Publications

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Preprints/Submitted

 12. Cao, X.*, C. Liu*, D. Liu*, J.L. Steenwyk, X. Zhong, Y. Wang, H. Liu, Y. Wang, Q. Zhang, X.-X. Shen, Z. Qu^, Y. Li^ (2025). *Equal co-first authors; ^Corresponding authors. The evolution and function of eukaryote-to-cyanobacteria horizontal gene transfer. Submitted.

11. Gonçalves, C.*, J.L. Steenwyk*, D.C. Rinker, D.A. Opulente, A.L. LaBella, M.-C. Harrison, J.F. Wolters, X. Zhou, X.-X. Shen, S. Covo, M. Groenewald, C.T. Hittinger, & A. Rokas (2025). *Equal co-first authors. Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species. bioRxiv. DOI: 10.1101/2025.03.15.643480.

10. Steenwyk, J.L.^ & T.J. Buida III (2025). ^Corresponding author. RCVT: a diagnostic to quantify compositional biases among taxa for large phylogenomic studies. bioRxiv. DOI: 10.1101/2024.11.28.625917.

9. Steenwyk, J.L.^ & N. King^ (2025). ^Corresponding authors. Integrative phylogenomics positions sponges at the root of the animal tree. Submitted.

8. Steenwyk, J.L.^, T.J. Buida III, A. Rokas, & N. King (2024). ^Corresponding author. OrthoHMM: Improved Inference of Ortholog Groups using Hidden Markov Models. bioRxiv. DOI: 10.1101/2024.12.07.627370.
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7. Ros-Rocher, N., J. Reyes-Rivera, U. Horo, C. Combredet, Y. Foroughijabbari, B.T. Larson, M.C. Coyle, E.A.T. Houtepen, M.J.A. Vermeij, N. King, J.L. Steenwyk, & T. Brunet (2024). Clonal-aggregative multicellularity entrained by salinity in one of the closest relatives of animals. Submitted.

6. Feng, B.*, Y. Li*, H. Liu*, J.L. Steenwyk, K.T. David, X. Tian, B. Xu, C. Gonçalves, D.A. Opulente, A.L. LaBella, M.-C. Harrison, J.F. Wolters, S. Shao, Z. Chen, K.J. Fisher, M. Groenewald, C.T. Hittinger, X.-X. Shen, A. Rokas^, X. Zhou^, & Y. Li^ (2024). *Equal contributors; ^Corresponding authors. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage. bioRxiv. DOI: 10.1101/2024.06.05.597512.

5. O. Lemke*, B.M. Heineike*, S. Viknander, N. Cohen, J.L. Steenwyk, L. Spranger, F. Li, F. Agostini, C.T. Lee, S.K. Aulakh, J. Nielsen, A. Rokas, J. Berman, A. Zelezniak, T.I. Gossmann, & M. Ralser (2024). *Equal contributors. The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution. bioRxiv. DOI: 10.1101/2024.05.27.596037.

4. Fan, Y., M. Du, W. Zhang, W. Deng, E. Yang, S. Wang, L. Yan, L. Zhang, S. Kang, J.L. Steenwyk, Z. An, X. Liu, & M. Xiang (2024). The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism. bioRxiv. DOI: 10.1101/2024.03.21.586190.

3. Turnbull, R.*, J.L. Steenwyk*, S. Mutch, P. Scholten, V.W. Salazar, J.L. Birch, & H. Verbruggen (2023). *Equal contributors. Orthoflow: phylogenomic analysis and diagnostics with one command. Research Square. DOI: 10.21203/rs.3.rs-3699210/v2.
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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.

1. Zheng, Q., J.L. Steenwyk^, & A. Rokas^ (2022). ^Corresponding authors. Lack of universal mutational biases in a fungal phylum. bioRxiv. DOI: 10.1101/2022.03.29.486229.

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Peer-reviewed

79. Steenwyk, J.L.^, J.T. Loucks, & T.J. Buida III (2025). ClipKIT in the Browser: Fast Online Trimming of Multiple Sequence Alignments for Phylogenetics. Nucleic Acids Research: in press
Run ClipKIT in the browser and leave the computing up to us!

78. Delbaje, E., L. Pontes, J. Rhodes, J.L. Steenwyk, L. Lu, T.F. dos Reis, A. Rokas, & G.H. Goldman (2025). Aspergillus fumigatus mitogenomes and their influence on azole-resistant and -susceptible populations. npj Antimicrobials and Resistance. DOI: 10.1038/s44259-025-00083-6.

