Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa (2019)
Journal Article
Monnahan, P., Kolář, F., Baduel, P., Sailer, C., Koch, J., Horvath, R., …Yant, L. (2019). Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nature Ecology and Evolution, 3, 457-468. doi:10.1038/s41559-019-0807-4

Ploidy-variable species allow direct inference of the effects of chromosome copy number on fundamental evolutionary processes. While an abundance of theoretical work suggests polyploidy should leave distinct population genomic signatures, empirical d... Read More

Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep (2019)
Journal Article
Ahbara, A., Bahbahani, H., Almathen, F., Al Abri, M., Agoub, M. O., Abeba, A., …Mwacharo, J. M. (2019). Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep. Frontiers in Genetics, 9, doi:10.3389/fgene.2018.00699

Variations in body weight and in the distribution of body fat are associated with feed availability, thermoregulation, and energy reserve. Ethiopia is characterized by distinct agro-ecological and human ethnic farmer diversity of ancient origin, whic... Read More

Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity (2018)
Journal Article
Schurink, A., da Silva, V. H., Velie, B. D., Dibbits, B. W., Crooijmans, R. P., Franҫois, L., …Ducro, B. J. (2018). Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genetics, 19, doi:10.1186/s12863-018-0657-0

Background: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of man... Read More

The fecal metabolome as a functional readout of the gut microbiome (2018)
Journal Article
Zierer, J., Jackson, M. A., Kastenmüller, G., Mangino, M., Long, T., Telenti, A., …Menni, C. (2018). The fecal metabolome as a functional readout of the gut microbiome. Nature Genetics, 50(6), 790-795. doi:10.1038/s41588-018-0135-7

The human gut microbiome plays a key role in human health1, but 16S characterization lacks quantitative functional annotation2. The fecal metabolome provides a functional readout of microbial activity and can be used as an intermediate phenotype medi... Read More

Murine systemic thrombophilia and hemolytic uremic syndrome from a factor H point mutation (2017)
Journal Article
Ueda, Y., Mohammed, I., Song, D., Gullipalli, D., Zhou, L., Sato, S., …Song, W. (2017). Murine systemic thrombophilia and hemolytic uremic syndrome from a factor H point mutation. Blood, 129(9), (1184-1196). doi:10.1182/blood-2016-07-728253. ISSN 0006-4971

Complement plays a key role in host defense, but its dysregulation can cause autologous tissue injury. Complement activation is normally controlled by regulatory proteins, including factor H (FH) in plasma and membrane cofactor protein (MCP) on the c... Read More

Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways (2016)
Journal Article
Archer, N., Walsh, M. D., Shahrezaei, V., & Hebenstreit, D. (2016). Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways. Cell Systems, 3(5), 467-479. doi:10.1016/j.cels.2016.10.012

Experimental procedures for preparing RNA-seq and single-cell (sc) RNA-seq libraries are based on assumptions regarding their underlying enzymatic reactions. Here, we show that the fairness of these assumptions varies within libraries: coverage by se... Read More