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
- 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)
- 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)
- 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.
- 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)
- 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.
- Zheng, Q., J. L. Steenwyk^, & A. Rokas^. Lack of universal mutational biases in a fungal phylum. (^Senior authors)
Research Articles
- Crandall, J. G., X. Zhou, A. Rokas, & C. T. Hittinger. Specialization restricts the evolutionary paths available to yeast sugar transporters. Mol. Biol. Evol.: in press.
- 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.
- Danis, T. & A. Rokas (2024). The evolution of gestation length in eutherian mammals. Proc. R. Soc. B 291: 20241412.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.: in press.
- 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.: syae031.
- 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 - 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.
- 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.
- 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.
- 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.
- 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 - 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Steenwyk, J. L., Y. Li, X. Zhou, X.-X. Shen, & A. Rokas (2023). Incongruence in the phylogenomics era. Nature Rev. Genet. 24: 834–850.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Rokas, A. (2022). Evolution of the human pathogenic lifestyle in fungi. Nature Microbiol. 7: 607-619.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Steenwyk, J. L.^ & A. Rokas^ (2021). orthofisher: a broadly applicable tool for automated gene identification and retrieval. (^Senior authors) G3 11: jkab250.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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 - 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.
- 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.
- 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., 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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 - 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 - 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.
- 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.
- 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 - 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- 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
- 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
- Steenwyk, J. L. & A. Rokas (2019). treehouse: a user-friendly application to obtain subtrees from large phylogenies. BMC Res. Notes 12: 541. PDF
Download treehouse - 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
- 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 - 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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 - 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
- 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
- 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
- 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
Download data - 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- King, N. & A. Rokas (2017). Embracing uncertainty in early animal evolution. Curr. Biol. 27: R1081–R1088. PDF
- 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
- 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
- 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
- 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
- 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
- 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
- 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 - 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 - Steenwyk, J. & A. Rokas (2017). Extensive copy number variation in fermentation-related genes among Saccharomyces cerevisiae wine strains. G3 7: 1475-1485. PDF
- 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 - 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
- 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
- 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
Download iWGS - 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Phillips, J. B., P. Abbot, & A. Rokas (2015). Is preterm birth a human-specific syndrome? Evol. Med. Public Health 2015: 136-148. PDF
- 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
- 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 - Wisecaver, J. H., & A. Rokas (2015). Fungal metabolic gene clusters – caravans traveling across genomes and environments. Front. Microbiol. 6: 161. PDF
- 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
- 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
- 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 - Wisecaver, J. H.*, J. C. Slot*, & A. Rokas (2014). The evolution of fungal metabolic pathways. (*Equal contributors) PLoS Genet. 10: e1004816. PDF
- 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
- Polzin, K. and A. Rokas (2014). Evaluating rare amino acid substitutions (RGC_CAMs) in a yeast model clade. PLoS ONE 9: e92213. PDF
Retrieve scripts and data - 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
- Zhou, X. and A. Rokas (2014). Prevention, diagnosis, and treatment of high throughput sequencing data pathologies. Mol. Ecol. 23: 1679-1700. PDF
- Soria, P. S.*, K. L. McGary*, and A. Rokas (2014). Functional divergence for every paralog. (*Equal contributors) Mol. Biol. Evol. 31: 984-992. PDF
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Salichos, L., and A. Rokas (2013). Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-331. PDF
Retrieve data - 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 - 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
- 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 - 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
- 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
- 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
- Gibbons, J. G., and A. Rokas (2013). The function and evolution of the Aspergillus genome. Trends Microbiol. 21: 14-22. PDF
- 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
- 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
- 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
- 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
- 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
- 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 - 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
- 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 - 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
- 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
- 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
- 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
- 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 - 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
- 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
- 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
Retrieve data - Salichos, L., and A. Rokas (2011). Evaluating ortholog prediction algorithms in a yeast model clade. PLoS ONE 6: e18755. PDF
Retrieve cRBH script - 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 - 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 - 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
- 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
- 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 - Salichos, L. and A. Rokas (2010). The diversity and evolution of circadian clock proteins in fungi. Mycologia 102: 269-278. PDF
- 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 - 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 - 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 - Rokas, A. and P. Abbot (2009). Harnessing genomics for evolutionary insights. Trends Ecol. Evol. 24: 192-200. PDF
- 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
- Rokas, A. (2009). The effect of domestication on the fungal proteome. Trends Genet. (Genome Analysis section) 25: 60-63. PDF
- Rokas, A. (2008). The molecular origins of multicellular transitions. Curr. Opin. Genet. Dev. 18: 472-478. PDF
- 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
- Rokas, A., and S. B. Carroll (2008). Frequent and widespread parallel evolution of protein sequences. Mol. Biol. Evol.25: 1943-1953. PDF
- 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
- 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
- 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 - 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
- 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
- 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
- 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
- Rokas, A. and S. B. Carroll (2006). Bushes in the Tree of Life. PLOS Biology: 4: e352. PDF
- 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
- 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 - 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
- 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 - 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 - 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 - Rokas, A., E. Ladoukakis, and E. Zouros (2003). Animal mitochondrial DNA recombination revisited. Trends Ecol. Evol. 18: 411-417. PDF
- 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
- 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
- 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 - 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
- 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
- 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 - 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
- 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
- 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
- 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
- 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 - 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
- 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
- Rokas, A., & P. S. Soltis, Eds. (2015). Special issue on Genomes and Evolution.
Curr. Opin. Genet. Dev., volume 35: 1-126.
PDF
Book Chapters
- 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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
- Steenwyk, J. L.^ & A. Rokas^ (2023). The dawn of relaxed phylogenetics. (^Senior authors) PLoS Biol. 21: e3001998.
- 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.
- 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.
- 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.
- 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.
- Shropshire, J. D. & A. Rokas (2017). Heredity: The gene family that cheats Mendel. eLife 6: e28567.
- Abbot, P. & A. Rokas (2017). Mammalian pregnancy. Curr. Biol. 27: R127-R128.
- Rokas, A. (2013). My oldest sister is a sea walnut? Science 342: 1327-1329.
- Rokas, A. (2013). Aspergillus. Curr. Biol. 23: R187-R188.
- Rokas, A. (2008). Lining up to avoid bias. Science 319: 416-417.
- Rokas, A. & C. T. Hittinger (2007). Transcriptional rewiring: The proof is in the eating. Curr. Biol. 17: R626-R628.
- Rokas, A. (2006). Genomics and the tree of life. Science 313: 1897-1898.
- Rokas, A. (2006). Different paths to the same end. Nature 443: 401-402.
- 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.
- Rokas, A. (2002). Sexual selection driving spider diversification. Trends Ecol. Evol. 17: 304.
- Rokas, A. (2001). Getting it right for the wrong reason. Trends Ecol. Evol. 16: 668.
- 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.
- Rokas, A. (2001). Selfish element wars in a wasp battleground. Trends. Ecol. Evol. 16: 277.
- 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.
- Rokas, A. (2001). Evolutionary biology meets genomics. Trends Ecol. Evol. 16: 15-16.
- Rokas, A. & G. McVean (2000). A Bayesian guide to tree felling. Trends Ecol. Evol. 15: 396.
- 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.
- Rokas, A. (2000). Bacteria altering reproduction in gall wasps or what happens if you don’t take your antibiotics! Cecidology 15: 2-7.
- Rokas, A. (2000). Wolbachia as a speciation agent. Trends Ecol. Evol. 15: 44-45.