77. Li, N., D.M. Geiser, J.L. Steenwyk, C. Tsuchida, S. Koike, S. Slinski, & F.N. Martin (2025). A systematic approach for identifying unique genomic sequences for Fusarium oxysporum f. sp. lactucae race 1 and development of molecular diagnostic tools. Phytopathology. DOI: 10.1094/PHYTO-04-24-0142-R.

76. Sarratto, T., K. Visuri, J. Lehitenen, I. Ortega-Sanz, J.L. Steenwyk, & S. Sihvonen (2025). Solu: a cloud platform for real-time genomic pathogen surveillance. BMC Bioinformatics. DOI: 10.1186/s12859-024-06005-z.

75. Steenwyk, J.L., S. Knowles, R.W. Bastos, C. Balamurugan, D. Rinker, M.E. Mead, C.D. Roberts, H.A. Raja, Y. Li, A.C. Colabardini, P.A. de Castro, T.F. dos Reis, D. Canóvas, R.L. Sanchez, K. Lagrou, E. Torrado, F. Rodrigues, N.H. Oberlies, X. Zhou, G.H. Goldman^, & A. Rokas^ (2024). ^Corresponding authors. Evolutionary origin and population diversity of a cryptic hybrid pathogen. Nature Communications. DOI: 10.1038/s41467-024-52639-1.

74. Gonçalves, C., M.-C. Harrison, J.L. Steenwyk, D.A. Opulente, A.L. LaBella, J.F. Wolters, X. Zhou, X.-X. Shen, M. Groenewald, C.T. Hittinger, & A. Rokas (2024). Diverse signatures of convergent evolution in cacti-associated yeasts. PLOS Biology. DOI: 10.1371/journal.pbio.3002832.

73. Bjornson, S., H. Verbruggen, N.S. Upham^, & J.L. Steenwyk^ (2024). ^Corresponding authors. Reticulate Evolution: Detection and Utility in the Phylogenomics Era. Molecular Phylogenetics and Evolution. DOI: 10.1016/j.ympev.2024.108197.

72. Steenwyk, J.L., G.I. Martínez-Redondo, T.J. Buida III, E. Gluck-Thaler, X.-X. Shen, T. Gabaldón, A. Rokas, & R. Fernández (2024). PhyKIT: A Multitool for Phylogenomics. Current Protocols. DOI: 10.1002/cpz1.70016.
Cover Article

71. Liu, H., J.L. Steenwyk, X. Zhou, D.T. Schultz, K.M. Kocot, X.-X. Shen, A. Rokas^, & Y. Li^ (2024). ^Corresponding authors. A taxon-rich and genome-scale phylogeny of Opisthokonta. PLOS Biology. DOI: 10.1371/journal.pbio.3002794.

70. Pinzan, C.F., C. Valero, P.A. de Castro, J. Luiz da Silva, K. Earle, H. Liu, M.A.C. Horta, O. Kniemeyer, T. Krüger, A. Pschibul, D.N. Cömert, T. Heinekamp, A.A. Brakhage, J.L. Steenwyk, M.E. Mead, N. Hermsdorf, S.G. Filler, N.G. da Rosa-Garzon, E. Delbaje, M.J. Bromley, H. Cabral, C. Diehl, C.B. Angeli, G. Palmisano, A.S. Ibrahim, D.C. Rinker, T.J.C. Sauters, K. Steffen, A. Gumilang, A. Rokas^, S. Gago^, & T.F. dos Reis^, G.H. Goldman^ (2024). ^Corresponding authors. Aspergillus fumigatus conidial surface-associated proteome reveals factors for fungal evasion and host immunity modulation. Nature Microbiology. DOI: 10.1038/s41564-024-01782-y.

69. Zhang, W., Y. Fan, W. Deng, Y. Chen, S. Wang, S. Kang, J.L. Steenwyk, M. Xiang, & X. Liu (2024). Characterization of Genome-wide Phylogenetic Conflict Uncovers Evolutionary Modes of Carnivorous Fungi. mBio. DOI: 10.1128/mbio.02133-24.

68. Steenwyk, J.L. (2024). The discovery of a new lifespan-extending gene in insects. Crop Health. DOI: 10.1007/s44297-024-00032-1.

67. Steenwyk, J.L. & N. King (2024). The Promise and Pitfalls of Synteny in Phylogenomics. PLOS Biology. DOI: 10.1371/journal.pbio.3002632.

