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| 2. |
- Eriksson, Anders, 1975, et al.
(författare)
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Gene-history correlation and population structure.
- 2004
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Ingår i: Physical biology. - : IOP Publishing. - 1478-3967 .- 1478-3975. ; 1:3-4, s. 220-8
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Tidskriftsartikel (refereegranskat)abstract
- Correlation of gene histories in the human genome determines the patterns of genetic variation (haplotype structure) and is crucial to understanding genetic factors in common diseases. We derive closed analytical expressions for the correlation of gene histories in established demographic models for genetic evolution and show how to extend the analysis to more realistic (but more complicated) models of demographic structure. We identify two contributions to the correlation of gene histories in divergent populations: linkage disequilibrium, and differences in the demographic history of individuals in the sample. These two factors contribute to correlations at different length scales: the former at small, and the latter at large scales. We show that recent mixing events in divergent populations limit the range of correlations and compare our findings to empirical results on the correlation of gene histories in the human genome.
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| 3. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Towards an automated phylogenetic classification of homobasidiomycetes
- 2004
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Ingår i: Mycological Society of America (MSA) Meeting 2004.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The prospects of a phylogeny-driven classification of the higher fungi are discussed, and a new software package - mor - that seeks to facilitate such classifications is presented.
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| 4. |
- Alexandersson, Marina, 1972, et al.
(författare)
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Genome sequence of the Brown Norway rat yields insights into mammalian evolution
- 2004
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Ingår i: Nature. - 0028-0836 .- 1476-4687. ; 428:6982, s. 493-521
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Tidskriftsartikel (refereegranskat)abstract
- The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality ‘draft’ covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineageindependent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
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| 5. |
- Tamas, Ivica, et al.
(författare)
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50 million years of genomic stasis in endosymbiotic bacteria.
- 2002
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 296:5577, s. 2376-9
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Tidskriftsartikel (refereegranskat)abstract
- Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes of their closest free-living relatives, Escherichia coli and Salmonella spp., are more than 2000-fold more labile in content and gene order. The genomic stasis of B. aphidicola, likely attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola is no longer a source of ecological innovation for its hosts.
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| 6. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Phylogeny of the Hypochnicium punctulatum complex as inferred from ITS sequence data
- 2003
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Ingår i: Mycologia. ; 95:1, s. 54-50
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Tidskriftsartikel (refereegranskat)abstract
- Parsimony analysis based on ITS sequence data was carried out to investigate the Hypochnicium punctulatum complex (Basidiomycota). The study gives full support to earlier, crossing test-based species delimitations. Altogether, 18 specimens were sequenced and their spore sizes plotted together with measurements from the corresponding type specimens. Spore sizes were found to cluster readily into four groups, all of which were supported by the phylogenetic analysis. However, in the case of H. punctulatum and H. albostramineum, the morphological delimitation is unsatisfactory and a zone of potential spore size overlap is shown to exist. The new combination Hypochnicium cremicolor is proposed for a species previously known as a small-spored taxon in the H. punctulatum complex, and H. caucasicum is shown to be a younger synonym to H. wakefieldiae. A key to the species is provided.
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| 7. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Phylogeography of Hyphoderma setigerum (Basidiomycota) in the Northern Hemisphere
- 2003
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Ingår i: Mycological Research. ; 107:6, s. 645-652
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies of morphological variation in the homobasidiomycete Hyphoderma setigerum have lead to suspicions of a species complex. This study explores variation in DNA sequences from the nuclear ribosomal ITS region of 45 specimens from America, Asia, and Europe in a phylogeographic context. Based on molecular analysis, morphological studies, and crossing tests, nine preliminary taxa are shown to exist inside the species complex, and the two previously described segregate species H. subsetigerum and H. nudicephalum are confirmed. The molecular analysis shows evidence of allopatric differentiation over intercontinental distances. Only one of the nine well-supported clades has a geographic distribution spanning more than one continent, probably indicating the importance of vicariance in the evolution of this species complex. The basionym of H. setigerum, Thelephora setigera, is neotypified to fix the application of that name.
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| 8. |
- Dewey, C., et al.
(författare)
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Accurate Identification of Novel Human Genes Through Simultaneous Gene Prediction in Human, Mouse and Rat
- 2004
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Ingår i: Genome Research. - 1088-9051 .- 1549-5469. ; 14:4, s. 661-664
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Tidskriftsartikel (refereegranskat)abstract
- We describe a new method for simultaneously identifying novel homologous genes with identical structure in the human, mouse, and rat genomes by combining pairwise predictions made with the SLAM gene-finding program. Using this method, we found 3698 gene triples in the human, mouse, and rat genomes which are predicted with exactly the same gene structure. We show, both computationally and experimentally, that the introns of these triples are predicted accurately as compared with the introns of other ab initio gene prediction sets. Computationally, we compared the introns of these gene triples, as well as those from other ab initio gene finders, with known intron annotations. We show that a unique property of SLAM, namely that it predicts gene structures simultaneously in two organisms, is key to producing sets of predictions that are highly accurate in intron structure when combined with other programs. Experimentally, we performed reverse transcription-polymerase chain reaction (RT-PCR) in both the human and rat to test the exon pairs flanking introns from a subset of the gene triples for which the human gene had not been previously identified. By performing RT-PCR on orthologous introns in both the human and rat genomes, we additionally explore the validity of using RT-PCR as a method for confirming gene predictions.
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| 9. |
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| 10. |
- Willander, Magnus, 1948, et al.
(författare)
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Modelling living fluids with the subdivision into the components in terms of probability distributions
- 2004
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Ingår i: Math. Models Methods Appl. Sci.. - : World Scientific. - 0218-2025. ; 14:10, s. 1495-1520
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Tidskriftsartikel (refereegranskat)abstract
- As it follows from the results of C. H. Waddigton, F. E. Yates, A. S. Iberall, and other well-known bio-physicists, living fluids cannot be modelled within the frames of the fundamental assumptions of the statistical-mechanics formalism. One has to go beyond them. The present work does it by means of the generalized kinetics (GK), the theory enabling one to allow for the complex stochasticity of internal properties and parameters of the fluid particles. This is one of the key features which distinguish living fluids from the nonliving ones. It creates the disparity of the particles and hence breaks the each-fluid-component-uniformity requirement underlying statistical mechanics. The work deals with the corresponding modification of common kinetic equations which is in line with the GK theory and is the complement to the latter. This complement allows a subdivision of a fluid into the fluid components in terms of nondiscrete probability distributions. The treatment leads to one more equationthat describes the above internal parameters. The resulting model is the system of these two equations. It appears to be always nonlinear in case of living fluids. In case of nonliving fluids, the model can be linear. Moreover, the living-fluid model, as a whole, cannot have the thermodynamic equilibrium, only partial equilibriums (such as the motional one) are possible. In contrast to this, in case of nonliving fluids, the thermodynamic equilibrium is, of course, possible. The number of the fluid components is treated as the number of the modes of the particle-characteristic probability density. In so doing, a fairly general extension of the notion of the mode from the one-dimensional case to the multidimensional case is proposed. The work also discusses the variety of the time-scales in a living fluid, the simplest quantum-mechanical equation relevant to living fluids, and the non-equilibrium nonlinear stochastic hydrodynamics option. The latter is simpler than, but conceptually comparable to, stochastickinetic equations. A few directions for future research are suggested. The work notes a cohesion of mathematical physics and fluid mechanics with the living-fluid-related fields as a complex interdisciplinary problem.
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