Popular Science Articles

1. Steenwyk, J.L. & A. Rokas (2019). An outlaw yeast thrives with genetic chaos – and could provide clues for understanding cancer growth, The Conversation, May 21, 2019. Link


Preprint

3. Bodinaku, I., J. Shaffer, A.B. Connors, J.L. Steenwyk, E. Kastman, A. Rokas, A. Robbat, & B. Wolfe (2019). Rapid phenotypic and metabolomic domestication of wild Penicillium molds on cheese. bioRxiv preprint

2. Labella, A.L., D.A. Opulente, J.L. Steenwyk, C.T. Hittinger, & A. Rokas (2019). Variation and selection on codon usage bias across an entire subphylum. bioRxiv preprint

1. Steenwyk, J., J. St. Denis, J. Dresch, D. Larochelle, & R. Drewell (2017). Whole genome bisulfite sequencing reveals a sparse, but robust pattern of DNA methylation in the Dictyostelium discoideum genome. bioRxiv preprint


Publications

11. Steenwyk, J.L., X.-X. Shen, A.L. Lind, G.H. Goldman, & A. Rokas (2019). A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium. mBio. doi: 10.1128/mBio.00925-19. PDF

10. Steenwyk, J.L., D. Opulente, J. Kominek, X.-X. Shen, X. Zhou, A.L. LaBella, N.P. Bradley, B.F. Eichman, N. Čadež, D. Libkind, J. DeVirgilio, A.B. Hulfachor, C.P. Kurtzman, C.T. Hittinger^, & A. Rokas^ (2019). Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. (^Senior authors). PLoS Biology. doi: 10.1371/journal.pbio.3000255. PDF
@VanderbiltU highlight

9. Ries, L.N.A., J.L. Steenwyk, P.A. de Castro, P.B.A. de Lima, F. Almeida, L.J. de Assis, A.O. Manfiolli, A. Takahashi-Nakaguchi, Y. Kusuya, D. Hagiwara, H. Takahashi, X. Wang, J. Obar, A. Rokas, & G.H. Goldman. Nutritional heterogeneity among Aspergillus fumigatus strains has consequences for virulence in a strain- and host-dependent manner. Frontiers in Microbiology. doi: 10.3389/fmicb.2019.00854. PDF

8. Mead M.E., S.L. Knowles, H.A. Raja, S. R. Beattie, C.H. Kowalski, J.L. Steenwyk, L.P. Silva, J. Chiaratto, L.N.A. Ries, G.G. Goldman, R.A. Cramer, N.H. Oberlies, & A. Rokas (2019). Characterizing the pathogenic, genomic, and chemical traits of Aspergillus fischeri, the closest sequenced relative of the major human fungal pathogen Aspergillus fumigatus. mSphere. doi: 10.1128/mSphere.00018-19. PDF

7. Knowles, S.L., H.A. Raja, A.J. Wright, A.M.L. Lee, L.K. Caesar, N.B. Cech, M.E. Mead, J.L. Steenwyk, L. Ries, G.H. Goldman, A. Rokas, N.H. Oberlies (2019). Mapping the fungal battlefield: using in situ chemistry and deletion mutants to monitor interspecific chemical interactions between fungi. Frontiers in Microbiology. doi: 10.3389/fmicb.2019.00285. PDF

6. Eidem, H.R., J.L. Steenwyk, J. Wisecaver, J.A. Capra, P. Abbot, & A. Rokas (2018). integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth. BMC Medical Genomics. doi: 10.1186/s12920-018-0426-y. PDF

5. Shen, X.-X.*, D.A. Opulente*, J. Kominek*, X. Zhou*, J.L. Steenwyk, K.V. Buh, M.A.B. Haase, J.H. Wisecaver, M. Wang, D.T. Doering, J.T. Boudouris, R.M. Schneider, Q.K. Langdon, M. Ohkuma, R. Endoh, M. Takashima, R. Manabe, N. Čadež, D. Libkind, C.A. Rosa, J. DeVirgilio, A.B. Hulfachor, M. Groenewald, C.P. Kurtzman^, C.T. Hittinger^ & A. Rokas^ (2018). Tempo and mode of genome evolution in the budding yeast subphylum. Cell. doi: 10.1016/j.cell.2018.10.023. (*Equal contributors; ^Senior authors). PDF
The story behind the paper in Nature Ecology & Evolution blog
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4. Segal, E.S., V. Gritsenko, A. Levitan, B. Yadav, N. Dror, J.L. Steenwyk, Y. Silberberg, K. Mielich, A. Rokas, N.A.R. Gow, R. Kunze, R. Sharan, & J. Berman (2018). Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans. mBio. doi: 10.1128/mBio.02048-18. PDF
Editor's Pick

3. Steenwyk, J.L. & A. Rokas (2018). Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation. Frontiers in Microbiology. doi: 10.3389/fmicb.2018.00288. PDF

2. Steenwyk, J. & A. Rokas (2017). Extensive copy number variation in fermentation-related genes among Saccharomyces cerevisiae wine strains. G3: Genes | Genomes | Genetics. doi: 10.1534/g3.117.040105. PDF

1. Steenwyk, J.L., J.S. Soghigian, J.R. Perfect, & J.G. Gibbons (2016). Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest. BMC Genomics. doi: 10.1186/s12864-016-3044-0. PDF