66. Brown, A., J.L. Steenwyk, & A. Rokas (2024). Genome-wide patterns of non-coding sequence variation in the major fungal pathogen Aspergillus fumigatus. G3 Genes|Genomes|Genetics. DOI: 10.1093/g3journal/jkae091.

65. Opulente, D.A.*, A.L. LaBella*, M.-C. Harrison#, J.F. Wolters#, C. Liu, Y. Li, J. Kominek, J.L. Steenwyk, H.R. Stoneman, J. VanDenAvond, C.R. Miller, Q.K. Langdon, M. Silva, C. Gonçalves, E.J. Ubbelohde, Y. Li, K.V. Buh, M. Jarzyna, M.A.B. Haase, C.A. Rosa, N. Cadez, D. Libkind, J.H. DeVirgilio, A.B. Hulfachor, C.P. Kurtzman, J.P. Sampaio, P. Gonçalves, X. Zhou, X.-X. Shen, M. Groenewald, A. Rokas^, & C.T. Hittinger^ (2024). *Equal co-first authors; #Equal co-second authors; ^Corresponding authors. Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts. Science. DOI: 10.1126/science.adj4503.

64. Balamurugan, C., J.L. Steenwyk^, G.H. Goldman, & A. Rokas^ (2024). ^Corresponding authors. The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. G3 Genes|Genomes|Genetics. DOI:10.1093/g3journal/jkae063

63. Steenwyk, J.L., C. Balamurugan, H.A. Raja, C. Gonçalves, N. Li, F. Martin, J. Berman, N.H. Oberlies, J.G. Gibbons, G.H. Goldman, D.M. Geiser, D.S. Hibbett, & A. Rokas (2024). Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus. mSpectrum. DOI: 10.1128/spectrum.03980-23

62. O'Meara, M.^, J. Rapala, C.B. Nichols, C. Alexandre, B. Billmyre, J.L. Steenwyk, J.A. Alspaugh, & T. O'Meara^ (2024). ^Corresponding authors. CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair. PLOS Genetics. DOI: 10.1371/journal.pgen.1011158.

61. Haase, M.A.B.^, J.L. Steenwyk, & J.D. Boeke (2024). ^Corresponding author. Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum. Genetics. DOI: 10.1093/genetics/iyae008

60. Wang, J.-T.J., J.L. Steenwyk, & R. Brem (2024). Natural trait variation across Saccharomycotina species. FEMS Yeast Research. DOI: 10.1093/femsyr/foae002.

59. Yea, R., M. Biango-Daniels, J.L. Steenwyk, A. Rokas, N. Louwa, R. Nardellaa, & B.E. Wolfe (2024). Genomic, transcriptomic, and ecological diversity of Penicillium species in the cheese rind microbiome. Fungal Genetics and Biology. DOI: 10.1016/j.fgb.2023.103862.

58. Steenwyk, J.L.^, A. Rokas, & G.H. Goldman (2023). ^Corresponding author. Know the enemy and know yourself: addressing cryptic fungal pathogens and beyond. PLOS Pathogens. DOI: 10.1371/journal.ppat.1011704.

57. Liu, C., X. Han, J.L. Steenwyk, & X.-X. Shen (2023). Temporal transcriptomics provides insight into host-pathogen interactions: a case study of Didymella pinodella and disease-resistant and -susceptible pea varieties. Crop Health. DOI: 10.1007/s44297-023-00005-w.

56. Steenwyk, J.L., Y. Li, X. Zhou, X.-X. Shen, & A. Rokas (2023). Incongruence in the phylogenomics era. Nature Reviews Genetics. DOI: 10.1038/s41576-023-00620-x.

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.

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.

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. PNAS. DOI: 10.1073/pnas.2214076120.

52. Steenwyk, J.L.^ & A. Rokas^ (2023). ^Corresponding authors. The dawn of relaxed phylogenetics. PLOS Biology. DOI: 10.1371/journal.pbio.3001998.

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). ^Corresponding authors. Contrasting modes of macro- and micro-synteny evolution in a eukaryotic subphylum. Current Biology. DOI: 10.1016/j.cub.2022.10.025.

50. Steenwyk, J.L.^, D.C. Goltz, T.J. Buida III, Y. Li, X.-X. Shen, & A. Rokas^ (2022). ^Corresponding authors. OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees. PLOS Biology. DOI: 10.1371/journal.pbio.3001827.
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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.

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). ^Corresponding authors. Examination of genome-wide ortholog variation in clinical and environmental isolates of the fungal pathogen Aspergillus fumigatus. mBio. DOI: 10.1128/mbio.01519-22.

