Publications

Preprints

5. Steenwyk, J.L., M.E. Mead, P.A. Castro, C. Valero, A. Damasio, R.A.C. Santos, A.L. LaBella, Y. Li, S.L. Knowles, H.A. Raja, N.H. Oberlies, X. Zhou, O.A. Cornely, F. Fuchs, P. Koehler^, G.H. Goldman^, A. Rokas^ (2020). Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus. (^Senior authors). bioRxiv. doi: 10.1101/2020.11.06.371971 bioRxiv preprint

4. Steenwyk, J.L.^, T.J. Buida III, A.L. LaBella, Y. Li, X.-X. Shen, & A. Rokas^ (2020). PhyKIT: a UNIX shell toolkit for processing and analyzing phylogenomic data. (^Senior authors). bioRxiv. doi: 10.1101/2020.10.27.358143. bioRxiv preprint

3. Li, Y., J.L. Steenwyk, Y. Chang, Y. Wang, T.Y. James, J.E. Stajich, J.W. Spatafora, M. Groenewald, C. Dunn, C.T. Hittinger, X.-X. Shen^, A. Rokas^ (2020). A genome-scale phylogeny of Fungi; insights into early evolution, radiations, and the relationship between taxonomy and phylogeny. (^Senior authors). bioRxiv. doi: 10.1101/2020.08.23.262857. bioRxiv preprint

2. LaBella, A.L., D. Opulente, J.L. Steenwyk, C.T. Hittinger, & A. Rokas (2020). Signatures of optimal codon usage predict metabolic ecology in budding yeasts. bioRxiv. doi: 10.1101/2020.07.22.214635. 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. doi: 10.1101/166033. bioRxiv preprint

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Peer-reviewed

31. Steenwyk, J.L.^, T.J. Buida III, Y. Li, X.-X. Shen, & A. Rokas^ (2020). ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference. (^Senior authors). PLoS Biology: in press. bioRxiv preprint

30. Li, Y., K.T. David, X.-X. Shen, J.L. Steenwyk, K.M. Halanych, & A. Rokas (2020). Feature Frequency Profile-based phylogenies are inaccurate. PNAS. doi: 10.1073/pnas.2013143117. PDF

29. Shen, X.-X.^, J.L. Steenwyk, A.L. LaBella, D.A. Opulente, X. Zhou, J. Kominek, Y. Li, M. Groenewald, C.T. Hittinger, & A. Rokas^ (2020). Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. (^Senior authors). Science Advances. doi: 10.1126/sciadv.abd0079. PDF

28. Santos, R.A.C., O. Rivero-Menendez, J.L. Steenwyk, M.E. Mead, G.H. Goldman^, A. Alastruey-Izquierdo, & A. Rokas^ (2020). Draft genome sequences of four Aspergillus section Fumigati clinical strains. (^Senior authors) Microbiology Resource Announcements. doi: 10.1128/MRA.00856-20. PDF

27. Filho, A.P.C., G.T.P. Brancini, P.A. de Castro, J.A. Ferreira, L.P. Silva, M.C. Rocha, I. Malavazi, J.G.M. Pontes, T. Fill, R. Silva, F. Almeida, J.L. Steenwyk, A. Rokas, T.F. dos Reis, L.N.A. Ries, & G.H. Goldman (2020). Aspergillus fumigatus G-protein coupled receptors GprM and GprJ are important for the regulation of the cell wall integrity pathway, secondary metabolite production, and virulence. mBio. doi: 10.1128/mBio.02458-20. PDF

26. Steenwyk, J.L. (2020). A portrait of budding yeasts: A symbol of the arts, sciences and a whole greater than the sum of its parts. Yeast. doi: 10.1002/yea.3518. PDF

25. Steenwyk, J.L., M.E. Mead*, S.L. Knowles*, H.A. Raja, C.D. Roberts, O. Bader, J. Houbraken, G.H. Goldman, N.H. Oberlies, & A. Rokas (2020). Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species. (*Equal contributors). Genetics. doi: 10.1534/genetics.120.303549. PDF
Highlighted Article

24. Ries, L.N.A., L. Pardeshi, Z. Dong, K. Tan, J.L. Steenwyk, A.C. Colabardini, J.A.F. Filho, P.A. de Castro, L.P. Silva, N.W. Preite, F. Almeida, L.J. de Assis, R.A.C. dos Santos, P. Bowyer, M. Bromley, R.A. Owens, S. Doyle, M. Demasi, D.C.R. Hernández, L.E.S. Netto, M.T. Pupo, A. Rokas, F.V. Loures, K.H. Wong, & G.H. Goldman (2020). The Aspergillus fumigatus transcription factor RglT is important for gliotoxin biosynthesis and self-protection, and virulence. PLoS Pathogens. doi: 10.1371/journal.ppat.1008645. PDF

