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The Rokas Lab

Publications

Wordle made from abstracts of articles published between 1999 and 2023 

Synthetic Reviews on our Research Interests

Gonçalves, C., C. T. Hittinger, & A. Rokas (2024). Horizontal gene transfer in Fungi and its ecological importance. In: Hsueh, Y. P., Blackwell, M. (Eds.) Fungal Associations. The Mycota, vol 9. Springer, Cham., pp. 59-81.

Steenwyk, J. L., Y. Li, X. Zhou, X.-X. Shen, & A. Rokas (2023). Incongruence in the phylogenomics era. Nature Rev. Genet. 24: 834–850.

Rokas, A. (2022). Evolution of the human pathogenic lifestyle in fungi. Nature Microbiol. 7: 607-619.

Benton, M. L., A. Abraham, A. L. LaBella, P. Abbot, A. Rokas, & J. A. Capra (2021). The influence of evolutionary history on human health and disease. Nature Rev. Genet. 22: 269–283.

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 Rep. 37: 868–878.

Preprint Articles

  1. Steenwyk, J. L., T. J. Buida, A. Rokas, & N. King. OrthoHMM: Improved inference of ortholog groups using Hidden Markov Models.
  2. Riedling, O. L., K. T. David, & A. Rokas. Global patterns of species diversity and distribution in the biomedically and biotechnologically important fungal genus Aspergillus.
  3. Danis, T., D. Lin, D. S. Caetano, G. F. Funston, & A. Rokas. Gestation length drives brain size and litter size variation in eutherian mammals.
  4. Aranguiz, K.*, L. C. Horianopoulos*, L. Elkin, K. Segura Abá, R. L. Wrobel, S.-H. Shiu, A. Rokas, & C. T. Hittinger. Machine learning uncovers gene families impacting oxidative stress resistance across yeasts. (* Equal contributors)
  5. David, K. T., J. G. Schraiber, J. G. Crandall, A. L. LaBella, D. A. Opulente, M.-C. Harrison, J. F. Wolters, X. Zhou, X.-X. Shen, M. Groenewald, C. T. Hittinger^, M. Pennell^, & A. Rokas^. Convergent expansions of keystone gene families drive metabolic innovation in a major eukaryotic clade. (^Senior authors)
  6. Hatmaker, E. A., A. E. Barber, M. T. Drott, T. J. C. Sauters, A. Alastruey-Izquierdo, D. Garcia-Hermoso, O. Kurzai, & A. Rokas. Pathogenicity is associated with population structure in a fungal pathogen of humans.
  7. Feng, B., Y. Li, H. Liu, J. L. Steenwyk, K. T. David, X. Tian, B. Xu, C. Goncalves, 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^. Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage. (^Senior authors)
  8. Lemke, O., 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. The role of metabolism in shaping enzyme structures over 400 million years of evolution.
  9. Zheng, Q., J. L. Steenwyk^, & A. Rokas^. Lack of universal mutational biases in a fungal phylum. (^Senior authors)