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). ^Corresponding authors. BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data. Genetics. DOI: 10.1093/genetics/iyac079.
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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.
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45. Bradley, N.P.*, K.L. Wahl*, J.L. Steenwyk, A. Rokas, & B.F. Eichman (2022). *Equal contributors. Resistance-guided mining of bacterial genotoxins defines a family of DNA glycosylases. mBio. DOI: 10.1128/mbio.03297-21.

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.

43. J.L. Steenwyk^ & A. Rokas^ (2021). ^Corresponding authors. ggpubfigs: colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures. Microbiology Resource Announcements. DOI: 10.1128/MRA.00871-21.
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42. Phillips, M.A., J.L. Steenwyk^, X.-X. Shen, & A. Rokas^ (2021). ^Corresponding authors. Examination of gene loss in the DNA mismatch repair pathway and its mutational consequences in a fungal phylum. Genome Biology and Evolution. DOI: 10.1093/gbe/evab219.

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

40. Steenwyk, J.L.^ & A. Rokas^ (2021). ^Corresponding authors. orthofisher: a broadly applicable tool for automated gene identification and retrieval. G3 Genes|Genomes|Genetics. DOI: 10.1093/g3journal/jkab250.
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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. DOI: 10.1128/mBio.01682-21.

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

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). ^Corresponding authors. Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates of Aspergillus fumigatus. mSpectrum. DOI: 10.1128/Spectrum.00010-21.

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. DOI: 10.1371/journal.pbio.3001185.

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

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

33. Steenwyk, J.L.^, T.J. Buida III, A.L. LaBella, Y. Li, X.-X. Shen, & A. Rokas^ (2021). ^Corresponding authors. PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics. DOI: 10.1093/bioinformatics/btab096.
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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). ^Corresponding authors. A genome-scale phylogeny of the kingdom Fungi. Current Biology. DOI: 10.1016/j.cub.2021.01.074.
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. DOI: 10.1002/yea.3518.
Cover Article

30. Steenwyk, J.L.^, T.J. Buida III, Y. Li, X.-X. Shen, & A. Rokas^ (2020). ^Corresponding authors. ClipKIT: a multiple sequence alignment-trimming software for accurate phylogenomic inference. PLOS Biology. DOI: 10.1371/journal.pbio.3001007.
Run ClipKIT in the browser and leave the computing up to us!
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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. PNAS. DOI: 10.1073/pnas.2013143117.

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). ^Corresponding authors. Genome-scale phylogeny and contrasting modes of genome evolution in the fungal phylum Ascomycota. Science Advances. DOI: 10.1126/sciadv.abd0079.

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

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. DOI: 10.1128/mBio.02458-20.

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). *Equal contributors. Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species. Genetics. DOI: 10.1534/genetics.120.303549.
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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. DOI: 10.1371/journal.ppat.1008645.

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). *Equal contributors; ^Corresponding authors. Pathogenic allodiploid hybrids of Aspergillus fungi. Current Biology. DOI: 10.1016/j.cub.2020.04.071.
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Nature Reviews Microbiology Research Highlights
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22. Mead, M.E.*, A.T. Borowsky*, B. Joehnk, J.L. Steenwyk, X.-X. Shen, A. Sil, & A. Rokas (2020). *Equal contributors. Recurrent loss of abaA, a master regulator of asexual development in filamentous fungi, correlates with changes in genomic and morphological traits. Genome Biology and Evolution. DOI: 10.1093/gbe/evaa107.

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). ^Corresponding authors. Genomic and phenotypic heterogeneity of clinical isolates of the human pathogens Aspergillus fumigatus, Aspergillus lentulus and Aspergillus fumigatiaffinis. Frontiers in Genetics. DOI: 10.3389/fgene.2020.00459.

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.

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.

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).^Corresponding authors. Gliotoxin, a known virulence factor in the major human pathogen Aspergillus fumigatus, is also biosynthesized by the non-pathogenic relative A. fischeri. mBio. DOI: 10.1128/mBio.03361-19.

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.

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.

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.
Editor's Pick

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

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.
Github logo docs

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.

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.

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). ^Corresponding authors. Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLOS Biology. DOI: 10.1371/journal.pbio.3000255.

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.

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. DOI: 10.1128/mSphere.00018-19.

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.

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.
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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). *Equal contributors; ^Corresponding authors. Tempo and mode of genome evolution in the budding yeast subphylum. Cell. DOI: 10.1016/j.cell.2018.10.023.
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.
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.

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.

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.

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