deterministic and Approximate Bayesian Computation inferences, we found strong support for gene flow throughout the entire history of Central and Southern Africa, and an early divergence, some 250-370 kya ago, of Khoe-San ancestors from the lineage ancestral to all Central African populations. This event was followed, still in the presence of gene-flow, some 80-240 kya, by the divergence of lineages ancestral to rainforest hunter-gatherers and their neighbors. Finally, divergence between the different Khoe-San populations likely predated that of eastern and western rainforest hunter-gatherers which occurred 16-44 kya. Altogether, our results indicate that a tree-like history of Central Africa incorporating gene-flow among ancient lineages as well as among recent lineages can explain genomic variation observed among populations today.
  •  
7.
  • Breton, Gwenna (författare)
  • Human demographic history : Insights on the human past based on genomes from Southern through Central Africa
  • 2020
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Evidence from paleontology, archaeology and population genetics support that modern humans originated in Africa. While the out-of-Africa event and subsequent colonization of all continents are well documented, human history in Africa at that time and before is less studied. Some current-day hunter-gatherer populations trace most of their genetic lineages to populations who inhabited Sub-Saharan Africa until the arrival of farming. They are informative about human history before and after the arrival of farming.I studied high-coverage genomes from two such groups, the Khoe-San from Southern Africa and the rainforest hunter-gatherers from Central Africa. I generated a total of 74 genomes, significantly increasing the number of genomes from Sub-Saharan African hunter-gatherers. I compared several versions of a commonly used pipeline for high-coverage genomes and showed that using standard ascertained reference datasets has no significant impact on variant calling in populations from Sub-Saharan Africa. Using the full genome information, I described the genetic diversity in the Khoe-San and in the rainforest hunter-gatherers and showed that gene flow from agropastoralist groups increased the Khoe-San genetic diversity. I also detected a signal of population size decline in the Khoe-San around the time of the out-of-Africa event, and I evaluated the power of the method to detect bottlenecks by applying it to simulated data. I investigated the history of modern humans in Africa by estimating divergence times between populations and applying an Approximate Bayesian Computation analysis. We confirmed that the earliest divergence event was between the Khoe-San ancestral lineage and the rest of modern humans, ~250-350 kya. I also showed that the possibility of high gene flow should be incorporated in models of human evolution.I furthermore examined SNP array data for two BaTwa populations from Zambia and showed that 20-30% of their autosomal diversity is hunter-gatherer-like. The estimated times for the admixture between a presumably local hunter-gatherer population and incoming agropastoralist groups are consistent with archaeological records.In this thesis, I investigated questions related to human history in Sub-Saharan Africa, from the emergence of modern humans ~300 kya to recent events related to the expansion of farming.
  •  
8.
  • Breton, Gwenna, et al. (författare)
  • The “BaTwa” populations from remote areas in Zambia retain ancestry of past forager groups
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Sub-equatorial Africa is inhabited today predominantly by Bantu-speaking farmers of west African descent. However, before the arrival of agriculture and pastoralism ~2,000 years ago, the region was inhabited by hunter-gatherers. The incoming farmer populations replaced, displaced or admixed with local hunter-gatherer groups. In some regions such as southern and central Africa, current-day farming populations have absorbed a large local hunter-gatherer genetic component. In other regions, such as Malawi, and Mozambique current-day populations have absorbed little to none of the local component. In this study, we generated genome-wide SNP data from two populations from Zambia thought to represent former hunter-gatherers, known locally as “BaTwa”, but for which no direct evidence exists of a hunter-gatherer past, either in language or lifestyle. We compared the BaTwa data to three Bantu-speaker agropastoralist populations from Zambia, and to other African and non-African populations. We show that the two BaTwa populations harbor a hunter-gatherer-like genetic component, representing respectively ~20% and ~30% of their genetic ancestry, while the rest is similar to Bantu-speaker agropastoralists. Although the component is closest related to current-day Khoe-San populations from southern Africa, results still suggest a unique local hunter-gatherer component. These results accord with Middle and Late Holocene skeletal evidence from Zambia and Malawi for a regionally separate hunter-gatherer population, which is now only detectable among the BaTwa. A two-way admixture scenario between a Bantu-speaker agropastoralist-like source and a hunter-gatherer-like source is supported for the two populations, occurring ~40 and ~16 generations ago respectively. These estimates are consistent with archaeological records for the arrival of agropastoralists in northern and central Zambia respectively. The study demonstrate the value of studying underrepresented minority groups to better understand the complexity of regional population histories.
