Recent publications

A paper titled, "Dr.Nod: computational framework for discovery of regulatory non-coding drivers in tissue-matched distal regulatory elements" by Tomkova et al. 2023 was recently published in Nucleic Acid Research.

Published in Nature Methods in December 2022, the paper titled “SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads” by Denti, Khorsand, Bonizzoni, Hormozdiari, and Chikhi describes a newly developed method to discover structural variants. Structural variants are defined as medium to large size genetic variations and are shown to be important in human genomics, evolution, and diseases.

This post summarizes the publication "Counter the weaponization of genetics research by extremists" by Carlson et al. (2022) in Nature.

Every modern mammal, from a platypus to a blue whale, is descended from a common ancestor that lived about 180 million years ago. We don’t know a great deal about this animal, but the organization of its genome has now been computationally reconstructed by an international team of researchers. The work is published Sept. 30 in Proceedings of the National Academy of Sciences.

This post summarizes the findings of the paper  "Effects of pairing on color change and central gene expression in lined seahorses" by Mederos et al. published in Genes, Brain and Behavior (link).

Studies comparing animal genomes generally focus on the DNA sequence itself. A new study by researchers at the University of California, Davis shows how the three-dimensional scaffolding of chromosomes is related across several species of carnivores, offering a new approach of “comparative scaffotyping” that could be used to identify related genes across species and place them in context. The work, published the week of Feb.

Scientists are a step closer to breeding plants with genes from only one parent. New research led by plant biologists at the University of California, Davis, published Nov. 19 in Science Advances, shows the underlying mechanism behind eliminating half the genome and could make for easier and more rapid breeding of crop plants with desirable traits such as disease resistance.

A recent publication in Scientific Reports by Brydges et al. titled "Indoxyl sulfate, a gut microbiome-derived uremic toxin, is associated with psychic anxiety and its functional magnetic resonance imaging-based neurologic signature" investigated whether indoles in the gut microbiome are associated with depression and anxiety. The study found that abundance of indoles is correlated with anxiety, but anxiety treatment was not related to the modulation of indoles in the gut.

The first atlas of metabolites in the mouse brain has been published by a team led by UC Davis researchers. The dataset includes 1,547 different molecules across 10 brain regions in male and female laboratory mice from adolescence through adulthood and into advanced old age. The work is published Oct. 15 in the Nature Communications. The complete dataset is publicly available at https://mouse.atlas.metabolomics.us/.