Research Articles

  1. Crandall, J. G., X. Zhou, A. Rokas, & C. T. Hittinger (2024). Specialization restricts the evolutionary paths available to yeast sugar transporters. Mol. Biol. Evol.: msae228.
  2. Pontes, A., M.-C. Harrison, A. Rokas, & C. Gonçalves (2024). Convergent reductive evolution in bee-associated lactic acid bacteria. Appl. Environ. Microbiol. 90: e01257-24.
  3. Danis, T. & A. Rokas (2024). The evolution of gestation length in eutherian mammals. Proc. R. Soc. B 291: 20241412.
  4. Steenwyk, J. L., S. L. 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, A. Gumilang, M. Almagro-Molto, A. Alanio, D. Garcia-Hermoso, E. Delbaje, L. Pontes, C. Figueiredo Pinzan, A. Zaninelli Schreiber, D. Canovas, R. S. Luperini, 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. (^Senior authors). Nature Comms. 15: 8412.
  5. Goncalves, 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 cactus-associated yeasts. PLoS Biol. 22: e3002832.
  6. Harrison, M.-C., D. A. Opulente, J. F. Wolters, X.-X. Shen, X. Zhou, M. Groenewald, C. T. Hittinger, A. Rokas, & A. L. LaBella (2024). Exploring Saccharomycotina yeast ecology through an ecological ontology framework. Yeast 41: 615–628.
  7. Steenwyk, J. L., G. Martínez-Redondo, T. Buida, E. Gluck-Thaler, X.-X. Shen, T. Gabaldón, A. Rokas, & R. Fernández (2024). PhyKIT: a multitool for phylogenomics. Curr. Prot. 4: e70016.
  8. Zavala, B., L. Dineen, K. J. Fisher, D. A. Opulente, M.-C. Harrison, J. F. Wolters, X.-X. Shen, X. Zhou, M. Groenewald, C. T. Hittinger, A. Rokas, &. A. L. LaBella (2024). Genomic factors shaping codon usage across the Saccharomycotina subphylum. G3 14: jkae207.
  9. Rinker, D. C., T. J. C. Sauters, K. Steffen, A. Gumilang, H. A. Raja, M. Rangel-Grimaldo, C. F. Pinzan, P. A. de Castro, T. F. dos Reis, E. Delbaje, J. Houbraken, G. H. Goldman^, N. H. Oberlies^, & A. Rokas^ (2024). Strain heterogeneity in a non-pathogenic fungus highlights factors associated with virulence. (^Senior authors) Comms. Biol. 7: 1082.
  10. 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. (^Senior authors) PLoS Biol. 22: e3002794.
  11. Pinzan, C. F.*, C. Valero*, P. A. de Castro, J. L. da Silva, K. Earle, H. Liu, M. A. C. Horta, O. Kniemeyer, T. Krueger, A. Pschibul, D. N. Coemert, T. Heinekamp, A. Brakhage, J. L. Steenwyk, M. E. Mead, N. Hermsdorf, S. Filler, N. G da Rosa-Garzon, E. Deljabe, M. J. Bromley, H. Cabral, C. Diehl, C. B. Angeli, G. Palmisano, A. 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. (*Co-first authors; ^Senior authors) Nature Microbiol. 9: 2710–2726.
  12. Liu, C.*, X. Zhou*, Y. Li, C. T. Hittinger, R. Pan, J. Huang, X. Chen, A. Rokas, Y. Chen, & X.-X. Shen (2024). The influence of the number of tree searches on maximum likelihood inference in phylogenomics. (*Equal contributors). Syst. Biol. 73: 807–822.
  13. Tao, M., J. Chen, C. Cui, Y. Xu, J. Xu, Z. Shi, J. Yun, J. Zhang, G.-Z. Ou, C. Liu, Y. Chen, Z.-R. Zhu, R. Pan, S. Xu, X. Chen, A. Rokas, Y. Zhao, S. Wang, J. Huang, & X.-X. Shen (2024). Identification of a longevity gene through evolutionary rate covariation of insect mito-nuclear genomes. Nature Aging 4: 1076–1088.
    Cover article
  14. Harrison, M. C., E. J. Ubbelohde, A. L. LaBella, D. A. Opulente, J. F. Wolters, X. Zhou, X.-X. Shen, M. Groenewald, C. T. Hittinger^, & A. Rokas^ (2024). Machine learning enables identification of an alternative yeast galactose utilization pathway. (^Senior authors) Proc. Natl. Acad. Sci. USA 121: e2315314121.
  15. 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. Goncalves, 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. Goncalves, 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. (*Co-first authors; #Co-second authors; ^Senior authors) Science 384: eadj4503.
  16. Brown, A., J. L. Steenwyk, & A. Rokas (2024). Genome-wide patterns of non-coding sequence variation in the major fungal pathogen Aspergillus fumigatus. G3 14: jkae091.
  17. Balamurugan, C., J. L. Steenwyk^, G. H. Goldman, & A. Rokas^ (2024). The evolution of the gliotoxin biosynthetic gene cluster in Penicillium fungi. (^Senior authors) G3 14: jkae063.
  18. Sun, L., K. T. David, J. F. Wolters, S. D. Karlen, C. Goncalves, D. A. Opulente, A. L. LaBella, M. Groenewald, X. Zhou, X.-X. Shen, A. Rokas, & C. T. Hittinger (2024). Functional and evolutionary integration of a fungal gene with a bacterial operon. Mol. Biol. Evol. 41: msae045.
    Cover article
  19. 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 (2024). Phylogenomics reveals extensive misidentification of fungal strains from the genus Aspergillus. Microbiol. Spectr. 12: e03980-23.
  20. David, K. T., M.-C. Harrison, D. A. Opulente, A. L. LaBella, J. F. Wolters, X. Zhou, X.-X. Shen, M. Groenewald, M. Pennell, C. T. Hittinger, & A. Rokas (2024). Saccharomycotina yeasts defy longstanding macroecological patterns. Proc. Natl. Acad. Sci. USA 121: e2316031121.
  21. Pontes, A.^, F. Paraíso, Y.-C. Liu, S. Limtong, S. Jindamorakot, L. Jespersen, C. Gonçalves, C. A. Rosa, I. J. Tsai, A. Rokas, C. T. Hittinger, P. Gonçalves^, & J. P. Sampaio^ (2024). Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication. (^Senior authors) iScience 27: 108987.
  22. Ye, R., M. Biango-Daniels, J. L. Steenwyk, A. Rokas, N. Louw, R. Nardella, & B. E. Wolfe (2024). Genomic, transcriptomic, and ecological diversity of Penicillium species in cheese rind microbiomes. Fungal Genet. Biol. 171: 103862.
  23. Riedling, O., A. S. Walker, & A. Rokas (2024). Predicting fungal secondary metabolite activity from biosynthetic gene cluster data using machine learning. Microbiol. Spectr. 12: e03400-23.
  24. Chavez, C. M., M. Groenewald, A. B. Hulfachor, G. Kpurubu, R. Huerta, C. T. Hittinger, & A. Rokas (2024). The cell morphological diversity of Saccharomycotina yeasts. FEMS Yeast Res. 24: foad055.
  25. Jones, R. E., A. K. Tice, M. Eliáš, L. Eme, M. Kolísko, S. Nenarokov, T. Pánek, A. Rokas, E. Salomaki, J. F. H. Strassert, X.-X. Shen, D. Žihala, & M. W. Brown (2024). Create, analyze, and visualize phylogenomic datasets using PhyloFisher. Curr. Prot. 4: e969.
  26. Wolters, J. F., A. L. LaBella, D. Opulente, A. Rokas, & C. T. Hittinger (2023). Mitochondrial genome diversity across the subphylum Saccharomycotina. Front. Microbiol. 14: 1268944.
  27. Steenwyk, J. L., A. Rokas, & G. H. Goldman (2023). Know the enemy and know yourself: Addressing cryptic fungal pathogens of humans and beyond. PLoS Path. 19: e1011704.
  28. Steenwyk, J. L., Y. Li, X. Zhou, X.-X. Shen, & A. Rokas (2023). Incongruence in the phylogenomics era. Nature Rev. Genet. 24: 834–850.
  29. Bradshaw, M. J., M. C. Aime, A. Rokas, A. Maust, S. Moparthi, K. Jellings, A. M. Pane, D. Hendricks, B. Pandey, Y. Li, & D. H. Pfister (2023). Extensive intragenomic variation in the internal transcribed spacer (ITS) region of fungi. iScience 26: 107317.
  30. Hatmaker, E. A., J. E. Schmitz, & A. Rokas (2023). Draft genomes of Aspergillus nomiae and Aspergillus tamarii isolates from human eye infections. Microbiol. Resour. Announc. 12: e00391-23.
  31. Groenewald, M., C. T. Hittinger, K. Bensch, D. A. Opulente, X.-X. Shen, Y. Li, C. Liu, A. L. LaBella, X. Zhou, S. Limtong, S. Jindamorakot, P. Gonçalves, V. Robert, K. H. Wolfe, C. A. Rosa, T. Boekhout, N. Čadež, G. Péter, J. P. Sampaio, M.-A. Lachance, A. M. Yurkov, H.-M. Daniel, M. Takashima, K. Boundy-Mills, D. Libkind, & A. Rokas (2023). A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Stud. Mycol. 105: 1-22.
  32. Nalabothu, R. L., K. J. Fisher, A. L. LaBella, T. A. Meyer, D. A. Opulente, J. F. Wolters, A. Rokas, & C. T. Hittinger (2023). Codon optimization improves the prediction of xylose metabolism from gene content in budding yeasts. Mol. Biol. Evol. 40: msad111.
  33. Ngo, K., T. H. Gittens, D. I. Gonzalez, E. A. Hatmaker, S. Plotkin, M. Engle, G. A. Friedman, M. Goldin, R. E. Hoerr, B. F. Eichman, A. Rokas, M. L. Benton, & K. L. Friedman (2023). A comprehensive map of hotspots of de novo telomere addition in Saccharomyces cerevisiae. Genetics 224: iyad076.
  34. M. E. Mead, P. A. Castro, J. L. Steenwyk, J.-P. Gangneux, M. Hoenigl, J. Prattes, R. Rautemaa-Richardson, H. Guegan, C. B. Moore, C. Lass-Floerl, 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. (^Senior authors) Microbiol. Spectr. 11: e05128-22.
  35. Sole-Navais, P., C. Flatley, V. Steinthorsdottir, M. Vaudel, J. Juodakis, J. Chen, T. Laisk, A. L. LaBella, D. Westergaard, J. Bacelis, J. Juodakis, B. Brumpton, L. Skotte, M. C. Borges, O. Helgeland, A. Mahajan, M. Wielscher, F. Lin, C. Briggs, C. A. Wang, G.-H. Moen, R. N. Beaumont, J. P. Bradfield, A. Abraham, G. Thorleifsson, M. E. Gabrielsen, S. R. Ostrowski, D. Modzelewska, E. A. Nohr, E. Hypponen, A. Srivastava, O. Talbot, C. Allard, S. M. Williams, R. Menon, B. M. Shields, G. Sveinbjornsson, H. Xu, M. Melbye, L. Jr. William, L. Bouchard, E. Oken, O. B. Pedersen, D. F. Gudbjartsson, C. Erikstrup, E. Sorensen, Early Growth Genetics Consortium, Estonian Biobank Research Team, Danish Blood Donor Study Genomic Consortium, R. T. Lie, K. Teramo, M. Hallman, T. Juliusdottir, H. Hakonarson, H. Ullum, A. T. Hattersley, L. Sletner, M. Merialdi, S. Rifas-Shiman, T. Steingrimsdottir, D. Scholtens, C. Power, J. West, M. Nyegaard, J. A. Capra, A. H. Skogholt, P. Magnus, O. A. Andreassen, U. Thorsteinsdottir, S. F. A Grant, E. Qvigstad, C. E. Pennell, M.-F. Hivert, G. M. Hayes, M.-R. Jarvelin, M. I. McCarthy, D. A. Lawlor, H. S. Nielsen, R. Magi, A. Rokas, K. Hveem, K. Stefansson, B. Feenstra, P. Njolstad, L. J. Muglia, R. M. Freathy, S. Johanson, G. Zhang^, & B. Jacobsson^ (2023). Genetic effects on the timing of parturition and links to fetal birth weight. (^Senior authors) Nature Genet. 55: 559–567.
  36. Sierra-Patev, S., 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, J. Donoghue, 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. Proc. Natl. Acad. Sci. USA 120: e2214076120.
  37. Abraham, A., A. L. LaBella, M. L. Benton, A. Rokas, & J. A. Capra (2023). GSEL: A fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinformatics 39: btad037.
  38. Hugaboom, M., E. A. Hatmaker^, A. L. LaBella, & A. Rokas^ (2023). Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi. (^Senior authors). G3 13: jkac285.
  39. 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 microsynteny evolution in a eukaryotic subphylum. (^Senior authors) Curr. Biol. 32: 5335-5343.e4.
  40. Abraham, A.*, A. L. LaBella*, J. A. Capra^, & A. Rokas^ (2022). Mosaic patterns of selection in genomic regions associated with diverse human traits. (*Equal contributors; ^Senior authors). PLoS Genet. 18: e1010494.
  41. Hatmaker, E. A., M. Rangel-Grimaldo, H. A. Raja, H. Pourhadi, S. L. Knowles, K. Fuller, E. M. Adams, J. D. Lightfoot, R. W. Bastos, G. H. Goldman, N. H. Oberlies, & A. Rokas (2022). Genomic and phenotypic trait variation of the opportunistic human pathogen Aspergillus flavus and its non-pathogenic close relatives. Microbiol. Spectr. 10: e0306922.
  42. Hatmaker, E. A., D. L. Miller, I. Newton, & A. Rokas (2022). Draft Genome Sequence of an Aspergillus Strain Isolated from a Honey Bee Pupa. Microbiol. Resour. Announc. 11: e00798-22.
  43. 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. (^Senior authors) PLoS Biol. 20: e3001827.
  44. Abraham, A., B. L. Le, I. Kosti, P. Straub, D. R. Velez Edwards, L. K. Davis, L. Muglia, A. Rokas, A. Bejan, M. Sirota, & J. A. Capra (2022). Dense phenotyping from electronic health records enables machine-learning-based prediction of preterm birth. BMC Med. 20: 333.
  45. Li, Y., Z. Liu, C. Liu, Z. Shi, L. Pang, C. Chen, Y. Chen, R. Pan, W. Zhou, X. X. Chen, A. Rokas^, J. Huang^, & X.-X. Shen^ (2022). HGT is widespread in insects and contributes to male courtship in lepidopterans. (^Senior authors) Cell 185: 2975-2987.e10.
  46. Colabardini, A. C., N. Van Rhijn, A. L. LaBella, C. Valero, L. Dineen, A. Rokas, & G. H. Goldman (2022). Aspergillus fumigatus FhdA transcription factor is important for mitochondrial activity and codon usage regulation during the caspofungin paradoxical effect. Antimicrob. Agents Chemother. 66: e0070122.
