About

I have eclectic interests spanning the sciences and arts. My scientific work blends the fields of computer science, evolution, and genomics to better understand the evolution of fungi. Some questions I address include what causes some fungi to be pathogenic while others are harmless? My artistic endeavors are primarily purpose driven and aim to raise awareness of endangered animals (see my new SciArt shop here).

More broadly, I aim to make education more accessible, promote diversity, equity and inclusion, and build a bridge between scientists and the public. To this end, I am an instructor of an international workshop on phylogenomics, serve on committees across Vanderbilt University that aim to enhance diversity and inclusion, and organize/participate in science-based community engagement events.


Research Interests

Recent representative publications:
Steenwyk et al. (2021) Bioinformatics
Steenwyk et al. (2020) PLoS Biology
Steenwyk and Lind et al. (2020) Current Biology
Steenwyk et al. (2019) mBio
Steenwyk et al. (2019) PLoS Biology

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. I also develop computational tools to facilitate these studies.

Budding Yeasts

about_images/diversity_of_yeasts.jpg 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. Discoveries have also been made among specific lineages. For example, budding yeast from the genus Hanseniaspora have lost numerous cell cycle and DNA repair genes. This discovery is in direct conflict with the 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.

Representative publications:
Steenwyk et al. (2019) PLoS Biology
Shen et al. (2018) Cell
Steenwyk & Rokas (2017) G3

Filamentous Fungi

about_images/hybrids_graphical_abstract.jpg 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 while others produce 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 affairs while others are helpful. In collaboration with the Goldman Lab at Universidade de São Paulo and the Oberlies Lab at University of North Carolina at Greensboro, we have discovered globally distributed isolates of Aspergillus latus, which were obtained from patients with lung infections, are of allodiploid hybrid origin (see figure from Steenwyk, Lind et al. 2020, Current Biology). Aspergillus hybrids exhibited phenotypic heterogeneity across infection-relevant traits and were distinct from closely related species including their parents. These results suggest that allodiploid hybridization contributes to the evolution of filamentous fungal pathogens. We have also discovered that some factors that contribute to the virulence of the major fungal pathogen Aspergills fumigatus are also present among nonpathogenic species, which raises the question of "what makes a pathogen?"

Representative publications:
Steenwyk, Lind et al. (2020) Current Biology
Steenwyk et al. (2020) Genetics
Steenwyk et al. (2019) mBio

Software

about_images/about_images/clipkit_performance.jpg Nearly all research I'm involved in relies on computational tools to address questions in the field of evolutionary biology. As a result, part of my research program is to develop the necessary tools to conduct evolutionary analysis and/or explore 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, PLoS Biology). Also, I have written PhyKIT, a toolkit with 30 (and counting) functions that help process and analyze multiple sequence alignments and phylogenies for broad applications including diagnosing potential biases, conducting evolution-based screens of gene function, and identifying signatures of rapid radiation events.

Representative publications:
Steenwyk et al. (2021) Bioinformatics
Steenwyk et al. (2020) PLoS Biology
Steenwyk and 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 Goldman 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.

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