How does asymmetry in inheritance affect expected feminisation of sex chromosomes?
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How many transposonable elements can you fit in one asexual genome?
How does a normal multilocus hybrid zone look like?
How hard is to find a pattern in the chaos?
Published in Bioinformatics, 2013
A scalable method for prediction of candidates for horizontally transferred genes.
Recommended citation: Jaron, K.S., Moravec, J.C. and Martínková, N., 2013. "SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes." Bioinformatics, 30(8), pp.1081-1086. http://doi.org/10.1093/bioinformatics/btt727
Published in PLoS ONE, 2014
We have reported European bat species infected by White-nose syndrome, a disease devastating American population. We have also showed that the fungus is a generalist pathogen attacking bat species of very diverse ecological traits.
Recommended citation: Zukal, J., Bandouchova, H., Bartonicka, T., Berkova, H., Brack, V., Brichta, J., Dolinay, M., Jaron, K.S., Kovacova, V., Kovarik, M. and Martínková, N., 2014. "White-nose syndrome fungus: a generalist pathogen of hibernating bats." PLoS One, 9(5), p.e97224. http://doi.org/10.1371/journal.pone.0097224
White-nose syndrome without borders: Pseudogymnoascus destructans infection tolerated in Europe and Palearctic Asia but not in North America
Published in Scientific Reports, 2016
We have reported White-nose syndrome in Asia and quantified fungal loads of bat wings using qPCR. Surprisingly loads we observed were higher than loads detected in American bats that have way way worse response to the infection.
Recommended citation: Zukal, J., Bandouchova, H., Brichta, J., Cmokova, A., Jaron, K.S., Kolarik, M., Kovacova, V., Kubátová, A., Nováková, A., Orlov, O. and Pikula, J., 2016. "White-nose syndrome without borders: Pseudogymnoascus destructans infection tolerated in Europe and Palearctic Asia but not in North America." Scientific reports, 6. http://doi.org/10.1038/srep19829
Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography—A structure-retention study assisted by soft-modelling and molecular dynamics
Published in Journal of Chromatography A, 2016
We showed nearly-deterministic relation of retention times of trinucleotides with their nucleotide composition. We modeled properties of trinucleotide molecules that actually explained most of the variability of the original model. I was invited to this study to construct models.
Recommended citation: Mikulášek, K., Jaroň, K. S., Kulhánek, P., Bittová, M., & Havliš, J., 2016. "Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography—A structure-retention study assisted by soft-modelling and molecular dynamics." Journal of Chromatography A, (1469), 88-95. http://doi.org/10.1016/j.chroma.2016.09.060
Published in Molecular biology and evolution, 2018
Taken from the abstract: We find strong evidence for higher rates of deleterious mutation accumulation, lower levels of segregating polymorphisms and arrested GC-biased gene conversion in asexuals as compared with sexuals. Taken together, our study conclusively shows that predicted consequences of genome evolution under asexuality can indeed be found in natural populations.
Recommended citation: Bast, J., Parker, D.J., Dumas, Z., Jalvingh, K.M., Tran Van, P., Jaron, K.S., Figuet, E., Brandt, A., Galtier, N. and Schwander, T., 2018. "Consequences of asexuality in natural populations: insights from stick insects." Molecular biology and evolution, 35(7), pp.1668-1677. https://doi.org/10.1093/molbev/msy058
Published in bioRxiv, 2019
Are there any universal consequences of asexuality in animals? We have collected genomes of 26 asexual animals and found that indeed there is not any really universal.
Recommended citation: Jaron, K. S., Bast, J., Nowell R. W., Ranallo-Benavidez, T. R., Robinson-Rechavi, M., & Schwander, T., 2018. "Genomic features of asexual animals." bioRxiv, 497495. https://doi.org/10.1101/497495
Published in Nature Communication, 2020
Genome sequencing can be messy and genome assembly is complicated and non-transparent process. Here we provide tools that allow some elementary characterisation of genomes using directly short read data. Now also aiming to provide help for polyploid genomes.
Recommended citation: Ranallo-Benavidez, T. R., Jaron, K. S., Schatz, M. C., 2020. "GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes" Nature Communication, In press. https://doi.org/10.1101/s41467-020-14998-3
Published in University of Lausanne, Department of Ecology & Evolution, 2015
Students are sequencing a genome of bacteria using latest sequencing technologies, assemble genome, map sequencing reads and build a gene annotation.
Published in University of Lausanne, Department of Ecology & Evolution, 2016
This class is a genomics project and therefore it’s a different every year. I have participated in this class in years 2016 and 2017.
Published in Swiss Institute of Bioinformatics, 2016
This is course I have co-developed with Amina Echchiki, Walid Gharib and Julien Roux. The full description can be found at the webpage of SIB and the teaching materials are available at GitHub. The goals of this workshop was to get hands-on experience with :
Published in Swiss Institute of Bioinformatics, 2017
Published in University of Lausanne, Department of Ecology & Evolution, 2018
I assisted students on individual basis, helping them to understand the practical exercises and getting them done. The practicals I have assisted to were covering concepts like Hardy Weinberg equilibrium, statistical testing of the departure from HW, calculation and interpretation of fst statistics between populations, effect of selection on genotype frequencies in case of heterozygosity advantage, and migration.