  47. 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. Front. Fungal Biol. 3: 802494.
  48. Horta, M. A., J. L. Steenwyk, M. E. Mead, L. H. B. 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 13: e01519-22.
  49. Steenwyk, J. L.^, T. J. Buida III, C. Goncalves, 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. (^Senior authors) Genetics: iyac079.
  50. Markowitz, R. H., A. L. LaBella, M. Shi, A. Rokas, J. A. Capra, J. F. Ferguson, J. D. Mosley & S. R. Bordenstein (2022). Microbiome-associated human genetic variants impact phenome-wide disease risk. Proc. Natl. Acad. Sci. USA 119: e2200551119.
  51. Rokas, A. (2022). Evolution of the human pathogenic lifestyle in fungi. Nature Microbiol. 7: 607-619.
  52. Steenwyk, J. L., M. A. Phillips, F. Yang, S. S. Date, T. R. Graham, J. Berman, C. T. Hittinger, & A. Rokas (2022). A gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. Science Adv. 8: abn0105.
  53. 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 13: e03297-21.
  54. Castro, P. A., M. Moraes, A. C. Colabardini, M. A. Crivelente 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. (^Senior authors) PLoS Genet. 18: e1009965.
  55. Harrison, M. C., A. L. LaBella, C. T. Hittinger^, & A. Rokas^ (2022). The evolution of the GALactose utilization pathway in budding yeasts. (^Senior authors) Trends Genet. 38: 97-106.
  56. Colabardini, A. C., F. Wang, Z. Dong, L. Pardeshi, M. C. Rocha, J. H. Costa, T.F. dos Reis, A. Brown, Q. Z. Jaber, M. Fridman, T. Fill, A. Rokas, I. Malavazi, K. H. Wong, & G. H. Goldman (2022). Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin. Genetics 220: iyab183.
  57. Prattes, J., J. Wauters, D. R. Giacobbe, J. Salmanton-García, J. Maertens, M. Bourgeois, M. Reynders, L. Rutsaert, N. Van Regenmortel, P. Lormans, S. Feys, A. C. Reisinger, O. A. Cornely, T. Lahmer, M. Valerio, L. Delhaes, K. Jabeen, J. Steinmann, M. Chamula, M. Bassetti, S. Hatzl, R. Rautemaa-Richardson, P. Koehler, K. Lagrou, M. Hoenigl; ECMM-CAPA Study Group* (2022). Risk factors and outcome of pulmonary aspergillosis in critically ill coronavirus disease 2019 patients- a multinational observational study by the European Confederation of Medical Mycology. (ECMM-CAPA Study Group*: Y. Debaveye, M. H. Miceli, J.-J. Tudesq, G. Paul, R. Krause, M. Linhofer, J. Frost, P. Zechner, M. Kochanek, P. Eller, J. D. Jenks, S. Volpi, A.-P. Bellanger, P. L. White, G. H. Goldman, P. Bowyer, A. Rokas, S. Gago, P. Pelosi, C. Robba, J.-P. Gangneux, C. Lass-Floerl, M. Machado, P. Muñoz) Clin Microbiol. Infect. 28: 580–587.
  58. Steenwyk, J. L.^ & A. Rokas^ (2021). ggpubfigs: colorblind friendly color palettes and ggplot2 graphic system extensions for publication-quality scientific figures. (^Senior authors) Microbiol. Resour. Announc. 10: e00871-21.
  59. 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. (^Senior authors) Genome Biol. Evol. 13: evab219.
  60. Santos, R. A. C., M. E. Mead, J. L. Steenwyk, O. Rivero-Menendez, A. Alastruey-Izquierdo, G. H. Goldman^, & A. Rokas^ (2021). Examining signatures of natural selection in antifungal resistance genes across Aspergillus fungi. (^Senior authors) Front. Fungal Biol. 2: 723051.
  61. Kwon, M. J., C. Steiniger, T. C. Cairns, J. H. Wisecaver, A. Lind, C. Pohl, C. Regner, A. Rokas, &. V. Meyer (2021). Beyond the biosynthetic gene cluster paradigm: Genome-wide co-expression networks connect clustered and unclustered transcription factors to secondary metabolic pathways. Microbiol. Spectr. 9: e00898-21.
  62. Tice, A. K., D. Žihala,T. Pánek, R. E. Jones, E. Salomaki, S. Nenarokov, F. Burki, M. Eliáš, L. Eme, A. J. Roger, A. Rokas, X.-X. Shen, J. F. H. Strassert, M. Kolísko, & M. W. Brown (2021). PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PLoS Biol. 19: e3001365.
  63. Steenwyk, J. L.^ & A. Rokas^ (2021). orthofisher: a broadly applicable tool for automated gene identification and retrieval. (^Senior authors) G3 11: jkab250.
  64. Ries, L. N. A., P. A. Castro, L. P. Silva, C. Valero, T. F. Reis, R. Saborano, I. F. Duarte, G. F. Persinoti, J. L. Steenwyk, A. Rokas, F. Almeida , J. H. Costa, T. P. Fill, S. S. W. Wong, V. Aimanianda, F. Rodrigues, R. A. Gonçales, C. Duarte-Oliveira, A. Carvalho, & G. H. Goldman (2021). Aspergillus fumigatus acetate utilisation impacts virulence traits and pathogenicity. mBio 12: e01682-21.
  65. Li, Y., X.-X. Shen, B. Evans, C. W. Dunn^, & A. Rokas^ (2021). Rooting the animal tree of life. (^Senior authors) Mol. Biol. Evol. 38: 4322–4333.
  66. 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 218: iyab066.
  67. 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. (^Senior authors) Microbiol. Spectr. 9: e00010-21.
  68. 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 Biol. 19: e3001185.
  69. Shen, X.-X., J. L. Steenwyk, & A. Rokas (2021). Dissecting incongruence between concatenation- and quartet-based approaches in phylogenomic data. Syst. Biol. 70: 997–1014.
  70. 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. (^Senior authors) Bioinformatics 37: 2325–2331.
  71. Li, Y., J. L. Steenwyk, Y. Chang, Y. Wang, T. Y. James, J. E. Stajich, J. W. Spatafora, M. Groenewald, C. W. Dunn, C. T. Hittinger, X.-X. Shen^, & A Rokas^ (2021). A genome-scale phylogeny of the kingdom Fungi. (^Senior authors) Curr. Biol. 31: 1653–1665.
    Cover article
  72. Wu, M.-Y.*, M. E. Mead*, M.-K. Lee, G. F. Neuhaus, D. A. Adpressa, J. I. Martien, Y.-E. Son, H. Moon, D. Amador-Noguez, K.-H. Han, A. Rokas, S. Loesgen, J.-H. Yu, H.-S. Park (2021). Transcriptomic, protein-DNA interaction, and metabolomic studies of VosA, VelB, and WetA in Aspergillus nidulans asexual spores. (*Equal contributors) mBio 12: e03128-20.
  73. Haase, M. A. B., J. Kominek, D. Opulente, X.-X. Shen, A. L. LaBella, X. Zhou, J. DeVirgilio, A. Hulfachor, C. P. Kurtzman, A. Rokas^, & C. T. Hittinger^ (2021). Repeated horizontal gene transfer of GALactose metabolism genes violates Dollo’s law of irreversible loss. (^Senior authors) Genetics 217: iyaa012.
  74. Benton, M. L., A. Abraham, A. L. LaBella, P. Abbot, A. Rokas, & J. A. Capra (2021). The influence of evolutionary history on human health and disease. Nature Rev. Genet. 22: 269–283.
  75. Rokas, A., S. Mesiano, O. Tamam, A. L. LaBella, G. Zhang, & L. J. Muglia (2020). Developing a theoretical evolutionary framework to solve the mystery of parturition initiation. eLife 9: e58343.
  76. Hatmaker, E. A.*, X. Zhou*, M. E. Mead, H. Moon, J.-H. Yu, & A. Rokas (2020). Revised transcriptome-based gene annotation for Aspergillus flavus strain NRRL 3357. (*Equal contributors) Microbiol. Resour. Announc. 9: e01155-20.
  77. 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 Biol. 18: e3001007.
  78. Shen, X.-X.^, Y Li, C. T. Hittinger, X. Chen, & A. Rokas^ (2020). An investigation of irreproducibility in maximum likelihood phylogenetic inference. (^Senior authors) Nature Comm. 11: 6096.
  79. Li, Y., K. T. David, X.-X. Shen, J. L. Steenwyk, K. M. Halanych, & A. Rokas (2020). Feature Frequency Profile-based phylogenies are inaccurate. Proc. Natl. Acad. Sci. USA 117: 31580-31581.
  80. 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) Sci. Adv. 6: eabd0079.
  81. 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) Microbiol. Resour. Announc. 9: e00856-20.
  82. 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 11: e02458-20.
  83. 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 216: 481-497.
    Cover article
  84. LaBella, A. L.*, A. Abraham*, Y. Pichkar, S. L. Fong, G. Zhang, L. J. Muglia, P. Abbot, A. Rokas^, & J. A. Capra^ (2020). Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. (*Equal contributors; ^Senior authors) Nature Comm. 11: 3731.
    The story behind the paper in Nature Research Ecology & Evolution Community’s blog
  85. 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. 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 Path. 16: e1008645.
  86. James, T. Y., J. E. Stajich, C. T. Hittinger, & A. Rokas (2020). Toward a fully resolved fungal tree of life. Ann. Rev. Microbiol. 74: 291–313.
  87. Steenwyk, J. L.*, A. L. Lind*, L. N. A. Ries, T. F. dos Reis, L. P. Silva, F. Almeida, R. W. Bastos, T. F. C. F. 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) Curr. Biol. 30: 2495–2507.
    Cover article
  88. 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 Biol. Evol. 12: 1119–1130.
  89. 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 authors) Front. Genet. 11: 459.
  90. Drott, M. T., R. W. Bastos, A. Rokas, L.N.A. Ries, T. Gabaldon, G. H. Goldman, N. P. Keller, & C. Greco (2020). Diversity of secondary metabolism in Aspergillus nidulans clinical isolates. mSphere 5: e00156-20.
  91. 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 5: e00153-20.
  92. 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 Path. 16: e1008315.
  93. Knowles, S. L., H. A. Raja, I. H. Isawi, L. C. Flores Bocanegra, P. H. Reggio, C. J. Pearce, J. E. Burdette, A. Rokas, & N. H. Oberlies (2020). Wheldone: Characterization of a unique scaffold from the co-culture of Aspergillus fischeri and Xylaria flabelliformis. Org. Lett. 22: 1878–1882.
  94. Libkind, D., D. Peris Navarro, F. Cubillos, J. L. Steenwyk, D. Opulente, Q. Langdon, A. Rokas, & C. T. Hittinger (2020). Into the wild: new yeast genomes from natural environments and new tools for their analysis. FEMS Yeast Research 20: foaa008.
  95. Knowles, S. J., M. E. Mead, L. Pereira Silva, H. A. Raja, J. L. Steenwyk, G. H. Goldman^, N. H. Oberlies^, & A. Rokas^ (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 11: e03361-19.
  96. 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 Rep. 37: 868–878.
  97. Zhou, X., S. Lutteropp, L. Czech, A. Stamatakis, M. von Looz, & A. Rokas (2020). Quartet-based computations of internode certainty provide accurate and robust measures of phylogenetic incongruence. Syst. Biol. 69: 308-324.
  98. Knowles, S. L., N. Vu, D. A. Todd, H. A. Raja, A. Rokas, Q. Zhang, & N. H. Oberlies (2019). Orthogonal method for double bond placement via ozone-induced dissociation mass spectrometry (OzID-MS). J. Nat. Prod. 82: 3421-3431. PDF
  99. 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 10: e02445-19. PDF
  100. 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. Microbiol. Resour. Announc. 8: e00890-19. (*Equal contributors; ^Senior authors) PDF
  101. Steenwyk, J. L. & A. Rokas (2019). treehouse: a user-friendly application to obtain subtrees from large phylogenies. BMC Res. Notes 12: 541. PDF
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  102. Ely, Z. A., J. M. Moon, G. R. Sliwoski, A. K. Sangha, X.-X. Shen, A. L. LaBella, J. Meiler, J. A. Capra, & A. Rokas (2019). The impact of natural selection on the evolution and function of placentally expressed galectins. Genome Biol. Evol. 11: 2574–2592. PDF
  103. Krassowski, T., J. Kominek, X.-X. Shen, D. A. Opulente, X. Zhou, A. Rokas, C. T. Hittinger, & K. H. Wolfe (2019). Multiple reinventions of mating-type switching during budding yeast evolution. Curr. Biol. 29: 2555–2562. PDF
    Commentary in Current Biology
  104. 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 15: e1008304. PDF
  105. dos Reis, T. F., L. P. Silva, P. A. de Castro, R. A. do Carmo, M. M. Marini, J. F. da Silveira, B. H. Ferreira, F. Rodrigues, A. L. Lind, A. Rokas, & G. H. Goldman (2019). The Aspergillus fumigatus mismatch repair MSH2 homologue is important for virulence and azole resistance. mSphere 4: e00416-19. PDF
  106. Moon, J. M., J. A. Capra, P. Abbot, & A. Rokas (2019). Immune regulation in eutherian pregnancy: Live birth co-evolved with novel immune genes and gene regulation. BioEssays 41: 1900072. PDF
  107. Moon, J. M., J. A. Capra, P. Abbot, & A. Rokas (2019). Signatures of recent positive selection in enhancers across 41 human tissues. G3 9: 2671-2774. PDF
  108. Steenwyk, J. L., X.-X. Shen, A. L. Lind, G. G. Goldman, &. A. Rokas (2019). A robust phylogenomic timetree for biotechnologically and medically important fungi in the genera Aspergillus and Penicillium. mBio 10: e00925-19. PDF
