You need to find what makes you happy, what makes your curiosity and heart tick. For many years I thought academia was that for me but I’ve come to understand that it’s not. In my pursuit of happiness, I have accepted a position as a data scientist at Phylagen, a startup in San Francisco committed to harnessing the unseen world of microbes to improve our daily lives. I’ll get to work with large sequencing datasets, combining my love for bioinformatics, big data, and biodiversity.
Here’s to a new start, a new path, and a whole new adventure!
As a postdoc at the University of Michigan, I have been working on building the Fungal Tree of Life using all the Sanger data available on Genbank! I couldn’t have done it alone though, my advisor Stephen Smith and ~10 other collaborators—each one an expert on a single fungal lineage—were instrumental in the project, so thank you!
The final phylogeny has data for 13 of the 15 fungal subphyla and has 29,993 tips—yes, that’s ~30K different species of fungi! 🍄🍄🍄
It’s, of course, way too big to display correctly, but here it is anyways! 😊
I’m very excited to have accepted a Postdoctoral Research Fellow position at the University of Michigan in Ann Arbor! I’ll be working with StephenSmith on bioinformatic and genomic methods for phylogenetics with a strong focus on angiosperms. This is a great opportunity for me to expand my computational skills and learn new approaches to generating large genomic datasets!
My latest paper on Burmeistera was just published in Molecular Phylogenetics and Evolution! In this paper, we investigated the best approach to combine complete plastome data generated with high-throughout sequencing and traditional Sanger sequences. This is really important because there are many publicly available Sanger data that people tend to forget about, and it would be a waste not to use them. We also produced the largest Burmeistera phylogeny to date, laying a foundation for a future taxonomic revision of the group.
I was invited to give my first Department Seminar at Oklahoma State University! I presented (September 14th, 2016) work from my dissertation on Neobartsia as well as current and future work on speciation and the accumulation of species properties. I spent two days in Stillwater and everything went really well. My host, Mark Fishbein, and his students were great and I had many good and stimulating conversations with them and other people in the department.
My latest paper on Neobartsia was published today in Systematic Botany! 🙂
This paper is the culmination of five years of hard work during my Ph.D., summarizing results from many analyses and types of data. The main result of this publication is the creation of Neobartsia, a new genus containing every Andean species (47) of the former genus Bartsia. I couldn’t be more excited and proud of this paper, besides, it’s really cool to name a genus! 😉
Our paper on target enrichment and high-throughput sequencing was publish today! 🙂
We developed a method to amplify multiple loci using microfluidic PCR from both the chloroplast and nuclear genome. The enriched loci can then be sequenced using a high-throughput sequencing platform, in our case Illumina. The paper also includes a pipeline to process the raw reads, recover alleles, and asses ploidy levels of the samples—exciting!