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2. A simple in silico approach to generate gene-expression profiles from subsets of cancer genomics dataMohammed Khurshed, Remco J. Molenaar, Cornelis J. F. van Noorden, 2019, original scientific article Abstract: In biomedical research, large-scale profiling of gene expression has become routine and offers a valuable means to evaluate changes in onset and progression of diseases, in particular cancer. An overwhelming amount of cancer genomics data has become publicly available, and the complexity of these data makes it a challenge to perform in silico data exploration, integration and analysis, in particular for scientists lacking a background in computational programming or informatics. Many web interface tools make these large datasets accessible but are limited to process large datasets. To accelerate the translation of genomic data into new insights, we provide a simple method to explore and select data from cancer genomic datasets to generate gene-expression profiles of subsets that are of specific genetic, biological or clinical interest.
Keywords: cancer genomics, cBioPortal, data mining, epigenetics, gene expression, in silico
Published in DiRROS: 24.07.2024; Views: 218; Downloads: 451
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3. Genomic evidence of recombination in the basidiomycete Wallemia mellicolaSun Xiaohuan, Cene Gostinčar, Fang Chao, Janja Zajc, Hou Yong, Song Zewei, Nina Gunde-Cimerman, 2019, original scientific article Abstract: One of the most commonly encountered species in the small basidiomycetous sub-phylum Wallemiomycotina is Wallemia mellicola, a xerotolerant fungus with a widespread distribution. To investigate the population characteristics of the species, whole genomes of twenty-five strains were sequenced. Apart from identification of four strains of clonal origin, the distances between the genomes failed to reflect either the isolation habitat of the strains or their geographical origin. Strains from different parts of the world appeared to represent a relatively homogenous and widespread population. The lack of concordance between individual gene phylogenies and the decay of linkage disequilibrium indicated that W. mellicola is at least occasionally recombining. Two versions of a putative mating-type locus have been found in all sequenced genomes, each present in approximately half of the strains. W. mellicola thus appears to be capable of (sexual) recombination and shows no signs of allopatric speciation or specialization to specific habitats.
Keywords: population genomics, halotolerance, xerotolerance, basidiomycete, allergenic fungus, recombination
Published in DiRROS: 23.07.2024; Views: 139; Downloads: 78
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4. How genomics can help biodiversity conservationKathrin Theissinger, Tine Grebenc, 2023, original scientific article Abstract: The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
Keywords: genomics, biodiversity conservation
Published in DiRROS: 22.02.2023; Views: 585; Downloads: 415
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5. Using genomic information for management planning of an endangered perennial, Viola uliginosaKyung Min Lee, Pertti Ranta, Jarmo Saarikivi, Lado Kutnar, Branko Vreš, Maxim Dzhus, Marko Mutanen, Laura Kvist, 2020, original scientific article Abstract: Species occupying habitats subjected to frequent natural and/or anthropogenic changes are a challenge for conservation management. We studied one such species, Viola uliginosa, an endangered perennial wetland species typically inhabiting sporadi-cally flooded meadows alongside rivers/lakes. In order to estimate genomic diversity, population structure, and history, we sampled five sites in Finland, three in Estonia, and one each in Slovenia, Belarus, and Poland using genomic SNP data with double-digest restriction site-associated DNA sequencing (ddRAD-seq). We found mono-phyletic populations, high levels of inbreeding (mean population FSNP = 0.407-0.945), low effective population sizes (Ne = 0.8-50.9), indications of past demographic ex-pansion, and rare long-distance dispersal. Our results are important in implementing conservation strategies for V. uliginosa, which should include founding of seed banks, ex situ cultivations, and reintroductions with individuals of proper origin, combined with continuous population monitoring and habitat management.
Keywords: nature conservation, demography, genomic diversity, population genomics, RAD sequencing, Viola
Published in DiRROS: 20.01.2022; Views: 1051; Downloads: 830
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