  •  
9.
  • Cotgreave, Ian, et al. (författare)
  • Pyriproxifen and microcephaly: an investigation of potential ties to the ongoing "Zika epidemic"
  • 2016
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • As part of the Swetox mission to react to emerging concerns in chemical health and environmental safety, a preliminary litterature investigation was undertaken to gather all readily available scientific information on PPF with respect to safety assessment, in order to better understand potential links between chemical exposure and the devopment of microcephaly in affected areas. Therefore the contents of the report do not constitute an attempt at either questioning the use of existing regulatory data in the manner prescribed by international regulatory proceedures, or as a new risk assessment, based on the scientific information and concepts discussed. Here we report our findings, with particular emphasis on exisiting regulatory information, potential for lack of translation of results from regulatory animal testing to humans, lack of human exposure data and suggestions on plausible mode(s) of action of PPF in human neurodevelopmental adversities such as microcephaly.
  •  
10.
  • Coutinho, Alexandra, et al. (författare)
  • The Evolution of Adaptive traits in Indigenous human populations in Sub-Saharan Africa
  • Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
    • Several well-known genetic variants that confer disease resistance or other adaptive advantages have been investigated in modern-day populations across the globe. In particular, sub-Saharan African populations display variation for many of these loci. In this study, we investigate allele frequencies underlying functional variants of interest in sub-Saharan African populations. By also investigating sequence data from ancient human remains from excavated sites in sub-Saharan Africa, we can start to get an indication of the allele frequency trajectories of adaptive variants, how they have diffused through the African genetic landscape, and how much migration and admixture played a role in the distribution of these variants in modern-day African populations. Our results show that as well as selection, migration has had a large influence on changing allele frequency through time in variants associated with disease resistance, salt sensitivity and metabolism. Yet in other variants, such as some associated with skin pigmentation, allele frequencies have changed little over time. Lastly, this study emphasizes the need for continued study of African populations, as due to the sheer genetic diversity present in Africa, different functional variants may confer similar means of adaptation than those we know for out-of-Africa populations. This study is the first to comprehensively investigate adaptive variants in both ancient and modern Africans, and further research will continue to reveal how the genetic landscape of modern humans has changed, and continues to change through time.
  •  
Skapa referenser, mejla, bekava och länka
  • Resultat 1-10 av 63
Typ av publikation
annan publikation (24)
doktorsavhandling (21)
tidskriftsartikel (11)
konferensbidrag (3)
licentiatavhandling (2)
rapport (1)
visa fler...
bokkapitel (1)
visa färre...
Typ av innehåll
Författare/redaktör
Jakobsson, Mattias (42)
Schlebusch, Carina, ... (10)
Jakobsson, Mattias, ... (10)
Günther, Torsten (8)
Götherström, Anders (7)
Malmström, Helena (7)
visa fler...
Sjödin, Per (6)
Skoglund, Pontus (6)
Bernhardsson, Caroli ... (4)
Soodyall, Himla (4)
Valdiosera, Cristina (4)
Storå, Jan (3)
Fraser, Magdalena (3)
Vicente, Mário (3)
Breton, Gwenna (3)
Coutinho, Alexandra (3)
Daskalaki, Evangelia (3)
Naidoo, Thijessen (3)
Simões, Luciana G. (3)
Jakobsson, Erik, 198 ... (3)
Li, Sen, 1983- (3)
McKenna, James, 1987 ... (3)
Persson, Per (2)
Agnès E., Sjöstrand (2)
Per, Sjödin (2)
Mattias, Jakobsson (2)
Lidén, Kerstin (2)
Somel, Mehmet (2)
Edlund, Hanna (2)
Vretemark, Maria (2)
Koptekin, Dilek (2)
Kılınç, Gülşah Merve (2)
Pettersson, Robert (2)
Ausmees, Kristiina (2)
Fernaeus, Ylva (2)
Hollfelder, Nina (2)
Svensson, Emma, 1979 ... (2)
Sjöstrand, Agnès E. (2)
Heyer, Evelyne (2)
Verdu, Paul (2)
Lombard, Marlize (2)
Peyroteo Stjerna, Ri ... (2)
Rosenberg, Noah A. (2)
Gattepaille, Lucie (2)
Goldberg, Amy (2)
Omrak, Ayça (2)
Frisk, Erik, Profess ... (2)
Baird, Douglas (2)
Ozer, Fusun (2)
Schlebusch, Carina (2)
visa färre...
Lärosäte
Uppsala universitet (50)
Linköpings universitet (6)
Stockholms universitet (4)
Göteborgs universitet (1)
Lunds universitet (1)
Karlstads universitet (1)
Språk
Engelska (62)
Svenska (1)
Forskningsämne (UKÄ/SCB)
Naturvetenskap (49)
Humaniora (13)
Teknik (3)
Samhällsvetenskap (2)
Medicin och hälsovetenskap (1)
Lantbruksvetenskap (1)

År

Kungliga biblioteket hanterar dina personuppgifter i enlighet med EU:s dataskyddsförordning (2018), GDPR. Läs mer om hur det funkar här.
Så här hanterar KB dina uppgifter vid användning av denna tjänst.

 
pil uppåt Stäng

Kopiera och spara länken för att återkomma till aktuell vy