Publications

102.

Authors

Aime, M.C., U. Kõljalg, T.W. May, K. Bensch, M. Bradshaw, G. Cardinali, P.W. Crous, J.Z. Groenewald, L. Guzmán-Dávalos, D.L. Hawksworth, M. Hernández-Restrepo, D. Hibbett, K.D. Hyde, E. Malosso, R.H. Nilsson, A. Rosling, N. Schoutteten, M. Stadler, A.M. Vasco-Palacios, C.M. Visagie, N. Wijayawardene, A. Yurkov, K. Abarenkov, H.A. Ariyawansa, J.P.M. Araújo, C. Baschien, M. Bakhshi, M. Bendiksby, M. Chuvochina, A. Conti, E. D'hooge, V. Flores-Almaraz, B. Furneaux, G.W. Griffith, D. Hernández-Hernández, J. Houbraken, G. Jones, P. Kirk, Y. Marin-Felix, W. Meyer, I. Pyrri, T. Rämä, V. Robert, J.L. Steenwyk, D. Stephens, L. Tedersoo, M. Thines, D. Vu, J. Xu, N. Zhang, & R. Lücking.

How to name dark fungal taxa outside the Code: The International Standard to Catalogue Dark Fungal Taxa (ISCDFT).

Submitted.

101. Zhang, Q., H. Liu, J.L. Steenwyk, B. Feng, X. Tian, X. Zhou, X.-X. Shen, X. Cao, Z. Qu, & Y. Li.

Site Subsampling Based on Posterior Mean Site Frequency Improves Phylogenomic Estimation Accuracy.

Submitted.

100. 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^.

The evolution and function of eukaryote-to-cyanobacteria horizontal gene transfer.

Submitted.

99. Steenwyk, J.L. (2026).

Epistemic State Representations in Large Language Models.

Preprints. DOI: 10.20944/preprints202608.2226.v1.

98. Steenwyk, J.L. (2026).

A geometric atlas of how ESM3 organizes modalities across depth.

bioRxiv. DOI: 10.64898/2026.07.08.737319.

97. Steenwyk, J.L. (2026).

Structure tokens sharpen the feature vocabulary of protein language models.

bioRxiv. DOI: 10.64898/2026.05.12.724593.

96. Laurent, J.M., A. Bou, M. Pieler, C. Igoe, A. Andonian, S. Narayanan, J. Braza, A.S. Vassopoulos, J.L. Steenwyk, B. Lash, A.D. White, S.G. Rodriques (2026).

LABBench2: An Improved Benchmark for AI Systems Performing Biology Research.

arXiv. DOI: 10.48550/arXiv.2604.09554.

95.

Authors

van Rhijn, N., E. Gan, P. Hepo-oja, X. Wang, J. Li, S. Duggan, D. Firer, L. Alsharqi, H. Gifford, J.L. Steenwyk, A.P. Brackin, A. Abdolrasouli, A.M. Borman, C.A. Cuomo, M.C. Fisher, D. Armstrong-James, R.A. Farrer, J. Usher, & J. Rhodes (2026).

The Antarctic marine microplastics reveals environmental persistence and rapid evolution of Candida auris.

bioRxiv.. DOI: 10.64898/2026.03.13.711634.

94. Li, N., J.L. Steenwyk, S. O’Donnell, E. Gluck-Thaler, S.M. Kane, D.M. Geiser, & F.N. Martin (2026).

Assembling telomere-to-telomere genomes of Fusarium oxysporum f. sp. lactucae provides a roadmap for studying genome and phenotype evolution.

BMC Genomics. DOI: 10.21203/rs.3.rs-8100147.

93.

Authors

Bjornson, S., T.T. Bringloe, K. Uthanumallian, R. De Paoli-Iseppi, M. B. Clark, C.M.C. Cremen, R. Hossen, O. McGinley, T. Jalali, J. West, F. Leliaert, R. Wetherbee, O. De Clerck, S. Duchene, J.L. Steenwyk, & H. Verbruggen (2026).

