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Publications

Wordle made from abstracts of articles published between 1999 and 2017 


Preprint Articles

  1. 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^. Regulation of gliotoxin biosynthesis and protection in Aspergillus species. (^Senior authors) PDF
    Preprint on bioRxiv server
  2. Steenwyk, J. L., M. A. Phillips, F. Yang, S. S. Date, T. R. Graham, J. Berman, C. T. Hittinger, & A. Rokas. A gene coevolution network provides insight into eukaryotic cellular and genomic structure and function. PDF
    Preprint on bioRxiv server
  3. 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 (2020). Dense phenotyping from electronic health records enables machine-learning-based prediction of preterm birth. PDF
    Preprint on medRxiv server
  4. Walker, J. F., X.-X. Shen, A. Rokas, S. A. Smith, & E. Moyroud (2020). Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices. PDF
    Preprint on bioRxiv server
  5. Ortiz, J. F. & A. Rokas (2018). The genomic geography and evolution of clusters of tandemly duplicated genes in the human and mammal genomes. PDF
    Preprint on bioRxiv server
  6. Rinker, D. C., X. Zhou, R. J. Pitts, P. L. Jones, A. Rokas, & L. J. Zwiebel (2015). RNAseq in the mosquito maxillary palp: a little antennal RNA goes a long way. PDF
    Preprint on bioRxiv server