  109. Wang, M., H. Fu, X.-X. Shen, R. Ruan, A. Rokas, & H. Li (2019). Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata. Mol. Plant Pathol. 20: 1425–1438. PDF
  110. Steenwyk, J. L., D. A. 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. Hittinger^, & A. Rokas^ (2019). Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts. PLoS Biol. 17: e3000255. (^Senior authors) PDF
  111. Smith, S. P.*, J. B. Phillips*, M. L. Johnson, P. Abbot, J. A Capra, & A. Rokas (2019). Genome wide association analysis identifies genetic variants associated with reproductive variation across domestic dog breeds and uncovers links to domestication. (*Equal contributors) Evol. Med. Public Health 2019: 93-103. PDF
  112. Greco, C., N. P. Keller^, & A. Rokas^ (2019). Unearthing fungal chemodiversity and prospects for drug discovery. Curr. Opin. Microbiol. 51: 22-29. (^Senior authors) PDF
  113. Ries, L. N. A., J. L. Steenwyk, P. A. Castro, P. B. A. Lima, F. Almeida, L. J. Assis, A. O. Manfiolli, A. Takahashi-Nakaguchi, Y. Kusuya, D. Hagiwara, H. Takahashi, X. Wang, J. 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. Front. Microbiol. 10: 854. PDF
  114. Gao, S., S. E. Gold, J. H. Wisecaver, Y. Zhang, L. Guo, L.-J. Ma, A. Rokas, & A. E. Glenn (2019). Genome-wide analysis of Fusarium verticillioides reveals inter-kingdom contribution of horizontal gene transfer to the expansion of metabolism. Fungal Genet. Biol. 128: 60-73. PDF
  115. Kominek, J., D. T. Doering, D. A. Opulente, X.-X. Shen, X. Zhou, J. DeVirgilio, A. B. Hulfachor, M. Groenewald, M. A. Mcgee, S. D. Karlen, C. P. Kurtzman, A. Rokas, & C. T. Hittinger (2019). Eukaryotic acquisition of a bacterial operon. Cell 176: 1356-1366. PDF
    Commentary in Cell
  116. Wang, Y., X. Zhou, L. Wang, X. Liu, D. Yang, & A. Rokas (2019). Gene selection and evolutionary modeling affect phylogenomic inference of Neuropterida based on transcriptome data. Int. J. Mol. Sci. 20: 1072. PDF
  117. 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 4: e00018-19. PDF
  118. 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. Front. Microbiol. 10: 285. PDF
  119. 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. (*Equal contributors; ^Senior authors) Cell 175: 1533-1545. PDF
    The story behind the paper in Nature Research Ecology & Evolution Community’s blog
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  120. Eidem, H. R., J. L. Steenwyk, J H. 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 11: 107. PDF
  121. Segal, E. S., V. Gritsenko, A. Levitan, B. Yadav, B, 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 9: e02048-18. PDF
  122. Krause, D. J., J. Kominek, D. A. Opulente, X.-X. Shen, X. Zhou, Q. K. Langdon, J. DeVirgilio, A. B. Hulfachor, C. P. Kurtzman, A. Rokas, & C. T. Hittinger (2018). Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts. Proc. Natl. Acad. Sci. USA 115: 11030-11035. PDF
  123. Rokas, A., J. H. Wisecaver, & A. L. Lind (2018). The birth, evolution, and death of metabolic gene clusters in fungi. Nature Rev. Microbiol. 16: 731–744. PDF
  124. Sirota, M., C. G. Thomas, R. Liu, M. Zuhl, P. Banerjee, R. J. Wong, C. C. Quaintance, R. Leite, J. Chubiz, R. Anderson, J. Chappelle, M. Kim, W. Grobman, G. Zhang, A. Rokas, L. Muglia, C. Ober, S. K. England, G. Marcones, S. Parry, G. M. Shaw, D. K. Stevenson, J. L. Simpson, E. Thomson, & A. J. Butte (2018). Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Scientific Data 5: 180219. PDF
  125. Shi, R., X.-X. Shen, A. Rokas, & B. F. Eichman (2018). Structural biology of the HEAT-like repeat family of DNA glycosylases. BioEssays 40: 1800133. PDF
  126. Wu, M.-Y.*, M. E. Mead*, M.-K. Lee, E. M. Ostrem Loss, S. C. Kim, A. Rokas, & J.-H. Yu (2018). Systematic dissection of the evolutionarily conserved WetA developmental regulator across a genus of filamentous fungi. (*Equal contributors) mBio 9: e01130-18. PDF
  127. Huusko, J. M., M. K. Karjalainen, B. E. Graham, G. Zhang, E. G. Farrow, N. A. Miller, B. Jacobsson, H. R. Eidem, J. C. Murray, B. Bedell, F. L. Bødker, N. K. Litterman, P.-P. Jiang, L. Russell, D. A. Hinds, Y. Hu, the 23andMe Research Team, A. Rokas, K. Teramo, K. Christensen, S. M. Williams, M. Rämet, S. F. Kingsmore, K. K. Ryckman, M. Hallman, & L. J. Muglia (2018). Whole exome sequencing reveals HSPA1L as a genetic risk factor for spontaneous preterm birth. PLoS Genet. 14: e1007394. PDF
  128. Lim, F. Y., T. H. Won, N. Raffa, J. A. Baccile, J. H. Wisecaver, A. Rokas, F. Schroeder, & N. P. Keller (2018). Fungal isocyanide synthases and xanthocillin biosynthesis in Aspergillus fumigatus. mBio 9: e00785-18. PDF
  129. Krassowski, T., A. Y. Coughlan, X.-X. Shen, X. Zhou, J. Kominek, D. A. Opulente, R. Riley, I. V. Grigoriev, N. Maheshwari, D. C. Shields, C. P. Kurtzman, C. T. Hittinger, A. Rokas, & K. H. Wolfe (2018). Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nature Comm. 9: 1887. PDF
  130. Gonçalves, C., J. H. Wisecaver, J. Kominek, M. Salema-Oom, M. J. Leandro, X.-X. Shen, D. Opulente, X. Zhou, D. Peris, C. P. Kurtzman, C. T. Hittinger, A. Rokas, & P. Gonçalves (2018). Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage. eLife 7: e33034. PDF
  131. Lind, A. L., F. Y. Lim, A. Soukup, N. P. Keller, & A. Rokas (2018). A LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus. mSphere 3: e00050-18. PDF
  132. Moon, J. M., D. M. Aronoff, J. A. Capra, P. Abbot, & A. Rokas (2018). Genes involved in human sialic acid biology do not harbor signatures of recent positive selection. G3 8: 1315-1325. PDF
  133. Opulente, D. A., E. J. Rollinson, C. Bernick-Roehr, A. B. Hulfachor, A. Rokas, C. P. Kurtzman, C. T. Hittinger (2018). Factors driving metabolic diversity in the budding yeast subphylum. BMC Biol. 16: 26. PDF
  134. Fidler, A. L., S. P. Boudko, A. Rokas, & B. G. Hudson (2018). The triple helix of collagens: an ancient protein structure that enabled animal multicellularity and tissue evolution. J. Cell Sci. 131: jcs203950. PDF
  135. Steenwyk, J. L. & A. Rokas (2018). Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation. Front. Microbiol. 9: 288. PDF
  136. K. Y. B. Lamm, M. L. Johnson, J. B. Phillips, M. B. Muntifering, J. M. James, H. N. Jones, R. W. Redline, A. Rokas, & L. J. Muglia (2018). Inverted formin 2 regulates intracellular trafficking, placentation, and pregnancy outcome. eLife 7: e31150. PDF
  137. Zhou, X., X.-X. Shen, C. T. Hittinger, & A. Rokas (2018). Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets. Mol. Biol. Evol. 35: 486-503. PDF
  138. Shi, R., E. A. Mullins, X.-X. Shen, K. T. Lay, P. K. Yuen, S. S. David, A. Rokas, & B. F. Eichman (2018). Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC. EMBO J. 37: 63-74. PDF
  139. Lind, A. L., J. H. Wisecaver, C. Lameiras, P. Wiemann, J. M. Palmer, N. P. Keller, F. Rodrigues, G. H. Goldman, & A. Rokas (2017). Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species. PLoS Biol. 15: e2003583. PDF
  140. King, N. & A. Rokas (2017). Embracing uncertainty in early animal evolution. Curr. Biol. 27: R1081–R1088. PDF
  141. Lojek, L. J., A. J. Farrand, J. H. Wisecaver, C. E. Blaby-Haas, S. S. Merchant, A. Rokas, & E. P. Skaar (2017). Chlamydomonas reinhardtii cMO is an IsdG family heme oxygenase. mSphere 2: e00176-17. PDF
  142. Eidem, H. R.*, K. L. McGary*, J. A. Capra, P. Abbot, & A. Rokas (2017). The transformative potential of an integrative approach to pregnancy. (*Equal contributors) Placenta 57: 204–215. PDF
  143. Valsecchi, I., O. Sarikayabayram, J. Wong Sak Hoi, L. Muszkieta, J. Gibbons, M.-C. Prevost, A. Mallet, J. Krijnse-Locker, O. Granet, I. Mouyna, P. Carr, M. Bromley, V. K. Aimanianda, J.-H. Yu, A. Rokas, G. Braus, C. Saveanu, O. Bayram, & J.-P. Latgé (2017). MybAp, a transcription factor involved in conidiation and conidial viability of the human pathogen Aspergillus fumigatus. Mol. Microbiol. 105: 880-900. PDF
  144. Wu, M.-Y., M. E. Mead, S.-C. Kim, A. Rokas, & J.-H. Yu (2017). WetA bridges cellular and chemical development in Aspergillus flavus. PLoS ONE 12: e0179571. PDF
  145. Zhao, L., X. Zhou, A. Rokas, & R. D. Cone (2017). Functional variants of the melanocortin-4 receptor associated with the Odontoceti and Mysticeti suborders of cetaceans. Sci. Rep. 7: 5684. PDF
  146. Fidler, A. L., C. E. Darris, S. V. Chetyrkin, V. K. Pedchenko, S. P. Boudko, K. L. Brown, W. G. Jerome, J. K. Hudson, A. Rokas, & B. G. Hudson (2017). Collagen IV and basement membrane at the evolutionary dawn of metazoan tissues. eLife 6: e24176. PDF
  147. Wisecaver, J. H., A. T. Borowsky, V. Tzin, G. Jander, D. J. Kliebenstein, & A. Rokas (2017). A global co-expression network approach for connecting genes to specialized metabolic pathways in plants. The Plant Cell 29: 944–959. PDF
    Commentary in The Plant Cell
  148. Shen, X.-X., C. T. Hittinger, & A. Rokas (2017). Contentious relationships in phylogenomic studies can be driven by a handful of genes. Nature Ecol. Evol. 1: 0126. PDF
    The story behind the paper in Nature Research Ecology & Evolution Community’s blog
    Download data
  149. Steenwyk, J. & A. Rokas (2017). Extensive copy number variation in fermentation-related genes among Saccharomyces cerevisiae wine strains. G3 7: 1475-1485. PDF
  150. Ortiz, J. F. & A. Rokas (2017). CTDGFinder: A novel homology-based algorithm for identifying closely spaced clusters of tandemly duplicated genes. Mol. Biol. Evol. 34: 215-229. PDF
    Download CTDGFinder
  151. Lind, A. L., T. Satterlee, T. D. Smith, A. M. Calvo, & A. Rokas (2016). Regulation of secondary metabolism by the Velvet complex is temperature-responsive in Aspergillus. G3 6: 4023-4033. PDF
  152. Shen, X.-X., X. Zhou, J. Kominek, C. P. Kurtzman, C. T. Hittinger, & A. Rokas (2016). Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3 6: 3927-3939. PDF
  153. Zhou, X., D. Peris, C. T. Hittinger, & A. Rokas (2016). in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies. G3 6: 3655-3662. PDF
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  154. Shen, X.-X., L. Salichos, & A. Rokas (2016). A genome-scale investigation of how sequence-, function-, and tree-based gene properties influence phylogenetic inference. Genome Biol. Evol. 8: 2565–2580. PDF
  155. Riley, R., S. Haridas, K. H. Wolfe, M. R. Lopes, C. T. Hittinger, M. Göker, A. Salamov, J. H. Wisecaver, T. M. Long, C. H. Calvey, A. L. Aerts, K. Barry, C. Choi, A Clum, A. Y. Coughlan, S. Deshpande, A. P. Douglass, S. J. Hanson, H.-P. Klenk, K. LaButti, A. Lapidus, E. Lindquist, A. Lipzen, J. P. Meier-Kolthoff, R. A. Ohm, R. P. Otillar, J. Pangilinan, Y. Peng, A. Rokas, C. A. Rosa, C. Scheuner, A. A. Sibirny, J. C. Slot, J. B. Stielow, H. Sun, C. P. Kurtzman, M. Blackwell, I. V. Grigoriev, & T. W. Jeffries (2016). Comparative genomics of biotechnologically important yeasts. Proc. Natl. Acad. Sci. USA 113: 9882–9887. PDF
  156. Ackerman IV, W. E., I. A. Buhimschi, H. R. Eidem, D. C. Rinker, A. Rokas, K. Rood, G. Zhao, T. L. Summerfield, M. B. Landon, & C. S. Buhimschi (2016). Comprehensive RNA profiling of villous trophoblast and decidua basalis in pregnancies complicated by preterm birth following intra-amniotic infection. Placenta 44: 23-33. PDF
  157. Wisecaver, J. H., W. G. Alexander, S. B. King, C. T. Hittinger, & A. Rokas (2016). Dynamic evolution of nitric oxide detoxifying flavohemoglobins, a family of single-protein metabolic modules in bacteria and eukaryotes. Mol. Biol. Evol. 33: 1979–1987. PDF
  158. Eidem, H. R., D. C. Rinker, W. E. Ackerman IV, I. A. Buhimschi, C. S. Buhimschi, C. Dunn-Fletcher, S. G. Kallapur, M. Pavlicev, L. J. Muglia, P. Abbot, & A. Rokas (2016). Comparing human and macaque placental transcriptomes to disentangle preterm birth pathology from gestational age effects. Placenta 41: 74-82. PDF
  159. Alexander, W. G., J. H. Wisecaver, A. Rokas, & C. T. Hittinger (2016). Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proc. Natl. Acad. Sci. USA 113: 4116–4121. PDF
