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1.
  • Säll, T., et al. (författare)
  • Chloroplast DNA indicates a single origin of the allotetraploid Arabidopsis suecica
  • 2003
  • Ingår i: Journal of Evolutionary Biology. - : John Wiley & Sons Inc.. - 1010-061X .- 1420-9101. ; 16:5, s. 1019-1029
  • Tidskriftsartikel (refereegranskat)abstract
    • DNA sequencing was performed on up to 12 chloroplast DNA regions [giving a total of 4288 base pairs (bp) in length] from the allopolyploid Arabidopsis suecica (48 accessions) and its two parental species, A. thaliana (25 accessions) and A. arenosa (seven accessions). Arabidopsis suecica was identical to A. thaliana at all 93 sites where A. thaliana and A. arenosa differed, thus showing that A. thaliana is the maternal parent of A. suecica. Under the assumption that A. thaliana and A. arenosa separated 5 million years ago, we estimated a substitution rate of 2.9 x 10(-9) per site per year in noncoding single copy sequence. Within A. thaliana we found 12 substitution (single bp) and eight insertion/deletion (indel) polymorphisms, separating the 25 accessions into 15 haplotypes. Eight of the A. thaliana accessions from central Sweden formed one cluster, which was separated from a cluster consisting of central European and extreme southern Swedish accessions. This latter cluster also included the A. suecica accessions, which were all identical except for one 5 bp indel. We interpret this low level of variation as a strong indication that A. suecica effectively has a single origin, which we dated at 20 000 years ago or more.
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5.
  • Anava, Sarit, et al. (författare)
  • Illuminating Genetic Mysteries of the Dead Sea Scrolls
  • 2020
  • Ingår i: Cell. - : CELL PRESS. - 0092-8674 .- 1097-4172. ; 181:6, s. 1218-
  • Tidskriftsartikel (refereegranskat)abstract
    • The discovery of the 2,000-year-old Dead Sea Scrolls had an incomparable impact on the historical understanding of Judaism and Christianity. "Piecing together'' scroll fragments is like solving jigsaw puzzles with an unknown number of missing parts. We used the fact that most scrolls are made from animal skins to "fingerprint'' pieces based on DNA sequences. Genetic sorting of the scrolls illuminates their textual relationship and historical significance. Disambiguating the contested relationship between Jeremiah fragments supplies evidence that some scrolls were brought to the Qumran caves from elsewhere; significantly, they demonstrate that divergent versions of Jeremiah circulated in parallel throughout Israel (ancient Judea). Similarly, patterns discovered in non-biblical scrolls, particularly the Songs of the Sabbath Sacrifice, suggest that the Qumran scrolls represent the broader cultural milieu of the period. Finally, genetic analysis divorces debated fragments from the Qumran scrolls. Our study demonstrates that interdisciplinary approaches enrich the scholar's toolkit.
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6.
  • Andersson, Mattias, et al. (författare)
  • Intrinsic and extrinsic influences on the temperature dependence of mobility in conjugated polymers
  • 2008
  • Ingår i: Organic electronics. - : Elsevier. - 1566-1199 .- 1878-5530. ; 9:5, s. 569-574
  • Tidskriftsartikel (refereegranskat)abstract
    • The temperature dependence of charge carrier mobility in conjugated polymers and their blends with fullerenes is investigated with different electrical methods, through field effect transistor (FET), space charge limited current (SCLC) and charge extraction (CELIV) measurements. Simple models, such as the Gaussian disorder model (GDM), are shown to accurately predict the temperature behavior, and a good correlation between the different measurement methods is obtained. Inconsistent charge carrier concentrations in the modeling are explained through intrinsic non-equilibrium effects, and are responsible for the limited applicability of existing numerical models. A severe extrinsic influence from water in FETs with a hydrophilic insulator interface is also demonstrated. The presence of water leads to a significant overestimate of the disorder in the materials from measurements close to room temperature and erratic behavior in the 150-350 K range. To circumvent this problem it is shown to be necessary to measure under ultra high vacuum (UHV) conditions. © 2008 Elsevier B.V. All rights reserved.
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8.
  • Ausmees, Kristiina (författare)
  • Efficient computational methods for applications in genomics
  • 2019
  • Licentiatavhandling (övrigt vetenskapligt)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.
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9.
  • Ausmees, Kristiina (författare)
  • Methodology and Infrastructure for Statistical Computing in Genomics : Applications for Ancient DNA
  • 2022
  • Doktorsavhandling (övrigt vetenskapligt)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.
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10.
  • Babiker, Hiba, et al. (författare)
  • Genetic variation and population structure of Sudanese populations as indicated by 15 Identifiler sequence-tagged repeat (STR) loci.
  • 2011
  • Ingår i: Investigative Genetics. - 2041-2223 .- 2041-2223. ; 2:1
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: There is substantial ethnic, cultural and linguistic diversity among the people living in east Africa, Sudan and the Nile Valley. The region around the Nile Valley has a long history of succession of different groups, coupled with demographic and migration events, potentially leading to genetic structure among humans in the region.RESULT: We report the genotypes of the 15 Identifiler microsatellite markers for 498 individuals from 18 Sudanese populations representing different ethnic and linguistic groups. The combined power of exclusion (PE) was 0.9999981, and the combined match probability was 1 in 7.4 × 1017. The genotype data from the Sudanese populations was combined with previously published genotype data from Egypt, Somalia and the Karamoja population from Uganda. The Somali population was found to be genetically distinct from the other northeast African populations. Individuals from northern Sudan clustered together with those from Egypt, and individuals from southern Sudan clustered with those from the Karamoja population. The similarity of the Nubian and Egyptian populations suggest that migration, potentially bidirectional, occurred along the Nile river Valley, which is consistent with the historical evidence for long-term interactions between Egypt and Nubia.CONCLUSION: We show that despite the levels of population structure in Sudan, standard forensic summary statistics are robust tools for personal identification and parentage analysis in Sudan. Although some patterns of population structure can be revealed with 15 microsatellites, a much larger set of genetic markers is needed to detect fine-scale population structure in east Africa and the Nile Valley.
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