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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
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Posts
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Blog Post number 1
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portfolio
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publications
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex
Published in Microbial Genomics, 2020
Bacteria are notorious for horizontal gene transfer, and it has often been asserted that this process will blur the boundaries between species to the extent that species cannot be clearly defined. Our study provides strong evidence that this is not necessarily so. Using 196 newly sequenced genomes of the Rhizobium leguminosarum species complex, we find five clearly distinct genospecies that occur in sympatry but show little evidence of recent between-species gene transfer affecting either the core or the accessory genome, except for a few highly mobile genetic regions.
Recommended citation: Cavassim, et al. (2020). "Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex." Microbial Genomics. 1(1). http://izabelcavassim.github.io/files/mgen000351.pdf
Recombination Facilitates Adaptive Evolution in Rhizobial Soil
Published in Molecular Biology and Evolution, 2021
By using a population genetics approach, this work demonstrates that homologous recombination directly impacts the efficacy of natural selection in the core genome of prokaryotes (genus Rhizobium), as previously reported in eukaryotes
Recommended citation: Cavassim, et al. (2021). "Recombination Facilitates Adaptive Evolution in Rhizobial Soil." Journal 1. 1(2). http://izabelcavassim.github.io/files/msab247.pdf
PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2
Published in bioRxiv (in print PNAS), 2022
In mammals and likely throughout vertebrates, the gene PRDM9 specifies the location of meiotic double strand breaks (DSBs) which are catalyzed by SPO11; in mice and humans at least, PRDM9 also aids in their repair. PRDM9 arose before the origin of vertebrates but was lost many times, either partially or entirely, and with it, it also lost its role in recombination. In this study, we leverage the PRDM9 interdigitation along the vertebrate phylogeny to identify genes whose presence coincides with that of PRDM9 and thus may be interacting with it.
Recommended citation: Cavassim, et al. (2021). "PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2." bioRxiv. 1(3). http://izabelcavassim.github.io/files/prdm9_pnas.pdf
talks
QCBio Research Seminar
Published:
In sexually reproducing organisms, meiotic recombination is initiated by the deliberate infliction of numerous double-strand breaks (DSBs) in the genome, the repair of which yields crossover and non-crossover resolutions. In most mammals, these DSBs are specified through the binding of PRDM9 and the deposition of H3K4me3 and H3K36me3 marks. Despite its evolutionary importance, PRDM9 has been independently lost numerous times across vertebrate’s evolution. Here, we take advantage of the multiple independent PRDM9 losses to infer the co-evolution of PRDM9 with other meiosis-related genes.
teaching
Next Generation Sequencing
Summer course, Aarhus University, Bioinformatics Research Center, 2016
This course was organized by Professors at BiRC (Mikkel Schierup) and the Dept. of Molecular Biology (Stig Andersen). I helped in the development of the exercises and I was the Teaching Assistant for two consecutive years.
Tree of life
Undergraduate/Masters level course, Aarhus University, BiRC, 2017
This course was organized and lectured by Professor Mikkel Schierup, and I was the Teaching Assistant for three consecutive years.
Population Genetics on genomes
Masters level course, Aarhus University, Bioinformatics Research Centre, 2018
This course was organized by Professors at BiRC (Mikkel Schierup, Kasper Munch, and Søren). I helped in the development of the exercises and I was the Teaching Assistant.