  160. Kobert, K., L. Salichos, A. Rokas, & A. Stamatakis (2016). Computing the Internode Certainty and related measures from partial gene trees. Mol. Biol. Evol. 33: 1606-1617. PDF
  161. Staehlin, B. M., J. G. Gibbons, A. Rokas, T. V. O’Halloran, & J. C. Slot (2016). Evolution of a heavy metal homeostasis/resistance island reflects increasing copper stress in Enterobacteria. Genome Biol. Evol. 8: 811-826. PDF
  162. Kim, M., B. A. Cooper, R. Venkat, J. B. Phillips, H. R. Eidem, J. Hirbo, S. Nutakki, S. M. Williams, L. J. Muglia, J. A. Capra, K. Petren, P. Abbot, A. Rokas, & K. L. McGary (2016). GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. Nucleic Acids Res. 44, Database issue: D908-916. PDF
  163. Wang, Y., X. Zhou, D. Yang, & A. Rokas (2015). A genome-scale investigation of incongruence in Culicidae mosquitoes. Genome Biol. Evol. 7: 3463-3471. PDF
  164. Hirbo, J., H. R. Eidem, A. Rokas, & P. Abbot (2015). Integrating diverse types of genomic data to identify genes that underlie adverse pregnancy phenotypes. PLoS ONE 10: e0144155. PDF
  165. Hittinger, C. T., A. Rokas, F.-Y. Bai, T. Boekhout, P. Gonçalves, T. W. Jeffries, J. Kominek, M.-A. Lachance, D. Libkind, C. A. Rosa, J. P. Sampaio, & C. P. Kurtzman (2015). Genomics and the making of yeast biodiversity. Curr. Opin. Genet. Dev. 35: 100–109. PDF
  166. Zhou, X., A. Rokas, S. L. Berger, J. Liebig, A. Ray, & L. J. Zwiebel (2015). Chemoreceptor evolution in Hymenoptera and its implications for the evolution of eusociality. Genome Biol. Evol. 7: 2407-2416. PDF
  167. Phillips, J. B., P. Abbot, & A. Rokas (2015). Is preterm birth a human-specific syndrome? Evol. Med. Public Health 2015: 136-148. PDF
  168. Eidem, H. R., W. E. Ackerman IV, K. L. McGary, P. Abbot, & A. Rokas (2015). Gestational tissue transcriptomics in term and preterm human pregnancies: A systematic review and meta-analysis. BMC Med. Genomics 8: 27. PDF
  169. Lind, A. L., J. H. Wisecaver, T. D. Smith, X. Feng, A. M. Calvo, & A. Rokas (2015). Examining the evolution of the regulatory circuit controlling secondary metabolism and development in the fungal genus Aspergillus. PLoS Genet. 11: e1005096. PDF
    Aspergillus fumigatus data in FungiDB
    Aspergillus nidulans data in FungiDB
  170. Wisecaver, J. H., & A. Rokas (2015). Fungal metabolic gene clusters – caravans traveling across genomes and environments. Front. Microbiol. 6: 161. PDF
  171. Eidem, H. R.*, K. L. McGary*, & A. Rokas (2015). Shared selective pressures on fungal and human metabolic pathways lead to divergent yet analogous genetic responses. (*Equal contributors) Mol. Biol. Evol. 32: 1449–1455. PDF
  172. Elmore, M. H.*, K. L. McGary*, J. H. Wisecaver, J. C. Slot, D. M. Geiser, S. Sink, K. O’Donnell, & A. Rokas (2015). Clustering of two genes putatively involved in cyanate detoxification evolved recently and independently in multiple fungal lineages. (*Equal contributors) Genome Biol. Evol. 7: 789-800. PDF
  173. Neafsey, D. E., R. M. Waterhouse, 117 other authors including X. Zhou, D. C. Rinker, A. Rokas and L. J. Zwiebel, & N. J. Besansky (2015). Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science 347: 43. PDF
    Commentary in Science
    Cover article
    Commentary in Nature Genetics
  174. Wisecaver, J. H.*, J. C. Slot*, & A. Rokas (2014). The evolution of fungal metabolic pathways. (*Equal contributors) PLoS Genet. 10: e1004816. PDF
  175. Zhou, X.*, D. C. Rinker*, R. J. Pitts, A. Rokas, and L. J. Zwiebel (2014). Divergent and conserved elements comprise the chemoreceptive repertoire of the non-blood feeding mosquito Toxorhynchites amboinensis. (*Equal contributors) Genome Biol. Evol. 6: 2883-2896. PDF
  176. Polzin, K. and A. Rokas (2014). Evaluating rare amino acid substitutions (RGC_CAMs) in a yeast model clade. PLoS ONE 9: e92213. PDF
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  177. Salichos, L., A. Stamatakis, and A. Rokas (2014). Novel information theory-based measures for quantifying incongruence among phylogenetic trees. Mol. Biol. Evol. 31: 1261-1271. PDF
  178. Zhou, X. and A. Rokas (2014). Prevention, diagnosis, and treatment of high throughput sequencing data pathologies. Mol. Ecol. 23: 1679-1700. PDF
  179. Soria, P. S.*, K. L. McGary*, and A. Rokas (2014). Functional divergence for every paralog. (*Equal contributors) Mol. Biol. Evol. 31: 984-992. PDF
  180. Greene, G. H., K. L. McGary, A. Rokas, and J. C. Slot (2014). Ecology drives the distribution of specialized tyrosine metabolism modules in fungi. Genome Biol. Evol. 6: 121-132. PDF
  181. Samuels, D. C., C. Li, B. Li, Z. Song, E. Torstenson, H. B. Clay, A. Rokas, T. Thornton-Wells, J. H. Moore, T. Hughes, R. Hoffman, J. L. Haines, D. G. Murdock, D. P. Mortlock, and S. M. Williams (2013). Recurrent tissue-specific mtDNA mutations are common in humans. PLoS Genetics 9: e1003929. PDF
  182. Rinker, D. C.*, X. Zhou*, R. J. Pitts, The AGC Consortium, A. Rokas, and L. J. Zwiebel (2013). Antennal transcriptome profiles of anopheline mosquitoes reveal human host olfactory specialization in Anopheles gambiae. (*Equal contributors) BMC Genomics 14: 749. PDF
  183. Dhingra, S., A. L. Lind, H-C. Lin, Y. Tang, A. Rokas, and A. M. Calvo (2013). The fumagillin gene cluster, an example of hundreds of genes under veA control in Aspergillus fumigatus. PLoS ONE 8: e77147. PDF
  184. Campbell, M. A., M. Staats, J. L. A. van Kan, A. Rokas, and J. C. Slot (2013). Repeated loss of an anciently horizontally transferred gene cluster in Botrytis. Mycologia 105: 1126–1134. PDF
  185. McGary, K. L., J. C. Slot, and A. Rokas (2013). The physical linkage of metabolic genes in fungi is an adaptation against the accumulation of toxic intermediate compounds. Proc. Natl. Acad. Sci. USA 110: 11481–11486. PDF
  186. Predazzi, I. M., A. Rokas, A. Deinard, N. Schnetz-Boutaud, N. D. Williams, W. S. Bush, A. Tacconelli, K. Friedrich, S. Fazio, G. Novelli, J. L. Haines, G. Sirugo, and S. M. Williams (2013). Putting pleiotropy and selection into context defines a new paradigm for interpreting genetic data. Circ. Cardiovasc. Genet. 6: 299-307. PDF
  187. Salichos, L., and A. Rokas (2013). Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-331. PDF
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  188. Rinker, D. C., R. J. Pitts, X. Zhou, E. Suh, A. Rokas, and L. J. Zwiebel (2013). Blood meal-induced changes to antennal transcriptome profiles reveal shifts in odor sensitivities in the malaria vector mosquito Anopheles gambiae. Proc. Natl. Acad. Sci. USA 110: 8260-8265. PDF
    Cover article
  189. Bradshaw, R. E., J. C. Slot, G. G. Moore, P. Chettri, P. J. G. M. de Wit, K. C. Ehrlich, A. R. D. Ganley, M. A. Olson, A Rokas, I. Carbone, and M. P. Cox (2013). Fragmentation of an aflatoxin-like gene cluster in a forest pathogen. New Phytol. 198: 525–535. PDF
  190. Xu, Y., P. Ma, P. Shah, A. Rokas, Y. Liu, and C. H. Johnson (2013). Non-optimal codon usage is a post-transcriptional mechanism to achieve conditionality of circadian clock function. Nature 495: 116-120. PDF
    Commentary in Nature
    Commentary in Nature Reviews Microbiology
  191. Adhikary, S., M. C. Cato, K. L. McGary, A. Rokas, and B. F. Eichman (2013). Non-productive DNA damage binding by DNA glycosylase-like protein Mag2 from Schizosaccharomyces pombe. DNA Repair 12: 196-204. PDF
  192. Muszkieta, L., A. Beauvais, V. Pähtz, J. G. Gibbons, V. A. Leberre, R. Beau, K. Shibuya, A. Rokas, J. M. Francois, O. Kniemeyyer, A. A. Brakhage, and J.-P. Latge (2013). Investigation of Aspergillus fumigatus biofilm formation by various “omics” approaches. Front. Microbiol. 4: 13. PDF
  193. Ubaida Mohien, C., D. R. Colquhoun, D. K. Mathias, J. G. Gibbons, J. S. Armistead, M. del Carmen-Rodriguez, M. H. Rodriguez, N. J. Edwards, J. Hartler, G. G. Thallinger, D. R. Graham, J. Martinez-Barnetche, A. Rokas, and R. R. Dinglasan (2013). A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites. Mol. Cell. Proteomics 12: 120-131. PDF
  194. Gibbons, J. G., and A. Rokas (2013). The function and evolution of the Aspergillus genome. Trends Microbiol. 21: 14-22. PDF
  195. Rokas, A., J. G. Gibbons, X. Zhou, A. Beauvais, and J.-P. Latge (2012). The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus. Ann. N. Y. Acad. Sci. 1273: 25-34. PDF
  196. Elmore, M. H.*, J. G. Gibbons*, and A. Rokas (2012). Assessing the genome-wide effect of promoter region tandem repeat natural variation on gene expression. (*Equal contributors) G3 2: 1643-1649. PDF
  197. Zhou, X.*, J. D. Slone*, A. Rokas, S. L. Berger, J. Liebig, A. Ray, D. Reinberg, and L. J. Zwiebel (2012). Phylogenetic and transcriptomic analysis of chemosensory receptors in a pair of divergent ant species reveals sex-specific signatures of odor coding. (*Equal contributors) PLoS Genet. 8: e1002930. PDF
  198. League, G. P., J. C. Slot, and A. Rokas (2012). The ASP3 locus in Saccharomyces cerevisiae originated by horizontal gene transfer from Wickerhamomyces. FEMS Yeast Res. 12: 859-863. PDF
  199. Zhang, H., A. Rokas, and J. C. Slot (2012). Two different secondary metabolism gene clusters occupied the same ancestral locus in fungal dermatophytes of the Arthrodermataceae. PLoS ONE 7: e41903. PDF
  200. Gibbons, J. G., L. Salichos, J. C. Slot, D. C. Rinker, K. L. McGary, J. G. King, M. A. Klich, D. L. Tabb, W. H. McDonald, and A. Rokas (2012). The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Curr. Biol. 22: 1403-1409. PDF
    Retrieve sequence alignment data
    Dataset of the Week, The Global Proteome Machine
  201. Stergiopoulos, I., Y. A. I. Kourmpetis, J. C. Slot, F. T. Bakker, P. J. G. M. De Wit, and A. Rokas (2012). In silico characterization and molecular evolutionary analysis of a novel superfamily of fungal effector proteins. Mol. Biol. Evol. 29: 3371-3384. PDF
  202. Floudas, D., M. Binder, 68 other authors including A. Rokas and J. C. Slot, and D. S. Hibbett (2012). The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336: 1715-1719. PDF
    Commentary in Science
  203. Martínez-Barnetche, J., R. E. Gómez-Barreto, M. Ovilla-Muñoz, J. Téllez-Sosa, D. E. García López, R. R. Dinglasan, C. Ubaida-Mohien, R. M. MacCallum, S. N. Redmond, J. G. Gibbons, A.Rokas, C. A. Machado, F. Cazares-Raga, L. González-Cerón, S. Hernández-Martínez, and M. H. Rodríguez López (2012). Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. BMC Genomics 13: 207. PDF
  204. Wei, C., L. Salichos, C. M. Wittgrove, A. Rokas, and J. G. Patton (2012). Transcriptome-wide analysis of small RNA expression in early zebrafish development. RNA 18: 915-929. PDF
  205. Campbell, M. A., A. Rokas, and J. C. Slot (2012). Horizontal transfer and death of a fungal secondary metabolic gene cluster. Genome Biol. Evol. 4: 289-293. PDF
  206. Klaassen,C. H. W.*, J. G. Gibbons*, N. D. Fedorova, J. F. Meis, and A. Rokas (2012). Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus. (*Equal contributors) Mol. Ecol. 21: 57-70. PDF
  207. Gibbons, J. G., A. Beauvais, R. Beau, K. L. McGary, J.-P. Latge, and A. Rokas (2012). Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. Euk. Cell 11: 68-78. PDF
    Cover article
    Spotlight
  208. Rokas, A. (2011). Phylogenetic analysis of protein sequence data using the Randomized Axelerated Maximum Likelihood (RAxML) program. Curr. Prot. Mol. Biol. 96:19.11.1-19.11.14. PDF
  209. Pitts, R. J.*, D. C Rinker*, P. L. Jones*, A. Rokas, and L. J. Zwiebel (2011). Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding. (*Equal contributors) BMC Genomics 12: 271. PDF
  210. Scannell, D. R., O. A. Zill, A. Rokas, C. Payen, M. J. Dunham, M. B. Eisen, J. Rine, M. Johnston, C. T. Hittinger (2011). The awesome power of yeast evolutionary genetics: New genome sequences and strain resources for the Saccharomyces sensu stricto genus. G3 1: 11-25. PDF
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  211. Salichos, L., and A. Rokas (2011). Evaluating ortholog prediction algorithms in a yeast model clade. PLoS ONE 6: e18755. PDF
    Retrieve cRBH script
  212. Slot, J. C. and A. Rokas (2011). Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi. Curr. Biol. 21: 134-139. PDF

