7. Steenwyk, J.L.^, D.C. Goltz, T.J. Buida III, Y. Li, X.-X. Shen, & A. Rokas^ (2021). orthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. ^Corresponding authors. bioRxiv. DOI: 10.1101/2021.10.30.466607. bioRxiv preprint
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6. Brown, A., M.E. Mead, J.L. Steenwyk, G.H. Goldman, & A. Rokas (2021). Extensive sequence divergence of non-coding regions between Aspergillus fumigatus, a major fungal pathogen of humans, and its relatives. bioRxiv. DOI: 10.1101/2021.10.26.465918. bioRxiv preprint

5. Bradley, N.P.*, K.L. Wahl*, J.L. Steenwyk, A. Rokas, & B.F. Eichman (2021). Resistance-guided mining of bacterial genotoxins defines a family of DNA glycosylases. *Equal contributors. bioRxiv. DOI: 10.1101/2021.10.29.466481. bioRxiv preprint

4. Steenwyk, J.L.^, T.J. Buida III, C. Gonçalves, D.C. Goltz, G.H. Morales, M.E. Mead, A.L. LaBella, C.M. Chavez, J.E. Schmitz, M. Hadjifrangiskou, Y. Li, & A. Rokas^ (2021). BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. ^Corresponding authors. bioRxiv. DOI: 10.1101/2021.10.02.462868. bioRxiv preprint
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3. P.A. de Castro, A. Moraes, A.C. Colabardini, M.A.C. Horta, S.L. Knowles, H.A. Raja, N.H. Oberlies, Y. Koyama, M. Ogawa, K. Gomi, J.L. Steenwyk, A. Rokas, L.N.A. Ries, & G.H. Goldman (2021). Regulation of gliotoxin biosynthesis and protection in Aspergillus species. bioRxiv. DOI: 10.1101/2021.08.16.456458. bioRxiv preprint

2. Steenwyk, J.L., M.A. Phillips, F. Yang, S.S. Date, T. Graham, J. Berman, C.T. Hittinger, & A. Rokas (2021). An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. bioRxiv. DOI: 10.1101/2021.07.09.451830. 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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43. J.L. Steenwyk^ & A. Rokas^ (2021). ggpubfigs: colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures. ^Corresponding authors. Microbiology Resource Announcements. DOI: 10.1128/MRA.00871-21. PDF
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42. Phillips, M.A., J.L. Steenwyk^, X.-X. Shen, & A. Rokas^ (2021). Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum. ^Corresponding authors. Genome Biology and Evolution. PMID: 34554246; DOI: 10.1093/gbe/evab219. PDF

41. Santos, R.A.C., M.E. Mead, J.L. Steenwyk, O. Rivero-Menéndez, A. Alastruey-Izquierdo, G.H. Goldman^, & A. Rokas^ (2021). Examining signatures of natural selection in antifungal resistance genes across Aspergillus fungi. ^Corresponding authors. Frontiers in Fungal Biology. DOI: 10.3389/ffunb.2021.723051. PDF

40. Steenwyk, J.L.^ & A. Rokas^ (2021). orthofisher: a broadly applicable tool for automated gene identification and retrieval. ^Corresponding authors. G3 Genes|Genomes|Genetics. PMID: 34544141; PMCID: PMC8496211; DOI: 10.1093/g3journal/jkab250. PDF
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39. Ries, L., P. de Castro, L. Silva, C. Valero, T. dos Reis, R. Saborano, I. Duarte, G. Persinoti, J.L. Steenwyk, A. Rokas, F. Almeida, J. Costa, T. Fill, S.S.W. Wong, V. Aimanianda, F. Rodrigues, R. Gonçales, C. Duarte-Oliveira, A. Carvalho, & G.H. Goldman (2021). Aspergillus fumigatus acetate utilization impacts virulence traits and pathogenicity. mBio. PMID: 34311583; PMCID: PMC8406206; DOI: 10.1128/mBio.01682-21. PDF

38. Mead, M.E.*, J.L. Steenwyk*, L.P. Silva, P.A. de Castro, N. Saeed, F. Hillmann, G.H. Goldman, & A. Rokas (2021). An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi. *Equal contributors. Genetics. PMID: 33944921; PMCID: PMC8225353; DOI: 10.1093/genetics/iyab066. PDF

37. 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^ (2021). Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus. ^Corresponding authors. Microbiology Spectrum. PMID: 34106569; PMCID: PMC7654854; DOI: 10.1128/Spectrum.00010-21. PDF

36. LaBella, A.L., D. Opulente, J.L. Steenwyk, C.T. Hittinger, & A. Rokas (2021). Signatures of optimal codon usage in metabolic genes inform budding yeast ecology. PLOS Biology. PMID: 33872297; PMCID: PMC8084343; DOI: 10.1371/journal.pbio.3001185. PDF