Stepwise evolutionary transitions in Cladophorales plastid genomes reveals origins of hairpin chromosomes.

Current Biology. DOI: 10.1016/j.cub.2026.02.038.

92. 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 (2026).

Clonal-aggregative multicellularity entrained by salinity in one of the closest relatives of animals.

Nature. DOI: 10.1038/s41586-026-10137-y.

Flexible paths to multicellularity. Nature News and Views Article by Lotharkupong and Coelho.

91. O’Donnell, S., N. Li, J.L. Steenwyk, D. Geiser, F.N. Martin, & E. Gluck-Thaler (2026).

PAQman: reference-free ensemble evaluation of long-read eukaryotic genome assemblies.

G3 Genes|Genomes|Genetics. DOI: 10.1093/g3journal/jkag034.

90. David, K.T., L. Horianopoulos, C. Goncalves, J.L. Steenwyk, A. Pontes, P. Goncalves, C.T. Hittinger, M. Pennell, & A. Rokas (2026).

Discovery of additional ancient genome duplications in yeasts.

Current Biology. DOI: 10.1016/j.cub.2025.12.053.

89. Steenwyk, J.L.^ & T.J. Buida III (2025).

RCVT: a diagnostic to quantify compositional biases among taxa for large phylogenomic studies.

bioRxiv. DOI: 10.1101/2024.11.28.625917.

88. Steenwyk, J.L.^ & N. King^ (2025).

Retracted: Integrative phylogenomics positions sponges at the root of the animal tree.

Science. DOI: 10.1126/science.adw9456.

87.

Authors

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).

Stable hypermutators revealed by the genomic landscape of DNA repair genes among yeast species.

Molecular Biology and Evolution. DOI: 10.1093/molbev/msaf285.

86.

Authors

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 (2025).

The Genomes of Nematode-Trapping Fungi Provide Insights into the Origin and Diversification of Fungal Carnivorism.

Molecular Phylogenetics and Evolution. DOI: 10.1016/j.ympev.2025.108423.

85.

Authors

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 (2025).

The role of metabolism in shaping enzyme structures over 400 million years.

Nature. DOI: 10.1038/s41586-025-09205-6.

84.

Authors

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^ (2025).

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage.

Molecular Systems Biology. DOI: 10.1038/s44320-025-00118-0.

83. 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. DOI: 10.1093/nar/gkaf325.

Run ClipKIT in the browser and leave the computing up to us!

82. 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.

81. 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.

80. 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.

79. Steenwyk, J.L.^, T.J. Buida III, A. Rokas, & N. King (2024).

OrthoHMM: Improved Inference of Ortholog Groups using Hidden Markov Models.

bioRxiv. DOI: 10.1101/2024.12.07.627370.

78.

Authors

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).

Evolutionary origin and population diversity of a cryptic hybrid pathogen.

Nature Communications. DOI: 10.1038/s41467-024-52639-1.

77. 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.

76. Bjornson, S., H. Verbruggen, N.S. Upham^, & J.L. Steenwyk^ (2024).

Reticulate Evolution: Detection and Utility in the Phylogenomics Era.

Molecular Phylogenetics and Evolution. DOI: 10.1016/j.ympev.2024.108197.

75. 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

74. Liu, H., J.L. Steenwyk, X. Zhou, D.T. Schultz, K.M. Kocot, X.-X. Shen, A. Rokas^, & Y. Li^ (2024).

A taxon-rich and genome-scale phylogeny of Opisthokonta.

PLOS Biology. DOI: 10.1371/journal.pbio.3002794.

73.

Authors

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).

Aspergillus fumigatus conidial surface-associated proteome reveals factors for fungal evasion and host immunity modulation.

Nature Microbiology. DOI: 10.1038/s41564-024-01782-y.

72. 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.

71. Steenwyk, J.L. (2024).

The discovery of a new lifespan-extending gene in insects.

Crop Health. DOI: 10.1007/s44297-024-00032-1.