    Cover article
    Video abstract
    Commentary in Current Biology
  213. Kent, B. N., L. Salichos, J. G. Gibbons, A. Rokas, I. L. G. Newton, M. E. Clark, and S. R. Bordenstein (2011). Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture. Genome Biol. Evol. 3: 209-218. PDF
    Cover article
  214. Carnahan, R. H.*, A. Rokas*, E. A. Gaucher, and A. B. Reynolds (2010). The molecular evolution of the p120-catenin subfamily and its functional associations. (*Equal contributors) PLoS ONE 5: e15747. PDF
  215. Slot, J. C. and A. Rokas (2010). Multiple GAL pathway gene clusters evolved independently and by different mechanisms in fungi. Proc. Natl. Acad. Sci. USA 107: 10136-10141. PDF
  216. Hittinger, C. T., P. Gonçalves, J. P. Sampaio, J. Dover, M. Johnston and A. Rokas (2010). Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature 464: 54-58. PDF
    Commentary in Nature Reviews Genetics
  217. Salichos, L. and A. Rokas (2010). The diversity and evolution of circadian clock proteins in fungi. Mycologia 102: 269-278. PDF
  218. Gibbons, J. G., M. A. Klich and A. Rokas (2010). Developing highly conserved microsatellite markers: a case study in the filamentous fungal genus Aspergillus. Mol. Ecol. Resources 10: 404-408.
    Summary article: PDF
    Full article: PDF
  219. Hittinger, C. T., M. Johnston, J. T. Tossberg and A. Rokas (2010). Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc. Natl. Acad. Sci. USA 107: 1476-1481. PDF
    Biotechniques article
    UCD advocate article
  220. Gibbons, J. G., E. Janson, C. T. Hittinger, M. Johnston, P. Abbot and A. Rokas (2009).
    Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol. Biol. Evol. 26: 2731-2744. PDF
  221. Rokas, A. and P. Abbot (2009). Harnessing genomics for evolutionary insights. Trends Ecol. Evol. 24: 192-200. PDF
  222. Gibbons, J. G. and A. Rokas (2009). Comparative and functional characterization of intragenic tandem repeats in ten Aspergillus genomes. Mol. Biol. Evol. 26: 591-602. PDF
  223. Rokas, A. (2009). The effect of domestication on the fungal proteome. Trends Genet. (Genome Analysis section) 25: 60-63. PDF
  224. Rokas, A. (2008). The molecular origins of multicellular transitions. Curr. Opin. Genet. Dev. 18: 472-478. PDF
  225. Rokas, A. (2008). The origins of multicellularity and the early history of the genetic toolkit for animal development. Ann. Rev. Genet. 42: 235-251. PDF
  226. Rokas, A., and S. B. Carroll (2008). Frequent and widespread parallel evolution of protein sequences. Mol. Biol. Evol.25: 1943-1953. PDF
  227. Mathee, K., G. Narasimhan, C. Valdes, X. Qiu, J. M. Matewish, M. Koehrsen, A. Rokas, C. N. Yandava, R. Engels, E. Zeng, R. Olavarietta, M. Doud, R. S. Smith, P. Montgomery, J. R. White, P. A. Godfrey, C. Kodira, B. Birren, J. E. Galagan, and S. Lory (2008). Dynamics of Pseudomonas aeruginosa genome evolution. Proc. Natl. Acad. Sci. USA 105: 3100-3105. PDF
  228. King, N., M. J. Westbrook, S. L. Young, A. Kuo, M. Abedin, J. Chapman, S. Fairclough, U. Hellsten, Y. Isogai, I. Letunic, M. Marr, D. Pincus, N. Putnam, A. Rokas, K. J. Wright, R. Zuzow, W. Dirks, M. Good, D. Goodstein, D. Lemons, W. Li, J. Lyons, A. Morris, S. Nichols, D. J. Richter, A. Salamov, JGI Sequencing, P. Bork, W. A. Lim, G. Manning, W. T. Miller, W. McGinnis, H. Shapiro, R. Tjian, I. V. Grigoriev, and D. Rokhsar (2008). The genome of the choanoflagellate Monosiga brevicollis and the origins of metazoan multicellularity. Nature 451: 783-788.PDF
  229. Stone, G. N., R. J. Atkinson, A. Rokas, J.-L.Nieves-Aldrey, G. Melika, Z. Acs, G. Csóka, A. Hayward, R. Bailey, C. Buckee and G. A. T. McVean (2008). Evidence for widespread cryptic sexual generations in apparently purely asexual Andricus gallwasps. Mol. Ecol. 17: 652-665. PDF
    Cover article
  230. Rokas, A., G. Payne, N.D. Fedorova, S.E. Baker, M. Machida, J. Yu, D. R. Georgianna, R. A. Dean, D. Bhatnagar, T.E. Cleveland, J.R. Wortman, R. Maiti, V. Joardar, P. Amedeo, D.W. Denning and W.C. Nierman (2007). What can comparative genomics tell us about species concepts in the genus Aspergillus? Studies in Mycology 59: 11-17. PDF
  231. Stone, G. N., R. J. Challis, R. J. Atkinson, G. Csóka, A. Hayward, G. Melika, S. Mutun, S. Preuss, A. Rokas, E. Sadeghi, and K. Schönrogge (2007). The phylogeographic clade trade: Tracing the impact of human-mediated dispersal on the colonisation of northern Europe by the oak gallwasp Andricus kollari. Mol. Ecol. 16: 2768-2781. PDF
  232. Challis, R. J., S. Mutun, J.-L. Nieves-Aldrey, S. Preuss, A. Rokas, A. Aebi, E. Sadeghi, M. Tavakoli, and G. N. Stone (2007). Longitudinal range expansion and cryptic eastern species in the western Palaearctic oak gallwasp Andricus coriarius. Mol. Ecol. 16: 2103-2114. PDF
  233. Ane, C., B. Larget, D. A. Baum, S. D. Smith, and Rokas, A. (2007). Bayesian estimation of concordance among gene trees. Mol. Biol. Evol.: 24: 412-426. PDF
  234. Rokas, A. and S. B. Carroll (2006). Bushes in the Tree of Life. PLOS Biology: 4: e352. PDF
  235. Jeong, S., A. Rokas and S. B. Carroll (2006). Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution. Cell 125: 1387-1399. PDF
  236. Prud’homme, B., N. Gompel, A. Rokas, V. A. Kassner, T. M. Williams, S.-D. Yeh, J. R. True and S. B. Carroll (2006). Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature 440: 1050-1053. PDF

