I have eclectic interests spanning the sciences and arts including music, graphic art, and poetry. My scientific work blends the fields of computer science and evolution to better understand the evolution of fungi. Some questions I address include what causes some species of fungi to be pathogenic while close relatives are harmless? My artistic endeavors are primarily purpose driven and aim to raise awareness of endangered animals (see my new SciArt shop here).
Beyond research and the arts, I aim to make education more accessible, promote diversity and inclusion, as well as build a bridge between scientists and the general public. To this end, I am an instructor of an internal workshop on phylogenomics, serve as a co-chair of the Early Career Scientist Communication and Outreach Subcommittee, and serve on committees across Vanderbilt University that aim to enhance diversity and inclusion.
In brief, my research interests integrate the fields of computer science, evolution, and genomics. More specifically, current research objectives leverage the diversity of budding yeasts and filamentous fungi to study the principles and pace of evolution. To address research objectives, I also develop computational tools.
The fungal subphylum of budding yeasts, Saccharomycotina, are a remarkably diverse group of organisms. In fact, budding yeast diversity is roughly on par with the animal and plant kingdoms (see figure from Shen et al. 2018, Cell). Together with the Hittinger lab at University of Wisconsin-Madison, we are undertaking the major effort of sequencing and analyzing 1,000+ species of budding yeasts. This project, named Y1000+ has yielded many insights into budding yeast evolution. Broadly, we have determined the tempo and mode of genome evolution across their approximately 400 million year evolutionary history and evaluated the selective pressures among codon usage. Discoveries have also been made among specific lineages. For example, the genus Hanseniaspora has lost numerous cell cycle and DNA repair genes. This discovery is in direct contrast to current wisdom that suggests these genes are important to all life. Undoubtedly, evolutionary studies of budding yeasts are likely to yeild more insights into evolutionary principles as well as highlight the amazing flexibility of genome evolution.
Steenwyk et al. (2019) PLoS Biology
Shen et al. (2018) Cell
Steenwyk & Rokas (2017) G3
Filamentous fungi including species from the genera Aspergillus and Penicillium are of great medical and technologic interest. For example, some species pose threats to human or plant health; in contrast, some species are producers of mainstay pharmaceuticals like penicillin or are used in cheese-making. Studies into these genera will help uncover the evolutionary processes that make some microbes harmful to human health while others are relatively harmless or helpful. Additionally, investigations of the genetic architecture of the genes responsible for making mainstay pharmaceuticals—termed secondary metabolites—may help discover new natural products and antimicrobials. In collaboration with the Goldman Lab at Universidade de São Paulo, Oberlies Lab at University of North Carolina at Greensboro, and the Wolfe Lab at Tufts University, we have investigated the evolutionary drivers and secondary metabolites of filamentous fungi important to medical and technologic human affairs. For example, we have discovered globally distributed isolates of Aspergillus latus, which were obtained from patients with lung infections, are of allodiploid hybrid origin and have a large genetic repetriore responsible for the production of secondary metabolites (see figure from Steenwyk, Lind et al. (2020) Current Biology).
Steenwyk, Lind et al. (2020) Current Biology
Steenwyk et al. (2019) mBio
Bodinaku et al. (2019) mBio
Nearly all research I do is at the intersection of evolution, computer science, and genomics. Often, our projects feature analyses of large-scale datasets spanning hundreds of species and thousands of genes. In order to analyze these large datasets, computational tools are required. Thus, part of my research program is to develop the tools necessary to enable researchers to conduct evolutionary analysis or explore their datasets. For example, I have written an alignment trimming algorithm, ClipKIT, that retains phylogenetically informative sites from multiple-sequence alignments and removes the rest. Performance assessment of ClipKIT and other alignment trimming software across a total of ~140 thousand alignments revealed ClipKIT often outperformed other alignment trimming methods (see figure from Steenwyk, et al. (2020) bioRxiv). Additionally, to enable researchers to be able to use phylogenies with hundreds to thousands of tips, I have written GUI software that allows researchers to obtain subtrees from large phylogenies.
Steenwyk, et al. (2020) bioRxiv
Steenwyk (2020) ggpubfigs source code
Steenwyk & Rokas (2019) BMC Research notes
Addressing these evolutionary questions has been enabled by collaborative efforts. A non-exhaustive list of collaborator/friend labs include the following: Rokas, Shen, Hittinger, Oberlies, and the Wolfe laboratories. I am always interested in collaboration because what we can achieve together is far greater than what we can achieve alone - please feel free to get in touch.