35. Steenwyk, J.L. (2021). Evolutionary divergence in the DNA damage response among fungi. mBio. PMID: 33727357; PMCID: PMC8092291; DOI: 10.1128/mBio.03348-20. PDF

34. Shen, Xing-Xing, J.L. Steenwyk, & A. Rokas (2021). Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data. Systematic Biology. PMID: 33616672; DOI: 10.1093/sysbio/syab011. PDF

33. Steenwyk, J.L.^, T.J. Buida III, A.L. LaBella, Y. Li, X.-X. Shen, & A. Rokas^ (2021). PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. ^Corresponding authors. Bioinformatics. PMID: 33560364; PMCID: PMC8388027; DOI: 10.1093/bioinformatics/btab096. PDF
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32. 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^ (2021). A genome-scale phylogeny of the kingdom Fungi. ^Corresponding authors. Current Biology. PMID: 33607033; PMCID: PMC8347878; DOI: 10.1016/j.cub.2021.01.074. PDF
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31. Steenwyk, J.L. (2021). A portrait of budding yeasts: A symbol of the arts, sciences and a whole greater than the sum of its parts. Yeast. PMID: 32869892; DOI: 10.1002/yea.3518. PDF
Cover Article

30. Steenwyk, J.L.^, T.J. Buida III, Y. Li, X.-X. Shen, & A. Rokas^ (2020). ClipKIT: a multiple sequence alignment-trimming software for accurate phylogenomic inference. ^Corresponding authors. PLOS Biology. PMID: 33264284; PMCID: PMC7735675; DOI: 10.1371/journal.pbio.3001007. PDF
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29. Li, Y., K.T. David, X.-X. Shen, J.L. Steenwyk, K.M. Halanych, & A. Rokas (2020). Feature Frequency Profile-based phylogenies are inaccurate. Proceedings of the National Academy of Sciences of the United States of America. PMID: 33234569; PMCID: PMC7749326; DOI: 10.1073/pnas.2013143117. PDF

28. 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. ^Corresponding authors. Science Advances. PMID: 33148650; PMCID: PMC7673691; DOI: 10.1126/sciadv.abd0079. PDF

27. 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. ^Corresponding authors. Microbiology Resource Announcements. PMID: 33004453; PMCID: PMC7530925; DOI: 10.1128/MRA.00856-20. PDF

26. 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. PMID: 33051372; PMCID: PMC7554674; DOI: 10.1128/mBio.02458-20. 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. PMID: 32817009; PMCID: PMC7536862; DOI: 10.1534/genetics.120.303549. PDF
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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. PMID: 32667960; PMCID: PMC7384679; 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; ^Corresponding authors. Current Biology. PMID: 32502407; PMCID: PMC7343619; 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. PMID: 32442273; PMCID: PMC7531577; 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. ^Corresponding authors. Frontiers in Genetics. PMID: 32477406; PMCID: PMC7236307; 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. PMID: 32269156; PMCID: PMC7142298; 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. PMID: 32106242; PMCID: PMC7046185; 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. ^Corresponding authors. mBio. PMID: 32047138; PMCID: PMC7018655; 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. PMID: 32009143; PMCID: PMC7067299; 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. PMID: 31898704; PMCID: PMC7332410; 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. PMID: 31615965; PMCID: PMC6794487; DOI: 10.1128/mBio.02445-19. PDF
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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; ^Corresponding authors. Microbiology Resource Announcements. PMID: 31537670; PMCID: PMC6753274; 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. PMID: 31455362; PMCID: PMC6712805; DOI: 10.1186/s13104-019-4577-5. PDF
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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. PMID: 31365533; PMCID: PMC6701816; 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. PMID: 31289177; PMCID: PMC6747717; 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. ^Corresponding authors. PLoS Biology. PMID: 31112549; PMCID: PMC6528967; 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. PMID: 31105662; PMCID: PMC6492530; 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. PMID: 30787113; PMCID: PMC6382966; 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. PMID: 30837981; PMCID: PMC6389630; 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. PMID: 30453955; PMCID: PMC6245874; 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. PMID: 30415838; PMCID: PMC6291210; DOI: 10.1016/j.cell.2018.10.023. *Equal contributors; ^Corresponding 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. PMID: 30377286; PMCID: PMC6212825; 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. PMID: 29520259; PMCID: PMC5826948; 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. PMID: 28292787; PMCID: PMC5427499; 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. PMID: 27590805; PMCID: PMC5009542; DOI: 10.1186/s12864-016-3044-0. PDF

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