    Commentary in Nature
    Science Daily article
  237. Rokas, A., D. Krueger and S. B. Carroll (2005). Animal evolution and the molecular signature of radiations compressed in time. Science 310: 1933-1938. PDF
  238. Rokas, A. and S. B. Carroll (2005). More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22: 1337-1344. PDF
    Retrieve data
  239. Hittinger, C. T., A. Rokas and S. B. Carroll (2004). Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc. Natl. Acad. Sci. USA 101: 14144-14149. PDF
    Commentary in Heredity
  240. Rokas, A.*, B. L. Williams*, N. King and S. B. Carroll (2003). Genome-scale approaches to resolving incongruence in molecular phylogenies. (*Equal contributors) Nature 425: 798-804. PDF

    Retrieve data
    Commentary in Nature
  241. Rokas, A., E. Ladoukakis, and E. Zouros (2003). Animal mitochondrial DNA recombination revisited. Trends Ecol. Evol. 18: 411-417. PDF
  242. Rokas, A., R. J. Atkinson, L. W. I. Webster and G. N. Stone (2003). Out of Anatolia: Longitudinal gradients in genetic diversity support a Turkish origin for a circum-mediterranean oak gallwasp Andricus quercustozae. Mol. Ecol. 12: 2153-2174. PDF
  243. Cummings, M. P., S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas and K. Winka (2003). Comparing bootstrap and posterior probability values in the four taxon case. Syst. Biol. 52: 477-487. PDF
  244. Rokas, A.*, N. King*, J. R. Finnerty and S. B. Carroll (2003). Conflicting phylogenetic signals at the base of the metazoan tree. (*Equal contributors) Devel. Evol. 5: 346-359. PDF

