Publications
Preprints/Submitted
4. Balamurugan, C., J.L. Steenwyk^, G.H. Goldman, & A. Rokas^ (2023). The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. ^Corresponding authors. bioRxiv. DOI: 10.1101/2023.01.17.524442.bioRxiv preprint
3. Steenwyk, J.L., C. Balamurugan, H.A. Raja, C. Goncalves, N. Li, F. Martin, J. Berman, N.H. Oberlies, J.G. Gibbons, G.H. Goldman, D.M. Geiser, D.S. Hibbett, A. Rokas (2022). Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus. bioRxiv. DOI: 10.1101/2022.11.22.517304. bioRxiv preprint
2. Le, H.G.B.H.^,*, J.L. Steenwyk*, N. Manske, M. Smolin, A. Abdulali, A. Kamat, R. Kanchana, K. Giffin, A. Andere, K. Workman^ (2022). *Equal contributors; ^Corresponding authors. Latch Verified Bulk-RNA Seq toolkit: a cloud-based suite of workflows for bulk RNA-seq quality control, analysis, and functional enrichment. bioRxiv. DOI: 10.1101/2022.11.10.516016. bioRxiv preprint
1. Zheng, Q., J.L. Steenwyk^, A. Rokas^ (2022). Lack of universal mutational biases in a fungal phylum. ^Corresponding authors. bioRxiv. DOI: 10.1101/2022.03.29.486229. bioRxiv preprint
Peer-reviewed
56. Steenwyk, J.L., Y. Li, X. Zhou, X.-X. Shen, & A. Rokas (2023). Incongruence in the phylogenomics era. Nature Reviews Genetics: in press.55. Drewell, R.A., T.C. Cormier, J.L. Steenwyk, J. St. Denis, J.F. Tabima, J.M. Dresch, & D.A. Larochelle (2023). The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing. NAR Genomics and Bioinformatics. DOI: 10.1093/nargab/lqad035. PDF
54. Mead, M.E., P.A. de Castro, J.L. Steenwyk, J. Gangeux, M. Hoenigl, J. Prattes, R. Rautemaa-Richardson, H. Guegan, C.B. Moore, C. Lass-Flörl, F. Reizine, C. Valero, N. Van Rhijn, M.J. Bromley, A. Rokas, G.H. Goldman, & S. Gago (2023). COVID-19 Associated Pulmonary Aspergillosis isolates are genomically diverse but similar to each other in their responses to infection-relevant stresses. mSpectrum. DOI: 10.1128/spectrum.05128-22. PDF
53. Sierra-Patev, Sean, B. Min, M. Naranjo-Ortiz, B. Looney, Z. Konkel, J.C. Slot, Y. Sakamoto, J.L. Steenwyk, A. Rokas, J. Carro, S. Camarero, P. Ferreira, G. Molpeceres, F.J. Ruiz-Dueñas, A. Serrano, B. Henrissat, E. Drula, K.W. Hughes, J.L. Mata, N.K. Ishikawa, R. Vargas-Isla, S. Ushijima, C.A. Smith, S. Ahrendt, W. Andreopoulos, G. He, K. LaButti, A. Lipzen, V. Ng, R. Riley, L. Sandor, K. Barry, A.T. Martínez, Y. Xiao, J.G. Gibbons, K. Terashima, I.V. Grigoriev, & D. Hibbett (2023). A Global Phylogenomic Analysis of the Shiitake Genus Lentinula. Proceedings of the National Academy of Sciences of the United States of America (PNAS). DOI: 10.1073/pnas.2214076120. PDF
52. Steenwyk, J.L.^ & A. Rokas^ (2023). The dawn of relaxed phylogenetics. ^Corresponding authors. PLOS Biology. DOI: 10.1371/journal.pbio.3001998. PDF
51. Li, Y.^, H. Liu, J.L. Steenwyk, A.L. LaBella, M.C. Harrison, M. Groenewald, X. Zhou, X.-X. Shen, T. Zhao, C.T. Hittinger, A. Rokas^ (2022). Contrasting modes of macro- and micro-synteny evolution in a eukaryotic subphylum. ^Corresponding authors. Current Biology. DOI: 10.1016/j.cub.2022.10.025. PDF
50. Steenwyk, J.L.^, D.C. Goltz, T.J. Buida III, Y. Li, X.-X. Shen, & A. Rokas^ (2022). OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. ^Corresponding authors. PLOS Biology. DOI: 10.1371/journal.pbio.3001827. PDF
49. Brown, A., M.E. Mead, J.L. Steenwyk, G.H. Goldman, & A. Rokas (2022). Extensive sequence divergence of non-coding regions between Aspergillus fumigatus, a major fungal pathogen of humans, and its relatives. Frontiers in Fungal Biology. DOI: 10.3389/ffunb.2022.802494. PDF
48. Horta, M.A., J.L. Steenwyk, M.E. Mead, L.H.B. dos Santos, S. Zhao, J.G. Gibbons, M. Marcet-Houben, T. Gabaldón, A. Rokas^, & G.H. Goldman^ (2022). Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus. ^Corresponding authors. mBio. DOI: 10.1128/mbio.01519-22. PDF
47. 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^ (2022). BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. ^Corresponding authors. Genetics. DOI: 10.1093/genetics/iyac079. PDF
46. Steenwyk, J.L., M.A. Phillips, F. Yang, S.S. Date, T. Graham, J. Berman, C.T. Hittinger, & A. Rokas (2022). An orthologous gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. Science Advances. DOI: 10.1126/sciadv.abn0105. PDF
Featured Image
45. Bradley, N.P.*, K.L. Wahl*, J.L. Steenwyk, A. Rokas, & B.F. Eichman (2022). Resistance-guided mining of bacterial genotoxins defines a family of DNA glycosylases. *Equal contributors. mBio. DOI: 10.1128/mbio.03297-21. PDF
44. 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 (2022). Regulation of gliotoxin biosynthesis and protection in Aspergillus species. PLOS Genetics. DOI: 10.1371/journal.pgen.1009965. PDF
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
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
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. mSpectrum. 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
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
Cover Article
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
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
Cover Article
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
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; ^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
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.H. 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
Journal Covers
Li et al. 2021
Steenwyk 2021
Steenwyk et al. 2020
Steenwyk and Lind et al. 2020
Popular Science
6. Steenwyk, J.L. & K. Giffin. The silver lining of bioinformatics. Genes to Genomes. September 12, 2022. Link5. Simopoulos, M.A.C., A.F. Cisneros, A.D. Mendoza, C. Bautista, J.L. Steenwyk, & N. Ahmad. Hurdles and advances to making science gender-neutral. ecrLife. November 26, 2020. Link
4. Mendoza, A.D., C. Bautista, E.A. Marnik, C.M.A. Simopoulos, & J.L. Steenwyk. Navigating fake news as a scientist. ecrLife. October 8, 2020. Link
3. Steenwyk, J.L. & M. Jonika. How to get started in science communication. ecrLife. August 21, 2020. Link
2. Steenwyk, J.L. & A. Rokas. A new hybrid fungus is found in hospitals and linked to lung disease. The Conversation. June 4, 2020. Link
1. Steenwyk, J.L. & A. Rokas. An outlaw yeast thrives with genetic chaos – and could provide clues for understanding cancer growth. The Conversation. May 21, 2019. Link