Research Articles

  1. 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. Heterogeneity in the transcriptional response of the human pathogen Aspergillus fumigatus to the antifungal agent caspofungin. Genetics: in press.
    Preprint on bioRxiv server
  2. 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.: in press. PDF
  3. 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* (2021). 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.: in press. PDF
  4. Harrison, M. C., A. L. LaBella, C. T. Hittinger^, & A. Rokas^ (2021). The evolution of the GALactose utilization pathway in budding yeasts. (^Senior authors) Trends Genet.: in press. PDF
  5. 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. PDF
  6. 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. PDF
  7. 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. PDF
  8. Steenwyk, J. L.^ & A. Rokas^ (2021). orthofisher: a broadly applicable tool for automated gene identification and retrieval. (^Senior authors) G3 11: jkab250. PDF
  9. 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. PDF
  10. Li, Y., X.-X. Shen, B. Evans, C. W. Dunn^, & A. Rokas^ (2021). Rooting the animal tree of life. (^Senior authors) Mol. Biol. Evol.: in press. PDF
  11. 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. PDF
  12. 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. PDF
  13. 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. PDF
  14. 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. PDF
  15. 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. PDF
  16. 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. PDF
    Cover article
  17. 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. PDF
  18. 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. PDF
  19. 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. PDF
  20. 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. PDF
  21. Hatmaker, E. A.*, X. Zhou*, M. E. Mead, H. Moon, J.-H. Yu, & A. Rokas (2020). A revised transcriptome-based gene annotation for Aspergillus flavus strain NRRL 3357. (*Equal contributors) Microbiol. Resour. Announc. 9: e01155-20. PDF
  22. 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. PDF
  23. 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. PDF
  24. 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. PDF
  25. 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. PDF
  26. 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. PDF
  27. 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. PDF
  28. 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. PDF
    Cover article
  29. 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. PDF
    The story behind the paper in Nature Research Ecology & Evolution Community’s blog
  30. 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. PDF
  31. 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. PDF
  32. 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. PDF
    Cover article
  33. 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. PDF
  34. 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. PDF
  35. 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. PDF
  36. 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. PDF
  37. 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. PDF
  38. 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. PDF
  39. 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. PDF
  40. 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. PDF
  41. 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. PDF
  42. 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. PDF
  43. 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
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. King, N. & A. Rokas (2017). Embracing uncertainty in early animal evolution. Curr. Biol. 27: R1081–R1088. PDF
  86. 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
  87. 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
  88. 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
  89. 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
  90. 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
  91. 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
  92. 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
  93. 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
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  94. Steenwyk, J. & A. Rokas (2017). Extensive copy number variation in fermentation-related genes among Saccharomyces cerevisiae wine strains. G3 7: 1475-1485. PDF
  95. 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
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  96. 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
  97. 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
  98. 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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  99. 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
  100. 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
  101. 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
  102. 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
  103. 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
  104. 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
  105. 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
  106. 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
  107. 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
  108. 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
  109. 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
  110. 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
  111. 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
  112. Phillips, J. B., P. Abbot, & A. Rokas (2015). Is preterm birth a human-specific syndrome? Evol. Med. Public Health 2015: 136-148. PDF
  113. 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
  114. 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
  115. Wisecaver, J. H., & A. Rokas (2015). Fungal metabolic gene clusters – caravans traveling across genomes and environments. Front. Microbiol. 6: 161. PDF
  116. 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
  117. 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
  118. 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
  119. Wisecaver, J. H.*, J. C. Slot*, & A. Rokas (2014). The evolution of fungal metabolic pathways. (*Equal contributors) PLoS Genet. 10: e1004816. PDF
  120. 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
  121. 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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  122. 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
  123. Zhou, X. and A. Rokas (2014). Prevention, diagnosis, and treatment of high throughput sequencing data pathologies. Mol. Ecol. 23: 1679-1700. PDF
  124. Soria, P. S.*, K. L. McGary*, and A. Rokas (2014). Functional divergence for every paralog. (*Equal contributors) Mol. Biol. Evol. 31: 984-992. PDF
  125. 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
  126. 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
  127. 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
  128. 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
  129. 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
  130. 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
  131. 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
  132. Salichos, L., and A. Rokas (2013). Inferring ancient divergences requires genes with strong phylogenetic signals. Nature 497: 327-331. PDF
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  133. 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
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  134. 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
  135. 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
  136. 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
  137. 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
  138. 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
  139. Gibbons, J. G., and A. Rokas (2013). The function and evolution of the Aspergillus genome. Trends Microbiol. 21: 14-22. PDF
  140. 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
  141. 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
  142. 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
  143. 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
  144. 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
  145. 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
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    Dataset of the Week, The Global Proteome Machine
  146. 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
  147. 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
  148. 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
  149. 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
  150. 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
  151. 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
  152. 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
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    Spotlight
  153. 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
  154. 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
  155. 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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  156. Salichos, L., and A. Rokas (2011). Evaluating ortholog prediction algorithms in a yeast model clade. PLoS ONE 6: e18755. PDF
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  157. 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
  158. 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
  159. 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
  160. 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
  161. 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
  162. Salichos, L. and A. Rokas (2010). The diversity and evolution of circadian clock proteins in fungi. Mycologia 102: 269-278. PDF
  163. 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
  164. 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
  165. 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
  166. Rokas, A. and P. Abbot (2009). Harnessing genomics for evolutionary insights. Trends Ecol. Evol. 24: 192-200. PDF
  167. 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
  168. Rokas, A. (2009). The effect of domestication on the fungal proteome. Trends Genet. (Genome Analysis section) 25: 60-63. PDF
  169. Rokas, A. (2008). The molecular origins of multicellular transitions. Curr. Opin. Genet. Dev. 18: 472-478. PDF
  170. 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
  171. Rokas, A., and S. B. Carroll (2008). Frequent and widespread parallel evolution of protein sequences. Mol. Biol. Evol.25: 1943-1953. PDF
  172. 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
  173. 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
  174. 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
  175. 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
  176. 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
  177. 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
  178. 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
  179. Rokas, A. and S. B. Carroll (2006). Bushes in the Tree of Life. PLOS Biology: 4: e352. PDF
  180. 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
  181. 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
  182. 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
  183. 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
  184. 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
  185. 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
  186. Rokas, A., E. Ladoukakis, and E. Zouros (2003). Animal mitochondrial DNA recombination revisited. Trends Ecol. Evol. 18: 411-417. PDF
  187. 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
  188. 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
  189. 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
  190. 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
  191. 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
  192. 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
  193. 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
  194. 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
  195. 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
  196. 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
  197. 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
  198. 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
  199. 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. 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
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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. 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. PDF
  2. 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. PDF
  3. 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. PDF
  4. Shropshire, J. D. & A. Rokas (2017). Heredity: The gene family that cheats Mendel. eLife 6: e28567. PDF
  5. Abbot, P. & A. Rokas (2017). Mammalian pregnancy. Curr. Biol. 27: R127-R128. PDF
  6. Rokas, A. (2013). My oldest sister is a sea walnut? Science 342: 1327-1329. PDF
  7. Rokas, A. (2013). Aspergillus. Curr. Biol. 23: R187-R188. PDF
  8. Rokas, A. (2008). Lining up to avoid bias. Science 319: 416-417. PDF
  9. Rokas, A. & C. T. Hittinger (2007). Transcriptional rewiring: The proof is in the eating. Curr. Biol. 17: R626-R628. PDF
  10. Rokas, A. (2006). Genomics and the tree of life. Science 313: 1897-1898. PDF
  11. Rokas, A. (2006). Different paths to the same end. Nature 443: 401-402. PDF
  12. 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.
  13. Rokas, A. (2002). Sexual selection driving spider diversification. Trends Ecol. Evol. 17: 304.
  14. Rokas, A. (2001). Getting it right for the wrong reason. Trends Ecol. Evol. 16: 668.
  15. 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.
  16. Rokas, A. (2001). Selfish element wars in a wasp battleground. Trends. Ecol. Evol. 16: 277.
  17. 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.
  18. Rokas, A. (2001). Evolutionary biology meets genomics. Trends Ecol. Evol. 16: 15-16.
  19. Rokas, A. & G. McVean (2000). A Bayesian guide to tree felling. Trends Ecol. Evol. 15: 396.
  20. 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.
  21. Rokas, A. (2000). Bacteria altering reproduction in gall wasps or what happens if you don’t take your antibiotics! Cecidology 15: 2-7.
  22. Rokas, A. (2000). Wolbachia as a speciation agent. Trends Ecol. Evol. 15: 44-45. PDF