    Cover article
  245. Rokas, A., G. Melika, Y. Abe, J.-L. Nieves-Aldrey, J. M. Cook and G. N. Stone (2003). Lifecycle closure, lineage sorting, and hybridization revealed in a phylogenetic analysis of European oak gallwasps (Hymenoptera: Cynipidae: Cynipini) using mitochondrial sequence data. Mol. Phylog. Evol. 26: 36-45. PDF
  246. Cook, J. M., A. Rokas, M. Pagel and G. N. Stone (2002). Evolutionary shifts between host oak species and host plant organs in Andricus gallwasps. Evolution 56: 1821-1830. PDF
  247. Rokas, A., R. J. Atkinson, J.-L. Nieves-Aldrey, S. A. West and G. N. Stone (2002).
    The incidence and diversity of Wolbachia in gallwasps (Hymenoptera; Cynipidae) on oak. Mol. Ecol. 11: 1815-1829. PDF
  248. Rokas, A., J. A. A. Nylander, F. Ronquist and G. N. Stone (2002). A maximum likelihood analysis of eight phylogenetic markers in gallwasps (Hymenoptera: Cynipidae); implications for insect phylogenetic studies. Mol. Phylog. Evol. 22: 206-219. PDF
  249. Stone, G. N., R. J. Atkinson, G. Brown and A. Rokas (2002). The population genetic consequences of range expansion: a review of pattern and process, and the value of oak gallwasps as a model system. Biodiversity Science: 10: 80-97. PDF
  250. Rokas, A., R. J. Atkinson, G. S. Brown, S. A. West and G. N. Stone (2001). Understanding patterns of genetic variation in the oak gallwasp Biorhiza pallida: demographic history or a Wolbachia selective sweep? Heredity 87: 294-304. PDF
  251. Stone, G. N., R. J. Atkinson, A. Rokas, G. Csoka and J.-L. Nieves-Aldrey (2001). Differential success in northwards range expansion between ecotypes of the marble gallwasp Andricus kollari: a tale of two refugia. Mol. Ecol. 10: 761-778. PDF
  252. Rokas, A. and P. W. H. Holland (2000). Rare genomic changes as a tool for phylogenetics. Trends Ecol. Evol. 15: 454-459. PDF
    Cover article
  253. Averof, M., A. Rokas, K. H. Wolfe and P. M. Sharp (2000). Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science 287: 1283-1286. PDF
  254. Rokas, A., J. Kathirithamby and P. W. H. Holland (1999). Intron insertion as a phylogenetic character: the engrailed homeobox of Strepsiptera does not indicate affinity with Diptera. Insect Mol. Biol. 8: 527-530. PDF

Edited Volumes

  1. Rokas, A., & P. S. Soltis, Eds. (2015). Special issue on Genomes and Evolution.
    Curr. Opin. Genet. Dev., volume 35: 1-126.
    PDF

Book Chapters

  1. Strullu-Derrien, C., A. Rokas, T. Y. James, & M. Berbee (2024). Fungal evolution: aquatic–terrestrial transitions. In: (Eds.) Encyclopedia of Evolutionary Biology, 2nd edition, Elsevier. In press.
  2. Gonçalves, C., C. T. Hittinger, & A. Rokas (2024). Horizontal gene transfer in Fungi and its ecological importance. In: Hsueh, Y. P., Blackwell, M. (Eds.) Fungal Associations. The Mycota, vol 9. Springer, Cham., pp. 59-81.
  3. Abbot, P., H. R. Eidem, & A. Rokas (2018). Preterm birth. In: Encyclopedia of Evolutionary Psychological Science, Shackelford T., & V. Weekes-Shackelford (Eds.),Springer, Cham. PDF
  4. Rokas, A. (2016). Systematics in the age of genomics. In “Next Generation Systematics“, Olson P. D., J. Hughes, & J. A. Cotton (Eds.), Cambridge University Press, pp. 219-228.
  5. Rokas, A. & S. Chatzimanolis (2008). From gene-scale to genome-scale phylogenetics; the data flood in but the challenges remain. In “Phylogenomics“, Murphy, W. J. (Ed.), Methods in Molecular Biology series, Humana Press, pp. 1-12.
  6. Geiser, D. M., R. A. Samson, J. Varga, A. Rokas, & S. M. Witiak (2008). A review of molecular phylogenetics in Aspergillus, and prospects for a robust genus-wide phylogeny. In “Aspergillus in the genomics era“, Varga, J. & R. A. Sampson (Eds.), Wageningen Academic Publishers, pp. 17-32.
  7. Rokas, A. & J. E. Galagan (2007). The Aspergillus nidulans genome and comparative analysis with other Aspergilli. In “The Aspergilli: Genomics, Medical Applications, Biotechnology, and Research Methods”, Osmani, S. A. & G. H. Goldman (Eds.), CRC Press, pp. 43-55.
  8. Atkinson, R. J., A. Rokas, & G. N. Stone (2007). Longitudinal patterns in species richness and genetic diversity in European oaks and oak gallwasps. In: “Phylogeography in southern European refugia: Evolutionary Perspectives on the origins and conservation of European Biodiversity“, Weiss S. & N. Ferrand (Eds.), Springer Netherlands, pp. 127-151.
  9. Stone, G. N., R. J. Atkinson, G. Brown, A. Rokas, & G. Csoka (2003). The population geenetic consequences of range expansion: oak gallwasps as a model system. In: “Genes in the Environment“, Hails R. S., J. E. Beringer, & H. C. J. Godfray (Eds.), Blackwell and the British Ecological Society, pp. 46-62.

Commentaries and Book Reviews

  1. Steenwyk, J. L.^ & A. Rokas^ (2023). The dawn of relaxed phylogenetics. (^Senior authors) PLoS Biol. 21: e3001998.
  2. Liu, C., Y. Li, Y. Chen, X. X. Chen, J. Huang, A. Rokas, & X.-X. Shen (2022). How has horizontal gene transfer shaped the evolution of insect genomes? Environ. Microbiol.: in press.
  3. Dunning Hotopp, J. C., D. A. Baltrus, V. M. Bruno, J. J. Dennehy, S. R. Gill, J. A. Maresca, J. Matthijnssens, I. L. G. Newton, C. Putonti, D. A. Rasko, A. Rokas, S. Roux, J. E. Stajich, K. M. Stedman, F. J. Stewart, J. C. Thrash (2020). Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements. Microbiol. Resour. Announc. 9: e00763-20.
  4. Baltrus, D. A., C. A. Cuomo, J. J. Dennehy, J. C. Dunning Hotopp, J. A. Maresca, I. L. G. Newton, D. A. Rasko, A. Rokas, S. Roux, J. E. Stajich (2019). Future-proofing your Microbiology Resource Announcements genome assembly for reproducibility and clarity. Microbiol. Resour. Announc. 8: e00954-19.
  5. Riquelme, M., M. C. Aime, S. Branco, A. Brand, A. Brown, L. Glass, R. Kahmann, M. Momany, A. Rokas, & F. Trail (2018). The power of discussion: support for Women at the fungal Gordon Research Conference. Fungal Genet. Biol. 121: 65-67.
  6. Shropshire, J. D. & A. Rokas (2017). Heredity: The gene family that cheats Mendel. eLife 6: e28567.
  7. Abbot, P. & A. Rokas (2017). Mammalian pregnancy. Curr. Biol. 27: R127-R128.
  8. Rokas, A. (2013). My oldest sister is a sea walnut? Science 342: 1327-1329.
  9. Rokas, A. (2013). Aspergillus. Curr. Biol. 23: R187-R188.
  10. Rokas, A. (2008). Lining up to avoid bias. Science 319: 416-417.
  11. Rokas, A. & C. T. Hittinger (2007). Transcriptional rewiring: The proof is in the eating. Curr. Biol. 17: R626-R628.
  12. Rokas, A. (2006). Genomics and the tree of life. Science 313: 1897-1898.
  13. Rokas, A. (2006). Different paths to the same end. Nature 443: 401-402.
  14. Rokas, A. (2004). What determines the direction of evolutionary change? Book Review of: Biased Embryos and Evolution by W. Arthur, Cambridge University Press, 2004. Trends Ecol. Evol. 19: 287-288.
  15. Rokas, A. (2002). Sexual selection driving spider diversification. Trends Ecol. Evol. 17: 304.
  16. Rokas, A. (2001). Getting it right for the wrong reason. Trends Ecol. Evol. 16: 668.
  17. Rokas, A. (2001). What is a character? Book Review of: The Character Concept in Evolutionary Biology by G. P. Wagner (Ed.), Academic Press, 2000. Trends Ecol. Evol. 16: 590.
  18. Rokas, A. (2001). Selfish element wars in a wasp battleground. Trends. Ecol. Evol. 16: 277.
  19. Rokas, A. & D. Charlesworth (2001). Book Review of: Molecular Evolution and Phylogenetics by M. Nei and S. Kumar, Oxford University Press, 2000. Genet. Res. 77: 117-119.
  20. Rokas, A. (2001). Evolutionary biology meets genomics. Trends Ecol. Evol. 16: 15-16.
  21. Rokas, A. & G. McVean (2000). A Bayesian guide to tree felling. Trends Ecol. Evol. 15: 396.
  22. Cook, J. M. & A. Rokas (2000). Influential passengers come of age, 1st International Wolbachia Conference, Orthodox Academy, Kolymbari, Crete, Greece, 7-12 June 2000. Trends Genet. 16: 378-379.
  23. Rokas, A. (2000). Bacteria altering reproduction in gall wasps or what happens if you don’t take your antibiotics! Cecidology 15: 2-7.
  24. Rokas, A. (2000). Wolbachia as a speciation agent. Trends Ecol. Evol. 15: 44-45.