dadi-cli preprint posted June 16, 2023 Former postdoc Xin Huang and research professional Travis Struck have spearheaded the development of a command-line interface for dadi. This interface not only makes dadi much easier to use, it also supports parallel and distributed computing. Read about it in our preprint, and find the code on GitHub. Read more Image
Polyploid inference paper published June 9, 2023 Our paper modeling homeologous exchange between chromosomes within polyploids is now published in Genetics. Read more Image
donni preprint posted May 25, 2023 PhD student Linh Tran has developed a remarkably efficient approach to infer demographic history models from allele frequency spectra using feedforward neural networks. The preprint shows that this approach is just as accurate as likelihood optimization using dadi, while being instantaneous with a pre-trained model. To enable usage, we have pre-trained a wide selection of models, which our software donni will automatically download from the CyVerse DataCommons. Read more Image
Welcome Justin March 1, 2023 Justin Conover has been awarded and NSF Postdoctoral Research Fellowship in Biology to work together with our group and Mike Barker's group. Justin's research will focus on the effects of polyploidy on distributions of fitness effects. He will testing whether DFEs differ between an allotetraploid and its diploid progenitors, and he will also extend our joint DFE approach to test the correlation of fitness effects between subgenomes. Read more Image
Congratulations Olivia Feb. 28, 2023 Undergraduate student Olivia Fernflores has been named a 2023 Beckman Scholar. This prestigious award will fund Olivia's research for two summers plus an academic year and enable her to travel to several conferences. Read more
Polyploid inference preprint posted Sept. 17, 2022 We've recently added the ability to model polyploidy and infer rates of exchange between subgenomes to dadi. A preprint describing and applying the method is now posted. To avoid some bioinformatic biases, in our approach we collapse the data from across the subgenomes into a single site frequency spectrum. In this collapsed spectrum, fixed differences between the subgenomes create a spike at 50% frequency. Allelic exchange between the subgenomes generates distinctive shoulders to the spike. Consequently, we can precisely infer model parameters describing the events after the formation of the polyploid. Justin Conover will be building on this work when he joins us to model DFEs in polyploids. Read more
Welcome Emanuel May 2, 2022 Emanuel Fonseca has joined our group, coming from Bryan Carsten's group. Emanuel has an ecology background and will be working to apply our joint DFE inference method to many interesting evolutionary and ecological situations. Read more Image
Welcome Olivia Fernflores March 8, 2022 Olivia is a Freshman Bioinfomatics major. She has been accepted into UBRP for summer funding, and her project is still being defined. Read more
Welcome Amy Fan Dec. 2, 2021 Amy is an undergraduate at the U of Arizona who is double-majoring in Molecular & Cellular Biology and Statistics & Data Science and planning to complete an Accelerated Master's Degree program Read more Image
Welcome Dr. David Castellano Dec. 1, 2021 Dr. David Castellano has joined the Gutenkunst group. His research with the group will focus on novel methods and applications of DFE inference. With strong personal reasons for not moving from Spain, David will be working with the group remotely for the foreseeable future. Read more Image