23. Steenwyk, J.L.*, A.L. Lind*, L.N.A. Ries, T.F. dos Reis, L.P. Silva, F. Almeida, R.W. Bastos, T.F. de Campos Fraga da Silva, V.L.D. Bonato, A.M. Pessoni, F. Rodrigues, H.A. Raja, S.L. Knowles, N.H. Oberlies, K. Lagrou, G.H. Goldman^, A. Rokas^ (2020). Pathogenic allodiploid hybrids of Aspergillus fungi. (*Equal contributors; ^Senior authors). Current Biology. doi: 10.1016/j.cub.2020.04.071. PDF
Cover Article
Nature Reviews Microbiology Research Highlights

22. Mead, M.E.*, A.T. Borowsky*, B. Joehnk, J.L. Steenwyk, X.-X. Shen, A. Sil, & A. Rokas (2020). Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, correlates with changes in genomic and morphological traits. (*Equal contributors) Genome Biology and Evolution. doi: 10.1093/gbe/evaa107. PDF

21. Santos, R.A.C., J.L. Steenwyk, O. Rivero-Menendez, M.E. Mead, L.P. Silva, R.W. Bastos, A. Alastruey-Izquierdo, G.H. Goldman^, & A. Rokas^ (2020). Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus and Aspergillus fumigatiaffinis. (^Senior contributors). Frontiers in Genetics. doi: 10.3389/fgene.2020.00459. PDF

20. Bastos, R.W., C. Valero, L.P. Silva, T. Schoen, M. Drott, V. Brauer, R. Silva-Rocha, A. Lind, J.L. Steenwyk, A. Rokas, F. Rodrigues, A. Resendiz-Sharpe, K. Lagrou, M. Marcet-Houben, T. Gabaldon, E. McDonnell, I. Reid, A. Tsang, B.R. Oakley, F. Loures, F. Almeida, A. Huttenlocher, N.P. Keller, L. Ries, & G.H. Goldman (2020). Functional characterization of clinical isolates of the opportunistic fungal pathogen Aspergillus nidulans. mSphere. doi:10.1128/mSphere.00153-20. PDF

19. Rokas, A., M.E. Mead, J.L. Steenwyk, N.H. Oberlies, & G.H. Goldman (2020). Evolving moldy murderers: Aspergillus section Fumigati as a model for studying the repeated evolution of fungal pathogenicity. PLoS Pathogens. doi: 10.1371/journal.ppat.1008315. PDF

18. Knowles, S.L., M.E. Mead, L.P. Silva, H.A. Raja, J.L. Steenwyk, G.H. Gustavo^, A. Rokas^, & N.H. Oberlies^ (2020). Gliotoxin, a known virulence factor in the major human pathogen Aspergillus fumigatus, is also biosynthesized by the non-pathogenic relative A. fischeri. (^Senior authors) mBio. doi: 10.1128/mBio.03361-19. PDF

17. Libkind, D., D. Peris, F.A. Cubillos, J.L. Steenwyk, D.A. Opulente, Q.K. Langdon, N. Bellora, A. Rokas, & C.T. Hittinger (2020). Into the wild: new yeast genomes from natural environments and new tools for their analysis. FEMS Yeast Research. doi: 10.1093/femsyr/foaa008. PDF

16. Rokas, A., M.E. Mead, J.L. Steenwyk, H.A. Raja, & N.H., Oberlies (2020). Biosynthetic gene clusters and the evolution of fungal chemodiversity. Natural Product Reports. doi: 10.1039/C9NP00045C. PDF

15. 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. mBio. doi: 10.1128/mBio.02445-19. PDF
Editor's Pick

14. Mead, M.E.*, H.A. Raja*, J.L. Steenwyk, S.L. Knowles, N.H. Oberlies^, & A. Rokas^ (2019). Draft genome sequence of the griseofulvin-producing fungus Xylaria flabelliformis strain G536. (*Equal contributors; ^Senior authors) Microbiology Resource Announcements. doi: 10.1128/MRA.00890-19. PDF

13. Steenwyk, J.L. & A. Rokas (2019). treehouse: a user-friendly application to obtain subtrees from large phylogenies. BMC Research Notes. doi: 10.1186/s13104-019-4577-5. PDF
Download treehouse

12. 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. PLoS Genetics. doi: 10.1371/journal.pgen.1008304. PDF

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

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 (2019). 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

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

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