A new position and a new direction

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!

Fungal Tree of Life 🍄

Wow, what an awesome project!

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! 😊


Evolution of Woodiness

Lately, I have been working on mapping the evolution of woodiness on the Plant Tree of Life.

For this project, I used the trait data collected by Botanic Gardens Conservation International (BGCI)—available through GlobalTreeSearch—and the phylogeny built by Stephen Smith and Joseph W. Brown. The tree contains almost every plant species (~353,000!!)  and the paper describing the process of building it can be accessed here.

The main findings are 1) that being herbaceous might be the ancestral state and 2) that the evolution of wood has happened many times but only on certain clades.

Here is a figure of this super cool project that uses amazing data and research by others—I’m definitively standing on the shoulders of giants.

New Position!

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 Stephen Smith 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!

#Go Blue!

My latest and first paper as a postdoc!

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.

You can find the article in the “Publications” tab on my website or here: http://www.sciencedirect.com/science/article/pii/S1055790316304158

Department Seminar at OSU!

simon-at-osu 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.

What a fantastic experience! 🙂


New paper on Neobartsia

Bartsia_Mosaique_SmallMy 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! 😉

You can read the publication here: http://www.bioone.org/doi/abs/10.1600/036364416X692299

New Paper on Genomics and Phylogenomics!

Screen Shot 2016-02-02 at 5.43.17 PM

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!

Check it out here: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0148203

My first talk as a postdoc

Screen Shot 2015-11-13 at 5.59.18 AM

I gave my first talk as a postdoc today 🙂

It was at BioLunch, a weekly department wide seminar at the University of Missouri-St.Louis Biology Department. I presented my work on Bartsia and people really liked it.

I was honored by the presence of eminent scientists like Bob RicklefsPeter Stevens, Bob Marquis, and of course my current postdoctoral advisor Nathan MuchhalaIvan Jimenez, Eric Knox, all my lab mates, and students from across the department!

It was a great experience and a great way to start this new stage in my life.