70. Steenwyk, J.L. & N. King (2024).

The Promise and Pitfalls of Synteny in Phylogenomics.

PLOS Biology. DOI: 10.1371/journal.pbio.3002632.

69. 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.

68.

Authors

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).

Genomic factors shape carbon and nitrogen metabolic niche breadth across Saccharomycotina yeasts.

Science. DOI: 10.1126/science.adj4503.

67. Balamurugan, C., J.L. Steenwyk^, G.H. Goldman, & A. Rokas^ (2024).

The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi.

G3 Genes|Genomes|Genetics. DOI:10.1093/g3journal/jkae063

66.

Authors

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

65. O'Meara, M.^, J. Rapala, C.B. Nichols, C. Alexandre, B. Billmyre, J.L. Steenwyk, J.A. Alspaugh, & T. O'Meara^ (2024).

CryptoCEN: A Co-Expression Network for Cryptococcus neoformans reveals novel proteins involved in DNA damage repair.

PLOS Genetics. DOI: 10.1371/journal.pgen.1011158.

64. Haase, M.A.B.^, J.L. Steenwyk, & J.D. Boeke (2024).

Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum.

Genetics. DOI: 10.1093/genetics/iyae008

63. Wang, J.-T.J., J.L. Steenwyk, & R. Brem (2024).

Natural trait variation across Saccharomycotina species.

FEMS Yeast Research. DOI: 10.1093/femsyr/foae002.

62. 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.

61. Turnbull, R.*, J.L. Steenwyk*, S. Mutch, P. Scholten, V.W. Salazar, J.L. Birch, & H. Verbruggen (2023).

Orthoflow: phylogenomic analysis and diagnostics with one command.

Research Square. DOI: 10.21203/rs.3.rs-3699210/v2.

60. Steenwyk, J.L.^, A. Rokas, & G.H. Goldman (2023).

Know the enemy and know yourself: addressing cryptic fungal pathogens and beyond.

PLOS Pathogens. DOI: 10.1371/journal.ppat.1011704.

59. 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.

58. 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.

57. 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.

56.

Authors

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.

55.

Authors

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.

54. Steenwyk, J.L.^ & A. Rokas^ (2023).

The dawn of relaxed phylogenetics.

PLOS Biology. DOI: 10.1371/journal.pbio.3001998.

53. 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).

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.

52. Zheng, Q., J.L. Steenwyk^, & A. Rokas^ (2022).

Lack of universal mutational biases in a fungal phylum.

bioRxiv. DOI: 10.1101/2022.03.29.486229.

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.

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).

OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees.

PLOS Biology. DOI: 10.1371/journal.pbio.3001827.

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).

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).

BioKIT: a versatile toolkit for processing and analyzing diverse types of sequence data.

Genetics. DOI: 10.1093/genetics/iyac079.

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.

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.

mBio. DOI: 10.1128/mbio.03297-21.

44.

Authors

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).

ggpubfigs: colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures.

Microbiology Resource Announcements. DOI: 10.1128/MRA.00871-21.

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.

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).

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).

orthofisher: a broadly applicable tool for automated gene identification and retrieval.

G3 Genes|Genomes|Genetics. DOI: 10.1093/g3journal/jkab250.

39.

Authors

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).

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.

Authors

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.

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).

PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data.

Bioinformatics. DOI: 10.1093/bioinformatics/btab096.

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.

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).

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!

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).

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).

Draft genome sequences of four Aspergillus section Fumigati clinical strains.

Microbiology Resource Announcements. DOI: 10.1128/MRA.00856-20.

26.

Authors

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).

Variation Among Biosynthetic Gene Clusters, Secondary Metabolite Profiles, and Cards of Virulence Across Aspergillus Species.

Genetics. DOI: 10.1534/genetics.120.303549.

Cover Article
Highlighted Article

24.

Authors

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.

Authors

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.

Current Biology. DOI: 10.1016/j.cub.2020.04.071.

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.

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).

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.

Authors

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).

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.

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